Monday, February 20, 2006

Know your audience, or improving 60 year-old ideas isn't anti-Darwinian

In the followup on Paul Nelson's piece discussed a few days ago, Nelson responds to two criticisms another blogger raised.

PZ Myers has done a nice write-up of the paper Nelson was commenting on, relieving me of the need to do so. The take-home message is that there are striking similarities in the sets of genes involved in development of many complex structures, shared by widely divergent species. These "kernels" are highly conserved, and may well date back to the pre-Cambrian. The kernels themselves are seen as likely evolving via standard evolutionary processes, but "Once they were assembled, they could not be disassembled or basically rewired, only built on to."

Paul Nelson insists that this work undermines neo-Darwinism, and that Davidson agrees. Nelson also insists that neo-Darwinism is well-defined, but leaves the proof as an exercise for the reader. For reference, we'll take the Wikipedia definition:

The modern evolutionary synthesis (often referred to simply as the modern synthesis or the evolutionary synthesis), neo-Darwinian synthesis or neo-Darwinism, generally denotes the combination of Charles Darwin's theory of the evolution of species by natural selection, Gregor Mendel's theory of genetics as the basis for biological inheritance, and mathematical population genetics.
Nelson is correct that this is different from "evolutionary diversification and adaptation happened by some process, and we know natural selection was involved, mainly, probably, somehow." It means that there are genes, that they mutate in the ways I described earlier, that natural selection can change gene frequencies, that genetic drift and gene flow can also shift allele frequencies in populations, and those are all forms of evolution. Indeed, one could say that these are the only ways evolution happens.

This leaves the endosymbiotic hypothesis outside the mainstream of neo-Darwinism. It's silly to insist that we refer to neo-Darwinism (neo=new!) or the "modern synthesis" (modern=new!) only in ways compatible with what we knew in the 1930s and '40s (before my parents were born ≠ new!). We can talk about modern evolutionary biology as distinct from the "modern synthesis" and make an effort to refer to ideas which have developed in the last 60 years as neo-neo-Darwinism, or we can just recognize that scientific knowledge is a moving target. Nelson, like many creationists, is missing a key point here. It's a point that non-creationists can miss as well, so it bears some explaining.

Out of the simple mutations, natural selection, genetic drift, and gene flow, a number of complex patterns can emerge over long time-scales. The kernels Davidson and Erwin describe are one such pattern. A series of gene duplications, the simultaneous evolution (by all four methods found in any definition of neo-Darwinism) of a series of developmental pathways, all add up to a highly integrated system of interacting genes which regulate the development of, for instance, the heart in flies and in people. Davidson and Erwin don't dispute that the evolutionary mechanisms we teach in college biology are sufficient to explain this (as explained further by Myers, or at Deinonychus antirrhopus):
Critically, these kernels would have formed through the same processes of evolution as affect the other components, but once formed and operating to specify particular body parts, they would have become refractory to subsequent change.
Davidson and Erwin are building on the neo-Darwinism of the 1940s, not overturning it. What they are dealing with is integrating the ways genes interact throughout an organism's development, the way genes are regulated, and the way all of this ties into the evolution of the ways organisms develop. These are new things, exciting capabilities that have only existed for a couple decades. The field of evolutionary developmental biology (evo-devo to the cool kids) is new enough that KU just created an evo-devo position in the last few years. The techniques used and the major findings in the field are younger than I am.

Nelson justifies his claim that Davidson is a non-neo-Darwinist by quoting from Genomic Regulatory Systems: Development and Evolution by Eric H. Davidson:

classical Darwinian evolution could not have provided an explanation, in a mechanistically relevant way, of how the diverse forms of animal life actually arose during evolution, because it matured before molecular biology provided explanations of the developmental process. To be very brief, the evolutionary theory that grew up before the advent of regulatory molecular biology dealt with the problem of the origin of novel organismal structures in two ways. The first has been to treat the mechanisms generating novel morphological structures as a black box. New forms were considered to arise "because" the environment changed. But while changes in Precambrian or Ordovician weather, continental shifts, or temperature may have contributed crucial selective forces, they do not generate heads or appendicular forms; only genes do that. The second mode of classical argument was that organismal evolution is the product of minute changes in genes and gene products, which occur as point mutations and which accumulate little by little, providing the opportunity for selection and ultimately reproductive isolation. The major forms this argument has taken have focused on stepwise, adaptive changes in protein sequence, but this is probably largely irrelevant to the evolution of any salient features of animal morphology (see, e.g., Miklos, 1993).
My emphasis. Note that he's specifying point mutations. There are other kinds, as we've discussed, and similar language occurs in Nelson's previous post. Asked by Nelson what could explain a developmental pathway Davidson had described, Nelson recounts that he said:

"Well, I'm not sure, but I know that standard single-base-pair mutations won't do it" -- meaning, as he later explained to me, the textbook neo-Darwinism every college biology student learns.
There's an enormous gap between single-base pair mutations (same as point mutations) and "textbook neo-Darwinism every college student learns." Paul Nelson is not a biologist. That's fine, I like seeing interested people explore new topics. And I suspect that Nelson is not trying to misrepresent Davidson in any massive way. He may know he's stretching, but I suspect he doesn't realize what he's wading into.

From the context, it's clear that Davidson is interested is disabusing people of the idea that all evolutionary change happens by point mutations followed by selection, drift and gene flow. Good. We do that in the college classes I've taken and those that I've taught. Davidson's argument is directed at other biologists. He's telling them to get it together and think seriously about developmental genetics, a new and exciting field which integrates standard evolutionary biology (including gene duplications and other non-point mutations) into a broader framework based on the details of the operation of the genome and new insights we're gaining into the process by which a fertilized egg becomes a complete organism.

This is a subtle distinction, and it may be that it went right past Nelson. Nelson is right that most evo-devo researchers would say that the 60 year-old version of the "modern synthesis" is showing its age. But that's what science does, it moves forward.

Paul Nelson is a young earth creationist. It used to be that a YEC could basically say that there was debate about evolution, and everyone said "gee, that must mean creationism is true." Those days are over. People understand that scientists debate the details of the mechanism without wanting to toss the mechanism out altogether. YEC has stayed the same for 100 years easily, while the science has changed. It's gotten better.

Intelligent design has no positive case for anything. Nelson said:

Easily the biggest challenge facing the ID community is to develop a full-fledged theory of biological design. We don’t have such a theory right now, and that’s a problem. Without a theory, it’s very hard to know where to direct your research focus. Right now, we’ve got a bag of powerful intuitions, and a handful of notions such as ‘irreducible complexity’ and ‘specified complexity’-but, as yet, no general theory of biological design.
Biologists have such a theory. It's evolution. Not necessarily the same thing people were talking about in the 1940s, let alone the 1860s. We have learned some new things, after all, but we have a Grand Unified Theory of biology, and that is evolution. We're working out all the details, but the core is sound. Questioning neo-Darwinism in the sense Davidson, evo-devo or Lynn Margulis do doesn't mean you're anti-evolution, or even doubtful. These are all clearly supporters of the modern modern synthesis, a synthesis which pulls developmental biology in, adds new insights from molecular biology and genomics, and mixes that all in with the old modern synthesis. They may dispute the simplistic nature of what we understood in the 1940s, but they don't doubt Darwin. They are improving on it. See Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom by Sean B. Carroll for more on the modern modern synthesis.