Monday, July 26, 2004

Mutation Bias?

Have a look at this short review of the new book Biased Embryos and Evolution by Wallace Arthur. The reviewer is Armond Leroi, a British biologist.

I mention this book for two reasons. The first is that Leroi praises the book as a good, clear introduction to the subject of evo-devo, one comprehensible to non-biologists. Personally, I've been looking for such an introduction for a while now, and I will probably pick up a copy of this book eventually.

The other reason is that Arthur apparently discusses the idea of orthogenesis. This refers to the possibility that evolution is effectively channeled into certain directions via design and developmental constraints. If this is true, then the trajectories traced out by evolving populations are not as random as is commonly thought. Such a discovery could also provide a compelling explanation for evolutionary convergence.

Orthogenesis has been very unpopular among scientists since no one has proposed a plausible mechanism by which it happens. Arthur seeks to change that. Here's Leroi summarizing Arthur's argument:

These are brave words. Orthogenesis has been a cause without mainstream sympathizers for at least 60 years. The reason for this is that no one has provided a mechanism by which it might work. Most biologists believe that the evolutionary direction of lineages is largely determined by natural selection; a minority make great play of contingency (the non-selective effects of meteor strikes and the like). So what is going on? Has Arthur discovered a new principle of evolution?

Not really, no. The fuel in his orthogenetic engine is 'mutation bias'. Mutation produces novel phenotypes, but it does not produce all novel phenotypes in equal frequency in a given population. For example, mutations that cause an animal to become smaller than normal might be more common than those that cause it to become larger. This bias is the result of the way body size is specified in development — a bias that might influence the direction that evolution takes, causing small animals to evolve more often than large ones.

And later:

Mutation bias is not enough to produce orthogenesis, however. If there is a single fitness optimum, or if the population is sufficiently large to ensure that all possible mutations are always present, then the direction of evolution will be dictated by natural selection alone. But if the landscape is rugged and population sizes small, the particular peak climbed by a population could depend on what mutations happen to be available. This is not orthogenesis of old — which posited a force independent of, or even capable of opposing, natural selection — but a reassignment of influence over evolutionary trajectories from natural selection to the kind of genetic variation available for it to work on.

If 'mutation bias' turns out to be a new term for an old idea, the same seems to be true for another unusual term: 'internal selection'. This is the idea that as one part of an organism evolves, it exerts selective pressure on other parts to change as well. Suppose a mutation increasing the length of an animal becomes fixed in a population. This might cause the subsequent fixation of another mutation that increases the animal's width, so restoring an original, harmonious, proportion. Arthur makes great play of this, but I think the interaction at the heart of this process is well known to population geneticists as 'fitness epistasis' and has often been experimentally demonstrated.

Leroi's conclusion is that Arthur's ideas are interesting, but far from proved.

I mention this here because, if Arthur is correct and mutation bias does lead to certain evolutionary pathways being favored over others, then this throws yet another monkey wrench into William Dembski's scheme for inferring design in organisms. Remember, Dembski's key ideas are that if an object is highly improbable and conforms to some independently describable pattern, then we can conclude it was designed. As has been documented elsewhere, his whole system is shot through with holes. But one of the biggest is his claim that we can carry out meaningful probability calculations regarding the formation of complex, biological structures.

Arthur's ideas would have to be taken into consideration in any such calculation. If certain sorts of phenotypes are more likely to be found in a population than others, than this will effect our measurement of how likely it is to evolve a particular complex system. And unless we can quantify very precisely which sorts of mutations are more likely to be found than others, it will be effectively impossible to carry out any such computation.

The evolution of complex systems dempends on far more variables than can possibly be captured in any elementary probability calculation. Arthur's ideas, if correct, would make that problem even more acute.


At 5:14 PM, Blogger Arlin Stoltzfus said...

This comment has been removed by a blog administrator.

At 5:16 PM, Anonymous Anonymous said...

This is a topic where synthesis is badly needed. First, theoretically, there is not any doubt that mutation bias can, under some circumstances, cause evolution to favor one direction over another. The population-genetic mechanism is shown in the theoretical paper that Leroi cites in his review (Yampolsky, L.Y., and Stoltzfus, A. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3: 73-83).

Second, there is no doubt that mutation-biased evolution is common. Every molecular evolutionist knows that mutation biases like GC/AT bias or transition/transversion bias or CpG bias have a major influence on molecular evolution. This influence is not an effect of "constraint" preventing some kinds of mutations from occurring: transversion mutations do occur, they just occur at a lower rate.

Third, one should not think of this as a special property of neutral evolution. It is true that in most cases one could dismiss mutation-biased sequence evolution as an aspect of neutral evolution, since (whether or not its true) it is hard to exclude neutral evolution for the majority of changes. However, neutral evolution is not theoretically necessary for mutation-biased evolution (see Yampolsky & Stoltzfus). There are even cases in which experimental adaptive evolution is influenced by mutation bias (see Rokyta, et al. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet 37: 441-444).

Finally, there is no obvious reason that developmental biases on phenotypic variation could not have a similar effect as mutational biases (see Yampolsky & Stoltzfus).


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