A visit from the architects of the fly hourglass paper

A similar study, including checkerspot butterflies, and especially the ones in the genus Euphydryas (like E. editha, E. colon, E. chalcedona, etc.) would also be very interesting.

"The major challenge we had to overcome was to convince people that the evolutionary divergence of the Drosophila species we used is sufficient to make arguments about phylum-level morphological patterns."

But it appears that you have indeed accomplished that task. Now that you have developed the methods and types of analysis required, and demonstrated the molecular basis of the hour glass phenomena, there is nothing stopping anyone from applying this same technique to larger divergence times. Many whole genome sequences are already available. You may have founded the new field of evo devo temporal/spatial gene expression pattern analysis. OK, maybe that name could use a little work.

The next step might be to examine the evolution of the regulatory mechanisms responsible for producing this pattern. I am sure that when confronted with the scientific evidence for evolution at this level that every honest creationist will be convinced of the reality of evolution.

DS said: I am sure that when confronted with the scientific evidence for evolution at this level that every honest creationist will be convinced of the reality of evolution.

It’s been pretty obvious the last few decades that there is no such thing.

To my knowledge there are exactly two Creationists who genuinely do understand evolution, Kurt Wise and Todd Wood. Both of these guys are very upfront about how evolution is scientifically valid... and Wise, at least, is equally upfront about rejecting evolution because it conflicts with his religious beliefs. Apart from that pair, however, it's honest; informed; Creationist -- pick two.

Cubist said: To my knowledge there are exactly two Creationists who genuinely do understand evolution, Kurt Wise and Todd Wood. Both of these guys are very upfront about how evolution is scientifically valid... and Wise, at least, is equally upfront about rejecting evolution because it conflicts with his religious beliefs. Apart from that pair, however, it's honest; informed; Creationist -- pick two.

And they are both sell-outs and frauds I have no regard for.

Yay Dale!

you're absolutely right. to hold those two up as "honest" is to horribly malign the term "intellectual honesty".

I've looked at what they have written. Honesty in name only.

simply claiming you can deny evidence because your religion dictates it does NOT make for an intellectually honest argument.

Paul Burnett said:

DS said: I am sure that when confronted with the scientific evidence for evolution at this level that every honest creationist will be convinced of the reality of evolution.

"Honest creationist" - wherever do you suppose something like that might be found? It's been pretty obvious the last few decades that there is no such thing.

Ichthyic said: And they are both sell-outs and frauds I have no regard for. Yay Dale! you're absolutely right. to hold those two up as "honest" is to horribly malign the term "intellectual honesty". I've looked at what they have written. Honesty in name only. simply claiming you can deny evidence because your religion dictates it does NOT make for an intellectually honest argument.

I would like to thank, and welcome Pavel Tomancak. There have been years of attacks on evolution, and science teaching in general based on the perceived "fraud" of Haeckel's embryo drawing.

What I now hope we will see is a new, and independently derived set of science results from embryology giving further confirmation of evolution.

At the risk of being repetitive and boring, I resubmit an earlier post from June, that seems even more poignant here:

If AIG or CMI is one’s authority you might think that “Ontogeny recapitulates Phylogeny” (and the similarities of developmental forms in general) is a false concept long abandoned and dis-proven (now providing evidence against evolution), and therefore cannot be included in any biology textbook or classroom today.

But such is not the case. Stephen Jay Gould wrote a 500 page tome, Ontogeny and Phylogeny* where he says in his opening sentence on page 1, 'I am aware that I treat a subject currently unpopular.'

He continues, “I tell a colleague that I am writing a book about parallels between ontogeny and phylogeny. He takes me aside, makes sure that no one is looking, checks for bugging devices, and admits in markedly lowered voice: ‘You know, just between you, me, and that wall, I think there really is something to it after all.’ “

Because there is indeed something to it. It’s not a false concept. It just needs modification in light of what we know today about biology. And that’s what Gould did.

On page 213 he writes, “The embryonic features that we share with all vertebrates represent no previous adult state, only the unaltered identity of early development. Thought they do not allow us to trace the actual course of our descent in any way, they are full of evolutionary significance nonetheless; for, as Darwin argued, community of embryonic structure reveals community of descent.”

All you have to do is look at those photographs and you know he’s right.

*-Belknap Press of Harvard University Press, 1977

(PS-No one at AIG or CMI has the record of field work of Gould. No one at AIG or CMI has the scholarship to write an Ontogeny and Phylogeny like Gould. Yet they expect us to bow to their pronouncements.)

"Our ability to recapitulate the known phylogeny from the divergence data is in my opinion remarkable.."
"We are developing fancy transgenic.."
"It’s well-funded.."

you know, if you keep doing that, you're going to go blind.

John Vanko -

Well, Gould was obviously correct, and even if embryoes were more divergent morphologically, what we now know about the conservation of basic major genes families in development across diverse lineages would prove that point.

However, to some degree, although Haeckel is probably excessively maligned, as Gould said in the quote you presented - "The embryonic features that we share with all vertebrates represent no previous adult state, only the unaltered identity of early development".

I haven't read Haeckel in the original and probably never will, but relying on summaries, I thought this was kind of the point. He thought that they did represent or recapitulate previous adult states.

They certainly do seem to resemble adult states of some members of the vertebrate lineage, and they certainly do often seem to resemble more ancient lineages closer to the beginning of development (I'm not sure if there are counter-examples), but at a vastly smaller physical scale. Without meaning to be unfair to someone whose work I have not read in the original, didn't Haeckel perhaps, unlike Gould, take this resemblance to literally?

harold said: ... didn't Haeckel perhaps, unlike Gould, take this resemblance too literally?

Pavel Tomancak may well be disappointed in some of the people here right now. He and his associates probably did the study so as to learn something, and not so that the results would be used solely (or partly) as a weapon in the war on ID/creationism, unless he and his associates intended it to be solely (or partly) that weapon of course.

Since science "ignores religious beliefs" (yeah right) that of course couldn't be the case. But, that surely hasn't stopped some of you from instantly adding the study to your arsenal of weapons against ID/creationism.

So, whatever you do, don't just find the study interesting and informative for its own sake (which I hope is what the authors intended). Think of it only as another scientific weapon against ID/creationism, while you keep saying that "science ignores religious beliefs".

Yep, that pretty much summarizes it.

Haeckel was working at a very early but very, very active time in the history of biology. I guess every period in biology since Linnaeus has been something of an explosive period of new knowledge, but the late nineteenth century still probably stands out in many ways.

Because the science was early, it was a time of brilliant minds forming rather extreme ideas, some of which turned out to be prescient, some of which were brilliant but wrong.

Golgi and Cajal supposedly came close to a fist fight at the Nobel Prize ceremonies (technically that was in the early twentieth century). Cajal realized that the central nervous system was made up of individual cells, Golgi thought it was some kind of syncitium. (Cajal was also an early weight training enthusiast; I have no idea what kind of shape Golgi would have been in for his age at the time - they were probably both about 60.)

In fact, I recently discovered to my amazement that some science-denying anti-medicine cranks are accurate advocates of once very important ideas from that time.

So in that context, Haeckel's admitted over-interpretation of his basically valid observations, and his mildly over-emphatic (but not grotesquely wrong) drawings, are really not that shocking. It's worth noting that before photomicrographs, artistic ability was an important scientific skill.

The real message is that the study of development, beside having applications to medical research, provides a lot of strong evidence for evolution and common descent.

So, whatever you do, don’t just find the study interesting and informative for its own sake (which I hope is what the authors intended). Think of it only as another scientific weapon against ID/creationism, while you keep saying that “science ignores religious beliefs”.

He and his associates probably did the study so as to learn something

Pavel Tomancak may well be disappointed in some of the people here right now.

He and his associates probably did the study so as to learn something, and not so that the results would be used solely (or partly) as a weapon in the war on ID/creationism,

unless he and his associates intended it to be solely (or partly) that weapon of course.

Since science “ignores religious beliefs” (yeah right) that of course couldn’t be the case.

But, that surely hasn’t stopped some of you from instantly adding the study to your arsenal of weapons against ID/creationism.

So, whatever you do, don’t just find the study interesting and informative for its own sake (which I hope is what the authors intended).

Think of it only as another scientific weapon against ID/creationism, while you keep saying that “science ignores religious beliefs”.

Because Natural Selection can destroy, it can therefore build.

This is the central fallacy of Darwinism. Just because something can destroy does not mean it can build.

This is the central fallacy of Darwinism

you mean your own personal fallacious strawman.

sounds catchy, but it makes no sense, and has nothing to do with evolution.

fail.

Michael Behe said: Because Natural Selection can destroy, it can therefore build. This is the central fallacy of Darwinism. Just because something can destroy does not mean it can build.

here's a hint for you:

what's the most basic definition of the word: evolution?

change.

heh.

jinx!

see, sometimes we DO think alike, Dale.

:)

Michael Behe said: Because Natural Selection can destroy, it can therefore build. This is the central fallacy of Darwinism. Just because something can destroy does not mean it can build.

harold said: We don't use antibiotics to deny that demons cause disease instead of microbes, but when they work, they provide evidence that microbes, not demons, cause some diseases.

Paul Burnett said:

harold said: We don't use antibiotics to deny that demons cause disease instead of microbes, but when they work, they provide evidence that microbes, not demons, cause some diseases.

Ah, but can you prove that demons don't cause microbes? (/snark) Some (most?) creationists attribute creative powers to their various devils and demons, committing a variant of the Manichaean Heresy (not that they have a clue).

Michael Behe said: Because Natural Selection can destroy, it can therefore build. This is the central fallacy of Darwinism. Just because something can destroy does not mean it can build.

Anybody notice that the trolls here are not actually discussing the science? It's almost as if they don't really understand the paper at all. You know, it's almost as if they never even read the paper! Imagine that, going to a web site devoted to defending evolution and ridiculing people for defending evolution, all the while ignoring the science and still claiming you are on their side. Amazing.

If anyone thinks that this paper refutes religion, just ask yourself, what religion? If anyone thinks that this paper refutes a religious belief, just ask yourself, what belief? As Flint correctly pointed out, whenever anyone makes claims about the natural world, science can and should address those claims. The science should be used to refute the scientific claims, not the religious motivation behind them.

As for the authors being disappointed, well why not just ask them? You know, the authors who specifically came to a blog devoted to defending evolution against creationism. Ask them if they are disappointed that their paper has been used for such a vile purpose as defending evolution. Why not hear it straight from the scientists mouth?

Notice.

First, I'll go further than RBH: if you are assuming that the commenter who refers to him/herself as "Michael Behe" is in fact the author of Darwin's Black Box, then you're a lot dumber than he is.

Second, and related, all comments by Kris -- and responses to her/him -- are on their way to the Bathroom Wall, as are any and all comments far afield of the interesting topics discussed by our guest bloggers. Seriously, guys, do you not have any experience in dealing succinctly with trolls? I can demonstrate the use of href tags to create links if that would help.

RBH said:

Michael Behe said: Because Natural Selection can destroy, it can therefore build. This is the central fallacy of Darwinism. Just because something can destroy does not mean it can build.

Absent verification of IP and email, I strongly recommend that folks not uncritically or naively accept this commenter as the Michael Behe of Lehigh University. We do not have auto-verification of commenters, so anyone can post under that name.

Kris -

It doesn't really matter what your motivation is. The quality of your comments is what it is. This will be my last "feeding" of you.

Michael Behe said: Because Natural Selection can destroy, it can therefore build. This is the central fallacy of Darwinism. Just because something can destroy does not mean it can build.

It’s simple. I just remove everything that doesn’t look like David.

I was assuming (naïvely) that the poster “Michael Behe” really was Michael Behe. If he was, then he will expand on his argument and show us the logic underlying it.

If he behaves like a drive-by troll and just disappears and refuses to explain his argument then I will give the real Michael Behe the benefit of the doubt and assume that the commenter wasn't Michael Behe.

Feel free to put this comment on the Bathroom Wall, but an important chance to highlight something about the history of ID presents itself.

ID was originally marketed as a means for getting some stealth creationism into public schools, without invoking court challenges. We can debate whether the DI ever intended for it to actually perform that function, but that's how it was marketed.

Hence, it was common during the pre-Dover era for science-denying trolls to ostentatiously claim not to be religious, to claim that ID/creationism wasn't religious, and so on. Simultaneous obsessive construction of a "discard science or discard all religious behavior" false dichotomy was characteristic of this. Canned remarks claiming persecution, often in ludicrous contexts, were also common (the "Expelled" strategy).

All of this was nothing more than a strategy that lying follower bots were instructed to observe.

We see a lot less of it since Dover, given that Judge Jones specifically called out people using this strategy for lying under oath, and wrote a decision making it almost impossible for this strategy to ever succeed.

However, there are a few dolts who haven't abandoned this grotesquely dishonest strategy yet, and Kris seems to be a "living fossil" of this type. If not, he is coincidentally a perfect mimic.

Well, now that the trolls are taken care of we can get back to discussing the science. If the author is still around, I have some questions.

Is it necessary to use species specific microarrays? Would it be possible to design microarrays that would allow for this type of analysis using a greater divergence time, especially for phylogenetically conserved genes such as hox genes? If that were possible, it would make this approach much less costly and time consuming? If not, how difficult is it to design and construct such arrays? Do you have any plans for looking at more fly species or expanding the divergence time? Could such an approach be used for vertebrates as well? Could the molecular developmental hour glass be demonstrated in the organisms used for Haeckel's drawing? Would you be disappointed if your work was used to fight creationism?

Thanks for doing such ground breaking work and for helping us to understand it.

RBH said: Absent verification of IP and email, I strongly recommend that folks not uncritically or naively accept this commenter as the Michael Behe of Lehigh University. We do not have auto-verification of commenters, so anyone can post under that name.

DS said: Anybody notice that the trolls here are not actually discussing the science? It's almost as if they don't really understand the paper at all. You know, it's almost as if they never even read the paper! Imagine that, going to a web site devoted to defending evolution and ridiculing people for defending evolution, all the while ignoring the science and still claiming you are on their side. Amazing. If anyone thinks that this paper refutes religion, just ask yourself, what religion? If anyone thinks that this paper refutes a religious belief, just ask yourself, what belief? As Flint correctly pointed out, whenever anyone makes claims about the natural world, science can and should address those claims. The science should be used to refute the scientific claims, not the religious motivation behind them. As for the authors being disappointed, well why not just ask them? You know, the authors who specifically came to a blog devoted to defending evolution against creationism. Ask them if they are disappointed that their paper has been used for such a vile purpose as defending evolution. Why not hear it straight from the scientists mouth?

Yeah, I would LOVE to hear from the authors of the study as to how they feel about the way some of you have totally detoured from the topic of the study. If they're smart, they're distancing themselves as far as possible from this website as fast as they can, unless of course if their study was simply intended to find and supply more weapons for the war on creationism/religious beliefs.

Kris, you seem not to be reading the thread. (What a surprise!) Your own opening comment about expanding the analysis has been left in. And your question about whether DS is "discussing the science" made me laugh out loud. (...ignoring the science of the study." LOL!)

So, Kris, we await your comments on "the science of the study." From this point on, comments on other topics by anyone will be sent straight to the wall. That means all other topics. There are plenty of threads around here where you can whine idiotically about mistreatment of "creationists." This is not one of them.

If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

To DS: I'll invite the authors to tackle some of the questions. I do think they're planning as similar analysis in other taxa, and for sure they plan to do the phylostratigraphic analysis of Domazet-Loso & Tautz on their fly data.

To everyone else: don't bother typing comments about trolls, creationists, deities, or ISPs on this thread. I'm quite sure that your time is better spent on other efforts, unless your buddies are really impressed when you cc them.

Thanks Steve. I appreciate it.

Steve Matheson said: I'll invite the authors to tackle some of the questions. I do think they're planning as similar analysis in other taxa, and for sure they plan to do the phylostratigraphic analysis of Domazet-Loso & Tautz on their fly data.

Mike Elzinga -

Interestingly - http://www.ncbi.nlm.nih.gov/pubmed/20512118

I don't at all know what the maximum range of temperatures that permit any viable development of drosophila embryos of any species is. I would guess that it is extremely narrow relative to the range of temperatures even that can be experienced on the surface of the earth, but relatively wide compared to the temperature range needed for viable mammalian development. But that would just be a guess.

harold said: Mike Elzinga - Interestingly - http://www.ncbi.nlm.nih.gov/pubmed/20512118 I don't at all know what the maximum range of temperatures that permit any viable development of drosophila embryos of any species is. I would guess that it is extremely narrow relative to the range of temperatures even that can be experienced on the surface of the earth, but relatively wide compared to the temperature range needed for viable mammalian development. But that would just be a guess.

Mike Elzinga said: A variable that doesn’t seem appear explicitly in these studies is temperature.

harold said: I don't at all know what the maximum range of temperatures that permit any viable development of drosophila embryos of any species is. I would guess that it is extremely narrow relative to the range of temperatures even that can be experienced on the surface of the earth, but relatively wide compared to the temperature range needed for viable mammalian development.

Yep, those plant embryos (seeds) can be amazingly hardy. There's a certain analogy to cysts. Some bacteria, and some eukaryotes like certain Amoeba species, can morph into hardy cysts when the environment becomes threatening and then transform back to their normal "adult" form when things return to ideal. I have no idea how long cysts can theoretically remain dormant but viable, but it's probably a very long time.

(For completeness, every beer enthusiast knows that brewer's yeast from bottles of beer recovered from 19th century shipwrecks has produced cultures that were used to brew excellent beer well over a century and a half later, but that's only because humans provided the sealed glass bottle environment.)

The last common ancestor of Jack Pine and Drosophila lived quite a while ago, of course :).

I'm no PZ Myers, but I do seem to recall that gravity plays a major role in early embryonic development of some animals - the contents of the actual zygotic cell become polarized, and that has a major impact on everything else.

Also, I think there are other Drosophila mutations that have an expression that is affected by temperature. That paper just happened to be a very elegant and in depth modern look at how this works for one example. I could be wrong, but I have a nagging feeling that I have heard of this before.

Michael Behe said: This is what Richard Dawkins believes: 1. I don't how life began 2. Therefore, I know it's not designed. That is a fallacy

“Michael Behe” [sic] said:

Joe Felsenstein said: Was Michaelangelo unable to “build”?

Michelangelo was an intelligent designer

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

Then why are you feeding the troll? Please refrain, if not for me (I made it completely clear that this thread is not the place for off-topic bickering) then out of respect for our guest bloggers.

Steve Matheson said: Then why are you feeding the troll? Please refrain, if not for me (I made it completely clear that this thread is not the place for off-topic bickering) then out of respect for our guest bloggers.

Once again a thread has turned into an ID/creationism/creationist bash fest. So much for the science.

I wonder why the authors of the study haven't been back and aren't participating in the 'discussion'. LOL!

Science Daily (and others) kicks this site's ass when it comes to providing interesting scientific information.

John Harshman said:

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

No, because a genus, like any other taxonomic rank, has no actual meaning. You could call the same clade a genus, a family, or even a phylum depending on your personal taste. Now, there have been occasional proposals to give ranks a real meaning. Charles Sibley proposed to do it based on genetic distance values, as you seem to imply. John Avise (and others before him) proposed to do it based on time of origin, which is not quite the same thing given that different genomes can evolve at different rates (not to mention different parts of the same genome). So far, though, none of these attempts has been popular, probably because they just aren't practical -- we don't have the necessary data to make the determinations in most cases -- and because if applied across a wide taxonomic scope it would require massive re-assignment of ranks. As with the case you raise: either Drosophila becomes a class (or higher), or Amniota becomes a genus. Neither of these is likely to be accepted.

Kris said: That's just one of the problems with science. Personal tastes have way too much to do with the way things are even named/labeled, let alone with how those things may be related to each other, or how they originated, or interact with their environment, etc., etc., etc.

Well one of the best criteria for identification of species is genetic discontinuity. Any gene pools that are are isolated from each other and have little or no gene glow will undergo genetic divergence. Often times this occurs in a clock like manner, at least for certain portions of certain genes. So the same genetic data that can be used to reconstruct phylogenetic relationships can also be used to identify isolated gene pools, i.e. species. This is in fact why the Barcode of life project has been so successful. It provides a relatively consistent framework for species identification using the mitochondrial COI gene.

What is interesting to me is that the spatio-temporal patterns of gene expression in these species can be used to reconstruct the exact same phylogenetic pattern produced by other data sets. So, there is obviously phylogenetic information in this data as well. Once again, the same result, produced by independent data sets and different methods of analysis, increases confidence in the result.

I would end with a comment about how this is yet another stunning example of the predictions of the theory of evolution and how it represents yet another nail in the coffin of creationism. But then our resident troll would have yet another excuse to fixate on that and once again complete ignore the science in order to whine and moan about how we don't really understand anything so we might as well give up and let the butt heads win. So I won't do that.

gene glow = gene flow obviously

gene glow is only for fireflies

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

Robin,

The concept of a molecular clock refers to the observation that there is a relatively constant rate of mutation for certain parts of certain genes for certain periods of time in certain groups of organisms. This can be determined by calibrating the times of divergence using the fossil record. For example, the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years. So, if we can calibrate the clock, we can estimate divergence times based on genetic divergence.

However, you are correct. Things are usually a lot messier than this. that is why there are so many restrictions and qualifiers required. For example, the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy.

Still, the mitochondrial COI gene has proven to be extraordinarily useful for many different groups. Thus it is currently the basis of the Barcode of Life project. However, the various taxonomic ranks are still somewhat arbitrary, due to rate heterogeneity in different groups. So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

The vertebrate example was for the hemoglobin gene.

Shoot. I forgot to mention that creationists have no explanation for the molecular clock data, or for the nested hierarchy of genetic similarities that it produces. They lose again.

DS said: Robin, The concept of a molecular clock refers to the observation that there is a relatively constant rate of mutation for certain parts of certain genes for certain periods of time in certain groups of organisms. This can be determined by calibrating the times of divergence using the fossil record. For example, the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years. So, if we can calibrate the clock, we can estimate divergence times based on genetic divergence.

However, you are correct. Things are usually a lot messier than this. that is why there are so many restrictions and qualifiers required. For example, the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy. Still, the mitochondrial COI gene has proven to be extraordinarily useful for many different groups. Thus it is currently the basis of the Barcode of Life project. However, the various taxonomic ranks are still somewhat arbitrary, due to rate heterogeneity in different groups. So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

DS said: the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy.

Well, if you must know I do various things in science, mostly involving Paleontology, and Lepidoptera.

I really can't avoid most of the problems since most scientists won't listen to anything that might improve the status quo. They get angry and defensive when problems are pointed out and potentially helpful suggestions are made (not just by me). I have been dealing with it for a long time.

Some scientists would like to fix some of the problems but too many are entrenched in old, non-productive ways. In some cases it's the chaos and confusion that keeps them employed.

It's kind of like having a huge work crew but no one is in charge, or at least no one takes charge. The result? Chaos, waste, and confusion. You know, kind of like a typical government.

Have you ever noticed that religion is often called "organized religion"? Have you ever heard anyone call science 'organized science'? I haven't, and for good reason.

Think about this; throughout history many churches/religions have been very well organized. They have a hierarchy of people who hold certain positions of leadership within the church or religion and they answer to each other a lot like managerial employees do in a large company.

I'm sure you've heard of the "Salvation Army", and the words, "Onward Christian soldiers", and "Holy Wars", and other such things that imply organization and a common cause. Yeah, I know, religions and churches are often at war with each other but some of them are still way more organized than science is. Maybe that's part of the reason they're so successful and science is so poorly known and accepted by the masses.

Yep, it's all my fault. Just thought I'd say that before I'm viciously attacked for pointing out some realities.

Something else to think about: if the 'scientific method' is allegedly so standardized and is truly accepted and practiced by scientists, then why do so many scientists fight with each other so often, including over the methods and standards they use?

I won't be a bit surprised if someone comes along (not necessarily here) and challenges the standards and methods used in the study that is the original subject of this thread, and they might even have some legitimate complaints. Time will tell.

Think of the recent Mono Lake arsenic study. Oh sure, it will be "self correcting", someday. What a lame argument.

So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

harold said:

So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

But it is also important to note that the nested hierarchy that we acknowledge when we apply taxonomic labels is real, even though the labels necessarily subdivide it at somewhat arbitrary points, and even though not every single lineage's relationship with every other lineage is known. The imaginary "ideal" molecular clock is a shared region of DNA, present in all lineages of interest, that does not have any coding, regulatory, or sequence-related structural function (note that such a region of DNA could not, thus, even exist in prokaryotes). The idea would be that mutations in such an allele would occur at the frequency of mutation rates, and not be selected against. Looking at the sequence of the allele in different lineages, the approximate time of divergence from a common allele could be estimated. Obviously - 1) No such perfect allele exists. 2) DNA repair rates, exposure to environmental mutagens, and possibly even other factors impacting underlying mutation frequencies, vary in different cell types and lineages. 3) Other types of molecular clocks can be and have been used. Having said all that, molecular clock studies have proved very useful, are in strong fundamental agreement with other types of studies, and continue to be refined.

Kris -

If you can get everything right the first time, more power to you. You are indeed superior to scientists and to everyone who posts here. It must be frustrating that lesser beings refuse to acknowledge your glory, but hey, that's life.

The rest of us need feedback and corrections to get things right, and that is why science is grounded in peer review and ultimate self-correction.

The Mono Lake bacterial study is a perfect example of the power of the self-correcting nature of science.

A useful discovery was made (arsenic resistant bacterial lineage), mildly excessive scientific claims were made, and the media reported irresponsibly. But in the end, the useful discovery will be what remains.

And sometimes they are in strong fundamental disagreement with other types of studies.

Kris said: Something else to think about: if the 'scientific method' is allegedly so standardized and is truly accepted and practiced by scientists, then why do so many scientists fight with each other so often, including over the methods and standards they use?

Kris said: I really can't avoid most of the problems since most scientists won't listen to anything that might improve the status quo.

Kris said: Maybe that's part of the reason [religions are] so successful and science is so poorly known and accepted by the masses.

Don't worry, Kris will no doubt provide examples where scientific studies disagree with creationist claims. He will then go on to claim that the studies were done specifically to destroy creationism, so science is really religion after all. That will prove how close minded those awful scientists are. What can you expect from an amateur butterfly collector?

Apparently he still hasn't read the paper and yet he has the audacity to whine about how others ignore the science. Perhaps he has simply failed to notice that this is a stunning example of where independent data sets agree. I wonder what explanation he has for that?

Steve needs to purge this thread again. If Kris were banished to the bathroom wall permanently we could give him the type of feedback he so richly deserves.

Kris said: Nothing in nature cares one iota what we humans call it. If we humans can't even agree on what the labels mean, how are we ever going to really figure out anything else, and agree on that too?

John Harshman said:

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

No, because a genus, like any other taxonomic rank, has no actual meaning. You could call the same clade a genus, a family, or even a phylum depending on your personal taste. Now, there have been occasional proposals to give ranks a real meaning. Charles Sibley proposed to do it based on genetic distance values, as you seem to imply. John Avise (and others before him) proposed to do it based on time of origin, which is not quite the same thing given that different genomes can evolve at different rates (not to mention different parts of the same genome). So far, though, none of these attempts has been popular, probably because they just aren't practical -- we don't have the necessary data to make the determinations in most cases -- and because if applied across a wide taxonomic scope it would require massive re-assignment of ranks. As with the case you raise: either Drosophila becomes a class (or higher), or Amniota becomes a genus. Neither of these is likely to be accepted.

Religion tells people what they mostly want to hear...In a nutshell, that’s why religion is more popular than science.

Flint said: I suggest this is only part of the story. Religion offers Absolute Truths, and the best science can do is offer conditional, tentative, probabilistic statements. One of the most common religious critiques of science revolves around this issue. Scientific "truths" are not guaranteed, they don't hold still, they are generally wrong or incomplete, scientific theories must be in principle subject to change at any time. Even when science self-corrects, it doesn't replace Wrong with Right, but rather replaces a little more wrong with a little less wrong.

Although some individual religions offer claims of absolute truth and rules for every aspect of life, taken together, a collection of untestable and contradictory claims of "absolute truth" is the result. In short, even if you think that one "absolute truth" based religion is true, you still have to randomly pick the right one. So the "absoluteness" is illusionary. At best your chances are as absolute as a lottery ticket. (My subjectively belief is that there is absolutely no risk of going to hell after you die no matter what you do, but that's another matter.)

This is much less of a problem for religions that are more ecumenical and more grounded in the idea of universal ethical standards.

Although science deals only with measurement and description of the physical world, and does not claim absolute truth (which is not the same thing as saying that it does not claim that some things are well-established), the result of scientific activity is an ever-expanding understanding of the physical world, and a high degree of consensus about many things.

Although some individual religions offer claims of absolute truth and rules for every aspect of life, taken together, a collection of untestable and contradictory claims of “absolute truth” is the result.

Science has faith that the universe is consistent, and that scientific disputes can ALWAYS be resolved by appropriately focused research.

Flint -

Since we mainly agree on things, I won't belabor the point, but I will make one more comment.

I can't read the minds of religious people, nor of anyone else.

There is kind of a fashion on the internet of insisting that the religious are brainwashed automatons who are convinced of some arbitrary "absolute truth", in a way so hard-wired and unchangeable as to resemble the fly-snapping neural circuitry of a frog.

The appeal of this claim is obvious. It allows a strong sense of superiority, while simultaneously declaring creationists to be innocent of machinations, thus avoiding the awkwardness of confronting potentially ugly underlying motivations.

I personally think this oversimplifies.

I think many religious behaviors are beneficial to those who choose them (although they aren't what I choose) and harmless to others, and are emotional in nature. Singing inspiring songs in church, praying in symbolic empathy with those who face some hardship, and so on. However, these behaviors ultimately rely on the idea of an invisible friend, who may or may not be able to affect things here on earth, but who is infinitely sympathetic and trustworthy. Science denial isn't really necessary. Certainly that's the kind of religion I was raised with. My grandparents went to Baptist church on every possible occasion, and would have gone more often if it had been possible (which, mercifully, it was not). The emphasis was almost entirely on what a wonderful, kind man Jesus was, how people mistreated him but know better now, how much Jesus cares whenever people or warm-blooded animals that aren't raised for food are suffering, and in general, how much better he is than everyone else but how much he likes us anyway, and what a good idea it is to try to be more like him. Which it generally was, as he was presented as being compassionate, honest, forgiving, intelligent, perceptive, tolerant, standing up for the underdog, making bad people decide to be good, etc. This was not a "liberal" church except by decadent post-modern standards that label any criticism of infantile narcissistic self-indulgence as "liberal"; it was deservedly considered very strict and austere by other denominations.

Another type of "religious behavior", which is not mutually exclusive, is to identify with a group or political movement and adopt religious views associated with that group or ideology, partly for group identity and partly as a defense against ethical criticisms ("since Gawd sed to kill teh gayz it must be moral to discriminate against them"). This can be done somewhat sincerely, grossly insincerely (Tom Tancredo, Bobby Jindal, Ann Coulter), or in a manner indicating a profoundly disturbed psyche (Christine O'Donnell). I'm sorry for mentioning politicians, but they make such great examples. Plenty of repulsive politicians have been communist or ostentatiously, hypocritically "liberal", let's not side track any further than the side track we're already on.

Yet another type is to attempt to indulge authoritarian fantasies up by self-identifying as the "one true prophet". Examples of this abound, and are often associated with violent events.

While it's true that people are unlikely to easily give up these reinforcing behaviors easily, many creationists would switch in a flash. Tom Tancredo probably "converted" from Catholicism to creationism because the Pope is only hard core right wing on issues that have something to do with sex, and can be outright "progressive" on issues like war, torture, death penalty, health care, programs for the needy, etc. Meanwhile, you can find a Protestant clergyman who is right wing on every issue (or "progressive" on every issue), so Tancredo presumably found someone whose God coincidentally commands exactly what you need to support to get elected in some designer-forsaken gated community and "converted".

A lot of the other creationists, from the trolls here on up, are just wanna-be authoritarian rulers or the like, and their sincerity is about as deep as I perceive that of some of those I have mentioned here to be.

(On a side note, IMO instead of saying “science has faith …” it might be more accurate to say “the people involved in science have faith …”.)

DS said: Robin, The concept of a molecular clock refers to the observation that there is a relatively constant rate of mutation for certain parts of certain genes for certain periods of time in certain groups of organisms. This can be determined by calibrating the times of divergence using the fossil record. For example, the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years. So, if we can calibrate the clock, we can estimate divergence times based on genetic divergence. However, you are correct. Things are usually a lot messier than this. that is why there are so many restrictions and qualifiers required. For example, the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy. Still, the mitochondrial COI gene has proven to be extraordinarily useful for many different groups. Thus it is currently the basis of the Barcode of Life project. However, the various taxonomic ranks are still somewhat arbitrary, due to rate heterogeneity in different groups. So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

stevaroni said:

Kris said: I really can't avoid most of the problems since most scientists won't listen to anything that might improve the status quo.

Huh? You do realize that true fame in science comes not maintaining the status quo, but from upending it, and proving that the current explanation is wrong, or at least incomplete, don't you? After all, Copernicus and Galileo are famous for demonstrating that, contrary to common belief, the Earth did move and orbited the Sun. Newton is famous for upending two millenia of "classical" mechanics. Einstein if famous for demonstrating that Newton wasn't all that and a bag of chips. And, of course, Darwin is famous for making an, ahem, slightly controversial observation about the origins of man. The way forward in science is to disturb the status quo. That's how you get famous.

Robin said:

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

Actually, this was what I was wondering as well. I don't really know what molecular clocking is, so I have no feel for the practicality or validity of use such as a marker. It strikes me though that counting...say...the number of changes that have occurred between two species wouldn't necessarily correlate meaningfully to the number of changes between two other species. I understand evolution (as a process), and nature in general, to be more dynamic and irregular than that. For instance, I would expect (though I've not done any research on this personally) that some biological/behavioral characteristics in some species would manifest after but a few changes while other biological/behavior characteristics would only manifest after many varied changes in certain species. It think that a fair amount in terms of measuring change and determining genus level differentiation, as it were, would depend both on the species itself and the environment that species was in/pioneering into.

DS said: Robin, The concept of a molecular clock refers to the observation that there is a relatively constant rate of mutation for certain parts of certain genes for certain periods of time in certain groups of organisms. This can be determined by calibrating the times of divergence using the fossil record. For example, the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years. So, if we can calibrate the clock, we can estimate divergence times based on genetic divergence. However, you are correct. Things are usually a lot messier than this. that is why there are so many restrictions and qualifiers required. For example, the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy. Still, the mitochondrial COI gene has proven to be extraordinarily useful for many different groups. Thus it is currently the basis of the Barcode of Life project. However, the various taxonomic ranks are still somewhat arbitrary, due to rate heterogeneity in different groups. So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

Kris said:

DS said: Robin, The concept of a molecular clock refers to the observation that there is a relatively constant rate of mutation for certain parts of certain genes for certain periods of time in certain groups of organisms. This can be determined by calibrating the times of divergence using the fossil record. For example, the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years. So, if we can calibrate the clock, we can estimate divergence times based on genetic divergence. However, you are correct. Things are usually a lot messier than this. that is why there are so many restrictions and qualifiers required. For example, the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy. Still, the mitochondrial COI gene has proven to be extraordinarily useful for many different groups. Thus it is currently the basis of the Barcode of Life project. However, the various taxonomic ranks are still somewhat arbitrary, due to rate heterogeneity in different groups. So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

Are you saying that the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years by using the fossil record? Yeah, if only we could agree on a definition of "species". This seems to be the appropriate time to insert this (form another thread): Stuart Weinstein replied to comment from darwinism.dogbarf() December 16, 2010 2:45 PM darwinism.dogbarf() said: "None of those essays explains how complex specified information rises in a cognitively isloated system." Stuart Weinstein said: "To do that we require the formula to compute what the complex specified information is.You can’t explain something if you can’t define it. “Complex specification” is the Zen of ID theory. IDists can’t explain it, but they know what is. If you’re punking us, very well done. “cognitively isolated”. Unfortunately ID proponents suffer cognitive disbaility." Notice this sentence: "You can’t explain something if you can’t define it." Seems to me that that applies (or at least should) to ID/creationism AND science.

eric said:

Kris said: Something else to think about: if the 'scientific method' is allegedly so standardized and is truly accepted and practiced by scientists, then why do so many scientists fight with each other so often, including over the methods and standards they use?

You are confusing method writ large with method writ small. When creationists attack the scientific method, they are attacking basic principles like the limitation of evidence to empirical observables. The concept of reproducibility and the scientific rule of thumb that says irreproducible and unconfirmable results will not be give much weight (if any). They are not talking about whether in last Tuesday's extraction Bob should've held the pipette at 90 degrees instead of 45 degrees. That is also a scientific methodology question. Scientists can argue about those sorts of details until the cows come home and there is no real significance to the scientific method writ large. You are falling for a classic creationist argument which claims that disagreements between scientists about how an experiment was performed somehow invalidates major scientific findings. This argument is bogus. Its bogus first because findings like evolution and so on are the result of enormous numbers of independent experiments reaching the same conclusion; no individual experiment wipes the slate clean. Its bogus second because they have no alternative method to put in its place. When (my example) Alice and Bob argue about pipettes, Alice is proposing an alternative methodology that we can test. When Behe (in reality) argues that science should allow for supernatural causes, he proposes no method at all for doing so. Nothing we can test. He wants to sneak divine revelation in without ever going through the process of determining whether science + revelation is better than science - revelation.

DS said: Don't worry, Kris will no doubt provide examples where scientific studies disagree with creationist claims. He will then go on to claim that the studies were done specifically to destroy creationism, so science is really religion after all. That will prove how close minded those awful scientists are. What can you expect from an amateur butterfly collector? Apparently he still hasn't read the paper and yet he has the audacity to whine about how others ignore the science. Perhaps he has simply failed to notice that this is a stunning example of where independent data sets agree. I wonder what explanation he has for that? Steve needs to purge this thread again. If Kris were banished to the bathroom wall permanently we could give him the type of feedback he so richly deserves.

jkc said:

Kris said: Nothing in nature cares one iota what we humans call it. If we humans can't even agree on what the labels mean, how are we ever going to really figure out anything else, and agree on that too?

This is precisely why the theory of evolution is so attractive. If life presented us with nice neat categories and easy definitions we might be inclined to conclude that everything was create a few thousand years ago according to those categories and had changed little since then. Since, in fact, life is not neat and clean, but rather, full of overlap and discontinuity (among many other evidences), we conclude that life has been changing for millions of years. The fact that science cannot neatly categorize all of life is more a function of the complexity of life than it is the fallibility of science. Oh, and if you have a better idea, let's hear it...

harold said: Flint - Since we mainly agree on things, I won't belabor the point, but I will make one more comment. I can't read the minds of religious people, nor of anyone else. There is kind of a fashion on the internet of insisting that the religious are brainwashed automatons who are convinced of some arbitrary "absolute truth", in a way so hard-wired and unchangeable as to resemble the fly-snapping neural circuitry of a frog. The appeal of this claim is obvious. It allows a strong sense of superiority, while simultaneously declaring creationists to be innocent of machinations, thus avoiding the awkwardness of confronting potentially ugly underlying motivations. I personally think this oversimplifies. I think many religious behaviors are beneficial to those who choose them (although they aren't what I choose) and harmless to others, and are emotional in nature. Singing inspiring songs in church, praying in symbolic empathy with those who face some hardship, and so on. However, these behaviors ultimately rely on the idea of an invisible friend, who may or may not be able to affect things here on earth, but who is infinitely sympathetic and trustworthy. Science denial isn't really necessary. Certainly that's the kind of religion I was raised with. My grandparents went to Baptist church on every possible occasion, and would have gone more often if it had been possible (which, mercifully, it was not). The emphasis was almost entirely on what a wonderful, kind man Jesus was, how people mistreated him but know better now, how much Jesus cares whenever people or warm-blooded animals that aren't raised for food are suffering, and in general, how much better he is than everyone else but how much he likes us anyway, and what a good idea it is to try to be more like him. Which it generally was, as he was presented as being compassionate, honest, forgiving, intelligent, perceptive, tolerant, standing up for the underdog, making bad people decide to be good, etc. This was not a "liberal" church except by decadent post-modern standards that label any criticism of infantile narcissistic self-indulgence as "liberal"; it was deservedly considered very strict and austere by other denominations. Another type of "religious behavior", which is not mutually exclusive, is to identify with a group or political movement and adopt religious views associated with that group or ideology, partly for group identity and partly as a defense against ethical criticisms ("since Gawd sed to kill teh gayz it must be moral to discriminate against them"). This can be done somewhat sincerely, grossly insincerely (Tom Tancredo, Bobby Jindal, Ann Coulter), or in a manner indicating a profoundly disturbed psyche (Christine O'Donnell). I'm sorry for mentioning politicians, but they make such great examples. Plenty of repulsive politicians have been communist or ostentatiously, hypocritically "liberal", let's not side track any further than the side track we're already on. Yet another type is to attempt to indulge authoritarian fantasies up by self-identifying as the "one true prophet". Examples of this abound, and are often associated with violent events. While it's true that people are unlikely to easily give up these reinforcing behaviors easily, many creationists would switch in a flash. Tom Tancredo probably "converted" from Catholicism to creationism because the Pope is only hard core right wing on issues that have something to do with sex, and can be outright "progressive" on issues like war, torture, death penalty, health care, programs for the needy, etc. Meanwhile, you can find a Protestant clergyman who is right wing on every issue (or "progressive" on every issue), so Tancredo presumably found someone whose God coincidentally commands exactly what you need to support to get elected in some designer-forsaken gated community and "converted". A lot of the other creationists, from the trolls here on up, are just wanna-be authoritarian rulers or the like, and their sincerity is about as deep as I perceive that of some of those I have mentioned here to be.

Here's something else you all may find interesting:

http://www.sciencedaily.com/releases/2010/12/101216142523.htm

Kris said:

John Harshman said:

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

No, because a genus, like any other taxonomic rank, has no actual meaning. You could call the same clade a genus, a family, or even a phylum depending on your personal taste. Now, there have been occasional proposals to give ranks a real meaning. Charles Sibley proposed to do it based on genetic distance values, as you seem to imply. John Avise (and others before him) proposed to do it based on time of origin, which is not quite the same thing given that different genomes can evolve at different rates (not to mention different parts of the same genome). So far, though, none of these attempts has been popular, probably because they just aren't practical -- we don't have the necessary data to make the determinations in most cases -- and because if applied across a wide taxonomic scope it would require massive re-assignment of ranks. As with the case you raise: either Drosophila becomes a class (or higher), or Amniota becomes a genus. Neither of these is likely to be accepted.

That's just one of the problems with science. Personal tastes have way too much to do with the way things are even named/labeled, let alone with how those things may be related to each other, or how they originated, or interact with their environment, etc., etc., etc. E.g., how many definitions of the word "species" are there? Yeah. Nothing in nature cares one iota what we humans call it. If we humans can't even agree on what the labels mean, how are we ever going to really figure out anything else, and agree on that too?

Kris said:

stevaroni said:

Kris said: I really can't avoid most of the problems since most scientists won't listen to anything that might improve the status quo.

Huh? You do realize that true fame in science comes not maintaining the status quo, but from upending it, and proving that the current explanation is wrong, or at least incomplete, don't you? After all, Copernicus and Galileo are famous for demonstrating that, contrary to common belief, the Earth did move and orbited the Sun. Newton is famous for upending two millenia of "classical" mechanics. Einstein if famous for demonstrating that Newton wasn't all that and a bag of chips. And, of course, Darwin is famous for making an, ahem, slightly controversial observation about the origins of man. The way forward in science is to disturb the status quo. That's how you get famous.

So then, you're saying that scientists are or should be motivated by a desire for fame?

I would say that some scientists are motivated by that but some just want to stay employed (or keep the grant money coming in).

Either can cause a scientist to accept or rebuke any criticisms of, or proposed changes to, the status quo. Their status quo. Was Darwin's work really about the "origins of man"?

Stuart Weinstein said:

Kris said:

John Harshman said:

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

No, because a genus, like any other taxonomic rank, has no actual meaning. You could call the same clade a genus, a family, or even a phylum depending on your personal taste. Now, there have been occasional proposals to give ranks a real meaning. Charles Sibley proposed to do it based on genetic distance values, as you seem to imply. John Avise (and others before him) proposed to do it based on time of origin, which is not quite the same thing given that different genomes can evolve at different rates (not to mention different parts of the same genome). So far, though, none of these attempts has been popular, probably because they just aren't practical -- we don't have the necessary data to make the determinations in most cases -- and because if applied across a wide taxonomic scope it would require massive re-assignment of ranks. As with the case you raise: either Drosophila becomes a class (or higher), or Amniota becomes a genus. Neither of these is likely to be accepted.

That's just one of the problems with science. Personal tastes have way too much to do with the way things are even named/labeled, let alone with how those things may be related to each other, or how they originated, or interact with their environment, etc., etc., etc. E.g., how many definitions of the word "species" are there? Yeah. Nothing in nature cares one iota what we humans call it. If we humans can't even agree on what the labels mean, how are we ever going to really figure out anything else, and agree on that too?

Unfortunately nature doesn't always oblige us by putting objects into nice neat categories. Its not a problem of Science, but a problem for Science. Putting things into categories and understanding patterns is how humans come to understand the world. Similar problem in geology is characterizing rocks. You harp on the disagreement above, but ignore the thousands of points of agreement that exist. Isn't it past your bed time?

Kris said:

stevaroni said:

Kris said: I really can't avoid most of the problems since most scientists won't listen to anything that might improve the status quo.

Huh? You do realize that true fame in science comes not maintaining the status quo, but from upending it, and proving that the current explanation is wrong, or at least incomplete, don't you? After all, Copernicus and Galileo are famous for demonstrating that, contrary to common belief, the Earth did move and orbited the Sun. Newton is famous for upending two millenia of "classical" mechanics. Einstein if famous for demonstrating that Newton wasn't all that and a bag of chips. And, of course, Darwin is famous for making an, ahem, slightly controversial observation about the origins of man. The way forward in science is to disturb the status quo. That's how you get famous.

So then, you're saying that scientists are or should be motivated by a desire for fame?

Was Darwin's work really about the "origins of man"?

Stuart Weinstein said:

Kris said:

stevaroni said:

Kris said: I really can't avoid most of the problems since most scientists won't listen to anything that might improve the status quo.

Huh? You do realize that true fame in science comes not maintaining the status quo, but from upending it, and proving that the current explanation is wrong, or at least incomplete, don't you? After all, Copernicus and Galileo are famous for demonstrating that, contrary to common belief, the Earth did move and orbited the Sun. Newton is famous for upending two millenia of "classical" mechanics. Einstein if famous for demonstrating that Newton wasn't all that and a bag of chips. And, of course, Darwin is famous for making an, ahem, slightly controversial observation about the origins of man. The way forward in science is to disturb the status quo. That's how you get famous.

So then, you're saying that scientists are or should be motivated by a desire for fame?

No. He's pointing out that your claim that scientists don't want to upset the *status quo* is stupid. For if that were the case, momentous discoveries would never happen or be acknowledged. Science is about challenging the status quo. That is why tests upon tests have been performed on fundamental theory like Quantum Mechanics or GR. Even though QM has in some cases been tested to a precision of one part in a billion billions, new and more precise experiments will be done in the future. Why? cuz any deviation from theory would be important. If science was overly concerned with status quo, such research would have ended decades ago.

I would say that some scientists are motivated by that but some just want to stay employed (or keep the grant money coming in).

You have completely missed the point.

Either can cause a scientist to accept or rebuke any criticisms of, or proposed changes to, the status quo. Their status quo. Was Darwin's work really about the "origins of man"?

You are familiar with Darwin's work, "Descent of Man"? Isn't it past your bed time?

Kris, you keep writing that science has "messes" and needs to "clean up its act."

What specific changes do you advocate?

Kris said: When considering, claiming, or referring to the 'scientific method', the scientific methods should be standardized (as much as possible) if scientists want anyone else to take 'scientific method' seriously.

Of course different people have different ways of defining standards, methods, and the 'scientific method', but that's one of the problems in science. There are too many 'personal tastes', even with some of the most basic things.

Obviously, many scientists (and most people here whether scientists or not) expect ID/creationists to use very strict standards and methods to support or prove their claims. I don't think it's unreasonable to expect the same from scientists.

SWT said: Kris, you keep writing that science has "messes" and needs to "clean up its act." What specific changes do you advocate?

Kris said:

Stuart Weinstein said:

Kris said:

John Harshman said:

Stanton said: If D. melanogaster and D. virilis are molecularly clocked as being as distant as humans are to lizards, would that quality alone, merit splitting the Drosophila subgenera (Sophophora, D. Drosophila spp, etc) into separate, distinct genera?

No, because a genus, like any other taxonomic rank, has no actual meaning. You could call the same clade a genus, a family, or even a phylum depending on your personal taste. Now, there have been occasional proposals to give ranks a real meaning. Charles Sibley proposed to do it based on genetic distance values, as you seem to imply. John Avise (and others before him) proposed to do it based on time of origin, which is not quite the same thing given that different genomes can evolve at different rates (not to mention different parts of the same genome). So far, though, none of these attempts has been popular, probably because they just aren't practical -- we don't have the necessary data to make the determinations in most cases -- and because if applied across a wide taxonomic scope it would require massive re-assignment of ranks. As with the case you raise: either Drosophila becomes a class (or higher), or Amniota becomes a genus. Neither of these is likely to be accepted.

That's just one of the problems with science. Personal tastes have way too much to do with the way things are even named/labeled, let alone with how those things may be related to each other, or how they originated, or interact with their environment, etc., etc., etc. E.g., how many definitions of the word "species" are there? Yeah. Nothing in nature cares one iota what we humans call it. If we humans can't even agree on what the labels mean, how are we ever going to really figure out anything else, and agree on that too?

Unfortunately nature doesn't always oblige us by putting objects into nice neat categories. Its not a problem of Science, but a problem for Science. Putting things into categories and understanding patterns is how humans come to understand the world. Similar problem in geology is characterizing rocks. You harp on the disagreement above, but ignore the thousands of points of agreement that exist. Isn't it past your bed time?

I must say I'm surprised at you Stuart, well, maybe not all that much, based on what I've seen around here. I thought you might see how your statement about defining something applies (or at least should) to science as well as ID/creationism. I'll bet you regret ever making that statement now, because it can be reasonably held against you, or pretty much anyone else who expects ID/creationists to define something and instantly bashes them when they don't or won't do it to your satisfaction.

Kris said:

eric said:

Kris said: Something else to think about: if the 'scientific method' is allegedly so standardized and is truly accepted and practiced by scientists, then why do so many scientists fight with each other so often, including over the methods and standards they use?

You are confusing method writ large with method writ small. When creationists attack the scientific method, they are attacking basic principles like the limitation of evidence to empirical observables. The concept of reproducibility and the scientific rule of thumb that says irreproducible and unconfirmable results will not be give much weight (if any). They are not talking about whether in last Tuesday's extraction Bob should've held the pipette at 90 degrees instead of 45 degrees. That is also a scientific methodology question. Scientists can argue about those sorts of details until the cows come home and there is no real significance to the scientific method writ large. You are falling for a classic creationist argument which claims that disagreements between scientists about how an experiment was performed somehow invalidates major scientific findings. This argument is bogus. Its bogus first because findings like evolution and so on are the result of enormous numbers of independent experiments reaching the same conclusion; no individual experiment wipes the slate clean. Its bogus second because they have no alternative method to put in its place. When (my example) Alice and Bob argue about pipettes, Alice is proposing an alternative methodology that we can test. When Behe (in reality) argues that science should allow for supernatural causes, he proposes no method at all for doing so. Nothing we can test. He wants to sneak divine revelation in without ever going through the process of determining whether science + revelation is better than science - revelation.

When considering, claiming, or referring to the 'scientific method', the scientific methods should be standardized (as much as possible) if scientists want anyone else to take 'scientific method' seriously. The standards and/or methods scientists use is foundational to the 'scientific method'.

Obviously, many scientists (and most people here whether scientists or not) expect ID/creationists to use very strict standards and methods to support or prove their claims. I don't think it's unreasonable to expect the same from scientists.

If any claim by science is based on non-standardized methods, or variable standards, don't be too surprised when people are reluctant to accept those claims.

I think you'd find that the average person will usually accept claims by science that have strong evidence in their favor AND fit into how that person perceives strong evidence. If a scientist says that a cement sidewalk is 'hard', the average person will agree and quickly accept it. But, if a scientist says that studies of mitochondrial DNA help prove evolutionary theory, the average person (and other scientists) may not be so quick to agree and accept it, especially if that person (or scientist) has studied some or all of the standards and/or methods used by the scientists making the claim, and finds them questionable or faulty. (Think arsenic/bacteria for example, in regard to methods/standards.)

There are many scientific studies that contradict each other, even though the same things were studied and allegedly with the same methods and/or standards. There are also many scientific studies that contradict each other simply because they didn't use the same standards and/or methods, yet each study claims to have used accepted or proven methods and/or standards, and of course each scientist or team of scientists vouches for the quality and veracity of their study.

Kris said:

DS said: Robin, The concept of a molecular clock refers to the observation that there is a relatively constant rate of mutation for certain parts of certain genes for certain periods of time in certain groups of organisms. This can be determined by calibrating the times of divergence using the fossil record. For example, the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years. So, if we can calibrate the clock, we can estimate divergence times based on genetic divergence. However, you are correct. Things are usually a lot messier than this. that is why there are so many restrictions and qualifiers required. For example, the calibration used for vertebrates cannot be used for insects and the clock ticks at different rates for mitochondrial DNA than for nuclear genes and for different rates for different mitochondrial genes. So yes, things can get very messy. Still, the mitochondrial COI gene has proven to be extraordinarily useful for many different groups. Thus it is currently the basis of the Barcode of Life project. However, the various taxonomic ranks are still somewhat arbitrary, due to rate heterogeneity in different groups. So even if we can agree on a definition of species, higher groups may still remain an artificial construct, regardless of degree of divergence or even phylogenetic relationships.

Are you saying that the rate of amino acid replacements in vertebrates can be shown to be relatively constant for hundreds of millions of years by using the fossil record? Yeah, if only we could agree on a definition of "species".

eric said:

Kris said: When considering, claiming, or referring to the 'scientific method', the scientific methods should be standardized (as much as possible) if scientists want anyone else to take 'scientific method' seriously.

However, I may also actively choose to use a different method to measure the same quantity. This is extremely valuable as a means of eliminating systemic errors. If there are no systemic errors, two entirely different methods should yield the same result (within their respective margins of error). Good scientists sometimes intentionally choose to use multiple methods to gather the same information because it helps you identify any biases in the methods used. So your thing about being taken seriously makes no sense to me. Moreover, using different methods may help you identify something you would've never discovered with any single method. Without GALLEX and Super Kamiokande yielding different results, we may not have discovered the oscillation of solar neutrinos.

Of course every real scientist knows that the scientific method is "standardized" as much as it possible already. Now matter what the study question or the methods, the same important issues are always addressed in any good study:

1) Testable hypothesis

2) Good experimental design

3) Appropriate methods

4) Ability to be reproduced

5) Sufficient sample size

6) Appropriate analysis and statistical significance

7) Peer review

If "someone" has a problem with any particular scientific study. then"someone" can publish a rebuttal paper. Whining and moaning about things you don't understand isn't really going to help now is it?

Now if "someone" has any suggestions for improvement, then "someone" might take that other "someone" seriously. Until then, "someone" can piss off.

Kris said: I'm not condemning all of science. Why are you guys so defensive? You act like a gung-ho, angry, religious zealot who just had someone tell him/her there's no such thing as God and that absolutely everything he/she ever believed in is false.

Kris: Actually, I haven’t and don’t ignore the thousands of points of agreement that exist in science. I agree with many of those points but not just because others agree with them. The amount of people agreeing or disagreeing about something doesn’t necessarily have an effect on me. If it did, I’d probably be religious. What if a creationist were to say that you ignore the points of agreement (whether thousands or otherwise) that exist between creationists? Would that change your mind about the veracity, reputation, and/or trustworthiness of the concept or practice of ID/creationism, either in whole or in part?

Robin -

You are not being "defensive".

The term "defensive" implies unreasonable objection to valid criticism.

Kris is defensive.

I can note objectively that every post Kris puts up consists of some combination of the following - worthlessly vague claims that "science" is somehow horribly flawed, worthlessly vague claims that he could tell "scientists" what to do, an uproariously evasive lack of specifics, and an implied worthless post-modern argument that creationism is "just as good" as science because science is so bad.

I will stick to that objective observation.

Kris said: So then, you're saying that scientists are or should be motivated by a desire for fame?

I would say that some scientists are motivated by that but some just want to stay employed (or keep the grant money coming in). Either can cause a scientist to accept or rebuke any criticisms of, or proposed changes to, the status quo. Their status quo.

Was Darwin's work really about the "origins of man"?

harold said: ... that creationism is "just as good" as science because science is so bad.

ben said:

SWT said: Kris, you keep writing that science has "messes" and needs to "clean up its act." What specific changes do you advocate?

Kris isn't here to advocate specific changes, Kris is here to cast as much aspersion as possible on science while pretending to value it. Note that although Kris has claimed to be a scientist, "science" and "scientists" are always referred to in 3rd person, and not a single example of anything has been offered from his/her own work or experience. Dishonest concern troll. Nothing to see here, move along.

Kris said: Does it matter who I am, or what I do, or where I work, or what my credentials are?

I pay attention to what people say, not how many diplomas they have on their walls.

Kris said:

ben said:

SWT said: Kris, you keep writing that science has "messes" and needs to "clean up its act." What specific changes do you advocate?

Kris isn't here to advocate specific changes, Kris is here to cast as much aspersion as possible on science while pretending to value it. Note that although Kris has claimed to be a scientist, "science" and "scientists" are always referred to in 3rd person, and not a single example of anything has been offered from his/her own work or experience. Dishonest concern troll. Nothing to see here, move along.

I don't have much time right now so I'll respond to some comments and questions from others later, but I simply have to respond to you right now. You're not the first one who has said or implied that I'm not a scientist, or has asked me where I work or what kind of science I work at. Does it matter who I am, or what I do, or where I work, or what my credentials are? Why would it matter? Is it so that you or someone else can compare me to themselves and see if they can beat my credentials, degrees, GPA, or some other irrelevant 'qualification' and then try to use it against me in a debate? Would you also ask who my teachers, associates, or mentors are or were, or which books or papers I have read, for the same reason? If I said I graduated from Harvard, or Princeton, or MIT, or some obscure community college, would it make any relevant difference? If I told you the size of my dick would you compare it to yours and hope to beat me there too? Unlike many (most?) people I don't rely on my credentials, including GPA, places of employment, mentors, teachers, degrees, schools, cited articles/papers/books, etc., just to impress others, or to use in a blustering attempt to bolster what I say. If I bring up any of that stuff it will be because it's relevant at the time and to the points I'm making. I know and have met people with tons of fancy credentials who are dumber than a post and I also know and have met people with no fancy credentials who are very sharp and knowledgeable. I pay attention to what people say, not how many diplomas they have on their walls. I don't worship anyone and I'm not intimidated by anyone. I know some things and there are lots of things I don't know. I have an insatiable thirst for knowledge about nature and I try very hard to keep as open a mind as possible. I don't care which or how many degrees you or anyone has or which schools you or they attended or graduated from. I don't care how many times someone's writings have been cited. I don't care where you or anyone else has worked or what your title is. I care about substance, not braggadocios fluff.

I don’t have much time right now so I’ll respond to some comments and questions from others later, but I simply have to respond to you right now. You’re not the first one who has said or implied that I’m not a scientist, or has asked me where I work or what kind of science I work at. Does it matter who I am, or what I do, or where I work, or what my credentials are? Why would it matter? Is it so that you or someone else can compare me to themselves and see if they can beat my credentials, degrees, GPA, or some other irrelevant ‘qualification’ and then try to use it against me in a debate? Would you also ask who my teachers, associates, or mentors are or were, or which books or papers I have read, for the same reason? If I said I graduated from Harvard, or Princeton, or MIT, or some obscure community college, would it make any relevant difference? If I told you the size of my dick would you compare it to yours and hope to beat me there too? Unlike many (most?) people I don’t rely on my credentials, including GPA, places of employment, mentors, teachers, degrees, schools, cited articles/papers/books, etc., just to impress others, or to use in a blustering attempt to bolster what I say. If I bring up any of that stuff it will be because it’s relevant at the time and to the points I’m making. I know and have met people with tons of fancy credentials who are dumber than a post and I also know and have met people with no fancy credentials who are very sharp and knowledgeable. I pay attention to what people say, not how many diplomas they have on their walls. I don’t worship anyone and I’m not intimidated by anyone. I know some things and there are lots of things I don’t know. I have an insatiable thirst for knowledge about nature and I try very hard to keep as open a mind as possible. I don’t care which or how many degrees you or anyone has or which schools you or they attended or graduated from. I don’t care how many times someone’s writings have been cited. I don’t care where you or anyone else has worked or what your title is. I care about substance, not braggadocios fluff.

So the answer is no, Kris is not a real scientist as he claimed. ANd the answer is no, he has no intention of actually reading the paper that is the topic of this thread or actually discussing any of the science in it. Glad he cleared that up once and for all.

Now Kris, if you want to argue about the molecular clock, you really should understand what you are talking about. Here area few references to get you started. If you are a real scientist you will read them. If not, you will be admitting that you cannot. In that case, my original diagnosis about you just having a bad case of science envy will once again be confirmed.

Goodman (1987) Globins: A case study in molecular phylogeny. Cold Spring Harbor Symp Quant Biol 52:875-890.

Ayala et. al. (1998) Origin of the Metazoan phyla: Molecular clocks confirm paleontological estimates. PNAS 95(2):606-611.

Lynch (1993) A method for calibrating molecular clocks and its application to animal mitochondrial DNA. 135:1197-1208.

Kris said:

ben said:

SWT said: Kris, you keep writing that science has "messes" and needs to "clean up its act." What specific changes do you advocate?

Kris isn't here to advocate specific changes, Kris is here to cast as much aspersion as possible on science while pretending to value it. Note that although Kris has claimed to be a scientist, "science" and "scientists" are always referred to in 3rd person, and not a single example of anything has been offered from his/her own work or experience. Dishonest concern troll. Nothing to see here, move along.

I don't have much time right now so I'll respond to some comments and questions from others later, but I simply have to respond to you right now. You're not the first one who has said or implied that I'm not a scientist...etc., etc.

I care about substance

I don’t have much time right now so I’ll respond to some comments and questions from others later, but I simply have to respond to you right now.

Robin said, quoting Chris the Creationist Christmas troll: "You made the claim that you are a scientist, without any prompting from anyone here. If it doesn't matter (and it is certainly irrelevant to most folks here) why did you bring it up?"

"Robin said, in response to..."

Anybody wanna bet he's either an engineer or a "computer scientist"? Anyone?

fnxtr said: Anybody wanna bet he's either an engineer or a "computer scientist"? Anyone?

John Vanko said: "Robin said, in response to..."

Robin said:

John Vanko said: "Robin said, in response to..."

??? Was this a misfire, John?

fnxtr said: Anybody wanna bet he's either an engineer or a "computer scientist"? Anyone?

while amoebas evolved the ability to blog.

stevaroni -

In defense of engineers -

1) Many creationist trolls who claim to be or imply that they are engineers or computer scientists are outright lying. They simply hope that biomedical people won't know enough about engineering to know that they are lying. They are usually wrong.

2) Many are technically doing a task with an occupational description of "(something) engineer" but don't have, and would not be able to obtain, an actually engineering degree.

That's not to say that there aren't some creationist engineers, but the numbers are exaggerated by the pretenders.

I have never seen an amoeba blogging, and I rotated through a clinical parasitology lab - although that was in the early days of the internet.

That should be "actual engineering degree" of course.

harold said: 1) Many creationist trolls who claim to be or imply that they are engineers or computer scientists are outright lying.

mrg -

Yes, it is indeed true that even the self-proclaimed engineers who actually are engineers are not qualified.

However, self-declaration of "engineer" or "computer scientist" status in trolls should be viewed with great skepticism.

Robin said: ??? Was this a misfire, John?

John Vanko said:

Robin said: ??? Was this a misfire, John?

(hoping you are a ma'am): "My Dear, I never misfire."

Robin said:

John Vanko said:

Robin said: ??? Was this a misfire, John?

(hoping you are a ma'am): "My Dear, I never misfire."

Heh! Well, though I'm a guy, that's still funny. I teed that one up without thinking about it.