The thick plottens

Pngarrison helpfully pointed us a day or two ago to a recent article in the context of the randomness of variation. It does raise some interesting issues from The Hump’s perspective. So I’ll very briefly summarise it in the knowledge that it’s open-access, and those with a better background can bypass my meanderings.

The study takes cystic fibrosis transmembrane conductance regulator (CFTR) as a typical example of a very ancient and essential gene (ie present for “hundreds of millions of years”), that has gained many variants through point mutations – otherwise known as single nucleotide polymorphisms (SNPs).

The article explains the plasticity of the gene – many variants work well – but also how catastrophic the loss of function is (as every respiratory physician knows from experience). It examines the relative ease by which accumulating mutations will suddenly render the gene non-functional.

The meat of the dish is the detailed examination of one problem: how over such a long evolutionary period this single gene has not simply degenerated by Muller’s ratchet to the point where higher life simply runs out of steam. One can multiply that problem by the very many similarly conserved ancient genes. It looks in detail at the conventionally accepted mechanisms such as sexual recombination, purifying selection, and neutral drift, and concludes that they would be fundamentally incapable of preventing this degeneration.

In other words, the pattern of variation observed now cannot be random, and they propose that there must be a mechanism in place that simply prevents many of the possible variants from ever forming, thus enabling purifying selection and so on to keep abreast of the job. Now, the controversial issue here, though such controversy is now becoming routine, is that it gives solid evidence of the non-comprehensiveness of Neodarwinian theory, even including Neutral theory. The authors insist that there are further mechanisms to be discovered, which would clearly affect our understanding of biology at every level.

I understood enough of the argument to see why they require this new understanding. In passing, however, they exclude other possible explanations, such as “directed evolution” and “Intelligent Design”. I think the paper would have been improved by more discussion of just what they were discounting in these, and why, since their argument was basically “We’ve shown these theories don’t explain the issue”, with bare references to sources on the theories in question.

My understanding would be that by “directed evolution” they mean something like James Shapiro’s natural genetic engineering in which mutations have some adaptive direction, and I can understand how their data might suggest that what variation there is in CFTR shows no sign of such adaptiveness. Incidentally, this only shows that in such cases NGE has no place; the evidence for it in other cases remains, and so we have only added one other non-Darwinian mechanism to the complicated mix that’s emerging.

On Intelligent Design, it’s hard to be sure what they’re actually denying, since they only reference Stephen Meyer’s Darwin’s Doubt, whose conclusions on mechanisms for detailed instantiation of design are intentionally minimal. But one can suggest they’re making a case for a plausible naturalistic explanation that Meyer didn’t discuss (though he wasn’t, of course, addressing genetic degeneration at all as far as I know).

This explanation of theirs turns out to be that, hidden deep in evolutionary history, life evolved a mechanism that would limit the nature and variety of SNPs in such essential genes, in the same way that it seems to have found a way of preventing the degeneration of the DNA code itself. This would explain the pattern of the data, ie that many of the variants that would inevitably accumulate deleteriously simply haven’t appeared, and so presumably are actively prevented from doing so.

The conclusion that there must be such a mechanism seems reasonable, and must change how evolution is viewed, by suggesting that evolution itself has evolved beyond the plausible simplicity of the Darwinian model. The more such a thing is accepted, the less fortuitous the “endless forms most beautiful” seem, and indeed the less fortuitous they are.

What is easy to forget, though, is that an actual mechanism has not yet been found, before the means of its arrival has been hypothesised. And the means suggested for its arrival, according to this paper, appear simply to be the standard Neodarwinian mechanisms that it claims to be incomplete now. Except that these simple Darwinian mechanisms have been endowed by the authors with almost supernatural powers of teleological foresight, that Darwin’s theory was formulated to avoid. Look at these quotes from the article:

The pathway was best interpreted as another device that co-evolved with both the genetic code and codon usage to help preserve the exome of higher organisms…

Based on the analysis presented here and the vital imperative to avert “meltdown” of protein coding DNA, we speculate that the introme, itself, might not only serve as an evolutionary strategy to support the generation of diversity (through alternative splice variants, microRNAs, gene network regulation, etc.), but as a specific alternative to meddling with the exons.

…but would be essential for selfish genomes attempting to cope with environmental challenge over an evolutionary timeframe.

The first quote implies that “life” was somehow aware of the need to preserve the exome and devised a strategy specifically to do so. Well, OK, at a stretch one might re-interpret that teleological design-language to mean that organisms happening to develop this grand new mechanism did fortuitously preserve their exome and de eventu didn’t die out and take the whole biosphere with them. That was another bit of luck, then.

The second quote, though, is even harder to extricate from its language of “evolutionary strategy” and the “vital imperative to avoid meltdown.” Quite apart from “the introme’s” quite unconscious realisation that “meddling with exons” would all end in tears.

But the third quote, starting from the already anthropomorphic “selfish gene” analogy, extends their wilfulness to an “attempt to cope” not in their own time, but “over an evolutionary timeframe”. In other words, the picture is like one of these ancient sci-fi civilisations planning over millions of years to survive the loss of their atmosphere or some other predicted catastrophe.

But is it not the whole point of evolution that it makes short-term fixes for today’s problem, and cannot make provision for the future? “Just good enough for today” is one of the commonly used arguments against divine design. But the only way the blind watchmaker knows his gene is at the point of meltdown is that his organism becomes extinct. At that point it’s a little late to start evolving a sophisticated mechanism to ensure your descendants stick around for 3 billion years. And if randomness were able to simulate such wise foresight, you’d have thought it could just as easily have found a way to ensure that all mutations were adaptive and all species successful, thus saving much bloodshed and heartache for egocentric genes.

I have three points, in conclusion, to make on this interesting, and increasingly typical, piece of research, other than the obvious one that overly simple theories should have had their day in the light of complicated reality.

Firstly, on randomness, which is where we came in. Taken overall, the study shows that the SNPs hitherto thought to be random are clearly not – they are only a subset of what is possible, the rest being universally prevented by whatever the magic mechanism is, ostensibly with the longevity of Gaia in mind. In this case randomness was an assumption found wanting on closer examination. And that endorses the point I’ve been making over a few posts that randomness is nothing more than a pattern one hasn’t yet understood. At this point in evolution, such mutations are constrained by a front-loaded mechanism, just as Shapiro’s NGE has some kind of bias inherited from the past.

Secondly, arising from that, it’s a little disingenuous to explain the teleology that one now observes (preventing genetic meltdown is just as teleological as designing mutations) by pushing the random process back into an unreachable past. “Evolution is cunningly constrained now, because random mutation, selection and drift at the dawn of life happened to create those sophisticated mechanisms, though nobody can now say how.” Somebody’s already coined the term “randomness of the gaps”, and there’s a danger of an endless regress in that: perhaps some other even earlier evolutionary strategy governed how the selfish genes became alerted to the genetic danger they were in so they could start to save the planet (for entirely self-centred reasons, of course). Perhaps molecules randomly became self-replicating. Perhaps only useful proteins are likely to be found by evolution. Perhaps the environment naturally favours rational intelligence. Perhaps the dice are naturally loaded.

Thirdly, on my other leitmotif of the theory-laden nature of science (and indeed, all knowledge), it goes without saying that many people reading this article from a thoroughly Neodarwinian mindset would only be able to perceive through those eyes. There are various ways that could be achieved.

For example, most paradigmatically one can always find some way of accommodating the data to the existing theory (or any existing theory). In effect, the article creates just such an epicycle by saying, “Look, we’ve found a non-Darwinian phenomenon, but we suggest it could have evolved in a Darwinian way, so nothing’s really changed.”

Alternatively, one could shrug off the problem as an unimportant anomaly which, “undoubtedly” will be explained by the standard theory one of these days.

Or one could simply deny the findings of the paper altogether. At best, the authors don’t understand evolution. Or maybe they’ve even skewed their data to make a name for themselves. Or best of all, since the research team is based in Birmingham, Alabama, you just have to suspect that some of them may be Southern Baptists and therefore closet creationists, if indeed they have real degrees at all.

But I come to it with a different theory-load. I think it’s intriguing work that shows the secondary causes to be a bit more adequate for the job of populating God’s cosmos as he purposed – but it does little to explain sufficiently how those secondary causes came to be what they are.