Us Darwin lobbyists try to solve the mystery of Uncommon Descent

Why use cars, or whirl winds in junkyards producing 747's? Why not do some research?

I used to enjoy UD when the whole gang was there flailing, and blustering away. Now Dembski is at some religious dump bowing and scraping before his nut job OEC bosses, desperately denying his earlier vague admissions that the earth is actually older than a Bristle Cone Pine. The others have just kind of quietly abandoned Mrs O'Leary, making occasional half hearted attempts at keeping the flame burning. Now that it's Denise by her IQ challenged self, skulking behind the moniker 'News' it's lost any humourous appeal it once had. A sad Canadian hurling insults at a dead genious ('that British toff') and generally harming the image of a country I greatly admire; their health care system is sublime.

"Darwin lobbyists" apparently are in cahoots with Einstein lobbyists, Galileo lobbyists, and Lavoisier lobbyists.

All grand conspirators in the evil plan to demand actual cause and effect relationships in science (yes, in classical science, don't quibble), rather than resorting to demonic possession and unseen spirits as the forces behind observable phenomena.

Glen Davidson

Not to mention the James Clerk Maxwell lobbyists, the Shannon-Kolgorov lobbyists, the Godel lobbyists, and so on. As a response to the Isaac Newton lobbyists, it reminds me of Intelligent Falling.

This is just getting weird.

Chris Lawson said: Shannon-Kolgorov lobbyists,

Chris Lawson said: As a response to the Isaac Newton lobbyists, it reminds me of Intelligent Falling.

So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

Stephen Meyer: So the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

Mike Elzinga said: So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

robert van bakel said: The others have just kind of quietly abandoned Mrs O'Leary, making occasional half hearted attempts at keeping the flame burning.

Stephen Meyer: the discovery of digital information in DNA provides strong grounds for inferring that intelligence played a causal role in its origin.

O’Leary has misunderstood my 2007 paper

She looked at me uncomprehendingly Like cows at a passing train

Mike Elzinga said: So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

"First she quotes the paleontologist T. Berra as saying that cars, like fossils, show “descent with modification”. Then she puts words in Berra’s mouth, implying that Berra has said that cars have genes and offspring, and that Berra has called automotive engineers liars."

Well, according to Gould, Mickey Mouse displays "descent with modification" as well. Somehow, I don't think he was using this analogy to disprove evolution though.

Here it is:

http://www.monmsci.net/~kbaldwin/mickey.pdf

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 a great paper in Nature on the subject of the digital code in DNA: http://www.nature.com/nature/journal/v421/n6921/abs/nature01410.html

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.

There is no naturalistic explanation for the existence of both digital codes and information. Felsenstein is right that the genetic code itself is an issue for abiogenesis / origin of life researchers whereas the information contained in protein sequences is a problem for the molecular evolutionist. The belief is that natural selection and random drift (a blind and open search) can somehow conspire to build novel motifs from scratch even though there is absolutely no evidence that they can.

Atheistoclast, please show us exactly where the paper states that its findings demonstrate irrefutable proof of an Intelligent Designer, aka God of the Bible, while simultaneously magically disproving evolution as never having existed and or is evil.

You know, like you constantly falsely state.

There is no naturalistic explanation for the existence of both digital codes and information.

Matt G said: Once again we have an example of people using the same word (or phrase) to mean different things. What do you suppose the authors of that paper would have to say about Meyer's use of "digital information" and the conclusion he rationalizes using it? I only glanced at the paper, but good luck finding anything ID-friendly in that paper, Joseph.

harold said: DNA is a naturally occurring organic chemical. Whether it "did" first occur naturally - a question for the field of abiogenesis - it unequivocally CAN. Therefore by your own standards, DNA provides an example of a "naturalistic" occurrence of what you refer to as a "digital code".

Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can't resist. Thanks.

Matt G said: Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can't resist. Thanks.

Matt G said: Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can't resist. Thanks.

Harold, the code and DNA are not the same thing. The code does not exist in DNA as some people seem to believe. It is just the format or procedure used by the translational machinery (enzymes and ribosomes) for constructing proteins, amino acid by amino acid, based on what is transcribed from DNA. You could use the genetic code outside of the context of molecular biology to represent just about everything.

And, in any case, there is no naturalistic explanation for the origination of DNA. Sure, it is natural in the sense that gasoline is natural and not supernatural. But you need to refine gasoline from crude oil - DNA needs to be synthesized from other chemicals. It does not spontaneously arise in Nature like carbon dioxide

Matt G said: Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can't resist. Thanks.

There is a digital code in DNA and it is used to represent digital(discrete) information. The reason why you don’t see this as supporting ID is because you spectacularly fail to realize that codes and information theory always relate to the work of intelligent designers and not to natural processes.

The mysterious digital information turns out to be nothing more than the usual genetic information that codes for the features of life, information that makes the organism well-adapted.

If we have a population of DNA sequences, we can imagine a case with four alleles of equal frequency. At a particular position in the DNA, one allele has A, one has C, one has G, and one has T. There is complete uncertainty about the sequence at this position. Now suppose that C has 10% higher fitness than A, G, or T (which have equal finesses). The usual equations of population genetics will predict the rise of the frequency of the C allele. After 84 generations, 99.9001% of the copies of the gene will have the C allele.

This is an increase of information: the fourfold uncertainty about the allele has been replaced by near-certainty. It is also specified information — the population has more and more individuals of high fitness, so that the distribution of alleles in the population moves further and further into the upper tail of the original distribution of fitnesses.

So the only law we have is one that does predict the creation of specified information by natural selection.

harold said: There used to be scientific idea called "vitalism". It was the idea that life could not be understood in terms of underlying physical principles. It was abandoned when urea was synthesized. Not because anyone claimed that the chemical synthesis of urea was identical to the biochemical synthesis - it wasn't - but because it proved that a biochemical wasn't magical - it COULD be synthesized.

Atheistoclast said:

The reason why you don't see this as supporting ID is because you spectacularly fail to realize that codes and information theory always relate to the work of intelligent designers and not to natural processes.

You keep making this unsupported assertion.

Not only is the genetic code a work of immaculate design but it is also designed to be as fault-tolerant and effective as possible.

Another unsupported assertion. And why do you use the word immaculate? Is that a scientific term I'm just not familiar with?

Let me ask you something: Why are you so resistive to the inferential evidence for ID?

Because it is not an inference, it is a rationalization. In science, if the evidence were different, the conclusions would be different. In ID, the conclusion is always the same: the Intelligent Designer did it this way (and we mere humans can't understand how, why, etc.).

Why are you so scared at the prospect that there may be an Intelligent Agency at work in the universe and life? Why is this so upsetting for you?

I am not scared, though I suspect you are projecting your own fear which you remedy by believing in this Intelligent Agency. I am not upset, except by those who misrepresent science (of which I am rather fond) to pursue ideological agendas. Doesn't it scare you that this agency might be tampering with your brain and that your thoughts and feelings might not be your own...?

I find it absolutely intriguing that there exists a Being who is so much more intelligent than any human. It opens up my mind to the true nature of reality.

You sound more passionate than dispassionate here, Joseph. Your religious beliefs seem to have blinded you to the nature of science as well as the nature of reality. Your invoking of supernatural agency adds nothing to our understanding of the natural world, and in fact takes from it by opening the door to empty "inferences."

harold said:

Matt G said: Sorry to be OT, but could someone please point me to instructions for breaking up a post so I can respond sentence by sentence? Athiestoclast has blood in the water and I can't resist. Thanks.

Use the greater than and less than signs where I use "[". The html code is "[blockquote]text[/blockquote]

harold said: That's a semantic argument. It's equally true of a computer program. It's not a set of instructions except in the proper context.

At the end of the day, the very final ID argument that people fall back on always seems to be declaring human technological work to be magic. That's a fascinating and ancient impulse. In fact, technology has indeed always seemed like magic to those who did not understand it fully. Over and over again, the "a human did it so it must too be magic" argument appears.

There used to be scientific idea called "vitalism". It was the idea that life could not be understood in terms of underlying physical principles. It was abandoned when urea was synthesized. Not because anyone claimed that the chemical synthesis of urea was identical to the biochemical synthesis - it wasn't - but because it proved that a biochemical wasn't magical - it COULD be synthesized.

Both DNA and gasoline can be synthesized without magic.

Now, if you want to argue that DNA was, nevertheless, synthesized once by magic, at the dawn of cellular life, be my guest - that gap will be there to jam your god into for a while, until a really good model of the origin of DNA genomes is developed. After all, the Flying Spaghetti Monster can magically synthesize anything humans can naturally synthesize.

But the salient point is that DNA does not NEED to be synthesized by magic.

Matt G said:

Atheistoclast said:

The reason why you don't see this as supporting ID is because you spectacularly fail to realize that codes and information theory always relate to the work of intelligent designers and not to natural processes.

You keep making this unsupported assertion.

Not only is the genetic code a work of immaculate design but it is also designed to be as fault-tolerant and effective as possible.

Another unsupported assertion. And why do you use the word immaculate? Is that a scientific term I'm just not familiar with?

Let me ask you something: Why are you so resistive to the inferential evidence for ID?

Because it is not an inference, it is a rationalization. In science, if the evidence were different, the conclusions would be different. In ID, the conclusion is always the same: the Intelligent Designer did it this way (and we mere humans can't understand how, why, etc.).

Why are you so scared at the prospect that there may be an Intelligent Agency at work in the universe and life? Why is this so upsetting for you?

I am not scared, though I suspect you are projecting your own fear which you remedy by believing in this Intelligent Agency. I am not upset, except by those who misrepresent science (of which I am rather fond) to pursue ideological agendas. Doesn't it scare you that this agency might be tampering with your brain and that your thoughts and feelings might not be your own...?

I find it absolutely intriguing that there exists a Being who is so much more intelligent than any human. It opens up my mind to the true nature of reality.

You sound more passionate than dispassionate here, Joseph. Your religious beliefs seem to have blinded you to the nature of science as well as the nature of reality. Your invoking of supernatural agency adds nothing to our understanding of the natural world, and in fact takes from it by opening the door to empty "inferences."

Atheistoclast said: Btw, Joe Felsenstein wrote a response to Bill Dembksi a while ago about the issue of "information" and "digital codes": http://ncse.com/rncse/27/3-4/has-natural-selection-been-refuted-arguments-william-dembski Here are some excerpts of his remarks and my responses to them:

The mysterious digital information turns out to be nothing more than the usual genetic information that codes for the features of life, information that makes the organism well-adapted.

OK, but it is digital information and one has to ask how this molecular communication arose.

We know that the digital information we use has an intelligent source so it logically follows that this is so for that encoded in our chromosomes.

No. Because fitness has nothing to do with information.

The C allele can still be advantageous (reproductively) but actually serve to degrade functionality and add noise to information. There are countless examples of such loss-of-function mutations having adaptive effects.

So the only law we have is one that does predict the creation of specified information by natural selection.

Natural selection has no creative powers. It cannot create specified information like this because it can only select what is useful and functional (the homeobox motif): RRRKRTAYTRYQLLELEKEFLFNRYLTRRRRIELAHSLNLTERHIKIWFQNRRMKWKKEN At most it can fine-tune, optimize or conserve it.

Matt G said: You sound more passionate than dispassionate here, Joseph. Your religious beliefs seem to have blinded you to the nature of science as well as the nature of reality. Your invoking of supernatural agency adds nothing to our understanding of the natural world, and in fact takes from it by opening the door to empty "inferences."

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: So information does have to do with fitness. You just don't know anything much about evolutionary theory or information.

Atheistoclast said: There is no naturalistic explanation for the existence of both digital codes and information.

Atheistoclast: Felsenstein is right that the genetic code itself is an issue for abiogenesis / origin of life researchers whereas the information contained in protein sequences is a problem for the molecular evolutionist.

Atheistoclast said:

Matt G said: You sound more passionate than dispassionate here, Joseph. Your religious beliefs seem to have blinded you to the nature of science as well as the nature of reality. Your invoking of supernatural agency adds nothing to our understanding of the natural world, and in fact takes from it by opening the door to empty "inferences."

If there were a valid naturalistic explanation for the origins and diversity of life I would accept it - as would everybody else. But there isn't.

Instead I see manifest evidence for design in Nature and at a level of sophistication far in excess of what we could possibly achieve.

The basic problem is that the natural and material world we perceive is not the totality of reality. It is not self-contained, self-governing and self-originating as naturalists believe it to be.

That is why they continue to fail to understand it.

You are welcome to believe that blind and dumb forces can conspire to produce such exquisite complexity but this relies on a large amount of faith in the inherent creativity of Nature.

Atheistoclast said:

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: So information does have to do with fitness. You just don't know anything much about evolutionary theory or information.

No, information may contribute to fitness but one can still be fitter but with less information.

A loss of function mutation can be reproductively advantageous - i.e improve fitness - but still serve to degrade information.

A compensatory mutation can be beneficial but only serve to restore information.

Genetic information is preserved by selection because it confers function necessarily for survival. However, information relates to biochemical functionality and not to fertility levels.

Bacteria are reproductively very fit and adaptable - but our own genomes contain more information then they do.

Atheistoclast said: Let me ask you something: Why are you so resistive to the inferential evidence for ID? Why are you so scared at the prospect that there may be an Intelligent Agency at work in the universe and life? Why is this so upsetting for you? I find it absolutely intriguing that there exists a Being who is so much more intelligent than any human. It opens up my mind to the true nature of reality.

Atheistoclast said: Instead I see manifest evidence for design in Nature...

(Of course UD News posts never insult people, do they?)..First she quotes...O’Leary has misunderstood...

— Joe Felsenstein

Joe Felsenstein said: By the way I will be monitoring this discussion and brutally sending folks off the Wall if they get off topic.

Joe Felsenstein said: I am not going to play word games.

Atheistoclast said: Unfortunately, the abiogenesis has completely and utterly failed after 60 years of research. It is time to throw the naturalistic explanation away and onto the ash heap of history where it deserves to end up.

SWT said:

Chris Lawson said: As a response to the Isaac Newton lobbyists, it reminds me of Intelligent Falling.

Hey, don't underestimate the gravity of the situation!

Mike Elzinga said:

robert van bakel said: The others have just kind of quietly abandoned Mrs O'Leary, making occasional half hearted attempts at keeping the flame burning.

It’s Denyse O’Leary having her usual cow. And speaking of flames and cows; wasn’t it Mrs. O’Leary’s cow that was responsible for burning down half of Chicago back in 1871? Maybe this time (fingers crossed) it will be the Discovery Institute.

Joe Felsenstein said: Wrong. In my 2007 paper I gave a simple example of information arising by natural selection choosing one allele out of a mix of four alleles. The first paper to show that processes like that can happen (not counting Darwin/Wallace etc.) was written by William Ernest Castle in 1903.

Atheistoclast has cited my example, and then baldly declared that I am wrong to call this information. No. He doesn't get to redefine words at will. I am not going to play word games.

The vitalist approach to chemistry was dead after Friedrich Woehler sythesized urea in 1826.

Atheistoclast is following his usual approach, the one followed by most creationists -- making bald assertions of impossibility without evidence, and holding evolutionary biologists to the standard that they must provide complete scenarios for everything to disprove that.

Shouldn’t they be doing some kind of legitimate work for the money?

Atheistoclast said: If there were a valid naturalistic explanation for the origins and diversity of life I would accept it - as would everybody else. But there isn't.

Instead I see manifest evidence for design in Nature

and at a level of sophistication far in excess of what we could possibly achieve.

The basic problem is that the natural and material world we perceive is not the totality of reality.

It is not self-contained, self-governing and self-originating as naturalists believe it to be.

That is why they continue to fail to understand it.

You are welcome to believe that blind and dumb forces can conspire to produce such exquisite complexity but this relies on a large amount of faith in the inherent creativity of Nature.

Atheistoclast said:

Joe Felsenstein said: Atheistoclast has cited my example, and then baldly declared that I am wrong to call this information. No. He doesn't get to redefine words at will. I am not going to play word games.

Well, what exactly is your biological definition of information? It seems to be a reduction in variation. I will define a gain in biochemical information as "the qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome."

oe wrote:

"In other words, there is more to life than just atoms and molecules (which we all deep down know)."

In other words, there is no more to life than just atoms and molecules (which we all deep down know).

See, I can make unsubstantiated assertations without a shred of evidence just as easily. Doesn't make it true (which we all deep down know).

Vitalism was discredited two hundred years ago. Joe just hasn't gotten the memo.

Atheistoclast said:

The vitalist approach to chemistry was dead after Friedrich Woehler sythesized urea in 1826.

I don't think so - that is a massive extrapolation. Vitalism is not limited to the production of certain chemicals used in the body nor does it insist that many life processes cannot be explained in terms of physics and chemistry. It is, rather, an attempt to explain living organisms not as physico-chemical machines (which you as a materialist and reductionist accept) but as fundamentally living organisms. In other words, there is more to life than just atoms and molecules (which we all deep down know).

Atheistoclast said: I will define a gain in biochemical information as "the qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." The reason why the sequences of nucleotides in DNA represent "information" is because they convey and communicate precisely how proteins are constructed and how they function and behave. You seem to ignore this point preferring to focus solely on population genetics and math.

Well, it does come down to improbability to the point of impossibility. Creating a specified string (motif) of 60 characters is a daunting prospect unless there exists one heck of a smooth fitness landscape with a comprehensive set of intermediate states that are all beneficial.

Creating a specified string (motif) of 60 characters is a daunting prospect unless there exists one heck of a smooth fitness landscape with a comprehensive set of intermediate states that are all beneficial. Unfortunately, a blind and open search has to operate over a very rough landscape if it is supposed to achieve this.

Mike Elzinga said: How does “information” push atoms and molecules around? How does “information” organize them and make them dance in particular patterns?

Paul Burnett said:

Mike Elzinga said: How does “information” push atoms and molecules around? How does “information” organize them and make them dance in particular patterns?

This is one of the great weaknesses of intelligent design creationism. The intelligent design creationists hypothesize an "intelligent designer" but not a corresponding "intelligent (or unintelligent) creator."

Ron Okimoto said: What do losers like O'Leary and Luskin get paid by the Discovery Institute (to do)?

Richard B. Hoppe said: That conjunction of sentences makes it clear that though Atheistoclast knows how to type a bunch of words, his ability to combine them into meaningful sentences and paragraphs is woefully deficient. It's word salad. The second sentence in particular is nonsense.

Joe Felsenstein said:

Atheistoclast said:

Joe Felsenstein said: Atheistoclast has cited my example, and then baldly declared that I am wrong to call this information. No. He doesn't get to redefine words at will. I am not going to play word games.

Well, what exactly is your biological definition of information? It seems to be a reduction in variation. I will define a gain in biochemical information as "the qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome."

I apologize. I said that Atheistoclast doesn't get to redefine words at will. But I was wrong. He does get to redefine words at will. It is just that he cannot expect that anyone will pay attention to his definitions.

Mike Elzinga said:

Atheistoclast said: I will define a gain in biochemical information as "the qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." The reason why the sequences of nucleotides in DNA represent "information" is because they convey and communicate precisely how proteins are constructed and how they function and behave. You seem to ignore this point preferring to focus solely on population genetics and math.

How does “information” push atoms and molecules around? How does “information” organize them and make them dance in particular patterns? What is the difference between your definition of "information" and vitalism?

Atheistoclast said:

Mike Elzinga said:

Atheistoclast said: I will define a gain in biochemical information as "the qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." The reason why the sequences of nucleotides in DNA represent "information" is because they convey and communicate precisely how proteins are constructed and how they function and behave. You seem to ignore this point preferring to focus solely on population genetics and math.

How does “information” push atoms and molecules around? How does “information” organize them and make them dance in particular patterns? What is the difference between your definition of "information" and vitalism?

We now have solid empirical evidence for the vital factor. Most scientists call it a "self-organizing program": Self-organizing optic-cup morphogenesis in three-dimensional culture http://www.sjos.org/stem_retinol.pdf

Richard B. Hoppe said: From scratch, yes, it's daunting. But evolution doesn't create strings from scratch; a reproducing population 'creates' (via random mutations) new strings in the mutational vicinity of already viable strings in the parent generation

Further, it is not necessary that all intermediate states be beneficial; neutral drift plays a significant role. For example, in an analysis of the history of the irreducible core of the strings evolved in the case study lineage from Lenski, et al. (lineage given in the Supplemental Information), I found that several mutations that occurred early during that history were adaptively neutral when they first occurred, but (preserved by pure chance) subsequently were co-opted and generations downstream became indispensable to the performance of complex functions that evolved later. Neutral mutations, of course, can be preserved in a population via a purely stochastic process and can provide the raw material--variation--for later adaptive evolution.

The search metaphor for evolution by random mutations and natural selection is a snare and a deception. Evolution does not "search" for adaptive solutions; it adventitiously finds adaptive solutions (in the vicinity of already viable 'solutions') as a by-product of the operation of random mutations and differential reproductive success.

Mike Elzinga said:

Atheistoclast said:

Mike Elzinga said:

Atheistoclast said: I will define a gain in biochemical information as "the qualitative increase in operational capability and functional specificity with no resultant uncertainty of outcome." The reason why the sequences of nucleotides in DNA represent "information" is because they convey and communicate precisely how proteins are constructed and how they function and behave. You seem to ignore this point preferring to focus solely on population genetics and math.

How does “information” push atoms and molecules around? How does “information” organize them and make them dance in particular patterns? What is the difference between your definition of "information" and vitalism?

We now have solid empirical evidence for the vital factor. Most scientists call it a "self-organizing program": Self-organizing optic-cup morphogenesis in three-dimensional culture http://www.sjos.org/stem_retinol.pdf

How does your labeling of well-known and well-understood physical processes by the term “vital factor” suddenly make such physical processes non-physical? You are word-gaming again.

Atheistoclast said: Random drift may allow so-called "stochastic tunneling" between adaptive valleys.

Atheistoclast said: Just read the article in full. The researchers were astounded with what they discovered - it was not what they expected.

Joe is simply misrepresenting the findings of others once again. There is no evidence whatsoever of any vital force anywhere in the paper or anywhere else. You can play word games all you want, but that is the truth. Oh well, what can you expect from some one who doesn't believe that genes direct development?

The discussion seems to have taken a turn off-topic. Why am I not surprised. Perhaps this would be a good time to move the discussion to the bathroom wall once again, so we can all tell Joe exactly what we think of his lies.

OK, folks, enough of the vitalism discussion.

This has moved too far from the original subject and all further vitalism discussion will take place on the Bathroom Wall.

Joe Felsenstein said: OK, folks, enough of the vitalism discussion. This has moved too far from the original subject and all further vitalism discussion will take place on the Bathroom Wall.

"The “digital information” is just the presence of sequences that code for RNA and proteins — sequences that lead to high fitness.

Atheistoclast said:

Joe Felsenstein said: OK, folks, enough of the vitalism discussion. This has moved too far from the original subject and all further vitalism discussion will take place on the Bathroom Wall.

I agree. The thread is about Joe Felsensten's statement that was quoted by UD:

"The “digital information” is just the presence of sequences that code for RNA and proteins — sequences that lead to high fitness.

Now, does the eminent professor really mean that the more information an organism has, the higher its level of fitness? What about bacteria whose capacity to survive, adapt and reproduce far surpasses our own - but their genomes contain less information. Is the Darwinian view of genetic information that it exists purely to contribute to ever-greater fitness? Or is it that the more complex an organism's design is, the more information it requires in order to survive and reproduce? In any case, invoking fitness is not a viable explanation for how information arises naturally in a stepwise and incremental manner. "HELLO WORLD" is meaningless if you reduce the message to its individual characters.

Atheistoclast said: The thread is about Joe Felsensten's statement that was quoted by UD:

"The “digital information” is just the presence of sequences that code for RNA and proteins — sequences that lead to high fitness.

Now, does the eminent professor really mean that ...

Joe Felsenstein said:

Atheistoclast said: The thread is about Joe Felsensten's statement that was quoted by UD:

"The “digital information” is just the presence of sequences that code for RNA and proteins — sequences that lead to high fitness.

Now, does the eminent professor really mean that ...

The statement is clear in context. Stephen Meyer was going on about something mysterious called "digital information" found in genomes. His audiences, as far as I could tell, thought this meant some new magical pattern that, by itself, could only come from ID (not ordinary evolutionary processes). So I pointed out that all this "digital information" meant was ... (well, read the statement above).

I'm not bothering to reply to Atheistoclast, but to those who are interested in what the papers really say. The Bozorgmehr paper ("Is gene duplication a viable explanation for the origination of biological information and complexity?") uses mathematical approximations and some examples to argue that gene duplication is insufficient to explain all biological diversity. My feeling is that the paper is somewhat limited by its reliance on approximations and its small sample of examples, but it is still an interesting paper. It does not say, though, what the ID crowd pretend it is saying, i.e. that evolutionary processes cannot create novel genetic information; it just says that one mechanism (i.e. gene duplication) is insufficient to explain all novel genetic information.

As for the Eiraku et al paper ("Self-organizing optic-cup morphogenesis in three-dimensional culture"), it shows that geometrically complex structures can arise from "an intrinsic self-organizing program involving stepwise and domain-specific regulation of local epithelial properties." In other words, a complex eye structure can be encoded by a small set of genetic instructions. This is, of course, further evidence for Charles Darwin's classic argument that evolution can create the complex structure of the eye. Atheistoclast, rather than recognising this paper as yet another nail in the coffin of the "life is too complex to have evolved" argument, pretends that it actually supports Intelligent Design and calls it "solid empirical evidence for the vital factor."

What all this shows is that Atheistoclast serves one useful purpose on these boards: to bring to our attention fascinating papers that say the exact opposite to what he presents them as saying.

Atheistoclast said: Explaining the specified complexity of gene sequences in terms of fitness requirements is problematic. Sure, these sequences do contribute to our ability to survive and reproduce, but reproductive fitness doesn't explain how they evolved in the first instance - unless you believe in truly expansive fitness landscapes whereby a motif sequence can be built one character at a time and yet confer a selective advantage. But that sounds more like something only artificial selection could achieve.

I forgot to add: Bozorgomehr's paper concludes, "Any alternative/revision to Neo-Darwinism has to consider the holistic nature and organization of information encoded in genes, which specify the interdependent and complex biochemical motifs that allow protein molecules to fold properly and function effectively." IDists may take note that Bozorgomehr does NOT say that any alternative/revision to neo-Darwinism requires a supernatural designer.

Chris Lawson said: As for the Eiraku et al paper ("Self-organizing optic-cup morphogenesis in three-dimensional culture"), it shows that geometrically complex structures can arise from "an intrinsic self-organizing program involving stepwise and domain-specific regulation of local epithelial properties." In other words, a complex eye structure can be encoded by a small set of genetic instructions. This is, of course, further evidence for Charles Darwin's classic argument that evolution can create the complex structure of the eye. Atheistoclast, rather than recognising this paper as yet another nail in the coffin of the "life is too complex to have evolved" argument, pretends that it actually supports Intelligent Design and calls it "solid empirical evidence for the vital factor." What all this shows is that Atheistoclast serves one useful purpose on these boards: to bring to our attention fascinating papers that say the exact opposite to what he presents them as saying.

Chris Lawson said: As for the Eiraku et al paper ("Self-organizing optic-cup morphogenesis in three-dimensional culture"), it shows that geometrically complex structures can arise from "an intrinsic self-organizing program involving stepwise and domain-specific regulation of local epithelial properties." In other words, a complex eye structure can be encoded by a small set of genetic instructions. This is, of course, further evidence for Charles Darwin's classic argument that evolution can create the complex structure of the eye. Atheistoclast, rather than recognising this paper as yet another nail in the coffin of the "life is too complex to have evolved" argument, pretends that it actually supports Intelligent Design and calls it "solid empirical evidence for the vital factor.

Atheistoclast said:

Chris Lawson said: As for the Eiraku et al paper ...

Oh my, Joseph, I read the Nature article you posted more carefully, and it doesn't look good for you. It mentions the high mutation rate in the antibody-producing B cells which, combined with V(D)J recombination, generates the astoundingly high diversity among antibodies. Now is this high mutation rate part of the intelligently-designed information system you keep talking about? While this approach can generate great diversity, it's also awfully wasteful. Wouldn't an intelligent designer use something a bit more efficient to fight off all those pathogens it created to attack us? If these mutations are generating random sequences, how can you even call that designed information since those sequences are completely novel and therefore constitute new information?

Sorry folks, the two before this one were vitalism discussions, so do that on the Wall.

I don't know why I'm removed to the bathroom wall. Surely a few mocking words at the eminently mockable should be allowed, have you read the tripe at UD. And let's face it O'Leary and 'the Clastmeister' are designed to be mocked:)

robert van bakel said: I don't know why I'm removed to the bathroom wall. Surely a few mocking words at the eminently mockable should be allowed, have you read the tripe at UD. And let's face it O'Leary and 'the Clastmeister' are designed to be mocked:)

Atheistoclast said: You're wrong. The paper makes no reference whatsoever to genetics or genetic instructions. It refers to a self-organizing principle that coordinates the formation of the constituents of a complex structure.

Chris Lawson said:

Atheistoclast said: You're wrong. The paper makes no reference whatsoever to genetics or genetic instructions. It refers to a self-organizing principle that coordinates the formation of the constituents of a complex structure.

Let's see. There are 33 mentions in the paper of the Pax6 gene, 31 mentions of the Chx10 gene, 6 mentions of the Mitf gene and a lot of other genes mentioned. There is an extensive discussion of the switching off and on of genes leading to differences in tissue development. It even includes the list of primers used for genetic analysis with their genetic sequence in the Methods section. You don't know enough about this subject to recognise it when scientists talk about genes at length and in detail. You have no insight into the research and yet you continue to quote these papers as if you understand them. I think it's sad that you use your ignorance to shield yourself from understanding the fascinating implications of the papers you quote.

Now, the genetic code is the trump card of ID: why?

1) It is a digital code (like binary except that it is quaternary).
2) It is optimal (especially fault-tolerant).
3) It has no naturalistic explanation.
4) Without it there can be no life as we know it.
5) It intimately links biology with information theory.

This is why Dr. Felsenstein is being far too dismissive of Meyers. He should know better simply because he actually writes computer programs...lots of it (like PHYLIP).

Give it up guys. Joe will never be convinced that genes control development. No matter what the evidence, even in papers he cites himself, he will always claim that it is the magic invisible hologram. It doesn't matter what the actual authors did or concluded, he knows he is right and that is that. Arguing with him is like throwing your pearls before swine. That is why he always gets dumped to the bathroom wall. That is where he should be now.

And of course all of his crap about "binary codes" is complete nonsense. But then again, I guess you could have figured that out from him complete ignorance of anything to do with genetics. He is not a geneticist or a developmental biologist, or any kind of real scientist. By his won criteria he should be ignored.

Has a message from a Designer been discovered? When DNA sequences are read, can they be converted into English sentences such as: “Copyright 4004 bce by the intelligent designer; all rights reserved”?

Atheistoclast said: Now, the genetic code is the trump card of ID: why? 1) It is a digital code (like binary except that it is quaternary). 2) It is optimal (especially fault-tolerant). 3) It has no naturalistic explanation. 4) Without it there can be no life as we know it. 5) It intimately links biology with information theory. This is why Dr. Felsenstein is being far too dismissive of Meyers. He should know better simply because he actually writes computer programs...lots of it (like PHYLIP).

Ron Okimoto said: What game are you playing? If the genetic code was some kind of trump card why are the guys that perpetrated the intelligent design scam running the bait and switch on their own creationist support base? Why not use the trump card? Are they saving it for a special occasion? When is it going to be time to play the card? The bait and switch has been going down for over 9 years since Ohio in 2002. Whenever the IDiot rubes pop up and claim to be able to teach the wonderful ID science the guys that perpetrated the ID scam run the bait and switch and only give the rubes a switch scam that doesn't even mention that ID ever existed. You could test it out yourself. Just get your local school board to "voluntarily" teach that the intelligent designer is responsible for creating the genetic code and watch how fast the switch goes down on you. What did the guys at the Discovery Institute just do to Michele Bachmann when she claimed that she supported teaching intelligent design in the public schools. It was only a matter of days before they countered, and ran in the switch. If ID was so wonderful, why is it only being used to scam the ignorant and incompetent?

Atheistoclast said: Well, I suggest you map each amino acid in an encoded peptide sequence to a corresponding Hebrew character. It might spell out some message.

Atheistoclast said: I don't want to get too much into the politics of ID.

Anyone who studies the genetic code is essentially staring into the mind of a supreme intelligence. It is a profoundly religious experience derived from scientific observation.

Atheistoclast said: I don't want to get too much into the politics of ID.

DS said: Give it up guys. Joe will never be convinced that genes control development. No matter what the evidence, even in papers he cites himself, he will always claim that it is the magic invisible hologram. It doesn't matter what the actual authors did or concluded, he knows he is right and that is that. Arguing with him is like throwing your pearls before swine. That is why he always gets dumped to the bathroom wall. That is where he should be now.

Atheistoclast said: Felsenstein mockingly jeers Meyers:

Has a message from a Designer been discovered? When DNA sequences are read, can they be converted into English sentences such as: “Copyright 4004 bce by the intelligent designer; all rights reserved”?

Well, I suggest you map each amino acid in an encoded peptide sequence to a corresponding Hebrew character. It might spell out some message. There are 20 amino acids and 1 stop site in the genetic code. There are 22 characters in Hebrew, although one of the letters is redundant I believe. You might even find yourself mentioned in your own DNA. If you do, you will win the Nobel Prize and be praised by every yeshiva in the country. Good luck! Btw, it wouldn't be 4004BCE. It would be year zero on the Hebrew calendar.

In Stephen Meyer's (by the way not "Meyers") statement he was not (in that case) talking about the origin of the genetic code. Sometimes (as in his later book) he uses the exact same phrase, the origin of digital information, to refer to the origin of the code table and the translation machinery.

William Dembski's arguments refer to the "origin" of digital information in the former sense, the origin of the particular sequences that we find in organisms and the origin of the differences between them in different species.
He has his theorems and seems to think that they are valid and prevent us from using natural selection to explain that.

As far as I know his arguments cannot be used (at least without a lot of modification) to address the origin of life or the origin of the genetic code.

Given all that, I am going to rule that further discussion of whether the genetic code can / cannot be explained, either by ordinary scientific explanations or by Something Else, is off-topic and will go to the Wall. Along with Bible Codes.

Joe Felsenstein said: Given all that, I am going to rule that further discussion of whether the genetic code can / cannot be explained, either by ordinary scientific explanations or by Something Else, is off-topic and will go to the Wall. Along with Bible Codes.

Joe Felsenstein said: In Stephen Meyer's (by the way not "Meyers") statement he was not (in that case) talking about the origin of the genetic code. Sometimes (as in his later book) he uses the exact same phrase, the origin of digital information, to refer to the origin of the code table and the translation machinery.

William Dembski's arguments refer to the "origin" of digital information in the former sense, the origin of the particular sequences that we find in organisms and the origin of the differences between them in different species. He has his theorems and seems to think that they are valid and prevent us from using natural selection to explain that.

As far as I know his arguments cannot be used (at least without a lot of modification) to address the origin of life or the origin of the genetic code.

apokryltaros said: Perhaps it would be best to relegate anything related to Atheistoclast to the Bathroom Wall?

Atheistoclast said: [JF: Stuff on origin of genetic codes snipped as off-topic]

William Dembski's arguments refer to the "origin" of digital information in the former sense, the origin of the particular sequences that we find in organisms and the origin of the differences between them in different species. He has his theorems and seems to think that they are valid and prevent us from using natural selection to explain that.

You define sequence information in terms of fitness functions and reduction of possibility(variation). Dem[b]ski defines sequence information in terms of the improbability of specific arrangements arising naturally.

Atheistoclast: I define information in terms of biochemical functionality. I think I am the most correct of all of us.

Atheistoclast: me: As far as I know his arguments cannot be used (at least without a lot of modification) to address the origin of life or the origin of the genetic code.

They can. The genetic code is specified. The mapping of amino acids to codons is neither random nor arbitrary but fits in with the idea of "specified complexity". It is designed for optimality and fault-tolerance, among other reasons.

Btw, you were the one who (sarcastically) brought up the possibility of hidden messages in DNA in your 2007 paper. All I did was suggest a way in which you could go about looking for them. You do actually find the string "LIES" in many peptide sequences.

Joe Felsenstein said:

apokryltaros said: Perhaps it would be best to relegate anything related to Atheistoclast to the Bathroom Wall?

If he does his usual trollish raising of side-issues and then dancing around and raising more side issues, all the while preening himself and telling everyone what a great scientist he is, then sure, all that will go to the Wall. This is an experiment in trying to keep a thread on-topic. Can it be done? (The signs aren't good as it is a rare phenomenon for a thread to stay on topic).

Atheistoclast said:

Ron Okimoto said: What game are you playing? If the genetic code was some kind of trump card why are the guys that perpetrated the intelligent design scam running the bait and switch on their own creationist support base? Why not use the trump card? Are they saving it for a special occasion? When is it going to be time to play the card? The bait and switch has been going down for over 9 years since Ohio in 2002. Whenever the IDiot rubes pop up and claim to be able to teach the wonderful ID science the guys that perpetrated the ID scam run the bait and switch and only give the rubes a switch scam that doesn't even mention that ID ever existed. You could test it out yourself. Just get your local school board to "voluntarily" teach that the intelligent designer is responsible for creating the genetic code and watch how fast the switch goes down on you. What did the guys at the Discovery Institute just do to Michele Bachmann when she claimed that she supported teaching intelligent design in the public schools. It was only a matter of days before they countered, and ran in the switch. If ID was so wonderful, why is it only being used to scam the ignorant and incompetent?

I don't want to get too much into the politics of ID. I wouldn't recommend actually teaching that the genetic code is the work of an intelligent designer. What I would like to impress on both educators and teachers alike is that its origin comports with that of a Designer and I would attempt to explain why. Anyone who studies the genetic code is essentially staring into the mind of a supreme intelligence. It is a profoundly religious experience derived from scientific observation. It is where the demarcation between religion and science disappears.

Atheistoclast said: (Stephen Meyer) has a new paper over on the counter-establishment ID journal,Biocompexity

(Stephen Meyer) frequently talks about the digital code of DNA given every speaking opportunity:

I'm just a layman but it seems to me that "reproductive success" is what life is; nature doesn't give a flying dog turd about what, how much, or whether "biochemical functionality" is involved. Whatever works, works.

Ron Okimoto said: You even admit that you wouldn't teach that the genetic code is the work of some intelligent designer. Yet you would hawk your religious belief in the science class anyway. That isn't science education, that is politics.

Atheistoclast said: I define information in terms of biochemical functionality. I think I am the most correct of all of us.

fnxtr said: I'm just a layman but it seems to me that "reproductive success" is what life is; nature doesn't give a flying dog turd about what, how much, or whether "biochemical functionality" is involved. Whatever works, works.

Mike Elzinga said: I think everyone here can agree that in well over 40 years, ID/creationists have never explained what they mean by “information” and how this “information” pushes stuff around.

Atheistoclast said:

Ron Okimoto said: You even admit that you wouldn't teach that the genetic code is the work of some intelligent designer. Yet you would hawk your religious belief in the science class anyway. That isn't science education, that is politics.

No. I would teach that there is a thing as a digital code and digital information in molecular biology as there is in ICT and ask students to make the only possible deduction that both have an intelligent origin. The fact is that the current scientific and educational establishment teaches that (atheistic) naturalistic philosophy is the only game in town. That is unconstitutional as it promotes non-religion in the classroom.

Atheistoclast said: ...the current scientific and educational establishment teaches that (atheistic) naturalistic philosophy is the only game in town.

That is unconstitutional as it promotes non-religion in the classroom.

Because it is physical position that is important on DNA, some further indication is required to determine the direction of reading, as reading from the “wrong” end would make the rubbish between STOP and START appear as the encoded data and vice versa

Atheistoclast said:

Mike Elzinga said: I think everyone here can agree that in well over 40 years, ID/creationists have never explained what they mean by “information” and how this “information” pushes stuff around.

We didn't coin the term - Francis Crick did. We didn't coin the term "genetic code" either. http://profiles.nlm.nih.gov/ps/retrieve/Narrative/SC/p-nid/143 We also didn't coin the terms "Darwinism" and "Evolutionism". Don't blame us for your own definitions that you have since disavowed yourself from.

Joe wrote:

"Natural selection is not a viable causal factor for the particular arrangement of codons in gene sequences - but it does explain how they are preserved."

Natural selection is a viable causal factor for the particular arrangement of codons in gene sequences - and it does explain how they are preserved.

There, fixed that for you.

Atheistoclast said: [Snip stuff about his definition of information] Moreover, the idea that natural selection and evolution can produce information is flawed because it takes many mutations to arrive at anything having of adaptive value.

Joe Felsenstein said: Ludicrous. It simply waves away the possibility that a favorable mutation could exist, in principle. I'm so happy to hear that there is no such thing as mutation leading to antibiotic resistance in bacteria, antiviral resistance in HIV, insecticide resistance in insect pests, etc.

The only way the statement could be rescued would be for a major semantic argument to be mounted that excludes all those favorable mutations from being counted as "anything having of [sic] adaptive value." And if that is attempted it will just be word games. Will not play.

DS said: Joe wrote: "Natural selection is not a viable causal factor for the particular arrangement of codons in gene sequences - but it does explain how they are preserved." Natural selection is a viable causal factor for the particular arrangement of codons in gene sequences - and it does explain how they are preserved. There, fixed that for you.

Everyone, without wishing to sound like an attention whore, I strongly advise you all to carefully read my peer-reviewed papers on the subject of information and evolution.

http://onlinelibrary.wiley.com/doi/10.1002/cplx.20365/abstract

http://www.sciencedirect.com/science/article/pii/S0303264711000797

It explains what naturals selection can and cannot do.

Atheistoclast said: Everyone, without wishing to sound like an attention whore, I strongly advise you all to carefully read my peer-reviewed papers on the subject of information and evolution. It explains what naturals selection can and cannot do.

Atheistoclast said:

DS said: Joe wrote: "Natural selection is not a viable causal factor for the particular arrangement of codons in gene sequences - but it does explain how they are preserved." Natural selection is a viable causal factor for the particular arrangement of codons in gene sequences - and it does explain how they are preserved. There, fixed that for you.

No, you haven't. The manner in which natural selection preserves existing genetic information is well known - deleterious mutations are filtered out and prevented from fixing. The belief that it can create new information is just a statement of faith in naturalism and has no scientific basis whatsoever. Selection has no creative powers whatsoever other than perhaps to optimize or compensate for prior degeneration.

Atheistoclast quoted my statements:

Joe Felsenstein said: Ludicrous. It simply waves away the possibility that a favorable mutation could exist, in principle. I'm so happy to hear that there is no such thing as mutation leading to antibiotic resistance in bacteria, antiviral resistance in HIV, insecticide resistance in insect pests, etc.

...

me again: The only way the statement could be rescued would be for a major semantic argument to be mounted that excludes all those favorable mutations from being counted as “anything having of [sic] adaptive value.” And if that is attempted it will just be word games. Will not play.

And if you knew anything about antibiotic resistance in bacteria, as of course you do, you would know that mutations that affect proteins in the outer membrane reduce cellular permeability ... Indeed, most instances of disease resistance are caused by mutations that degrade existing information. .... These "beneficial" mutations don't add new information, Joe - they destroy or degrade it but still increase fitness in certain environments. They cannot be used to explain how natural election creates new sequence motifs which are admired by the ID community and hailed as "digital information". You do know what I mean when I talk of protein motifs and domains, don't you? Because it seems like we are not on the same wavelength.

Atheistoclast: Often, what is of "adaptive value" may actually represent a loss of function or even the physical deletion of genetic information. I repeat, fitness refers to reproductive success and not to biochemical complexity and functionality - what Dembski and myself are referring to.

Atheistoclast said:

Joe Felsenstein said: Ludicrous. It simply waves away the possibility that a favorable mutation could exist, in principle. I'm so happy to hear that there is no such thing as mutation leading to antibiotic resistance in bacteria, antiviral resistance in HIV, insecticide resistance in insect pests, etc.

And if you knew anything about antibiotic resistance in bacteria, as of course you do, you would know that mutations that affect proteins in the outer membrane reduce cellular permeability, thereby inhibiting the admittance of the antibiotic and some good materials as well (Delcour et al 2009). Indeed, most instances of disease resistance are caused by mutations that degrade existing information. Deletions in a proline-rich motif of the Pi21 gene in strains of Japanese rice inhibit the slowing of optimal defense mechanisms, typical of the wild type, in response to a debilitating blast fungus disease (Fukuoka et al 2009). The mutations of genes involved in polysaccharide O-acetylation for the angiosperm, Arabidopsis thaliana, serve to lower necessary amounts of acetic acid in cell walls. This has the equivalent effect of conferring resistance to another fungal pathogen.(Manabe et al 2011). These "beneficial" mutations don't add new information, Joe - they destroy or degrade it but still increase fitness in certain environments. They cannot be used to explain how natural election creates new sequence motifs which are admired by the ID community and hailed as "digital information". You do know what I mean when I talk of protein motifs and domains, don't you? Because it seems like we are not on the same wavelength.

The only way the statement could be rescued would be for a major semantic argument to be mounted that excludes all those favorable mutations from being counted as "anything having of [sic] adaptive value." And if that is attempted it will just be word games. Will not play.

Often, what is of "adaptive value" may actually represent a loss of function or even the physical deletion of genetic information. I repeat, fitness refers to reproductive success and not to biochemical complexity and functionality - what Dembski and myself are referring to.

For a minute there I thought this might have been an interesting discussion, but it's just "genetic entropy" in a stolen lab coat.

Yawn.

DS said: So [the other] Joe, perhaps you can tell us, exactly why is it that you believe that no beneficial mutations can arise? Exactly why is it that all mutations must be degradatory? You do know that mutations are random don't you? You do know that what is beneficial is determined by the environment don't you? You do know that some random mutations are beneficial in some environments and that these can increase in frequency due to selection don't you?

THe discussion has gone way off-topic - again. I don;t know why the real Joe is so tolerant of the fake Joe and his word games and crap. The bathroom wall await for him - again. Better sooner that later.

fnxtr said: For a minute there I thought this might have been an interesting discussion, but it's just "genetic entropy" in a stolen lab coat. Yawn.

Atheistoclast said:

Ron Okimoto said: You even admit that you wouldn't teach that the genetic code is the work of some intelligent designer. Yet you would hawk your religious belief in the science class anyway. That isn't science education, that is politics.

No. I would teach that there is a thing as a digital code and digital information in molecular biology as there is in ICT and ask students to make the only possible deduction that both have an intelligent origin. The fact is that the current scientific and educational establishment teaches that (atheistic) naturalistic philosophy is the only game in town. That is unconstitutional as it promotes non-religion in the classroom.

If the intentions of Meyer is to be discussed here (and not just the ignorance and repetitive presuppositions of the guy who'd like to break atheists), this is worth watching:

Is the Bible reliable?

Note especially the beginning, where he says "The worldview of scientific naturalism has not only affected our view of of [sic] nature, it's also affected our view of theology and the Bible." It's a promo for "Is the Bible reliable?"

Yes, treating the Bible like it arose "naturally" is every bit as evil as understanding life as "natural." As if they could ever do anything but attack all honest scholarship, along with science. Their intentions are extremely obvious, only slightly muffled before secular audiences, not at all in front of Xian audiences. Btw, this course seems to be nothing but finding later parts of the Bible that accord fairly well with history, ergo the Bible is true. Never mind where it fails historically, let alone scientifically...

Another video, one where Meyer crows that they "own the metaphors." Oh yes, the mere fact that the metaphors used for life often are taken from technology is something that they intend to exploit as much as possible--indeed, his book and Felsenstein's observations indicate as much. There are four other parts to the interview, available from the menus on the side.

Was there ever a time when ID was intended to be honest, at least by those who knew anything about science?

Glen Davidson

This Atheistoclast character is a perfect example of what happens when one thinks he can do modern biology by using 16th and 17th century ideas about matter and life.

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: Another video, one where Meyer crows that they "own the metaphors." Oh yes, the mere fact that the metaphors used for life often are taken from technology is something that they intend to exploit as much as possible--indeed, his book and Felsenstein's observations indicate as much. There are four other parts to the interview, available from the menus on the side. Was there ever a time when ID was intended to be honest, at least by those who knew anything about science? Glen Davidson

Joe Felsenstein said: Well said, but I can predict how this question will turn out -- Atheistoclast will have his own private definition of "beneficial".

Was there ever a time when ID was intended to be honest, at least by those who knew anything about science?

At a mathematical level, let's say we have a protein motif that is 60 character long:

There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

DS said: So Joe, perhaps you can tell us, exactly why is it that you believe that no beneficial mutations can arise? Exactly why is it that all mutations must be degratory? You do know that mutations are random don't you? You do know that what is beneficial is determined by the environment don't you? You do know that some random mutations are beneficial in some environments and that these can increase in frequency due to selection don't you?

Atheistoclast said:

Joe Felsenstein said: Well said, but I can predict how this question will turn out -- Atheistoclast will have his own private definition of "beneficial".

No. I accept "beneficial" as s is greater than 0, as do you.

Often, as I have repeated ad nauseum here

the information content of a gene is degraded but, for various reasons, this nonetheless leads to a gain in fitness. A new mutation which degrades functionality - and does not add anything else - is not "new information" but is rather "noise", even if it proves to be "beneficial" under certain conditions.

In some instances, actual sequences are deleted (a loss in "information" however you wish to define it) and selection will still favor such a development.

Dembski, if I can defend him for a moment, is insistent that the syntactically specific and complex arrangement of codons in gene sequences (such as those for protein motifs/domains) represents "information" largely because their existence is "improbable" (when you consider how many possibilities there are of constructing a peptide sequence 100 residues long).

What differentiates information from random noise is the fact that the former is very difficult to arrive at by chance.

The only question that remains is whether natural selection can generate this information. Felsenstein and virtually all Neo-Darwinists believe that it can although many also recognize there are real constraints to this. Like Dembksi I see no evidence, theoretical or empirical, that natural selection can create or design anything at all.

Atheistoclast said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

Joe (the real one) wrote:

"OK, so Atheistoclast doesn’t deny that beneficial mutations can occur, just that ones that increase functionality can occur. And his (own, private) definition of “information” needs to be used if you want to say that evolution cannot increase information."

Well, I already demolished that misconception. So I guess now the other Joe will have to redefine "functionality". I can't wait to see how he plays word games long enough to define degrading more antibiotics as not adding a new function. Frankly, by the time he get through redefining all the terms to mean exactly what he says they mean, I don't know why anyone would care what his point was, if he ever had one in the first place.

Any way you cut it, no atheists were converted, so another epic fail by Joe.

Mike Elzinga said: So does this mean that you think such “characters” in a string of 60 are just lying around to be randomly picked up and plopped into position? Are you suggesting that this is what happens every time; just start all over again and keep doing uniform, random selection until we get a hit?

And what constitutes a “hit?” What is this “functionality” that you are talking about?

Is “functionally” specified ahead of time? Who decides what is “functional?”

DS said: Joe (the real one) wrote: "OK, so Atheistoclast doesn’t deny that beneficial mutations can occur, just that ones that increase functionality can occur. And his (own, private) definition of “information” needs to be used if you want to say that evolution cannot increase information."

Mike,

GIve it up. This guy will never understand the concept of neutral variation. He will never admit the role of duplications in the evolution of new functions. He will never even admit that genes control development. Why bother with him? Let him wallow in his own willful ignorance.

Atheistoclast said:

DS said: Joe (the real one) wrote: "OK, so Atheistoclast doesn’t deny that beneficial mutations can occur, just that ones that increase functionality can occur. And his (own, private) definition of “information” needs to be used if you want to say that evolution cannot increase information."

OK: let's look at the possibilities: 1) Information refers to the coded sequences in DNA and nothing more. In which case it is really synonymous with "data". A nucleotide is like a "bit". 2) Information is that which confers reproductive fitness. 3) Information is that which encodes biochemical functionality. 4) Information is that which reduces uncertainty. Now, I don't favor any one of these possible definitions. I think all are valid.

DS said: The random mutations in the beta lactamase gene create now information by any and all of these definitions. You are wrong again, as always.

Atheistoclast said:

DS said: The random mutations in the beta lactamase gene create now information by any and all of these definitions. You are wrong again, as always.

Betalactamase is an anti-antibiotic enzyme. There are no "random mutations" involved. It is part of some bacteria's immune system. Animals also have proteins that fight off disease and infection. Once again, you fail to show any understanding of biochemistry. Why? Cos you don't know how to read a scientific paper.

Atheistoclast said: Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero.

Well, there is zero chance of a random walk arriving at a specific 60 character motif.

Joseph, I am still waiting for an answer to my question: where is the "designed" information in the high mutation rate found in B lymphocytes which helps generate the tremendous diversity in antigen binding sites? These sequences are generated randomly and produce "information" which was not there before. Generating sequences randomly is wasteful and therefore not something you'd expect from intelligence. I reiterate that this immune response would not even be necessary if there did not exist a wide array of pathogens, also a product of design in your model.

DS said: Mike, GIve it up. This guy will never understand the concept of neutral variation. He will never admit the role of duplications in the evolution of new functions. He will never even admit that genes control development. Why bother with him? Let him wallow in his own willful ignorance.

It's perfectly legitimate to distinguish the theory of evolution from theories about the origin of life, but the two topics share an indistinct border since selection effects can occur in very rudimentary chemical systems such as those that might have obtained in the postulated RNA world. In fact, the genetic code itself looks very much like the result of a Monte Carlo simulation. If an intelligent designer, by which in the instance I mean a human chemist, sets out to optimize a genetic code for a chemical system, as may actually happen one of these days, the obvious way to proceed would be to use a genetic algorithm of some sort. Indeed, it's not obvious that there would be any other way to arrive at an efficient and robust code. Andreas Wagner discusses these issues in his book Robustness and Evolvability in Living Systems.

Atheisto@$$#ole said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

dalehusband said: If you don't know the difference between improbable and impossible, you disqualify yourself from any further discussion of either evolution or abiogenesis.

Atheistoclast said: Well, there is zero chance of a random walk arriving at a specific 60 character motif.

dalehusband said: If you don't know the difference between improbable and impossible, you disqualify yourself from any further discussion of either evolution or abiogenesis.

After Mike patiently explained exactly why such a calculation was completely worthless and fundamentally dishonest, Joe went ahead and did it anyway. Now why am I not surprised? Anyone who doesn't believe in random mutations, or that genes control development, or that there are beneficial mutations, is basically beyond any hope of rationality. It's almost as if he is proud of his complete lack of ability to learn. It's almost as if he is proud that nothing at all will ever penetrate to the core of his delusions.

I ask again, why was this fool allowed to derail so many threads with all of this off-topic nonsense?

Atheistoclast said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

In other hands, Atheistoclast is employing the Texas Sharpshooter and Lottery fallacies.

*shrug*

Somebody tell me why he thinks he's some sort of god of science, again?

mplavcan said:

Atheistoclast said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

Oh God this just makes me feel ill seeing this. OK, atheistoclast, here is a little exercise for you. How many sperm does a human male crank out each day? What is the reproductive life span of a human male? How many eggs does each human female have? What is the reproductive span of a human female? How many humans were in the world when you were conceived? What is the random probability that your mother and father would have met and your particular sperm and your particular egg would have fused? Not improbable enough? Take it back a generation or two until satisfied. See, you don't exist! I just proved it by your own logic. Now, if you see the flaw in this, take a close look at this protein argument. Then take a close look at Dembski's stuff, and even Behe's stuff. You see, by simply asking the wrong question and applying the wrong logic, you can make anything look impossible. Yet here you are.

What is it about this computer meme that makes it co compelling to ID/creationists? Compared to chemistry and physics, computer code is too linear, and too much of a straight jacket.

Atheistoclast said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

Henry J said:

What is it about this computer meme that makes it co compelling to ID/creationists? Compared to chemistry and physics, computer code is too linear, and too much of a straight jacket.

Exactly. Some evolution deniers use that metaphor to imply that such a straight jacket exists, and proceed to argue that it prevents evolution beyond some level or other. Henry

Atheistoclast said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

Mike Elzinga said: Compared to chemistry and physics, computer code is too linear, and too much of a straight jacket.

Scott F said: It seems that all of the gold veins in the California mountains were formed by heat and water percolating, filtering, and concentrating specks of gold from (literally) mountains of "manure" (ie otherwise "useless" rock) into identifiable gold nuggets.

Mike Elzinga said: So I guess that all someone has to do to disprove the evolution of cars is to find a Precambrian Volkswagen Rabbit.

Scott F said:

Mike Elzinga said: Compared to chemistry and physics, computer code is too linear, and too much of a straight jacket.

Now, now, don't be so hasty. Only *some* computer code is too linear. Prolog is anything but linear, and there are lots of parallel algorithms that don't have much linearity. I like to imagine that life imitates computer science. :-) But then, I'm kind of biased.

mplavcan said: What is the random probability that your mother and father would have met and your particular sperm and your particular egg would have fused? Not improbable enough? Take it back a generation or two until satisfied. See, you don't exist! I just proved it by your own logic. ... Yet here you are.

Atheistoidiot, do yourself and everyone else a favor and NEVER come back here again! We will simply laugh at you until hell freezes over, because you have discredited yourself beyond redemption with yet another of your lame, totally worthless arguments here, like every other Creationist moron does!

stevaroni said:

dalehusband said: If you don't know the difference between improbable and impossible, you disqualify yourself from any further discussion of either evolution or abiogenesis.

Michael Behe had the same problem. One of the highlights of the Dover trial was when Behe took the stand to defend his "this mutation is way to improbable to ever happen" argument. The opposing council made him methodically work out the actual probability and it turns out that, given the just number of cells presently inside the courtroom making up the participants, this particular mutation was happening on average every hour and a half. The odds of dealing a Royal Flush are 311 million to one. Nonetheless, I would hazard a guess that one got dealt somewhere on Earth today.

dalehusband said:

Atheisto@$$#ole said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

If you don't know the difference between improbable and impossible, you disqualify yourself from any further discussion of either evolution or abiogenesis.

Kevin B said:

dalehusband said:

Atheisto@$$#ole said: At a mathematical level, let's say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that's just me.

If you don't know the difference between improbable and impossible, you disqualify yourself from any further discussion of either evolution or abiogenesis.

It's this "digital information". With the finite mantissa of a floating point number on a computer, 10^78 + 1 is equal to 10^78. AC has used a computer program to calculate 1 in 10^78, and has believed the answer.

DS said: After Mike patiently explained exactly why such a calculation was completely worthless and fundamentally dishonest, Joe went ahead and did it anyway. Now why am I not surprised? Anyone who doesn't believe in random mutations, or that genes control development, or that there are beneficial mutations, is basically beyond any hope of rationality. It's almost as if he is proud of his complete lack of ability to learn. It's almost as if he is proud that nothing at all will ever penetrate to the core of his delusions. I ask again, why was this fool allowed to derail so many threads with all of this off-topic nonsense?

DS said: I ask again, why was this fool allowed to derail so many threads with all of this off-topic nonsense?

Atheistoclast said: Well, there is a 1 in 10^78 chance of finding an exact 60 character motif but, of course, some variation in the peptide sequence is allowed (that doesn't impact on function) so it is actually a little less than that. But I am fairly sure that anything more than 10^40 or thereabouts is regarded as being scientifically impossible, not just improbable. You also have to understand that the mutation rate itself is rare which further complicates matters. The only way for the likes of Felsenstein to approach this problem is to try and break it down by imagining the existence of sub-motifs that are relatively short (for example 6 residues long). But there are complications with this approach as well. And, of course, there are motifs that are 3 times as large (like the T-domain).

Joe Felsenstein said: So mea culpa, I let my moderation standards slide. On the other hand ... Youra culpa too, because you all had to get just one more comment in (and then complained about how the discussion was continuing unreasonably).

DS said: Thanks Joe. You are absolutely right. Unfortunately, giving this guy the benefit of the doubt never seems to work out for anyone. His only goals seems to be word games and gratuitous displays of ignorance.

rossum said:

Atheistoclast said: Well, there is a 1 in 10^78 chance of finding an exact 60 character motif but, of course, some variation in the peptide sequence is allowed (that doesn't impact on function) so it is actually a little less than that. But I am fairly sure that anything more than 10^40 or thereabouts is regarded as being scientifically impossible, not just improbable. You also have to understand that the mutation rate itself is rare which further complicates matters. The only way for the likes of Felsenstein to approach this problem is to try and break it down by imagining the existence of sub-motifs that are relatively short (for example 6 residues long). But there are complications with this approach as well. And, of course, there are motifs that are 3 times as large (like the T-domain).

There is a rule in computer science, GIGO: Garbage In, Garbage Out. The output from a calculation is critically dependent on the quality of the information input to the calculation. Your numbers are garbage because the input to your calculation reflects a garbage caricature of evolution. Evolution does not develop proteins from nothing. Evolution requires a successfully reproducing population. If the population can't reproduce it goes extinct. Given that the starting population is successfully reproducing, then it is not a random starting point. It is a highly non-random starting point, well enough adapted to its environment to be able to reproduce itself. Unless your calculation can include that non-random factor in its inputs then it has no relation to the actual theory of evolution. All your calculation shows is that the creationist strawman "tornado in a junkyard" version of evolution is incorrect. rossum

Mike Elzinga said: ID/creationists are still attempting to make their pseudo-science into something new that can get around the law rather than actually do anything that real scientists do. For example, look at this grotesquely silly challenge that just popped up over on the Unintelligibly Dense site.

DS said:

Joe Felsenstein said: So mea culpa, I let my moderation standards slide. On the other hand ... Youra culpa too, because you all had to get just one more comment in (and then complained about how the discussion was continuing unreasonably).

Thanks Joe. You are absolutely right. Unfortunately, giving this guy the benefit of the doubt never seems to work out for anyone. His only goals seems to be word games and gratuitous displays of ignorance.

DS said: It's no use rossum. Mike already explained all of this to Joe. He just doesn't get it, he never will. When I told him that mutations were observed in the lab and in nature that allowed bacteria to metabolize a broader spectrum of antibiotics, he simply denied that any random mutations could be beneficial! The degree of ignorance is astounding. The degree of self-delusion is even more astounding. You will never meet some more proud of the fact that they are emotionally incapable of ever learning anything.

Atheistoclast said:

DS said: It's no use rossum. Mike already explained all of this to Joe. He just doesn't get it, he never will. When I told him that mutations were observed in the lab and in nature that allowed bacteria to metabolize a broader spectrum of antibiotics, he simply denied that any random mutations could be beneficial! The degree of ignorance is astounding. The degree of self-delusion is even more astounding. You will never meet some more proud of the fact that they are emotionally incapable of ever learning anything.

No. You were referring to enzymes belonging to a bacteria's immune system, not to random mutations. As I have already explained here, there are mutations that affect outer membrane permeability thus impeding the invasion of the antibiotic. They are indeed "beneficial" in that they improve the organism's survival chances and so represent a gain in fitness. However, they don't represent a gain in information as all they do is serve to degrade biochemical functionally whilst inadvertently allowing the organism to survive. But remove the antibiotic and these strains are at a selective disadvantage compared to the wild type. The benefit is ephemeral.

Atheistoclast said: So what is your definition of genetic information then?

What is your response to the fact this information is digitally encoded?

What is your explanation for the origination of protein motifs?

Could it be that you don't like the necessary conclusions and seek the moderators to prevent you from dealing with them?

Atheistoclast said:

DS said:

Joe Felsenstein said: So mea culpa, I let my moderation standards slide. On the other hand ... Youra culpa too, because you all had to get just one more comment in (and then complained about how the discussion was continuing unreasonably).

Thanks Joe. You are absolutely right. Unfortunately, giving this guy the benefit of the doubt never seems to work out for anyone. His only goals seems to be word games and gratuitous displays of ignorance.

So what is your definition of genetic information then? What is your response to the fact this information is digitally encoded? What is your explanation for the origination of protein motifs? Could it be that you don't like the necessary conclusions and seek the moderators to prevent you from dealing with them?

DS said: Wrong again. If you want to argue about it go to the bathroom wall. You haven't read the paper, you can't read the paper, you won't read the paper. You don't have the slightest clue what you are talking about, as usual.

DS said:

Atheistoclast said:

DS said:

Joe Felsenstein said: So mea culpa, I let my moderation standards slide. On the other hand ... Youra culpa too, because you all had to get just one more comment in (and then complained about how the discussion was continuing unreasonably).

Thanks Joe. You are absolutely right. Unfortunately, giving this guy the benefit of the doubt never seems to work out for anyone. His only goals seems to be word games and gratuitous displays of ignorance.

So what is your definition of genetic information then? What is your response to the fact this information is digitally encoded? What is your explanation for the origination of protein motifs? Could it be that you don't like the necessary conclusions and seek the moderators to prevent you from dealing with them?

Random mutations and natural selection. But then again you already know this. The fact that refuse to believe it is not evidence of anything but your own delusions. Deal with it.

So what is your definition of genetic information then?

What is your response to the fact this information is digitally encoded?

What is your explanation for the origination of protein motifs?

Could it be that you don’t like the necessary conclusions and seek the moderators to prevent you from dealing with them?

Atheistoclast said:

DS said: Wrong again. If you want to argue about it go to the bathroom wall. You haven't read the paper, you can't read the paper, you won't read the paper. You don't have the slightest clue what you are talking about, as usual.

Stop being such a whiner and cite this paper of your so I can read it. You can't expect me to refuse reading a paper you haven't even bothered to cite.

Atheistoclast said:

DS said:

Atheistoclast said:

DS said:

Joe Felsenstein said: So mea culpa, I let my moderation standards slide. On the other hand ... Youra culpa too, because you all had to get just one more comment in (and then complained about how the discussion was continuing unreasonably).

Thanks Joe. You are absolutely right. Unfortunately, giving this guy the benefit of the doubt never seems to work out for anyone. His only goals seems to be word games and gratuitous displays of ignorance.

So what is your definition of genetic information then? What is your response to the fact this information is digitally encoded? What is your explanation for the origination of protein motifs? Could it be that you don't like the necessary conclusions and seek the moderators to prevent you from dealing with them?

Random mutations and natural selection. But then again you already know this. The fact that refuse to believe it is not evidence of anything but your own delusions. Deal with it.

I note you didn't answer the first two questions. Btw, "information theory" is a science (as the moderator knows full well). Anyway, you have your hypothesis about random mutations and natural selection being responsible for the creation of protein motifs. OK, but how do you propose testing this idea? How can we at least theoretically, if not empirically, demonstrate this? Science is about observables - things we can measure. How are you going to show all of us skeptics how natural selection and random mutations works to produce novel motifs?

Thanks Harold. I didn't have the patience.

DS said: Thanks Harold. I didn't have the patience.

harold said:

[Atheistoclast] What is your response to the fact this information is digitally encoded?

It is perfectly valid to note that the nucleotide-based genetic code functions in a "digital" way - it is a quartenary code, with values usually designated as A, T, C, G. This does not mean it was magically created.

DS said:

Atheistoclast said:

DS said: Wrong again. If you want to argue about it go to the bathroom wall. You haven't read the paper, you can't read the paper, you won't read the paper. You don't have the slightest clue what you are talking about, as usual.

Stop being such a whiner and cite this paper of your so I can read it. You can't expect me to refuse reading a paper you haven't even bothered to cite.

OK Joe, here you go: Barlow and Hall (2002) Predicting evolutionary potential: In vitro evolution accurately reproduces natural evolution of theTEM beta lactamase. Genetics 160:823-832.

harold said: In some cases, protein motifs can easily be seen to have evolved from prior proteins or protein motifs.

What the first entity(ies) we would recognize as a cell(s) looked like, what proteins they already had genes for, and where those genes came from is a very interesting question. It involves events that took place at least once billions of years ago (and most certainly not 5711 years ago). That field of inquiry is known as "abiogenesis".

Atheistoclast said:

DS said:

Atheistoclast said:

DS said: Wrong again. If you want to argue about it go to the bathroom wall. You haven't read the paper, you can't read the paper, you won't read the paper. You don't have the slightest clue what you are talking about, as usual.

Stop being such a whiner and cite this paper of your so I can read it. You can't expect me to refuse reading a paper you haven't even bothered to cite.

OK Joe, here you go: Barlow and Hall (2002) Predicting evolutionary potential: In vitro evolution accurately reproduces natural evolution of theTEM beta lactamase. Genetics 160:823-832.

This paper concerns in vitro directed evolution by artificial selection. The researchers claim they are imitating/mimicking natural processes but acknowledge that the effects need to be observed in vivo. Until they do, I don't see what their little experiment proves since they controlled the outcome.

harold said: In some cases, protein motifs can easily be seen to have evolved from prior proteins or protein motifs.

Really? Can you elucidate on the “easily” understood evolutionary origins of the forkhead box, the homeobox, the T-box, or the cyclin box among others? I’d like to know. I’m being deadly serious.

What the first entity(ies) we would recognize as a cell(s) looked like, what proteins they already had genes for, and where those genes came from is a very interesting question. It involves events that took place at least once billions of years ago (and most certainly not 5711 years ago). That field of inquiry is known as “abiogenesis”.

No. Because not all protein motifs were created with the first cellular organism. Most motifs/domains for development genes (like transcription factors) obviously came later on. Therefore, it is very much an issue for evolutionary biology - and an unanswered one.

harold said: Information is determined by the observer. What is or is not information depends on the question being asked and the level of resolution.

DS said: See, this is exactly why I didn't trust you to read the paper. One part was done in the lab, it did NOT include any directed anything. And, it accurately predicted exactly what they eventually found in nature. You just can't say it was not random mutations, you just can't. The effects were observed in the lab AND in nature. You are so wrong it is absolutely silly. Why can't you ever believe any author of any real paper? Why must you always misrepresent everything? Why must you always be sop predictably wrong. Piss off.

harold said: It's trivial to note that there are many members of these families, and that there is overwhelming evidence of a common descent relationship. But the question of how these domains first became involved in regulation of mutlicellular development is very interesting.

Atheistoclast said: The authors of the paper are merely guessing that the in vitro experiments would mimick the complex biochemical environment of the in vivo case. Moreover, they (artificially) directed the selection process. It is not a valid demonstration of natural evolution.

Joe Felsenstein said: Unless the authors of the paper directed the mutation process and directed exactly what substitutions would occur, they aren't "direct[ing] the selection process" (or the mutation process).

This objection of Atheistoclast is the same one used by creationists to any animal breeding evidence: "but it's intelligently designed! It's not natural!". However, in animal breeding experiments the breeder selects for an overall phenotype but does not control what precise variations occur or increase in frequency. The breeder typically has little idea what genetic or developmental systems are used to get the response. The whole point is, that there is a good analogy to natural selection in that respect.

Atheistoclast said:

DS said: See, this is exactly why I didn't trust you to read the paper. One part was done in the lab, it did NOT include any directed anything. And, it accurately predicted exactly what they eventually found in nature. You just can't say it was not random mutations, you just can't. The effects were observed in the lab AND in nature. You are so wrong it is absolutely silly. Why can't you ever believe any author of any real paper? Why must you always misrepresent everything? Why must you always be sop predictably wrong. Piss off.

Nobody asked you to join this discussion with Atheistoclast. Why don't you take a hike out of here if you don't like the answers you get? The authors of the paper are merely guessing that the in vitro experiments would mimick the complex biochemical environment of the in vivo case. Moreover, they (artificially) directed the selection process. It is not a valid demonstration of natural evolution.

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: Another video, one where Meyer crows that they "own the metaphors." Oh yes, the mere fact that the metaphors used for life often are taken from technology is something that they intend to exploit as much as possible--indeed, his book and Felsenstein's observations indicate as much. There are four other parts to the interview, available from the menus on the side. Was there ever a time when ID was intended to be honest, at least by those who knew anything about science? Glen Davidson

Joe wrote:

"Well, directed mutagenesis and artificial selection is actually what goes on in these experiments. The researchers induce changes and screen the mutants for the next round as part of an iterative and intelligent process until they get to their desired outcome.:

Bullshit. That is not the definition of directed. It does not produce beneficial mutations in a frequency above that expected by chance. And that is absolutely positively NOT what they did to find the mutations in the samples from nature. You are lying plain and simple.

Nobody asked you to trash up this thread with off-topic nonsense. Joe has been more than lenient with you but you are just being an ass now. Do yourself a favor, go away and don;t come back. I will respond to you only on the bathroom wall from now on.

Mike Elzinga said: The biggest difference between the parallel code on computer processors and the parallel activities of chemistry and physics is that the activities of chemistry and physics don’t have to end up anywhere in particular and at any particular time. If something falls out of these processes that “works,” that’s good enough. I would be a little bit like running a bunch of parallel computer code and not caring about timing or what came out. Make as big a mess as you want; “somebody” may like the result.

Scott F said: Scale those toy systems up to the complexity of a mosquito's neuro-system, and it becomes pretty clear that we have some basic understandings of the ways in which "information" itself can self-assemble.

Mike Elzinga said:

Scott F said: Scale those toy systems up to the complexity of a mosquito's neuro-system, and it becomes pretty clear that we have some basic understandings of the ways in which "information" itself can self-assemble.

Yeah, neural networks produce some pretty amazing things. But one doesn’t have to even go to that level of complexity to demonstrate what a few simple rules will do. One of the more interesting parts of emergent phenomena in systems of atoms and molecules is that there is often a relatively large energy gap between levels of complexity. Energies within the nucleus of atoms are on the order of millions of electron volts. Chemistry happens with energies on the order of an electron volt. When we get to solids such as metals, we are in the tenths of an eV range. But when we get into the levels of complexity of organic systems, we are starting to enter energy windows on the order of hundredths of an eV. And now the myriads of potential wells, interactions, and constraints are so enormous that it becomes extremely likely that many interesting things will happen. Much of what takes place depends on what properties have already emerged and will not depend on what goes on in, say, the nucleus of an atom, for example (other than the fact that the nucleus set a template upon which higher levels of complexity and properties can emerge. And sometimes, only two or three rules can result in some very complex behavior. I never get the impression that ID/creationists have ever learned any of this stuff. It’s like they have never had any chemistry or physics. They can’t even observe phenomena happening right in front of their noses every second of their existence. Even the atomist Greeks wondered about solids and liquids. ID/creationists don’t seem to notice it or get it.

Atheistoclast said:

[quoting me]: This objection of Atheistoclast is the same one used by creationists to any animal breeding evidence: "but it's intelligently designed! It's not natural!". However, in animal breeding experiments the breeder selects for an overall phenotype but does not control what precise variations occur or increase in frequency. The breeder typically has little idea what genetic or developmental systems are used to get the response. The whole point is, that there is a good analogy to natural selection in that respect.

Except that intelligent design is what is going on in these labs, Joe: The intelligent design of evolution http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681497/

Atheistoclast: More generally, artificial selection does not concern itself with reproductive fitness (as natural selection does) or else how could we produce things like seedless fruit. Breeders can select variations Nature would never do.

Mike Elzinga said: Much of what takes place depends on what properties have already emerged and will not depend on what goes on in, say, the nucleus of an atom, for example (other than the fact that the nucleus set a template upon which higher levels of complexity and properties can emerge. And sometimes, only two or three rules can result in some very complex behavior. I never get the impression that ID/creationists have ever learned any of this stuff. It’s like they have never had any chemistry or physics. They can’t even observe phenomena happening right in front of their noses every second of their existence. Even the atomist Greeks wondered about solids and liquids. ID/creationists don’t seem to notice it or get it.

Atheistoclast said: What is your response to the fact this information is digitally encoded?

Joe Felsenstein said: The point of the work of Stuart Kauffman and others from the Santa Fe school is that random connections can produce interesting patterns. Which just says that not all that looks (selected, designed) is. Stuart actually is a great fan of evolution and natural selection.

Joe Felsenstein said: Utterly irrelevant -- Atheistoclast failed to notice that this was a different experiment by different people! And not intending to be an experimental evolution study. That reply is therefore meaningless.

The debate between intelligent design and evolution in education may still rage in school boards and classrooms, but intelligent design is making headway in the laboratory. In this case, though, the designer turned out to be just some clever scientist. A recent paper in Nature (Yoshikuni et al, 2006) presented the iterative evolution of highly specific catalysts from a promiscuous wild-type enzyme via what the authors refer to as designed divergent evolution.

Which is just what I said (see above!) creationists always say: "it's not natural". And I gave reasons why artificial selection experiments are relevant. Which were not addressed. So that reply too was a meaningless non-reply.

Scott F said: I would argue (perhaps gratuitously) that the "information" in life is not "digitally encoded" at all.

Atheistoclast said:

Joe Felsenstein said: Utterly irrelevant -- Atheistoclast failed to notice that this was a different experiment by different people! And not intending to be an experimental evolution study. That reply is therefore meaningless.

Yeah, I can imagine you didn't like reading that. Atheistoclast noticed this comment: ... [quote irrelevant to ID "controversy" snipped] Who would have ever thought IDevolution could be demonstrated and observed? After all, it is supposed to be a "pseudo-science" that cannot be tested.

[Atheistoclast again:]

[quoting me:] Which is just what I said (see above!) creationists always say: "it's not natural". And I gave reasons why artificial selection experiments are relevant. Which were not addressed. So that reply too was a meaningless non-reply.

The point is that you can't use artificial selection to explain natural selection - as most Darwinists, including the founding father himself, always have done. The efficacy of artificial selection compared to natural evolution illustrates the power of ID.

Joe Felsenstein said: Thanks to DS for bringing up the Barlow and Hall paper as a particularly clear experimental evolution paper in which Atheistoclasts's arguments are exposed for that they are ... utterly wrong. And which pushed Atheistoclast into repetition, irrelevant arguments, and finally boldfacing, since he had run out of anything else. What next? A fancy font, maybe Comic Sans? Capital letters? Very large print? Flashing text?

Atheistoclast said:

Joe Felsenstein said: Thanks to DS for bringing up the Barlow and Hall paper as a particularly clear experimental evolution paper in which Atheistoclasts's arguments are exposed for that they are ... utterly wrong. And which pushed Atheistoclast into repetition, irrelevant arguments, and finally boldfacing, since he had run out of anything else. What next? A fancy font, maybe Comic Sans? Capital letters? Very large print? Flashing text?

Gee, I never thought natural evolution involved any direction, control, intervention and intelligence - I though that was the remit of humans and the "Something Else" you refer to. Also, natural evolution only works in the complex biochemical environment of in vivo and not in vitro. That's another flaw in this argument. You can't just make up assumptions and not allow them to be falsified.

What goes on in the cell is ICT, pure and simple.

Re: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1681497/

"At the protein level, at least, it looks like irreducible complexity is out and a rather reducible simplicity is in.

Isn't this thread
relevant for the basic paradigm of ID?

Joe Felsenstein said: Hilarious! We'll have to tell all those little critters growing in petri dishes to stop evolving. Their conditions are "artificial" so they've got to stop mutating, growing at different rates, and sometimes dying. Atheistoclast has spoken, they should listen.

Rolf said:

What goes on in the cell is ICT, pure and simple.

Yeah, "There is a digital quaternary code", except I don't see the machine code that reads and process the data? In fact, I don't see any digital computing technology in the cell at all. What I see is chemistry at work. Microchips aren't performing ICT, it is just electronics at work.

These findings stem from the design principles of the two systems: robustness for biological systems and cost effectiveness (reuse) for software systems.

Joe Felsenstein said:

Atheistoclast said:

Joe Felsenstein said: Utterly irrelevant -- Atheistoclast failed to notice that this was a different experiment by different people! And not intending to be an experimental evolution study. That reply is therefore meaningless.

Yeah, I can imagine you didn't like reading that. Atheistoclast noticed this comment: ... [quote irrelevant to ID "controversy" snipped] Who would have ever thought IDevolution could be demonstrated and observed? After all, it is supposed to be a "pseudo-science" that cannot be tested.

Wow. Astonishing that Atheistoclast would think that this is an argument. He has suddenly discovered that people can design things, and thinks that this proves something about ID!

[Atheistoclast again:]

[quoting me:] Which is just what I said (see above!) creationists always say: "it's not natural". And I gave reasons why artificial selection experiments are relevant. Which were not addressed. So that reply too was a meaningless non-reply.

The point is that you can't use artificial selection to explain natural selection - as most Darwinists, including the founding father himself, always have done. The efficacy of artificial selection compared to natural evolution illustrates the power of ID.

Same old argument, but put into boldface to (supposedly) make the point. Thanks to DS for bringing up the Barlow and Hall paper as a particularly clear experimental evolution paper in which Atheistoclasts's arguments are exposed for that they are ... utterly wrong. And which pushed Atheistoclast into repetition, irrelevant arguments, and finally boldfacing, since he had run out of anything else. What next? A fancy font, maybe Comic Sans? Capital letters? Very large print? Flashing text?

I think it's interesting to see how much ground Bozorgmehr actually ceded in this discussion (although I'm not sure he's recognized it).

In accepting the effectiveness of directed evolution, he has also accepted the effectiveness of ... how shall I put it? ... non-random survival of randomly varying replicators.

In doing so, he has implicitly recognized that evolutionary mechanisms can explain exactly what modern evolutionary theory says they can: the diversity of life as we know it.

Everyone should notice that Joe has failed to answer the questions I asked about the paper he supposedly read. I will post them again on the bathroom wall. HIs inability to answer proves that he is dead wrong about the paper and he knows it.

SWT said: I think it's interesting to see how much ground Bozorgmehr actually ceded in this discussion (although I'm not sure he's recognized it). In accepting the effectiveness of directed evolution, he has also accepted the effectiveness of ... how shall I put it? ... non-random survival of randomly varying replicators. In doing so, he has implicitly recognized that evolutionary mechanisms can explain exactly what modern evolutionary theory says they can: the diversity of life as we know it.

Atheistoclast said: A directed and artificial mechanism of selection can achieve almost anything, though still availing itself of chance mutations. An undirected mechanism can achieve almost nothing. It is as simple as that. The ID movement is based on the fact that blind and undirected processes fail to explain the complexity of life.

For all of Atheistoclast's carefully designed sciency camouflage, the argument from probability fails at a breathtakingly inane level: In order to go from small probability to an inference of design, you need an argument that assumes its own conclusion. This is the point at which, when forced into a corner, the IDers whine about the scientific method being unfair and inadequate in its insistence on logical progressions and rejection of non sequiturs. Without the assumption of purpose, which can't be logically supported, all of ID is reduced to pure religion or at best, idol idle navel-gazing.

SWT said:

Atheistoclast said: A directed and artificial mechanism of selection can achieve almost anything, though still availing itself of chance mutations. An undirected mechanism can achieve almost nothing. It is as simple as that. The ID movement is based on the fact that blind and undirected processes fail to explain the complexity of life.

I suspect you're confused by the nomenclature here. Why do you think it's called "directed evolution"?

Intelligently designed libraries and improved search techniques are consequently important for future advances. In this regard, combining experimental and computational methods holds particular promise for the creation of tailored protein receptors and catalysts for tasks unimagined by nature.

wynne3617#39925 said: For all of Atheistoclast's carefully designed sciency camouflage, the argument from probability fails at a breathtakingly inane level: In order to go from small probability to an inference of design, you need an argument that assumes its own conclusion. This is the point at which, when forced into a corner, the IDers whine about the scientific method being unfair and inadequate in its insistence on logical progressions and rejection of non sequiturs. Without the assumption of purpose, which can't be logically supported, all of ID is reduced to pure religion or at best, idol idle navel-gazing.

Atheistoclast said:

SWT said:

Atheistoclast said: A directed and artificial mechanism of selection can achieve almost anything, though still availing itself of chance mutations. An undirected mechanism can achieve almost nothing. It is as simple as that. The ID movement is based on the fact that blind and undirected processes fail to explain the complexity of life.

I suspect you're confused by the nomenclature here. Why do you think it's called "directed evolution"?

Because it is change effected purposefully under the direction of intelligent designers.

Yes, whole families depend on these domains as their “backbone” - although members of the homeobox superfamily may contain other motifs. But the fact is that there is no evolutionary relationship between the protein domains themselves.

That is the crucial point. There are many on this forum who believe everything is just a modification of something else.

Sorry, but any attempt to claim a common ancestry among all gene families will inevitably fail…and so with it does the theory of evolutionism

Atheistoclast said:

wynne3617#39925 said: For all of Atheistoclast's carefully designed sciency camouflage, the argument from probability fails at a breathtakingly inane level: In order to go from small probability to an inference of design, you need an argument that assumes its own conclusion. This is the point at which, when forced into a corner, the IDers whine about the scientific method being unfair and inadequate in its insistence on logical progressions and rejection of non sequiturs. Without the assumption of purpose, which can't be logically supported, all of ID is reduced to pure religion or at best, idol idle navel-gazing.

ID is a valid inference in astronomy (SETI) and paleontology (tool use) so why not in biology? The only reason there is opposition to it is because it necessarily implies the existence of Something Else that materialistic science cannot directly observe......but then this is true for Dark Energy as well.

ID is a valid inference in astronomy (SETI) and paleontology (tool use) so why not in biology?

The only reason there is opposition to it is because it necessarily implies the existence of Something Else that materialistic science cannot directly observe.…..

but then this is true for Dark Energy as well.

Atheistoclast said:

wynne3617#39925 said: For all of Atheistoclast's carefully designed sciency camouflage, the argument from probability fails at a breathtakingly inane level: In order to go from small probability to an inference of design, you need an argument that assumes its own conclusion. This is the point at which, when forced into a corner, the IDers whine about the scientific method being unfair and inadequate in its insistence on logical progressions and rejection of non sequiturs. Without the assumption of purpose, which can't be logically supported, all of ID is reduced to pure religion or at best, idol idle navel-gazing.

ID is a valid inference in astronomy (SETI) and paleontology (tool use) so why not in biology? The only reason there is opposition to it is because it necessarily implies the existence of Something Else that materialistic science cannot directly observe......but then this is true for Dark Energy as well.

SWT said: No. It is called directed evolution because the technique typically imposes variation in a target gene rather than the entire genome of an organism. The "directed" part distinguishes the technique from classical mutagenesis.

harold said: That's just pure denial of reality. http://www.ncbi.nlm.nih.gov/pubmed?term=homeobox%20evolution

Ultimately where genes come from is a question that relates to abiogenesis.

harold said: It IS a valid inference in biology, when used in an analogous way. Starting with known characteristics of a designer (in SETI, which has been unsuccessful to date, human-like psychology and technology is implicitly sought)

If an ornithologist is in an unexplored area, and finds a bird's nest that does not match any known species, they can still infer that it was designed by a bird. Likewise a biologist finding an insect hive that is not exactly like any characterized before. Because we know about designs of birds and insects.

Bullshit. I've been asking for positive evidence for ID for years. You must have 100 comments in this thread. One comment would have been sufficient if you had positive evidence to support your claims.

Dark energy is entirely material, and was predicted and detected entirely via methodological materialism.

Atheistoclast said:

harold said: It IS a valid inference in biology, when used in an analogous way. Starting with known characteristics of a designer (in SETI, which has been unsuccessful to date, human-like psychology and technology is implicitly sought)

SETI has been unsuccessful, not because of poor methodology but because the extraterrestrial intelligent agents don't seem to leave any evidence behind.

This is not so in the case of the cell.

Atheistoclast said:

Dark energy is entirely material, and was predicted and detected entirely via methodological materialism.

It has not been directly observed and measured which means it is not "natural" or "material". But we know if must exist to explain the motion of the stars. Follow my drift?

The evidence is in the cell - this includes the information storage in DNA, the digital code, the decoding and translation process, the editing, the splicing, the nano-scale factories and assembly lines that exist within it. These point to only one possible conclusion - the cell is the product of a designing intelligence. Your resistance to this is because you don’t like such a conclusion not because it is unjustified.

What's stunning about this particular troll is that he blares out his religion-first attitude with his nym, Atheistoclast, then tries to tell us that it's all science.

OK, it's not like we're fooled by Meyer's dissembling, nor with the BS of any of the rest of them, but at least most of them aren't as brazen as this buffoon. The mere fact that he can't think, doesn't know science, and is clearly a religionist first and foremost are supposed to be ignored by us as we lap up his "wisdom."

Even most IDiots aren't quite as clueless as this one.

Glen Davidson

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: What's stunning about this particular troll is that he blares out his religion-first attitude with his nym, Atheistoclast, then tries to tell us that it's all science. OK, it's not like we're fooled by Meyer's dissembling, nor with the BS of any of the rest of them, but at least most of them aren't as brazen as this buffoon. The mere fact that he can't think, doesn't know science, and is clearly a religionist first and foremost are supposed to be ignored by us as we lap up his "wisdom." Even most IDiots aren't quite as clueless as this one. Glen Davidson

For goodness sake, Harold, is it so hard for you to understand? I said is there any indication of an evolutionary relationship among protein domains of unrelated function ,such as cyclins and integrins, not if there is molecular evolution within a gene family (which I have written papers on).

No, because not all genes were around 3.8 billion years ago. Bone morphogenetic proteins only arose when vertebrates did. Therefore, it is a problem for evolutionary theory.

SETI has been unsuccessful, not because of poor methodology but because the extraterrestrial intelligent agents don’t seem to leave any evidence behind. This is not so in the case of the cell.

Not knowing the possible or probable identity of the designer does not invalidate the inference for design.

The evidence is in the cell - this includes the information storage in DNA, the digital code, the decoding and translation process, the editing, the splicing, the nano-scale factories and assembly lines that exist within it.

These point to only one possible conclusion - the cell is the product of a designing intelligence.

Your resistance to this is because you don’t like such a conclusion not because it is unjustified.

It has not been directly observed and measured which means it is not “natural” or “material”. But we know if must exist to explain the motion of the stars. Follow my drift?

Atheistoclast said:

SWT said: No. It is called directed evolution because the technique typically imposes variation in a target gene rather than the entire genome of an organism. The "directed" part distinguishes the technique from classical mutagenesis.

What???? No.Then it would be called targeted evolution, it is called "directed" evolution - evolution directed by an intelligent agency.

Harold wrote:

"You are an unusual person. You appear to have high baseline academic ability, but some sort of neuro-cognitive problem that interferes with logic, and a somewhat impressive but incomplete autodidactic scientific education."

If only he would use his meager skills for good instead of evil. Since he seem to be emotionally incapable of accepting any finding of any publication in any science journal, even his own, I can only conclude that he is delusional beyond reason. Why anyone with such a low opinion of real scientists would want to become one is beyond me.

I suggest that we engage his delusions only on the bathroom wall, since this thread is the perfect example of what happens when his fantasies are indulged.

SWT said:

Atheistoclast said:

SWT said: No. It is called directed evolution because the technique typically imposes variation in a target gene rather than the entire genome of an organism. The "directed" part distinguishes the technique from classical mutagenesis.

No SWT, you just don't get it. He has his own definition of "random" and "directed" and "targeted" so why not his own definition of "information". That way he can have his cake, eat it, digest it and crap it out, use it as fertilizer, grow flowers and pretend they are made of gold. He wouldn't be able to describe an experiment involving site directed mutagenesis if his miserable life depended on it, because then he would have to admit that he is wrong wrong wrong. The bathroom wall is the appropriate place to respond to someone using their own dictionary with their own definitions, if there. What???? No.Then it would be called targeted evolution, it is called "directed" evolution - evolution directed by an intelligent agency.

What??? Classical mutagenesis and selective breeding are also "evolution directed by an intelligent agency" but are methodologies distinct from DE. Do you even know how DE is typically carried out? Of course, this side discussion obscures a key point: non-random survival of randomly varying replicators can be a source of what ID people call "information".

This one seems to believe that he is THE ONE TRUE JILTED GENIUS on this planet, and perhaps in the entire universe. I would love to see all these characters confined to a big coliseum somewhere. Toss a few knives onto the playing field and watch the fun.

Joe Felsenstein said:

This one seems to believe that he is THE ONE TRUE JILTED GENIUS on this planet, and perhaps in the entire universe. I would love to see all these characters confined to a big coliseum somewhere. Toss a few knives onto the playing field and watch the fun.

Watch it! This borders on encouragement of, or threats of, violence. Will be sent to Wall if more of this occurs. Ridiculing is fine, though.

harold said: It is EXtREMELY COMMON for scientists to infer the existence of something based on its effect on other things.

Atheistoclast said: There are, of course, natural laws at work but they don't explain why there exists an elaborate and complex set-up of machinery, communication and factories (all words are used by scientists) in place. It is not like you mix chemical A and chemical B and you get a digital information system.You wouldn't explain the design of a car engine in terms of the laws of physics, now would you?

Joe Felsenstein said:

This one seems to believe that he is THE ONE TRUE JILTED GENIUS on this planet, and perhaps in the entire universe. I would love to see all these characters confined to a big coliseum somewhere. Toss a few knives onto the playing field and watch the fun.

Watch it! This borders on encouragement of, or threats of, violence. Will be sent to Wall if more of this occurs. Ridiculing is fine, though.

Mike Elzinga said:

Atheistoclast said: There are, of course, natural laws at work but they don't explain why there exists an elaborate and complex set-up of machinery, communication and factories (all words are used by scientists) in place. It is not like you mix chemical A and chemical B and you get a digital information system.You wouldn't explain the design of a car engine in terms of the laws of physics, now would you?

As I just said, ID/creationists are not known for their understanding of metaphor.

Atheistoclast said: What gives me comfort is that I will have the last laugh...maybe not now, but definitely in 2059...

Cellular activities are no more attributable simply to a matter of “physics and chemistry” than a silicon chip’s operation is.

Paul Burnett said:

Atheistoclast said: What gives me comfort is that I will have the last laugh...maybe not now, but definitely in 2059...

Okay - I'll bite: What happens in 2059? Is this another one of those Mayan Calendar / UFO / Pyramidology things?

Atheistoclast said: Digital information is no "metaphor" when applied to the sequences in DNA. It is the correct term - deal with it.

You wouldn't explain the design of a car engine in terms of the laws of physics, now would you?

Atheistoclast said:

Joe Felsenstein said:

This one seems to believe that he is THE ONE TRUE JILTED GENIUS on this planet, and perhaps in the entire universe. I would love to see all these characters confined to a big coliseum somewhere. Toss a few knives onto the playing field and watch the fun.

Watch it! This borders on encouragement of, or threats of, violence. Will be sent to Wall if more of this occurs. Ridiculing is fine, though.

I don't mind any ridicule or reproach. What gives me comfort is that I will have the last laugh...maybe not now, but definitely in 2059 (if I'm around then). I'd rather be a maverick than a conservative member of a rotten establishment.

harold said:

Paul Burnett said:

Atheistoclast said: What gives me comfort is that I will have the last laugh...maybe not now, but definitely in 2059...

Okay - I'll bite: What happens in 2059? Is this another one of those Mayan Calendar / UFO / Pyramidology things?

http://en.wikipedia.org/wiki/2059 Could be a reference to either or both, I guess. This guy is absolutely my favorite creationist.

Mike Elzinga said:

harold said:

Paul Burnett said:

Atheistoclast said: What gives me comfort is that I will have the last laugh...maybe not now, but definitely in 2059...

Okay - I'll bite: What happens in 2059? Is this another one of those Mayan Calendar / UFO / Pyramidology things?

http://en.wikipedia.org/wiki/2059 Could be a reference to either or both, I guess. This guy is absolutely my favorite creationist.

Maybe a pretty good poe.

Mike Elzinga said:

harold said:

Paul Burnett said:

Atheistoclast said: What gives me comfort is that I will have the last laugh...maybe not now, but definitely in 2059...

Okay - I'll bite: What happens in 2059? Is this another one of those Mayan Calendar / UFO / Pyramidology things?

http://en.wikipedia.org/wiki/2059 Could be a reference to either or both, I guess. This guy is absolutely my favorite creationist.

Maybe a pretty good poe.

harold said:

Cellular activities are no more attributable simply to a matter of “physics and chemistry” than a silicon chip’s operation is.

We finally agree. Silicon chips work because of the flow of electrons - physics and chemistry.

Mike Elzinga said:

Atheistoclast said: Digital information is no "metaphor" when applied to the sequences in DNA. It is the correct term - deal with it.

Why DNA and not any other quasi-crystal? (I’m beginning to suspect that this character doesn’t even know what a metaphor is.)

See Harold? If one thing is designed then everything else must be. And if things can evolve by directed processes, then they can't evolve by any other processes. And if Joe is wrong about everything, that really means he is wrong about nothing. And if Joe gets to redefine one word, he gets to define all words.

You just can't argue with that logic, you really can't.

Atheistoclast said:

harold said:

Cellular activities are no more attributable simply to a matter of “physics and chemistry” than a silicon chip’s operation is.

We finally agree. Silicon chips work because of the flow of electrons - physics and chemistry.

Yes. But the transistors inside them have been designed and configured as part of a specifically complex plan. The operation of a silicon chip is explained in terms of ID, and not the laws of physics and chemistry. Btw, 2059 is the 200th anniversary of the publication of the Origin.

"The world has had enough of evolution � In the future, evolution will be remembered only as the crowning deception which the arch-enemy of human souls foisted upon the race in his attempt to lead man away from the Savior. The Science of the future will be creationism. As the ages roll by, the mysteries of creation week will be cleared up, and as we have learned to read the secrets of creative power in the lives of animals and plants about us, we shall understand much that our dim senses cannot now fathom. If we hope to continue scientific study in the laboratories and fields of the earth restored, we must begin to get the lessons of truth now. The time is ripe for a rebellion against the dominion of evolution, and for a return to the fundamentals of true science," Back To Creationism. - Harold W. Clark (1929) Back To Creationism, p. 139

Mike Elzinga said: This one seems to believe that he is THE ONE TRUE JILTED GENIUS on this planet, and perhaps in the entire universe.

Atheistoclast said: The operation of a silicon chip is explained in terms of ID, and not the laws of physics and chemistry (emphasis added).

Btw, 2059 is the 200th anniversary of the publication of the Origin.

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said:

Mike Elzinga said: This one seems to believe that he is THE ONE TRUE JILTED GENIUS on this planet, and perhaps in the entire universe.

Yes, most of these geniuses are almost certainly more interested in shoring up their world of belief than in projecting some great earth-shattering revolution in science. This troll seems to be close to the JAD model, though, interested in shoring up his world of belief, but also in the conviction that he's capable of overthrowing the science that all of those pathetic biologists use. It's not enough for him to say that he'll laugh at us as we burn in hell, which no doubt he intends to do, but he hopes that we'll yet grovel before his awesomeness prior to the (not too certain) triumph in an after-life. Delusive grandeur is part of his pathology. Glen Davidson

Mike Elzinga said: He seems to take great pride in just spewing out flippant bullshit. I don’t find one damned thing he has said that makes any sense. He never gets the point of any question; and his responses are complete non-sequiturs. He just strings words together like a parrot imitating what it hears.

Paul Burnett said: Tell that to the folks at Intel and Advanced Micro Devices. While their chips are admittedly "intelligently designed," I'm pretty sure they do follow all the laws of chemistry and physics.

...wherein Darwin's life and discoveries will once again be celebrated, while Stephen Meyer and Dembski and Behe and the other creationists will have been long relegated to the dustbin of history - gone and forgotten. I hope you're alive to see it.

Atheistoclast said:

Paul Burnett said: Tell that to the folks at Intel and Advanced Micro Devices. While their chips are admittedly "intelligently designed," I'm pretty sure they do follow all the laws of chemistry and physics.

I doubt the digital logic designers and chip architects consider the physics and chemistry of transistor-on-silicon. That is the responsibility of chemical engineers such as those involved in copper deposition and doping.

...wherein Darwin's life and discoveries will once again be celebrated, while Stephen Meyer and Dembski and Behe and the other creationists will have been long relegated to the dustbin of history - gone and forgotten. I hope you're alive to see it.

No, they will be regarded in a similar vein to that of Marx and Freud.

The 19th century produced some really crazy shit, the 21st century will hopefully sweep it away. Maybe the galactic alignment of 2012 really heralds the end of Darwinism.

I look forward to regime change within science with great anticipation.

Atheistoclast said: No, DNA is an information storage device. While you lot focus on the molecule's ability to self-replicate, linking it with the origin of life, you seem to forget that DNA only imposes a metabolic cost on the cell which it has to produce the nucleic bases, phosphates and sugars of which it is composed. DNA doesn't engage in any cellular functions or biochemical reactions. It is relatively inert, and serves as a repository for the sequences of proteins and RNAs that do play an essential part.

Kevin B said: Why have you italicised "regime change"? Is it because you've invented a new, and completely irrelevant, meaning to the phrase? If so, you ought to be consistent and do the same for all your other favourite words.

POWER TO THE LUNATICS!

dalehusband said:

Atheistoclast said: No, DNA is an information storage device. While you lot focus on the molecule's ability to self-replicate, linking it with the origin of life, you seem to forget that DNA only imposes a metabolic cost on the cell which it has to produce the nucleic bases, phosphates and sugars of which it is composed. DNA doesn't engage in any cellular functions or biochemical reactions. It is relatively inert, and serves as a repository for the sequences of proteins and RNAs that do play an essential part.

Excuse me while I die laughing...... Are you denying the connection between DNA, RNA, and proteins, you lunatic?! That without DNA, those other things wouldn't exist?! HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA HA!!!!!!!!!

Kevin wrote:

"Why have you italicised “regime change”? Is it because you’ve invented a new, and completely irrelevant, meaning to the phrase? If so, you ought to be consistent and do the same for all your other favourite words."

And so he has.

Atheistoclast said:

Kevin B said: Why have you italicised "regime change"? Is it because you've invented a new, and completely irrelevant, meaning to the phrase? If so, you ought to be consistent and do the same for all your other favourite words.

If regime change can happen in politics, it can also happen in science. The current establishment is corrupt and must be overthrown. We need a new system.

Atheistoclast said: DNA encodes proteins and RNAs...but it has no biochemical function within the cell other than to store the information relating to their sequences. It is designed purely to serve as a medium for the conveying of this information.

dalehusband said:

Atheistoclast said: DNA encodes proteins and RNAs...but it has no biochemical function within the cell other than to store the information relating to their sequences. It is designed purely to serve as a medium for the conveying of this information.

And this is an issue to you......why? Sounds like DNA is EXTREMELY important to me. What you just said is as dumb as saying Barack Obama is "only" the President of the United States!

Atheistoclast said: It has not been directly observed and measured which means it is not "natural" or "material".

Atheistoclast said: It has not been directly observed and measured which means it is not "natural" or "material".

The operation of a silicon chip is explained in terms of ID, and not the laws of physics and chemistry.

AC, you're killing me! As a former chip designer myself, pray tell, what is a "transistor-on-silicon?" Don't consider the physics and chemistry? You're joking, right? That was a creationist's attempt at humor. So funny I forgot to laugh.

Tell you what, move out to Cupertino, take your material and ply the open mic nights at the local comedy clubs. I think you'll be a hit with the Geek Crowd, and probably the Biotechies, too.

I mean, this is comedy gold if you're into abject stupidity and cluelessness.

So far, AC, you've demonstrated you are completely ignorant of "intelligent design" theory (you've made several mistakes there!), biology, chemistry, physics and, now, electrical engineering! Brilliant! I love it so.

Take my advice and augment your material with funny words like penguin, banana and kumquat and weave in some driving gags (Oy, traffic jams! They can't just happen, they had to be created!) and you've got a career, my friend. Live long and proselytize.

Erm, maybe SETI hasn't discovered aliens for the same reason ID hasn't identified the designer: they ain't there.

In a nutshell:

Harold: How do you know the cell was designed?
Theistoclown: Well, just look at it!

Unlike the crew of the Enterprise, we are in no danger from Theistoclown's logic.

Doc Bill said: I've been dealing with creationists for a long, long time, going back to Garner Ted Armstrong and "The World Tomorrow" and I thought I was tard-proof, but this is quite possibly the stupidest thing I've ever seen a creationist write.* Thank you, AC, you made my day!

The operation of a silicon chip is explained in terms of ID, and not the laws of physics and chemistry.

Holy OMG, Batman, stick a fork in this thread 'cause it's done! *possibly with the exception of Joe G's claim that ice and water were two different things, not just different states of matter, but Two Different Things.

Atheistoclast said: I look forward to regime change within science with great anticipation.

fnxtr said: In a nutshell: Harold: How do you know the cell was designed? Theistoclown: Well, just look at it!

I’m not sure that analogy was a good one to use here. Odds on, AC is a Birther as well. Next thing, we’ll have him demanding that Obama publish his DNA sequence!

I don’t go over to that Unimaginably Dense website much; but my last few looks at that site suggest it is getting to be a really big paranoid pity party over there. So much whining, carping, and projecting.

AiG is also getting crabbier.

It appears that ID/creationists are just doubling down on their already bad ideas. No effort whatsoever to learn any science.

I don’t mind any ridicule or reproach. What gives me comfort is that I will have the last laugh…maybe not now, but definitely in 2059 (if I’m around then). I’d rather be a maverick than a conservative member of a rotten establishment.

Rolf said: One thing stands out: No amount of facts or evidence can shake that kind of creationists.

Rolf said: Whereas the foundation of ID remains just an argument from incredulity. One thing stands out: No amount of facts or evidence can shake that kind of creationists.

Atheistoclast said:

Rolf said: Whereas the foundation of ID remains just an argument from incredulity. One thing stands out: No amount of facts or evidence can shake that kind of creationists.

I would contend that the argument from personal incredulity lies solely with the atheists. They cannot accept that there could be a super-intelligent being responsible for the origination of the cell and so they become all upset whenever this is postulated. But a true scientist keeps his options open and does not make unsubstantiated assumptions that preclude certain possible explanations. If there is a viable naturalistic option, he should investigate it. If the evidence points to a supernatural intervention, then he should acknowledge that too. The truth relates to the way things actually are, not as how we would wish them to be.

Doc Bill said: AC, you're killing me! As a former chip designer myself, pray tell, what is a "transistor-on-silicon?" Don't consider the physics and chemistry? You're joking, right? That was a creationist's attempt at humor. So funny I forgot to laugh.

dalehusband said: Assumptions are not evidence. When you ASSUME there must be a designer but never produce a way to access the Designer directly, that's not science. It's not about atheism, you liar. It's about bigots like you using religious bullcrap where it never belongs.

Atheistoclast said:

dalehusband said: Assumptions are not evidence. When you ASSUME there must be a designer but never produce a way to access the Designer directly, that's not science. It's not about atheism, you liar. It's about bigots like you using religious bullcrap where it never belongs.

No, the assumption I am referring to is the one that scientists make when they maintain that there must be a naturalistic explanation. But what if there isn't? What if the Designer-really-did-do-it?

AC, your brand of "OMG science is so bad because it insists that the material world is all there is" is tiresome and wrong to boot. Science doesn't demand that the material is all there is. It simply says that it is not equipped to deal with the supernatural.

You think that's a mistake? I'd suggest that the field is wide open for a bold creationist to figure out a way to actually make the supernatural accessible to the scientific method. Go ahead, show all those nasty materialists the folly of their ways.

But first, a caution. You are not likely to get results that please you. The two likely results are that either you will come to the conclusion that the supernatural does not exist, or that if it does exist it's existence is indistinguishable from non existence (well, I mean if you were honest with yourself anyway, I think we both know you'd never accept such results). Secondly if you were able to investigate something that you believed was in the realm of the supernatural you would likely inadvertently demote it to world of the natural instead. A crude analogy might be starting with the understanding that disease is caused by supernatural bad spirits, and progressing to the germ theory. It's not so much that we gained the ability to research the bad spirits, but we found out what was really causing the disease, and surprise surprise, it was actually a natural explanation after all.

In any case, if all you've got is saying "well, I don't know how it works, so I guess assuming that an invisible, undetectable, immaterial entity did it instead is just as useful as working to come up with an explanation that works and that leads to useful predictions that can be followed to further develop the understanding" then, well, there's not much more to say, is there?

Atheistoclast said:But what if there isn't? What if the Designer-really-did-do-it?

Atheistoclast said: No, the assumption I am referring to is the one that scientists make when they maintain that there must be a naturalistic explanation. But what if there isn't? What if the Designer-really-did-do-it?

Atheistoclast said:

Doc Bill said: AC, you're killing me! As a former chip designer myself, pray tell, what is a "transistor-on-silicon?" Don't consider the physics and chemistry? You're joking, right? That was a creationist's attempt at humor. So funny I forgot to laugh.

Digital logic designers do not consider the underlying transistor physics (on the silicon chip)- they just write lots of Vhdl/Verilog code. Been there, done that.

Atheistoclast said: No, the assumption I am referring to is the one that scientists make when they maintain that there must be a naturalistic explanation. But what if there isn't? What if the Designer-really-did-do-it?

The way to deal with poseurs like Atheistoclast is to make sure they don't wriggle out of the corner they've painted themselves into. Keep it basic, and keep pounding on the basics--the argument from probability is fatally flawed, and cdesign proponentsists avoid discussion of mechanisms as though it were a rabid dog. At the moment they start insisting that methodological naturalism isn't fair, and that scientists are wrong for insisting on testable hypotheses, laugh at them and turn your attention to someone or something rational. You can't argue rationally against ideas that aren't rationally formed.

Rumraket said:

Atheistoclast said:But what if there isn't? What if the Designer-really-did-do-it?

Then there should be some evidence of it. There isn't. Oh wait, you are suggesting we just stop the search for an explanation and declare goddidit? I see, I see... sounds like an excellent way to do science. What is thunder and lightning? How does it work? Hmmm... I can't immediately figure it out, so I'm just going to posit an undetectable, unknowable, unfathomably intelligent designer. Oh wait, I have to correct myself. The designer is THE ELOHIM, of course. How do we know this? Oh, we don't? You're just making it up? Ahh, I see... excellent science there again clastie, most excellent.

And yet, the only evidence for life being designed are your own arrogant assertions that life is designed, as well as your colossally arrogant claims that you've magically overturned the totality of science and atheism with your inane and insignificant papers.

Atheistoclast said: The only way to refute (the assertion that life is designed by a Designer) is is to offer a naturalistic explanation that can be sufficiently demonstrated - not just based on speculation. That hasn't happened, so we must still necessarily accept intentional design as the best explanation.

How that design was achieved and implemented, and the identity of the designer,is another matter altogether.

wynne3617#39925 said: The way to deal with poseurs like Atheistoclast is to make sure they don't wriggle out of the corner they've painted themselves into. Keep it basic, and keep pounding on the basics--the argument from probability is fatally flawed, and cdesign proponentsists avoid discussion of mechanisms as though it were a rabid dog. At the moment they start insisting that methodological naturalism isn't fair, and that scientists are wrong for insisting on testable hypotheses, laugh at them and turn your attention to someone or something rational. You can't argue rationally against ideas that aren't rationally formed.

If Atheistoclast's nonsense is true, then water is intelligently designed to fit whatever container it's poured into.

"The only way to refute (the assertion that life is designed by a Designer) is is to offer a naturalistic explanation that can be sufficiently demonstrated - not just based on speculation. That hasn’t happened, so we must still necessarily accept intentional design as the best explanation."

Of course, even if a natural explanation is provided, even if it stands the test of time, even if it passes all testing for one hundred and fifty years, even if all of the experts agree that it is valid beyond a reasonable doubt, you can still just clamp your hands over your ears and scream "it ain't so" at the top of your lungs and deny it. When asked to justify your infantile denials, all you have to do is lie and make shit up. If anyone challenges you to defend your made up crap, just clamp your hands over your ears and scream once again. That way, you can go on believing any fool thing you choose, regardless of the evidence.

apokryltaros said: So you're casually dismissing over a century and a half's worth of evidence for evolution in favor of GODIDIT because why? Why is evidence that is apparently offensive to your own hypersensitive religious bigotries merely philosophical speculation, while your own arrogant and inane assertions are to be treated as holy law?

How that design was achieved and implemented, and the identity of the designer,is another matter altogether.

No. 150 years of naturalistic materialism in science has manifestly failed to answer these 4 big issues in biology: 1) The Origin of Life: the evolution of life from non-life. 2) The Origin of Information: the specific motif sequences in DNA. 3) The Origin of Form: the morphology of complex traits and systems. 4) The Origin of Consciousness and Behavior: Self-awareness and psychology. These are the fundamentally important questions, not whether black peppered moths thrive in polluted environments or how the polar bear came to look white because of a lack of eumelanin in its hair.

DS said: Exactly. That's why I keep posting the questions that Joe cannot answer. The paper that the claimed to read specifically stated that the mutations were RANDOM. Joe of course declared that they were "directed".

Atheistoclast said:

DS said: Exactly. That's why I keep posting the questions that Joe cannot answer. The paper that the claimed to read specifically stated that the mutations were RANDOM. Joe of course declared that they were "directed".

Oh, for goodness sake! In directed evolution, mutations may be either purposefully or randomly induced. That isn't the issue. It is a directed process because selection (in this case the screening process) is not natural, but artificial. Breeders don't create new mutations - they select them. They are successful, because the select natural and spontaneous variation that Nature would dispose of.

Atheistoclast said:

DS said: Exactly. That's why I keep posting the questions that Joe cannot answer. The paper that the claimed to read specifically stated that the mutations were RANDOM. Joe of course declared that they were "directed".

Oh, for goodness sake! In directed evolution, mutations may be either purposefully or randomly induced. That isn't the issue. It is a directed process because [s]selection (in this case the screening process) is not natural, but artificial[/s] I say it is.

Ack, I messed up the tags. What I meant to convey was that in simpler terms, it's a "directed process" because AC says it is. Close the labs and go home.

BTW, AC, tell us about your mechanisms.

Atheistoclast said: The evidence for a designer is the unmistakable signature he leaves behind in his design.

You just reject any logical inference for this design in life, preferring to believe it is the outcome of chance and necessity. That is a philosophical position, but it has no scientific merit whatsoever.

The only way to refute this is to offer a naturalistic explanation that can be sufficiently demonstrated - not just based on speculation. That hasn't happened,

Atheistoclast said: Intelligent Design is the very basis for our modern civilization...and science itself.

Atheistoclast said:

DS said: Exactly. That's why I keep posting the questions that Joe cannot answer. The paper that the claimed to read specifically stated that the mutations were RANDOM. Joe of course declared that they were "directed".

Oh, for goodness sake! In directed evolution, mutations may be either purposefully or randomly induced. That isn't the issue. It is a directed process because selection (in this case the screening process) is not natural, but artificial. Breeders don't create new mutations - they select them. They are successful, because the select natural and spontaneous variation that Nature would dispose of.

Atheistoclast said: Oh, for goodness sake! In directed evolution, mutations may be either purposefully or randomly induced. That isn't the issue.

Breeders don't create new mutations - they select them.

eric said:

Atheistoclast said: Oh, for goodness sake! In directed evolution, mutations may be either purposefully or randomly induced. That isn't the issue.

Yeah, it is the issue, because you keep claiming a digital code can only be the result of intelligent action. If you are now admitting that random mutation can produce codes on which selection can act, you have just conceded that natural, unintelligent forces can create novel digital code. There is simply no way to simultaneously claim that the existence of digital code is evidence of design (which you've been doing for the past several days), and yet admit that random mutation can produce new digital code on which selection can act (which you've just done).

Breeders don't create new mutations - they select them.

Exactly. Which is why the existence of a code is not evidence of design...because intelligent agents aren't needed to create new mutations.

dalehusband said:

Atheistoclast said: Intelligent Design is the very basis for our modern civilization...and science itself.

No, that is simply an outright lie. And since you lied about that basic truth, nothing else you say can ever be taken seriously again.

That is what Joe must now admit he was wrong about.

That is what Joe must now admit he was wrong about.

Atheistoclast said: No, DNA is an information storage device. While you lot focus on the molecule's ability to self-replicate, linking it with the origin of life, you seem to forget that DNA only imposes a metabolic cost on the cell which it has to produce the nucleic bases, phosphates and sugars of which it is composed. DNA doesn't engage in any cellular functions or biochemical reactions. It is relatively inert, and serves as a repository for the sequences of proteins and RNAs that do play an essential part.

The evidence for a designer is the unmistakable signature he leaves behind in his design.

You just reject any logical inference for this design in life, preferring to believe it is the outcome of chance and necessity.

That is a philosophical position, but it has no scientific merit whatsoever.

Atheistoclast said: 150 years of naturalistic materialism in science has manifestly failed to answer these 4 big issues in biology: 1) The Origin of Life: the evolution of life from non-life. 2) The Origin of Information: the specific motif sequences in DNA. 3) The Origin of Form: the morphology of complex traits and systems. 4) The Origin of Consciousness and Behavior: Self-awareness and psychology.

These are the fundamentally important questions, not whether black peppered moths thrive in polluted environments or how the polar bear came to look white because of a lack of eumelanin in its hair.

And this, ironically, highlights the fact that neither you, nor any other Intelligent Design proponent is even interested, let alone physically capable of demonstrating how Intelligent Design can explain anything, or is even scientific to begin with.

Intelligent Design is the very basis for our modern civilization...and science itself.

dalehusband said:

Atheistoclast said: Intelligent Design is the very basis for our modern civilization...and science itself.

No, that is simply an outright lie. And since you lied about that basic truth, nothing else you say can ever be taken seriously again.

apokryltaros said: When did we ever take Atheistoclast seriously to begin with?

harold said:

dalehusband said:

Atheistoclast said: Intelligent Design is the very basis for our modern civilization...and science itself.

No, that is simply an outright lie. And since you lied about that basic truth, nothing else you say can ever be taken seriously again.

It's a particularly annoying lie, too. One of the more obnoxious aspects of ID/creationism is the nebulous, weasley nature of the term "intelligent design". Constantly shifting the meaning of a term is most annoying. Did humans "intelligently design" modern civilization and science? I guess so. Does that have anything to do with clams that the Elohim magically created cells out of nothing and continue to interfere magically with cellular metabolism? No.

DS said:

apokryltaros said: When did we ever take Atheistoclast seriously to begin with?

I know I never did. He has been so wrong about so many things, it's hard to believe he is even a real person. Look at the mess he made of this thread. He claimed that mutations must always degrade biological systems and that they can never produce any new information or new functions. When confronted with a paper that proved that they did just that, he tried to claim that the process was somehow "directed" and that that somehow meant if could not happen naturally. Of course he completely failed to notice that the paper included analysis of populations from nature. And of course he is absolutely wrong about the difference between natural and artificial selection as well. His claim is now reduced to the unfounded assertion that bacteria can never encounter antibiotics in nature! Exactly where does he think that antibiotics come from? Exactly why does he think that it makes any difference where they come from? He shot himself in the foot and danced up and down in a fit claiming victory! How can anyone take that seriously?

Atheistoclast said:

Rumraket said:

Atheistoclast said:But what if there isn't? What if the Designer-really-did-do-it?

Then there should be some evidence of it. There isn't. Oh wait, you are suggesting we just stop the search for an explanation and declare goddidit? I see, I see... sounds like an excellent way to do science. What is thunder and lightning? How does it work? Hmmm... I can't immediately figure it out, so I'm just going to posit an undetectable, unknowable, unfathomably intelligent designer. Oh wait, I have to correct myself. The designer is THE ELOHIM, of course. How do we know this? Oh, we don't? You're just making it up? Ahh, I see... excellent science there again clastie, most excellent.

The evidence for a designer is the unmistakable signature he leaves behind in his design.

Atheistoclast said:You just reject any logical inference for this design in life, preferring to believe it is the outcome of chance and necessity. That is a philosophical position, but it has no scientific merit whatsoever.

Atheistoclast said:When we see digitally encoded information, intracellular communication and signal transduction systems, assembly lines and factories present, we naturally compare it with our own designing intelligence: we seek causes based on our own experience.

Atheistoclast said:The only possible deduction we can therefore make is that the appearance of design in life is because there exists a real design.

Atheistoclast said:The only way to refute this is to offer a naturalistic explanation that can be sufficiently demonstrated - not just based on speculation. That hasn't happened, so we must still necessarily accept intentional design as the best explanation.

Atheistoclast said:How that design was achieved and implemented, and the identity of the designer,is another matter altogether.

Rumraket wrote:

"This is hilarious coming from the guy who blatantly postulates “design” with no evidence of when, where or how design took place, or by whom. Though, you have been seen piling more assertions on top of your design-assertion, when you go and declare that the design is the product of the will of THE ELOHIM."

Blasphemer. The only true god is ELOHER.

Atheistoclast said: sigh. 1. Directed evolution experiments do not count because natural evolution is undirected. The researcher has control of the experiment and can decide what to select and what not to select. In the wild, only Nature has that decision power.

Unfortunately, neither you nor Felsenstein have the specialist expertise to be able to understand what is going on in these experiments and the significance of them.

Atheistoclast said: Where would we all be without intelligent design and intelligent scientists? You need intelligence just to study science which is why I am so good at it.

Atheistoclast said: 1. Directed evolution experiments do not count because natural evolution is undirected. The researcher has control of the experiment and can decide what to select and what not to select. In the wild, only Nature has that decision power.

2. In vitro experiments cannot be used to account for natural evolution which always occurs a biochemically complex in vivo environment.

3.Even if the experiment did show mutations that confer pathogen resistance, we still don't know of the pleiotropic effect this may have. How does this affect other functionality and behavior? Does it adversely affect other areas?

Unfortunately, neither you nor Felsenstein have the specialist expertise to be able to understand what is going on in these experiments and the significance of them.

The only way to refute (the assertion that life is designed by a Designer) is is to offer a naturalistic explanation that can be sufficiently demonstrated - not just based on speculation. That hasn’t happened, so we must still necessarily accept intentional design as the best explanation.

DS said:

apokryltaros said: When did we ever take Atheistoclast seriously to begin with?

I know I never did. He has been so wrong about so many things, it's hard to believe he is even a real person.

Rumraket said:

Atheistoclast said:

Rumraket said:

Atheistoclast said:But what if there isn't? What if the Designer-really-did-do-it?

Then there should be some evidence of it. There isn't. Oh wait, you are suggesting we just stop the search for an explanation and declare goddidit? I see, I see... sounds like an excellent way to do science. What is thunder and lightning? How does it work? Hmmm... I can't immediately figure it out, so I'm just going to posit an undetectable, unknowable, unfathomably intelligent designer. Oh wait, I have to correct myself. The designer is THE ELOHIM, of course. How do we know this? Oh, we don't? You're just making it up? Ahh, I see... excellent science there again clastie, most excellent.

The evidence for a designer is the unmistakable signature he leaves behind in his design.

Oh you mean like "Made in china" or "painted by John"? That kind of unmistakable signature?

A special for AC: Dark matter at work

Anyway, I am declaring total victory in this thread. Joe Felsenstein, whom I personally have nothing whatsoever against, was exposed for his complete insouciance and indifference regarding the fact that we need to appreciate genetic information in terms of biochemistry and biophysics, and not just probability and variety. But the fact remains that only an infinitesimally small number of character combinations produce viable and functional peptide sequences. Selection just simply has no way of reaching this by way of a blind and open search. Any logical person must come to the same conclusion.

Atheistoclast said: Anyway, I am declaring total victory in this thread. Joe Felsenstein, whom I personally have nothing whatsoever against, was exposed for his complete insouciance and indifference regarding the fact that we need to appreciate genetic information in terms of biochemistry and biophysics, and not just probability and variety. But the fact remains that only an infinitesimally small number of character combinations produce viable and functional peptide sequences. Selection just simply has no way of reaching this by way of a blind and open search. Any logical person must come to the same conclusion.

Atheistoclast said: Selection just simply has no way of reaching this by way of a blind and open search.

Any logical person must come to the same conclusion.

Atheistoclast said: Anyway, I am declaring total victory in this thread. Joe Felsenstein, whom I personally have nothing whatsoever against, was exposed for his complete insouciance and indifference regarding the fact that we need to appreciate genetic information in terms of biochemistry and biophysics, and not just probability and variety. But the fact remains that only an infinitesimally small number of character combinations produce viable and functional peptide sequences. Selection just simply has no way of reaching this by way of a blind and open search. Any logical person must come to the same conclusion.

https://me.yahoo.com/a/JxVN0eQFqtmgoY7wC1cZM44ET_iAanxHQmLgYgX_Zhn8#57cad said: Which is why evolution starts from a reproducing population, not from a random starting point. If you can't reproduce then you can't join the game.

Atheistoclast said: I don't see your point. How do reproducing populations somehow make the search for an improbable sequence that much easier?

rossum said:

Atheistoclast said: I don't see your point. How do reproducing populations somehow make the search for an improbable sequence that much easier?

Because your starting point is not random, it is already on an island of functionality within the search space. You are starting from a point that can reproduce itself. Unless you include the nature of the starting point in your calculations, you are not modelling evolution. Starting from a random 6 billion bases of DNA, you are highly improbable. Starting from your parents' DNA you are much less improbable. A non-random starting point changes the calculation. rossum

Mike Elzinga said:

rossum said:

Atheistoclast said: I don't see your point. How do reproducing populations somehow make the search for an improbable sequence that much easier?

Because your starting point is not random, it is already on an island of functionality within the search space. You are starting from a point that can reproduce itself. Unless you include the nature of the starting point in your calculations, you are not modelling evolution. Starting from a random 6 billion bases of DNA, you are highly improbable. Starting from your parents' DNA you are much less improbable. A non-random starting point changes the calculation. rossum

This is an example of Atheistoclast’s complete ignorance of the field; he has been faking it right along. Anybody who can’t understand initial and boundary conditions in any kind of physical phenomena has not had an education in even the most elementary aspects of the subject. Not getting the point of reproducing populations is just plain jaw-droppingly stupid.

DS said:

Mike Elzinga said:

rossum said:

Atheistoclast said: I don't see your point. How do reproducing populations somehow make the search for an improbable sequence that much easier?

Because your starting point is not random, it is already on an island of functionality within the search space. You are starting from a point that can reproduce itself. Unless you include the nature of the starting point in your calculations, you are not modelling evolution. Starting from a random 6 billion bases of DNA, you are highly improbable. Starting from your parents' DNA you are much less improbable. A non-random starting point changes the calculation. rossum

This is an example of Atheistoclast’s complete ignorance of the field; he has been faking it right along. Anybody who can’t understand initial and boundary conditions in any kind of physical phenomena has not had an education in even the most elementary aspects of the subject. Not getting the point of reproducing populations is just plain jaw-droppingly stupid.

Well it's not like you didn't try to explain it to him before. It's not like he didn't have the opportunity to learn. He simply declined. Now why do I get the feeling that the reception of his new "paper" is going to receive the same sort of reception?

rossum said:

Atheistoclast said: I don't see your point. How do reproducing populations somehow make the search for an improbable sequence that much easier?

Because your starting point is not random, it is already on an island of functionality within the search space. You are starting from a point that can reproduce itself. Unless you include the nature of the starting point in your calculations, you are not modelling evolution. Starting from a random 6 billion bases of DNA, you are highly improbable. Starting from your parents' DNA you are much less improbable. A non-random starting point changes the calculation. rossum

I told you he didn't get it. I told you he couldn't get it. I told you he won't get it.

Same thing will happen with his rejection letter.

DS said: I told you he didn't get it. I told you he couldn't get it. I told you he won't get it. Same thing will happen with his rejection letter.

Atheistoclast said:

DS said:

Mike Elzinga said:

rossum said:

Atheistoclast said: I don't see your point. How do reproducing populations somehow make the search for an improbable sequence that much easier?

Because your starting point is not random, it is already on an island of functionality within the search space. You are starting from a point that can reproduce itself. Unless you include the nature of the starting point in your calculations, you are not modelling evolution. Starting from a random 6 billion bases of DNA, you are highly improbable. Starting from your parents' DNA you are much less improbable. A non-random starting point changes the calculation. rossum

This is an example of Atheistoclast’s complete ignorance of the field; he has been faking it right along. Anybody who can’t understand initial and boundary conditions in any kind of physical phenomena has not had an education in even the most elementary aspects of the subject. Not getting the point of reproducing populations is just plain jaw-droppingly stupid.

Well it's not like you didn't try to explain it to him before. It's not like he didn't have the opportunity to learn. He simply declined. Now why do I get the feeling that the reception of his new "paper" is going to receive the same sort of reception?

If you want to read my paper, I can send you an advance copy. It is going to cause a lot of commotion. It marks the beginning of the end for evo-devo and the birth of a new approach.

I mean, really, if your latest inane paper really is going to "shake things up," how come you can not bring yourself to name which "doubters of Darwinism" you've been able to convert to Creationism?

If I didn't know better, I'd suspect you're just making a childish boast in a pitiful attempt to wow and taunt us into worshiping you.

Atheistoclast said: It is going to cause a lot of commotion. It marks the beginning of the end for evo-devo and the birth of a new approach.

Atheistoclast said: But the fact remains that only an infinitesimally small number of character combinations produce viable and functional peptide sequences....

Atheistoclast said:

DS said: I told you he didn't get it. I told you he couldn't get it. I told you he won't get it. Same thing will happen with his rejection letter.

And, yet, you can't seem to explain why having a reproducing population makes a virtually impossible search a probable one.

Atheistoclast said: It is going to cause a lot of commotion. It marks the beginning of the end for evo-devo and the birth of a new approach.

Arthur Hunt said: This statement was wrong the first time it was made, and it is still wrong. Heck, it's pretty easy to find for oneself that functionality is relatively common in sequence space. I guess the indifference to the evidence that refutes the claim means that I can claim victory.

Mike Elzinga said: (snip) In order to adequately sample a function, it is necessary to sample at a frequency (temporal or spatial) that is at least twice the highest frequency in the function being sampled. If that is not done, the result is called “aliasing” which means that the frequencies in the Fourier transform of the function get mixed and “folded together.” (snip)

fnxtr said:

Mike Elzinga said: (snip) In order to adequately sample a function, it is necessary to sample at a frequency (temporal or spatial) that is at least twice the highest frequency in the function being sampled. If that is not done, the result is called “aliasing” which means that the frequencies in the Fourier transform of the function get mixed and “folded together.” (snip)

Hence 44.1 KHz.

mplavcan said:

Atheistoclast said: It is going to cause a lot of commotion. It marks the beginning of the end for evo-devo and the birth of a new approach.

We would love to see the reviews, if it gets that far.

Atheistoliar said: Well, I'm basically saying that evo-devo is a big hoax...and I have the evidence to back this assertion up.

Atheistoclast said: You are still making no sense. Reproduction just means you can have another go with the search. It doesn't magically make the search any easier.

rossum said:

Atheistoclast said: You are still making no sense. Reproduction just means you can have another go with the search. It doesn't magically make the search any easier.

Consider the statement: "I am a 15 minutes walk from Central Park, New York." Now calculate the probabilities of that statement being true under two different starting conditions: 1. My current location is a randomly selected point on the surface of the Earth. 2. My current location is a randomly selected point on Manhattan Island. Where you start from can affect the probability of your destination being reachable. Evolution restricts itself to a subset of all possible DNA sequences, sequences that can reproduce. Unless your calculation includes that fact then your calculation is not representative of evolution. GIGO: Garbage In, Garbage Out. rossum

dalehusband said:

Atheistoliar said: Well, I'm basically saying that evo-devo is a big hoax...and I have the evidence to back this assertion up.

Sure, and while you are at it, try proving the Earth is flat too! LOL!

Atheistoclast said: So what you are basically saying is that there is variation in a group. Gee, thanks for telling me this!

They don't make the main task of reaching the target any easier.

I told you he couldn't get it. Rossum even pointed out the exact problem with his calculations and he still doesn't get it. No analogy can penetrate such willful blindness. Give it up already.

As for the abstract being "divinely inspired", I guess the reviewers will have to be divinely inspired as well.

The words just flowed from my brain to the keyboard.

rossum said: Correct. Now you have to make sure that this variation in the group is included in your probability calcualtions. In particular you have to include the limited variability inherent in evolution requiring a reproducing population.

How long does it take to walk from Tierra del Fuego to Central Park? How long does it take to walk from Battery Park to Central Park? Different starting points have an impact on how easy it is to reach a destination. How do you incorporate the effect of the starting point in your calculation?

DS said: I told you he couldn't get it. Rossum even pointed out the exact problem with his calculations and he still doesn't get it. No analogy can penetrate such willful blindness. Give it up already. As for the abstract being "divinely inspired", I guess the reviewers will have to be divinely inspired as well.

Doc Bill said:

The words just flowed from my brain to the keyboard.

The only thing that flows from your head to your keyboard is drool. I do like your style, though, sort of an FL without all the biblical literalism. Ever thought about getting a degree in philosophy of biology? I'm sure Paul Nelson would mentor you.

Joe has it all figured out. He can prove that you definitely can't get from here to there. All he has to do is to not define "here" or "there" and presto!

I'll make one last try on this issue. If Atheistoclast happens not to be persuaded, and goes around saying he's "won", so be it -- you can't persuade every last person on earth.

Calculations of how rare functional sequences are in protein space are mostly irrelevant to the issue of whether evolution can find functional sequences, starting from a previous functional sequence. Dembski's No Free Lunch argument in effect assumes that fitnesses are randomly associated with sequences (that is the kind of fitness surface you get when you average over all the ways a set of fitnesses could be associated with a set of genotypes). In Dembski's model, when you change the base at one particular site in the genome, you arrive at a sequence whose fitness is (in effect) randomly chosen from the fitnesses of all possible genotypes. Mostly that means it's totally non-functional.

This would be a disaster for the ability of natural selection to improve fitness. But note that if you instead change all sites in the genome at the same time, you also get (in the NFL model) a fitness randomly chosen from the fitnesses of all possible genotypes. So if we have that kind of fitness surface, changing the base at one site should be equivalent to changing the bases at all sites. Now obviously, evidently, blatantly we are not in that situation. Changing one base is on average worse, but not nearly as disastrous as changing all of them.

So the fitness surface is not like the the "white noise" fitness surface assumed by NFL, and by Atheistoclast. Functional sequences are near each other in sequence space. There are large "islands" of functional sequences and evolution is often within these islands. The fact that those islands are a small fraction of sequence space (if they are) is irrelevant, as long as you can find functional sequences by moving locally.

This point was made against Dembski's argument by a whole bunch of people starting with Richard Wein and with Jason Rosenhouse in 2002. It is also why Atheistoclast's objection is wrong, and what all the people here have been trying to get across to him.

Joe Felsenstein said: Calculations of how rare functional sequences are in protein space are mostly irrelevant to the issue of whether evolution can find functional sequences, starting from a previous functional sequence.

Dembski's No Free Lunch argument in effect assumes that fitnesses are randomly associated with sequences (that is the kind of fitness surface you get when you average over all the ways a set of fitnesses could be associated with a set of genotypes). In Dembski's model, when you change the base at one particular site in the genome, you arrive at a sequence whose fitness is (in effect) randomly chosen from the fitnesses of all possible genotypes. Mostly that means it's totally non-functional.

This would be a disaster for the ability of natural selection to improve fitness. But note that if you instead change all sites in the genome at the same time, you also get (in the NFL model) a fitness randomly chosen from the fitnesses of all possible genotypes. So if we have that kind of fitness surface, changing the base at one site should be equivalent to changing the bases at all sites. Now obviously, evidently, blatantly we are not in that situation. Changing one base is on average worse, but not nearly as disastrous as changing all of them.

So the fitness surface is not like the the "white noise" fitness surface assumed by NFL, and by Atheistoclast. Functional sequences are near each other in sequence space. There are large "islands" of functional sequences and evolution is often within these islands. The fact that those islands are a small fraction of sequence space (if they are) is irrelevant, as long as you can find functional sequences by moving locally.

This point was made against Dembski's argument by a whole bunch of people starting with Richard Wein and with Jason Rosenhouse in 2002. It is also why Atheistoclast's objection is wrong, and what all the people here have been trying to get across to him.

And there you have it from a real expert. Joe, (the fake Joe), is absolutely wrong. His nonsense was categorically refuted almost ten years ago. He refuses to listen when informed of the facts. He refuses to learn anything at all. He just keep repeating the same old tired nonsense over and over.

Now why do I get the distinct impression that he has done the exact same thing in his "review article"? Why do I get the impression that real reviewers of a real journal will not be so tolerant of his willful ignorance? Why do I get the feeling that no one else will be as patient as the real Joe? Why do I get the feeling that another lawsuit is coming?

Atheistoclast said: No, I don't. Because variation is usually limited to SNP differences.

The evolution of the sequence is about getting all the characters into a specific arrangement.

You can have a near infinite population and it won't really help.

Joe wrote:

"It is my duty to convince you, not the other way round."

Hey, he finally got something right.

rossum wrote:

"You are walking to Central Park from somewhere on Manhattan Island. Calculating as if you could be walking from Tierra del Fuego will give you an incorrect answer."

Yes, but it's even worse than that. All you have to do is walk to some park somewhere. And you don't have to go there directly, you can stop off at a store along the way. And you can make copies of yourself that can also end up in any park anywhere and they can stop off anywhere along the way.

DS said: And there you have it from a real expert. Joe, (the fake Joe), is absolutely wrong. His nonsense was categorically refuted almost ten years ago. He refuses to listen when informed of the facts. He refuses to learn anything at all. He just keep repeating the same old tired nonsense over and over.

Now why do I get the distinct impression that he has done the exact same thing in his "review article"? Why do I get the impression that real reviewers of a real journal will not be so tolerant of his willful ignorance? Why do I get the feeling that no one else will be as patient as the real Joe? Why do I get the feeling that another lawsuit is coming?

Atheistoclast said:

DS said: And there you have it from a real expert. Joe, (the fake Joe), is absolutely wrong. His nonsense was categorically refuted almost ten years ago. He refuses to listen when informed of the facts. He refuses to learn anything at all. He just keep repeating the same old tired nonsense over and over.

Joseph Felsenstein is a real expert - the leading theoretical population geneticist in the world (and perhaps ever according to Professor Paul Harvey of the University of Oxford) - I am not denying that. But he is talking in abstract terms that are divorced from the biochemical reality of which he is unfamiliar. He has recently mentioned something interesting about "islands of functionality" that can be the steps towards the realization of the final product but I have already considered this possibility and it only serves to reduce the sheer improbability but not to eliminate it.

Now why do I get the distinct impression that he has done the exact same thing in his "review article"? Why do I get the impression that real reviewers of a real journal will not be so tolerant of his willful ignorance? Why do I get the feeling that no one else will be as patient as the real Joe? Why do I get the feeling that another lawsuit is coming?

Well, I have published in real journals...you?...no chance.

Atheistoclast said: If you want to read my paper, I can send you an advance copy. postdarwinism@ymail.com It is going to cause a lot of commotion. It marks the beginning of the end for evo-devo and the birth of a new approach.

DS said: Wrong again, on both counts.

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

SWT said:

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

DS, if you want to play this game without outing yourself, send a DOI or citation for one of your publications to me at the email address above and I'll provide an independent verification of the number of publications I see associated with your name in Scopus. I think I know your first and last names; however, I don't know your middle initial so I can't just do a search to get an accurate publication count.

I suspect most people here can see the game that Bozo Joe is playing.

Ever since Henry Morris and Duane Gish formed the Institute for Creation “Research” back in the early 1970s, ID/creationists have always wanted to ride on the coattails of scientists; and if they can do it on the coattails of a Nobel laureate, so much the better. In fact, they have whined that it is not worth their time to “debate” “lesser scientists.”

They did this by taunting until the scientific community caught on. Now they stalk scientists on websites attempting the same thing.

Bozo is engaging in brazen taunting and mumbo-jumbo replies in order to “stay in the game” with scientists as he attempts to set up phony debates to make himself look good.

Just looking at that last reply to Joe Felsenstein shows a perfect example. Bozo has strung together words that make it look like he is arguing knowledgeably. But his replies are the replies of a palm reader or an astrologist.

We have already demonstrated that he can’t even handle the most elementary questions in science, be it biology, chemistry, or physics. Place his comments in that context.

SWT said:

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

DS, if you want to play this game without outing yourself, send a DOI or citation for one of your publications to me at the email address above and I'll provide an independent verification of the number of publications I see associated with your name in Scopus. I think I know your first and last names; however, I don't know your middle initial so I can't just do a search to get an accurate publication count.

DS said: Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

DS said:

SWT said:

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

DS, if you want to play this game without outing yourself, send a DOI or citation for one of your publications to me at the email address above and I'll provide an independent verification of the number of publications I see associated with your name in Scopus. I think I know your first and last names; however, I don't know your middle initial so I can't just do a search to get an accurate publication count.

Thanks SWT. I appreciate it. I really don't see any point in getting into a pissing contest with a willfully ignorant fool. He can either accept that my publication record is vastly superior to his, or he can piss off. I could care less either way. Perhaps he will then learn about evidence and making unwarranted assumptions. Besides, if that is the criteria, then he should STFU and stop dissing Sean Carroll. Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

Atheistoclast said: All I can tell is that you are amateur evo-nut who collects scientific papers, reads only the abstracts, and thinks he knows something about the subject. You don't come across as being a published author.

Atheistoclast said:

DS said:

SWT said:

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

DS, if you want to play this game without outing yourself, send a DOI or citation for one of your publications to me at the email address above and I'll provide an independent verification of the number of publications I see associated with your name in Scopus. I think I know your first and last names; however, I don't know your middle initial so I can't just do a search to get an accurate publication count.

Thanks SWT. I appreciate it. I really don't see any point in getting into a pissing contest with a willfully ignorant fool. He can either accept that my publication record is vastly superior to his, or he can piss off. I could care less either way. Perhaps he will then learn about evidence and making unwarranted assumptions. Besides, if that is the criteria, then he should STFU and stop dissing Sean Carroll. Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

Well, what is your field? Where did you graduate from? Do you have your own lab? At which university or institute? All I can tell is that you are amateur evo-nut who collects scientific papers, reads only the abstracts, and thinks he knows something about the subject. You don't come across as being a published author.

DS said:

Atheistoclast said:

DS said:

SWT said:

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

DS, if you want to play this game without outing yourself, send a DOI or citation for one of your publications to me at the email address above and I'll provide an independent verification of the number of publications I see associated with your name in Scopus. I think I know your first and last names; however, I don't know your middle initial so I can't just do a search to get an accurate publication count.

Thanks SWT. I appreciate it. I really don't see any point in getting into a pissing contest with a willfully ignorant fool. He can either accept that my publication record is vastly superior to his, or he can piss off. I could care less either way. Perhaps he will then learn about evidence and making unwarranted assumptions. Besides, if that is the criteria, then he should STFU and stop dissing Sean Carroll. Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

Well, what is your field? Where did you graduate from? Do you have your own lab? At which university or institute? All I can tell is that you are amateur evo-nut who collects scientific papers, reads only the abstracts, and thinks he knows something about the subject. You don't come across as being a published author.

Guess.

Atheistoclast said: All I can tell is that you are amateur evo-nut who collects scientific papers, reads only the abstracts, and thinks he knows something about the subject. You don't come across as being a published author.

Atheistoclast said:

DS said:

Atheistoclast said:

DS said:

SWT said:

Atheistoclast said:

DS said: Wrong again, on both counts.

Really? Well, let's see what you have got published. Post the links here or forever be mute.

DS, if you want to play this game without outing yourself, send a DOI or citation for one of your publications to me at the email address above and I'll provide an independent verification of the number of publications I see associated with your name in Scopus. I think I know your first and last names; however, I don't know your middle initial so I can't just do a search to get an accurate publication count.

Thanks SWT. I appreciate it. I really don't see any point in getting into a pissing contest with a willfully ignorant fool. He can either accept that my publication record is vastly superior to his, or he can piss off. I could care less either way. Perhaps he will then learn about evidence and making unwarranted assumptions. Besides, if that is the criteria, then he should STFU and stop dissing Sean Carroll. Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

Well, what is your field? Where did you graduate from? Do you have your own lab? At which university or institute? All I can tell is that you are amateur evo-nut who collects scientific papers, reads only the abstracts, and thinks he knows something about the subject. You don't come across as being a published author.

Guess.

I suspect it is bioinformatics....something like that. Or perhaps the philosophy of biology? You are certainly no technical research scientist. I can tell that much easily.

Mike Elzinga said:

DS said: Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

Bozo is also trying to subtly extract personal information from people here. It seems that all these creationists attempt this at some point in their taunting.

prongs said:

Mike Elzinga said:

DS said: Every time this asshat lose an argument he starts hurling insults and trying to get people into pissing contests. Who cares? He lost, that's enough.

Bozo is also trying to subtly extract personal information from people here. It seems that all these creationists attempt this at some point in their taunting.

Bozorgmehr, Mike, Bozorgmehr. My Bozo ancestors take offense.

Looks like Clastie is still pushing the idiotic strawman that evolution is contingent on inventing vast stretches of new, complex biochemistry and protein-sequence.
Hey Clasti, looks like you missed this paper: http://pandasthumb.org/archives/2011/04/the-true-story.html

Turns out most of what has been going on in the evolution of new multicelluclar species(like from ape to man) is a combination of HGT, Recombination and gene-duplication. It certainly wasn't contingent on inventing entirely novel, 300 AA stretches of protein polymer or anything like that.

Another fact you neglect to consider in your mindless assertion that sequence space is vast, with isolated islands of function, is that the environment determines the shape of the landscape. And in fact, that part of this environment, is often other sequences.

What may be a stretch of nonfunctionality now in a cold environment, may be be an adaptive valley or even steep slope for selection to climb in a hotter environment. And then there's the fact that vast amounts of sequence is simply "binding material" where one stretch of polymer sticks to another. Mutating one may break or degrade the binding site, mutating the target site may reenable it.(Which is what happens in the evolution of antibody targeting) The possibilities are endless.

You're trying to speak authoritively on matters you don't have a clue about. You don't know the shape of the fitness landscape, you never did any research to find out. And you certainly don't know how it looked in the ~4 billion year past history of life. All you are offering here is blind assertion: Hey look, if this enzyme mutates in these 3-6 specific sites, it stops working: Therefore evolution is false. Hah!

ROFL.

And please don't come back crying that I'm arguing the evolution of multicellular life is contingent on HGT. In that case, it would be mostly recombination, duplication and drift.

And by the way, Clastie, how come when I beat you about the head with that paper over on talkrational, you suddenly retracted your entire "evolution can't happen because enzymes can't chane into each other"-line of argument and instead started whining about how life started to begin with?

Looks like you are knowingly pushing a strawman here, then. That's a bit dishonest, I would say.

He cites the writings of others but avoids any attempt to put together a coherent thought of his own.

Rumraket said: And by the way, Clastie, how come when I beat you about the head with that paper over on talkrational, you suddenly retracted your entire "evolution can't happen because enzymes can't chane into each other"-line of argument and instead started whining about how life started to begin with? Looks like you are knowingly pushing a strawman here, then. That's a bit dishonest, I would say.

Rumraket said: Turns out most of what has been going on in the evolution of new multicelluclar species(like from ape to man) is a combination of HGT, Recombination and gene-duplication. It certainly wasn't contingent on inventing entirely novel, 300 AA stretches of protein polymer or anything like that.

Atheistoclast said: Sorry, but evolutionist have failed to present a tree showing the common descent of all genes from a single ancestor. They admit that most gene types have "independently evolved". There is no homology, in either sequence or function, between most different classes of protein. Dyneins come from Mars, cyclins come from Venus.

Atheistoclast said:

Rumraket said: Turns out most of what has been going on in the evolution of new multicelluclar species(like from ape to man) is a combination of HGT, Recombination and gene-duplication. It certainly wasn't contingent on inventing entirely novel, 300 AA stretches of protein polymer or anything like that.

Sorry, but evolutionist have failed to present a tree showing the common descent of all genes from a single ancestor. They admit that most gene types have "independently evolved". There is no homology, in either sequence or function, between most different classes of protein. Dyneins come from Mars, cyclins come from Venus.

And even if we were to agree that we don't know how gene-families with zero structural or sequence-homology ultimately originated, your knee-jerk response is just goddidit, right? Never mind the complete lack of evidence for that. We don't know how, and it's really improbable, therefore god. Well trolled clastie.

Atheistoclast said:

Joe Felsenstein said: Calculations of how rare functional sequences are in protein space are mostly irrelevant to the issue of whether evolution can find functional sequences, starting from a previous functional sequence.

That would depend on how much homology exists between the previous sequence and that which proceeds from it. If there is very little, both in terms of sequence and function, you have a big problem because there isn't a smooth "fitness landscape" or wide "adaptive valley" that could provide such a solution.

Matt G said:

stevaroni said:

dalehusband said: If you don't know the difference between improbable and impossible, you disqualify yourself from any further discussion of either evolution or abiogenesis.

Michael Behe had the same problem. One of the highlights of the Dover trial was when Behe took the stand to defend his "this mutation is way to improbable to ever happen" argument. The opposing council made him methodically work out the actual probability and it turns out that, given the just number of cells presently inside the courtroom making up the participants, this particular mutation was happening on average every hour and a half. The odds of dealing a Royal Flush are 311 million to one. Nonetheless, I would hazard a guess that one got dealt somewhere on Earth today.

And for those interested in small, incremental changes in evolution, and those interested in how an organism can see without having eyes, an article from Science Daily (original article in PNAS): http://www.sciencedaily.com/releases/2011/06/110630111538.htm

Joe Felsenstein said: This is the closest we will see to Atheistoclast saying "oops, I guess I was wrong about that!" He was assuming that rarity of functional sequences (in sequence space) meant that mutations would not come up with functional sequences. Now he qualifies this by saying that there is a problem "if there is very little [homology]" between the original sequences and the mutants. For point mutation there is lots of homology between the mutant and the original sequence as typically only one site has changed. So the fitness surfaces have ample opportunity to be smooth which means Atheistoclast was wrong to take supposed rarity of functional sequences as evidence that mutation could not find functional sequences.

Translation: am not , am not.

Rumraket said: And by the way, Clastie, how come when I beat you about the head with that paper over on talkrational, you suddenly retracted your entire "evolution can't happen because enzymes can't chane into each other"-line of argument and instead started whining about how life started to begin with? Looks like you are knowingly pushing a strawman here, then. That's a bit dishonest, I would say.

Henry said: It looks like a pretty good design--they were made that way.

Atheistoclast said: Really, Prof. Felsenstein? I think not. We're not talking about single nucleotide adaptations. We are talking about the generation of any functional coded elements within sequence motifs. If we are using artificial selection, any sequence homology makes things a lot easier because you can select for each nucleotide. But natural selection doesn't work that way, Joe. Even if there is a lot of sequence homology, this can still be functionally useless.For example, if the third letters of each codon are the same between any two sequences then this doesn't help us as amino acids tend to be specified by the first two base pairs. You need to consider the particular context in question.

Atheistoclast | September 11, 2011 4:42 PM | Reply | Edit At a mathematical level, let’s say we have a protein motif that is 60 character long: There are exactly 1.15292 * 10^78 ways of constructing a sequence of this length using all proteinogenic 20 amino acids. The vast vast majority will be non-viable as polypeptides. Only an infinitesimally small number of combinations will prove to be functional. That is the basic problem facing Felsenstein et al. Can natural selection filter out a speck of gold from a mountain of manure? That is the million dollar question. I think the chances are virtually zero. But that’s just me.

Joe Felsenstein said: It was the million dollar question, according to Atheistoclast (back then). Sadly, he lost the million dollars, as I explained above. So now, suddenly, the question isn't rarity of functional polypeptides in sequence space. Suddenly it's generation of new functions. But that was not the point under discussion. It was finding functional sequences, whether new function or not. Sorry, no million dollars today.

Atheistoclast said:

Joe Felsenstein said: It was the million dollar question, according to Atheistoclast (back then). Sadly, he lost the million dollars, as I explained above. So now, suddenly, the question isn't rarity of functional polypeptides in sequence space. Suddenly it's generation of new functions. But that was not the point under discussion. It was finding functional sequences, whether new function or not. Sorry, no million dollars today.

Well, Joseph, that is what we are trying to find out. How do new functions and new protein motifs arise as opposed to old ones. It is the question that the DI repeatedly asks you. A homeobox and a cyclin box are two distinct protein motifs. They share no relationship with each other whatsoever. However, this doesn't preclude the possibility, at least, that some new stuff may contain functional elements from older stuff (composite sequences), but we still require new peptide arrangements of adaptive function. You know, Joe, your knowledge of the math involved is way superior to everyone here combined - probably a million times over. Science is about quantifying what you observe and theorize - you know as much as that is what you do as a scientist. Can you produce an equation that clearly shows how your evolutionary method for the generation of novel sequence motifs works in practice, rather than just say how it might work? That would convince me and a lot of other folks. Honest.

DS said:

Atheistoclast said:

Joe Felsenstein said: It was the million dollar question, according to Atheistoclast (back then). Sadly, he lost the million dollars, as I explained above. So now, suddenly, the question isn't rarity of functional polypeptides in sequence space. Suddenly it's generation of new functions. But that was not the point under discussion. It was finding functional sequences, whether new function or not. Sorry, no million dollars today.

Well, Joseph, that is what we are trying to find out. How do new functions and new protein motifs arise as opposed to old ones. It is the question that the DI repeatedly asks you. A homeobox and a cyclin box are two distinct protein motifs. They share no relationship with each other whatsoever. However, this doesn't preclude the possibility, at least, that some new stuff may contain functional elements from older stuff (composite sequences), but we still require new peptide arrangements of adaptive function. You know, Joe, your knowledge of the math involved is way superior to everyone here combined - probably a million times over. Science is about quantifying what you observe and theorize - you know as much as that is what you do as a scientist. Can you produce an equation that clearly shows how your evolutionary method for the generation of novel sequence motifs works in practice, rather than just say how it might work? That would convince me and a lot of other folks. Honest.

I already provided you with the calculation. Did you find the reference yet?

Atheistoclast said:

Joe Felsenstein said: It was the million dollar question, according to Atheistoclast (back then). Sadly, he lost the million dollars, as I explained above. So now, suddenly, the question isn't rarity of functional polypeptides in sequence space. Suddenly it's generation of new functions. But that was not the point under discussion. It was finding functional sequences, whether new function or not. Sorry, no million dollars today.

Well, Joseph, that is what we are trying to find out. How do new functions and new protein motifs arise as opposed to old ones. It is the question that the DI repeatedly asks you.

Atheistoclast said: I asked Dr. Felsenstein, not some math amateur like yourself.

Joe Felsenstein said: Atheistoclast is wrong again, and that can be seen -- I quoted the comment of his that we were all responding to, and it was not about "new functions and new protein domains". It was about rarity of functional (both new and old) sequences in sequence space, and whether this proved that mutation and selection could not improve species.

Atheistoclast is simply unable to say, on any issue "gee, I guess I was wrong about that". I say it all the time -- there is at least one mistake in each paper I have written, and many of those get retracted in subsequent papers. But Atheistoclast just tries to divert our attention to some new topic and/or redefine some word.

Atheistoclast said: I asked Dr. Felsenstein, not some math amateur like yourself.

Atheistoclast said: Of the 3 papers I have written, not one technical erratum can be found. If you can find one, please write a letter to the editor and I will respond in kind. If not, then please retract your undeserved comment about there being mistakes.

Joe Felsenstein said:

Atheistoclast said: Of the 3 papers I have written, not one technical erratum can be found. If you can find one, please write a letter to the editor and I will respond in kind. If not, then please retract your undeserved comment about there being mistakes.

How naive does Atheistoclast take us to be? I made it clear: I assert error in the argument he made here and have documented (a) what his argument was and (b) what his error was. Did I ever assert any errors in his papers? (No, I asserted that there were errors in my papers). Atheistoclast will say almost anything, apparently, to avoid having to say "gee, I guess I was wrong about that".

Joe Felsenstein said: Atheistoclast is simply unable to say, on any issue "gee, I guess I was wrong about that".

phhht said: However, if your basis of truth is faith, then the concession of error in any regard undermines the entire basis of knowledge.

Atheistoclast said: Let me repeat for the benefit of everybody. There is scope for "pockets of functionality" within seemingly irreducibly complex gene sequences. But these functional blocks themselves will consist of multi-codon elements AND they must synergistically interact with each other to produce the final and complete function. Any sequence homology may or may not prove useful as there is no clear correlation between sequence idenity and function. While a divide and conquer strategy and approach to the evolution of motif sequences may reduce the problem somewhat, it does not eliminate it by any means. There is still a quintessentially rough fitness landscape that must be overcome. Unfortunately, Professor Felsenstein has yet to author a peer-reviewed paper that adequately deals with this. Perhaps it is now time he did. If not, I will just have to fill the void for him.

Joe Felsenstein said:

phhht said: However, if your basis of truth is faith, then the concession of error in any regard undermines the entire basis of knowledge.

Actually, what is at stake is much less than that. Any religious person could, in principle, concede that a particular argument they made in support of their faith was wrong. It would not undermine their overall belief system. They would just be saying "well, I guess that argument is not convincing, but I have other arguments". However, for some folks it doesn't seem to work that way.

Atheistoclast said:

Joe Felsenstein said:

phhht said: However, if your basis of truth is faith, then the concession of error in any regard undermines the entire basis of knowledge.

Actually, what is at stake is much less than that. Any religious person could, in principle, concede that a particular argument they made in support of their faith was wrong. It would not undermine their overall belief system. They would just be saying "well, I guess that argument is not convincing, but I have other arguments". However, for some folks it doesn't seem to work that way.

In this argument, Joe, I am not arguing from a religious viewpoint. I am arguing from a purely scientific one. I don't see how a blind and open search algorithm can generate a specific motif sequence conferring biochemical functionality. If it could be demonstrated that it does, I would accept it. Many non-Darwinian biologists would agree with me on this point even if they are non-religious or even anti-religious. The fact that the information encoded in DNA does appear to require a teleological explanation...well...that leads to a particular conclusion. It is indeed attractive to suppose that natural selection, a blind and unconscious process, could produce such amazing complexity - but then so is much in the world of science fiction. Let's stick to the hard facts.

Atheistoclast said: In this argument, Joe, I am not arguing from a religious viewpoint. I am arguing from a purely scientific one.

I don’t see how a blind and open search algorithm can generate a specific motif sequence conferring biochemical functionality.

If it could be demonstrated that it does, I would accept it.

Many non-Darwinian biologists would agree with me on this point even if they are non-religious or even anti-religious.

The fact that the information encoded in DNA does appear to require a teleological explanation…well…that leads to a particular conclusion.

It is indeed attractive to suppose that natural selection, a blind and unconscious process, could produce such amazing complexity - but then so is much in the world of science fiction.

Not only has de novo gene origination been documented in flies, it has been documented in humans as well. It has also been documented in yeast, in a paper we discussed here three years ago. Apparently Joe didn't get the memo. Maybe he will next provide the equation proving that bumble bees can't fly, but only if it is written by a real expert in theoretical insect aerodynamics.

DS said:

Atheistoclast said:

Joe Felsenstein said:

phhht said: However, if your basis of truth is faith, then the concession of error in any regard undermines the entire basis of knowledge.

Actually, what is at stake is much less than that. Any religious person could, in principle, concede that a particular argument they made in support of their faith was wrong. It would not undermine their overall belief system. They would just be saying "well, I guess that argument is not convincing, but I have other arguments". However, for some folks it doesn't seem to work that way.

In this argument, Joe, I am not arguing from a religious viewpoint. I am arguing from a purely scientific one. I don't see how a blind and open search algorithm can generate a specific motif sequence conferring biochemical functionality. If it could be demonstrated that it does, I would accept it. Many non-Darwinian biologists would agree with me on this point even if they are non-religious or even anti-religious. The fact that the information encoded in DNA does appear to require a teleological explanation...well...that leads to a particular conclusion. It is indeed attractive to suppose that natural selection, a blind and unconscious process, could produce such amazing complexity - but then so is much in the world of science fiction. Let's stick to the hard facts.

It has been demonstrated. Accept it.

DS said: Not only has de novo gene origination been documented in flies, it has been documented in humans as well. It has also been documented in yeast, in a paper we discussed here three years ago. Apparently Joe didn't get the memo. Maybe he will next provide the equation proving that bumble bees can't fly, but only if it is written by a real expert in theoretical insect aerodynamics.

Atheistoclast said: I didn't see a fancy equation that explains how natural selection can create genetic information - one through which we can make scientific predictions.

Atheistoclast said: Where did Joe Felsenstein demonstrate anything on this forum? I didn't see a fancy equation that explains how natural selection can create genetic information - one through which we can make scientific predictions. All the great professor of genomics has ever talked about his how natural selection reduces genetic variation. And that, my friend, is all that natural selection can possibly do.

Atheistoclast said:

DS said: Not only has de novo gene origination been documented in flies, it has been documented in humans as well. It has also been documented in yeast, in a paper we discussed here three years ago. Apparently Joe didn't get the memo. Maybe he will next provide the equation proving that bumble bees can't fly, but only if it is written by a real expert in theoretical insect aerodynamics.

Nonsense. Some researchers have alleged that an entire reading frame can be just recruited from non-coding DNA - almost magically - but all the papers I have read on this subject are really pseudogenes that have been reactivated or genes that have been deactivated in all lineages but one, hence they look like they are novel. In reality, de novo recruitment is limited to the exonization of very small bits, such as the the 20 or so codons at the N-terminus of the Sdic gene. You really need to read my papers.

DS said: Joe did not demonstrate this. He simply noted that you moved the goalposts and then gave up on you and your whining. I told you that there was empirical evidence for this, look it up for yourseef and stop your whining.

DS said:

Atheistoclast said: Where did Joe Felsenstein demonstrate anything on this forum? I didn't see a fancy equation that explains how natural selection can create genetic information - one through which we can make scientific predictions. All the great professor of genomics has ever talked about his how natural selection reduces genetic variation. And that, my friend, is all that natural selection can possibly do.

Joe did not demonstrate this. He simply noted that you moved the goalposts and then gave up on you and your whining. I told you that there was empirical evidence for this, look it up for yourseef and stop your whining.

Atheistoclast said: No he didn't. I asked from the outset where new protein motifs came from. It is something which evolutionists have so far been unable to explain. All we get from the likes of Felsenstein is same old evo-babble and nothing of any rigor. You'd expect more from a scientist who has been studying evolutionary theory for over 40 years. People like yourself, DS, exhibit only the most superficial understanding of the science involved.

DS said:

Atheistoclast said: No he didn't. I asked from the outset where new protein motifs came from. It is something which evolutionists have so far been unable to explain. All we get from the likes of Felsenstein is same old evo-babble and nothing of any rigor. You'd expect more from a scientist who has been studying evolutionary theory for over 40 years. People like yourself, DS, exhibit only the most superficial understanding of the science involved.

Really? That's why I'm familiar with the literature and you aren't? But more importantly, you are not willing to be educated. None of this bullshit has anything whatsoever to do with the topic of this thread. Any further response to you by me will be on the bathroom wall. As usual, you have worn out your welcome once again. Now you are reduced to insults, since, as usual, you were wrong and refuse to admit it.

Atheistoclast lying again: No, you are not. You read the titles and abstracts of papers that is about it. You never question the methods and conclusions of the authors because you have no discerning ability whatsoever. You are neither a scientist nor an intellectual. Felsenstein tried but miserably failed to suggest that somehow random mutations and natural selection can explain the origination of extremely improbable and highly specific sequence motifs. He provided nothing substantive other than there may be functional bits within sequence space. There is nothing rigorous about this. He doesn't say how these "islands of functionality" syngeristically group together to form an archipelago. He has had 40 years to think about this but nothing has emerged. The game is up for Darwinism. It is time for regime change and paradigm shift.

Atheistoclast said: The game is up for Darwinism. It is time for regime change and paradigm shift.

Atheistoclast said:

DS said: Joe did not demonstrate this. He simply noted that you moved the goalposts and then gave up on you and your whining. I told you that there was empirical evidence for this, look it up for yourseef and stop your whining.

No he didn't. I asked from the outset where new protein motifs came from.

The game is up for Darwinism. It is time for regime change and paradigm shift.

Atheistoclast said: The game is up for Darwinism. It is time for regime change and paradigm shift.

Joe Felsenstein said: Oh, really? So the different question that you declared to be the "million dollar question" wasn't?

You asked that other question, and got hammered, and you still won't admit that.

[Yawn].

Let me just explain by illustration:

Joe Felsenstein thinks that a motif sequence can be broken down in functional elements. I don't dispute that this may be so. Let us look at the consensus sequence for the homebox. Let us now assume he is right by diving the 60 character sequence into 10 blocks, each consisting of just 6 residues.

RRRKRT-AYTRYQ-LLELEK-EFLFNR-YLTRRR-RIELAH-SLNLTE-RHIKIW-FQNRRM-KWKKEN

OK. All we need to do is evolve each element independently, assuming they are functional by themselves, and just hope they combine with each other to form the helix-turn-helix structure. There is no doubt that this helps reduce the issue of extreme improbability identified by Dembski, but it does not eliminate it. We need 20^6 (64 million) rounds of mutation to produce just one element. And,as we have had to partition the sequence by a factor of 10, the mutations are going to be spread over the whole sequence and so it will take 10 times as many rounds at least.

Ahteistoclast has chugalugged the Cool Aid.

The latest four-part video by Mike Riddle over on AiG is clear evidence that the ID/creationists are just doubling down on their lies.

I would a least give Riddle the credit for stating those lies in a very clear manner. If one suppresses the gag reflex and goes through that sequence of videos, it is a pretty clear outline of all the major misconceptions and misrepresentations that are the core of ID/creationism.

I know I keep beating on this, but Riddle inevitably plunges into the second law of thermodynamics and Henry Morris’s original construction of a fake conflict between evolution and the second law.

From that follows the misrepresentation of “information” as something placed in DNA to build a “program” for “capturing energy” and “directing” that energy into the construction of living organisms.

It is an understatement to say that Riddle’s ID/creationist scenario is wrong. It is a grotesque mischaracterization of physics, chemistry, and biology.

It is vitalism at its worst. At least the 18th and 19th century vitalists had better reasons in their day for what they thought. But they were, and still are, wrong.

I don’t think Bozo Joe here has the educational background to figure it out.

I told you he would never learn. Joe has been told repeatedly, by several posters over a long period of time, that sequences do NOT arise from nothing. He refuses to accept this basic fact, relying instead on calculations for the "poof" hypothesis. Too bad for him that we know where hox genes came from. They evolved from simpler NK genes found in the ancestral lineage leading to animals. I can provide references, but Joe will just say that the authors are wrong and that he n=knows better than they do. He has used this ploy dozens of times now. You would think that at some point he might consider the possibility that someone somewhere might know a little bit more than he does. At the very least, he should feel shame at once again being completely ignorant of the literature.

I have no idea why the real Joe continues to allow the fake Joe to abuse this thread with his own brand of misguided ignorance. It should be obvious by ow that he is incapable of learning anything, or of ever admitting to a mistake, even those that are still there for all to see.

Atheistoclast said:

harold said: The logical thing for you to do is to present me with a testable explanation of “design” by a “designer”, and the evidence that supports it. Not false analogies, not mere use of words like “nano-machine”, certainly not arguments against evolution - a mechanism and positive evidence for “design”.

Read the works of Dembski and Meyer. They have provided clear methods for inferring design from non-design. If you can't be bothered to understand them, then that is your problem. They are very similar to the techniques that SETI use.

Now get started with some positive evidence for “design”.

Start with the genetic code. It is the foundation of molecular biology and also the best evidence for design in Nature because, among other things, it is extremely improbable (there are 1.51*10^84 possible ways of mapping 64 codons to 20 amino acids and a stop site), extremely fault-tolerant and extremely elegant.

dornier.pfeil said: Atheistoclast, You think very highly of your ID mathematics. So put it to work and show us something. WNGVM NVVNW NNSVN VNNVW NYNLV VAHHK PQPSF SPLPC VCCDP ASGGV VNKKF PTTNF TTKSV RWDTV GEEAK WGEGW PLEDS SHKGS SIIGE TAKSG WFWSW RITFQ NCTGS CVAHD RSTCS EIMPF FLKCD RCFFY ALHCW HAKLQ AQLDD DTKSN LFFLF GSWFE WGEWT PNLLS QMRDK CSIAS EMELR HWQSG VEDTS ALSAL YLGKL EGGFH LKPVF LRLKV DDDYE ELANH GRYSI PDIGH FLIGP CKGVT KTWEV TLVFN ESLHF AEAQD ATNVN LAAVS QVKPL TFACV Some of those letter strings represent real proteins. Some of them are just random strings of letters. I am not going to tell you how many there are of either or even ask you to tell which is which. I just want to know what your ID math has to say about ANY of them. For instance, how much CSI do they all have?

This is not exactly the test I wanted to make, but I thought of a diagram I want to prepare for Arthuriandaily that will take a day or so to make so I dashed this out as a cheap substitute.

DS said: I told you he would never learn. Joe has been told repeatedly, by several posters over a long period of time, that sequences do NOT arise from nothing.

Atheistoclast said: That is just not going to happen.

Atheistoclast said: Let me just explain by illustration: Joe Felsenstein thinks that a motif sequence can be broken down in functional elements. I don't dispute that this may be so. Let us look at the consensus sequence for the homebox. Let us now assume he is right by diving the 60 character sequence into 10 blocks, each consisting of just 6 residues. RRRKRT-AYTRYQ-LLELEK-EFLFNR-YLTRRR-RIELAH-SLNLTE-RHIKIW-FQNRRM-KWKKEN OK. All we need to do is evolve each element independently, assuming they are functional by themselves, and just hope they combine with each other to form the helix-turn-helix structure. There is no doubt that this helps reduce the issue of extreme improbability identified by Dembski, but it does not eliminate it. We need 20^6 (64 million) rounds of mutation to produce just one element. And,as we have had to partition the sequence by a factor of 10, the mutations are going to be spread over the whole sequence and so it will take 10 times as many rounds at least.

rossum said:

Atheistoclast said: Let me just explain by illustration: Joe Felsenstein thinks that a motif sequence can be broken down in functional elements. I don't dispute that this may be so. Let us look at the consensus sequence for the homebox. Let us now assume he is right by diving the 60 character sequence into 10 blocks, each consisting of just 6 residues. RRRKRT-AYTRYQ-LLELEK-EFLFNR-YLTRRR-RIELAH-SLNLTE-RHIKIW-FQNRRM-KWKKEN OK. All we need to do is evolve each element independently, assuming they are functional by themselves, and just hope they combine with each other to form the helix-turn-helix structure. There is no doubt that this helps reduce the issue of extreme improbability identified by Dembski, but it does not eliminate it. We need 20^6 (64 million) rounds of mutation to produce just one element. And,as we have had to partition the sequence by a factor of 10, the mutations are going to be spread over the whole sequence and so it will take 10 times as many rounds at least.

Look at the first element: RRRKRT. We know that element works in that position. How many other possible elements could also work well enough in that position? Would RRRLRT be effective enough for the organism carrying it to be able to survive long enough to reproduce? We know that there is at least one functional target. Until you know the total number of possible functional targets then you will not be able to do any accurate calculations on the likelihood of hitting one of the possible targets. Yockey (1992) calculated that there were 2.3 x 10^93 different ways to make a working Cytochrome C. A number like 2.3 x 10^93 can make a very big difference to the result of a calculation. I am sure you would criticise any scientist who was incorrect by such a large factor. rossum

DS said: The whole thing is one big smoke screen, Joe just isn't man enough to admit his errors and misrepresentations.

rossum said: Look at the first element: RRRKRT. We know that element works in that position. How many other possible elements could also work well enough in that position? Would RRRLRT be effective enough for the organism carrying it to be able to survive long enough to reproduce?,/blockquote. Well, we know that variations in important motifs are possible and so you may not have to get exactly the specific target - but you do have to get very close to it for it to be functional. RRRLRT might be ok, but not RRLLRT.

We know that there is at least one functional target. Until you know the total number of possible functional targets then you will not be able to do any accurate calculations on the likelihood of hitting one of the possible targets.

Well, in a multifunctional target motif there may be many sub-targets.

Yockey (1992) calculated that there were 2.3 x 10^93 different ways to make a working Cytochrome C. A number like 2.3 x 10^93 can make a very big difference to the result of a calculation. I am sure you would criticise any scientist who was incorrect by such a large factor.rossum

Well, I suspect their assertion is ulitmately untestable. WE know that CYTC is still a conserved protein, so this kind of undermines what they are saying. About half of its residues are conserved among all taxa. In any case, I am referring to highly specific domains like the homeobox - the scope for variation in it is greatly limited.

Atheistoclast said: In any case, I am referring to highly specific domains like the homeobox - the scope for variation in it is greatly limited.

rossum said:

Atheistoclast said: In any case, I am referring to highly specific domains like the homeobox - the scope for variation in it is greatly limited.

How limited? What are the number of possible variations? What is the impact of that number on the calculations in your papers? Without knowing the number of allowed variations we cannot tell how accurate are the numbers you have shown us up to now. How can anyone be sure that you are not in error by 93 orders of magnitude? rossum

rossum said:

Atheistoclast said: In any case, I am referring to highly specific domains like the homeobox - the scope for variation in it is greatly limited.

How limited? What are the number of possible variations? What is the impact of that number on the calculations in your papers? Without knowing the number of allowed variations we cannot tell how accurate are the numbers you have shown us up to now. How can anyone be sure that you are not in error by 93 orders of magnitude? rossum

Let us also do one more calculation.

Suppose that in the 60 residue homeobox motif, each amino acid can be replaced by just one other. That means that the probability of chancing upon it is the inverse of (20/2)^60 or 1*10^60.

Let us suppose that each residue can be replaced by as many as 4 other amino acids. This means that the probability now becomes the inverse of (20/4)^60 or 8.67*10^41.

So we now manage to reduce some of the improbability, but not to the extent where it helps the Darwinist. Sorry. Just accept that the math is against you.

Atheistoclast said: OK, let us say for the sake of argument that 50% of the 60 residues in the homeobox motif can be replaced with any other amino acid. This is not true, but let us countenance the idea all the same. That leaves 30 residues which cannot be changed. As such, the probability of reaching the target is reduced from the inverse of 20^60 (1.15*10^78) to the inverse of 20^30 (1.073*10^39). That is a difference of 39 orders of magnitude. But does it really help? We still have a greatly improbable feat which, for all intents and purposes, is impossible. Let us also do one more calculation. Suppose that in the 60 residue homeobox motif, each amino acid can be replaced by just one other. That means that the probability of chancing upon it is the inverse of (20/2)^60 or 1*10^60. Let us suppose that each residue can be replaced by as many as 4 other amino acids. This means that the probability now becomes the inverse of (20/4)^60 or 8.67*10^41. So we now manage to reduce some of the improbability, but not to the extent where it helps the Darwinist. Sorry. Just accept that the math is against you.

dalehusband said:

Atheistoclast said: OK, let us say for the sake of argument that 50% of the 60 residues in the homeobox motif can be replaced with any other amino acid. This is not true, but let us countenance the idea all the same. That leaves 30 residues which cannot be changed. As such, the probability of reaching the target is reduced from the inverse of 20^60 (1.15*10^78) to the inverse of 20^30 (1.073*10^39). That is a difference of 39 orders of magnitude. But does it really help? We still have a greatly improbable feat which, for all intents and purposes, is impossible. Let us also do one more calculation. Suppose that in the 60 residue homeobox motif, each amino acid can be replaced by just one other. That means that the probability of chancing upon it is the inverse of (20/2)^60 or 1*10^60. Let us suppose that each residue can be replaced by as many as 4 other amino acids. This means that the probability now becomes the inverse of (20/4)^60 or 8.67*10^41. So we now manage to reduce some of the improbability, but not to the extent where it helps the Darwinist. Sorry. Just accept that the math is against you.

Your comments keep getting dumber, Atheistofraud. You only show why most mutations of the homeobox genes are harmful, which would be one explanation of why miscarriages happen so often. You don't rule out completely changes in the homeobox sequences, you idiot.

Let's actually look at some homeobox sequences [cd00068 at NCBI] - of the 60 amino acids that comprise the motif, there are only 14 positions where the consensus amino acid is present in the MAJORITY of proteins. There are only SIX positions where the consensus amino acid is present in three-quarters of the proteins - heck, you could almost define a homeobox as being [F19, V44 or I44, W47, F48, N50, R52] but that would leave out my favorite homeoprotein, which LACKS amino acids 46 and 47 !!).

Getting 14 positions exactly right (not that we need to) is a one in 10^18 chance.

But the HomeoBox is a subgroup of a more diverse H-T-H family of DNA binding proteins.

Let's look at H-T-H sequences [cd00093], there are only 9 positions where the consensus amino acid is present in the majority of proteins, and getting nine amino acids exactly right is one in 10^11 (which number is, appropriately, the number of bacteria in one gram of excrement). Your calculations appear to be off by up to 10^20.

Finally, we actually know what is involved in moving from one H-T-H protein to another with a completely different function (provides resistance to superinfection by a different bacteriophage...) one in 10^5.

See pmid 4033758 and 3413061.

The H-T-H family, and its homeobox subset, are a fairly good example of of how accessible variations on a theme can create diverse functionality. I am surprised that you would pick them as your example of inaccessible sequence space. But then again, you did claim that the degeneracy in the genetic code mirrors the prevalence of the amino acids, which is wonderfully, wonderfully wrong (compare M with C, and K with S)

DNAJock

Sorry, cd00068 should read cd00086.

https://me.yahoo.com/a/VCNNdkJ8n848znvV2Pa9Jx6fbjhynPM5Uw--#7e243 said:

Let's actually look at some homeobox sequences [cd00068 at NCBI] - of the 60 amino acids that comprise the motif, there are only 14 positions where the consensus amino acid is present in the MAJORITY of proteins. There are only SIX positions where the consensus amino acid is present in three-quarters of the proteins - heck, you could almost define a homeobox as being [F19, V44 or I44, W47, F48, N50, R52] but that would leave out my favorite homeoprotein, which LACKS amino acids 46 and 47 !!).

Getting 14 positions exactly right (not that we need to) is a one in 10^18 chance.

But the HomeoBox is a subgroup of a more diverse H-T-H family of DNA binding proteins.

Let's look at H-T-H sequences [cd00093], there are only 9 positions where the consensus amino acid is present in the majority of proteins, and getting nine amino acids exactly right is one in 10^11 (which number is, appropriately, the number of bacteria in one gram of excrement). Your calculations appear to be off by up to 10^20.

Finally, we actually know what is involved in moving from one H-T-H protein to another with a completely different function (provides resistance to superinfection by a different bacteriophage...) one in 10^5.

See pmid 4033758 and 3413061.

The H-T-H family, and its homeobox subset, are a fairly good example of of how accessible variations on a theme can create diverse functionality. I am surprised that you would pick them as your example of inaccessible sequence space. But then again, you did claim that the degeneracy in the genetic code mirrors the prevalence of the amino acids, which is wonderfully, wonderfully wrong (compare M with C, and K with S)

DNAJock

DS said: 1) Proteins don;t evolve, genes evolve. He isn't even talking about the right molecule, let alone considering the genetic code.

2) Genes don't evolve from nothing. In this case, we know the ancestral sequences from which the hox genes evolved, they were not random, so his starting point is meaningless.

3) His target is meaningless. We know that a wide variety of sequences work just fine, joe hasn't done anything but hand waving, even though he knows that this dramatically affects the probability. Besides, with gene duplication which occurs frequently in hox gene evolution, nonfunctional intermediates or new functions can also arise.

4) THe calculations assume that all amino acids are equally frequent. This is not the case, but Joe hasn't even considered this possibility.

1) Joe is completely ignorant and is doing nothing more that attempting to fool people with fake calculations. Meanwhile, he can't even begin to calculate the "information" in any real sequence. And all of this while he crows about what an expert he is!

2) The probability of a new protein arising through repeated rounds of random mutation and natural selection is undoubtedly many orders of magnitude greater than anything that Joe will ever admit to. That makes it a virtual certainly in billions of living organisms reproducing over billions of years.

3) Joe is still ignoring all of the examples and all of the real mechanisms by which new genes and new functions are known to arise. He is completely ignorant of the literature in this field. Who would take his word for anything?

OK, enough. Everyone has had their say and everyone can claim victory, and now everyone is calling each other names. Further discussion can take place on the Wall. I am closing comments for this discussion.