Gene duplication enables a novel function to evolve

In particular, whether chance mutations and unguided natural selection are sufficient to produce the relevant genetic changes is almost never assessed.

Followed by "You can't prove it was unguided". (headshake)

This one has been getting raked over the coals in the comments on PHYSORG:

http://www.physorg.com/news/2011-01-gene-functions.html

Complete with scriptural citations. One good thing I've noticed in my other work with conspiracy theorists: they never quote sacred texts.

Gasp! A link to my humble blog by Panda's Thumb. My cup runneth over.

Followed by “You can’t prove it was unguided”. (headshake)

gate.net: Xylitol is also not normally metabolized, but Mortlock and his colleagues were able to develop strains (generally through spontaneous mutations, but sometimes with u.v. ray or chemical induced mutations) that could use it because ribitol dehydrogenase (which is usually present in the cells to convert ribitol to D-ribulose) was able to slightly speed up the conversion of xylitol to D-xylulose, for which metabolic pathways already exist. The ability of the strains to utilize xylitol was increased as much as 20 fold when first production of ribitol dehydrogenase was deregulated (the enzyme was produced all the time, not just when ribitol was present), then duplication of the ribitol dehydrogenase genes occurred, then the structure of the enzyme was changed such that its efficiency at working with xylitol was improved, and finally, in at least one case, a line regained control of the modified ribitol dehydrogenase gene so that the enzyme was only produced in the presence of xylitol. Here we have a complete example of a new metabolic pathway being developed through duplication and modification of an existing pathway.

Any one willing to bet on how far back Luskin and dupes will move the goalposts on this one? My prediction: First they'll shot in the dark trying to make it look like something else, then they'll move the posts back by saying something like "....but it hasn't been observed in nature...."

Whenever ID/creationist carping about “new information” comes up, I wonder why they have never observed the properties of water compared with the properties of hydrogen and oxygen.

Or, if one wants a little more drama, the properties of salt compared with the properties of sodium and chlorine.

And one doesn't even have to get beyond the brainpower of ID/creationists by using compounds as examples. Why does a solid piece of lead have different properties than a single atom of lead? And why do these properties vary with temperature?

All they have to do to win a Nobel is demonstrate that the laws of physics and chemistry no longer apply to complex phenomena at some level and why. Then they should be able to demonstrate at which particular level of complexity this kicks in and also the mechanism that prevents further assemblies of matter and/or prevents the emergence of new phenomena as complexity increases.

Piece of cake, Casey; go get ‘em!

Casey will take his cue from Behe and call it a trivial change. Simple microevolution. Parlor trick. See it all the time. Fly is still a fly. Move on, folks, no evolution to see here. Same for whales. Pish posh.

Not sure if I should mention this, but you can get a full preliminary copy of the article here:

http://www.life.illinois.edu/ccheng/Deng%20et%20al%20PNAS2010_online.pdf

It's very, very thick, but interesting.

OgreMkV said: It's very, very thick, but interesting.

Gee, gene duplication and divergence documented as a major mechanism of evolution. What a shock! Who would have guessed?

Now all Dembski has to to is to calculate the exact amount of CCSSII before the duplication and after in order to see what evolution is capable of. He can still claim that it can't do better than this of course, but he can't claim that there are no beneficial mutations, or that there is no new information, or that no new protein has evolved, or any of that other crap. Not that anyone was ever fooled by his hand waving in the first place.

My bet is on the 'design' of the lab experiment.

"This only proves that intelligence can create novel systems."

Of course this would be a complete misread of the article because the researchers didn't actually do experiments. They just (hah!) analyzed the gene sequences from a variety of fish.

There's some golden quote-mine material in there too. I can't wait to see one of the sentences from the first two paragraphs and then hammer them with the rest of the material.

Comon attack gerbil, don't let us down.

Doc Bill said: Casey will take his cue from Behe and call it a trivial change. Simple microevolution. Parlor trick. See it all the time. Fly is still a fly. Move on, folks, no evolution to see here. Same for whales. Pish posh.

But it's ... just MICROEVOLUTION! Not MACROEVOLUTION! It doesn't ADD information! And there are NO transtional fossils! And DARTH VADER was an EVOLUTIONIST!

OgreMkv,

Thanks for the link.

OgreMkV said: Comon attack gerbil, don't let us down.

"Attack mouse." I like it.

You don't have to wait to find out how the cdesign proponentsits will react, there was already a recent Cornelius Hunter trackback on Uncommon Descent addressing the research about new genes becoming essential for survival in fruit flies. DID THOSE DARWINISTS EVER CONSIDER THAT THE GENES WERE NOT THE PRODUCT OF EVOLUTION? WHY NO, OF COURSE NOT!

They also have posts up addressing the recent scandals that the NCSE (via the New Mexico CESME) calls ID "Creationism re-labeled" and that they endorse teaching evolution a fact!

I guess it's nice of them to finally pay attention after all these years?

Wheels said: They also have posts up addressing the recent scandals that the NCSE (via the New Mexico CESME) calls ID "Creationism re-labeled" and that they endorse teaching evolution a fact!

Someday I need to tell you guys about the time I was chased out of Herman park by a pack/gang/samurai army of squirrels.

Mike Elzinga said: Whenever ID/creationist carping about “new information” comes up, I wonder why they have never observed the properties of water compared with the properties of hydrogen and oxygen. Or, if one wants a little more drama, the properties of salt compared with the properties of sodium and chlorine. (snip)

Someday I need to tell you guys about the time I was chased out of Herman park by a pack/gang/samurai army of squirrels.

Doc Bill said:

Someday I need to tell you guys about the time I was chased out of Herman park by a pack/gang/samurai army of squirrels.

In Kew Gardens I saw a tourist trying to take a picture of a swan with its wings out, and he had his wife behind him flapping her arms up and down to attract the swan. Well, it worked. The swan chased the lady, knocked her down and tried to mate with her. (I didn't think she was all that attractive, but I'm not a swan.) Anyway, the tourist thought it was great and kept taking pictures ignoring his wife's screams.

The Curmudgeon said: Gasp! A link to my humble blog by Panda's Thumb. My cup runneth over.

RBH said:Did the trackback make the trip?

The Curmudgeon said:

RBH said:Did the trackback make the trip?

I haven't allowed trackbacks for a year or two. They're often spammy. But I just enabled them for that one post. Nothing shows up, at least not yet.

fnxtr said: The snow on the roof would never turn to icicles on the eaves if not for the local temperature fluctations, or even the heat leaking through from inside the house. And the icicles would never form if the heat leakage from inside the house was greater.

You guys can mock Luskin all you want. He will still continue to embarrass Darwinists on a daily basis. For the latest smackdown see his post here:

http://www.evolutionnews.org/2011/01/marsupials_embryos_develop_dif042271.html#more

More and more data like this is being uncovered, which completely contradicts the myth of common descent. Darwinists have no choice but to ignore it.

As for gene duplication leading to novel functions, this phenomenon is perfectly consistent with ID. Let me know when you guys can find an example of DNA forming spontaneously from random arrangements of chemicals...

MSG said: Let me know when you guys can find an example of DNA forming spontaneously from random arrangements of chemicals...

You guys can mock Luskin all you want.

why, thanks!

...and please send our thanks also to Casey for his continued permission to allow us to mock his inanity publicly, with no fear of either libel suit or factual disagreement.

say, do you know when Casey is gonna finish his book:

"The Mouse that Squeaked Very Loudly"

Where do you hang your Nobel Prize medal?

MSG said: Have you read Signature in the Cell?

MSG said: Right next to the evidence of DNA spontaneously creating itself... Have you read Signature in the Cell?

MSG said: As for gene duplication leading to novel functions, this phenomenon is perfectly consistent with ID.

Mike Elzinga said: Yeah; it’s pretty lousy science fiction pretending to be something more than it is.

http://pandasthumb.org/archives/2009/12/signature-in-th.html#more

That's the one where Meyer couldn't even bother to make his assertions consistent, or avoid the tired creationist canard about abiogenesis and a 'hurricane in a junkyard', right?

http://www.talkorigins.org/indexcc/CB/CB010.html

Nah, not at the top of my reading list -- there are other brave souls who risk their sanity to take down trash like that.

(Note to self: ID-apologist troll will complain about 'ID isn't creationism!' and 'That analysis is for proteins, not DNA!' and greatly belabor pretending to miss the actual merits of the argument.)

MSG

None for me thanks, I have an allergy.

MSG said:

Where do you hang your Nobel Prize medal?

Right next to the evidence of DNA spontaneously creating itself... Have you read Signature in the Cell?

MSG said: You guys can mock Luskin all you want. He will still continue to embarrass Darwinists on a daily basis. For the latest smackdown see his post here: http://www.evolutionnews.org/2011/01/marsupials_embryos_develop_dif042271.html#more

The 2011 edition of Ken Miller textbook Biology states, "Similar patterns of embryological development provide further evidence that organisms have descended from a common ancestor." (p. 469) But what happens when supposedly similar types of organisms have very different patterns of embryological development? Would that count as evidence against common ancestry? In fact, researchers are finding striking differences in the development of vertebrates.

— Luskin

MSG said: You guys can mock Luskin all you want. He will still continue to embarrass Darwinists on a daily basis. For the latest smackdown see his post here: http://www.evolutionnews.org/2011/01/marsupials_embryos_develop_dif042271.html#more More and more data like this is being uncovered, which completely contradicts the myth of common descent. Darwinists have no choice but to ignore it. As for gene duplication leading to novel functions, this phenomenon is perfectly consistent with ID. Let me know when you guys can find an example of DNA forming spontaneously from random arrangements of chemicals...

MSG said: ...gene duplication leading to novel functions... is perfectly consistent with ID.

jkc said:

The 2011 edition of Ken Miller textbook Biology states, "Similar patterns of embryological development provide further evidence that organisms have descended from a common ancestor." (p. 469) But what happens when supposedly similar types of organisms have very different patterns of embryological development? Would that count as evidence against common ancestry? In fact, researchers are finding striking differences in the development of vertebrates.

— Luskin

MSG -

I want to be fair.

I want to compare the theory of intelligent design to the theory of evolution, and see which, if either, is the better explanation of the diversity and nested hierarchical relationships we see in the biosphere.

The problem is, although I have read pretty extensively on the subject, I don't know what that theory of intelligent design it.

It all just seems to be lame evolution denial.

But again, I want to be fair, so answer a few basic questions for me.

1) Who is the designer?

2) Exactly what did the designer design?

3) How did the designer design it?

4) When did the designer design it?

5) What is an example of something that might not have been designed?

Is there anything which isn’t “perfectly consistent with ID”?

Great, more Trolling For Credits(tm).

1) Who is the designer?

2) Exactly what did the designer design?

3) How did the designer design it?

4) When did the designer design it?

5) What is an example of something that might not have been designed?

Let me know when you guys can find an example of DNA forming spontaneously from random arrangements of chemicals…

MSG said:

Is there anything which isn’t “perfectly consistent with ID”?

Sure. One example would be a plausible naturalistic explanation for the origin of life. Scientists have been struggling for over a hundred years to come up with such an explanation, but all we've got so far are a few wildly imaginative guesses that don't hold up under even the slightest amount of scrutiny. How long will it take for Darwinists to admit the obvious: that the information-rich sequences found in DNA could only have arisen by means of intelligence? Another example that would be inconsistent with ID is junk DNA. Scientists have long claimed that the non-coding portions of our DNA serve as evidence for descent with modification, but this paradigm has been shattered by recent genomic research. For starters, check out the following: http://www.nature.com/nature/journal/v465/n7301/pdf/nature09144.pdf http://www.pnas.org/content/early/2010/07/01/1004139107.short Now let's get back to gene duplication. You all are touting the recent research by Cheng et al. as some massive victory over ID. (Strange how Darwinists take so much delight in "defeating" a theory which is supposed to be so largely irrelevant. But anyway...) Even though we MAY have found evidence for gene duplication leading to new functionality, the larger body of evidence still points to the process being insufficient overall. This point is made nicely in the following peer-reviewed paper: http://onlinelibrary.wiley.com/doi/10.1002/cplx.20365/abstract

MSG said:

Is there anything which isn’t “perfectly consistent with ID”?

Sure. One example would be a plausible naturalistic explanation for the origin of life.

MSG said: Scientists have been struggling for over a hundred years to come up with such an explanation, but all we've got so far are a few wildly imaginative guesses that don't hold up under even the slightest amount of scrutiny. How long will it take for Darwinists to admit the obvious: that the information-rich sequences found in DNA could only have arisen by means of intelligence?

Even though we MAY have found evidence for gene duplication leading to new functionality, the larger body of evidence still points to the process being insufficient overall. This point is made nicely in the following peer-reviewed paper: http://onlinelibrary.wiley.com/doi/[…]365/abstract

All life depends on the biological information encoded in DNA with which to synthesize and regulate various peptide sequences required by an organism's cells. Hence, an evolutionary model accounting for the diversity of life needs to demonstrate how novel exonic regions that code for distinctly different functions can emerge.

BTW, I strongly recommend that MSG read about T. Ryan Gregory's Onion Test and tell us how ID handles it. In particular, how does ID account for the 5-fold range of genome sizes in Allium?

MSG said: I believe the designer is YHWH, God of the Bible and Father of Jesus Christ. However, ID is compatible with almost any sort of designer and it has no inherent religious implications. We have good evidence to suggest that the designer was responsible for the origin of life. The designer likely has intervened several other times in life's history. As Michael Behe has aptly demonstrated, a design event seems to have been necessary in order to form the first prokaryotic (and later eukaryotic) cells. The fossil record also points to a design event during the Cambrian. I suspect further research may uncover additional instances of design. The designer's mechanism is not currently known, but we shouldn't let this distract us. Remember when Alfred Wegener first proposed the theory of continental drift, he was unable to describe the exact mechanism that caused the continents to move. Like the initial theory of continental drift, ID has significant explanatory power, and it should not be dismissed because it currently lacks a precise mechanism.

MSG said: …gene duplication leading to novel functions… is perfectly consistent with ID.

casey Luskin: More and more data like this is being uncovered, which completely contradicts the myth of common descent. Darwinists have no choice but to ignore it.

msg: Let me know when you guys can find an example of DNA forming spontaneously from random arrangements of chemicals…

csh.org: Finally, DiMauro and coworkers have recently reported that 3′, 5′-cyclic AMP and GMP will spontaneously form homo-A and homo-G oligonucleotides, respectively, in aqueous solution (Costanzo et al. 2009). These authors propose that nucleotides activated as cyclic monophosphates are potentially prebiotic, based on their earlier demonstration of 3′, 5′-cyclic AMP formation in formamide solutions containing phosphate minerals (Costanzo et al. 2007).

Don't let the troll derail this conversation. A nice tidy example of exaptation at the molecular level. I picked up various objects today (a bar magnet, a screwdriver, a pair of tongs) and passed them off to my students as a knife, fork and spoon. It's basically the same stunt from Dover in which a partial mousetrap served as a tie clip. Something serves one purpose well, and is merely OK at another; through duplication and modification, one copy can come to serve the second function better, and then perhaps exclusively. Did anyone happen to catch the article a few years back called 52 uses for a bat wing? It essentially addresses Dawkins' old question: "what good is half a wing?".

msg: How long will it take for Darwinists to admit the obvious: that the information-rich sequences found in DNA could only have arisen by means of intelligence?

How long will it take for Darwinists to admit the obvious

How long will it be until the profoundly ignorant admit that assertion /= evidence?

well, probably we'll have to wait until they also can admit that lying /= honesty.

given the history of the efficacy of lying, I'd say...

we'll be waiting a long, long time.

“Atheistoclast,”

THAT'S who this is?

*headdesk*

some people just should not be allowed near computers.

Ichthyic said: “Atheistoclast,” THAT'S who this is? *headdesk* some people just should not be allowed near computers.

“Atheistoclast,” THAT’S who this is?

Ichthyic said: MSG None for me thanks, I have an allergy.

Ichthyic said: “Atheistoclast,” THAT'S who this is? *headdesk* some people just should not be allowed near computers.

RBH said: As it happens, I know something about that author. He's a long-time internet crank, currently spreading his nonsense on TalkRational as "Atheistoclast," terming himself a neoLamarkian.

Well that explains it. No wonder he made such a transparently fallacious argument. He claimed that a plausible explanation for the origin of life would be inconsistent with ID, while at the same time claiming that a plausible explanation, (well supported by fifty years of evidence), for the origin of new genes and new functions and new information was NOT incompatible with ID. He didn't have to move the goalposts, he just used different shaped goalposts for every own goal!

MSG said:

2) Exactly what did the designer design?

In short, everything.

5) What is an example of something that might not have been designed?

Any micro-evolutionary feature - e.g. the ability of certain bacteria to consume nylon.

raven said:

“Atheistoclast,” THAT’S who this is?

Fake non-intellectual is right. I saw him on Jerry Coyne's blog. He posts links to science abstracts and papers. They have nothing to do with whatever point he is trying and failing to make and often instead contradict it. He doesn't have enough background to actually understand what he is linking to. Which is what he did above with the Cheng paper.

I believe the designer is YHWH, God of the Bible and Father of Jesus Christ.

However, ID is compatible with almost any sort of designer and it has no inherent religious implications.

In short, everything.

We have good evidence to suggest that the designer was responsible for the origin of life.

The designer likely has intervened several other times in life’s history. As Michael Behe has aptly demonstrated, a design event seems to have been necessary in order to form the first prokaryotic (and later eukaryotic) cells.

The fossil record also points to a design event during the Cambrian.

I suspect further research may uncover additional instances of design.

The designer’s mechanism is not currently known, but we shouldn’t let this distract us. Remember when Alfred Wegener first proposed the theory of continental drift, he was unable to describe the exact mechanism that caused the continents to move. Like the initial theory of continental drift, ID has significant explanatory power, and it should not be dismissed because it currently lacks a precise mechanism.

Now let’s get back to gene duplication. You all are touting the recent research by Cheng et al. as some massive victory over ID. (Strange how Darwinists take so much delight in “defeating” a theory which is supposed to be so largely irrelevant. But anyway…) Even though we MAY have found evidence for gene duplication leading to new functionality, the larger body of evidence still points to the process being insufficient overall. This point is made nicely in the following peer-reviewed paper:

"The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case."

"Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms."

RBH: Wait wait wait–the author of the paper in Complexity that MSG linked to is Atheistoclast. I’m not identifying MSG.

Wiley publishing: Effective with the 2011 volume, this journal (Complexity) will be published in an online-only format. Complexity is a bi-monthly, cross-disciplinary journal focusing on the rapidly expanding science of complex adaptive systems. The purpose of the journal is to advance the science of complexity. Articles may deal with such methodological themes as chaos, genetic algorithms, cellular automata, neural networks, and evolutionary game theory. Papers treating applications in any area of natural science or human endeavor are welcome, and especially encouraged are papers integrating conceptual themes and applications that cross traditional disciplinary boundaries. Complexity is not meant to serve as a forum for speculation and vague analogies between words like "chaos," "self-organization," and "emergence" that are often used in completely different ways in science and in daily life.

Is gene duplication a viable explanation for the origination of biological information and complexity? Joseph Esfandiar Hannon Bozorgmehr Article first published online: 22 DEC 2010 Complexity Author Information 39 Princedom Street, Manchester M9 4GQ, United Kingdom Email: Joseph Esfandiar Hannon Bozorgmehr (bozorgmehr@hotmail.co.uk) Abstract All life depends on the biological information encoded in DNA with which to synthesize and regulate various peptide sequences required by an organism's cells. Hence, an evolutionary model accounting for the diversity of life needs to demonstrate how novel exonic regions that code for distinctly different functions can emerge. Natural selection tends to conserve the basic functionality, sequence, and size of genes and, although beneficial and adaptive changes are possible, these serve only to improve or adjust the existing type. However, gene duplication allows for a respite in selection and so can provide a molecular substrate for the development of biochemical innovation. Reference is made here to several well-known examples of gene duplication, and the major means of resulting evolutionary divergence, to examine the plausibility of this assumption. The totality of the evidence reveals that, although duplication can and does facilitate important adaptations by tinkering with existing compounds, molecular evolution is nonetheless constrained in each and every case. Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. © 2010 Wiley Periodicals, Inc. Complexity, 2011

Rapid evolutionary innovation during an Archaean genetic expansion The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers1, 2. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events3, 4, 5, 6. Here we use an explicit model of macroevolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways. Genes arising after this expansion show increasing use of molecular oxygen (P = 3.4 × 10−8) and redox-sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere.

MSG said: Let me know when you guys can find an example of DNA forming spontaneously from random arrangements of chemicals...

MSG said: Have you read Signature in the Cell?

Gary Hurd said: My Amazon review has recently been voted off the front page by creationists, but they cannot actually make a reply.

Jose Fly said: Don't know if the Pandas Thumb denizens saw this, but I thought it was amazing... http://www.nature.com/nature/journal/v469/n7328/abs/nature09649.html

Rapid evolutionary innovation during an Archaean genetic expansion The natural history of Precambrian life is still unknown because of the rarity of microbial fossils and biomarkers1, 2. However, the composition of modern-day genomes may bear imprints of ancient biogeochemical events3, 4, 5, 6. Here we use an explicit model of macroevolution including gene birth, transfer, duplication and loss events to map the evolutionary history of 3,983 gene families across the three domains of life onto a geological timeline. Surprisingly, we find that a brief period of genetic innovation during the Archaean eon, which coincides with a rapid diversification of bacterial lineages, gave rise to 27% of major modern gene families. A functional analysis of genes born during this Archaean expansion reveals that they are likely to be involved in electron-transport and respiratory pathways. Genes arising after this expansion show increasing use of molecular oxygen (P = 3.4 × 10−8) and redox-sensitive transition metals and compounds, which is consistent with an increasingly oxygenating biosphere.

The evolutionary history of almost 4,000 gene families figured out, and it just happens to independently confirm a major event in the history of the earth. Wow. Remind me again what structures or systems ID creationists have clearly identified as "designed" and given detailed accounts of how they were designed? Oh that's right.....

Sylvilagus said: This sounds amazing! Would one of the scientists here post an overview of these findings for us laymen?

I have no idea who this YHWH guy is.

The Designer is most definitely YMCA. There's even a song.

Mike Elzinga said:

Gary Hurd said: My Amazon review has recently been voted off the front page by creationists, but they cannot actually make a reply.

Ah yes; "science" by political action.

Gary Hurd said: It makes sense, after a fashion. The most likely person to be looking at that book is a creationist. They cannot actually follow the argument, but they can vent their objection to science by voting critical reviews "off the island."

mrg said: No doubt I'm not the only Panda who rang the bell after following up the link ... hmm, obviously an evil plan to stack the deck.

For some strange reason, you skipped my question about WHEN the designer designed. Could you please answer that question?

— harold

Frank J said: Keep asking, and ask lots of specific "when" questions. e.g. when life first appeared on Earth, when our lineage split from that of chimps, etc.

Sure. One example would be a plausible naturalistic explanation for the origin of life.

harold said: Why don’t you just design a thought experiment that you could use to hypothetically demonstrate the presence of magic design in a biological system?

Terenzio the Troll said: (Yes: I stole this one from Sagan).

raven said: Complexity is an obscure online journal that Wiley lists under Mathematics. The publisher description doesn't indicate if it is even peer reviewed.

In my professional work I studied fluid phases and I am always impressed by how the local order in a fluid somehow manages to blow up to include the entire bulk during the transition to solid. It's amazing that you can get a single crystal at all, when you think about the huge numbers of atoms that have to be involved. It can't all be due to random motions, can't it?

So I've been lobbying for my theory of intelligent crystalization. The atoms in a crystal are painstakingly arranged by the souls of departed grad students passing through Purgatory.

Gabriel Hanna said: In my professional work I studied fluid phases and I am always impressed by how the local order in a fluid somehow manages to blow up to include the entire bulk during the transition to solid. It's amazing that you can get a single crystal at all, when you think about the huge numbers of atoms that have to be involved. It can't all be due to random motions, can't it?

So I've been lobbying for my theory of intelligent crystallization. The atoms in a crystal are painstakingly arranged by the souls of departed grad students passing through Purgatory.

Mike Elzinga said:

So I've been lobbying for my theory of intelligent crystallization. The atoms in a crystal are painstakingly arranged by the souls of departed grad students passing through Purgatory.

Having their souls annealed?

Mike Elzinga said:

Gabriel Hanna said: In my professional work I studied fluid phases and I am always impressed by how the local order in a fluid somehow manages to blow up to include the entire bulk during the transition to solid. It's amazing that you can get a single crystal at all, when you think about the huge numbers of atoms that have to be involved. It can't all be due to random motions, can't it?

Depending on the atoms or molecules and the rate at which energy is carried away, you can form anything from amorphous solids to polycrystals to pure crystals having long range order. But then annealing near the melting point can often produce what rapid cooling cannot. Much of what happens depends on inclusions, dislocations, and the presence of other elements, the atomic and molecular structure of the vessel in which the condensing matter is contained, and the stresses produced within the condensing material if bond angles between atoms or molecules are not quite commensurate with the emerging crystalline lattice structure. It is extremely difficult to make a pure substance that doesn’t have trace amounts of other elements in it. And tiny amounts of trace elements on the order of one part in 10⁹ can have enormous effects on the properties of the host element when it condenses. In fact, that is what the semiconductor industry is all about.

Gabriel Hanna said: Snowflakes are my favorite examples of the spontaneous creation of order, especially for arguing with creationists.

It's funny that a DRAWING of a snowflake is full of "information" and obviously intelligently designed, but an ACTUAL snowflake, too complicated to be drawn, is totally DEVOID of "information".

Gabriel Hanna said: It's funny that a DRAWING of a snowflake is full of "information" and obviously intelligently designed, but an ACTUAL snowflake, too complicated to be drawn, is totally DEVOID of "information".

SWT said:

Mike Elzinga said:

So I've been lobbying for my theory of intelligent crystallization. The atoms in a crystal are painstakingly arranged by the souls of departed grad students passing through Purgatory.

Having their souls annealed?

Given the purported nature of purgatory, wouldn't zone refining be more apt?

In my paper "is gene duplication a viable explanation for the origination of biological information and complexity", I make it clear that gene duplication can indeed facilitate adaptation, but it is of a very limited nature - usually just the tweaking or tinkering of an existing function. Natural selection has the ability to optimize and elaborate on a function but not to create it from scratch.

I believe I debunked the farcical hogwash of the speculative conversion of a trypsinogen-like enzyme into an antifreeze protein in their 1997 paper where they also claimed a "completely new function" had evolved.

In this latest pathetic attempt of theirs, they claim the subfunctionalization of a bifunctional gene (read the paper) is some great example of biological innovation. It is not.

Gabriel Hanna said: Snowflakes are my favorite examples of the spontaneous creation of order, especially for arguing with creationists.

Atheistoclast said: In this latest pathetic attempt of theirs, they claim the subfunctionalization of a bifunctional gene (read the paper) is some great example of biological innovation. It is not.

Atheistoclast said: I believe I debunked the farcical hogwash ...

I wish the Darwinists on this site would actually care to read the papers they claim champion their ideology.

"The capacity to code for a functional signal peptide (SP), in fact, existed in the precursor sequence in LdSAS-B, because we found comparable levels of AFPIII-exporting activity by the SP precursor-mature AFPIII construct and the native pre-AFPIII cDNA."

"Thus, the incipient ice activity of the ancestral SAS molecule or its detached C-terminal peptide would be quite sufficient in inhibiting ice-crystal expansion
in the fish body fluids."

"A clear example of EAC-compelled duplication of a bifunctional ancestral gene and additionally, acceleration of conflict resolution through intragenic domain deletion in one duplicate and its neofunctionalization into a protein of distinctive function."

None of these observations show how any new functionality has been created - only that it has been optimized and elaborated. None of this, therefore, detracts from the conclusions in my own paper.

*Atheistoclast*

Atheistoclast, can you show us the data you got from your lab work? What sort of experiments did you perform to debunk every single example of gene duplication?

BTW, what's particularly amusing about a'clasts paper is that he has basically cobbled together a few of his Talk Rational posts, submitted it to a journal and they've published it. He even talks about "kinds". Along with his recent magnum opus in the Journal of Bioeconomics, it's arguably the best example of journals (albeit crap ones) being trolled since Sokal put pen to paper. It's really quite hilarious.

What with blabbering on about holocaust denial, conspiracies involving the "British establishment" or threatening to sue the editor of Journal of Bioeconomics, it's a wonder he has time to troll journals.

Stanton said: Atheistoclast, can you show us the data you got from your lab work? What sort of experiments did you perform to debunk every single example of gene duplication?

Atheistoclast said: In my paper "is gene duplication a viable explanation for the origination of biological information and complexity", I make it clear that gene duplication can indeed facilitate adaptation, but it is of a very limited nature - usually just the tweaking or tinkering of an existing function. Natural selection has the ability to optimize and elaborate on a function but not to create it from scratch. I believe I debunked the farcical hogwash of the speculative conversion of a trypsinogen-like enzyme into an antifreeze protein in their 1997 paper where they also claimed a "completely new function" had evolved. In this latest pathetic attempt of theirs, they claim the subfunctionalization of a bifunctional gene (read the paper) is some great example of biological innovation. It is not.

Atheistoclast said:

Stanton said: Atheistoclast, can you show us the data you got from your lab work? What sort of experiments did you perform to debunk every single example of gene duplication?

I didn't perform any lab experiments. I simply downloaded the relevant data from the NCBI website and analyzed it using a number of tools such as BLAST. The paper is a *review* of previous research, including Christina's 1997 paper on antifreeze glycoproteins. If you cannot access the paper using your library system or do not wish to pay for it, send me an email and I will provide a private copy: bozorgmehr@hotmail.co.uk

DS said: Well all (Atheistoclast has) to do is give us a copy of the paper where you did this.

I give Mr. Bozorgmehr credit for submitting something to a journal for peer review, even if the paper is a review - this is something the professionals at the Discovery Institute and the Biologic Institute rarely do themselves.

The problem is, it still counts as a PR victory in creationist circles, something else for the likes of Casey Luskin to talk about. Papers that the ID crowd manage to get published (typically reviews, with the Meyer paper being an archetype) have had no impact whatsoever upon the actual study of evolutionary biology. ID is all PR, religion, and politics, presenting no refutation of evolution or - most tellingly - alternative mechanisms to evolution in peer-reviewed scientific research papers.

Stanton said: Thank you for your generous offer: I will consider it. I just want to give you some advice, in that, you would gain and carry much more authoritative weight if you were to verify your conclusions with labwork and experimentation, and not just reviewing other scientists' work. I'm sorry to say, but, you're not going to impress anyone by just going "This can not be" in a bad review, while flinging the term "Darwinist" around like a racist epitaph.

DS said: I would like to second this sentiment. Why would anyone think that the opinion of someone who hasn't actually done any real research be given more consideration than the thousands of scientists who actually did the work and collected the data? Why should the opinion of one person, who wrote one review paper somewhere, be considered as important as the thousands of papers where the authors reached exactly the opposite conclusion?

DS said: I would like to second this sentiment. Why would anyone think that the opinion of someone who hasn't actually done any real research be given more consideration than the thousands of scientists who actually did the work and collected the data? Why should the opinion of one person, who wrote one review paper somewhere, be considered as important as the thousands of papers where the authors reached exactly the opposite conclusion?

Stanton said:

DS said: Well all (Atheistoclast has) to do is give us a copy of the paper where you did this.

He's offering to do that here, actually

Why should the opinion of one person, who wrote one review paper somewhere, be considered as important as the thousands of papers where the authors reached exactly the opposite conclusion?

Atheistoclast said: You are making a flawed argument from authority. Science isn't based on votes. I could be right and the entire scientific community could be wrong. If you can't be bothered to read the paper, let alone consider its conclusions, then you are not interested in gaining any knowledge. Darwin himself had to oppose conventional thinking in his day when he published his magnum opus.

Well all you have to do is give us a copy of the paper where you did this. You know, the peer reviewed journal article. What...? It wasn't a real journal? Well why not?

Atheistoclast said:

Why should the opinion of one person, who wrote one review paper somewhere, be considered as important as the thousands of papers where the authors reached exactly the opposite conclusion?

You are making a flawed argument from authority. Science isn't based on votes. I could be right and the entire scientific community could be wrong. If you can't be bothered to read the paper, let alone consider its conclusions, then you are not interested in gaining any knowledge. Darwin himself had to oppose conventional thinking in his day when he published his magnum opus.

Atheistoclast said:

Well all you have to do is give us a copy of the paper where you did this. You know, the peer reviewed journal article. What...? It wasn't a real journal? Well why not?

Complexity is a peer-reviewed journal published by Wiley-Blackwell.It is cross-discipline and intended for all scientists. The subject of the paper was too broad for just a bog standard biology/genetics journal. I have 3 more papers under review at mainstream journals and am writing up one more. This is just the beginning of the end of the Darwinian paradigm.

DS said: End of evolution eh. Now where have I heard that before?

mrg said:

DS said: End of evolution eh. Now where have I heard that before?

"The windmills are weakening!"

DS said: "Stand still while I braineth thee."

The thing is that in order to overthrow "Darwinism" you have to propose some alternative. That alternative has to explain all of the evidence. It has to have more predictive and explanatory power than the original theory. Now so far all you have got is lots of "I don't think that could happen". What alternative are you proposing? What journal are you proposing it in?

See, the thing is, that even if it could be conclusively proven that gene duplication could not be a mechanism of evolution, it would not mean the end of evolutionary theory. Darwin didn't know anything about genes let alone duplication. The theory does not rest on that mechanism. Are you going to destroy common descent, random mutation and natural selection as well? What journal will that be in again?

mrg said:

DS said: "Stand still while I braineth thee."

I can't figure out if that's Month Python, Bugs Bunny, the Three Stooges -- or if it matters which.

DS said: It's Jim Carey in The Cable Guy.

DS said: When you get those papers in real journals, I and everyone else will have a look at them. Assuming you can get them past the peer review process of course.

For those playing at home, Complexity has an impact factor of 0.948. It's a real journal with a really low impact factor.

Atheistoclast said: I oppose "hierocracy" within science.

Atheistoclast said: Btw, "Darwinist" is a term that refers to those evolutionists who regard natural selection as the principal mechanism behind biological change. It was invented by Darwin's disciples.

Scott F said: "the principal [sic] mechanism behind biological change"?

Atheistoclast said:

DS said: When you get those papers in real journals, I and everyone else will have a look at them. Assuming you can get them past the peer review process of course.

Please tell me why Complexity is not a "real journal"? Maybe you would like to email its editors, two leading scientists in their fields, Hubbler and Schuster, and tell them that they are wasting their time. I have already published another piece in Bioeconomics. http://www.springerlink.com/content/q767h613177m34r1/ All you have to offer is an argument from authority. You defer to the interpretations of others. And then people have the gall to wonder why Darwinism is called a religion? I oppose "hierocracy" within science.

If you want to claim that requiring research to be published in peer reviewed journals is an argument form authority, so be it. You still ain't got none. And you still have provided no alternative, now why is that?

Atheistoclast said: It really is pathetic to dismiss a paper you refuse to read: What are you afraid of, Darwinist? You scared you might find something you don't like?? Awww.....

Atheistoclast said: Btw, "Darwinist" is a term that refers to those evolutionists who regard natural selection as the principal mechanism behind biological change. It was invented by Darwin's disciples.

Atheistoclast said:

If you want to claim that requiring research to be published in peer reviewed journals is an argument form authority, so be it. You still ain't got none. And you still have provided no alternative, now why is that?

Good science sometimes means going over old ground. Evidently, you are not aware of this habit. If you actually read the paper, you will see that there is lots of new perspectives on the best examples of gene duplication. There are also new sequence alignments that have never been presented before. It really is pathetic to dismiss a paper you refuse to read: What are you afraid of, Darwinist? You scared you might find something you don't like?? Awww.....

Atheistoclast said: In my paper "is gene duplication a viable explanation for the origination of biological information and complexity", I make it clear that gene duplication can indeed facilitate adaptation, but it is of a very limited nature - usually just the tweaking or tinkering of an existing function. Natural selection has the ability to optimize and elaborate on a function but not to create it from scratch. I believe I debunked the farcical hogwash of the speculative conversion of a trypsinogen-like enzyme into an antifreeze protein in their 1997 paper where they also claimed a "completely new function" had evolved. In this latest pathetic attempt of theirs, they claim the subfunctionalization of a bifunctional gene (read the paper) is some great example of biological innovation. It is not.

I wish the Darwinists on this site would actually care to read the papers they claim champion their ideology. "The capacity to code for a functional signal peptide (SP), in fact, existed in the precursor sequence in LdSAS-B, because we found comparable levels of AFPIII-exporting activity by the SP precursor-mature AFPIII construct and the native pre-AFPIII cDNA." "Thus, the incipient ice activity of the ancestral SAS molecule or its detached C-terminal peptide would be quite sufficient in inhibiting ice-crystal expansion in the fish body fluids." "A clear example of EAC-compelled duplication of a bifunctional ancestral gene and additionally, acceleration of conflict resolution through intragenic domain deletion in one duplicate and its neofunctionalization into a protein of distinctive function." None of these observations show how any new functionality has been created - only that it has been optimized and elaborated. None of this, therefore, detracts from the conclusions in my own paper. *Atheistoclast*

I didn't perform any lab experiments. I simply downloaded the relevant data from the NCBI website and analyzed it using a number of tools such as BLAST. The paper is a *review* of previous research, including Christina's 1997 paper on antifreeze glycoproteins. If you cannot access the paper using your library system or do not wish to pay for it, send me an email and I will provide a private copy: bozorgmehr@hotmail.co.uk

Good science sometimes means going over old ground. Evidently, you are not aware of this habit. If you actually read the paper, you will see that there is lots of new perspectives on the best examples of gene duplication. There are also new sequence alignments that have never been presented before. It really is pathetic to dismiss a paper you refuse to read: What are you afraid of, Darwinist? You scared you might find something you don't like?? Awww.....

Atheistoclast said:

If you want to claim that requiring research to be published in peer reviewed journals is an argument form authority, so be it. You still ain't got none. And you still have provided no alternative, now why is that?

Good science sometimes means going over old ground. Evidently, you are not aware of this habit. If you actually read the paper, you will see that there is lots of new perspectives on the best examples of gene duplication. There are also new sequence alignments that have never been presented before. It really is pathetic to dismiss a paper you refuse to read: What are you afraid of, Darwinist? You scared you might find something you don't like?? Awww.....

Well if Atheistoclast is so keen on reading papers, perhaps he will want to read this one posted by Joe Fly on this very thread:

http://www.nature.com/nature/journa[…]re09649.html

It documents the importance of gene duplication in evolutionary time. Now when he can explain this actual data, published in the most respected scientific journal in the world, then maybe someone will want to read his paper. Until then, it seems rather pointless.

Thanks to Joe for the link.

That should be Jose Fly. Sorry Jose.

If anyone is interested in a real review of some of the evidence for the importance of gene duplications as a mechanism of evolution in a journal specializing in reviews in this field, here is a good article:

Zhang (2003) Evolution by gene duplication: an update. Trends in Ecology and Evolution 18(6):292-298.

It has 78 references, all of which disagree with atheistoclast. But then I'm sure he is well aware of this evidence, since he wrote a review paper of his own on the subject. If he hasn't read it, I'm sure he will. I'm sure he will not be afraid to read it. I'm sure he is not scared that he will find something he overlooked, or something he won't like.

This reminds of a segment on This American Life, recommended for all.

http://www.thisamericanlife.org/radio-archives/episode/293/a-little-bit-of-knowledge

ACT THREE. SUCKER MC-SQUARED.
Bob Berenz had a good job as an electrician. But he wanted to do something bigger. He came up with an idea for an invention. But as he studied physics texts to see if his invention could work, he happened upon the biggest idea of his life: A revelation about physics that would disprove Einstein, and Newton. That is, if Bob's right. Bob's friend, Robert Andrew Powell, reports the story. He's a sports writer and the author of We Own This Game, about youth football. (16 minutes)

James F said: This reminds of a segment on This American Life, recommended for all. http://www.thisamericanlife.org/radio-archives/episode/293/a-little-bit-of-knowledge ACT THREE. SUCKER MC-SQUARED. Bob Berenz had a good job as an electrician. But he wanted to do something bigger. He came up with an idea for an invention. But as he studied physics texts to see if his invention could work, he happened upon the biggest idea of his life: A revelation about physics that would disprove Einstein, and Newton. That is, if Bob's right. Bob's friend, Robert Andrew Powell, reports the story. He's a sports writer and the author of We Own This Game, about youth football. (16 minutes)

atheistoclast: All you have to offer is an argument from authority.

and also wanted someone to invest in a motor that put out more energy than it took in.

To be fair on atheistoclast, I see no problem in analysing publicly available data and calling it "research". But that isn't what a review is, and Bozorgmehr's paper is not a "review".

It's an attempt to make an argument from data, which is a perfectly worthy exercise, in principle.

It's also one of the worst pieces of work I've ever seen get past peer-review.

raven said: All you, atheistoclast, have is outright lies and insults.Starting with this thread which references a lot of data on gene duplication and exaptation, data being the opposite of appeal to authority. I can't read anything but the Complexity abstract which is just a series of assertions without proof. It is behind a paywall and I refuse on moral grounds to pay for crackpot reading material.

DS said: Well dude, if you think that you have new evidence that will destroy Darwinism, why don't you publish it in a reputable journal? I'm sure that Nature or Science would be glad to have it. As for your paper, I read the abstract. I was not impressed. I decided not to read the rest. "New perspectives" do not destroy well studied and well documented mechanisms. Only new evidence can do that. You don't have any. Now, one last time, just to be fair. What is your alternative? Don't have one you are willing to admit to do you? Thought not.

Atheistoclast said: It's also one of the worst pieces of work I've ever seen get past peer-review.

raven said: I can't read anything but the Complexity abstract which is just a series of assertions without proof. It is behind a paywall and I refuse on moral grounds to pay for crackpot reading material.

For those of you who can't get access to the Cheng paper you can access it on her site.

http://www.life.illinois.edu/ccheng/Deng%20et%20al%20PNAS2010_online.pdf

It does help to read the paper *before* you rant on about how it supports evolution by exaptation.

AC: It really is pathetic how you want to diss a paper you haven’t even bothered to read.

Let's bear in mind that "published in a peer-reviewed journal" is not synonymous" with "admitted to the canon." The vast majority of published papers in peer reviewed journals sink beneath the waves, never to be cited or heard about again.

Passing peer review, however shakily, means only that a couple of reviewers and an editor thought it was worth putting out there to see if it might fly. My bet is that in this case, it won't.

Atheistoclast said: Nature don't publish review articles that are not solicited. The same goes for PNAS or Science. Also, you have to suppose that the editors of these champions of naturalism and evolutionism are prepared to shoot themselves in the foot by publishing a paper that exposes all the deceit and extrapolation regarding gene duplication and neofunctionalization. I don't think so. Anyway, like I say, more papers are on the way - these are all original research papers. The levees that buttress Darwinism can only be expected to hold out for so long. The game is up.

Atheistoclast said:

raven said: All you, atheistoclast, have is outright lies and insults.Starting with this thread which references a lot of data on gene duplication and exaptation, data being the opposite of appeal to authority. I can't read anything but the Complexity abstract which is just a series of assertions without proof. It is behind a paywall and I refuse on moral grounds to pay for crackpot reading material.

Did you actually read the paper by Cheng? Reading abstracts alone will hardly get you anywhere. If you want to read my paper, I can send you a private copy which backs up all of the claims made in the abstract: bozorgmehr@hotmail.co.uk. If you don't want to learn anything, that is your problem. It really is pathetic how you want to diss a paper you haven't even bothered to read.

Atheistoclast lying: nobody has been able to refute or even dispute anything in it.

swt: If you’d like a copy, drop me an email at swt.onpt at yahoo.com … I think sending a single copy to someone as part of a discussion of the content is probably within the bounds of fair use.

RBH said: Let's bear in mind that "published in a peer-reviewed journal" is not synonymous" with "admitted to the canon." The vast majority of published papers in peer reviewed journals sink beneath the waves, never to be cited or heard about again. Passing peer review, however shakily, means only that a couple of reviewers and an editor thought it was worth putting out there to see if it might fly. My bet is that in this case, it won't.

Peer review at Biocomplexity is evidently a joke. They’ve been trolled.

Infinite Energy (magazine) - Wikipedia, Infinite Energy is a bi-monthly magazine published in New Hampshire that details theories and experiments concerning alternative energy. ... en.wikipedia.org/wiki/Infinite_Energy_(magazine) - Cached - Similar

Peer review at Biocomplexity is evidently a joke. They've been trolled.

SteveF said:

Peer review at Biocomplexity is evidently a joke. They've been trolled.

Whoops. Meant Complexity, not Biocomplexity (where peer review probably is a joke, but that's not the journal we're talking about here).

Yes...you really do have your knickers in a twisst. Complexity is a mainstream journal that has been around for two decades.

For the record: "Kinds" or "Types" of gene/protein do exist. http://en.wikipedia.org/wiki/List_of_types_of_proteins

As for holocaust denial....I am a revisionist not a denialist. The account of the holocaust has changed since Nuremberg with the death toll at Auschwitz-Birkenau going down from 9 millon to less than 1 million - and it keeps falling as new research is done.

BTW, while Complexity deserve a fair bit of criticism for being trolled, worse still is the Journal of Bioeconomics. They published atheistoclasts first paper and, if anything, it's even worse.

http://www.springerlink.com/content/q767h613177m34r1/

Atheistoclast said: My belief is not to believe anything unless it can be demonstrated. Darwinism is a *belief* desperate for evidence.

I never included anything about a "mighty creator"....I was tempted to include an "intelligent artificer" but did not do so.

It seems like ,unless I publish in Nature, it doesn't count for you lot...tell that to all those millions of scientists who don't get the opportunity to get their work published in the top journals.

If you know the editor, you have a good chance. If the editor hates you, as do most evolutionist editors, then the chance of even being sent for review are zero.

Sean Carrol over at PNAS hates my guts.

I never included anything about a "mighty creator"....I was tempted to include an "intelligent artificer" but did not do so.

DS said:

Atheistoclast said: My belief is not to believe anything unless it can be demonstrated. Darwinism is a *belief* desperate for evidence.

Unfortunately for you, gene duplication has been conclusively demonstrated to be a major mechanism for evolution. Even if it had some limitations, which you have failed to demonstrate, evolution would still be true and you would still be wrong. So all you have to do is ignore all of the evidence and then you can believe anything you want. Did you learn that trick from Behe, or did you come up with that all on your own. Now let's see, ignores all evidence, performs no research, offers no alternative. Now where have we seen such tactics before?

Indeed, the place and extent of natural selection as a force for change in molecular biology have been questioned in recent years [8].

Population genetics methods typically involve measuring levels of heterogeneity and polymorphism at sites including and in proximity to the one under investigation [36]. It can lead to confusing results because the effects of Darwinian selection are often the same as those of background selection—the purging of neutral alleles due to their spatial proximity to deleterious ones [37]

Further evidence for the role of selection in the development of Sdic includes a possible sweep found in the low levels of polymorphism across neighboring loci and a skewed frequency distribution of allelic variation. However, it is noted that a reduced level of heterozygosity in a region of low recombination, such as at the base of the X-chromosome where Sdic is located, is also consistent with background selection because of the effect of deleterious mutations [49].

In any case, as a mechanism for the creation of novel motifs and protein domains, de novo recruitment of noncoding DNA would seem extremely improbable and implausible.

[D]e novo gene origination from non-coding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes

Indeed, the place and extent of natural selection as a force for change in molecular biology have been questioned in recent years [8].

Population genetics methods typically involve measuring levels of heterogeneity and polymorphism at sites including and in proximity to the one under investigation [36]. It can lead to confusing results because the effects of Darwinian selection are often the same as those of background selection—the purging of neutral alleles due to their spatial proximity to deleterious ones [37]

Further evidence for the role of selection in the development of Sdic includes a possible sweep found in the low levels of polymorphism across neighboring loci and a skewed frequency distribution of allelic variation. However, it is noted that a reduced level of heterozygosity in a region of low recombination, such as at the base of the X-chromosome where Sdic is located, is also consistent with background selection because of the effect of deleterious mutations [49].

A key problem associated with the Darwinian mechanism of evolution is that many of the putative incipient and intermediate stages in the development of a biological trait may not be useful themselves and may even be harmful.

Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms.

Therefore, I have decided to define any gain in exonic information as: "The qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome."

Atheistoclast said: As for holocaust denial....I am a revisionist not a denialist. The account of the holocaust has changed since Nuremberg with the death toll at Auschwitz-Birkenau going down from 9 millon to less than 1 million - and it keeps falling as new research is done.

My belief is not to believe anything unless it can be demonstrated. Darwinism is a *belief* desperate for evidence.

Sorry about the double post.

Atheistoclast said: It seems like ,unless I publish in Nature, it doesn't count for you lot...tell that to all those millions of scientists who don't get the opportunity to get their work published in the top journals.

If you know the editor, you have a good chance. If the editor hates you, as do most evolutionist editors, then the chance of even being sent for review are zero. Sean Carrol over at PNAS hates my guts.

"A key problem associated with the Darwinian mechanism of evolution is that many of the putative incipient and intermediate stages in the development of a biological trait may not be useful themselves and may even be harmful."

Exactly. That's why gene duplication is such an important mechanism. By removing sequences form functional constraint, it provides the opportunity for exploring the adaptive topology.

"Therefore, although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms."

And there it is in black and white, the old conservation of information argument. And not just any information, but "highly complex information" at that. So gene duplication has been a major factor in shaping the genome, but it can't in any way make any new genes, even though they could be produced from non coding sequences. No wonder this guy can't get published in any real biology journals.

Thanks to Dave for the reference. I'm sure that anyone who has written a review would already be familiar with it.

Atheistoclast said: I never included anything about a "mighty creator"....I was tempted to include an "intelligent artificer" but did not do so. It seems like ,unless I publish in Nature, it doesn't count for you lot...tell that to all those millions of scientists who don't get the opportunity to get their work published in the top journals. If you know the editor, you have a good chance. If the editor hates you, as do most evolutionist editors, then the chance of even being sent for review are zero. Sean Carrol over at PNAS hates my guts.

DS said: Now I wonder why Sean has such a low opinion of you? Could it be that he sees right through your bullshit? Could it be that he wants to protect science form nut jobs who proclaim the end of the most tested and successful theory in all of science based on nothing but their own ignorance and incredulity? Could that have anything to do with it? You know Sean has actually done real experiments, right? You know he has earned the right to write review articles, right?

Atheioclast, do you consider your paper in Complexity to be original research?

RBH said: Let's bear in mind that "published in a peer-reviewed journal" is not synonymous" with "admitted to the canon." The vast majority of published papers in peer reviewed journals sink beneath the waves, never to be cited or heard about again. Passing peer review, however shakily, means only that a couple of reviewers and an editor thought it was worth putting out there to see if it might fly. My bet is that in this case, it won't.

So in one paper he argues that selection alone cannot produce any new information. In another paper he argues that gene duplication and mutation alone cannot produce new information. Sound familiar?

This is probably what got the Japanese in trouble in WWII. They figured that the US had boats, but they could not attack from the air and the US had planes but they could not fly far enough to attack. Therefore, it was impossible for any US planes to attack any targets in the Pacific! Perfect logic.

Mike Elzinga said: One of my “famous” papers is three blank pages in the Journal of Vacuum Science and Technology.

Atheioclast, precisely how much highly complex information is in the genome? How did you calculate it? Please be specific. Thanks.

DS said:

Mike Elzinga said: One of my “famous” papers is three blank pages in the Journal of Vacuum Science and Technology.

And yet that paper still had more highly complex information than the paper in Complexity. Go figure.

Mike Elzinga said: One of my “famous” papers is three blank pages in the Journal of Vacuum Science and Technology. In March 1990 the military swooped in and stopped the presses just as the journal was going to print. It’s still classified.

Atheistoclast doesn’t actually back this assertion up, but here’s a paper directly contradictiing his assertion: Zhou Q, G Zhang, Y Zhang, S Xu, R Zhao, Z Zhan, X Li, Y Ding, SYang & WWang (2008). On the origin of new genes in Drosophila. Genome Research gr.076588.108. From the paper (my emphasis):

[D]e novo gene origination from non-coding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes

That’s a pretty big percentage for such an improbable and implausible mechanism. Yet another example of the execrable quality of typical ID scholarship.

mrg said:

DS said:

Mike Elzinga said: One of my “famous” papers is three blank pages in the Journal of Vacuum Science and Technology.

And yet that paper still had more highly complex information than the paper in Complexity. Go figure.

"If a tree falls in a forest, and if it's classified information, does it still make a sound?"

Atheistoclast said: The problem with evolution science is that it is more a matter of *interpretation* than anything objective and determinable. Sometimes people want to see what actually isn't there.

Atheistoclast said:

Atheistoclast doesn’t actually back this assertion up, but here’s a paper directly contradictiing his assertion: Zhou Q, G Zhang, Y Zhang, S Xu, R Zhao, Z Zhan, X Li, Y Ding, SYang & WWang (2008). On the origin of new genes in Drosophila. Genome Research gr.076588.108. From the paper (my emphasis):

[D]e novo gene origination from non-coding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes

That’s a pretty big percentage for such an improbable and implausible mechanism. Yet another example of the execrable quality of typical ID scholarship.

Actually, I do back it up. In the case of CLLU1 - the "de novo" gene is more than likely a reactivated pseudogene (it was affected by a frameshift) and I explain why: the same is likely true for BSC4 in baker's yeast. Either that or the parallel deactivation in lineages was the responsible factor. Always look for the most parsimonious explanation. The research on fruit flies again only shows that in some lineages coding DNA has become non-coding. The dishonest evolutionists - notably Zhang et al - perverts this observation and claims that a sequence of non-coding DNA became coding. They fail to also describe what these "de novo" genes exactly do - *FAIL*. The idea that a random string of ncDNA can become exonized as a functional domain is derisory. The problem with evolution science is that it is more a matter of *interpretation* than anything objective and determinable. Sometimes people want to see what actually isn't there.

Stanton said: So why is a reactivated pseudogene not "new information" ...

Stanton said: So why is a reactivated pseudogene not "new information" and why do you call these people dishonest if the only crime they've committed is to come to a conclusion different than what your religious bigotries permit?

Atheistoclast said:

Stanton said: So why is a reactivated pseudogene not "new information" and why do you call these people dishonest if the only crime they've committed is to come to a conclusion different than what your religious bigotries permit?

In the case of CLLU1, one of two things happened: 1) A gene became pseuodogenized and then was reactivated in humans. It only took a single nucleotide indel. 2) A gene was psudogenized by parallel evolution in chimps and other primates but not in humans. Either way, no new information was created - it may only have been restored. It is *dishonest* to claim that a gene was created "de novo" when the more plausible explanations are given above. This is the latest *gimmick* of the Darwinists - namely that new genes and functionality can arise spontaneously and even miraculously. They tried as much with the frameshift mutation until I and others debunked this nonsense. They are running out of ideas....and time.

Atheistoclast said:

Stanton said: So why is a reactivated pseudogene not "new information" and why do you call these people dishonest if the only crime they've committed is to come to a conclusion different than what your religious bigotries permit?

In the case of CLLU1, one of two things happened: 1) A gene became pseuodogenized and then was reactivated in humans. It only took a single nucleotide indel. 2) A gene was psudogenized by parallel evolution in chimps and other primates but not in humans. Either way, no new information was created - it may only have been restored. It is *dishonest* to claim that a gene was created "de novo" when the more plausible explanations are given above. This is the latest *gimmick* of the Darwinists - namely that new genes and functionality can arise spontaneously and even miraculously. They tried as much with the frameshift mutation until I and others debunked this nonsense. They are running out of ideas....and time.

Atheistoclast said:

Stanton said: So why is a reactivated pseudogene not "new information" and why do you call these people dishonest if the only crime they've committed is to come to a conclusion different than what your religious bigotries permit?

In the case of CLLU1, one of two things happened: 1) A gene became pseuodogenized and then was reactivated in humans. It only took a single nucleotide indel. 2) A gene was psudogenized by parallel evolution in chimps and other primates but not in humans. Either way, no new information was created - it may only have been restored. It is *dishonest* to claim that a gene was created "de novo" when the more plausible explanations are given above. This is the latest *gimmick* of the Darwinists - namely that new genes and functionality can arise spontaneously and even miraculously. They tried as much with the frameshift mutation until I and others debunked this nonsense. They are running out of ideas....and time.

Malchus said: By the way, the correct term is "evolutionary biologist".

Atheioclast, you said that your forthcoming papers were original research. What lab did you use?

Do you consider your Complexity paper to be original research?

How much information is in the genome in question? How did you calculate it?

What prevents mutation from creating an exon from non-coding DNA?

Stanton said: Do you know what the original functions of the alleged pseudogenes are? Why do you insist on continuing using the slur "Darwinist," (sic) and alleging they're "running out of ideas....and time" if you have no desire or stomach to verify your claims with lab or field work?

Why do you insist on continuing using the slur "Darwinist," (sic) and alleging they're "running out of ideas....and time" if you have no desire or stomach to verify your claims with lab or field work?

Malchus said: Atheioclast, you said that your forthcoming papers were original research. What lab did you use? Do you consider your Complexity paper to be original research? How much information is in the genome in question? How did you calculate it? What prevents mutation from creating an exon from non-coding DNA?

SteveF said: He's trolling. It's all about getting attention and getting a reaction from people. At the moment he's succeeding.

Atheistoclast said:

Atheistoclast doesn’t actually back this assertion up, but here’s a paper directly contradictiing his assertion: Zhou Q, G Zhang, Y Zhang, S Xu, R Zhao, Z Zhan, X Li, Y Ding, SYang & WWang (2008). On the origin of new genes in Drosophila. Genome Research gr.076588.108. From the paper (my emphasis):

[D]e novo gene origination from non-coding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes

That’s a pretty big percentage for such an improbable and implausible mechanism. Yet another example of the execrable quality of typical ID scholarship.

Actually, I do back it up. In the case of CLLU1 - the "de novo" gene is more than likely a reactivated pseudogene (it was affected by a frameshift) and I explain why: the same is likely true for BSC4 in baker's yeast. Either that or the parallel deactivation in lineages was the responsible factor. Always look for the most parsimonious explanation. The research on fruit flies again only shows that in some lineages coding DNA has become non-coding. The dishonest evolutionists - notably Zhang et al - perverts this observation and claims that a sequence of non-coding DNA became coding. They fail to also describe what these "de novo" genes exactly do - *FAIL*. The idea that a random string of ncDNA can become exonized as a functional domain is derisory. The problem with evolution science is that it is more a matter of *interpretation* than anything objective and determinable. Sometimes people want to see what actually isn't there.

SteveF said: He's trolling. It's all about getting attention and getting a reaction from people. At the moment he's succeeding.

It was all done using some computer program.

Atheistoclast said:

Stanton said: Do you know what the original functions of the alleged pseudogenes are? Why do you insist on continuing using the slur "Darwinist," (sic) and alleging they're "running out of ideas....and time" if you have no desire or stomach to verify your claims with lab or field work?

Yes, it is a *gimmick*. They need "hopeful monsters" to explain phenomena: In the past, the frameshift mutation was one such option for them, now it is the turn of ncDNA. Evolutionism is a pseudo-religion as much in need of miracles as any faith-based cult. Btw, The "Darwinists" actually do call themselves as such: http://en.wikipedia.org/wiki/Neo-Darwinism They are proud of it!

Which was hashed out over at TalkRational. As a programmer, I can assure everyone that his programming skills are at the very best no better than his biology skills. Furthermore, they have much in common, in that both start with foregone conclusions and get tweaked until those conclusions are produced.

above should read:

You are correct that clastie is an hilariously awful programmer, howeveer the computer program being referred to in this instance is BLAST:

however even. jesus.

Actually, I do back it up. In the case of CLLU1 - the “de novo” gene is more than likely a reactivated pseudogene (it was affected by a frameshift) and I explain why: the same is likely true for BSC4 in baker’s yeast. Either that or the parallel deactivation in lineages was the responsible factor. Always look for the most parsimonious explanation.

However, this inference may be incorrect. Rather than the deletion creating a new stretch of translated DNA, it is likely that a back mutation restored the original ORF that became essentially divided in two as a result of an insertion— a very common phenomenon observed in indelinduced frameshifts [92].

The disabler [the additional adenine nuxcelotide-- DW] is also shared by gorilla and gibbon indicating it is ancestral

Mike Elzinga said: But this troll still hasn’t figured out the blatant misconceptions he has; and nobody should tell him.

Correction: the disabler is not present in orangutans. However, if you peruse the phylogenetic relationships of these species, it is present in the ancestral groups.

Atheistoclast said: snip 1) A gene became pseuodogenized and then was reactivated in humans. It only took a single nucleotide indel. 2) A gene was psudogenized by parallel evolution in chimps and other primates but not in humans. Either way, no new information was created - it may only have been restored. snip

If your answer to any of those is ‘NO’, then new information, by your own definition, is created. If your answer to all of the above is yes, then, what actually happened was, by your definition, nothing.

Here is another example of what atheistoclast says can't happen:

Arnegard et. al. (2010) Old gene duplication facilitates origin and diversification of an innovative communication system - twice. PNAS 107(51): 22172-22177.

It always amuses me what excuses creationists will make up for things they say can't happen when they are given examples of just that thing happening. They always find some ad hoc excuse for disqualifying the example. Of course no one is fooled by that. Oh well, there is always quote mining.

mrg said:

Mike Elzinga said: But this troll still hasn’t figured out the blatant misconceptions he has; and nobody should tell him.

"Should"? You might as well try to give a clue to a concrete block.

Mike Elzinga said: The psychology of con artists is certainly peculiar.

Apparently there must be some kind of reward they get for faking it. By playing to the rube market, they more quickly elevate themselves socially; and they don’t have to go through the discomfort of rigorous training.

One IDer I've been dealing with tried to tell me the fitness of a stable population was zero. When I pointed out the basic incoherence of his argument and suggested a course in population genetics, you know, so that he could get his basic facts straight, he admitted having taken it, but complained that it was a "waste of time" because the concept of fitness was nonsensical since it was based on differential reproductive success. Thoughts on the staircase: I should have replied that it wasn't a waste of time, it was just wasted on him.

Dave Wisker said: It's something peculiar to cranks. The true crank believes training in a subject blinds one to seeing the simple truth that the crank has discovered.

mrg said: In one sense, the "forest for the trees" observation is entirely correct. When an expert says: "This is obvious." -- the novice is better qualified than the expert to observe: "No, it is not."

mrg said: When an expert says: "This is obvious." -- the novice is better qualified than the expert to observe: "No, it is not."

Mike Elzinga said: My old, first edition copy of J.D. Jackson’s Classical Electrodynamics has several pages in it in which, as a grad student, I responded in frustration and wrote in pen “Damnit; this is not obvious!”

My old, first edition copy of J.D. Jackson’s Classical Electrodynamics has several pages in it in which, as a grad student, I responded in frustration and wrote in pen “Damnit; this is not obvious!” Then the next day, it was obvious; and it has been obvious ever since. Sometimes our brains fry when we are dog tired while trying to study.

mrg said: Well, if ID arguments start incorporating vector calculus, now you'll know who to blame.

Mike Elzinga said:

mrg said: In one sense, the "forest for the trees" observation is entirely correct. When an expert says: "This is obvious." -- the novice is better qualified than the expert to observe: "No, it is not."

My old, first edition copy of J.D. Jackson’s Classical Electrodynamics has several pages in it in which, as a grad student, I responded in frustration and wrote in pen “Damnit; this is not obvious!” Then the next day, it was obvious; and it has been obvious ever since. Sometimes our brains fry when we are dog tired while trying to study.

"Obvious in hindsight" is, also not quite the same as "obvious".

DS said: Here is another example of what atheistoclast says can't happen: Arnegard et. al. (2010) Old gene duplication facilitates origin and diversification of an innovative communication system - twice. PNAS 107(51): 22172-22177. It always amuses me what excuses creationists will make up for things they say can't happen when they are given examples of just that thing happening. They always find some ad hoc excuse for disqualifying the example. Of course no one is fooled by that. Oh well, there is always quote mining.

PNAS has become pure evolutionist propaganda in recent weeks. It is really sickening to see the editors determined to publish any garbage that supports their dying ideology.

Dave Wisker said: RA Fisher was one of those biologists who would casually toss off something as if it were obvious, and leave us mortals struggling to figure it out, then eventually kicking ourselves when it did become obvious.

Gabriel Hanna said: When you die, if you go to heaven, you may then understand Jackson.

Atheistoclast said: PNAS has become pure evolutionist propaganda in recent weeks. It is really sickening to see the editors determined to publish any garbage that supports their dying ideology.

I heard a story that the hospital room where Pauli died was Room 137.

Atheistoclast said: PNAS has become pure evolutionist propaganda in recent weeks. It is really sickening to see the editors determined to publish any garbage that supports their dying ideology.

In my forthcoming paper I question whether the really essential stuff in our genome - the encoded and conserved protein domains - could have been generated by a process of chance and selection. I think I may have a anti-evolutionist mathematical theorem to finally settle this issue once and for all. It is time that Darwinism collapses just as Marxism did. The Berlin wall moment is nigh!

The Soviet empire collapsed in 5 years...so shall Darwinism.

It is time for regime change.

Stanton said:

Atheistoclast said: PNAS has become pure evolutionist propaganda in recent weeks. It is really sickening to see the editors determined to publish any garbage that supports their dying ideology.

Tell us again why we should assume that you're an authority on Evolutionary Biology even though you've confessed that you have neither the funds, nor desire to do actual research? How come you refuse to spell out exactly how and why saying "DESIGNERDIDIT" is supposed to have greater explanatory power than assuming common descent?

Atheistoclast said:

Stanton said:

Atheistoclast said: PNAS has become pure evolutionist propaganda in recent weeks. It is really sickening to see the editors determined to publish any garbage that supports their dying ideology.

Tell us again why we should assume that you're an authority on Evolutionary Biology even though you've confessed that you have neither the funds, nor desire to do actual research? How come you refuse to spell out exactly how and why saying "DESIGNERDIDIT" is supposed to have greater explanatory power than assuming common descent?

No, I do do original research - just not with this particular paper which was a meta-analysis. I am a computational biologist and so don't need chemicals, freezers and a lab coat.

I am convinced that Randy Schekman, editor of PNAS, has given orders to admit any paper that is seen as defending Darwinism whilst rejecting those papers that question it. He even told me to not email him any more he was so upset with me.

Ah, good! We've entered the violent rhetoric stage of the discussion.

Will the revolution occur before or after Atheistoclast provides substantive responses to all the questions that have been posted here?

Stanton said: So, how does being a computational biologist make you smarter than all of the other biologists in the whole wide world?

Atheistoclast said: In my forthcoming paper I question whether the really essential stuff in our genome - the encoded and conserved protein domains - could have been generated by a process of chance and selection. I think I may have a anti-evolutionist mathematical theorem to finally settle this issue once and for all. It is time that Darwinism collapses just as Marxism did. The Berlin wall moment is nigh! The Soviet empire collapsed in 5 years...so shall Darwinism. It is time for regime change.

SWT said: Ah, good! We've entered the violent rhetoric stage of the discussion. Will the revolution occur before or after Atheistoclast provides substantive responses to all the questions that have been posted here?

So Atheistoclast,

I would really like to know the answers to these questions. They have stumped you guys for decades. I can't wait for an answer.

1) What is the difference in complexity between a designed thing and a non-designed thing?

2) How (units and process) does one measure complexity?

3) What is the value of the above measure for a designed thing?

4) What is the value of the above measure for a non-designed thing?

5) Does ID only apply to a) the universe b) living things c)small parts of living things? Why?

6) In reference to '5' above, who is the designer. (I do hope you realize that the answer to '5' depends on the answer to '6' and that the wrong answer just means that it is logically impossible for the designer one envisions to exist.)

Thanks in advance.

Atheistoclast said:

Stanton said: So, how does being a computational biologist make you smarter than all of the other biologists in the whole wide world?

I never claimed I was.

Atheistoclast said:

SWT said: Ah, good! We've entered the violent rhetoric stage of the discussion. Will the revolution occur before or after Atheistoclast provides substantive responses to all the questions that have been posted here?

I already have. At the end of the day, this boils down to a matter of interpretation. You are prepared to ignore all sense and believe that natural selection is essentially divine (the real creator god)...fine...but this is a *religious* belief.

mrg said: I heard a story that the hospital room where Pauli died was Room 137.

No, I do do original research - just not with this particular paper which was a meta-analysis.

SWT said: Ah, good! We've entered the violent rhetoric stage of the discussion. Will the revolution occur before or after Atheistoclast provides substantive responses to all the questions that have been posted here?

Atheistoclast said:

Stanton said: So, how does being a computational biologist make you smarter than all of the other biologists in the whole wide world?

I never claimed I was. I just don't indulge in any speculation and extrapolation to justify my research grant as the others do. Science, including evolutionary theory, is big business. Do you think the likes of Lenski, Miller and Carrol are just in it for the honor? Dawkins has made a small fortune selling Darwinism to the masses. Seriously, I would be an evolutionist if I was paid well enough. Give me $100,000 and I will write a paper praising the innovation resulting from gene duplication.

Atheistoclast said: In my forthcoming paper I question whether the really essential stuff in our genome - the encoded and conserved protein domains - could have been generated by a process of chance and selection.

I think I may have a anti-evolutionist mathematical theorem to finally settle this issue once and for all.

It is time that Darwinism collapses just as Marxism did. The Berlin wall moment is nigh! The Soviet empire collapsed in 5 years...so shall Darwinism. It is time for regime change.

Atheistoclast said: Yes, it is a *gimmick*. They need "hopeful monsters" to explain phenomena: In the past, the frameshift mutation was one such option for them, now it is the turn of ncDNA. Evolutionism is a pseudo-religion as much in need of miracles as any faith-based cult. Btw, The "Darwinists" actually do call themselves as such: http://en.wikipedia.org/wiki/Neo-Darwinism They are proud of it!

Dale Husband said:

Atheistoclast said: Yes, it is a *gimmick*. They need "hopeful monsters" to explain phenomena: In the past, the frameshift mutation was one such option for them, now it is the turn of ncDNA. Evolutionism is a pseudo-religion as much in need of miracles as any faith-based cult. Btw, The "Darwinists" actually do call themselves as such: http://en.wikipedia.org/wiki/Neo-Darwinism They are proud of it!

Gee, it seems that when Creationist trolls lie, they lie outright. Can't you be a bit more clever and tell half-truths?

Stanton said: You might as well ask for the Moon, then.

Rog said: So we have established you are a prostitute.

Dave Wisker said: Atheistoclast writes:

No, I do do original research - just not with this particular paper which was a meta-analysis.

Choosing a few papers and extrapolating from them is not meta-analysis. Considering that you missed one important study on the Drosophila genome that didn't support your thesis tells us your search criteria for studies that should have been included in the meta-analysis are laughable. And if you think you made any kind of legitimate statistical analysis of your data, you are sadly mistaken. You are nothing but a poseur.

mrg said:

Rog said: So we have established you are a prostitute.

"Now, we're just discussing the price."

I'm sure, you're diligently working on the questions.

Thanks

Atheistoclast said: Come one, everyone, just admit that Darwinism is a cult.

OgreMkV said: I'm sure, you're diligently working on the questions. Thanks

A common objection to natural selection as the mechanism for evolution is that while it may act as an editor, it cannot be an author. That is, it may change genetic information through mutation, but it cannot cause genetic information to increase. And they are right, but genetic information can still increase across the generations of organisms through a process called nondisjunction. This occurs when an unequal amount of genetic material is passed on to two daughter cells after the process of a cell dividing. One cell will have slightly less genetic material, and the other will have slightly more. The most famous example of nondisjunction is the kind that causes Down’s Syndrome, when a human embryo receives three 21st chromosomes from its parents rather than the normal number of two. But nondisjunction can occur regarding any chromosome in any organism and may not even involve chromosomes at all, such as in the case of bacteria. Let us imagine that three billion years ago, a bacterial cell was dividing, but because of a chemical malfunction, slightly less genetic material ended up in one daughter cell, and slightly more in the other. The cell with less material will probably end up smaller, while the cell with more material may end up larger, because a greater amount of genetic material can produce a greater amount of proteins, the molecules that provide the structural basis for all organisms. Larger cells (assuming the reproductive potential of the different cells was the same) would have an advantage over smaller cells in the race to gain food, thus natural selection would favor larger cells. If this process was repeated many times, then it is possible that over a billion years a bacterial cell would have emerged that had hundreds of times more genetic material than the first primitive organisms that arose on Earth about four billion years ago. And that would have enabled the evolution of more complex organisms than bacteria…including us!

Atheistoclast said: It amuses me that people like yourself never actually these pro-Darwinist papers beyond the title and abstract. I actually read the paper on the sodium channel gene duplication and I can tell you that the authors were making an extraordinary extrapolation - just as Cheng and the Chinese team are exaggerating the "novelty" of the antifreeze gene. I wrote a letter to PNAS but it was rejected. I have written another one for the Cheng paper. As for CLLU1, what you are amazingly claiming is that a single nucleotide insertion created a brand new gene!! I am saying that the disabling mutation's presence in the African apes is the result of a parallel deactivation (as the authors considered but chose not to accept) or, to assume a common descent, that the disabler was already inherited in the hominid lineage. Come on, it is pretty obvious that an immune system gene can become disabled.

Atheistoclast said: Evolutionists are the biggest attention whores...just remember this time last year with all the hype and sensationalism surrounding the discovery of Australopithecus sediba. And what about "Ida" - it was even called the "Holy Grail"....and the "Lost Ark"!!! http://www.timesonline.co.uk/tol/comment/columnists/guest_contributors/article6360606.ece Come one, everyone, just admit that Darwinism is a cult.

Dale Husband said:

Atheistoclast said: Evolutionists are the biggest attention whores...just remember this time last year with all the hype and sensationalism surrounding the discovery of Australopithecus sediba. And what about "Ida" - it was even called the "Holy Grail"....and the "Lost Ark"!!! http://www.timesonline.co.uk/tol/comment/columnists/guest_contributors/article6360606.ece Come one, everyone, just admit that Darwinism is a cult.

You are lying yet again. The media blew those up, not scientists. Remember, assertions made without evidence can be dismissed without evidence. And you are full of them!

Yes, a brand new gene is formed every time a single nucleotide changes, you idiot! How is that even controversial??? And no one denies that genes become disabled. What about all that "junk DNA" that is thought to result from disabled genes from millions of years ago?

You are a classic example of a clueless person who overestimates himself.

Wait...didn't "darwinism" fall and the "regime change" with the release of Expelled? Or was it when the ID experts took the stand in Dover?

Dang, you need a scorecard to keep up with all the deaths of the TOE!

The paper was on gene duplication and not “de novo” creation. I mentioned the latter in passing because I focused on an example of alleged “de novo” recruitment in a case of gene duplication. The subject probably requires another paperand getting access to ncDNA data is tricky.

We find that, 1) tandem gene duplication has generated about 80% of the nascent duplicates that are limited to single species (D. melanogaster or D. yakuba); 2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional

I am especially proud of my debunking of frameshifts. I put a lot of effort into the alignment in Figure 2.

-clast, I'm hurt, you haven't responded to my questions that actually blow whatever it is you are claiming out of the water.

Nevermind, hard questions never get answered from intellectual cowards.

Atheistoclast said: It is time that Darwinism collapses just as Marxism did. The Berlin wall moment is nigh! The Soviet empire collapsed in 5 years...so shall Darwinism. It is time for regime change.

OgreMkV said: -clast, I'm hurt, you haven't responded to my questions that actually blow whatever it is you are claiming out of the water. Nevermind, hard questions never get answered from intellectual cowards.

Mike Elzinga said:

RBH said: Let's bear in mind that "published in a peer-reviewed journal" is not synonymous" with "admitted to the canon." The vast majority of published papers in peer reviewed journals sink beneath the waves, never to be cited or heard about again. Passing peer review, however shakily, means only that a couple of reviewers and an editor thought it was worth putting out there to see if it might fly. My bet is that in this case, it won't.

One of my “famous” papers is three blank pages in the Journal of Vacuum Science and Technology. In March 1990 the military swooped in and stopped the presses just as the journal was going to print. It’s still classified.

Atheistoclast said:

Yes, a brand new gene is formed every time a single nucleotide changes, you idiot! How is that even controversial??? And no one denies that genes become disabled. What about all that "junk DNA" that is thought to result from disabled genes from millions of years ago?

LOL. Never heard of a synonymous change before? Even non-synonymous changes don't lead to "brand new genes". ATP6 has been mutating in different lineages for billions of years and it is still...ATP6.

CLLU1 ,and also BSC4, are examples of either parallel deactivation or a reactivation. Psueodgenes are technically part of ncDNA. Either way, the probability of creating a new gene by exonizing a random piece of ncDNA is ridculously small.

Remember that a generic protein ,consisting of 300 residues, is one out of 20^300 possible combinations.

You are a classic example of a clueless person who overestimates himself.

I'm part of the peer-reviewed authorship and you are not! Deal with it. My panda's thumb to you.

Atheistoclast said: Seriously, I would be an evolutionist if I was paid well enough. Give me $100,000 and I will write a paper praising the innovation resulting from gene duplication.

Stuart Weinstein said:

Mike Elzinga said:

RBH said: Let's bear in mind that "published in a peer-reviewed journal" is not synonymous" with "admitted to the canon." The vast majority of published papers in peer reviewed journals sink beneath the waves, never to be cited or heard about again. Passing peer review, however shakily, means only that a couple of reviewers and an editor thought it was worth putting out there to see if it might fly. My bet is that in this case, it won't.

One of my “famous” papers is three blank pages in the Journal of Vacuum Science and Technology. In March 1990 the military swooped in and stopped the presses just as the journal was going to print. It’s still classified.

In other words, Mike could tell us more, but then he'd have to kill us.

For Atheistoclast's attention: a new protein-coding gene in the maize mitochondrial genome, cobbled together from different segments of the genome that did not code for proteins before: TURF-13. PT contributor Art Hunt posted about it here:

http://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html

Dave Wisker said: For Atheistoclast's attention: a new protein-coding gene in the maize mitochondrial genome, cobbled together from different segments of the genome that did not code for proteins before: TURF-13. PT contributor Art Hunt posted about it here: http://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html

DS said:

Dave Wisker said: For Atheistoclast's attention: a new protein-coding gene in the maize mitochondrial genome, cobbled together from different segments of the genome that did not code for proteins before: TURF-13. PT contributor Art Hunt posted about it here: http://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html

That doesn't count because ... well give me a minute here. I didn't actually bother to read the paper, but I know it can't be a good enough example, because then everything I want to believe would be wrong and people would be justified in ignoring me. So there has to be some reason why I refuse to accept it. Let's see, it really is a new gene with a completely new function. And it really didn't just poof out of nowhere, they really do know where it came form. And it does have information, which I guess has to be new information, so I can't use that old ploy again. Well, it's just a plant right? that doesn't count because very everyone knows that plants aren't intelligent, so where did the new information come from? Yea, I'm going with that. See cause selection couldn't produce new information and mutation couldn't produce it, at least by some definition that I won't define. Now all I have to do is convince some editor in Landscape Digest Monthly to publish this wild speculation and everyone will be fooled. I'm sure I'll get the Nobel Prize or something just as good. This science stuff isn't so hard after all.

What I don't understand is, if this guy is so keen on being one of those rich and famous scientists, why doesn't he actually do some research and find the real mechanisms of evolution? If mutation, selection, gene duplication, drift, etc. aren't enough, then what is? How does it really work? Where is the evidence for it? Now that would be a way to get rich and famous, finding a new molecular mechanism for evolutionary change. After all, it worked for Sean Carrol.

Now why do you suppose anyone would just whine and cry about how nobody else is right? Why would anyone refuse to do any research to demonstrate an alternative? It couldn't be because "poof" is really the answer could it? Well, that sure would explain a lot.

DS said: What I don't understand is, if this guy is so keen on being one of those rich and famous scientists, why doesn't he actually do some research and find the real mechanisms of evolution? If mutation, selection, gene duplication, drift, etc. aren't enough, then what is? How does it really work? Where is the evidence for it? Now that would be a way to get rich and famous, finding a new molecular mechanism for evolutionary change. After all, it worked for Sean Carrol. Now why do you suppose anyone would just whine and cry about how nobody else is right? Why would anyone refuse to do any research to demonstrate an alternative? It couldn't be because "poof" is really the answer could it? Well, that sure would explain a lot.

Dave Wisker said: For Atheistoclast's attention: a new protein-coding gene in the maize mitochondrial genome, cobbled together from different segments of the genome that did not code for proteins before: TURF-13. PT contributor Art Hunt posted about it here: http://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html

OgreMkV said: No no, it was done in a lab and therefore only shows that intelligent is needed to do something with it. Or observe it or something.

Atheistoclast said:

Dave Wisker said: For Atheistoclast's attention: a new protein-coding gene in the maize mitochondrial genome, cobbled together from different segments of the genome that did not code for proteins before: TURF-13. PT contributor Art Hunt posted about it here: http://pandasthumb.org/archives/2007/05/on-the-evolutio-1.html

Sorry, but is this an actual paper on a maize gene or just a thought experiment? I could not find any link? Just to point out. I debunk the following "new genes" and "evolutionary innovation" in my paper: 1) I debunked the bullshit on Sdic. 2) I debunked the bullshit on "nylonase" and frameshifts in general. 3) I debunked the bullshit on Kua-UEV. 4) I debunked the bullshit on "jingwei" 5) I debunked the bullshit on RNASE1B 6) I debunked the bullshit on the trypsingogen-AFGP conversion. 7) I debunked the bullshit on CLLU1. Perhaps I needed to go further but the paper was getting too long in any case. If you want me to write another paper on some other examples of "new genes" or on this latest antifreeze, I will do so. As I say, I have already sent a letter to the editor of PNAS. Just give me your list and I will do the research.

Dave Wisker said: Typical phony poseur scholarship. Now you want me to do your research for you. Frak off. By the way, Art Hunt included all the necessary references in that post. Or do you need to be spoon-fed?

Debunked = made up excuses

Keep going genius, only 100,000 more examples to "debunk". When you're finished with that there will be a million more. In the end, all you will just have to admit that the things you denied are happening all the time whether you like it or not. It is logically impossible to disprove a mechanism by disproving individual examples.

Here is another paper for you to "debunk" (along with all of the references included therein):

Long M, Betran B, Thornton K, Wang W. 2003. The origin of new genes: Glimpses from the young and old. Nature Rev Genet. 4: 865-875.

Now, exactly what is your point in all of this hand waving? Are you trying to show that we don't know everything about how evolution works, therefore there is an excuse to believe in god? How do you know we don't already believe in god? How do you know if we need any excuses? You do know that there is definitive v=evidence that evolution actually occurred don't you? You do now that no matter what the mechanism was, it has no bearing on whether you have to believe in a god or not, right? You do know that god of the gaps arguments never work, right?

DS said: Debunked = made up excuses Keep going genius, only 100,000 more examples to "debunk". When you're finished with that there will be a million more. In the end, all you will just have to admit that the things you denied are happening all the time whether you like it or not. It is logically impossible to disprove a mechanism by disproving individual examples. Here is another paper for you to "debunk" (along with all of the references included therein): Long M, Betran B, Thornton K, Wang W. 2003. The origin of new genes: Glimpses from the young and old. Nature Rev Genet. 4: 865-875. Now, exactly what is your point in all of this hand waving? Are you trying to show that we don't know everything about how evolution works, therefore there is an excuse to believe in god? How do you know we don't already believe in god? How do you know if we need any excuses? You do know that there is definitive v=evidence that evolution actually occurred don't you? You do now that no matter what the mechanism was, it has no bearing on whether you have to believe in a god or not, right? You do know that god of the gaps arguments never work, right?

Btw, up to 80% of the genes in your genome are recongnizably paralogs of more basic genes.

They have not functionally diverged in any major way since most are redundant. You can knock one out and another will take over. Many duplicates have degenerated and you can see this when you align their sequences.

Gene duplication increases the size and versatility of the genome - especially in plants - but does not add to its information content and certainly not to organismic complexity.

The sooner you lot realize this the sooner we can kill off this satanic paradigm.

Atheistoclast said: Gene duplication increases the size and versatility of the genome - especially in plants - but does not add to its information content and certainly not to organismic complexity.

Atheistoclast said: The sooner you lot realize this the sooner we can kill off this satanic paradigm.

Atheistoclast said: Btw, up to 80% of the genes in your genome are recongnizably paralogs of more basic genes. They have not functionally diverged in any major way since most are redundant. You can knock one out and another will take over. Many duplicates have degenerated and you can see this when you align their sequences.

Gene duplication increases the size and versatility of the genome - especially in plants - but does not add to its information content and certainly not to organismic complexity. The sooner you lot realize this the sooner we can kill off this satanic paradigm.

eric said:

Atheistoclast said: The sooner you lot realize this the sooner we can kill off this satanic paradigm.

And there you have the real motivation, in a single, simple sentence. For these guys, its not about finding a better explanation for how species arise; its about removing a good explanation that is religiously threatening.

Mike Elzinga said: Either he is just mooning everybody here and getting a big kick out of it, or he is so damned deluded that he stands naked before the entire world imagining himself dressed in the robes of a king.

Atheistoclast said: Btw, up to 80% of the genes in your genome are recongnizably paralogs of more basic genes. They have not functionally diverged in any major way since most are redundant. You can knock one out and another will take over. Many duplicates have degenerated and you can see this when you align their sequences. Gene duplication increases the size and versatility of the genome - especially in plants - but does not add to its information content and certainly not to organismic complexity. The sooner you lot realize this the sooner we can kill off this satanic paradigm.

Atheistoclast the attention whoresaid: The sooner you lot realize this the sooner we can kill off this satanic paradigm.

Atheistoclast said:

DS said: Debunked = made up excuses Keep going genius, only 100,000 more examples to "debunk". When you're finished with that there will be a million more. In the end, all you will just have to admit that the things you denied are happening all the time whether you like it or not. It is logically impossible to disprove a mechanism by disproving individual examples. Here is another paper for you to "debunk" (along with all of the references included therein): Long M, Betran B, Thornton K, Wang W. 2003. The origin of new genes: Glimpses from the young and old. Nature Rev Genet. 4: 865-875. Now, exactly what is your point in all of this hand waving? Are you trying to show that we don't know everything about how evolution works, therefore there is an excuse to believe in god? How do you know we don't already believe in god? How do you know if we need any excuses? You do know that there is definitive v=evidence that evolution actually occurred don't you? You do now that no matter what the mechanism was, it has no bearing on whether you have to believe in a god or not, right? You do know that god of the gaps arguments never work, right?

There are 100,000 examples now? Where did you get that figure from, may I ask? Could it be somewhere dark and where the sun don't shine? The Long, Thornton and Betran paper was actually the review I used to select the "juiciest" examples of new gene evolution. From their list of about 30 or so "new genes" the following are included in my paper: 1) Sdic 2) FUT3/6 3) AFGP genes 4) Kua-UEV 5) TRE 6) RNASE1B 7) Jingwei 8) Adh-twain/ Adh-finnegan All comprehensively debunked and exposed. I am tempted to write a rejoinder to the latest paper by Long et al. - and explain what has really happened - but it is going to take time. Darwinism is running out of ideas.

I also note, in passing, that Bozorgmehr or Atheioclast, is not a computational biologist; is not affiliated with any labs or educational institutions; and is merely a failed businessman. This does not necessarily make him wrong; but it does seriously undermine his credibility when he lies about his profession.

Malchus said: Interestingly, I note that your claim to have "debunked" any of these is categorically false. Each "debunking" seems to consist of your claim that you simply don't believe it. But you provide no actual support for your opinion. Your understanding of genetics is, it appears, sadly superficial.

Atheistoclast said:

DS said: Debunked = made up excuses Keep going genius, only 100,000 more examples to "debunk". When you're finished with that there will be a million more. In the end, all you will just have to admit that the things you denied are happening all the time whether you like it or not. It is logically impossible to disprove a mechanism by disproving individual examples. Here is another paper for you to "debunk" (along with all of the references included therein): Long M, Betran B, Thornton K, Wang W. 2003. The origin of new genes: Glimpses from the young and old. Nature Rev Genet. 4: 865-875. Now, exactly what is your point in all of this hand waving? Are you trying to show that we don't know everything about how evolution works, therefore there is an excuse to believe in god? How do you know we don't already believe in god? How do you know if we need any excuses? You do know that there is definitive v=evidence that evolution actually occurred don't you? You do now that no matter what the mechanism was, it has no bearing on whether you have to believe in a god or not, right? You do know that god of the gaps arguments never work, right?

There are 100,000 examples now? Where did you get that figure from, may I ask? Could it be somewhere dark and where the sun don't shine? The Long, Thornton and Betran paper was actually the review I used to select the "juiciest" examples of new gene evolution. From their list of about 30 or so "new genes" the following are included in my paper: 1) Sdic 2) FUT3/6 3) AFGP genes 4) Kua-UEV 5) TRE 6) RNASE1B 7) Jingwei 8) Adh-twain/ Adh-finnegan All comprehensively debunked and exposed. I am tempted to write a rejoinder to the latest paper by Long et al. - and explain what has really happened - but it is going to take time. Darwinism is running out of ideas.

Malchus said: I also note, in passing, that Bozorgmehr or Atheioclast, is not a computational biologist; is not affiliated with any labs or educational institutions; and is merely a failed businessman. This does not necessarily make him wrong; but it does seriously undermine his credibility when he lies about his profession.

Actually, you are a confirmed internet troll; your postings on Pharyngula established that you are unable to deal with discussion or argument, and that your understanding of genetics is highly limited.

You are not an independent scientist; you are a failed businessman with too much time on his hands. What science are you doing? What lab do you use in your work? What actual original research have you done?

You are the kind of person who gives Christians a bad name by continuing to bear false witness.

You are also remarkably poor at actual discussion; I am disappointed.

Atheistoclast said: There are 100,000 examples now? Where did you get that figure from, may I ask? Could it be somewhere dark and where the sun don't shine? The Long, Thornton and Betran paper was actually the review I used to select the "juiciest" examples of new gene evolution. From their list of about 30 or so "new genes" the following are included in my paper: 1) Sdic 2) FUT3/6 3) AFGP genes 4) Kua-UEV 5) TRE 6) RNASE1B 7) Jingwei 8) Adh-twain/ Adh-finnegan All comprehensively debunked and exposed. I am tempted to write a rejoinder to the latest paper by Long et al. - and explain what has really happened - but it is going to take time. Darwinism is running out of ideas.

As additional evidence for your dishonesty, I note the pesudonym you used to author this paper: http://www.wepapers.com/Papers/52959/Report_on_the_Iranian_presidential_election_2009.

I also note that your business was shut down because you broke the law.

You have not established the credibility required for us to even take your opinions seriously.

Malchus said: I also note, in passing, that Bozorgmehr or Atheioclast, is not a computational biologist; is not affiliated with any labs or educational institutions; and is merely a failed businessman. This does not necessarily make him wrong; but it does seriously undermine his credibility when he lies about his profession.

He posts under various aliases on the net; he has at least twenty-seven for Richard Dawkin's site because he keeps being banned for trolling.

He appears fundamentally dishonest and remarkable egocentric.

Btw, up to 80% of the genes in your genome are recongnizably paralogs of more basic genes.

They have not functionally diverged in any major way since most are redundant.

You can knock one out and another will take over.

Many duplicates have degenerated and you can see this when you align their sequences.

Gene duplication increases the size and versatility of the genome - especially in plants - but does not add to its information content and certainly not to organismic complexity.

The sooner you lot realize this the sooner we can kill off this satanic paradigm.

OgreMkV said: "Becoming a scientist to get rich and famous is like becoming a Bishop to get girls."

It isn’t being a failed businessman that makes him wrong; it’s being wrong that makes him wrong.

Atheistoclast said: I never claimed I was affiliated with any institution. But computational biologist I am. I am an independent scientist.

Anyway, my next papers are soon to be published causing more anguish and disappointment for the Panda folks here.

I’d also love to hear why, after you’ve told us in multiple posts how neither deletions nor duplications increase information content, why information content matters at all for evolution.

How do you measure complexity (values, units, and process for determination)? How do you measure information (values, units, and process for determination)? What’s the difference in complexity between a designed thing and a non-designed thing of equal mass and makeup? What values of complexity indicate design? Why? What values of complexity indicate evolution? Why? And you do realize that by ignoring these questions again, you are admitted that all the things you’ve been peddling are BS.

eric said: As an aside, this guy's posts have provoked some great science-containing responses. Thanks for that to all, but especially Dave Whisker.

The sooner you lot realize this the sooner we can kill off this satanic paradigm.

From what I can tell, the oft repeated taunt that IDiots and Creationists haven’t published in peer reviewed journals is just red meat for the trolls to feed on. In the end it doesn’t matter what journal you get published in. What matters are your ideas.

Scott F said: Having never published a thing (and my apologies to those who struggle to make a living at it), which publication you get your article in appears to be merely counting coup among real scientists. From what I can tell, the oft repeated taunt that IDiots and Creationists haven't published in peer reviewed journals is just red meat for the trolls to feed on. In the end it doesn't matter what journal you get published in. What matters are your ideas. If your ideas don't fly, even getting published in "Science" (once) won't do you a bit of good.

Atheistoclast said: Just to point out. I debunk the following "new genes" and "evolutionary innovation" in my paper: 1) I debunked the bullshit on Sdic. 2) I debunked the bullshit on "nylonase" and frameshifts in general. 3) I debunked the bullshit on Kua-UEV. 4) I debunked the bullshit on "jingwei" 5) I debunked the bullshit on RNASE1B 6) I debunked the bullshit on the trypsingogen-AFGP conversion. 7) I debunked the bullshit on CLLU1. Perhaps I needed to go further but the paper was getting too long in any case. If you want me to write another paper on some other examples of "new genes" or on this latest antifreeze, I will do so. As I say, I have already sent a letter to the editor of PNAS. Just give me your list and I will do the research.

Flint said: While bad ideas deserve to be forgotten, good ideas are more likely to be noticed if they are not buried in mountains of chaff.

Dale Husband said: Yet the loon won't show his work where he did all that debunking. I cry fraud! Creationists have been claiming to debunk evolution for at least a century, and they always fail.

DS said: It's worse than that. No matter how many examples he claims are now good enough for him, his basic premise is that you can't create information without intelligence. He has not demonstrated any theoretical reason for supposing that this is the case, let alone any evidence that this is the case. On the other hand, he has admitted that lots of important things happen because of mutation and gene duplication, but I guess this doesn't count as highly specified and complexified information (whatever that might be).

Mike Elzinga said: It’s like setting off a firecracker behind someone who doesn’t flinch; and you realize the person is stone deaf.

This “Code of Life” series is the latest example of a creationist chattering without understanding the significance of the examples she is using.

Mike Elzinga said: This “Code of Life” series is the latest example of a creationist chattering without understanding the significance of the examples she is using.

mrg said:

Mike Elzinga said: This “Code of Life” series is the latest example of a creationist chattering without understanding the significance of the examples she is using.

I like to time myself when listening to nutjob videos. I got about 15 seconds into this one. At moments she reminded me of Byers. Hand me one of the BIG firecrackers, will ya?

Mike Elzinga said: This “Code of Life” series is the latest example of a creationist chattering without understanding the significance of the examples she is using.

Dave Wisker said:

Mike Elzinga said: This “Code of Life” series is the latest example of a creationist chattering without understanding the significance of the examples she is using.

I love how she makes the assumptions about increasing complexity = increased information = larger genomes, then when there are exceptions to it, it's all of a sudden a problem for the evolutionists.

Mike Elzinga said:

Dave Wisker said:

Mike Elzinga said: This “Code of Life” series is the latest example of a creationist chattering without understanding the significance of the examples she is using.

I love how she makes the assumptions about increasing complexity = increased information = larger genomes, then when there are exceptions to it, it's all of a sudden a problem for the evolutionists.

It is such a characteristic of creationists to just make up crap as they go. There are no exceptions. They do this right out in public where everyone can watch, and they don’t seem to care that experts can observe them making complete fools of themselves. It speaks volumes about the coercive subculture in which they live. It’s even scarier that they have such gullible audiences.

Dave Wisker said: What's truly infuriating is how they will tailor their responses to different audiences. Jonathan Wells, for example, will not say "Peppered moths do not rest on tree trunks" to a knowledgeable audience because they know this is false, but I have personally heard him say exactly that at an ID conference.

Flint said:

From what I can tell, the oft repeated taunt that IDiots and Creationists haven’t published in peer reviewed journals is just red meat for the trolls to feed on. In the end it doesn’t matter what journal you get published in. What matters are your ideas.

It's been my impression that peer review exists for some good reason, and that even those scientists whose efforts don't get past peer review seem to agree it's a Good Thing. Something about improving the chances that your ideas ARE good ones, that your conclusions are supported by your data, that your data were obtained appropriately, stuff like that. While bad ideas deserve to be forgotten, good ideas are more likely to be noticed if they are not buried in mountains of chaff.

Impact factor isn't that good an indicator of quality IMO. In fact some of the top journals have some of the worst papers, I suspect because big names tend to be treated with too much respect, and because really cool findings are sought after by the biggest journals, and really cool findings that are also true are rarer than really cool findings that turn out to be flakey.

The most reliable findings are the replicated ones, and replications tend not to find their way into the coolest journals.

The only real way to tell a good paper from a bad one is to read it really thoroughly.

Not even peer-reviewers always do that.

I agree about the impact factor. I was looking at the impact factors of journals. The biggies like Nature, Science, and PNAS have huge numbers compared to the Royal Society Transactions. I haven't seen anybody looking down their noses at the Royal Society lately.

As I mentioned a few pages ago, making judgments about impact factor is to some extent discipline-dependent. In chemical engineering (my discipline), it's generally considered a good thing to be published in AIChE Journal and Chem. Eng. Science, both of which have impact factors around 2. My students are frequently pushing to submit manuscripts to "better" (higher impact factor) journals, when they're actually likely to get better citation results by getting their material in front of the eyes of the people who care most about their field of research. I also remind my students that the very best way to get good citation results is to do outstanding work and present it with great precision and clarity.

DS said:

Atheistoclast said:

Why should the opinion of one person, who wrote one review paper somewhere, be considered as important as the thousands of papers where the authors reached exactly the opposite conclusion?

You are making a flawed argument from authority. Science isn't based on votes. I could be right and the entire scientific community could be wrong. If you can't be bothered to read the paper, let alone consider its conclusions, then you are not interested in gaining any knowledge. Darwin himself had to oppose conventional thinking in his day when he published his magnum opus.

No I'm not. I am simply saying that the people who actually did the research and submitted the papers for peer review in real journals have all reached a different conclusion than you have. You must prove them all wrong to be taken seriously. So far, you haven't even done any real research so you haven't earned the right to review anything. You have no new evidence, you just have your own conclusion. Science is based on evidence not authority. You have neither.

If IBIG wants a response to his moronic bullshit, he can take it to the bathroom wall.

It's always so amusing, in a sad, pathetic, struggling-fly-with-its-wings-pulled-off sort of way, to watch IBelieve demonstrate himself to be a colossal idiot with each and every post he makes.

Here he whines about having a double standard, and yet, he wants us to believe that Science is really an evil rival religion run by devil-worshipers, and he also wants us to abandon Science in favor of worshiping him as the Godhead.

Simply because he has "FAITH" (sic).

And he's also stupid enough to think that we've forgotten of all of the stupid gotcha games he's tried to pull on us where he makes inane rhetorical questions in order to lie about how we couldn't respond to him.

AS for gene duplication, it is indeed a well documented mechanism of evolution. I really can't tell exactly what the problem is for the atheist guy, but he seem to desperately need to find some excuse why no example is good enough for him. Seems like the only requirements would b:

1) A gene duplication

2) A new gene derived from the duplicate copy

3) A new function (maybe a new name or new information or innovation or something)

Of course, somehow none of the well documented examples are good enough to fulfill this nebulous yet rigorous criteria. They are all important to evolution, but somehow not important enough. Well what about these examples:

1) Hemoglobin genes (Well they all have a somewhat related function so I guess they really shouldn't count for something or other, maybe they are just not innovative enough. Yea that's it. I won't define the term, or say how much would be enough, but I'm sure they don't count)

2) Ribosomal genes (Well they all have something to do with a ribosome, so I guess they must not really be innovative enough either. It really doesn't matter how different thy are or who different their functions really are, no one will notice if I just ignore all the messy little details.)

3) Hox genes (They all have something to do with development so they don't count because ... give me a minute ... well I really can't think of a reason why they can't count ,,, I'm sure I'll find some reason to ignore them anyway.)

Now where can I publish my magnum opus? I know, Mad magazine. If only the editor didn't hate me so much.

DS said: AS for gene duplication, it is indeed a well documented mechanism of evolution. I really can't tell exactly what the problem is for the atheist guy, but he seem to desperately need to find some excuse why no example is good enough for him. ... (They all have something to do with development so they don't count because ... give me a minute ... well I really can't think of a reason why they can't count ,,, I'm sure I'll find some reason to ignore them anyway.)

Now where can I publish my magnum opus? I know, Mad magazine. If only the editor didn't hate me so much.

IBelieveInGod said: PROVE them wrong? It's funny how it's always a requirement for Creationists/IDers to prove something, but it is never a requirement for you to prove evolution, abiogenesis, etc..., science is not about proving anything, science only attempts to find a better explanation for observations. It's funny how there is such a double standard! You don't have to prove anything, yet Creationist/IDers must prove everything! Clearly this demonstrates the weakness of science when it comes to attempting to explain the origin of life, the universe, the physical laws, etc...

Dale Husband said:

IBelieveInGod said: PROVE them wrong? It's funny how it's always a requirement for Creationists/IDers to prove something, but it is never a requirement for you to prove evolution, abiogenesis, etc..., science is not about proving anything, science only attempts to find a better explanation for observations. It's funny how there is such a double standard! You don't have to prove anything, yet Creationist/IDers must prove everything! Clearly this demonstrates the weakness of science when it comes to attempting to explain the origin of life, the universe, the physical laws, etc...

You IGNORE all the evidence for evolution, and say there is "evidence" for Creationism and then give us none! So who has the double standard? YOU!

Richard,

The IBIG fool has been banned. Please dump all his posts to the bathroom wall. There is still a special thread just for him at After the Bar Closes, that's where he belongs.

Everyone else,

Please don't respond to this raving lunatic on this thread. All he wants to do is derail the thread with his incessant whining about abiogenesis and other meaningless bullshit. I guess he just couldn't stand to see the atheist guy getting his ass handed to him.

IBIG, you have thread at ATBC where you may spew. Until you have sufficient knowledge of the topic, I would encourage you to go there to babble.

We've all heard it. No one cares. No one here has to prove anything to you. No one here has to even address your concerns.

I have personally offered to teach you everything you would need to know about Biology, Chemistry, and how science works. I estimated that it would take about 9 months and some serious effort on your part. You have refused this at every opportunity.

Get thee to ATBC, IBIGgy.

Scott F said: But from a layman's perspective, while I'm aware that there is a difference, I really couldn't tell the difference between a high impact journal and a low one. (In fact, I just learned here that there is such a measure.) I just don't have the experience. What I care about is whether you can defend your ideas in rational, measured tones, without dropping to the level of school yard taunting like, "My CV is bigger than your CV."

IBelieveInGod said: It's all in the interpretation of the evidence as you should very well know. You interpret the evidence based on your presupposition that evolution by common descent is true, a Creationist/IDer interprets the same evidence very differently.

The reasons I can see are that Atheistoclast simply uses his inane programs to camouflage typical debunked Creationist appeals to incredulity in pseudoscientific jargon in the futile hope that no one will see through them, and that Atheistoclast is, hypocritically, an attention whore desperate for any sort of attention, and desperate to mock anyone and everyone who does not bow down to worship him as the Jesus of Science.

DS said: Richard, The IBIG fool has been banned. Please dump all his posts to the bathroom wall. There is still a special thread just for him at After the Bar Closes, that's where he belongs. Everyone else, Please don't respond to this raving lunatic on this thread. All he wants to do is derail the thread with his incessant whining about abiogenesis and other meaningless bullshit. I guess he just couldn't stand to see the atheist guy getting his ass handed to him.

Clean up on aisle 11.

All your questions have been answered at ATBC IBIG. The fact that you cannot understand the answers and don't want to understand them is not our fault. That's a personal failing and one that you should work hard to overcome.

I'm still willing to teach you.

Well, just use a bigger firecracker. A LOT bigger firecracker.

Karen S. said: Do you think even a nuke would make a difference?

IBelieveInGod lied: I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

mrg said:

Karen S. said: Do you think even a nuke would make a difference?

Well, what would you prefer? The Creation Museum, or a big smoking crater in the ground?

Elizabeth Liddle said: The only real way to tell a good paper from a bad one is to read it really thoroughly. Not even peer-reviewers always do that.

DS said: Now where can I publish my magnum opus? I know, Mad magazine. If only the editor didn't hate me so much.

Fortunately for us,any IDer papert that does slip by peer review will be praised to the skies by the Dishonesty Institute as the next toppler of Darwin's theory. That gives the rest of us a chance to go look at it and comment-- the only serious attention it most likely will ever get.

mrg said:

Karen S. said: Do you think even a nuke would make a difference?

Well, what would you prefer? The Creation Museum, or a big smoking crater in the ground?

Dave Wisker said: Fortunately for us,any IDer papert that does slip by peer review will be praised to the skies by the Dishonesty Institute as the next toppler of Darwin's theory. That gives the rest of us a chance to go look at it and comment-- the only serious attention it most likely will ever get.

Earlier in this thread I was critical of Atheistoclast for using violent rhetoric. Shouldn't we avoid that on our side, even in jest? Obliterate their arguments, attack their assumptions, but please don't joke about killing or harming anyone or physically destroying anything over this debate.

Yes, violent rhetoric and imagery, even used metaphorically and hyperbolicly, will inevitably be taken literally, or as some sort of coded message by the disturbed. You don't even have to be psycho to get what is implied by crosshairs on a map, "don't retreat, reload," "second amendment solutions," etc.

That and the fact that creationists often allege all sorts of perfidious and evil acts are committed by "Darwinists". Why add fuel to that fire?

Plus, we have the facts; we don't need the hyperbole.

SWT said: That and the fact that creationists often allege all sorts of perfidious and evil acts are committed by "Darwinists". Why add fuel to that fire? Plus, we have the facts; we don't need the hyperbole.

I must admit that escalating from firecrackers to tactical nukes was a bit of a jump. We should establish an arms-limitation treaty with the creobots to restrict both sides to Nerf(TM) munitions.

Dave Wisker said: Fortunately for us,any IDer papert that does slip by peer review will be praised to the skies by the Dishonesty Institute as the next toppler of Darwin's theory. That gives the rest of us a chance to go look at it and comment-- the only serious attention it most likely will ever get.

Stanton said:

IBelieveInGod lied: I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

Actually, yes you have been banned before, because you constantly derail every thread you visit, demanding that we worship you as the Godhead of Science, that you have "FAITH" (sic). That's why you have been repeatedly told that your comments are to be confined to the Bathroom Wall. And if you don't want us pointing out how you are a raving lunatic, stop talking like one.

Füttern das troll nichts.

Mike Elzinga said: Füttern das troll nichts.

IBelieveInGod said:

Stanton said:

IBelieveInGod lied: I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

Actually, yes you have been banned before, because you constantly derail every thread you visit, demanding that we worship you as the Godhead of Science, that you have "FAITH" (sic). That's why you have been repeatedly told that your comments are to be confined to the Bathroom Wall. And if you don't want us pointing out how you are a raving lunatic, stop talking like one.

I've been banned before? Tell me when? I have never had a problem posting here, even though my email address is the same, I have always posted as IBelieveInGod. Are you saying that I was banned and then unbanned?

If IBIGOT the lying troll wants anyone to respond to him, he can take it to After the Bar Closes. He's still getting his ass kicked over there. If not, he can shove a digit up his favorite orifice and rotate on it. This jackass isn't even welcome on the Bathroom Wall anymore. It took ten men working in shifts to purge the bathroom of 400 pages of his filth last time. Does anyone want to go through that bullshit again?

The guy is a raving lunatic and a satan worshiper. For all I know he sacrifices young virgins to the new moon. Why respond to such a deluded fool? He never posts anything on topic anyway. What the hell does abiogenesis have to do with gene duplication? Absolutely nothin, say it again.

If Richard won't purge his crap, we should all ignore him completely. Maybe then he will get the message that he is not welcome here.

I hope people have not forgotten that Atheistoclast has not even tried to address my pointing out his misrepresentation of the reference he claimed supported his contention that the Sdic gene was explained by "background selection".

SWT said: Earlier in this thread I was critical of Atheistoclast for using violent rhetoric. Shouldn't we avoid that on our side, even in jest? Obliterate their arguments, attack their assumptions, but please don't joke about killing or harming anyone or physically destroying anything over this debate.

Stanton said: Why should we neuter our hyperbole for the sake of creationist trolls?

Stanton said: Apparently, you are too stupid to remember the reason why you were originally restricted to the Bathroom Wall in the first place:

On Sept. 24th, 2010, IBIG said: "I read this on the ICR site and I really like it:) Since something exists (say, the universe), and since something cannot make itself (without violating the first principle of causality), then a cause outside that thing must exist (God)."

On Sept. 24th, 2010, OgreMkV said: "Well, we tried science… IBIG pretty much failed at that. We tried, logic… IBIG failed. We tried theology… fail. Now we’re back to witnessing… fail. And the cycle repeats… like a shirt that just isn’t getting clean.

Dave Luckett said on Feb 8, 2010: Playing chess with pigeons.

IBelieveInGod said on Feb 9, 2010: “I believe that God created life through natural causes, “

IBelieveInGod said on Feb 9, 2010: “I keep making analogies to attempt to help you all understand, but it appears that you aren’t capable, or you just don’t want to understand.”

IBelieveInGod said on Feb 9, 2010: “Why do you all think that God does everything supernaturally? “

IBelieveInGod said:

Dale Husband said: You IGNORE all the evidence for evolution, and say there is "evidence" for Creationism and then give us none! So who has the double standard? YOU!

It's all in the interpretation of the evidence as you should very well know. You interpret the evidence based on your presupposition that evolution by common descent is true, a Creationist/IDer interprets the same evidence very differently. You think that the evidence supports your opinion and the Creationist/Ider think the evidence supports their opinion. So, all we have are different OPINIONS of the same evidence. I prefer opinions rather then explanation, because that really all they are.

mrg said:

Stanton said: Why should we neuter our hyperbole for the sake of creationist trolls?

That's right. Call in a Nerfstrike on the lowlives.

Dave Wisker said: I hope people have not forgotten that Atheistoclast has not even tried to address my pointing out his misrepresentation of the reference he claimed supported his contention that the Sdic gene was explained by "background selection".

John Kwok said: You get a most enthusiastic second from me mrg!!!!

I meant to say the ancestral SAS precursor of the AFP.

Stanton said:

SWT said: Earlier in this thread I was critical of Atheistoclast for using violent rhetoric. Shouldn't we avoid that on our side, even in jest? Obliterate their arguments, attack their assumptions, but please don't joke about killing or harming anyone or physically destroying anything over this debate.

Why should we neuter our hyperbole for the sake of creationist trolls?

Stanton said:

IBelieveInGod said:

Stanton said:

IBelieveInGod lied: I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

Actually, yes you have been banned before, because you constantly derail every thread you visit, demanding that we worship you as the Godhead of Science, that you have "FAITH" (sic). That's why you have been repeatedly told that your comments are to be confined to the Bathroom Wall. And if you don't want us pointing out how you are a raving lunatic, stop talking like one.

I've been banned before? Tell me when? I have never had a problem posting here, even though my email address is the same, I have always posted as IBelieveInGod. Are you saying that I was banned and then unbanned?

Apparently, you are too stupid to remember the reason why you were originally restricted to the Bathroom Wall in the first place: that you continually pick fights on every thread, demanding that we give up Science in order to worship you, instead. Please stop posting your lies, inane anti-science screeds, and moronic lunacy.

SWT said:

Stanton said:

SWT said: Earlier in this thread I was critical of Atheistoclast for using violent rhetoric. Shouldn't we avoid that on our side, even in jest? Obliterate their arguments, attack their assumptions, but please don't joke about killing or harming anyone or physically destroying anything over this debate.

Why should we neuter our hyperbole for the sake of creationist trolls?

I'm suggesting the change in tone for the sake of the creationists and the "both siders" who might still be convinced by the scientific evidence.

Trolls are trolls and bad behavior is expected of them as long as they're fed. We can do better.

SWT said: Earlier in this thread I was critical of Atheistoclast for using violent rhetoric. Shouldn't we avoid that on our side, even in jest? Obliterate their arguments, attack their assumptions, but please don't joke about killing or harming anyone or physically destroying anything over this debate.

IBelieveInGod said: I beg to differ, I was never restricted to the bathroom, I had several posts sent to the bathroom and then I chose to post there instead.

I was never banned, so you lie again, tell me when will you quit your lying?

I have never demanded that you give up science to worship me, again another blatant lie by you. You are LIAR!!!

Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved.

There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

Stanton said:

IBelieveInGod said: I beg to differ, I was never restricted to the bathroom, I had several posts sent to the bathroom and then I chose to post there instead.

Your presence is not welcomed here, it never was welcomed here. We would greatly appreciate if you would stop posting here altogether.

I was never banned, so you lie again, tell me when will you quit your lying?

If I'm lying, then DS is really Pat Robertson, and the day I "quit lying" to you is the day DS also admits he's really Fred Phelps, which will also be the same day you admit to being the Pope.

I have never demanded that you give up science to worship me, again another blatant lie by you. You are LIAR!!!

Uh huh. And yet, why is it that you continue posting here, picking fights, conflating civility with groveling, and claiming how you know more about science than actual scientists, that Abiogenesis is really an atheistic recruitment mantra to turn children into God-hating zombies, or insisting that we're evil liars and God-hating atheists simply because we do not accept your Lies for Jesus? Give it up, IBelieve. No one here believes you, beyond the other Jesus trolls.

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved.

There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

IBelieveInGod said: Is this a public forum? If it is a public forum, then I would think you would welcome opposing views, if you don't want opposing views, then maybe those in charge should make this a private forum, and only accept membership from those believe in evolution from common descent.

Atheistoclast said:

Dave Wisker said: I hope people have not forgotten that Atheistoclast has not even tried to address my pointing out his misrepresentation of the reference he claimed supported his contention that the Sdic gene was explained by "background selection".

Not my contention at all. Charlesworth & Charlesworth suggested that background selection can mimick the effect of positive selection in a region of low recombination - such as the X chromosome. http://www.nature.com/nature/journal/v400/n6744/full/400519b0.html

Let me add that it is never okay to threaten anyone, even if it is jest. As I pointed out when Kris posted such despicable threats, that he shouldn't be just banned, but maybe even prosecuted. I have never posted anything of the sort. My posts have been opposing views, which it appears aren't welcome here. If opposing views aren't welcome here, why is that the case, could it be that many feel that evolution by common descent is threatened by such posts? Why should there even be a concern?

Stanton said:

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

In other words, God magically poofed everything into existence using magic.

Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved.

In other words, you don't understand, therefore, it didn't happen, and everyone who does actually understand it are really evil liars and God-hating atheists.

There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

And yet, you're claiming that I'm the liar. Hypocrite.

IBelieveInGod said: Let me add that it is never okay to threaten anyone, even if it is jest. As I pointed out when Kris posted such despicable threats, that he shouldn't be just banned, but maybe even prosecuted. I have never posted anything of the sort. My posts have been opposing views, which it appears aren't welcome here. If opposing views aren't welcome here, why is that the case, could it be that many feel that evolution by common descent is threatened by such posts? Why should there even be a concern?

IBelieveInGod said: I beg to differ, I was never restricted to the bathroom, I had several posts sent to the bathroom and then I chose to post there instead. I was never banned, so you lie again, tell me when will you quit your lying? I have never demanded that you give up science to worship me, again another blatant lie by you. You are LIAR!!!

IBelieveInGod said: Let me add that it is never okay to threaten anyone, even if it is jest. As I pointed out when Kris posted such despicable threats, that he shouldn't be just banned, but maybe even prosecuted. I have never posted anything of the sort. My posts have been opposing views, which it appears aren't welcome here. If opposing views aren't welcome here, why is that the case, could it be that many feel that evolution by common descent is threatened by such posts? Why should there even be a concern?

IBelieveInGod said: I don't know the actual physical process that God used, but I believe that God is Spirit and is not controlled by, nor is He subject to the physical universe. If He created the physical universe, then He also would have control over it. Magic and Poofing are nothing more then words, that you use to attempt to discredit a Creator.

Either the universe came from nothing by itself, or the universe came from nothing by a Creator. So, is it you belief that the universe poofed itself into existence by magic? You see no matter how you look at it, something had to come from nothing. So, tell me did the universe poof itself into existence by magic from nothing?

IBelieveInGod said: I don't know the actual physical process that God used,

but I believe that God is Spirit and is not controlled by, nor is He subject to the physical universe.

If He created the physical universe, then He also would have control over it. Magic and Poofing are nothing more then words, that you use to attempt to discredit a Creator.

Either the universe came from nothing by itself, or the universe came from nothing by a Creator.

Dale Husband said:

IBelieveInGod said: I beg to differ, I was never restricted to the bathroom, I had several posts sent to the bathroom and then I chose to post there instead. I was never banned, so you lie again, tell me when will you quit your lying? I have never demanded that you give up science to worship me, again another blatant lie by you. You are LIAR!!!

There are two possibilities, IBIG; you are either a liar or an idiot. If you were never confined to the Bathroom Wall, why would you post there and only there for many months and waste all that time and space? That's what an idiot does. The Bathroom Wall is for convos that have NO PLACE elsewhere on the Panda's Thumb! So you just admitted to everyone that you are an idiot! I think Stanton actually means you expect us to worship the bogus image of God in your head, which would be the same as worshipping you, since man tends to create God in his own image, rather than the other way around as the Book of Genesis falsely claims.

IBelieveInGod said: Let me add that it is never okay to threaten anyone, even if it is jest. As I pointed out when Kris posted such despicable threats, that he shouldn't be just banned, but maybe even prosecuted. I have never posted anything of the sort. My posts have been opposing views, which it appears aren't welcome here. If opposing views aren't welcome here, why is that the case, could it be that many feel that evolution by common descent is threatened by such posts? Why should there even be a concern?

If you want to present a legitimate opposing view, it still has to be based on the established rules of science. You never have followed those rules. If I knew a chess player was a habitual cheater, I'd never allow him to play in an international chess tournament.

IBelieveInGod said: Why don't you ask those in charge if I was banned? I posted there on purpose, and I am not an idiot.

No view that opposes your view of evolution from common descent would be legitimate. According to many here any that don't agree that evolution from common descent is true are idiots, ignorant, insane, lunatics, etc... There is no tolerance of Creationists here, nor is there tolerance of intelligent design proponents here.

IBelieveInGod said: Why don't you ask those in charge if I was banned? I posted there on purpose, and I am not an idiot.

No view that opposes your view of evolution from common descent would be legitimate. According to many here any that don't agree that evolution from common descent is true are idiots, ignorant, insane, lunatics, etc... There is no tolerance of Creationists here, nor is there tolerance of intelligent design proponents here.

There is no tolerance of Creationists here, nor is there tolerance of intelligent design proponents here

IBelieveInGod said to Stanton: I beg to differ, I was never restricted to the bathroom, ... You are LIAR!!!

Don't forget hypocrisy... hating science while using the tools that science has given him. BTW: There's a good question for you at ATBC. I bet you won't go answer it.

You never cited Charlesworth & Charlesworth in the paper-- I had to find and read it myself.

Furthermore, your explanation does not take into account the sharply increased codon usage bias, it ignores it. Therefore, you cannot propose--as you flatly do in the paper-- that it is "more logical" to propose a relaxed selection regime, without first explaining why such increased codon usage bias exists and persisted under relaxed selection.

SteveF said:

The reasons I can see are that Atheistoclast simply uses his inane programs to camouflage typical debunked Creationist appeals to incredulity in pseudoscientific jargon in the futile hope that no one will see through them, and that Atheistoclast is, hypocritically, an attention whore desperate for any sort of attention, and desperate to mock anyone and everyone who does not bow down to worship him as the Jesus of Science.

Atheistoclast has produced some inane programs of his own. See here for a humorous example: http://www.talkrational.org/showthread.php?t=15811 However, as I pointed out earlier, he isn't using an inane program in this instance. He's using BLAST. http://blast.ncbi.nlm.nih.gov/Blast.cgi

ben said:

There is no tolerance of Creationists here, nor is there tolerance of intelligent design proponents here

What there is no tolerance for, is people claiming that non-science (creationism) and anti-science (ID) are in fact legitimate science. Start following the established rules of science and you will find that people here will stop attacking you for falsely claiming that your moronic superstitions are scientific.

Atheistoclast, did you ever email Peter Seebach's superiors at Wind River to inform them he doesn't know how to code, as you threatened to do? Pity if you didn't, he gave you all their email addresses and encouraged you to do so.

Atheistoclast said:

Atheistoclast, did you ever email Peter Seebach's superiors at Wind River to inform them he doesn't know how to code, as you threatened to do? Pity if you didn't, he gave you all their email addresses and encouraged you to do so.

No. I didn't want Herr Seebach to lose his job with the company. His complete incomprehension of C++, along with confusion over dynamic memory allocation, would have been too embarrassing. I am just too nice of a guy.

Atheistoclast said:

ben said:

There is no tolerance of Creationists here, nor is there tolerance of intelligent design proponents here

What there is no tolerance for, is people claiming that non-science (creationism) and anti-science (ID) are in fact legitimate science. Start following the established rules of science and you will find that people here will stop attacking you for falsely claiming that your moronic superstitions are scientific.

Darwinism is destined to end up on the ash heap of failed pseudo-scientific ideologies. It is a case of when and not if. If it were so sound, it would not be in a constant battle to defend its contentions. The evidence would be overwhelming. However, hardly anything of the naturalistic argument makes any real sense.

John Vanko said:

IBelieveInGod said to Stanton: I beg to differ, I was never restricted to the bathroom, ... You are LIAR!!!

IBIG said he never lies, intentionally. I beg to differ. In the PT forum ‘Primordial Soup’ Ousted from the Origin of Life?!? by Dave Thomas, initiated Feb. 3, 2010, IBIG was banished to the Bathroom Wall Feb. 8th after spamming, railroading, and then derailing (take your pick of metaphor) the thread, panel 6. It is in the Feb 2010 Archives and the BW, go see for yourself. (I still can't see the old BW because IBIG clogged it with his effluent.) So did IBIG intentionally lie, or unintentionally lie? You be the judge.

Atheistoclast said: Darwinism is destined to end up on the ash heap of failed pseudo-scientific ideologies. It is a case of when and not if. If it were so sound, it would not be in a constant battle to defend its contentions. The evidence would be overwhelming. However, hardly anything of the naturalistic argument makes any real sense.

And yet, where is the evidence that all things can not evolve, where is the evidence that God is magically tinkering with everything under our noses?

More importantly, how come there all of the Creationists and the Intelligent Design proponents refuse to look for any evidence to support their claims that Creationism or Intelligent Design is supposed to be a legitimate science? I also see that you are still addicted to using Darwinism as a racist slur.

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

IBelieveInGod said: Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved. There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

Atheistoclast said: It is not that things cannot change - it is a question of the extent to which they can without the intervention of something beyond the natural and observed order.

You obviously never looked at the alignment. Sdic has LOST 100 codons at the N-terminus that are present in Cdic. This initial development would have been deleterious and so selected against.

The most likely scenario involves a population bottleneck, migration, or founder effect [51]. Any reduction in effective population size would also produce a further relaxation of selective constraints as (nearly) neutral drift would predominate

It appears that deletion in this instance was one of the necessary factors involved in gene fusion. As such, Sdic is shorter than Cdic, and this is true also for the hominoid oncogene, TRE2, which is 200 residues less than one of its parents, USP32 [52]. This presents a problem in terms of explaining any accretion of cistron size with reference to the most naturally applicableevolutionary process

Therefore, I have decided to define any gain in exonic information as: ‘‘The qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome

Atheistoclast said: Darwinism is destined to end up on the ash heap of failed pseudo-scientific ideologies. It is a case of when and not if.

If it were so sound, it would not be in a constant battle to defend its contentions.

The evidence would be overwhelming.

However, hardly anything of the naturalistic argument makes any real sense.

Atheistoclast said:

ben said:

There is no tolerance of Creationists here, nor is there tolerance of intelligent design proponents here

What there is no tolerance for, is people claiming that non-science (creationism) and anti-science (ID) are in fact legitimate science. Start following the established rules of science and you will find that people here will stop attacking you for falsely claiming that your moronic superstitions are scientific.

Darwinism is destined to end up on the ash heap of failed pseudo-scientific ideologies. It is a case of when and not if. If it were so sound, it would not be in a constant battle to defend its contentions. The evidence would be overwhelming. However, hardly anything of the naturalistic argument makes any real sense.

IBelieveInBearingFalseWitness said:

DS said: Richard, The IBIG fool has been banned. Please dump all his posts to the bathroom wall. There is still a special thread just for him at After the Bar Closes, that's where he belongs. Everyone else, Please don't respond to this raving lunatic on this thread. All he wants to do is derail the thread with his incessant whining about abiogenesis and other meaningless bullshit. I guess he just couldn't stand to see the atheist guy getting his ass handed to him.

I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

How do you know this? You don't cite any research demonstrating it. For example, is there any enzyme activity level data for the Cdic protein with such a deletion? Furthermore, if the Cdic gene was initially duplicated, and the copy underwent the deletion, what reason is there to expect negative selection to occur? This is where your argument—such as it is—goes off the rails. Let’s assume, for the moment, that the deletion in the Cdic gene was not negatively selected against (which is what you seem to be saying, though conventional evolutionary theory predicts this anyway, so you get no points for originality).

You are suggesting the likelihood of genetic drift as “the most likely” explanation, despite the fact that increased codon usage bias is not a pattern associated with it (in fact, it’s the reverse). That’s called special pleading.

Why must the Sdic gene be longer? Cistron length in this case doesn’t seem to have anything to do with your own definition of a gain in exonic information (my emphasis):

The logic in your Sdic argument leads to this conclusion: any novel adaptive function or capability acquired by the duplicated gene must involve an increase in cistron length. That doesn’t make sense, even by your own definition.

All that effort you put into the alignment, for which you are so proud, still doesn’t support your argument at all. You are consistently confusing effort with results.

John Kwok said:

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

Sorry IBelieveInNonsense, but the last time I checked, there are devout Christian scientists who accept that biological evolution is valid and is the means through which the Almighty has "created" life on earth: Francis Collins, Darrel Falk, Karl Giberson, Keith Miller, Ken Miller, Steve Matheson, Simon Conway Morris, and many, many others.

IBelieveInGod said: Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved. There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

Typical creotard breathtaking inanity from you, IBelieveInNonsense, since your comments ignore the role of geneaology - or to be more precise, phylogeny - in helping to define the "paths" in which descent through modification - to use Darwin's original term for biological evolution - occurs through countless lineages of bacteria, fungi, protists, plants and animals, and has resulted in the present complexity and diversity of life on Planet Earth. The complexity that you speak of is due to accidents of history, not through Divine Intervention of any kind whatsoever, and moreover, as others have noted here, the very processes responsible for microevolution are also responsible for macroevolution (the creation of new species, or rather, in other words, lineage splitting).

For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection.

I will be presenting this hypothesis in another paper.

phantomreader42 said:

IBelieveInBearingFalseWitness said:

DS said: Richard, The IBIG fool has been banned. Please dump all his posts to the bathroom wall. There is still a special thread just for him at After the Bar Closes, that's where he belongs. Everyone else, Please don't respond to this raving lunatic on this thread. All he wants to do is derail the thread with his incessant whining about abiogenesis and other meaningless bullshit. I guess he just couldn't stand to see the atheist guy getting his ass handed to him.

I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

Yes, you have. Almost a year ago. This has been pointed out repeatedly. Are you physically capable of telling the truth? Does jeebus like it when you lie?

Atheistoclast babbled:

And yet, where is the evidence that all things can not evolve, where is the evidence that God is magically tinkering with everything under our noses?

It is not that things cannot change - it is a question of the extent to which they can without the intervention of something beyond the natural and observed order.

Atheistoclast said: For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection. I will be presenting this hypothesis in another paper.

IBelieveInBearingFalseWitness said:

phantomreader42 said:

IBelieveInBearingFalseWitness said:

DS said: Richard, The IBIG fool has been banned. Please dump all his posts to the bathroom wall. There is still a special thread just for him at After the Bar Closes, that's where he belongs. Everyone else, Please don't respond to this raving lunatic on this thread. All he wants to do is derail the thread with his incessant whining about abiogenesis and other meaningless bullshit. I guess he just couldn't stand to see the atheist guy getting his ass handed to him.

I have never been banned here. Please don't call me a raving lunatic! When you can't respond to a post your answer is to call someone a raving lunatic.

Yes, you have. Almost a year ago. This has been pointed out repeatedly. Are you physically capable of telling the truth? Does jeebus like it when you lie?

No I was never banned, my posts were sent to the bathroom wall, and then I continued to post on the bathroom wall, if I had been banned I would not have been able to still post in the threads, which I was still able to do. Maybe you even have trouble comprehending what it means to be banned. Talk about ignorant!

Atheistoclast said: For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection. I will be presenting this hypothesis in another paper.

IBIG, like John Freshwater, can never admit he is wrong.

With Jesus in their hearts (and Jesus is without sin), they can do no wrong.

The Second Law of Creationist Dynamics: "The correctness of Creationists cannot decrease. It can only remain constant or increase." (And it can never go below zero.)

Could IBIG BE John Freshwater? Both seem to have had an awful lot of time on their hands last year!

Er.…yes I do know. For one, I made the alignment and ,secondly, the deletion at the amino end is also mentioned in a paper cited in the text. Ranz, J.M.; Ponce, A.R.; Hartl, D.L.; Nurminsky, D. (2003) .Origin and evolution of a new gene expressed in the Drosophila sperm axoneme Genetica, 118, 233–244.

The loss of the N-terminus meant Sdic could not function as a cytoplasmic dynein because it was unable to interact with dynactin. This meant that it was axonemal almost by default. This would have represented a deleterious development - at least initially.

Codon usage bias can be influenced, by among other things, background selection. That is what Nurminsky and Hartl report in their response to Charlesworth & Charlesworth.

The alignment clearly shows the bulk deletion at the N-terminus and the disabling of the 4th domain from the 5’ end by a frameshift mutation. It is a peach.

DS said:

Look dude, you obviously don't understand the concept of duplicated genes being removed from functional constraint. Go look it up and get back to Dave when you understand it. Or just look it up and get lost. You haven't got a broken leg to stand on.

Shoot, I forgot. ID = satanism. 111!

IBelieveInGod said to phantomreader42: "No I was never banned, my posts were sent to the bathroom wall, and then I continued to post on the bathroom wall, ... Maybe you even have trouble comprehending what it means to be banned. Talk about ignorant!"

IBelieveInGod said to Stanton: I beg to differ, I was never restricted to the bathroom, … You are LIAR!!!

DS said: Shoot, I forgot. ID = satanism. 111!

DS said: Shoot, I forgot. ID = satanism. 111!

IBelieveInGod said:

John Kwok said:

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

Sorry IBelieveInNonsense, but the last time I checked, there are devout Christian scientists who accept that biological evolution is valid and is the means through which the Almighty has "created" life on earth: Francis Collins, Darrel Falk, Karl Giberson, Keith Miller, Ken Miller, Steve Matheson, Simon Conway Morris, and many, many others.

IBelieveInGod said: Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved. There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

Typical creotard breathtaking inanity from you, IBelieveInNonsense, since your comments ignore the role of geneaology - or to be more precise, phylogeny - in helping to define the "paths" in which descent through modification - to use Darwin's original term for biological evolution - occurs through countless lineages of bacteria, fungi, protists, plants and animals, and has resulted in the present complexity and diversity of life on Planet Earth. The complexity that you speak of is due to accidents of history, not through Divine Intervention of any kind whatsoever, and moreover, as others have noted here, the very processes responsible for microevolution are also responsible for macroevolution (the creation of new species, or rather, in other words, lineage splitting).

Biological evolution (very broad term)? or biological evolution from common descent? where is your evidence that the complexity of limbs is due to accidents of history? Microevolution does not create new novel morphological structures, it only changes structures that already exist. I've already stated in the past that natural selection does not select for the future fitness of a mutation, so how would so many accidents (mutations) ultimately form a fully functioning limb with all of it's complexity?

John Kwok said: Biological evolution IS common descent, or as Darwin termed it, "Descent With Modification". The rest of your latest breathtaking inanity merely demonstrates your woeful ignorance and poor understanding as to what are the processes that are responsible for biological evolution.

John Kwok said:

IBelieveInGod said:

John Kwok said:

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

Sorry IBelieveInNonsense, but the last time I checked, there are devout Christian scientists who accept that biological evolution is valid and is the means through which the Almighty has "created" life on earth: Francis Collins, Darrel Falk, Karl Giberson, Keith Miller, Ken Miller, Steve Matheson, Simon Conway Morris, and many, many others.

IBelieveInGod said: Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved. There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

Typical creotard breathtaking inanity from you, IBelieveInNonsense, since your comments ignore the role of geneaology - or to be more precise, phylogeny - in helping to define the "paths" in which descent through modification - to use Darwin's original term for biological evolution - occurs through countless lineages of bacteria, fungi, protists, plants and animals, and has resulted in the present complexity and diversity of life on Planet Earth. The complexity that you speak of is due to accidents of history, not through Divine Intervention of any kind whatsoever, and moreover, as others have noted here, the very processes responsible for microevolution are also responsible for macroevolution (the creation of new species, or rather, in other words, lineage splitting).

Biological evolution (very broad term)? or biological evolution from common descent? where is your evidence that the complexity of limbs is due to accidents of history? Microevolution does not create new novel morphological structures, it only changes structures that already exist. I've already stated in the past that natural selection does not select for the future fitness of a mutation, so how would so many accidents (mutations) ultimately form a fully functioning limb with all of it's complexity?

Biological evolution IS common descent, or as Darwin termed it, "Descent With Modification". The rest of your latest breathtaking inanity merely demonstrates your woeful ignorance and poor understanding as to what are the processes that are responsible for biological evolution.

DS said: Shoot, I forgot. ID = satanism. 111!

Atheistoclast said: For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection.

Oops - got a little carried away there After posting this: STOP! MOVE ALONG - JUST A LITTLE TROLL CONTROL As you can see, I’ve sent IBIG to the Bathroom Wall. Engage with him there all you like! But not here, por favor. I gave him a chance to define what he meant by “Creation”, and he evaded with RNA/whatnot. For crying out loud - his handle was “I BELIEVE IN GOD”. For someone like that to pussyfoot with the definition of ‘creation’ is disingenuous. Thus, to the Bathroom Wall with him. Sorry about the Collateral Damage - I hope you’ll understand. And, it’s not like your comments get Disappeared - they just get a new room, with a cheaper wallpaper that’s got some cracks and pee stains. Cheers, Dave

Dale Husband said: Look at this: http://pandasthumb.org/archives/2010/02/primordial-soup-1.html#comment-205876

Oops - got a little carried away there After posting this: STOP! MOVE ALONG - JUST A LITTLE TROLL CONTROL As you can see, I’ve sent IBIG to the Bathroom Wall. Engage with him there all you like! But not here, por favor. I gave him a chance to define what he meant by “Creation”, and he evaded with RNA/whatnot. For crying out loud - his handle was “I BELIEVE IN GOD”. For someone like that to pussyfoot with the definition of ‘creation’ is disingenuous. Thus, to the Bathroom Wall with him. Sorry about the Collateral Damage - I hope you’ll understand. And, it’s not like your comments get Disappeared - they just get a new room, with a cheaper wallpaper that’s got some cracks and pee stains. Cheers, Dave

I was trying to send yet another of IBIG’s inane meanderings to the Bathroom Wall, when I apparently selected the whole raft of comments by accident. And wouldn’t you know, while there’s a way to send the raft to the Bathroom Wall”, there’s no way to fetch them back. My apologies. Consider it a scenery change for the discussion with IBIG. Cheers, Dave I think Dave meant he sent IBIG's posts to the Bathroom Wall, but not IBIG himself. Of course, the fact that IBIG continued to post for many months pointless quarrels on the BW instead of either going away completely or trying to understand evolution and science in general better only proves my point about his idiocy.

IBelieveInGod said: [A lot of old news from the Discovery Institute, along with fallacious crap.]

IBelieveInGod said: So, you admit that I wasn't banned? So, explain to me if my posts were so idiotic, so inane, so pointless why did so many even respond to them? Wouldn't it be idiotic to respond to pointless, inane, idiotic posts?

OK, IBIG, I'll ask you the same question that 'clast hasn't responded to.

What's the different (result, not process) between artificial selection and natural selection?

(i.e. what 'thing' will tell us whether a gene, organism, protein, or system evolved via artificial or natural selection? and why?)

Be careful... it is a trap... I doubt you'll understand it though.

BTW: There's another question for you at ATBC.

Maybe I haven't explained myself very well.

Microevolution (best described as adaptation) which can be observed in the laboratory and in nature, ie different breeds of dogs, birds, etc...

Macroevolution (best described as speciation and the origin of divisions within the taxonomic hierarchy, and the development of new complex novel morphological structures, organs, etc...) this has never been observed in the laboratory or in nature, this is where it ceases to be science and because a type of belief system.

IBelieveInGod said: So, you admit that I wasn't banned?

IBelieveInGod said: Maybe I haven't explained myself very well. Microevolution (best described as adaptation) which can be observed in the laboratory and in nature, ie different breeds of dogs, birds, etc... Macroevolution (best described as speciation and the origin of divisions within the taxonomic hierarchy, and the development of new complex novel morphological structures, organs, etc...) this has never been observed in the laboratory or in nature, this is where it ceases to be science and because a type of belief system.

IBelieveInGod said: Maybe I haven't explained myself very well. Microevolution (best described as adaptation) which can be observed in the laboratory and in nature, ie different breeds of dogs, birds, etc... Macroevolution (best described as speciation and the origin of divisions within the taxonomic hierarchy, and the development of new complex novel morphological structures, organs, etc...) this has never been observed in the laboratory or in nature, this is where it ceases to be science and because a type of belief system.

OgreMkV said:

Atheistoclast said: For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection. I will be presenting this hypothesis in another paper.

Please describe, in detail, the difference (results not process) between artifical selection and natural selection. i.e how can you tell if a structure, gene, protein, or organism was devevloped through artificial or natural selection?

Atheistoclast said:

OgreMkV said:

Atheistoclast said: For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection. I will be presenting this hypothesis in another paper.

Please describe, in detail, the difference (results not process) between artifical selection and natural selection. i.e how can you tell if a structure, gene, protein, or organism was devevloped through artificial or natural selection?

I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

ibig, I actually have a question for you: If everything on earth is specially created by god, why do the progressions we see if fossil records occur? Does God have a calendar and tuesday is cartaligineous (sp) fish, then firday the 13th of october is sharks and then for New Year, I'll create a bony fish. i mean since you know the mind of god, how does he keep track?

IBelieveInGod said: Maybe I haven't explained myself very well.

Macroevolution (best described as speciation and the origin of divisions within the taxonomic hierarchy, and the development of new complex novel morphological structures, organs, etc...) this has never been observed in the laboratory or in nature...

this is where it ceases to be science and because a type of belief system.

IBelieveInGod said: Maybe I haven't explained myself very well. Microevolution (best described as adaptation) which can be observed in the laboratory and in nature, ie different breeds of dogs, birds, etc... Macroevolution (best described as speciation and the origin of divisions within the taxonomic hierarchy, and the development of new complex novel morphological structures, organs, etc...) this has never been observed in the laboratory or in nature, this is where it ceases to be science and because a type of belief system.

eric said: Creationists assert that the mechanism for micro cannot accomplish the macro. But you have never explained why. On a biochemical scale such an assertion doesn't even make sense, as there is no possible way a mutation in the genetic code could "know" whether the result will be a dramatic change in development with positive value in the future organism's environment, a dramatic change in development with negative value in the future organism's environment, or no change in development at all. Is a duplication of sequence L to LL physically possible or physically impossible? Creationists need to know the developmental outcome before they make that assesment. But biochemical machinery never knows the outcome. But that isn't your biggest problem. You have not even defined the limit in any consistent manner. Evidently, the genetic difference between chimps and humans could not possibly be bridged, even though you accept that larger genetic differences in other family groups could be bridged. And it is transparently obvious to everyone involved that this irrational inconsistency arises not out of some scientific hypothesis about mutational mechanisms, but merely because you want to keep the biblical concept of kinds intact.

Macroevolution (best described as speciation and the origin of divisions within the taxonomic hierarchy, and the development of new complex novel morphological structures, organs, etc...) this has never been observed in the laboratory or in nature...

It has been observed. Here are many examples. We have pointed these examples out to you before. You simply pretend they don't exist.

Atheistoclast said: I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

OgreMkV said: That bolded bit is the most brilliant reasoning I've ever heard.

Yes, IBIG, please explain why the anatomical spectrum in Canis familaris is so much larger than in the rest of the entire order of carnivora (excluding that one species).

In all of the years that IBIGOT has been trolling here, he has utterly failed to convince even one single person of one single thing. He is consistently and obstinately wrong about every single thing he states and what is worse, he refuses to ever admit it.

I strongly recommend that no one respond to him anywhere but the bathroom wall. The jerk already has his own thread at ATBC, where he has similarly failed to convince anyone of anything. Obviously he only comes here for attention, don't give it to him. If the administrators of this site are unwilling or unable to ban him permanently, we can effectively do it ourselves.

eric said:

OgreMkV said: That bolded bit is the most brilliant reasoning I've ever heard.

Thank you. :)

Yes, IBIG, please explain why the anatomical spectrum in Canis familaris is so much larger than in the rest of the entire order of carnivora (excluding that one species).

I want to address a bad response before it crops up, because I think there's about a 90% likelihood that IBIG will try and use it. The fact that dogs are bred by people provides no answer to the question of how such a wide variation could arise genetically. And that is the micro/macrro issue: could mutations that lead to such wide developmental variations arise? Now, we humans did determine which dogs bred with which. But we did not introduce the variation into the dogs, we merely worked with what nature handed us. So the variation in dog genetics must've come from nature. And it is a very wide variation. And it only took maybe 15,00-20,000 years...a finger snap in terms of geological time.

OgreMkV said:

Atheistoclast said:

OgreMkV said:

Atheistoclast said: For those of you who want to know the mechanism behind IDvolution I am proposing that it is case of "directed hypermutation" and artificial selection. I will be presenting this hypothesis in another paper.

Please describe, in detail, the difference (results not process) between artifical selection and natural selection. i.e how can you tell if a structure, gene, protein, or organism was devevloped through artificial or natural selection?

I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

Interesting, because no scientist 'poofs' "new genetic information". There are several well defined processes for new genetic information. Gene duplication is one of them. I'm afraid that you're are attacking a strawman.

'clast... define information in this context.

Dale Husband said:

Atheistoclast said: I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

I thought you said earlier that "Darwinism" was going to be overthrown. Now you affirm that evolution can happen. Make up your mind!

It sure worked with Kris.

Drove him insane!

Atheistoclast said:

Dale Husband said:

Atheistoclast said: I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

I thought you said earlier that "Darwinism" was going to be overthrown. Now you affirm that evolution can happen. Make up your mind!

You fail to understand that *artificial* selection, or any kind of directed evolution, is essentially intelligent design. Once you allow for a supervisory element into the equation you are arguing against a naturalistic origination.

DS said about IBIG: ... If the administrators of this site are unwilling or unable to ban him permanently, we can effectively do it ourselves.

DS said: If the administrators of this site are unwilling or unable to ban him permanently, we can effectively do it ourselves.

"But troll bashing, like dwarf bowling, is wicked fun, more so after a few drinks!"

IBelieveInGod said:

John Kwok said:

IBelieveInGod said: Creationists believe that God created various kinds of life, and those various kinds of life have changed and adapted through the years. That change and adaptation is backed by the evidence (microevolution) These changes do not include the evolution of new novel morphological structures.

Sorry IBelieveInNonsense, but the last time I checked, there are devout Christian scientists who accept that biological evolution is valid and is the means through which the Almighty has "created" life on earth: Francis Collins, Darrel Falk, Karl Giberson, Keith Miller, Ken Miller, Steve Matheson, Simon Conway Morris, and many, many others.

IBelieveInGod said: Evolutionists believe that all life evolved from an extremely simple organism or organisms. (macroevolution) Which would require the evolution of new novel morphological structures. Limbs with all the complexity of bones, cartilage, ligaments, tendons, muscles, nerves would have had to evolved, and that is just one example of a complex morphological structure that would have evolved. There is evidence of microevolution, but macroevolution is nothing more then conjecture, and assumption based on ones belief that evolution from common descent happened.

Typical creotard breathtaking inanity from you, IBelieveInNonsense, since your comments ignore the role of geneaology - or to be more precise, phylogeny - in helping to define the "paths" in which descent through modification - to use Darwin's original term for biological evolution - occurs through countless lineages of bacteria, fungi, protists, plants and animals, and has resulted in the present complexity and diversity of life on Planet Earth. The complexity that you speak of is due to accidents of history, not through Divine Intervention of any kind whatsoever, and moreover, as others have noted here, the very processes responsible for microevolution are also responsible for macroevolution (the creation of new species, or rather, in other words, lineage splitting).

Biological evolution (very broad term)? or biological evolution from common descent? where is your evidence that the complexity of limbs is due to accidents of history? Microevolution does not create new novel morphological structures, it only changes structures that already exist. I've already stated in the past that natural selection does not select for the future fitness of a mutation, so how would so many accidents (mutations) ultimately form a fully functioning limb with all of it's complexity?

Atheistoclast said: You fail to understand that *artificial* selection, or any kind of directed evolution, is essentially intelligent design. Once you allow for a supervisory element into the equation you are arguing against a naturalistic origination.

I think you need to read this 'clast (and anyone else who is interested).

It's probably better than your paper and I wouldn't even consider it for publication, but it pretty much explains why your entire concept is wrong.

Enjoy.

https://docs.google.com/document/d/1A_EfiEhJxqDDobXENGaYSPcsrJrpycDvFlluVeypxv8/edit?hl=en

Oops... guess I should attach the link huh

OgreMkV said: I think you need to read this 'clast (and anyone else who is interested).

mrg said: "Intelligent Design is an attempt to elevate seeing faces in clouds to a science."

JASONMITCHELL said: are you saying that you accept that peeple can walk 100 feet but not 100 yards (or given enough time) 100 miles?

Atheistoclast said: You fail to understand that *artificial* selection, or any kind of directed evolution, is essentially intelligent design. Once you allow for a supervisory element into the equation you are arguing against a naturalistic origination.

DS said:

mrg said: "Intelligent Design is an attempt to elevate seeing faces in clouds to a science."

Just like astrology is a science?

The dividing line between artificial and natural selection is very fuzzy:

http://www.vectorsite.net/taevo_14.html#m3

See section 14.3 if the link doesn't register properly.

Atheistoclast said:

Dale Husband said:

Atheistoclast said: I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

I thought you said earlier that "Darwinism" was going to be overthrown. Now you affirm that evolution can happen. Make up your mind!

You fail to understand that *artificial* selection, or any kind of directed evolution, is essentially intelligent design. Once you allow for a supervisory element into the equation you are arguing against a naturalistic origination.

Stuart Weinstein said: If artifical selection can result in macroevolution, there is then no genetic barrier to macroevolution whether its due to articifical or natural selection.

Stuart Weinstein said:

Atheistoclast said:

Dale Husband said:

Atheistoclast said: I'm afraid you will have to wait until the paper is published. But artificial selection and a process known as "hypermutation" (as with somatic immune cells) can make profound changes in a very short space of time. The point is you don't need to "poof" new genetic information into existence - you just need to be able to manipulate the existing imperfection (though near perfected state) of the replication system.

I thought you said earlier that "Darwinism" was going to be overthrown. Now you affirm that evolution can happen. Make up your mind!

You fail to understand that *artificial* selection, or any kind of directed evolution, is essentially intelligent design. Once you allow for a supervisory element into the equation you are arguing against a naturalistic origination.

This is stupid. If artifical selection can result in macroevolution, there is then no genetic barrier to macroevolution whether its due to articifical or natural selection. And hence no reason why *Darwinism* is soon to bite the dust.

mrg said:

Stuart Weinstein said: If artifical selection can result in macroevolution, there is then no genetic barrier to macroevolution whether its due to articifical or natural selection.

A honeybee has enough brains to select flowers it finds more attractive in a population from those that are less attractive. Artificial selection or natural selection? In coevolutionary strategies, the partners are selecting each other; if we domesticate cattle and select for milk production, they end up selecting us for lactose tolerance.

SWT said: And, as was pointed out in another thread long ago, if we adopt Dembski's definition of intelligence as the "power and facility to choose between options", then natural selection is an intelligent agent. There's no distinction, mechanistically, between "natural" selection and "artificial" selection. It appears to me that one of the manifold problems with ID arguments is that they subtly conflate "intelligence" with "intention" and "consciousness".

Everyone here understands the difference between "artificial" selection and "natural" selection.

'clast, I will ask you again.

Given two organism, genes, or proteins, can you tell which one evolved by natural selection and which evolved by artificial selection. I need a detailed process so that I can test your results.

If you cannot do this, then your entire point (whatever that is) is moot and a complete waste of your time.

The former requires an intelligence to select those variations that meet the particular *purpose* in mind. The latter’s sole criterion is reproductive fitness and nothing else.

I'm still waiting for dog breeders to breed a dog with horns, or wings, or fins in place of legs:):):)

Artificial selection should theoretically, be able to create a new novel morphological structure much faster then natural selection, because the breeder would be able to choose the most suitable mutations for a new morphological structure. The difference is that natural selection can only select for the current fitness of a mutation, and not for any future fitness of a mutation, but artificial selection (breeder) can select for the future fitness of any mutation. If OgreMkV can't see the difference, then he is an awful scientist!

Artificial selection should theoretically, be able to create a new novel morphological structure much faster then natural selection

Flint said:

Artificial selection should theoretically, be able to create a new novel morphological structure much faster then natural selection

Only up to a point. Consider the genome as containing a certain amount of available variation. Breeders can focus and emphasize SOME of the existing variation while excluding others. But once the limit of existing variation has been reached, breeders are just like any environment - they must wait for NEW genetic variation before they can concentrate it. And that requires mutation, over which the breeders have no control. Not even the best breeders could select for "future fitness", EVEN IF they could foresee the future, if the raw material to be selected is simply not available. It remains beyond the state of the art to introduce genetic variation sufficient to stick wings or fins on a dog. But as GM foods illustrate, it IS currently possible to insert genes across species to a limited extent.

JASONMITCHELL said: are you saying that you accept that peeple can walk 100 feet but not 100 yards (or given enough time) 100 miles? THERE IS NO DIFFERENCE between "micro"evolution and "macro"evolution other than scale

IBelieveInGod said:

Flint said:

Artificial selection should theoretically, be able to create a new novel morphological structure much faster then natural selection

Only up to a point. Consider the genome as containing a certain amount of available variation. Breeders can focus and emphasize SOME of the existing variation while excluding others. But once the limit of existing variation has been reached, breeders are just like any environment - they must wait for NEW genetic variation before they can concentrate it. And that requires mutation, over which the breeders have no control. Not even the best breeders could select for "future fitness", EVEN IF they could foresee the future, if the raw material to be selected is simply not available. It remains beyond the state of the art to introduce genetic variation sufficient to stick wings or fins on a dog. But as GM foods illustrate, it IS currently possible to insert genes across species to a limited extent.

:):):) So evolution by common ancestor didn't occur?

So evolution by common ancestor didn’t occur?

Flint said:

The former requires an intelligence to select those variations that meet the particular *purpose* in mind. The latter’s sole criterion is reproductive fitness and nothing else.

This always amuses me. "Artificial selection" is nothing more than some external agent OTHER than the environment defining reproductive fitness. But whether artificial or natural (that is, regardless of who sets the fitness criteria), those who meet the reproductively-fit criteria are more likely to breed. I guess nature, despite doing selection, doesn't count as a selector because if it has an "intent" it's not obvious enough to meet religious criteria.

IBelieveInGod said: I'm still waiting for dog breeders to breed a dog with horns, or wings, or fins in place of legs:):):) Artificial selection should theoretically, be able to create a new novel morphological structure much faster then natural selection, because the breeder would be able to choose the most suitable mutations for a new morphological structure. The difference is that natural selection can only select for the current fitness of a mutation, and not for any future fitness of a mutation, but artificial selection (breeder) can select for the future fitness of any mutation. If OgreMkV can't see the difference, then he is an awful scientist!

Atheistoclast said: NONSENSE. We breed for such things as chihuahuas, sheep with short legs (that can't jump fences) or seedless grapes - organisms and traits that would not survive in the wild. We select what is useful to our society. Natural selection would oppose most of the changes we select as breeders...like with the examples above.

'clast, I'm sure you're just missing my posts with a critical question. I'll repeat it here for you.

Given an organism, gene, protein, or structure, can you tell whether it was developed via artificial selection or natural selection? I'll need a complete process so that I can try it on a few example organisms to make sure it works.

If you can't do that, then your entire point (whatever it is) is moot and you're wasting your time on the subject.

Atheistoclast said:

Flint said:

The former requires an intelligence to select those variations that meet the particular *purpose* in mind. The latter’s sole criterion is reproductive fitness and nothing else.

This always amuses me. "Artificial selection" is nothing more than some external agent OTHER than the environment defining reproductive fitness. But whether artificial or natural (that is, regardless of who sets the fitness criteria), those who meet the reproductively-fit criteria are more likely to breed. I guess nature, despite doing selection, doesn't count as a selector because if it has an "intent" it's not obvious enough to meet religious criteria.

NONSENSE. We breed for such things as chihuahuas, sheep with short legs (that can't jump fences) or seedless grapes - organisms and traits that would not survive in the wild. We select what is useful to our society. Natural selection would oppose most of the changes we select as breeders...like with the examples above. Of course, there are *limits* to artificial selection but this is because we don't know how to select individual mutations without an obvious phenotype. What I mean is that we could create a string of characters... "CLASTIEISKING" ..in a protein sequence if we decided to select each amino acid. We can do this now, but not in the past.

John Kwok said:

IBelieveInGod said: I'm still waiting for dog breeders to breed a dog with horns, or wings, or fins in place of legs:):):) Artificial selection should theoretically, be able to create a new novel morphological structure much faster then natural selection, because the breeder would be able to choose the most suitable mutations for a new morphological structure. The difference is that natural selection can only select for the current fitness of a mutation, and not for any future fitness of a mutation, but artificial selection (breeder) can select for the future fitness of any mutation. If OgreMkV can't see the difference, then he is an awful scientist!

Sorry IBIG you are wrong on all counts since you neglect the importance of genealogical history - what is better known as "phylogeny" - in the history of life. The reason why we will never see dogs with horns or wings or fins is because the dog lineage diverged long ago from those lineages which did produce eventually, horns or wings or fins. Artifical selection can produce "novel structures" faster than natural selection, as is clearly demonstrated by the "diversity" we see in dogs, ranging from tiny Pekinese to Great Danes and Greyhounds. But no dog breed can produce the very structures you desire because of historical constraints imposed on dogs via the prior phylogeny of the "dog" clade.

NONSENSE. We breed for such things as chihuahuas, sheep with short legs (that can’t jump fences) or seedless grapes - organisms and traits that would not survive in the wild. We select what is useful to our society. Natural selection would oppose most of the changes we select as breeders…like with the examples above.

Atheistoclast said:

Everyone here understands the difference between "artificial" selection and "natural" selection.

I'm afraid you don't. Both artificial and natural selection do indeed make use of an imperfect replication system (i.e random mutations). But that is where the similarity ends. The former requires an intelligence to select those variations that meet the particular *purpose* in mind. The latter's sole criterion is reproductive fitness and nothing else. If it is beneficial to lose functionality, because it confers a survival advantage, then natural selection will go down that route. Artificial selection always works by way of the conscious intent and will of the *artificer*.

Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Flint said: Normal people (those who have learned anything in their life) also tend to forget things never brought to mind. Normal people also tend to learn new things more immediately useful in their lives. You'll have to trust me on this.

IBelieveInGod babbled: But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish? If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Atheistoclast said: NONSENSE. We breed for such things as chihuahuas, sheep with short legs (that can't jump fences) or seedless grapes - organisms and traits that would not survive in the wild. We select what is useful to our society. Natural selection would oppose most of the changes we select as breeders...like with the examples above. Of course, there are *limits* to artificial selection but this is because we don't know how to select individual mutations without an obvious phenotype.

Stanton said:

IBelieveInGod babbled: But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish? If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Hey, moron. Tetrapod vertebrates have many traits in common with ancestral lobe-finned fishes. That is why the lobe-finned fishes are considered to be the closest relatives of tetrapod vertebrates. The loss of some traits, such as gills, occurred because they were selected against. If you keep saying stupid things with the intent to impress us into worshiping you, we're going to have to keep pointing out how you're a moronic lunatic.

IBelieveInGod said:

Stanton said:

IBelieveInGod babbled: But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish? If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Hey, moron. Tetrapod vertebrates have many traits in common with ancestral lobe-finned fishes. That is why the lobe-finned fishes are considered to be the closest relatives of tetrapod vertebrates. The loss of some traits, such as gills, occurred because they were selected against. If you keep saying stupid things with the intent to impress us into worshiping you, we're going to have to keep pointing out how you're a moronic lunatic.

So they are selected against? Tell me what prevents a repressed gene from being expressed in the future?

IBelieveInGod said:

Stanton said:

IBelieveInGod babbled: But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish? If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Hey, moron. Tetrapod vertebrates have many traits in common with ancestral lobe-finned fishes. That is why the lobe-finned fishes are considered to be the closest relatives of tetrapod vertebrates. The loss of some traits, such as gills, occurred because they were selected against. If you keep saying stupid things with the intent to impress us into worshiping you, we're going to have to keep pointing out how you're a moronic lunatic.

So they are selected against? Tell me what prevents a repressed gene from being expressed in the future?

The only question is whether natural selection could play an important role in producing the diversity of life found on earth. The answer is yes.

IBelieveInGod said: But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish? If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Stanton said:

IBelieveInGod said:

Stanton said:

IBelieveInGod babbled: But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish? If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

Hey, moron. Tetrapod vertebrates have many traits in common with ancestral lobe-finned fishes. That is why the lobe-finned fishes are considered to be the closest relatives of tetrapod vertebrates. The loss of some traits, such as gills, occurred because they were selected against. If you keep saying stupid things with the intent to impress us into worshiping you, we're going to have to keep pointing out how you're a moronic lunatic.

So they are selected against? Tell me what prevents a repressed gene from being expressed in the future?

If a gene is silenced due to mutation, then it can not be expressed anymore in the exact same way a recipe in a cookbook can no longer be read if someone were to pour ink on the page it is on. Once a gene has been rendered incapable of being expressed, it becomes a pseudogene, and the only way to reactivate a pseudogene is if another mutation places a start codon at its start. This has happened, but, not that you are capable of caring. If you have a rudimentary knowledge of Genetics and or Biology, you would have known this. But, you have made it clear that you find learning, science and knowledge to be tantamount to devil-worship and murder.

IBelieveInGod said:

John Kwok said: Sorry IBIG you are wrong on all counts since you neglect the importance of genealogical history - what is better known as "phylogeny" - in the history of life. The reason why we will never see dogs with horns or wings or fins is because the dog lineage diverged long ago from those lineages which did produce eventually, horns or wings or fins. Artifical selection can produce "novel structures" faster than natural selection, as is clearly demonstrated by the "diversity" we see in dogs, ranging from tiny Pekinese to Great Danes and Greyhounds. But no dog breed can produce the very structures you desire because of historical constraints imposed on dogs via the prior phylogeny of the "dog" clade.

But didn't all tetrapods evolve from lobe-finned fish? If so wouldn't dogs and all tetrapods still have those traits left over from lobe-finned fish?

If not why? Are you saying that there is a loss of information in the DNA over time? If so, why is there a loss of information?

mrg said: The dividing line between artificial and natural selection is very fuzzy:

Atheistoclast said: NONSENSE. We breed for such things as chihuahuas, sheep with short legs (that can't jump fences) or seedless grapes - organisms and traits that would not survive in the wild. We select what is useful to our society. Natural selection would oppose most of the changes we select as breeders...like with the examples above. Of course, there are *limits* to artificial selection but this is because we don't know how to select individual mutations without an obvious phenotype. What I mean is that we could create a string of characters... "CLASTIEISKING" ..in a protein sequence if we decided to select each amino acid. We can do this now, but not in the past.

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

Stanton said:

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

Ah, so you're playing games with percentages? Here's where IBelieve, the pompous, arrogant idiot deliberately ignores the fact that beneficial and neutral mutations are retained by their owning organisms because they either improve, or do not impair their owners' chances at reproduction in order to boast and brag about how evolution magically can not happen because there are more harmful mutations than beneficial mutations. Of course, IBelieve wouldn't be playing such a stupid gotcha-game if he were honest, and happened to like learning about science, rather than regarding it as being of the devil.

IBelieveInGod said: Playing a game with percentages? I'm asking what percentage of mutations are good, bad, and neutral. Are you afraid to answer that question, because you think it is a gotcha? Why would you be concerned about a gotcha?

IBelieveInGod said: So they are selected against? Tell me what prevents a repressed gene from being expressed in the future?

I’m asking what percentage of mutations are good, bad, and neutral. Are you afraid to answer that question, because you think it is a gotcha?

IBelieveInGod said: Playing a game with percentages? I'm asking what percentage of mutations are good, bad, and neutral. Are you afraid to answer that question, because you think it is a gotcha? Why would you be concerned about a gotcha?

Then 10 years from now, when for some reason I need to access a term paper I wrote in college.… pfffft.

Flint said:

Then 10 years from now, when for some reason I need to access a term paper I wrote in college.… pfffft.

The CD-ROM (remember those? Occasionally they're still used) was said to be the very first medium that was expected to outlast the ability to read it. That is, the physical item wouldn't deteriorate beyond recovery sooner than the hardware and software necessary to extract anything off of it.

IBelieveInGod said: Playing a game with percentages? I'm asking what percentage of mutations are good, bad, and neutral. Are you afraid to answer that question, because you think it is a gotcha? Why would you be concerned about a gotcha?

RBH said:

IBelieveInGod said: Playing a game with percentages? I'm asking what percentage of mutations are good, bad, and neutral. Are you afraid to answer that question, because you think it is a gotcha? Why would you be concerned about a gotcha?

Your question was answered. Read for comprehension or risk banishment to the Bathroom Wall.

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

Sheesh; if this ibig troll is a child that has been abandoned by its mother, one can hardly blame the mother.

Is disease an example of bad mutations?

Maybe I should clarify the previous question, are cancer, sickle cell anemia, muscular dystrophy, etc... examples of harmful mutations?

Cubist said:

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

As has already been pointed out, you really can't apply any of the terms "beneficial", "damaging", or "neutral" to a mutation until after you've specified the environment in which the mutation-carrying critter will live.
Consider a mutation which gives a critter pure white fur: For a critter which lives up north in the Arctic Circle, pure white fur would be effective camouflage, so that pure-white-fur mutation would be beneficial to an animal in the Arctic. But for a critter which lives in the swamps of Florida, pure white fur would make that critter stand out against its environment, hence make that critter an easier target for predators, so that pure-white-fur mutation would be damaging to an animal in Florida. So… is that pure-white-fur mutation beneficial, or damaging?
All the above said and acknowledged: The last time I checked, something like 90% of all mutations are 'neutral', meaning not really affecting the critter for good or ill; another 9%-or-so of mutations can be considered 'damaging' to those critters which carry them; and the remaining ≈1% of mutations can be considered 'beneficial' to those critters which carry them. What of it, IBIG?

What is Natural Genetic Engineering?

IBelieveInGod said: What is Natural Genetic Engineering?

IBelieveInGod said: [A]re cancer, sickle cell anemia, muscular dystrophy, etc... examples of harmful mutations?

stevaroni said:

IBelieveInGod said: So they are selected against? Tell me what prevents a repressed gene from being expressed in the future?

Actually, you would expect a truly repressed gene to fall apart over time. Genes duplicate imperfectly. That is a known fact. Eventually, every gene which is not repaired can be expected to accumulate enough mutations that it breaks. This happens to all genes. When it happens to an important gene, that animal usually dies is debilitated in such a way that nature selects against it ( an interesting example is the ancestor of great apes, including us, where the vitamin C synthesis gene broke about 10Mya, before humans and their crafty hunter-gathering, this limited the habitat of the great apes to tropical areas where vitamin C rich fruit was plentiful ). When an animal with a faulty important function is selected against, it's usually to the advantage of similar fully functional animal. Hence, it's quite likely that the broken gene is swept out of the gene pool, to be replaced by a better copy. In the case of a truly recessive gene, there's no tendancy to self-correct and fix it, since there's no loss of fitness assosiated to loosing a function that doesn't work. Since all genes mutate at a fixed rate, and no pressure is applied to fix broken genes, you would expect truly recessive genes to slowly turn into junk. This is a simple concept, IBIG. I expect all the parts on my computer to die eventually. If a significant function goes, liek the display or power supply, I will fix it immediately (nature can't fix it, of course, instead it just selects a better, working computer). If a recessive function goes, like my 5 1/4 floppy or parallel port, I probably won't even notice, and will never fix it. In fact, like my 5 1/4 inch floppy, I will probably slowly start to not have the right driver installed, because I never needed it anyway. Eventually, it's not even supported in the operating system. Then 10 years from now, when for some reason I need to access a term paper I wrote in college.... pfffft. That's how recessive genes work in the real world.

IBelieveInGod said:

Cubist said:

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

As has already been pointed out, you really can't apply any of the terms "beneficial", "damaging", or "neutral" to a mutation until after you've specified the environment in which the mutation-carrying critter will live.
Consider a mutation which gives a critter pure white fur: For a critter which lives up north in the Arctic Circle, pure white fur would be effective camouflage, so that pure-white-fur mutation would be beneficial to an animal in the Arctic. But for a critter which lives in the swamps of Florida, pure white fur would make that critter stand out against its environment, hence make that critter an easier target for predators, so that pure-white-fur mutation would be damaging to an animal in Florida. So… is that pure-white-fur mutation beneficial, or damaging?
All the above said and acknowledged: The last time I checked, something like 90% of all mutations are 'neutral', meaning not really affecting the critter for good or ill; another 9%-or-so of mutations can be considered 'damaging' to those critters which carry them; and the remaining ≈1% of mutations can be considered 'beneficial' to those critters which carry them. What of it, IBIG?

Please provide actual evidence that 90% of all mutations are 'neutral'. Please don't provide studies or research that have no basis in reality, i.e. Nachman and Crowell did a comparison of Human and Chimpanzee DNA; they then proceeded to use the Evolutionary assumption that Humans and Chimpanzees had a common ancestor that lived about 5 million years ago. Their estimate of 3 harmful mutations per generation had the same basis. This is not real science, because the entire research hinges on whether Chimpanzees and Humans, really had a common ancestor 5 million years ago. This study did not measure actual mutations in humans, so I call it a bogus study. So, please provide actual observable evidence to back up how many mutations are neutral, harmful, and beneficial. I've seen numbers and percentages, but are they have a basis in reality, are they really observed or are they calculated on the assumption like provided earlier in this paragraph.

Cubist said:

IBelieveInGod said:

Cubist said:

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

As has already been pointed out, you really can't apply any of the terms "beneficial", "damaging", or "neutral" to a mutation until after you've specified the environment in which the mutation-carrying critter will live.
Consider a mutation which gives a critter pure white fur: For a critter which lives up north in the Arctic Circle, pure white fur would be effective camouflage, so that pure-white-fur mutation would be beneficial to an animal in the Arctic. But for a critter which lives in the swamps of Florida, pure white fur would make that critter stand out against its environment, hence make that critter an easier target for predators, so that pure-white-fur mutation would be damaging to an animal in Florida. So… is that pure-white-fur mutation beneficial, or damaging?
All the above said and acknowledged: The last time I checked, something like 90% of all mutations are 'neutral', meaning not really affecting the critter for good or ill; another 9%-or-so of mutations can be considered 'damaging' to those critters which carry them; and the remaining ≈1% of mutations can be considered 'beneficial' to those critters which carry them. What of it, IBIG?

Please provide actual evidence that 90% of all mutations are 'neutral'. Please don't provide studies or research that have no basis in reality, i.e. Nachman and Crowell did a comparison of Human and Chimpanzee DNA; they then proceeded to use the Evolutionary assumption that Humans and Chimpanzees had a common ancestor that lived about 5 million years ago. Their estimate of 3 harmful mutations per generation had the same basis. This is not real science, because the entire research hinges on whether Chimpanzees and Humans, really had a common ancestor 5 million years ago. This study did not measure actual mutations in humans, so I call it a bogus study. So, please provide actual observable evidence to back up how many mutations are neutral, harmful, and beneficial. I've seen numbers and percentages, but are they have a basis in reality, are they really observed or are they calculated on the assumption like provided earlier in this paragraph.

Gosh, IBIG, how could anyone possibly get the idea that any ostensibly-innocent question of yours could be nothing more than a veiled attempt to play a 'gotcha' trick on those Ee-vil Darwinisticianistas?

Cubist said:

IBelieveInGod said:

Cubist said:

IBelieveInGod said: What percentage of mutations are beneficial? What percentage of mutations are damaging? What percentage of mutations are neutral?

As has already been pointed out, you really can't apply any of the terms "beneficial", "damaging", or "neutral" to a mutation until after you've specified the environment in which the mutation-carrying critter will live.
Consider a mutation which gives a critter pure white fur: For a critter which lives up north in the Arctic Circle, pure white fur would be effective camouflage, so that pure-white-fur mutation would be beneficial to an animal in the Arctic. But for a critter which lives in the swamps of Florida, pure white fur would make that critter stand out against its environment, hence make that critter an easier target for predators, so that pure-white-fur mutation would be damaging to an animal in Florida. So… is that pure-white-fur mutation beneficial, or damaging?
All the above said and acknowledged: The last time I checked, something like 90% of all mutations are 'neutral', meaning not really affecting the critter for good or ill; another 9%-or-so of mutations can be considered 'damaging' to those critters which carry them; and the remaining ≈1% of mutations can be considered 'beneficial' to those critters which carry them. What of it, IBIG?

Please provide actual evidence that 90% of all mutations are 'neutral'. Please don't provide studies or research that have no basis in reality, i.e. Nachman and Crowell did a comparison of Human and Chimpanzee DNA; they then proceeded to use the Evolutionary assumption that Humans and Chimpanzees had a common ancestor that lived about 5 million years ago. Their estimate of 3 harmful mutations per generation had the same basis. This is not real science, because the entire research hinges on whether Chimpanzees and Humans, really had a common ancestor 5 million years ago. This study did not measure actual mutations in humans, so I call it a bogus study. So, please provide actual observable evidence to back up how many mutations are neutral, harmful, and beneficial. I've seen numbers and percentages, but are they have a basis in reality, are they really observed or are they calculated on the assumption like provided earlier in this paragraph.

Gosh, IBIG, how could anyone possibly get the idea that any ostensibly-innocent question of yours could be nothing more than a veiled attempt to play a 'gotcha' trick on those Ee-vil Darwinisticianistas?

Would a mutation/mutations that cause the blood to loose ability to clot be considered beneficial? It would greatly reduce the risk of stroke, which could be considered a benefit, but then again the individual would most likely bleed to death, because of the inability of the blood to clot. So would it be considered a harmful mutation/mutations, neutral, or beneficial?

Atheistoclast said: Both artificial and natural selection do indeed make use of an imperfect replication system (i.e random mutations). But that is where the similarity ends.

Artificial selection always works by way of the conscious intent and will of the *artificer*.

IBIG is just doing the Gish gallup.

Everyone, look at his last several posts. He's stopped even pretending to answer questions, and now just posts a different question every time.

I tried to warn you guys. For some reason, you let this pathetic little twit completely screw up another perfectly good thread.

Maybe I can explain it in these terms. IBIGOT is a twelve year old boy who craves attention. His mother hates him, for obvious reasons, so she ignores him completely. She does however give him one dollar for every response he can get on internet blogs, this keeps him out of her hair while she drinks. Now IBIGOT uses the money to buy ammo for his assault rifle which he takes to school every day. Do you really want to respond to him again?

Ignore him and he will go away. Respond to him and you get exactly what you ask for. Ban him permanently and no one will have to deal with his crap. He already had his chance, he already blew it. Don't give him another chance. He still has his own thread, so why is he even here? That's just plain rude.

eric said: IBIG is just doing the Gish gallup. Everyone, look at his last several posts. He's stopped even pretending to answer questions, and now just posts a different question every time.

eric said: IBIG is just doing the Gish gallup. Everyone, look at his last several posts. He's stopped even pretending to answer questions, and now just posts a different question every time.

DS said: I tried to warn you guys. For some reason, you let this pathetic little twit completely screw up another perfectly good thread. Maybe I can explain it in these terms. IBIGOT is a twelve year old boy who craves attention. His mother hates him, for obvious reasons, so she ignores him completely. She does however give him one dollar for every response he can get on internet blogs, this keeps him out of her hair while she drinks. Now IBIGOT uses the money to buy ammo for his assault rifle which he takes to school every day. Do you really want to respond to him again? Ignore him and he will go away. Respond to him and you get exactly what you ask for. Ban him permanently and no one will have to deal with his crap. He already had his chance, he already blew it. Don't give him another chance. He still has his own thread, so why is he even here? That's just plain rude.

Eric, yes IBIG is trying to find someone, anyone, to play his 'gotcha' game. In fact... it is EXACTLY the same game he played several months ago on the BW... same questions, same inane responses to the answers he got.

If the answer he got didn't say what he wanted to hear to play his 'gotcha' game, then he would harangue the answerer and 'interpret' his answer until the answerer got fed up and left... at which point IBIG would state that his interpretation was correct, make some totally inane conclusion and declare victory.

I predict that, if this thread is allowed to continue, that he will begin complaining that all these questions are to show us that there are moral absolutes and God is the reason for that. Of course, he's wrong, as I recently showed on his thread at ATBC. He's just too chicken to have an actual conversation on the subject.

I'll note that he thinks we play gotcha games with him. However, he has to lie, 'interpret', attack strawmen, etc. We (I) just have to tell the truth and use logic.

BTW: Hey 'clast, I'm sure you'll get to answering how you can tell the difference between a gene, organism, protein, or strucutre developed (either artificial or natural selection) in just a few posts. I'd hate to have someone think that you can't deal with such an idiotically simple question.

DS said: Ignore him and he will go away.

IBelieveInGod said: I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done?

If this is a public forum about evolution, then I would think that you would welcome opposing views.

Granted, you learned “speciation has never been observed” instead of “polly want a cracker,” but that’s about the only difference.

It really doesn't matter who or what is doing the selecting, or what the "purpose" of the selector may be. All you're illustrating is that selection works, regardless of what does the selecting. And the limits to artifical selection are identical to the limits of natural selection - the variation in the current genome. And the reason they're identical is, selection is selection is selection. You are deliberately confusing the purpose of the selector, with the method used by the selector, which is differential reproductive rates. In both cases. To beat this dead horse a little further in to the ground, "artificial" selection is nothing more than a changed environment to the organism trying to breed. It really doesn't matter whether the organism knows or cares about the CAUSE of the change. It only matters which individuals end up breeding. For whatever reason.

eric said:

IBelieveInGod said: I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done?

What's egregious and despicable is you completely ignore the answers. You ask the same crap over and over again and refuse to converse about it. Here you claimed that speciation has never been observed. Here I linked to a whole list of observed speciations. So, converse with me instead of changing the subject. Do you admit your statment was incorrect? If not, how do you account for all those those observed speciations? Respond to evidence and counter-argument instead of just ignoring it.

If this is a public forum about evolution, then I would think that you would welcome opposing views.

When a parrot disagrees with me, I don't consider it an "opposing view." Its just a parrot. Your conversational capability appears to be that of a parrot: words come out, but you show no comprehension of the words going in. Granted, you learned "speciation has never been observed" instead of "polly want a cracker," but that's about the only difference.

In the previous post I meant who makes the determination?

IBelieveInGod said:

eric said:

IBelieveInGod said: I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done?

What's egregious and despicable is you completely ignore the answers. You ask the same crap over and over again and refuse to converse about it. Here you claimed that speciation has never been observed. Here I linked to a whole list of observed speciations. So, converse with me instead of changing the subject. Do you admit your statment was incorrect? If not, how do you account for all those those observed speciations? Respond to evidence and counter-argument instead of just ignoring it.

If this is a public forum about evolution, then I would think that you would welcome opposing views.

When a parrot disagrees with me, I don't consider it an "opposing view." Its just a parrot. Your conversational capability appears to be that of a parrot: words come out, but you show no comprehension of the words going in. Granted, you learned "speciation has never been observed" instead of "polly want a cracker," but that's about the only difference.

Really? So speciation has been observed? Or is it new species have been discovered? Are they really new species, or could it be that they were just never discovered before? Anyway let's get back to the topic at hand, mutations. Tell me how it is determined that any particular mutation is beneficial, harmful, or neutral? How makes the determination? If a mutation is beneficial in one aspect and harmful in another is it then determined to be beneficial, harmful or neutral?

IBelieveInGod said: In the previous post I meant who makes the determination?

Atheistoclast said: Let me just repeat for the *asininely dense* in this forum: Natural selection tends to oppose what artificial selection develops. As breeders, we have managed to produce animals and plants which cannot survive in the wild. A chihuahua cannot compete for resources against a wolf or fox - it is essentially a deformed canid. Natural selection would oppose such changes, as with seedless fruit. There is no "environment" with respect to artificial selection - instead there is a human "requirement". Now, what we have been doing for thousands of years is really a form of *genetic engineering*...something natural selection cannot do. Artificial selection means making use of chance mutations to construct something which does not represent an increase in reproductive fitness, but rather in economic or social utility. What you lot don't understand is that natural selection is the worst possible force to explain the diversity of life on earth. Why would anything other than the likes of cyanobacteria exist when they are the most adaptable and reproductively fit organisms that can survive in virtually every possible ecological niche?

IBelieveInGod said:

eric said:

IBelieveInGod said: I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done?

What's egregious and despicable is you completely ignore the answers. You ask the same crap over and over again and refuse to converse about it. Here you claimed that speciation has never been observed. Here I linked to a whole list of observed speciations. So, converse with me instead of changing the subject. Do you admit your statment was incorrect? If not, how do you account for all those those observed speciations? Respond to evidence and counter-argument instead of just ignoring it.

If this is a public forum about evolution, then I would think that you would welcome opposing views.

When a parrot disagrees with me, I don't consider it an "opposing view." Its just a parrot. Your conversational capability appears to be that of a parrot: words come out, but you show no comprehension of the words going in. Granted, you learned "speciation has never been observed" instead of "polly want a cracker," but that's about the only difference.

Really? So speciation has been observed? Or is it new species have been discovered? Are they really new species, or could it be that they were just never discovered before? Anyway let's get back to the topic at hand, mutations. Tell me how it is determined that any particular mutation is beneficial, harmful, or neutral? How makes the determination? If a mutation is beneficial in one aspect and harmful in another is it then determined to be beneficial, harmful or neutral?

IBelieveInGod said:

DS said: I tried to warn you guys. For some reason, you let this pathetic little twit completely screw up another perfectly good thread. Maybe I can explain it in these terms. IBIGOT is a twelve year old boy who craves attention. His mother hates him, for obvious reasons, so she ignores him completely. She does however give him one dollar for every response he can get on internet blogs, this keeps him out of her hair while she drinks. Now IBIGOT uses the money to buy ammo for his assault rifle which he takes to school every day. Do you really want to respond to him again? Ignore him and he will go away. Respond to him and you get exactly what you ask for. Ban him permanently and no one will have to deal with his crap. He already had his chance, he already blew it. Don't give him another chance. He still has his own thread, so why is he even here? That's just plain rude.

I'm not a twenty year old boy with and assault rifle, I don't even have a gun of any kind. How have I destroyed this perfectly good thread? I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done? If this is a public forum about evolution, then I would think that you would welcome opposing views. Opposing views would only strengthen the theory of evolution, if indeed evolution is true. So, if you really feel that evolution is true, then you should have nothing to worry about, as this would give you the opportunity to answer those opposing views with brilliant evidence backed by real observation.

IBelieveInGod said: In the previous post I meant who makes the determination?

'clast,

So, my understanding is that you cannot tell the difference between an organism that developed by natural selection and one developed by artificial selection. Is this correct?

If this is not correct, please describe the procedure that objectively classifies an organism as developing via natural or artificial selection.

Saying "artificial selection makes thngs that can't survive in the wild" is a simply ridiculous classification system. Without corrective lenses, I can't survive in the wild. Am I a product of artificial sslection then?

Any researcher should be able to apply your determinination procedure to any organism (or gene or protein or structure) and every single researcher should get the same result (i.e. this organism was developed via natural selection and not artificial selection).

So what criteria do you use to make this determination?

I maintain that you cannot do this. I maintain that there is no difference in the organism, gene, protein, or biologic structure that could possibly indicate artificial or natural selection. The reason is that they are the exact same thing. They use the same starting material, they use the same mutations, and they can result in the same changes. The only difference is the environment of the organism and that isn't reflected in the DNA.

For their environment (little old ladies homes*) the chihuahua is extremely well adapted. In fact, I bet they generally life longer lives than any truly wild dogs (wolves, coyotes, dingos, etc). The ones that do reproduce probably reproduce way more than wild dogs with a much, much higher of surviving offspring. By any measure, they are just as succesful, if not more-so than their wild counterparts.

If you cannot determine the difference between natural and artificial selection by observing the organism, then your entire argument is useless.

*This is a joke people.

IBelieveInGod said: Are they really new species, or could it be that they were just never discovered before?

fnxtr said: OT: I'm hoping CFL's will soon go the way of Laserdisc. Wiring a house for low-voltage LED's would be *so* much easier!

There is still an environment even for artificial selection, otherwise, how could natural selection oppose artificial selection? You contradicted yourself there.

Genetic engineering is not just selective breeding. You are once again mistaken.

Natural selection can produce complexity and diversity, it just depends on the environment and how it changes.

Bacteria are still with us, but other organisms have also evolved. You have provided no reason why they couldn't. Artificial selection is irrelevant to this argument. The fact that bacteria persist does not imply that nothing else could ever evolve. Or do you think that every biologist in the world is too stupid to realize that bacteria still exist?

Since you still cannot bring yourself to admit that you were wrong a bout duplicated genes, I'll make it easy for you. If I have two cars and one can will not start I can still drive to the store. There, do you get it now?

Atheistoclast said: The former requires an intelligence to select those variations that meet the particular *purpose* in mind. The latter's sole criterion is reproductive fitness and nothing else. If it is beneficial to lose functionality, because it confers a survival advantage, then natural selection will go down that route.

Gabriel Hanna said:

IBelieveInGod said:

eric said:

IBelieveInGod said: I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done?

What's egregious and despicable is you completely ignore the answers. You ask the same crap over and over again and refuse to converse about it. Here you claimed that speciation has never been observed. Here I linked to a whole list of observed speciations. So, converse with me instead of changing the subject. Do you admit your statment was incorrect? If not, how do you account for all those those observed speciations? Respond to evidence and counter-argument instead of just ignoring it.

If this is a public forum about evolution, then I would think that you would welcome opposing views.

When a parrot disagrees with me, I don't consider it an "opposing view." Its just a parrot. Your conversational capability appears to be that of a parrot: words come out, but you show no comprehension of the words going in. Granted, you learned "speciation has never been observed" instead of "polly want a cracker," but that's about the only difference.

Really? So speciation has been observed? Or is it new species have been discovered? Are they really new species, or could it be that they were just never discovered before? Anyway let's get back to the topic at hand, mutations. Tell me how it is determined that any particular mutation is beneficial, harmful, or neutral? How makes the determination? If a mutation is beneficial in one aspect and harmful in another is it then determined to be beneficial, harmful or neutral?

this is why people are calling you a troll. They gave you a link that stated clearly, THESE ARE OBSERVATIONS OF NEW SPECIES FORMING. You refused to look at the link and then just repeated yourself. "Are they really NEW species, or just newly discovered?" THEY ARE REALLY NEW, genius.

Gabriel Hanna said:

IBelieveInGod said: In the previous post I meant who makes the determination?

We can call a mutation anything we want, its effect on survival and reproduction is what determines whether its beneficial regardless of what we call it. Are you thinking there is some kind of Grand Council that confers gold medals on worthy mutations, or what? This is why the other commenters are calling you stupid.

IBelieveInGod said: Is disease an example of bad mutations?

IBelieveInGod said: So there is no way of actually knowing if a currently observed mutation is beneficial, harmful, or neutral?

I'm stupid for asking questions?

Atheistoclast said:

There is still an environment even for artificial selection, otherwise, how could natural selection oppose artificial selection? You contradicted yourself there.

There is no natural environment or fitness landscape. There is only the requirement of the breeder. Chihuahuas are bred to survive under human conditions, not those of Nature.

Genetic engineering is not just selective breeding. You are once again mistaken.

Evidently you have a problem reading English. I stated that selective breeding was a form of genetic engineering.

Natural selection can produce complexity and diversity, it just depends on the environment and how it changes.

Nonsense. Natural selection *reduces* diversity. It does not proliferate variation. How, may I ask, does the environment produce domains for DNA-binding or cell cycle regulation? Do you even know what I am talking about?

Bacteria are still with us, but other organisms have also evolved. You have provided no reason why they couldn't. Artificial selection is irrelevant to this argument. The fact that bacteria persist does not imply that nothing else could ever evolve. Or do you think that every biologist in the world is too stupid to realize that bacteria still exist?

The point is that bacteria are the most effective means of securing DNA replication. That is why there is no natural reason why anything should or would have evolved beyond prokaryotic life.

Since you still cannot bring yourself to admit that you were wrong a bout duplicated genes, I'll make it easy for you. If I have two cars and one can will not start I can still drive to the store. There, do you get it now?

How ,in any way, was I wrong about duplicated genes? Your inability to understand a basic sequence alignment really testifies to your lack of understanding in this subject. I will pass on your stupid analogy.

IBelieveInGod said:

Gabriel Hanna said:

IBelieveInGod said:

eric said:

IBelieveInGod said: I have asked questions about mutations, and somehow that is an egregious and despicable thing I have done?

What's egregious and despicable is you completely ignore the answers. You ask the same crap over and over again and refuse to converse about it. Here you claimed that speciation has never been observed. Here I linked to a whole list of observed speciations. So, converse with me instead of changing the subject. Do you admit your statment was incorrect? If not, how do you account for all those those observed speciations? Respond to evidence and counter-argument instead of just ignoring it.

If this is a public forum about evolution, then I would think that you would welcome opposing views.

When a parrot disagrees with me, I don't consider it an "opposing view." Its just a parrot. Your conversational capability appears to be that of a parrot: words come out, but you show no comprehension of the words going in. Granted, you learned "speciation has never been observed" instead of "polly want a cracker," but that's about the only difference.

Really? So speciation has been observed? Or is it new species have been discovered? Are they really new species, or could it be that they were just never discovered before? Anyway let's get back to the topic at hand, mutations. Tell me how it is determined that any particular mutation is beneficial, harmful, or neutral? How makes the determination? If a mutation is beneficial in one aspect and harmful in another is it then determined to be beneficial, harmful or neutral?

this is why people are calling you a troll. They gave you a link that stated clearly, THESE ARE OBSERVATIONS OF NEW SPECIES FORMING. You refused to look at the link and then just repeated yourself. "Are they really NEW species, or just newly discovered?" THEY ARE REALLY NEW, genius.

Gabriel Hanna said:

IBelieveInGod said: In the previous post I meant who makes the determination?

We can call a mutation anything we want, its effect on survival and reproduction is what determines whether its beneficial regardless of what we call it. Are you thinking there is some kind of Grand Council that confers gold medals on worthy mutations, or what? This is why the other commenters are calling you stupid.

So there is no way of actually knowing if a currently observed mutation is beneficial, harmful, or neutral? I'm stupid for asking questions? You see I hear percentages of what are harmful, beneficial, and neutral mutations.

Atheistoclast said: There is no natural environment or fitness landscape. There is only the requirement of the breeder. Chihuahuas are bred to survive under human conditions, not those of Nature.

Bullshit. You cannot breed without an environment. Humans cannot control all aspects of the environment or development. Therefore, you are wrong. Genetic engineering is more than just selective breeding. You are not using the term incorrectly. If you mean selective breeding then say so.

Nonsense. Natural selection *reduces* diversity. It does not proliferate variation. How, may I ask, does the environment produce domains for DNA-binding or cell cycle regulation? Do you even know what I am talking about?

I know you are talking bullshit. You once again conveniently forgot about mutation. That coupled with selection produces diversity. Get a clue.

The point is that bacteria are the most effective means of securing DNA replication. That is why there is no natural reason why anything should or would have evolved beyond prokaryotic life.

Bullshit. Bacteria are the best replicators in some environments. There is no reason why anything else had to evolve, but it did. You cannot deny that it did. All you can do is nitpick mechanisms. Since you still cannot bring yourself to admit that you were wrong a bout duplicated genes, I'll make it easy for you. If I have two cars and one can will not start I can still drive to the store. There, do you get it now?

How ,in any way, was I wrong about duplicated genes? Your inability to understand a basic sequence alignment really testifies to your lack of understanding in this subject. I will pass on your stupid analogy.

Here is a back of the envelope accounting.

If mutations occur evenly across the entire genome and only 2% of the DNA is coding. Then only 2% of the mutations have the potential to be immediately harmful and/or beneficial or more likely than not, neutral. Of the 98% of the remaining mutations, they will be de facto neutral (if a tree falls in the forest ...) with a potential upside to be beneficial if a new gene regulatory function results. (see Sean Carroll's work if truly interested)

You are of the mistaken notion that there is an ongoing catalog of all mutations and each gets classified into one of your categories immediately. Genome sequencing is making great advances but I assure you, your understanding is quite sophomoric. That you continue to insist on that delusion only adds to your irrelevancy to biological science reality.

Ever try explaining Quantum Mechanics to a four year old? Yes, they ask a lot of questions but the questions more often exposes the child's incompetence rather than indicate any deep understand of the material and the implications of any of the concepts. If you cannot add anything to the intelligence of the conversation, you are merely the four year old distracting child.

Gabriel Hanna said: this is why people are calling you a troll. They gave you a link that stated clearly, THESE ARE OBSERVATIONS OF NEW SPECIES FORMING. You refused to look at the link and then just repeated yourself.

Atheistoclast said: Natural selection tends to oppose what artificial selection develops. As breeders, we have managed to produce animals and plants which cannot survive in the wild. A chihuahua cannot compete for resources against a wolf or fox - it is essentially a deformed canid. Natural selection would oppose such changes, as with seedless fruit. What you lot don't understand is that natural selection is the worst possible force to explain the diversity of life on earth. Why would anything other than the likes of cyanobacteria exist when they are the most adaptable and reproductively fit organisms that can survive in virtually every possible ecological niche?

Atheistoclast said: Natural selection tends to oppose what artificial selection develops. As breeders, we have managed to produce animals and plants which cannot survive in the wild. A chihuahua cannot compete for resources against a wolf or fox

What you lot don’t understand is that natural selection is the worst possible force to explain the diversity of life on earth. Why would anything other than the likes of cyanobacteria exist when they are the most adaptable and reproductively fit organisms that can survive in virtually every possible ecological niche?

Atheistoclast said: Nonsense. Natural selection *reduces* diversity. It does not proliferate variation.

The point is that bacteria are the most effective means of securing DNA replication. That is why there is no natural reason why anything should or would have evolved beyond prokaryotic life.

The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

Mere quibbling. There is an environment. The actions of the breeder merely adjust the parameters somewhat. The human/Nature dichotomy is just another variant of the "It's Designed" fallacy.

Selection reduces variation. Gene duplication, point mutation, sexual reproduction, (and the rest....) generate the variation that selection discriminates for and against. The fact that you can even ask "does the environment produce domains for DNA-binding" shows that you simply do not have the slightest understanding of what you're trying to argue against.

What has sequence alignment got to do with this? You are just trying to confuse the issue with non-sequiturs. Try a programming analogy. Only yesterday I took a copy of a program and edited the copy to make it do something completely different. The original program remains and still works, and worked even during the period when the copy was incomplete and non-functional. Please explain why the same principle doesn't work for genes.

Atheistoclast said:

Mere quibbling. There is an environment. The actions of the breeder merely adjust the parameters somewhat. The human/Nature dichotomy is just another variant of the "It's Designed" fallacy.

No, the breeder proactively selects certain variations for their perceived utility and so alters the natural course.

Selection reduces variation. Gene duplication, point mutation, sexual reproduction, (and the rest....) generate the variation that selection discriminates for and against. The fact that you can even ask "does the environment produce domains for DNA-binding" shows that you simply do not have the slightest understanding of what you're trying to argue against.

Er...what is the difference between variation and genetic diversity? And I'd like to know how environmental pressures can generate something like the DNA-binding homeodomain.

What has sequence alignment got to do with this? You are just trying to confuse the issue with non-sequiturs. Try a programming analogy. Only yesterday I took a copy of a program and edited the copy to make it do something completely different. The original program remains and still works, and worked even during the period when the copy was incomplete and non-functional. Please explain why the same principle doesn't work for genes.

The most powerful piece of evidence presented in my paper was the sequence alignment showing that the classic examples of gene duplication and adaptation entailed significant deletions of information.

Your analogy is baseless. For the two succinct reasons: 1) Gene duplicates tend to serve as backups for each other. If you change the functionality of a duplicate it prevents it from compensating for any damage done to a paralog. 2) Natural selection has no intelligence and cannot change a gene or program as a human would. Trial and error can only get you so far.

All gene duplicates end up as variations of the same theme. You will find gene families with lots of paralogous members but all doing pretty much the same thing - albeit with minor and subtle differences in function and expression.

Atheistoclast said: All gene duplicates end up as variations of the same theme. You will find gene families with lots of paralogous members but all doing pretty much the same thing - albeit with minor and subtle differences in function and expression.

Atheistoclast said:

Mere quibbling. There is an environment. The actions of the breeder merely adjust the parameters somewhat. The human/Nature dichotomy is just another variant of the "It's Designed" fallacy.

No, the breeder proactively selects certain variations for their perceived utility and so alters the natural course.

Selection reduces variation. Gene duplication, point mutation, sexual reproduction, (and the rest....) generate the variation that selection discriminates for and against. The fact that you can even ask "does the environment produce domains for DNA-binding" shows that you simply do not have the slightest understanding of what you're trying to argue against.

Er...what is the difference between variation and genetic diversity? And I'd like to know how environmental pressures can generate something like the DNA-binding homeodomain.

What has sequence alignment got to do with this? You are just trying to confuse the issue with non-sequiturs. Try a programming analogy. Only yesterday I took a copy of a program and edited the copy to make it do something completely different. The original program remains and still works, and worked even during the period when the copy was incomplete and non-functional. Please explain why the same principle doesn't work for genes.

The most powerful piece of evidence presented in my paper was the sequence alignment showing that the classic examples of gene duplication and adaptation entailed significant deletions of information. Your analogy is baseless. For the two succinct reasons: 1) Gene duplicates tend to serve as backups for each other. If you change the functionality of a duplicate it prevents it from compensating for any damage done to a paralog. 2) Natural selection has no intelligence and cannot change a gene or program as a human would. Trial and error can only get you so far. All gene duplicates end up as variations of the same theme. You will find gene families with lots of paralogous members but all doing pretty much the same thing - albeit with minor and subtle differences in function and expression.

Atheistoclast said: Your analogy is baseless. For the two succinct reasons: 1) Gene duplicates tend to serve as backups for each other. If you change the functionality of a duplicate it prevents it from compensating for any damage done to a paralog. 2) Natural selection has no intelligence and cannot change a gene or program as a human would. Trial and error can only get you so far. All gene duplicates end up as variations of the same theme. You will find gene families with lots of paralogous members but all doing pretty much the same thing - albeit with minor and subtle differences in function and expression.

Atheistoclast said: What you lot don't understand is that natural selection is the worst possible force to explain the diversity of life on earth. Why would anything other than the likes of cyanobacteria exist when they are the most adaptable and reproductively fit organisms that can survive in virtually every possible ecological niche?

DS said: The atheist guy is somehow confusing the environment with selection pressure.

eric said:

DS said: The atheist guy is somehow confusing the environment with selection pressure.

He's also confusing mutation and selection. Or maybe he's just doing the old creationist goalpost move: start at 'it is physically impossible for that biochemical reaction to occur,' but when someone questions that, move to 'such an animal would not likely survive to pass on its genes.' Ah, the classics. My client was nowhere near the crime scene your honor, and anyway, it was self-defense.

RBH said:

IBelieveInGod said: Playing a game with percentages? I'm asking what percentage of mutations are good, bad, and neutral. Are you afraid to answer that question, because you think it is a gotcha? Why would you be concerned about a gotcha?

Your question was answered. Read for comprehension or risk banishment to the Bathroom Wall.

John Vanko said: Since this IS a public forum, and we live in a democracy, IF we voted on banishing IBIG to the BW (or out of PT altogether), could you get rid of him for us? On the other hand, if this forum is a meritocracy (like science), with peer review, could we not banish IBIG's posts to the BW for failing to pass muster (as they always fail)?

No, clastie never wrote my bosses. He does, however, continue to call me "Herr Seebach", presumably to go along with his repeated allegations that my side lost WWII (see, it's a German name, right, so that means I'm German!).

And to correct one of the other posters: I'm not "Dr. Seebach". I got a B.A. in psychology, and that's it. I'm just some guy who programs because it's fun.

I am so glad to see that he is continuing to amuse.

Hiya seebs! Long time no see!

RBH said:

John Vanko said: Since this IS a public forum, and we live in a democracy, IF we voted on banishing IBIG to the BW (or out of PT altogether), could you get rid of him for us? On the other hand, if this forum is a meritocracy (like science), with peer review, could we not banish IBIG's posts to the BW for failing to pass muster (as they always fail)?

The Thumb is neither a meritocracy nor a democracy, it's a (usually) benevolent dictatorship. The main goals (for me, at least) are education and intellectual recreation, and people like IBIG help advance both. His clueless comments provide the opportunity to correct him, for the lurkers if no one else, and thus serve the educational goal by exemplifying the sheer ignorance and perversity of the opposition. We need to be reminded of that, I think. And the recreation comes in the effort to solve the puzzles the cluelessness of his comments embody: 'Just what is he claiming now?'

RBH said:

John Vanko said: Since this IS a public forum, and we live in a democracy, IF we voted on banishing IBIG to the BW (or out of PT altogether), could you get rid of him for us? On the other hand, if this forum is a meritocracy (like science), with peer review, could we not banish IBIG's posts to the BW for failing to pass muster (as they always fail)?

The Thumb is neither a meritocracy nor a democracy, it's a (usually) benevolent dictatorship. The main goals (for me, at least) are education and intellectual recreation, and people like IBIG help advance both. His clueless comments provide the opportunity to correct him, for the lurkers if no one else, and thus serve the educational goal by exemplifying the sheer ignorance and perversity of the opposition. We need to be reminded of that, I think. And the recreation comes in the effort to solve the puzzles the cluelessness of his comments embody: 'Just what is he claiming now?'

No, clastie never wrote my bosses. He does, however, continue to call me "Herr Seebach", presumably to go along with his repeated allegations that my side lost WWII (see, it's a German name, right, so that means I'm German!).

Atheistoclast said:

No, clastie never wrote my bosses. He does, however, continue to call me "Herr Seebach", presumably to go along with his repeated allegations that my side lost WWII (see, it's a German name, right, so that means I'm German!).

I just bet you wish Deutsche was the national language of America. Your kith and kin on the other side of the Atlantic lost the war: now deal with it. Anyway, I didn't want to get you fired from your job - that is why I relented and did not write to your bosses. I also have a new and wonderful program which really will falsify the T of E.....even someone like yourself could understand it.

Which brings us full circle back to the research in the OP: A new function (antifreeze) from an old duplicated gene that did something quite different, much more than a "minor and subtle" difference.

DS said: The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

Atheistoclast said: I just bet you wish Deutsche was the national language of America. Your kith and kin on the other side of the Atlantic lost the war: now deal with it.

Dale Husband said:

DS said: The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

No, he is a con artist, like most Creationist bigots.

Atheistoclast said: I also have a new and wonderful program which really will falsify the T of E.....even someone like yourself could understand it.

SWT said:

Atheistoclast said: I also have a new and wonderful program which really will falsify the T of E.....even someone like yourself could understand it.

10 REM 20 REM PROGRAM ATHEISTOCLAST 30 REM 40 PRINT ("EVOLUTION IS FALSE!") 50 GO TO 40 60 END

Atheistoclast said:

Which brings us full circle back to the research in the OP: A new function (antifreeze) from an old duplicated gene that did something quite different, much more than a "minor and subtle" difference.

Except that neither you NOR ANYONE HERE *ACTUALLY READ THE PAPER* beyond the title and abstract! It does help to read the details and not just the attention whoring headlines! If you don't want to pay, here is a link from the author's website. You have no excuse to remain ignorant. http://www.life.illinois.edu/ccheng/Deng%20et%20al%20PNAS2010_online.pdf The authors make it quite clear the ancestral SAS gene was "bifunctional" and that its “C-terminus peptide would be quite sufficient in inhibiting ice-crystal expansion in the fish body fluids.” They also make it clear that the *loss* of the N-terminal domain was one of the key changes involved in the evolution of the antifreeze gene. In other words, this is an example of "subfunctionalization" followed by a process of specialization and optimization. And this really is the most "innovation" that natural selection can accomplish.

Atheistoclast said:

Dale Husband said:

DS said: The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

No, he is a con artist, like most Creationist bigots.

Says someone with a zero publication record. If you have something important to say, submit to the journals. Any fool can participate in a forum like this.

Dale Husband said:

Atheistoclast said:

Dale Husband said:

DS said: The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

No, he is a con artist, like most Creationist bigots.

Says someone with a zero publication record. If you have something important to say, submit to the journals. Any fool can participate in a forum like this.

So you admit to being a fool like the rest of us? If your publications are full of $#it, who cares?

Atheistoclast said: Says someone with a zero publication record. If you have something important to say, submit to the journals. Any fool can participate in a forum like this.

and still no simple yes/no answer for if he can tell natural selection from artificial selection by looking at the products.

Of course, he doesn't understand that his entire point is gone if he can't do this.

So, do keep babbling and I'll keep asking you until you admit that you can't do it.

DS said:

Atheistoclast said: Says someone with a zero publication record. If you have something important to say, submit to the journals. Any fool can participate in a forum like this.

Well I guess he did learn something after all. That's what you call a self describing prophecy.

Of course this guy has no idea who he is talking to. He has no idea of the publication record of anyone. He just assumes that his record is superior. Well I guess that's his whole argument in a nut shell, remain ignorant and make whatever unjustified assumptions are required in order to maintain you misconceptions. It works for him, kind of.

I almost forgot - the end of creationism is at hand! I got me a 'puter program what says so.

Atheistoclast said:

No, clastie never wrote my bosses. He does, however, continue to call me "Herr Seebach", presumably to go along with his repeated allegations that my side lost WWII (see, it's a German name, right, so that means I'm German!).

I just bet you wish Deutsche was the national language of America. Your kith and kin on the other side of the Atlantic lost the war: now deal with it.

Anyway, I didn't want to get you fired from your job - that is why I relented and did not write to your bosses.

I also have a new and wonderful program which really will falsify the T of E.....even someone like yourself could understand it.

seebs said:

Atheistoclast said:

No, clastie never wrote my bosses. He does, however, continue to call me "Herr Seebach", presumably to go along with his repeated allegations that my side lost WWII (see, it's a German name, right, so that means I'm German!).

I just bet you wish Deutsche was the national language of America. Your kith and kin on the other side of the Atlantic lost the war: now deal with it.

Dude, poisoning the well doesn't work when you do it so very obviously. Hint: I haven't got ancestors from Germany within the last hundred and many years. Calling me a Nazi by implication just makes you look like you've got no actual responsive arguments.

No, no, he's a revisionist. Yeah, that's it, revisionist.

Atheistoclast said:

Dale Husband said:

DS said: The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

No, he is a con artist, like most Creationist bigots.

Says someone with a zero publication record. If you have something important to say, submit to the journals. Any fool can participate in a forum like this.

Stanton said:

Dale Husband said:

Atheistoclast said:

Dale Husband said:

DS said: The atheist guy is somehow confusing the environment with selection pressure. Perhaps a reasonable mistake, but when corrected he once again refused to admit that he was wrong and persisted in his misconceptions. This is the only way in which he can continue to be a rebel without a clue. Or is he a maverick? I can't tell.

No, he is a con artist, like most Creationist bigots.

Says someone with a zero publication record. If you have something important to say, submit to the journals. Any fool can participate in a forum like this.

So you admit to being a fool like the rest of us? If your publications are full of $#it, who cares?

Atheistoclast cares, because he wants us to worship him like the God he thinks he is for writing his inane programs. After all, he isn't attention-whoring for just nothing.

Well I'll pass on "directed hypermutations". There is absolutely no evidence whatsoever that any mutation is ever "directed". If there were, you could publish in Nature and Science and probably win the Nobel Prize. Of course the atheist guy still can't explain who is doing the directing, how or why. No wonder he has no evidence with a "hypothesis" like that.

The atheist guy still can't bring himself to admit that he was wrong a bout duplicate copies not being selected against either. He must know he is wrong and is just too stubborn to admit it. Of course, he has also completely ignored all of the questions regarding the evolution of hox genes. Now I wonder why that is? It's so cute when someone with no background or training tries to play scientist. Everyone can see they haven't got a clue, except themselves.

Waterloo for creationism! 111 eleventy!

What was the name of that first paper he published in Complexity? ANyone know?

I'd like to do a little search and see if anyone has ever cited it. After all, that's a much more useful measure of how good it is. Anyone can write a paper, but will anyone else read it?

And isn't that really all that's needed for evolution to occur? What else were you expecting? Expecting genes to appear out of nothing is a Creationist idea, not an evolutionist idea. You seem to be arguing with us about.......nothing we have a problem with.

“This is the first clear demonstration - with strong supporting molecular and functional evidence - of escape from adaptive conflict as the underlying process of gene duplication and the creation of a completely new function in one of the daughter copies,” Cheng said. “This has not been documented before in the field of molecular evolution.”

The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function.

OgreMkV said: What was the name of that first paper he published in Complexity? ANyone know? I'd like to do a little search and see if anyone has ever cited it. After all, that's a much more useful measure of how good it is. Anyone can write a paper, but will anyone else read it?

Well I'll pass on "directed hypermutations". There is absolutely no evidence whatsoever that any mutation is ever "directed".

Atheistoclast said:

And isn't that really all that's needed for evolution to occur? What else were you expecting? Expecting genes to appear out of nothing is a Creationist idea, not an evolutionist idea. You seem to be arguing with us about.......nothing we have a problem with.

Firstly, evolutionists do claim that genes like CLLU1 and BSC4 can appear out of a random piece of non-coding DNA just as they lied for years about a frameshift mutation causing the "nylonase" oligomer-degrading enzyme. What did Cheng actually claim?

“This is the first clear demonstration - with strong supporting molecular and functional evidence - of escape from adaptive conflict as the underlying process of gene duplication and the creation of a completely new function in one of the daughter copies,” Cheng said. “This has not been documented before in the field of molecular evolution.”

Oh...an "entirely new function" which was also a preexisting sub-function. Hmmm. Except that she made such a claim back in 1997 with this paper: http://www.pnas.org/content/94/8/3811.full

The notothenioid trypsinogen to AFGP conversion is the first clear example of how an old protein gene spawned a new gene for an entirely new protein with a new function.

Thankfully, I debunked her stupid conversion process in the paper in Complexity. Evidently, she had already backed off.

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

OgreMkV said: What was the name of that first paper he published in Complexity? ANyone know? I'd like to do a little search and see if anyone has ever cited it. After all, that's a much more useful measure of how good it is. Anyone can write a paper, but will anyone else read it?

Atheistoclast said:

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

Do you have a citation to research on TURF-13 in a peer-reviewed journal? I can't find any mention of it

Dave Wisker said:

Atheistoclast said:

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

Do you have a citation to research on TURF-13 in a peer-reviewed journal? I can't find any mention of it

Stop asking me to keep spoon-feeding you. The references are in the Panda's Thumb post by Art Hunt.

John Kwok said:

Dave Wisker said:

Atheistoclast said:

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

Do you have a citation to research on TURF-13 in a peer-reviewed journal? I can't find any mention of it

Stop asking me to keep spoon-feeding you. The references are in the Panda's Thumb post by Art Hunt.

You have my condolences Dave in dealing with this absurd buffoon.

I know how one could one discriminate natural and artificial selection. For the former you will observe a satified grin on the face of a supernatural; for the latter, a satisfied grin from the human breeder.

I suppose then that means any supernatural is interchangeable with any humans. I think I'm on to something and could just beat Atheistoclast to that Nobel. Wha da ya all think?

Atheistoclast said:

Well I'll pass on "directed hypermutations". There is absolutely no evidence whatsoever that any mutation is ever "directed".

Except that humans have been directing molecular evolution for a long time now. http://peds.oxfordjournals.org/content/17/9/659.full.pdf+html The process is, of course, analogous with artificial selection.

Bobsie said: I know how one could one discriminate natural and artificial selection. For the former you will observe a satified grin on the face of a supernatural; for the latter, a satisfied grin from the human breeder. I suppose then that means any supernatural is interchangeable with any humans. I think I'm on to something and could just beat Atheistoclast to that Nobel. Wha da ya all think?

Dave Wisker said:

Atheistoclast said:

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

Do you have a citation to research on TURF-13 in a peer-reviewed journal? I can't find any mention of it

Stop asking me to keep spoon-feeding you. The references are in the Panda's Thumb post by Art Hunt.

Bobsie said: I know how one could one discriminate natural and artificial selection. For the former you will observe a satified grin on the face of a supernatural; for the latter, a satisfied grin from the human breeder. I suppose then that means any supernatural is interchangeable with any humans. I think I'm on to something and could just beat Atheistoclast to that Nobel. Wha da ya all think?

Atheistoclast said:

Dave Wisker said:

Atheistoclast said:

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

Do you have a citation to research on TURF-13 in a peer-reviewed journal? I can't find any mention of it

Stop asking me to keep spoon-feeding you. The references are in the Panda's Thumb post by Art Hunt.

Aha: so again you haven't actually read any papers - like a puppet you just repeat what you have been told.

Atheistoclast said:

Dave Wisker said:

Atheistoclast said:

TURF-13. A protein coding gene which arose from the cobbling together of non-protein-coding sequences.

Do you have a citation to research on TURF-13 in a peer-reviewed journal? I can't find any mention of it

Stop asking me to keep spoon-feeding you. The references are in the Panda's Thumb post by Art Hunt.

Aha: so again you haven't actually read any papers - like a puppet you just repeat what you have been told.

seebs said: Seriously, it's worth it. There is more to life than lying to yourself. The truth will set you free... You don't have to be afraid and angry all the time. There is another way...

This is the most ironic thing the atheist loon has posted yet. He can't be bothered to read the literature, or even make a coherent argument. He can't even deal with a simple analogy. Then he accuses others of not reading a paper! Man, there are whole branches of science this guy is ignoring. First observe the beam that is thine own eye. This is even worse then him claiming he has a superior publication record than that of complete strangers ( and I do mean stranger).

Atheistoclast said:

This is the most ironic thing the atheist loon has posted yet. He can't be bothered to read the literature, or even make a coherent argument. He can't even deal with a simple analogy. Then he accuses others of not reading a paper! Man, there are whole branches of science this guy is ignoring. First observe the beam that is thine own eye. This is even worse then him claiming he has a superior publication record than that of complete strangers ( and I do mean stranger).

Did you or did you not read the cited papers relating to T-URF13 or not? You are the baboon who brought it up! I would expect you to talk the talk on the subject Or do I have to painstakingly go through the citations and explain why you are so mistaken?

Atheistoclast said:

This is the most ironic thing the atheist loon has posted yet. He can't be bothered to read the literature, or even make a coherent argument. He can't even deal with a simple analogy. Then he accuses others of not reading a paper! Man, there are whole branches of science this guy is ignoring. First observe the beam that is thine own eye. This is even worse then him claiming he has a superior publication record than that of complete strangers ( and I do mean stranger).

Did you or did you not read the cited papers relating to T-URF13 or not? You are the baboon who brought it up! I would expect you to talk the talk on the subject Or do I have to painstakingly go through the citations and explain why you are so mistaken?

Atheistoclast said: Did you or did you not read the cited papers relating to T-URF13 or not? You are the baboon who brought it up! I would expect you to talk the talk on the subject Or do I have to painstakingly go through the citations and explain why you are so mistaken?

Bobsie said: I know how one could one discriminate natural and artificial selection. For the former you will observe a satified grin on the face of a supernatural; for the latter, a satisfied grin from the human breeder. I suppose then that means any supernatural is interchangeable with any humans. I think I'm on to something and could just beat Atheistoclast to that Nobel. Wha da ya all think?

Atheistoclast said:

This is the most ironic thing the atheist loon has posted yet. He can't be bothered to read the literature, or even make a coherent argument. He can't even deal with a simple analogy. Then he accuses others of not reading a paper! Man, there are whole branches of science this guy is ignoring. First observe the beam that is thine own eye. This is even worse then him claiming he has a superior publication record than that of complete strangers ( and I do mean stranger).

Did you or did you not read the cited papers relating to T-URF13 or not? You are the baboon who brought it up! I would expect you to talk the talk on the subject Or do I have to painstakingly go through the citations and explain why you are so mistaken?

Mike Elzinga said:

Bobsie said: I know how one could one discriminate natural and artificial selection. For the former you will observe a satified grin on the face of a supernatural; for the latter, a satisfied grin from the human breeder. I suppose then that means any supernatural is interchangeable with any humans. I think I'm on to something and could just beat Atheistoclast to that Nobel. Wha da ya all think?

This is sheer genius, Bobsie. You have set out the parameters for a research program that can go on for generations. Natural selection produces some really stupid and undesirable things (e.g., ID/creationists) whereas artificial selection aims for desired traits that look designed. So whenever we see the satisfied smirk on the face of an ID/creationist, we instantly think, “Ah, mutation; proof of natural selection.” The more I think about this, the better it gets.

What's hilarious is that (again), the scientists are doing more work in ID than the ID proponents.

'clast has refused to even acknowledge the single question that destroys his entire notion, but Bobsie comes up with a testable (sort of) idea.

I even have a way of testing it. According to the Bible, God destroyed his entire creation twice (once when he kicked Adam and Eve out and again with the Flud), so I'm guessing that he wasn't smiling then. We win... ummm... what do we win?

Atheistoclast said: No, the breeder proactively selects certain variations for their perceived utility and so alters the natural course.

Shebardigan said: There are no prison walls stronger than the ones we construct for ourselves.

One of the really powerful ideas [in religions] is the idea of sacred truths. And a sacred truth is one that even thinking about it is evil. Don’t even think about it! And when you can establish that about anything, when you can build that taboo against thinking and internalize it – and people internalize it – then they become their own jailers. They become very effective protectors of their own incarceration. (Emphases in Dennett’s intonation)

RBH said: quoting Daniel Dennett:

... then they become their own jailers. They become very effective protectors of their own incarceration.

OgreMkV said: Define 'natural course'. You are assuming that anything humans do is not natural. This is not a correct assumption.

DS said: Did you or did you not read all of the literature relating to hox gene duplications? I am the one who brought it up, you are the one who is avoiding the subject, just like you tried to duck the fact that you were wrong about selection pressure on duplicated genes.

Dave Wisker said: Atheistoclast gets this wrong-headed view on duplications and selection from a couple of studies suggesting that duplications contribute to genetic robustness, i.e., the ability to withstand null and degenerative mutations, and papers describing the concept of subfunctionalization. First of all, the studies on robustness do not establish that degenerative mutations to gene copies are bad as a general rule-- they point out that advantages--if any--related to robustness depend heavily on the individual circumstances surrounding the genes themselves. As for subfunctionalization, that is simply one way in which gene duplicates can avoid degeneration-- it in no way suggests that duplicate sequences must persist intact in a population as a general rule. Atheistoclast has taken these examples and made the completely unjustified conceptual leap to asserting that some purifying or stabilizing selection must be present preserving duplicate copy sequences. This does not follow logically at all.

Exactly. Well, maybe since he isn’t an expert and obviously has no real training or understanding, perhaps he can be forgiven for this misunderstanding.

Hox genes definitely arose by duplication, after which they absolutely underwent divergence. Indeed, this has been a major mechanism behind the evolution of all of the diversity of body forms seen throughout the animal kingdom. This one example absolutely demolishes the hypothesis that gene duplication is not important in the evolution of novel functions. There are literally thousands of papers on this topic, here are a few to get the atheist guy started:

Brooke et. al. (1998) The parahox gene cluster is an evolutionary sister of the hox gene cluster. Nature 392:920-922.

McClintock et. al. (2001) Consequences of hox gene duplication in the vertebrates: An investigation of zebrafish paralogous grouped genes. Development 128(13):2471-2481.

Lynch et. al. (2006) Adaptive evolution of hox gene homeodomains after cluster duplications. BMC Evolutionary Biology 6:86-94.

Any good review of gene duplication would certainly document this important mechanism of evolution. Unless of course a 1000 page story isn't "novel" enough for you.

Atheistoclast seems to think that a gene must be composed of entirely new sequences before it can be considered novel.That is like arguing a word cannot be considered new because it uses letters that older words have already used.

Dave Wisker said: Atheistoclast seems to think that a gene must be composed of entirely new sequences before it can be considered novel.That is like arguing a word cannot be considered new because it uses letters that older words have already used.

Dave Wisker said: Atheistoclast seems to think that a gene must be composed of entirely new sequences before it can be considered novel.That is like arguing a word cannot be considered new because it uses letters that older words have already used.

Did you or did you not read all of the literature relating to hox gene duplications? I am the one who brought it up, you are the one who is avoiding the subject, just like you tried to duck the fact that you were wrong about selection pressure on duplicated genes.

Oh yea and my publication record is better than yours, so you lose again. 11111

mrg said:

Dave Wisker said: Atheistoclast seems to think that a gene must be composed of entirely new sequences before it can be considered novel.That is like arguing a word cannot be considered new because it uses letters that older words have already used.

The mindset seems to be that the succession A B C D ... X Y Z (which is what evolution says) does not represent a creation of "new information" (whatever that is supposed to mean) -- it has to be straight from A to Z, or more exactly Z just appearing de novo, there never having been an A. In other words, it's a roundabout way of expressing creationism: "It couldn't have got from there to here by evolving through a succession of forms building on themselves by slow increments. It all had to be poofed into existence."

Atheistoclast said: I find it strange such a prolific author as yourself couldn't even be bothered to read the Cheng paper which is the subject of this thread. Indeed, nobody here actually read the paper. They just read the title and abstract and make up their minds based on just that. The "Devil", or rather the "Darwin" is in the detail.

And still no answers to the very simple question... can he tell the difference between natural and artificial selection when presented with the results?

Oh well, I guess it was too much to ask that he be a thinking person and interested in critical discussion of his works.

Dave Wisker said:

Exactly. Well, maybe since he isn’t an expert and obviously has no real training or understanding, perhaps he can be forgiven for this misunderstanding.

I'm not saying he should be forgiven. He did, after all, decide to leave the kiddies table by actually getting published. Unfortunately for him, as you, me and others are showing, his paper is very poor, and deserves the pointing and laughing it's getting.

Mike Elzinga said: The cruelest fate a paper can have is to be completely ignored. The next cruelest fate is to be mocked.

Atheistoclast said: What about hox genes? What are you babbling on about now? How was I "wrong" on the selective pressures of gene duplication? What are you actually trying to argue in favor of or against? Well, then you can post references to them here.

Dale Husband said:

Atheistoclast said: I find it strange such a prolific author as yourself couldn't even be bothered to read the Cheng paper which is the subject of this thread. Indeed, nobody here actually read the paper. They just read the title and abstract and make up their minds based on just that. The "Devil", or rather the "Darwin" is in the detail.

Why do you assume that? Because we don't reach the same conclusions about the subject matter you do? You could be suffering from psychotic delusions.

Now, admit you were wrong about the selection pressure on duplicated genes. Admit that they can be removed from functional constraint.

Then read the hox gene papers I cited and admit that you were wrong a bout duplicated genes not being able to take on new functions. Until then, piss off.

If you want my publication record you can just go online and search for it yourself. I have nothing top prove to you. After all, you are the one who makes baseless assertations that he accepts without evidence. You have absolutely no idea who you are talking to, don't pretend that you do.

Atheistoclast said:

Dale Husband said: Why do you assume that? Because we don't reach the same conclusions about the subject matter you do? You could be suffering from psychotic delusions.

I assume this because all of you have blindly bought into the spin and propaganda surrounding the Cheng paper - that of some wonderful new function created as a result of evolutionary exaptation. But if you had actually read the paper, and studied the provisional sequences, you would realize that this really isn't a case of "neofunctionalization" so much as that of "subfunctionalization" and specialization made possible by gene duplication.

This is the problem with you lot - you pay no attention to the details but only to the headlines. You fail to realize that evolutionist scientists are under pressure to find evidence at the molecular level to support their "theory" of innovation by evolution. As there is no evidence, they hyperbolize and extrapolate the data as best they can. They include words like "amazing", "remarkable", "extraordinary" and "astonishing" to try and deceive the reader into thinking something stupendous has happened when it has not.

So, I am not really that surprised that you have been brainwashed into thinking that the Darwinian mechanism of trial and error can explain just about anything and everything. But if you would care to read the small print you will understand that you are being conned...big time. The tragedy is that it is your money that is funding the research grants of these fraudsters. This is why you should lobby your legislature to cut life support to these scoundrels...divest from Darwinism.

Atheistoclast said: Then read the hox gene papers I cited and admit that you were wrong a bout duplicated genes not being able to take on new functions. Until then, piss off.

With no name or title, I might as well look up "Mickey Mouse" and see if he is on PubMed. Mind you, there might well be a Dr. Michael Mouse out there...you never know.

DS said: Hox genes definitely arose by duplication, after which they absolutely underwent divergence. Indeed, this has been a major mechanism behind the evolution of all of the diversity of body forms seen throughout the animal kingdom. This one example absolutely demolishes the hypothesis that gene duplication is not important in the evolution of novel functions. There are literally thousands of papers on this topic, here are a few to get the atheist guy started: Brooke et. al. (1998) The parahox gene cluster is an evolutionary sister of the hox gene cluster. Nature 392:920-922. McClintock et. al. (2001) Consequences of hox gene duplication in the vertebrates: An investigation of zebrafish paralogous grouped genes. Development 128(13):2471-2481. Lynch et. al. (2006) Adaptive evolution of hox gene homeodomains after cluster duplications. BMC Evolutionary Biology 6:86-94. Any good review of gene duplication would certainly document this important mechanism of evolution. Unless of course a 1000 page story isn't "novel" enough for you.

I assume this because all of you have blindly bought into the spin and propaganda surrounding the Cheng paper - that of some wonderful new function created as a result of evolutionary exaptation. But if you had actually read the paper, and studied the provisional sequences, you would realize that this really isn’t a case of “neofunctionalization” so much as that of “subfunctionalization” and specialization made possible by gene duplication.

This is the problem with you lot - you pay no attention to the details but only to the headlines. You fail to realize that evolutionist scientists are under pressure to find evidence at the molecular level to support their “theory” of innovation by evolution.

As there is no evidence, they hyperbolize and extrapolate the data as best they can. They include words like “amazing”, “remarkable”, “extraordinary” and “astonishing” to try and deceive the reader into thinking something stupendous has happened when it has not.

So, I am not really that surprised that you have been brainwashed into thinking that the Darwinian mechanism of trial and error can explain just about anything and everything.

But if you would care to read the small print you will understand that you are being conned…big time.

The tragedy is that it is your money that is funding the research grants of these fraudsters. This is why you should lobby your legislature to cut life support to these scoundrels…divest from Darwinism.

Yes, duplicate genes do evolve under a *relaxed* regime of purifying selection. My paper clearly states this. However, you are wrong to assume that a respite in selection facilitates innovation. Rather, it makes degeneration of sequence and function more likely. You would know this if you studied some gene duplicates.

DS : Then read the hox gene papers I cited and admit that you were wrong about duplicated genes not being able to take on new functions. Until then, piss off.

Atheistoclast said:

Now, admit you were wrong about the selection pressure on duplicated genes. Admit that they can be removed from functional constraint.

Yes, duplicate genes do evolve under a *relaxed* regime of purifying selection. My paper clearly states this.

Dave Wisker said: This guy is slipperier than Walter ReMine.

Mike Elzinga said: The cruelest fate a paper can have is to be completely ignored. The next cruelest fate is to be mocked. It isn’t getting a paper in a peer reviewed journal - no matter how obscure - that really counts. Sometimes that is the worst possible thing that can happen to you. This troll’s primary problem is that he hasn’t a clue about science at any level. He has cobbled together a bunch of words that he thinks makes him look and speak like a scientist. If this were a little five year old doing it, it might be cute and endearing. However, in this troll’s case, it makes him look totally insane.

Dale Husband said: You could be suffering from psychotic delusions.

In other words - A GAIN OF INFORMATION, since the fish still have the original SAS gene PLUS this new one !

What you are calling 'subfunctionalization' is idiocy - you are implying that SAS is NORMALLY used as an antifreeze when it isn't. Even tropical fish have SAS, and they aren't particularly freeze resistant.

It is more of an exploitable coincidence - like the FACT that multiple enzymes have been used as lens crystallins in the eyes of various critters. Would you whine that such a use isn't truly novel, but merely 'subfunctionalization'?

There is plenty of evidence that evolution can produce innovations - its just that IDiots and creotards shove their heads three feet up their own arses, wave their hands frantically and scream "THAT DOESN'T COUNT ! IT DOESN'T !! IT DOESN'T !! IT DOESNT' !!"

Too bad for you that something has happened, and is fully explainable via the known mechanisms of evolution.

Once a DUPLICATE is free of constraint, it can evolve into something else. Why is such a simple concept so hard for you to accept or understand ?

By DUPLICATIONS and divergence of course ! By your flaccid whinings, there shouldn't be so many, since 'duplicates, freed of constraints, degenerate'.

The Sdic gene of D melanogaster is a gain of information - all other species haveAnnX-Cdic next to each other; only D mel has AnnX - Sdic1-Sdic2-Sdic3-Sdic4-Cdic.

Much like jingwei arose in the ancestor of two closely related Drosophila species - all over species have ymp and Adh; only two species have ymp, Adh AND jgw.

Another example that you 'assert' you 'debunked' by flaccid whining and frantic handwaving : the AFGP of the notothenioids is unique to them - examination of genomic DNA reveals that it is evolved from trypsinogen. Other fish have trypsinogen; only notothenioids have their AFGP AND trypsinogen.The repeats that enable it to BE an antifreeze arose from repeat expansion of intronic DNA - these sequences are cleaved out of standard trypsinogen.

In other words - A GAIN OF INFORMATION, since the fish still have the original SAS gene PLUS this new one !

What you are calling 'subfunctionalization' is idiocy - you are implying that SAS is NORMALLY used as an antifreeze when it isn't. Even tropical fish have SAS, and they aren't particularly freeze resistant.

It is more of an exploitable coincidence - like the FACT that multiple enzymes have been used as lens crystallins in the eyes of various critters. Would you whine that such a use isn't truly novel, but merely 'subfunctionalization'?

There is plenty of evidence that evolution can produce innovations - its just that IDiots and creotards shove their heads three feet up their own arses, wave their hands frantically and scream "THAT DOESN'T COUNT ! IT DOESN'T !! IT DOESN'T !! IT DOESNT' !!"

Too bad for you that something has happened, and is fully explainable via the known mechanisms of evolution.

Once a DUPLICATE is free of constraint, it can evolve into something else. Why is such a simple concept so hard for you to accept or understand ?

By DUPLICATIONS and divergence of course ! By your flaccid whinings, there shouldn't be so many, since 'duplicates, freed of constraints, degenerate'.

The Sdic gene of D melanogaster is a gain of information - all other species haveAnnX-Cdic next to each other; only D mel has AnnX - Sdic1-Sdic2-Sdic3-Sdic4-Cdic.

Much like jingwei arose in the ancestor of two closely related Drosophila species - all over species have ymp and Adh; only two species have ymp, Adh AND jgw.

Another example that you 'assert' you 'debunked' by flaccid whining and frantic handwaving : the AFGP of the notothenioids is unique to them - examination of genomic DNA reveals that it is evolved from trypsinogen. Other fish have trypsinogen; only notothenioids have their AFGP AND trypsinogen.The repeats that enable it to BE an antifreeze arose from repeat expansion of intronic DNA - these sequences are cleaved out of standard trypsinogen.

Atheist,

You can pout and bluster all you want to about how one example or another isn't good enough for you, but you still have provided no reason whatsoever why evolution cannot occur. And you still have not addressed the hox genes you are just blowing smoke.

Look dude, it really doesn't matter if the function is new or not. Evolution occurred. Deal with it. There are now two genes where there was only one before. Finding the intermediate step doesn't mean that evolution never happened, it just means that we know exactly how it happened.

If the gene had only one function initially, then a completely new function did indeed evolve. All that means is that there is now one more mechanism known by which this could happen. Since you refuse to provide any real alternative, you can't really complain now can you?

Besides, your publication record stinks and mine is much better. You lose.

Atheist wrote:

"Yes, gene families can be formed by duplication - but if you actually bother to look at them the degeneration is obvious - you will find truncations and bulk deletions all over the place that would never be tolerated in a singleton."

Dude, this is only true of pesudogenes. The very existence of hox gene complexes completely falsifies this unhopeful monster argument.

Relaxed selection does NOT mean that the gene must ALWAYS degenerate. It means that, when freed from functional constraint, any sequence can evolve, even if the intermediates are nonfunctional. This provides tremendous opportunity to explore adaptive space. You just can't seem to get this simple concept through your head.

Still no examples of "directed" mutations? Well I guess we can forget about that nonsense then.

You can pout and bluster all you want to about how one example or another isn't good enough for you, but you still have provided no reason whatsoever why evolution cannot occur. And you still have not addressed the hox genes you are just blowing smoke.

Look dude, it really doesn't matter if the function is new or not. Evolution occurred. Deal with it. There are now two genes where there was only one before. Finding the intermediate step doesn't mean that evolution never happened, it just means that we know exactly how it happened.

If the gene had only one function initially, then a completely new function did indeed evolve. All that means is that there is now one more mechanism known by which this could happen. Since you refuse to provide any real alternative, you can't really complain now can you?

'clast,

Define information in this context. Thanks

Relaxed selection does NOT mean that the gene must ALWAYS degenerate. It means that, when freed from functional constraint, any sequence can evolve, even if the intermediates are nonfunctional. This provides tremendous opportunity to explore adaptive space. You just can't seem to get this simple concept through your head.

Still no examples of "directed" mutations? Well I guess we can forget about that nonsense then.

OgreMkV said: 'clast, Define information in this context. Thanks

Atheistoclast said:

OgreMkV said: 'clast, Define information in this context. Thanks

The instructions pertaining to the operational capability and functional specificity of the gene. In this case, we do see a quantitative *improvement* in ice-binding capability but with the *loss* of motifs that specify the functionality of the N-terminus domain. Again, why have you lot not read the paper? Is this what you always do - just accept an author's *interpretation* at face value? If so, why don't you accept all the points made in my own paper?

Atheistoclast said: Read about the controversy http://en.wikipedia.org/wiki/Directed_mutagenesis

It states: The hypothesis was first proposed in 1988 by John Cairns, of Harvard University,[citation needed] who was studying Escherichia coli that lacked the ability to metabolize lactose. He grew these bacteria in media in which lactose was the only source of energy. In doing so, he found that the rate at which the bacteria evolved the ability to metabolize lactose was many orders of magnitude higher than would be expected if the mutations were truly random.

Ah, I think I see the confusion. You're conflating information and meaning. That's a huge difference. Since the meaning hasn't changed (anti-freeze ability or whatever), then you think that information hasn't changed. This is incorrect and a common error.

Using slipperly language is just a method that either shows dishonesty or shoddy communication skills.

BTW: Have you ever figured out how to tell the difference between natural and artifical selection when only being able to review the results? I've got several examples ready to test for you, once you tell me the process and values to consider.

Atheistoclast said: So, we are dealing with a bifunctional ancestor that became subfunctionalized through gene duplication.

The key "innovation" was to *delete* the N-terminal domain to remove any adaptive conflict caused by pleiotropic antagonism.

Except that I debunked most of the classic examples of "evolutionary innovation" in my paper - which you also haven't read.

If it [a duplicate gene] is free of constraint, it will degenerate - it will not evolve into something else... [later]However, gene duplicates are still subject to purifying selection because they can serve as useful backups.

The Sdic gene of D melanogaster is a gain of information - all other species haveAnnX-Cdic next to each other; only D mel has AnnX - Sdic1-Sdic2-Sdic3-Sdic4-Cdic.

Again, you are mistaken because you haven't studied the gene sequences or read my paper. Sdic was formed by a bulk deletion at the N-terminus of a copy of Cdic and a frameshift disabling another domain.

Atheistoclast said: Your argument seems to be that if you let random mutations mess things about, you can end up with a brand new function. That is a case of wishful thinking.

In this case, we do see a quantitative *improvement* in ice-binding capability but with the *loss* of motifs that specify the functionality of the N-terminus domain.

Atheistoclast said: It is quite simple. Natural (positive) selection represents a gain in reproductive fitness. Artificial selection, however, represents a gain in utility as defined by human society. If something has been selected for reasons other than reproductive fitness, then it is a case of artificial selection.

Atheistoclast said:

Ah, I think I see the confusion. You're conflating information and meaning. That's a huge difference. Since the meaning hasn't changed (anti-freeze ability or whatever), then you think that information hasn't changed. This is incorrect and a common error.

The definition of information, by Shannon, is that it is the "reduction in uncertainty". It has to convey something meaningful within the particular context.

Using slipperly language is just a method that either shows dishonesty or shoddy communication skills.

I gave you an operational definition. Information is fundamentally a form of *communication*. This applies as much to human language as it does to molecular processes.

BTW: Have you ever figured out how to tell the difference between natural and artifical selection when only being able to review the results? I've got several examples ready to test for you, once you tell me the process and values to consider.

It is quite simple. Natural (positive) selection represents a gain in reproductive fitness. Artificial selection, however, represents a gain in utility as defined by human society. If something has been selected for reasons other than reproductive fitness, then it is a case of artificial selection.

Atheistoclast said: The definition of information, by Shannon, is that it is the "reduction in uncertainty". It has to convey something meaningful within the particular context. ... I gave you an operational definition. Information is fundamentally a form of *communication*. This applies as much to human language as it does to molecular processes. ... It is quite simple. Natural (positive) selection represents a gain in reproductive fitness. Artificial selection, however, represents a gain in utility as defined by human society. If something has been selected for reasons other than reproductive fitness, then it is a case of artificial selection.

So, atheistoclast is admitting that duplication and mutation can lead to a quantitative improvement in some capability, all the while arguing evolution does not occur???

Dave Lovell said:

Atheistoclast said: Read about the controversy http://en.wikipedia.org/wiki/Directed_mutagenesis

Did you read it? Or perhaps you wrote it.

It states: The hypothesis was first proposed in 1988 by John Cairns, of Harvard University,[citation needed] who was studying Escherichia coli that lacked the ability to metabolize lactose. He grew these bacteria in media in which lactose was the only source of energy. In doing so, he found that the rate at which the bacteria evolved the ability to metabolize lactose was many orders of magnitude higher than would be expected if the mutations were truly random.

As stated, surely the only conclusion a scientist can draw from this is that the starting material was contaminated. With no ability to use the only food source available, mutation rates would just not need to be orders of magnitude higher, but almost infinite. Did he manage to repeat his experiment?

In an earlier review, Lenski & Mittler (54) identified several effects that have the potential to mislead experimenters into concluding that directed mutation is occurring when, in fact, it is not. The lacZam and Mu cases indeed illustrate two of these effects; others will be brought out below when we discuss subsequent cases of apparently directed mutation. The "Poisson-like" distri- butions of lacZam revertants that Cairns et al observed in fluctuation tests were quite plausibly due to slow growth of some revertants, particularly amber suppressors, prior to selective plating. In the case of Mu excision, starvation and the presence of selective substrates were confounded; the observed discrepancy between rates of mutation to Lac(Ara)+ during growth and during starvation on lactose-arabinose medium was a nonspecific con- sequence of starvation rather than a specific response to the presence of lactose and arabinose. Indeed, the case of Mu excision illustrates the general point, made earlier, that the occurrence of mutations after the imposition of a selective agent does not demonstrate that the selective agent is the cause of those mutations.

Atheistoclast said: *IT HELPS TO READ THE PAPER*

Atheist,

And I am really losing patience with you. You refuse to read any papers and then scream at others READ THE PAPER! You are nothing but a hypocrite. Once again, you have offered no reason whatsoever that a new function could not evolve. Your incredulity is NOT evidence.

Look dude, I'll make this real easy for you. Just answer three simple yes/no questions:

1) Did hox genes arise by duplication?

2) Dis hox genes diverge?

3) Did hox genes take on new functions?

Until you answer those three simple yes./no questions, I see no point in continuing a discussion with someone who is so opposed to rationality.

Sorry, that's wrong. The string: "198540981641756490256098259" probably does not convey any meaning to you, yet it is information.

Sure, in context it may have some meaning, but that does not affect how the information is transmitted, which is the only thing that Shannon was concerned with.

The uncertainty is in whether the reciever actually got the bit that was transmitted, not whether he understood the transmission.

It's official, you are confusing meaning and information. Plus, you do not seem to know what Shannon was talking about.

You gave a definition that is meaningless. You have no method of measuring the information content of DNA. You have no method of determining the relationship between the product (meaning) and the source (DNA/information). Without this, your definition is utterly useless.

'clast, your last statement, just like all the others show just how much you don't know. EVERYTHING is related to reproductive fitness. If we choose to breed a cow because it produces more milk, then that's the measure of reproductive fitness. Other cows that produce less milk will have less of a chance to reproduce. Duh.

But that doesn't answer the question. Can you tell the difference between natural and artifical selection given only an organism, structure, gene, or protien? You don't know the history of the object. Just looking at, can you tell the difference?

"The author serves the reader, not the other way around."

Atheistoclast is such a lazy scholar. See this paper:

Atheistoclast said: I AM REFERRING TO THE CHENG PAPER, IDIOT!

Honestly, I have never encountered so many morons in so small of a forum. However, with all of the misconceptions around, it is no surprise that you lot are in the dark about biology and evolution.

My advice to you is to *read* scientific research and articles rather than just the summaries you find on sciencey sites. That way you will get a more nuanced perspective.

I can't be bothered explaining each point to all of you...I have my own research projects to worry about.

Atheistoclast said:

Sorry, that's wrong. The string: "198540981641756490256098259" probably does not convey any meaning to you, yet it is information.

It doesn't have to convey meaning or a message to me - but it does have to convey it to something or somebody.

Sure, in context it may have some meaning, but that does not affect how the information is transmitted, which is the only thing that Shannon was concerned with.

No, Shannon defines information as a reduction of uncertainty in a communication channel.

The uncertainty is in whether the reciever actually got the bit that was transmitted, not whether he understood the transmission.

Nonsense...you haven't read his paper.The definition applies to the nature and not to the transmission of information.

It's official, you are confusing meaning and information. Plus, you do not seem to know what Shannon was talking about.

How do you define information if it has no meaning or value - how do you distinguish it from random noise?

You gave a definition that is meaningless. You have no method of measuring the information content of DNA. You have no method of determining the relationship between the product (meaning) and the source (DNA/information). Without this, your definition is utterly useless.

It works perfectly. Genetic information contains the instructions to make functional proteins with a high degree of specificity. All biologists agree on this.

'clast, your last statement, just like all the others show just how much you don't know. EVERYTHING is related to reproductive fitness. If we choose to breed a cow because it produces more milk, then that's the measure of reproductive fitness. Other cows that produce less milk will have less of a chance to reproduce. Duh.

Overproducing milk represents a waste of metabolism and will be selected against in the wild. How is a chihuahua reproductively more fit than a wolf? Often, we produce breeds that are essentially deformed but still useful to us.

But that doesn't answer the question. Can you tell the difference between natural and artifical selection given only an organism, structure, gene, or protien? You don't know the history of the object. Just looking at, can you tell the difference?

I can tell if it is designed or not by applying the *design inference* already used in palaeontology and astrobiology (SETI). http://www.nature.com/nature/journal/v466/n7308/abs/nature09248.html http://spsr.utsi.edu/articles/markjbis2007.pdf You need to read up.

In other words - A GAIN OF INFORMATION, since the fish still have the original SAS gene PLUS this new one !

You represent the tragedy of when the scientifically illiterate and ignorant claim to be knowledgeable.

The research clearly shows that ice-binding activity was already present in the ancestral gene.

What you are calling ‘subfunctionalization’ is idiocy - you are implying that SAS is NORMALLY used as an antifreeze when it isn’t. Even tropical fish have SAS, and they aren’t particularly freeze resistant.

They also admit that… “The incipient ice activity of the ancestral SAS molecule or its detached C-terminal peptide would be quite sufficient in inhibiting ice-crystal expansion in the fish body fluids.” The key “innovation” was to *delete* the N-terminal domain to remove any adaptive conflict caused by pleiotropic antagonism.

Atheistoclast said: How do you define information if it has no meaning or value - how do you distinguish it from random noise?

I can tell if it is designed or not by applying the *design inference* already used in palaeontology and astrobiology (SETI).

Again, you are mistaken because you haven’t studied the gene sequences or read my paper. Sdic was formed by a bulk deletion at the N-terminus of a copy of Cdic and a frameshift disabling another domain.

Indeed it did…but jingwei is a chimeric gene whose function is still unknown. However, it is an alcohol dehydrogenase like Adh.

And I showed how this was pure speculation and nothing more on their part.

They authors have since distanced themselves from this nonsense when they found that both the AFGP and the trysinogen-like protease are biosynthesised in the pancreas: which explains some of the commonalities they share.

Atheistoclast said: Honestly, I have never encountered so many morons in so small of a forum. However, with all of the misconceptions around, it is no surprise that you lot are in the dark about biology and evolution. My advice to you is to *read* scientific research and articles rather than just the summaries you find on sciencey sites. That way you will get a more nuanced perspective. I can't be bothered explaining each point to all of you...I have my own research projects to worry about.

Atheistoclast said: That way you will get a more nuanced perspective.

Lenksi disputes the findings of Cairns and others. He is not the definitive word on the subject.

You claimed the idea of a “directed mutation” was my own invention - but it was coined by a Harvard professor.

From the paper : "Of the six conserved residues (Q9, T18, A16, T15, Q44, and N14) in Atlantic ocean pout AFPIII identified through structural studies to constitute a PUTATIVE flat ice-binding surface, two (T15 and T18) are ancestral, preexisting in the C-terminal domain of both SAS-A and SAS-B (T305 and T308, respectively) of L. dearborni and other teleost SAS. These MIGHT have constituted an ACCIDENTAL structural basis for RUDIMENTARY ice affinity in SAS."The ice binding wasn't a 'subfunction' - IT WAS A CONVENIENT ACCIDENT !

Boosting antifreeze capability KILLS SAS activity. So the ONLY way the ADDITIONAL MUTATIONS in AFPIII could evolve is if the SAS gene duplicated, freeing up one copy to evolve into an antifreeze protein. By boosting an ACCIDENTAL property.

WHICH IS A GAIN OF INFORMATION BY ALL SANE AND RATIONAL DEFINITIONS.

Again, simpleton : most fish have SAS-A and SAS-B. These eelpout have SAS-A, SAS-B, and a WHOLE FRECKING CLUSTER OF AFPIII genes located elsewhere on the chromosome ! Generated via duplication and translocation - both KNOWN to happen in genomes.

SAS-B does NOT have Q44 or N14. To see what would happen if they mutated the C-term of SAS-B, they changed 4 residues to match those of AFPIII - THIS KILLED SAS ACTIVITY.So the sane, rational and parsimonious explanation of how AFPIII arose is that SAS-B was duplicated, and the DUPLICATE evolved.

The capacity to code for a functional signal peptide (SP), in fact, existed in the precursor sequence in LdSAS-B, because we found comparable levels of AFPIII-exporting activity by the SP precursor-mature AFPIII construct and the native pre-AFPIII cDNA.

"...there was both a loss and modification of existing information."

John Vanko said:

"...there was both a loss and modification of existing information."

A "modification of existing information" in indeed "new" information.

Atheistoclast said: No, it isn't. Natural selection has the ability to tweak and tinker, optimize and compensate but not to create from scratch. Modification of existing genetic information is generally limited and only ever results in a closely related function. This is part of the problem with the theory of evolution. In order for something to evolve, there needs to be a functional system or component to begin with. Evolution should not be confused with origination.

Atheistoclast said:

John Vanko said:

"...there was both a loss and modification of existing information."

A "modification of existing information" in indeed "new" information.

No, it isn't. Natural selection has the ability to tweak and tinker, optimize and compensate but not to create from scratch. Modification of existing genetic information is generally limited and only ever results in a closely related function. This is part of the problem with the theory of evolution. In order for something to evolve, there needs to be a functional system or component to begin with. Evolution should not be confused with origination.

Dale Husband said: Your objections to evolution are pointless.

Hey, stupid! Your "problem" with evolution is exactly what we have said all along; evolution is by nature a gradual process in which preexisting features are modified to produce new features, like fish fins becoming amphibian legs. Only Creationists think life (or even new genes) must have arisen out of nothing.

But once the notions of information are breached, we know. Creationists don’t seem to know how it is we can pick up on this stuff so quickly; they think we are really stupid and can be bamboozled by bluster and scolding.

Yep, still conflating meaning and information, even after being told not to. He's too stuck in his biased belief to understand.

Oh, I'll try one more time.

If you have
123456789

and then you have

123456789123456789

the amount of information has increased. In terms of meaning the amount has doubled. In terms of Shannon, the amount has increased by a smaller amount (because this sequence is easily compressible).

If you then get

123456789123556789

There is a change in meaning and a change in information, including an increase in Shannon information because the sequence is less compressible than it was a moment ago.

Now replace all of the numbers with nucleotides and you'll find the exact same thing holds true.

If you add an entire copy of a gene, then you increase the information, especially the Shannon information.

What all this means, is that you are wrong. But that's not surprising to anyone who studies this stuff.

Oh, I'll try one more time. If you have 123456789 and then you have 123456789123456789 the amount of information has increased. In terms of meaning the amount has doubled. In terms of Shannon, the amount has increased by a smaller amount (because this sequence is easily compressible).

Atheistoclast said: Do you actually have anything useful to say other than ranting on about your phobia and paranoia regarding non-Darwinians?

Atheistoclast said:

Hey, stupid! Your "problem" with evolution is exactly what we have said all along; evolution is by nature a gradual process in which preexisting features are modified to produce new features, like fish fins becoming amphibian legs. Only Creationists think life (or even new genes) must have arisen out of nothing.

Interesting. How exactly did a fish fin evolve into a tetrapod limb by way of a gradual process? At some point in this hypothetical transition you would have an organ that was neither good as a fin nor as a functioning leg. In other words, the intermediate stage would be useless. It is a bit like the "apeman" ancestor who can neither walk fully upright nor can he knuckle-walk and brachiate. He is just a maladapted freak who is neither human nor ape. The fact is that the core information in the genome is not merely derived from pre-existing function, as APFIII clearly is. Where did the conserved protein domains that form the backbone of countless gene families come from? Your ignorance and personal gullibility can never be used as an argument in support of evolutionism.

Atheistoclast said: Stop embarrassing yourself.

"No, it isn't. Natural selection has the ability to tweak and tinker, optimize and compensate but not to create from scratch. Modification of existing genetic information is generally limited and only ever results in a closely related function."

Atheistoclast said: Well this "example" really demonstrates your profound idiocy and ignorance. The amount of information has not doubled in this case. Rather, the data has doubled. Information should never be confused with data. All you have done is to add redundancy to the number string. In data compression, one aims to achieve the minimum redundancy in order to convey all the necessary information. Please, do us a favor and not comment on things which you know so little. Stop embarrassing yourself.

Atheistoclast said:

Oh, I'll try one more time. If you have 123456789 and then you have 123456789123456789 the amount of information has increased. In terms of meaning the amount has doubled. In terms of Shannon, the amount has increased by a smaller amount (because this sequence is easily compressible).

Well this "example" really demonstrates your profound idiocy and ignorance. The amount of information has not doubled in this case. Rather, the data has doubled. Information should never be confused with data. All you have done is to add redundancy to the number string. In data compression, one aims to achieve the minimum redundancy in order to convey all the necessary information. Please, do us a favor and not comment on things which you know so little. Stop embarrassing yourself.

OgreMkV said: Tell me 'clast. Which has more information according to Shannon, a recording Obama's State of the Union Address or the same length of white noise?

Mike Elzinga said: This guy has been nailed with a railroad spike and he doesn’t even know it.

Mike Elzinga said:

OgreMkV said: Tell me 'clast. Which has more information according to Shannon, a recording Obama's State of the Union Address or the same length of white noise?

This is really getting funny. All this information laid out right in front of him and he doesn’t see. This guy has been nailed with a railroad spike and he doesn’t even know it.

Again, I'm reminded of a Molly Ivins column I read long ago. Seems something escaped from a military base in Colorado, killing thousands of sheep where they stood just downwind of the base boundary. Naturally the ranchers were angry, and wanted restitution.

So they held a meeting with military representatives. The meeting was held in a house near where many sheep died, so all attendees had to negotiate past the rotting corpses to reach the house, and the smell was so bad they had to wear masks.

"So, what's the problem?" asked the military spokesmen? (This was, like, a hint).

"You've killed thousands of our sheep", the ranchers replied. "We need to be reimbursed for them, or we will go broke."

"Sheep?", the military people responded. "What sheep? We don't see any sheep. We don't know what you're talking about."

And that was the end of the meeting. An exquisite example of what happens when evidence encounters doctrine or policy. The ranchers were armed with mere evidence. They never stood a chance. To them, evidence mattered. And now we're over 20 pages into a thread illustrating that, like the ranchers, we simply CAN NOT LEARN that evidence is irrelevant. After literally HUNDREDS of responses consistently showing otherwise, we have learned nothing.

And ironically, we pride ourselves on learning from the evidence!

Tell me 'clast. Which has more information according to Shannon, a recording Obama's State of the Union Address or the same length of white noise?

Atheistoclast said: Yeah, all you can offer is stupid and asinine talk. Put up or shut up, Mikey.

Flint said: Again, I'm reminded of a Molly Ivins column I read long ago. Seems something escaped from a military base in Colorado, killing thousands of sheep where they stood just downwind of the base boundary.

On 13 March 1968, an F-4 Phantom strike aircraft flew a test mission over the Dugway Proving Ground in Utah with chemical dispensers containing VX. One of the dispensers wasn't completely emptied during the test, and as the F-4 gained altitude after its bombing run, VX trickled out in a trail behind the aircraft to drift into Skull Valley, north of the proving ground, and settle over a huge flock of sheep. 6,000 sheep were killed, and the incident provoked national attention at a time of high public political unrest and suspicion of the government.

Flint said: And ironically, we pride ourselves on learning from the evidence!

"VX", incidentally, is a "persistent" nerve agent. Instead of evaporating, it sticks around on objects to make them toxic for a long time.

This is probably the event Ivins was talking about. She did relate that there was a meeting, and she did relate that (according to the ranchers) the military simply denied everything. Molly Ivins described the "designated military denier" who (she said) can look you straight in the eye, deny you are even there, and sincerely believe it.

What I'm seeing here is an interminable illustration of Dawkins' observation that there is no sensible limit to what the human mind is capable of believing, against any amount of contrary evidence. The only question is, how many head-bangers will fill how many pages with contrary evidence before (if ever) they understand what "any amount" actually means.

Flint said: This is probably the event Ivins was talking about. She did relate that there was a meeting, and she did relate that (according to the ranchers) the military simply denied everything.

Atheistoclast said:

Tell me 'clast. Which has more information according to Shannon, a recording Obama's State of the Union Address or the same length of white noise?

Is this supposed to be some trick question, Ogre? If I give you two copies of the NY Times, are you twice as well informed as a result of reading both of them? Consider the recipient at the other end of the communication channel: CLAST IS A GENIUS! Ok message understood. CLAST IS A GENIUS! Ok, we heard you the first time. CLAST IS A GENIUS! You have already said that twice! CLAST IS A GENIUS! For crying out loud, shut up!

mrg said:

Flint said: This is probably the event Ivins was talking about. She did relate that there was a meeting, and she did relate that (according to the ranchers) the military simply denied everything.

I would bet that at the outset there were some very stressed-out government people who had no idea of what they dared say. The facts did become known, but I would greatly doubt the folks in the hotseat were immediately forthcoming. Of course, they were more forthcoming than our visitor is ever likely to be.

OgreMkV said: If it was a secret test, it's likely that the people sent to the ranch didn't have a clue what was going on. Since they can't confirm or deny something they weren't involved with, they maintain nothing happened.

Mike Elzinga said:

Atheistoclast said: Yeah, all you can offer is stupid and asinine talk. Put up or shut up, Mikey.

So are you going to answer the question? It’s pretty basic; and we will know. Bluster isn't going to do it for you.

OgreMkV said:

Atheistoclast said:

Tell me 'clast. Which has more information according to Shannon, a recording Obama's State of the Union Address or the same length of white noise?

Is this supposed to be some trick question, Ogre? If I give you two copies of the NY Times, are you twice as well informed as a result of reading both of them? Consider the recipient at the other end of the communication channel: CLAST IS A GENIUS! Ok message understood. CLAST IS A GENIUS! Ok, we heard you the first time. CLAST IS A GENIUS! You have already said that twice! CLAST IS A GENIUS! For crying out loud, shut up!

So are you going to answer the question 'clast? I guess not. And yes, according to Shannon, two copies of the New York times has more information than one. QUIT THINKING ABOUT THE MESSAGE... I mean, are you really this misinformed? The message has nothing to do with it. Two copies of the New York Times takes twice as much to send, unless you compress them, and then the instructions for decompressing will take a fraction of the whole, which means that, yes. According to Shannon, two copies of the New York Times has more information. Humorously, the same applies to DNA. If an organism has multiple copies of a gene... guess what? They produce MORE of that protein. Duh. Of course, one or more of the copies is free to mutate without affecting the rest... which is the whole point of this damn conversation (or whatever it is). BTW: Answer the question, which has more information a 30 minute audio speech or a 30 minute batch of white noise (Shannon Info please)?

If it was a secret test, it’s likely that the people sent to the ranch didn’t have a clue what was going on. Since they can’t confirm or deny something they weren’t involved with, they maintain nothing happened.

I think about two years ago, creobots were still catching people a bit flat-footed with their "information-complexity" bafflegab. They're not any more. People who have heard it before don't just know it's bogus, they know specifically why it's bogus.

QUIT THINKING ABOUT THE MESSAGE... I mean, are you really this misinformed? The message has nothing to do with it.

According to Shannon, two copies of the New York Times has more information.

mrg said: I think about two years ago, creobots were still catching people a bit flat-footed with their "information-complexity" bafflegab. They're not any more. People who have heard it before don't just know it's bogus, they know specifically why it's bogus.

The discovery of the structure of DNA transformed biology profoundly, catalysing the sequencing of the human genome and engendering a new view of biology as an information science. Two features of DNA structure account for much of its remarkable impact on science: its digital nature and its complementarity, whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes.

Atheistoclast said: Here is one such paper authored by a "creobot".

Atheistoclast,

What is your definition of information? Be specific.

What is your definition of data? Be specific.

If you offer no definitions, I call BS.

DNA has two types of digital information — the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behaviour of the genes.

Atheistoclast said:

Sorry, that's wrong. The string: "198540981641756490256098259" probably does not convey any meaning to you, yet it is information.

It doesn't have to convey meaning or a message to me - but it does have to convey it to something or somebody.

How do you define information if it has no meaning or value - how do you distinguish it from random noise

Atheistoclast said: Interesting. How exactly did a fish fin evolve into a tetrapod limb by way of a gradual process? At some point in this hypothetical transition you would have an organ that was neither good as a fin nor as a functioning leg. In other words, the intermediate stage would be useless.

DS said: Hox genes definitely arose by duplication, after which they absolutely underwent divergence. Indeed, this has been a major mechanism behind the evolution of all of the diversity of body forms seen throughout the animal kingdom. This one example absolutely demolishes the hypothesis that gene duplication is not important in the evolution of novel functions. There are literally thousands of papers on this topic, here are a few to get the atheist guy started: Brooke et. al. (1998) The parahox gene cluster is an evolutionary sister of the hox gene cluster. Nature 392:920-922. McClintock et. al. (2001) Consequences of hox gene duplication in the vertebrates: An investigation of zebrafish paralogous grouped genes. Development 128(13):2471-2481. Lynch et. al. (2006) Adaptive evolution of hox gene homeodomains after cluster duplications. BMC Evolutionary Biology 6:86-94.

Atheistoclast said:

According to Shannon, two copies of the New York Times has more information.

Dear, oh dear. Can't tell the difference between data and information.

Rob said: Atheistoclast, What is your definition of information? Be specific. What is your definition of data? Be specific. If you offer no definitions, I call BS.

Atheistoclast said: Interesting. How exactly did a fish fin evolve into a tetrapod limb by way of a gradual process? At some point in this hypothetical transition you would have an organ that was neither good as a fin nor as a functioning leg. In other words, the intermediate stage would be useless.

It is a bit like the "apeman" ancestor who can neither walk fully upright nor can he knuckle-walk and brachiate. He is just a maladapted freak who is neither human nor ape.

The fact is that the core information in the genome is not merely derived from pre-existing function, as APFIII clearly is. Where did the conserved protein domains that form the backbone of countless gene families come from?

Your ignorance and personal gullibility can never be used as an argument in support of evolutionism.

Scott F said:

Atheistoclast said:

According to Shannon, two copies of the New York Times has more information.

Dear, oh dear. Can't tell the difference between data and information.

My dear Clast, of course two copies of the New York Times have more information. If I got two copies of the New York Times in my mail box, I would have two new pieces of information that I would not have had if I had received only one copy of the newspaper: 1) My neighbor also gets the New York Times; 2) He didn't get his today. Since we seem to have it wrong, what distinction do you draw between "data" and "information"? Please use your own words rather than a link. A simple link doesn't prove that you know what is contained in the link. I would prefer to hear your thoughts on the subject. Thank you for your participation.

Rob said: Atheistoclast, What is your definition of information? Be specific. What is your definition of data? Be specific. If you offer no definitions, I call BS.

Although the nucleotide sequences in DNA are commonly understood to carry/convey biological "information" [28], a precise scientific delineation for the term in the context of genetics is often found to be lacking. Therefore, it is impossible to test any hypothesis regarding the creation of new genetic information without offering at least a conceptual definition of what information means and what the criterion is for identifying it. In Shannon’s theory [29] of communication, information is termed the "reduction in uncertainty," where entropy is the measure of any stochastic dependencies -- the greater the level of uncertainty that exists in a particular situation, the less likely it is to predict the behaviors and outcomes because of the presence of random noise. Therefore, information is that which denotes a degree of determinism in a known relationship, although this would also have to involve a large measure of contingency to permit as many possible combinations to be conveyed. In the framework of molecular biology, information would refer to the inherent functionality of gene products: i.e., how they interact with the biochemical environment in which they operate. Therefore, I have decided to define any gain in exonic information as: "The qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." The two parts of the statement are complementary, because an appreciably great degree of specificity is required to reduce any uncertainty and problems regarding behavior and effect: this is especially true in the case of enzymes that catalyze only particular reactions, and to the exclusion of all others.

Atheistoclast said: READ THE PAPER! READ THE PAPER! READ THE PAPER! READ THE PAPER! READ THE PAPER! READ THE PAPER! READ THE PAPER! *IT HELPS TO READ THE PAPER* I AM REFERRING TO THE CHENG PAPER, IDIOT!

Although Atheistoclast has repeatedly offered to email us his crummy paper, I don't think it will do any difference.

After all, he's pulled out your typical Creationist appeals to ignorance and incredulity, like the moronic "what good is half a limb," and he's also demonstrated that the real reason why so many editors shun him is because he's an asshole who uses racial slurs on anyone who disagrees with him.

This is actually quite a well written and cogent piece and I have to say that I agree with many things that you say here that are not about biology. The problem is that the entire argument about natural selection is deeply flawed. You mistake rhetoric for logic when it comes to arguing against a mechanistic view of evolution. I think that you also mistake belief in particular mechanisms (i.e. natural selection) with a materialistic view of nature. Evolutionary biologists including myself are quite open to the fact possibility that natural selection is not as important as people generally think or that other processes may be at work in evolution in important ways. The literature is full of arguments to that effect and you seem to have read enough of that you should realize that. What I and most scientists are not open to is the idea that showing that a particular mechanism is less important means that there must be divine intervention in the history of life. Here, two world views clash in ways that are impossible to adjudicate within science much less with scientific peer review. Natural selection as a mechanism has withstood intense scientific scrutiny over the past century and a half. That being said, the average evolutionary biologist today probably ascribes less explanatory power to it today than Darwin did in his. Materialistic evolutionary theory, however, is increasingly coherent despite this relative downplaying of natural selection. That is because a materialistic view of evolution is not dependent on a particular mechanism. Even if you did present a coherent argument against natural selection, which I don't believe you do, it would not be an argument for creationism. That is an intellectual leap that has nothing to do with logic or science. Even if we had no good mechanistic explanation for evolution, as a scientist, I would look for mechanistic explanations for our observations about the diversity and history of life. If I simply threw my hands up and said i can't explain this, it must be divine intervention, then I've ceased to be a scientist. This is why your papers are not acceptable here in Evolutionary Biology. There is no scientific debate about creationism versus evolutionary theory. There is a cultural discourse on this topic that does not have a foundation in science. Evolutionary biology is a scientific journal. If you call the assumption that natural phenomena have materialistic explanations an ideology, then yes we do have that ideology. So does pretty much every other journal in science. So, please do not submit any more essays or papers to evolutionary biology as it is now very clear that you have an ideology that falls into creationism or intelligent design. We will not review them and I will not read any more of them. It will simply waste your time to submit more papers like this. The next paper you submit will not get to my desk and will simply be rejected at the editorial office, so there is really no point preparing any further submissions. Any response from you to this decision will not be read or answered. I'm sorry to be harsh with this, but your persistence in submitting papers, your emails demanding review and explanations for decisions and the alarmingly caustic phone message that you left on my voicemail leads me to be very direct in this.

Atheistoclast said:

According to Shannon, two copies of the New York Times has more information.

Dear, oh dear. Can't tell the difference between data and information.

You are even dumber than I thought. LOL! Ever heard of mudskippers?

Try googling "Oliver the 'Humanzee'", you idiot! He was actually an ordinary chimp that happened to be able to walk upright, just as our pre-human ancestors would have done. Yet he was a perfectly functioning animal in all other respects.

All genes (and protiens) are made from parts of DNA (and amino acids), which are in turn made from atoms.

Look who's talking! You haven't made a credible argument here yet, and we have just been laughing at you like hyenas.

Rob said: Atheistoclast, What is your definition of information? Be specific. What is your definition of data? Be specific. If you offer no definitions, I call BS.

SWT said:

Rob said: Atheistoclast, What is your definition of information? Be specific. What is your definition of data? Be specific. If you offer no definitions, I call BS.

According to his Complexity paper,

Although the nucleotide sequences in DNA are commonly understood to carry/convey biological "information" [28], a precise scientific delineation for the term in the context of genetics is often found to be lacking. Therefore, it is impossible to test any hypothesis regarding the creation of new genetic information without offering at least a conceptual definition of what information means and what the criterion is for identifying it. In Shannon’s theory [29] of communication, information is termed the "reduction in uncertainty," where entropy is the measure of any stochastic dependencies -- the greater the level of uncertainty that exists in a particular situation, the less likely it is to predict the behaviors and outcomes because of the presence of random noise. Therefore, information is that which denotes a degree of determinism in a known relationship, although this would also have to involve a large measure of contingency to permit as many possible combinations to be conveyed. In the framework of molecular biology, information would refer to the inherent functionality of gene products: i.e., how they interact with the biochemical environment in which they operate. Therefore, I have decided to define any gain in exonic information as: "The qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." The two parts of the statement are complementary, because an appreciably great degree of specificity is required to reduce any uncertainty and problems regarding behavior and effect: this is especially true in the case of enzymes that catalyze only particular reactions, and to the exclusion of all others.

Atheistoclast said:

According to Shannon, two copies of the New York Times has more information.

Dear, oh dear. Can't tell the difference between data and information.

Atheistoclast said: The question is: who or what specified this information? It is crucial to the debate on evolutionary origins.

Atheistoclast said:

Rob said: Atheistoclast, What is your definition of information? Be specific. What is your definition of data? Be specific. If you offer no definitions, I call BS.

Data is a quantity of objects/symbols that can *represent* information but which may still contain no information. This is because information is fundamentally a qualitative "substance". It conveys something of value or utility as part of an exchange of communication. For example, your hard drive may hold up to 100 Gigabits of data but it may nonetheless have no information content. It could just contain a random sequence of binary digits. Likewise the nucleotides in DNA would be meaningless stretches of chemicals except for the fact that they are specifically arranged to convey *information* pertinent to the functionality of the cell. The question is: who or what specified this information? It is crucial to the debate on evolutionary origins.

DS said: Hox genes definitely arose by duplication, after which they absolutely underwent divergence. Indeed, this has been a major mechanism behind the evolution of all of the diversity of body forms seen throughout the animal kingdom. This one example absolutely demolishes the hypothesis that gene duplication is not important in the evolution of novel functions. There are literally thousands of papers on this topic, here are a few to get the atheist guy started: Brooke et. al. (1998) The parahox gene cluster is an evolutionary sister of the hox gene cluster. Nature 392:920-922. McClintock et. al. (2001) Consequences of hox gene duplication in the vertebrates: An investigation of zebrafish paralogous grouped genes. Development 128(13):2471-2481. Lynch et. al. (2006) Adaptive evolution of hox gene homeodomains after cluster duplications. BMC Evolutionary Biology 6:86-94. Once you have read the papers you can answer these questions: 1) Did hox genes arise by duplication? 2) Dis hox genes diverge? 3) Did hox genes take on new functions? I can keep asking as many times as needed. Until you address this evidence you will not be taken seriously.

Atheistoclast said: The question is: who or what specified this information? It is crucial to the debate on evolutionary origins.

Ogre wrote:

"That’ll do for now. We can hit the other ones later. Hey, why don’t you head over to the forum, since we’re pretty OT here at this point?"

Seconded. We have now moved past the point of arguing about gene duplications. From here it will just degrade into GODDIDIT crap. THe moderators has been generous for the last twenty pages. I see no reason to clutter up the thread any further with off topic nonsense about ghosts and witches conjuring DNA out of their orifices. If this guy wants to continue the conversation, he can take it to the bathroom wall, or ATBC.

Oh well, at least he tried to discuss science for a while. That's a step up around here compared to IBIGOT and Kris.

Slight variation on everyone else's response to Atheistoclast's 'what specified the information':

Mutation produces a wide variety of different information in different individuals. Selective processes then do the specification. If a tiger kills and eats you before you could reproduce, natural selection has done the specifying. If you can avoid the tigers but no one wants to have sex with you, sexual selection has done the specifying. If our alien overlords abduct and sterilize you, artificial selection has done the specifying.

In terms of human evolution, I will continue to discount the latter until you show us evidence of alien overlord breeding programs. The mere presence of 'information' in the genome is not evidence of alien overlords, since there are at least two other selection processes that could account for it.

There's the germ of an interesting point here. It looks like 'clast imagines that evolution can only tinker with functional proteins, and there's some fundamental gap between simple precursor organic molecules and even the simplest functional protein. This harks back to a rather traditional, vitalist conception about matter: that matter is essentially inert.

But we who know anything about physics and chemistry know that matter isn't essentially inert. Every molecule does something- can react with something. There is no essential gap between base matter and functional proteins.

This is why 'clast keeps repeating that "evolution can only tinker" and imagines he's making a point. "Just tinkering" can get you all the way from the simplest precursor organic molecules to the most beautifully specific functional protein, because there are no fundamental gaps anywhere on the way.

SAWells said:This is why 'clast keeps repeating that "evolution can only tinker" and imagines he's making a point. "Just tinkering" can get you all the way from the simplest precursor organic molecules to the most beautifully specific functional protein, because there are no fundamental gaps anywhere on the way.

SAWells said: "Just tinkering" can get you all the way from the simplest precursor organic molecules to the most beautifully specific functional protein, because there are no fundamental gaps anywhere on the way.

http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=4d3eec405f2756ae;act=ST;f=14;t=7199

This thread is open and unused. It would be a fine place to discuss 'clast.

I would suggest you put the relevant parts of your paper (if you don't mind) or you could PM it to those interested (so it doesn't break out on the web).

Then we could really discuss it and use graphs and pictures and such... unlike this comment only thread.

RBH said: Which is, of course,descent with modification, which is what evolution is.

Boy howdy, I went over to ATBC to set up an Atheistoclast thread and RBH had already beat me to it.
Now THAT's service!

mrg said: Hey RBH, you're pretty good about closing down threads that go on too long. I suggest this one is well into diminishing returns and needs to go to the ATBC? We need to set up an "Athiestoclast" thread there. If he wants to be humored, no problem in humoring him.

Atheistoclast said:

Rob said: Atheistoclast, What is your definition of information? Be specific. What is your definition of data? Be specific. If you offer no definitions, I call BS.

Data is a quantity of objects/symbols that can *represent* information but which may still contain no information. This is because information is fundamentally a qualitative "substance". It conveys something of value or utility as part of an exchange of communication. For example, your hard drive may hold up to 100 Gigabits of data but it may nonetheless have no information content. It could just contain a random sequence of binary digits. Likewise the nucleotides in DNA would be meaningless stretches of chemicals except for the fact that they are specifically arranged to convey *information* pertinent to the functionality of the cell. The question is: who or what specified this information? It is crucial to the debate on evolutionary origins.