19 October 2008

Why I'm not a Behe fan: conclusion and a challenge

About 2 months ago, I finished a series on Michael Behe's latest book, The Edge of Evolution. I concluded that it was a terrible book, displaying significant errors of both fact and judgment. The book's main argument is a population genetics argument, and Behe seems to have little knowledge or understanding of that difficult subject. The book is a joke, and I believe it will someday be seen as one of the more disastrous mistakes made by the ID movement. But I think it's important to distinguish between Behe's errors (which reflect on his scientific credibility and on his decision-making habits) and his thesis. His book is full of mistakes, but that doesn't mean that his proposal is known to be false. So I'd like to make it clear what my verdict on his book actually is, then present an outline of one way to actually test Behe's hypothesis.

1. In The Edge of Evolution, Behe correctly identified a biological process – the generation of genetic variants that lead to evolutionary change – as a likely focus of deliberate design. Having concluded that common descent is true, he reasoned that the trajectory of change through the tree of life might be expected to show evidence of non-random direction. Design, as he and others in the ID movement conceive it, might be manifested in the pattern by which the tree of life came to be. (Some might go as far as to say that it must be manifested in such a way, but I don't think Behe suggests this.) My point is that there is nothing stupid, irrational, or unscientific about Behe's reasoning. So, Behe conceived a hypothesis, which I will restate as follows:
  • Based on the consideration of life's complexity, specifically on the consideration of the integrated complexity that characterizes the molecular machinery of the cell, it is proposed that random mutation and subsequent selection cannot fully account for the evolutionary development of biological systems.
  • Consequently, it is proposed that the process of mutation is non-random.
Again, I find nothing outrageous or stupid about the hypothesis, or even its rationale. Molecular machines are astoundingly complex and integrated, and I do think it's reasonable to wonder how such things can come about without the aid of a superintelligence. In other words, Behe's proposal is not inherently incoherent or otherwise easily dismissed. Might the machinery of life have emerged through non-random processes? Sure. EoE is a joke, but not because the proposal is a joke.

EoE is a joke because Behe seems not to have even attempted to establish the strength of the hypothesis. Very little of the book is devoted to this central concern, and those sections that take up the task are so laughably wrong that they have led me to question Behe's scientific integrity. (Sorry, no apologies: the errors are too basic, and the proposal too world-altering, to give someone who is vying for scientific immortality a pass on standards of scientific conduct.)

But this is important: Behe's failure to even attempt an honest defense of his proposal does not imply that the proposal has been falsified. It hasn't. It remains possible that the development of biological machines – especially in the early days of the tree of life – was characterized by a non-random, directed trajectory. (I happen to doubt this, but that's not relevant here.) Behe's book is a failure, but his hypothesis stands.

So here we are: an interesting and potentially revolutionary hypothesis has been advanced. It has a certain explanatory appeal, and it has unquestioned relevance for believers of many kinds. It is empirical and rational. And, I maintain, it is testable, at least in principle. And so I'm offering to collaborate on a real effort to test it.

2. Behe's proposal leads to certain types of testable predictions. He claims that the genetic changes that underlie certain levels of evolutionary change occurred non-randomly. In other words, he claims that there is a dramatic mismatch between rates of genetic mutation and rates of evolutionary change. His efforts in EoE were ridiculously inadequate. Here is an outline of an approach that could succeed.
  • One major mistake that Behe made was to devote most of his attention to a "case study" in which significant genetic change did not occur. His case study was poorly suited to his purpose, but even if it had been better conceived it would be worthless. We can't learn about how evolution works by analyzing examples in which it didn't occur. (Well, of course it did occur in Behe's case study, but the changes that he claims are non-random are different by his own definition.)
  • So, any approach to the detection of non-random influences on evolutionary change needs to focus on case studies that actually involve the relevant level of evolutionary change. Examples should be easy to find, by considering the tree of life and the branching levels at which one would hypothesize non-random change.
  • The evolutionary lineage(s) selected for analysis should be fairly well-documented, so that the nature of the relevant common ancestors can be reasonably inferred. This probably means that much deeper lineages (such as eukaryotes or even multicellular eukaryotes) would not make good subjects of analysis. Since Behe is pretty sure that design characterizes differences at the level of class (and deeper), this concern is not a barrier to addressing his hypothesis, at least at those levels of divergence. The tetrapod lineage could serve well, but there are any number of evolutionary trajectories that could be considered.
  • Within the selected lineage(s), one or more evolutionary changes would be selected for genetic analysis. Changes could be simple (such as the molecular evolution of a particular protein of interest) or more complex (such as the development of a particular attribute like teeth or feathers or lungs), and could even include the sum total of the genetic changes in a lineage, but must be amenable to genetic description. Most importantly, the evolutionary changes that are analyzed must be associated with the specific design postulate. The goal is to examine the genetic changes underlying an evolutionary transition that Behe would identify as designed.
  • Once the genetic changes of interest have been identified, analysis can proceed the way Behe pretended to proceed in EoE: inferred mutational trajectories can be considered in the light of estimated mutation rates and estimated generation numbers. If non-random mutation is clearly necessary for the evolutionary changes in question, it should be apparent that even the simplest mutational paths leading to change are well beyond the explanation of random mutation.
My description makes the undertaking sound straightforward, and in principle it is, but of course such examination of even a relatively simple evolutionary change is a significant and demanding project. Inferring the genetic makeup of the common ancestor is a project all by itself, and constructing postulated mutational pathways is the kind of work that occupies many professional biologists full-time. (Consider the work of Joe Thornton and his group, considered among the best analyses of this kind.) Estimates of generation number will span huge ranges even after the most careful consideration of the variables.

But this is the work that any real scientist and scholar would know has to be done. Behe's hypothesis is completely untested, and only the kind of study that I have outlined can change that. I invite any scholar with interest in undertaking this project to contact me. I would be interested in joining a collaborative effort to test the non-random mutation hypothesis, and I have some significant resources that could be brought to bear on the problem. This is a serious offer, and I would encourage readers to forward it to anyone who might be interested in discussing the details.

16 comments:

Martin LaBar said...

Well put. That's a serious research proposal, for sure.

John Farrell said...

Indeed. The problem, of course, is that Behe and the Institute that funds him decided long ago that only the merest fig leaf of science was necessary for them to present what is essentially an ideological, not a scientific, position. Bad faith argument is part of their game plane.

Any real publications on this question by Steve and prospective colleagues would be misunderstood, and worse, deliberately misrepresented by the ID movement's spokesmen.

Anonymous said...

One Word: FLAVERIA.
C3 and C4 photosynthesis in the same genus, plus C3-C4 intermediates, all extant. C3 is the ancestral state, since that's what most of the rest of the family (Asteraceae) has.

Some random papers on the topic:
Phylogeny of Flaveria
Evolution of C4 photosynthesis (PDF)
Many others on Google scholar.

It will only be used ideologically if the hypothesis of directed variation cannot be rejected. And frankly, it matters very little what scientists say about ID, since they are unlikely to alter their propaganda anyway.

Peter Parslow said...

As a lay observer (A level biology only; now an engineer), I'd encourage you not to worry about changing the minds of the "ID movement". Like any science, demonstrating the possibility/likelihood of non-random "design" should be independent of any pressure groups opinion.
(Of course, I know that doesn't often happen in many other areas of science either, often due to funding issues, but we can still be idealists!)

Stephen Matheson said...

John's right that the ID swamp is almost completely propaganda-based, and I think he's right that any research effort along the lines of my proposal would be misused from the beginning. That's true now, of all sorts of good science, and it will be true as long as well-funded culture warriors believe that scientific explanation is something to be feared.

So the question is not whether the bottom-feeders of the ID movement will make stuff up...the question is whether we should try to test the hypothesis of directed variation. (Hat tip to Prof. Wood.)

And the real problem is not propaganda -- it's worse: the analysis that will be required is demanding and will require the attention of diligent, intelligent, and honest scholars, probably an interdisciplinary team. So TCW, can I count you in? :-)

Now back to reading up on Flaveria, which is very interesting but would probably be labelled Darwinian by Behe, who identifies design in deeper distinctions than those that occur among species. (Silly, I know, but that's what he stuck us with.)

Dennis Venema said...

I'll admit I'm quite intrigued. The issue will be identifying an example Behe agrees is designed.

What sort of timescale are you proposing, Steve?

Another hat tip to Prof Wood - I've recently become familiar with your work, and I enjoyed your 2006 BSG paper so much I've assigned it to one of my classes for required reading later this fall.

Dennis Venema said...

Another thought: I agree that something in the tetrapod lineage would be a good choice, since you can use the Danio and Fugu genomes to root the trees and help infer the original tetrapod genome.

Anonymous said...

A few more comments:

You can't worry about what Behe would say about this test. Any test that falsifies "frontloading" will be shrugged off as an example of "Darwinian evolution," while the real evidence of "frontloading" must be somewhere else. Evidence just doesn't matter.

Given the constantly shifting propaganda claims (a problem that holds for any creationist folk science claim), it's necessary to pin things down to a specific claim that can be tested. In this case, Flaveria is particularly attractive because of the convergence involved. C4 occurs not just in Flaveria but in many flowering plant families and the biochemically related pathway of CAM occurs in even more. As far as I can tell, there's only two ways to explain the commonness of these pathways: either C4 and CAM are just minor, easily evolved variants of C3 (i.e., the probability of evolving them is higher than intuition might suggest); or God "stacked the deck" of variation (i.e., the variation is designed to occur in specific ways).

I think using the origin of tetrapods is a very bad idea simply because of the complexity involved. Take a different example: humanity. There are multiple primate genomes now available, and no genetic or biochemical system is as studied as human beings (ok, may C. elegans, but you get my point). I'm no human genetics expert, but I still don't think we're in any position to say definitively what genetic or other differences are involved in generating uniquely human traits. And you want to try to figure out what makes a tetrapod different from a fish? Good luck. C4 is attractive in this respect since the biochemical pathways are well-defined: We already know what enzymes are involved, and we can sequence those enzymes and examine their regulatory regions. There is a direct relationship between the genetics and phenotype that is already established. Makes the work a lot easier.

I think I'm the last person you want on the team, given who I am and my history with Flaveria in particular. Unless you have some secret funding source that is willing to overlook perceptions of bias or ideology? (On the other hand, Flaveria has been a long-standing obsession with me. I'd loved to be involved in cracking that particular nut. Maybe I could be a subcontract or chief bottlewasher?)

Dennis, thanks for the comments regarding that particular paper. It is easily the most popular thing I've ever written, and is directly responsible for an entire cadre of antievolutionists (including a well-known creationist organization whose initials may or may not include the letters I, C, and R) despising me. Fun times.

Stephen Matheson said...

TC, you're absolutely right that it would be foolish to try to characterize the specific differences between taxa. I think that's why an analysis within, say, the tetrapod lineage would have to focus on a specific gene or pathway, or perhaps a few, selected with an eye toward the kinds of higher-level distinctions that might be postulated to characterize the two taxa being compared. Placentation genes. Transcription factors like FOXP2. Lineage-specific genes in, say, birds or bats or fish would be excellent candidates, especially when they are known to underlie notable developmental phenotypes.

And, you have a good point about the ID response to a project of this kind. And so it seems that those interested in the project would have to decide if the goal is to look for directed variation, period, or to look for the kind of directed variation postulated by Behe. How one chooses will, I think, be mostly a function of whether one expects to find directed variation anywhere.

As for your claims to be a funding liability, I guess we'll just have to do that experiment too. :-)

Dennis Venema said...

Hello Prof Wood,

I'm not at all surprised that you've earned the ire of many for that paper. I'll freely admit part of the joy of reading that paper was its honesty . That paper is the only YEC paper I would even consider putting in from of my students, because it is the only one I have ever come across that doesn't distort the science.

Have any YEC organizations officially responded to that paper in print or on the web? If so I would be very interested in reading their responses. I'm in the early stages of writing a paper on baraminology: basically comparing discontinuity systematics with the standard approach in the genomics era. Your 2006 paper is already a centerpiece - so responses from outfits that may or may not have an I, C or R, or even an A, I or G would be most welcome.

(In case you're wondering who I am, exactly, I may or may not teach at an institution that employs a T, W or U in its name. Nice to make your acquaintance.)

John Farrell said...

TC, Steve, scientists have better things to do than wash bottles.

I'll volunteer for that duty if I can bring along my Sony VX2000 and cover this project for a kick-butt science documentary.

:)

Dennis Venema said...

Hey Steve,

Are you thinking actual benchwork for this? I.e. trying to recreate ancestral proteins, etc? Or is this strictly in silico ?

Anonymous said...

Steve:

FoxP2? Placentation genes? Those come across as too reductionist to me (and probably others of my ideological ilk). Now lineage specific genes are very interesting to me. They seem to be all over the place, and yet where do they come from? Are they just duplications? Very interesting puzzle. My advisor was interested in that, too, but I don't think he ever did anything with it.

As far as a funding liability, I've been dropped like a hot potato more times than I can count. I've even been cut off with no explanation. Just silence. I once got a peer review that was overt, though. Said I was an enemy of science and my paper should not be published under any circumstances. Editor agreed with him. Fortunately, I'm pretty anonymous so I can slip by sometimes. (In fact, I'm supposed to be writing a grant right now that's due Friday. It can wait, I guess.)

Dennis:

That paper is the only YEC paper I would even consider putting in from of my students, because it is the only one I have ever come across that doesn't distort the science.

You know, I've written more than one paper. Oh, you mean... never mind. I don't want to know.

I was told there would not be a "public response" to my paper. Antievolutionists think in explicitly militaristic terms, then Christianize them. "It's wrong to attack fellow creationists." Hmmmm.... if by "attack" you mean point out errors and encourage higher standards of scholarship and generally engage in healthy scholarly discourse, then I guess I'm guilty as charged. I don't see that as an attack, though. It's more like trying to dress a gaping wound.

Frankly, I would hate to see a response. I threw the gauntlet down on a problem I've worked on now my entire professional career. What could they possibly say that I haven't already thought of and discredited? [crickets]

T, W, and/or U? Texas Woman's University?

John:

No documentary. Publicity is too dangerous in my line of work. My anonymity is a precious commodity. In fact, why am I even posting this? Must be the sinus infection.

Dennis Venema said...

Hi Todd,

As of yet I haven't read any of your other work except a brief skim of your "Mitochondrial Eve" article for AiG. I'll be digging through more of your stuff for the baraminolgy paper, though, I'm sure.

Nope, not in Texas. Sorry, the acronym thing was a lame attempt at humour. There's a clue in that last word (i.e. it's not a typo).

if by "attack" you mean point out errors and encourage higher standards of scholarship and generally engage in healthy scholarly discourse, then I guess I'm guilty as charged. I don't see that as an attack, though. It's more like trying to dress a gaping wound.

You know, honesty in biology is not typically rewarded by Christians, regardless of the view one has of origins. It is very interesting to me to see that even though you hold to a YEC approach, you cannot openly discuss the problems - not even in an attempt to move the field forward and address said problems.

Best,

Dennis

Jimpithecus said...

The human fossil record has numerous transitions (in fact, transitional forms tend to be the rule) and it would be possible to test Behe's premise there. I agree with Steve Matheson, though, and it is getting harder and harder to tell the DI from the ICR in terms of propaganda. Sad.

Anonymous said...

This and this discuss a pretty interesting example of an IC system arising by chance, in a system whose life history, genetics, and molecular changes are very well-understood.

Silverswords might also be a good subject for this project. Of course, in this case, some actual research may be needed. But the general history and evolutionary relationships at the organismal level are well-established.