…and this is a 
Last week, I described the lectures I attended at the Chicago 2009 Darwin meetings (Science Life also blogged the event). Two of the talks that were highlights of the meeting for me were the discussions of stickleback evolution by David Kingsley and oldfield mouse evolution by Hopi Hoekstra — seriously, if I were half my age right now, I'd be knocking on their doors, asking if they had room for a grad student or post-doc or bottle-washer. They are using modern techniques in genetics and molecular biology to look at variation in natural populations in the wild, and working out the precise genetic changes that led to the evolution of differences in development and morphology. They are doing stuff that, back when I actually was a graduate student, would have been regarded as technically impossible; you needed model systems in the laboratory to have the depth of molecular information required to track down the molecular basis of novel morphs, and you couldn't possibly just grab some interesting but otherwise unknown species out on a beach or a pond and work out a map and localize genetic differences between individuals. They're doing it now, though, and making it look easy.
Then there were all the other talks in population genetics and paleontology (and the talks on history and philosophy, which I almost entirely neglected)…this was a meeting that everywhere demonstrated major advances in our understanding of evolution. Every talk was about the successes of evolutionary theory and directions to take to overcome incomplete areas of understanding; this was a wonderfully positive and promising event that should have impressed all the attendees with the quality of the work that has been done and the excitement of the potential for future research. Like I said, there were a whole bunch of people here that I want to be when I grow up.
Well, normal people would feel that way. Paul Nelson, that creationist, was also there. Nelson is a weird guy; he's always hanging around the edges of these scientific meetings, and you'd think that after all these years of lurking, he'd actually learn something, but no…the only skill he has mastered is the art of ignoring what he doesn't like and incorporating fragments of sentences into his armor of ignorance. It's very sad.
I talked with Nelson briefly at a reception at the meetings, and we both agreed on the quality of Kingsley's work — but that's about all. Nelson thought it supported ID better than neo-Darwinian evolutionary theory. His argument was that a) all anybody ever described was loss of features, and b) a large parent population was the source of all the allelic variation in the sub-populations studied, which is what ID predicts. He didn't mention their favorite magic word of "front-loading", but I could see what he was thinking.
How Nelson can hang about on the fringes of the evo-devo world and not notice that what was described by modern empirical research is exactly what the evo-devo theoreticians expected is a mystery — these were results that fit beautifully what science, not the wishful voodoo of intelligent design creationism, predicts.
Both Kingsley and Hoekstra are looking at recent species, subpopulations that separated from parent populations within the last ten thousand years, and have adapted relatively rapidly to new environmental conditions. The sticklebacks are fragments of marine species that were isolated in freshwater streams and lakes, while the beach mice are parts of a widespread population of oldfield mice that are adapting to gulf coast islands. They are also working with populations that can be bred back to the root stock, that retain the ability to do genetic crosses, so of course the variation is not on the magnitude of turning fins into limbs (we need large amounts of geological time to do that; it's the kind of work Neil Shubin would do, and unfortunately, he can't cross Tiktaalik with Acanthostega). Complaining that the variants the real scientists are looking at aren't the kind that the creationists want is a particularly clueless kind of whine, since the scientists are intentionally focusing on the variants that are amenable to dissection by their techniques.
The other aspect of their work that confirms evo-devo expectations is that what they're discovering is that the genetic mechanisms behind morphological variants are changes in regulatory DNA — that what's happening is that regulatory genes like Pitx1 or Mc1r are being switched off or on. We anticipate that a lot of morphological novelty is going to be generated by switching genes off and on, and by recombination of patterns of gene expression. Nelson and Behe are reduced to carping on the sidelines that observed variants are just the product of getting large effects by trivially flipping switches, while all the real biologists are out there in the middle of the work happily announcing that we can get large-scale morphological effects by simply flipping switches, and hey, isn't that cool, and doesn't that tell us a lot about the origins of evolutionary novelties? It's not just a to-may-to/to-mah-to difference in interpretation, this is a case of the creationists wilfully and ignorantly missing the whole point of an exciting line of research.
There's also a fundamental failure of comprehension. Creationists see loss of a feature like pelvic spines, or a reduction in pigmentation, and declare that the evolutionary evidence is "all breaking things and losing things". Wrong. What we have here is a complete lack of understanding of developmental genetics. What we typically find are changes in the pattern of expression of developmental genes, not wholesale losses. In the stickleback, Pitx1 is still there; what's different is that the places in the embryo where it is turned on have changed, the map of the pattern of gene expression has shifted. You cannot describe that as simply a broken gene. Similarly, in the mouse, Hoekstra showed that the expression of genes that reduce pigmentation has expanded. We've seen the same thing in the blind cavefish; a creationist looks at it and says it's just broken and has lost its eyes, but the scientists look closer and see that no, the fish have actually increased gene expression and expanded the domain of a midline gene.
Just wait for the detailed analysis of jaw morphology in cichlid fishes. These animals have radically different variants in feeding structures, which is thought to be the root of their adaptability and the radiation of different forms, and I guarantee you that the creationists will ignore the morphological novelties and focus on the fact that to achieve that, some genes will be downregulated (I also guarantee you that there will be such shifts in expression). It's "all breaking things and losing things", after all; just like baking a cake involves breaking eggs.
I don't know how the creationists fit known variations in the coding sequences of genes (how do you translate a single-nucleotide polymorphism into their vision of all change being a matter of losses?) into their idea that all evolution is a matter of breaking DNA, or how they can claim all novelty requires a designer when people can track the progression of morphological shifts in the tetrapod transition, for instance, across tens of millions of years. It seems to be their desperate 21st century excuse in the face of the overwhelming progression of information from 21st century biological science.
Nelson ends his skewed summary of the meeting with the comment that "It's a heck of a lot of fun to attend a conference like this, if you don't mind being the butt of jokes." I'm sure. I suppose Nelson could have even more fun if he put on a dunce cap and drooled a lot, because that's basically his role at these meetings anyway — he's the butt of jokes because he shows up and then happily demonstrates his ignorance about what's going on. It's not a role I'd enjoy, but the gang at the clown college called the Discovery Institute have a slightly different perspective, I suppose.
Life Science
Comments
Posted by: Valdyr | November 4, 2009 10:29 AM
Does this count as a Deep Rift? No? Maybe just a little one?
Posted by: David | November 4, 2009 10:36 AM
I am just getting into actually learning the nitty-gritty details about evolutionary processes, but it seems to me that the answer to this guy is simply, it is not a loss, there is no value other than what benefits it gives an animal or plant in a particular ecological niche. So "loss" of eyes under evolutionary theory is not really a "loss" but if anything a "gain" in saving resources for things a blind cave fish may need, since sight may no longer be a selective factor.
Posted by: Bodach | November 4, 2009 10:41 AM
I wish I could have had Nelson's seat in Chicago. I wouldn't have understood half of what I heard but I'd at least appreciate the work that was being discussed.
Posted by: David Marjanović, OM | November 4, 2009 10:44 AM
Our loss of fin rays made it possible to have separate fingers & toes. You can't have an opposable thumb inside a fin.
Yes, it is a loss. But so what?
Why do people laugh at creationists?
Only creationists don't understand why!
Posted by: Deepsix | November 4, 2009 10:46 AM
Science hard. Make brain hurt. /creationist mode off.
Posted by: Alan | November 4, 2009 10:52 AM
Unbelievable!!! Typical creationist; do nothing but moan about evolution and then when presented with real science done by actual researchers claim it actually supports their deluded views. A man who thinks the world is 6,000 years old should be banned from all scientific lectures and talks. He is clearly not interested in science, so why does he bother going?
His claims about the research supporting ID remind me of a video C0nc0rdance made - http://www.youtube.com/watch?v=c9dK_7_aGCs - at the end he says "if research biology were a sport, the Intelligent Design movement would be a bitter reject from the team, booing and yelling insults from the sidelines. Then claiming credit when the team scores."
Posted by: Glen Davidson
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November 4, 2009 10:55 AM
While I don't deny that adapting a leg from a fin is a lot harder to do than simply losing function, the problem for tards like Nelson is that even the former is about "breaking things." That's what a mutation is.
Then they'll accept the evidence of mutation plus natural selection for the one, and not the other, with not an iota of honest explanation for why they would do this. Only their prejudices will not allow that evidence for one will similarly be evidence for the other.
Glen D
http://tinyurl.com/mxaa3p
Posted by: SteveF | November 4, 2009 10:59 AM
This idea about breaking things is becoming an increasingly common one in creationist circles. They acknowledge that evolution and adaptation can do some funky things, but because it involved "breakages", ultimately you aren't ever going to be able to develop serious complexity from evolutionary mechanisms. Hopi Hoekstra's work has been attacked in this regard before, by Georgia Purdom of AiG. Commenting on this paper:
Hoekstra, H.E. et al. (2006) A single amino acid mutation contributes to adaptive color pattern in beach mice. Science. 313, 101-104.
Purdom writes:
From a creationist perspective, this research provides us with yet another example of a beneficial outcome of a mutation in a given environment allowing an organism a selectable advantage. Mutations lead to loss of information, and while the organism may be more well suited for its current environment, it may have lost the ability to adapt to other environments. The mutation described in this Science paper does not address the origin of the melanin gene or pigmentation, only the loss of them, thus it is not relevant to the discussion of molecules-to-man evolution.
http://www.answersingenesis.org/articles/aid/v1/n1/evolution-or-adaptation
At the opposite end of the creationist spectrum, Michael Behe made basically the same argument in response to a paper demonstrating that beneficial mutations are actually substantially more common than previously believed. That paper is:
Perfeito, L. et al. (2007) Adaptive mutations in bacteria: high rate and small effects. Science, 317, 813-815.
Behe wrote:
While the result is interesting, readers of The Edge of Evolution will not be very surprised by it. As I showed for mutations that help in the human fight against malaria, many beneficial mutations actually are the result of breaking or degrading a gene. Since there are so many ways to break or degrade a gene, those sorts of beneficial mutations can happen relatively quickly. For example, there are hundreds of different mutations that degrade an enzyme abbreviated G6PD, which actually confers some resistance to malaria. Those certainly are beneficial in the circumstances. The big problem for evolution, however, is not to degrade genes (Darwinian random mutations can do that very well!) but to make the coherent, constructive changes needed to build new systems. The bottom line is that the beneficial mutations reported in the new Science paper most likely are degradatory mutations, and so don’t address the challenges outlined in The Edge of Evolution.
So it's a pretty common argument among creationists. I think Behe wrote something similar in the past few weeks in response to the most recent paper from the Lenski lab in Nature, but I can't be arsed finding it.
Luskin regularly makes this argument too. Here he is attacking Sean Carroll's evo-devo discussions:
http://www.ideacenter.org/contentmgr/showdetails.php/id/1432
Posted by: Eric Mattingly | November 4, 2009 10:59 AM
"When a theory is defined by what it is not -– e.g., Darwinian evolution holds that a transcendent intelligence did not design living things -– then that theory cannot help but cart its opposition around, wherever it goes. 'Yes, I know he smells bad,' says Theory Q regretfully, about supposedly refuted Theory P, who is sitting in the back seat picking his nose, 'but I am defined in opposition to Mr. P, so he has to come along, whether we want him around or not.'
That's clever, but I doubt anyone really defines evolution in opposition to ID. It would be like saying TOE defines itself in opposition to Lamarckianism as well. Not to mention the infinite number of potential (if not actual) theories that contradict it.
Posted by: SteveF | November 4, 2009 11:01 AM
By the way, being slightly mischevious, this criticism based around "loss" isn't totally restricted to creationists. Funnily enough, Hopi Hoekstra and Jerry Coyne make a kind of related argument in their big Evo-Devo critique paper:
Hoekstra, H.E. and Coyne, J.A. (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution, 61, 995-1016.
they write:
Table 1 clearly shows that we have far more evidence for structural than for cis-regulatory changes. While the most well supported examples of cis-regulatory based adaptation (the first three entries of Table 1) have not yet identified precise causal mutations, there are, in contrast, many examples of individual structural mutations contributing to adaptation. Moreover, most of the cis-regulatory examples involve loss of an ancestral trait (usually via loss-of-function alleles), whereas the structural mutations involve both gains and losses of traits.
and
Finally, we must recall that these three studies focus primarily on the loss of traits (pelvic spines, wing spots, and trichomes). Supporting the evo devo claim that cis-regulatory changes are responsible for morphological innovations requires showing that promoters are important in the evolution of new traits, not just the losses of old ones.
Hoekstra and Coyne's critique of the evo-devo program is massively more sophisticated than that of the creationists, but it is interesting to note an echo of similarity.
Posted by: Foggg
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November 4, 2009 11:03 AM
Nelson could have instead spent his time at The Legacy of Darwin Conference, put on by the DI and Focus on the Family, with Nelson's compadres Meyer, Behe, West, Berlinski (featured in the movie Expelled: No Intelligence Allowed!) and assorted seminary professors and apologists.
And Danny Oertli, "who will be helping us with our mission of touching both the head and the heart by leading worship at various times during the conference."!
From the press release for secular media:
From the press release for religious organizations:
Too bad sciency Chicago couldn't have played some catchy "heart-touching music", dedicated to Nelson.
Posted by: freethinker | November 4, 2009 11:05 AM
Religion is the most powerful means of thought control ever invented, and science happens to be its most dangerous challenge. The Creationists attack on evolution is not about logic, but simply a means to preserve their influence and wealth.
Posted by: Alessa Mendes | November 4, 2009 11:06 AM
I fear that the "gaps" that Creationists seek within science will never be closed, even with applauding progress such as what you have now presented, in brief. It's not so much that gaps exist - they do, and scientists are thankful for them - but Creationists NEED gaps to exist. So, even if there were none, they would find something to validate their beliefs...
Thanks for the update. I love to hear about things like this.
Posted by: Steve
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November 4, 2009 11:09 AM
"...which is what ID predicts."
ID predicts something?
Posted by: co | November 4, 2009 11:22 AM
Love the statement on Nelson's blog:
Wow. Just . . .. Wow.
Posted by: Cheryl | November 4, 2009 11:33 AM
After reading this (and other recent postings) all I can say is - PZ, I want to be you when I grow up. The fact that I am older than you is not a deterrent.
Posted by: Hipple, Rev Paul T | November 4, 2009 11:50 AM
When will you darwinists ever understand that when God sets down to create a new species, it is better than any new species that has ever come before. God's Creation is one of ascendancy upon the ladder towards Perfection, with Man, and some women, resting in God's bosom at the pinnacle! This is His plan.
In contrast, Mutations are the toys lying about in the Demon's Sandbox, and therefore, always deleterious. Therefore, the subject matter of which you speak is immaterial. That is all Brother Nelson is trying to teach you.
As for the stickleback fish, did any of you bother to wonder WHY the fish is now "isolated" in fresh water lakes, away from its former marine habitat? Do you bother to think WHY God is punishing that creature?
Good grief!
-RPTH
Posted by: MrFire
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November 4, 2009 11:58 AM
@17:
You are sooooo a Poe.
Posted by: Rey Fox | November 4, 2009 12:31 PM
""When a theory is defined by what it is not -– e.g., Darwinian evolution holds that a transcendent intelligence did not design living things -– then that theory cannot help but cart its opposition around, wherever it goes."
Must be why we keep the phlogistonists and the luminierous etherists around after all these years. Or maybe it's just that Nelson still doesn't know how science works.
Posted by: Les Lane | November 4, 2009 1:03 PM
Paul T. Hipple appears to be as advertised (a dominionist no less). He nicely demonstrates a standard fundamentalist failing which is the inability to distinguish rationalizing from science (or perhaps he sees rationalizing as superior to science.)
Posted by: jbeck.myopenid.com
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November 4, 2009 1:21 PM
Paul Nelson is like a mangy cur scrabbling around an overlord's table for scraps, any scraps. He quotes Dr. Betty Smocovitis's paper on the Darwin Centennial event at U.Chicago in 1959 here http://bit.ly/366Alm to trot out some mangled and dishonest inference about the state of evolutionary biology then and now. Nelson probably imagines that his readers like his catatonic flunkies will not take the trouble to read up on his references, and goes as far as to paste the link into his screed. Reading the article is yet another confirmation of the depths that IDiots will plumb to cook up cause for their IDiocy. The paper is largely about the events leading to the conference and the deliberations that led to what was scheduled. And although Dr. Smocovitis does mention that the emphasis on natural selection provoked a other biologists to question, she paints a picture of an emerging discipline that with far less by way of science and evidence managed to unify knowledge from disparate discipline into an integrated field of study. Evolution as a theory and idea enjoyed little acceptance outside the scientific community and the better read folks of the day, unlike today. Nelson manages to hamhandedly twist these points, insisting that a unified discipline is now rent with dissension (as if that means anything from the POV of science.
Every time you think that the IDiots and Cretinists have reached a new low in dishonesty, they surprise you by opening a trap door and pointing through it, "There, that's how low I can go."
Posted by: taranaki
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November 4, 2009 1:21 PM
Nelson is friends with Ron Numbers. They talked about it in their Bloggingheads TV diavlog. This diavlog started the protests that culminated after the Behe/McWhorter fiasco. Unfortunately, Nelson got a Ph.D. in philosophy from the University of Chicago - he and Dembski have stained my degrees from UofC. So Nelson could find out about the conference from Numbers, regular alumni channels, and other ways.
Nelson's wife is a pediatrician at Northwestern and Children's Memorial. She is a young earth creationist like Nelson. Has impressive credentials - Northwestern and Harvard. This is what I do not understand - she rejects the fundamental underlying principles of biology but uses it to treat patients.
Posted by: PoxyHowzes | November 4, 2009 1:22 PM
@#9 and #19
Darwinian evolution proposes mechanisms for the observed diversity of living things without making reference to a transcendent intelligence.
— no need at all for "defining" it by what it is not.
And BTW, what are all the other "evolutions" from which "Darwinian Evolution" is singled out?
Posted by: DLC
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November 4, 2009 1:48 PM
Well, really, I blame Pee Zed for all this.
No, not the host of the blog, but the Deity's science adviser.
You know, he looks suspiciously familiar somehow.
Oh, wait.. we'd have gotten the eye with the blind spot anyhow. never-mind... Carry on!
Posted by: amphiox | November 4, 2009 1:49 PM
David #2:
The loss/gain issue is also about the mechanism. The ID people always insist that mutations can only produce destructive loss - ie a gene is damaged leading to loss of function leading to loss of some phenotypic character. They cannot seem to comprehend how mutations can result in gain of function as well.
While it is certainly possible that a destructive mutation can result in the loss of a characteristic, for example a mutation in one of the genes regulating eye development that knocks out its function could result in an eyeless cave fish, or a deletion of a gene involved in the development of the pelvis could result in a stickleback losing its pelvic spines, research has demonstrated that this is not, in fact what happens.
In these cases, no genes have been deleted or destroyed, no genetic function lost. Instead the pattern of regulation - where and when certain genes are turned on and off, has changed. For example, the gene responsible for regulating pelvic spine growth in the sticklebacks has been switched off a the time and place during development that results in reduction of the spines, but the gene itself is still fully functional and still working perfectly in all the other places in times in development where it normally functions. In some of the blind cavefish, it turns out that the region of expression of a gene involved in jaw development (I think) expanded to overlap the region where the gene involved in eye development normally would have been expressed, resulting in inhibition of development of the eye. So eye loss was actually a neutral side effect (neutral because the cavefish no longer needed good vision) of a positive gain of function of a more powerful jaw. And the gene responsible for eye development was not destroyed, but continued to function (it has many other roles).
This is a simplification of course, but that's the general gist of it.
Posted by: jbeck.myopenid.com
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November 4, 2009 2:00 PM
Taranaki,
Beliefs don't matter as long as you aren't acting by them. Paul's wife may be a YEC, but she sure as heck wouldn't drink poisons and handle snakes.
Posted by: llewelly | November 4, 2009 2:02 PM
Every now and then, the random quote is coincidentally appropriate:
Posted by: Sastra
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November 4, 2009 2:08 PM
Being a scientific theory, evolution provides a mechanism. ID has no mechanism. That's a critical distinction. ID isn't about how a transcendent designer went about designing things -- it's about how evolution couldn't happen here, or here, or here. That's the only place it can go.
And it can't even go there. Or there. Or there.
What a statement, coming from a creationist. Projection, much, Mr. Nelson?
Posted by: Yaque | November 5, 2009 5:22 AM
And how about gene duplication?
That just about kills the IDiot "argument" about how mutation can't "create" "information"
(running out of quotation marks here, heh)
Each gene than diverges, increasing the complexity of the system, or eventually doing different things altogether.
I understand that that is how the clotting system developed, not to mention the "motor" for the flagellum.
IIRC (you guys can fill me in) molecular biologists have worked out whole lineages of gene groups.
Posted by: Pierce R. Butler | November 5, 2009 10:40 AM
... I could see what he was thinking.
Further revelation of Professor Powers, y'all.
Take notes - this all grows from training your Student Powers of precognition as to what Will Be On The Test!
Posted by: bsmocovi | November 5, 2009 5:46 PM
How nice to have my name--and work--used in vain. Here is my revenge quotation about celebrity Kirk Cameron's push for a Christianized version of Origin (original source from Gainesville Sun).
Enjoy
http://sensuouscurmudgeon.wordpress.com/2009/10/24/kirk-cameron-out-of-his-mind-says-professor/
Posted by: baju
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February 2, 2010 5:29 AM
A man who thinks the world is 6,000 years old should be banned from all scientific lectures and talks
Posted by: John Morales
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February 2, 2010 5:44 AM
baju, you mean expelled? ;)