Monday, October 09, 2006

Review of "The Mystery of the Genome" (I)

A few months ago, I had a debate with Salvador Cordova over robustness and redundancy. At some point (in these comments) Salvador decided that I needed enlightening on matters evolutionary and gave me a copy of a book by John Sanford, an agricultural geneticist at Cornell University (Courtesy Associate Professor), suggestively titled Genetic Entropy & The Mystery of the Genome (and ominously subtitled: "the genome is degenerating"). I suppose that courtesy dictates that I should say a few words about it. I finally picked it up and have read the first 30 pages (Prologue and Chapters I and II).

Unsurprisingly Sanford's objective is to demolish what he calls the "Primary Axiom" of evolutionary biology "that man is merely the product of random mutations plus natural selection". This is not a good start for someone who claims professional expertise in biology. Bringing the term axiom from mathematics into a discussion of a theory in the natural sciences is not helpful. What he describes is a summary of a theory, not an axiom. But let's go with it for the moment. So why might Sanford be challenging this "Primary Axiom"? He provides a telling answer:
If the Primary Axiom could be shown to be wrong it would profoundly affect our culture [...] It could change the very way we think about ourselves. (Prologue)
So now we know where he's coming from. What next?

In Chapter 1 ("The genome is the book of life. Where did it come from?") he explains how "the genome is an instruction manual". Although I would put it slightly differently, I don't have a major problem with his description: he talks of DNA, proteins, regulation of gene expression, etc. He then introduces a complicated metaphor -- manuals for constructing wagons -- for the process of mutation and natural selection designed to highlight the improbability of evolution. He goes into full "personal incredulity" mode:
Isn't it remarkable that the Primary Axiom of biological evolution essentially claims that typographical errors plus some selective copying can transform a wagon into a spaceship, in the absence of any intelligence, purpose, or design? Do you find this concept credible?
No prizes for guessing which answer he's counting on. While his wagon metaphor could have been more elegant (and more elegantly expressed) it is not fundamentally wrong. At least he doesn't tell us that natural selection is pure randomness. However, his discussion is misleading in at least two respects. First, it does not convey the immensity of time allowed for evolution to operate. This might be because Sanford is a Young Earth creationist and doesn't believe there has been much time for anything, although I haven't read a statement by him to that effect yet, so I'll give him the benefit of the doubt. Second, he analogizes mutation to spelling mistakes in natural language, which is deeply misleading. Although it is true that randomly altering letters in source code written in a high level programming language is unlikely to produce beneficial mutations, that does not imply that evolutionary computation is impossible, far from it. (Indeed, evolutionary computation raises major problems for evolution deniers, but that's another discussion.) The problem with Sanford's characterization is that point mutations are more subtle than the spelling analogy would suggest. But since no analogy is perfect, we'll let it pass for now.

Chapter 2 ("Are random mutations good?") gets to one of the central points of his argument. According to Sanford the bad news for the "Primary Axiom" is that "it can very reasonably argued that random mutations are never good". If true, this would indeed be a problem. So what about the evidence? Sanford tries to back it up with the following assertions:
  1. Mutations are like misspellings in the "instruction manual".
  2. There no "clear cases of information-creating mutations".
  3. The few beneficial mutations that occur are nearly neutral.
  4. Repeated selection experiments in plant breeding have resulted in "no meaningful crop improvement"
  5. Geneticists never see beneficial mutations.
Most of these are standard, repeatedly refuted creationist claims. I've already explained why the first argument is based on a misleading analogy. The second argument sounds more serious but it is hard to say what Sanford has in mind since he never precisely defines information, and creationists cannot be trusted to do so with any accuracy (see also this). In any event, mutations can create new binding sites, duplicate genes, etc, so whatever he means cannot be meaningful (to use one of Sanford's favorite terms). Let me give you an example from my study organism, the nematode Caenorhabditis elegans. A single aminoacid substitution in the gene npr-1 (neuropeptide Y receptor homologue) can make worms (normally solitary) aggregate on food. Is that an increase or decrease in information? Does it matter?

The fifth argument is completely wrong. Define beneficial and I'll give you many examples. Just in the nematode C. elegans we have mutations that increase or decrease body size, that increase or decrease lifespan, that increase or decrease hermaphrodite self-fertility, that make it easier or more difficult to go into dauer (the worm equivalent of a spore), etc. Many of these mutations can be beneficial in certain environments.

The fourth argument is nothing short of delusional. Artificial selection has succeeded in getting selection responses in the desired direction for "improvement" in practically every instance tried. For example, Ken Weber selected for differences in wing shape on the order of a few cells in the fruitfly Drosophila melanogaster and got a response! Exceptions to this generalization are so few and far between (e.g., changing the primary sex ratio and directional asymmetry in Drosophila) that the existence of constraints is still debated in the pages of Nature. There may have been a few unsuccessful selection experiments in crop species (I'm less familiar with that literature), but I doubt that Sanford's summary is accurate. Indeed I know of at least one case that contradicts it: starting with 163 ears of corn Leng (1962) was able to increase oil content of kernels from 4-6% to about 16% within 60 generations using artificial selection. That may not count as "meaningful crop improvement" in Sanford's book, but it does in mine.

We're left with the third argument. This one is more subtle and will be the subject of the next installment of this review. By then I may have been able to read a couple more chapters as well.