Model Madness: Axe vs. Lynch and Abegg

I recently blogged about a paper by Lynch and Abegg 2010, which I thought was an important paper. It showed that, yes, there was time enough for evolution, mainly because neutral and even maladaptive variations could accumulate in sufficient numbers until they finally coalesced into a new beneficial function.

Douglas Axe, a leading scientist within the ID community, responded to the challenge inherent in this paper. Axe's position and research agenda has long been that there is not time enough for evolution.

At this point, I have to say that even though I disagree with Dr Axe, I give him credit for being the most professional and rigorous pro-ID scientist I have ever read. Yes, professional scientists can work themselves into a corner that eventually becomes crank science as they refuse to abandon a position - witness the Rubin group at the University of Oregon on "birds are not dinosaurs". Yes, I do think Axe is in this position, but he is trying in a principled, scientific way to address the issues. As such, he has demonstrated far more professional integrity than Stephen Meyer or William Dembski, neither of whom is a scientist.

Axe's response is The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations, which attempts to criticize Lynch and Abegg and to propose an alternative model.

For now, I'd like to focus on the differences in the models. Lynch and Abegg use a model assuming sexually reproducing diploid populations. Axe tries to refute them with an asexually reproducing haploid island population model. Are those differences appropriate?

One way to answer would be to look at the biochemistry that is being discussed, and ask when did it evolve. Is it eukaryotic or prokaryotic in origin? As I pointed out in my last post on this, eukaryotic sexual species with large populations have been around for a billion years. The larger portion of the biochemistry we operate with is eukaryotic - not shared with bacteria.

That calls into question the basic assumption of Axe's model. Another way to look at the issue is to question the realism of the asexual population genetic abstraction. We now know that in real life, as opposed to the test tube or a mathematical simplification, bacteria exchange genes rapidly. The process might be based in conjugation, or it might be through viral infection. In either case, the binary fission model of where genes come from isn't relevant.

Axe's model also incorporates an effective population size that is quite small - 10^9, a billion bacteria. This is justified by appealing to the island model dynamics of Maruyama and Kimura 1980. Even accepting these dynamics, a gene's eye view of the world has to incorporate the reservoirs afforded by other species and viruses. So I would argue that Axe's effective population size is too small.

Rarity vs. Isolation, a problem for Intelligent Design

Douglas Axe is a scientist, and a creationist, judging from his affiliation with Biola University. (Biola requires signing a faith statement.) He has occasionally published studies relating to the occurence of protein folds, using mutation as a way to determine the frequency of functional folds. His overall research program is to show that functional folds are so rare in nature that they could not arrive by chance mutation from an existing fold (killing evolution) or by chance from random polypeptides (killing abiogenesis).

Axe's most recent peer reviewed work is Axe 2004. Of course, anything even mildly supportive of ID in the peer reviewed literature gets a lot play, and this did. It has recently gotten some more, as Doug has blogged about some reactions to it from Steve Matheson and Art Hunt. Here are some of my observations.


Side point 1 - As with Guillermo Gonzales, advocating creationism seems to be negatively correlated with publishing. Gonzales couldn't get tenure because his publishing and grants dried up, and Axe publishes very infrequently.


Side point 2 - Axe's argument is essentially a variation on the argument from improbability - the universe doesn't possess the time/resources required for evolution to work. As such, it is a "bignum" argument, and the most important bignum in the ID memenet is Dembski's Universal Probability Bound. This UPB is usually stated as the odds of something happening have to be greater than 10^-150 before an ID supporter will allow that they might have natural causes. Well, Axe's work is well within that bound. The number usually plucked from Axe is 10^-77 as the "chance" for a functional protein. That is 80 orders of magnitude more likely than UPB, so Axe is really not supporting ID if these folks could keep their bignums straight.


The main point - rarity is not isolation. Even if we grant for the purposes of argument that Axe's rarity number is correct, that doesn't mean proteins, and the genes that make them, are isolated.


Here's an analogy. Gold is rare. But on land, gold is not isolated. If I find a piece of gold in one spot, my expectation (hope) is to find another piece of gold nearby. Lots of people will come and try to find gold nearby. Now there might actually be more gold in the ocean than on land, but if I find one gold atom in a bucket of seawater, I'm not going start my next gold mine where I found that one gold atom.


The difference is the distribution, and isolation is far more about distribution than it is about rarity. Gold on land is very unevenly distributed, rare but not isolated. Gold in seawater is evenly distributed and isolated. At another level, nucleons are extremely rare within the volume of an atom, but not isolated at all. They are all in one lump in the center of the atom.


Of course, there is an underlying process that accounts for this uneven distribution. And if you want to challenge evolution or abiogenesis, you have to challenge the underlying processes, not make hand waving arguments that always assume a uniform distribution. Rarity is not isolation.


Quintessence of Dust: Exploring the protein universe: a response to Doug Axe: "http://disqus.com/forums/quintessenceofdust/exploring_the_protein_universe_a_response_to_doug_axe/trackback/"