Tuesday, May 10, 2016

Darwin the Newtonian. Part IV. What is 'natural selection'?

If, as I suggested yesterday, genetic drift is a rather unprovable or even metaphysical notion, then what is the epistemological standing of its opposite: not-drift?  That concept implies that the reproductive success of the alternative genotypes under consideration is not equal. But since we saw yesterday that showing that two things are exactly equal is something of a non-starter, how different is its negation?  

Before considering this, we might note that to most biologists, those who think and those who just invoke explanations, non-drift means natural selection.  That is what textbooks teach, even in biology departments (and in schools 
of medicine and public health, where simple-Simon is alive and well). But natural selection implies systematic, consistent favoring of one variant over others, and for the same reason.  That is by far the main rationale for the routine if unstated assumption that today's functions or adaptations are due to past selection for those same functions: we observe today and retroactively extrapolate to the past.  It's understandable that we do that, and it was a major indirect way (along with artificial selection) in which Darwin was able to reconstruct an evolutionary theory that didn't require divine ad hoc creation events.   But there are problems with this sort of thinking--and some of them have long been known, even if essentially stifled by what amounts to a selectionist ideology, that is, a rather unquestioning belief in a kind of single-cause worldview.

What does exactly not-zero mean?
I suggested yesterday that drift, meaning exactly no systematic difference between states (like genotypes) was so illusive as to be essentially philosophical.  But zero-difference is a very specific value and may thus be especially hard to prove.  But non-zero is essentially an open-ended concept and might thus be trivially easy to show.  But it's not!

One alternative to two things being not zero is simply that they have some difference.  But need that difference be specifiable or of a fixed amount?  Need it be constant or similar over instances of time and place?  If not, we are again in rather spooky territory, because not being identical is not much if any help in understanding.  One wants to know by how much, and why--and if it's consistent or a fluke of sample or local circumstance.  But this is not a fixed set of things to check.

Instead of just 'they're different', what is usually implicitly implied is that the genotypes being compared have some particular, specific fitness difference amount, not just that they differ. That is what asserting different functional effects of the variants largely implies, because otherwise one is left asserting that they are different....sort of, sometimes, and this isn't very satisfying or useful.  It would be normal, and sensible, to argue that the difference need not be precisely, deterministically constant, because there's always a luck component, and ecological conditions change.  But if the difference varies widely among circumstances, it is far more difficult to make persuasive 'why' explanations. For example, small differences favoring variant A over variant B in one sample or setting might actually favor B over A in other times or places.  Then selection is a kind of willy-nilly affair--which probably is true!--but much more difficult to infer in a neat way, because it really is not different from being zero on average (though 'on average' is also easier to say than to account for causally).  If a difference is 'not zero', there are an infinity of ways that might be so, especially if it is acknowledged to be variable, as every sensible evolutionary biologist would probably agree is the case.

But then looking for causes becomes very difficult because among all the variants in a population, and all the variation in individual organisms' experience means that there may be an open-ended  number of explanations one would have to test to account for an observed small fitness difference between A and B.  And that leads to serious issues about statistical 'significance' and inference criteria.  That's because most alleged fitness differences are essentially local and comparative.  In turn that means the variant is not inherently selected but is context-dependent: fitness doesn't have a universal value, like, say, G, the universal Newtonian gravitational constant in physics, and to me that means that even an implicitly Newtonian view of natural selection is mistaken as a generality about life. 

If selection were really force-like in that sense, rather than an ephemeral, context-specific statistical estimate, its amount (favoring A over B) should approach the force's parameter, analogous to G, asymptotically: the bigger the sample and greater the number of samples analyzed the closer the estimated value would get to the true value.  Clearly that is not the way life is, even in most well-controlled experimental settings.  Indeed, even Darwin's idea of a constant struggle for existence is incompatible with that idea.

There are clearly many instances in which selective explanations of the classical sort seem specifically or even generally credible.  Infectious disease and the evolution of resistance is an obvious example.  Parallel evolution, such as independent evolution of, say, flight or similar dog-like animals in Australia and Africa, may be taken to prove the general theory of adaptation to environments.  But what about all the not dogs in these places?  We are largely in ad hoc explanatory territory, and the best of evolutionary theory clearly recognizes that.

So, in what sense does natural selection actually exist?  Or neutrality?  If they are purely comparative, local, ad hoc phenomena largely demonstrable only by subjective statistical criteria, we have trouble asserting causation beyond constructing Just-So stories.  Even with a plausible mechanism, this will often be the case, because plausibility is not the same as necessity.  Just-So stories can, of course, be true....but usually hard to prove in any serious sense.

Additionally, in regard to adaptive traits within or between populations or species, if genetic causation is due to contributions of many genes, as typically seems to be the case, there is phenogenetic drift, so that even with natural selection working force-like on a trait, there may be little if any selection on specific variants in that mix: even if the trait is under selection, a given allelic variant may not be.

Some other slippery issues
Natural selection is somewhat strange.  It is conceptually a passive screen of variation, but often treated as if an inherent property of a genotype (or an allele), whose value is determined on what else is in the same locus in the population.  Yet it's also treated as if this is inherent and unchanging property of the genotype...until any competing genotypes disappear.  As the favored allele becomes more common, its amount of advantage will increasingly vary because, due to recombination and mutation, the many individuals carrying the variant will also vary in the rest of their genomes, which will introduce differences in fitness among them (likewise, early on most carriers of the favored 'A' variant will be heterozygotes, but later on more and more will be homozygotes).  When the A variant becomes very common in the population, its advantage will hardly be detectable since almost all its peers fellws will have the same genotype at that site.  Continued adaptation will have to shift to other genes, where there still is a difference.  Some AA carriers will have detrimental variants at another gene, say B, and hence reduced fitness. Relatively speaking, some A's, or eventually maybe all A's, will have become harmful, because even in classical Darwinian terms selection is only relative and local.  So, selection even in the force-like sense, is very non-Newtonian, because it is so thoroughly context-dependent.  

Another issue is somatic mutation.  The genotypes that survive to be transmitted to the next generation are in the germ line.  But every cell division induces some mutations, and depending on when and where during development or later life a mutation occurs, it could affect the traits of the individual.  Even if selection were a deterministic force, it screens on individuals and hence that includes any effects of somatic mutation in those individuals.  But somatic mutations aren't inherited, so even if the mechanism is genetic their effects will appear as drift in evolutionary terms.  

Most models of adaptive selection are trait-specific.  But species do not evolve one trait at a time, except perhaps occasionally when a really major stressor sweeps through (like an epidemic).  Generally, a population is always subject to a huge diversity of threats and opportunities, contexts and changes.  Every one of our biological systems is always being tested, of in many ways at once. Traits are also often correlated with one another, so pushing on one may be pulling on another.  That means that even if each trait were being screened for separate reasons, the net effect on any one of the must typically be very very small, even if it is Newtonian in its force-like nature.  

The result is something like a Japanese pachinko machine.  Pachinko is popular type of gambling in Japan. A flurry of small metal balls bounces down from the top more or less randomly through a jungle of pins and little wheels, before finally arriving at the bottom.  The balls bounce off each other on the way in basically random collisions. The payoff (we could say it's analogous to fitness) is based on the balls that, after all this apparent chaos, end up in a particular pocket at the bottom.  In biological analogy, each ball can represent a different trait or perhaps individuals in a population. They bounce around rather randomly, constrained only by the walls and objects there--nothing steers them specifically. What's in the pocket is the evolutionary result. 

Pachinko machine (from Google images)
 (you can easily find YouTube videos showing pachinkos in action)

All similes limp, and these collisions are probably in truth deterministic, even if far too too complex to predict the outcome.  Nonetheless, this sort of dynamics among individuals with their differing genes of varying and context-specific effects, in diverse and complex environments, suggests why in this dynamic complex, change related to a given trait will be a lot like drift; there are so many that if each were too strongly force-like extinction would be more likely the result.  Further, since most traits are affected by many parts of the genome, the intensity of selection on any one of them must be reduced to be close to the expectations of drift. Adaptive complexity is another reason to think that adaptive change must be glacially slow, as Darwin stressed many times, but also that selection is much less force-like, as a rule.  After the fact, seeing what managed to survive, it looks compatible with force-like, straight-line selection.

Here, the process seems to rest heavily on chance.  But as we discussed in a post in 2014 in a series on the modes and nature of natural selection, we likened the course that species take through time to the geodesic paths that objects take through spacetime, that is determined (and there it really does seem to be 'determined') by the splattered matter and energy in any point it passes through.

An overall view
This leaves us in something of a quandary.  We can easily construct criteria for making some inferences, in the stronger cases, and testing them in some experimental settings.  We can proffer imaginative scenarios to account for the presence of organized traits and adaptations.  But evolutionary explanations are often largely or wholly speculative.  This applies comparably to natural selection and to genetic drift as well, and these are not new discoveries although they seem to be in few peoples' interest to acknowledge them fully.

Darwin wanted to show by plausibility argument that life on earth was the result of natural processes, not ad hoc divine creation events.  He had scant concepts of chance or genetic drift, because his ideas of the mechanism of inheritance were totally wrong.  Concepts of probabilism and statistical testing and the like were still rather new and only in restricted use.  Darwin would have no trouble acknowledging a role for drift.  How he would respond to the elusiveness of these factors, and that they really are not 'forces', is hard to say--but he probably would vigorously try to defend systematic selection by arguing that what is must have gotten here by selection as a force. 

The causal explanation of life's diversity still falls far short of the kind of mathematical or deterministic rigor of the core physical sciences, and even of more historical physical sciences like geology, oceanography, and meteorology.  Until someone finds better ways (if they indeed are there to be found), much of evolutionary biology verges on metaphysical philosophy for reasons we've tried to argue in this series.  We should be honest about that fact, and clearly acknowledge it.

One can say that small values are at least real values, or that you can ignore small values, as in genetic drift.  Likewise one can say that small selective effects will vary from sample to sample because of chance and so on.  But such acknowledgments undermine the kinds of smooth inferences we naturally hunger for.  The assumption that what we see today is what was the case in the past is usually little more than an assumption. This is a main issue we should confront in trying to understand evolution--and it applies as well to the promises being made of 'precision' prediction of genomic causation in health and medicine.  The moving tide of innumerable genotypic ways to get similar traits, at any time, within or between populations, and over evolutionary time, needs to be taken seriously. 

It may be sufficient and correct to say, almost tautologically, that today's function evolved somehow, and we can certainly infer that it got here by some mix of evolutionary factors.  Our ancestors and their traits clearly were evolutionarily viable or we wouldn't be here.  So even if we can't really trace the history in specifics, we can usually be happy to say that, clearly, whales evolved to be able to live in the ocean.  Nobody can question that.  But the points I've tried to make in this series are serious ones worth thinking seriously about, if we really want to understand evolution, and the genetic causal mechanisms that it has produced.


rich lawler said...

With reference to your pachinko machine, (if you are unfamiliar with it) you should check out the paper by Oliver P. Person in Ecology 1960 (http://www.jstor.org/stable/1933324). He built a "population dynamics" machine and it simulates all sorts of population processes using steel balls that fall through various holes and/or are channeled through various slots. I wish I could track this machine down, I would love to see it in person.

Ken Weiss said...

Thanks. I'll take a look as I didn't know about it. When I was in high school a friend, who had lived for some time in Japan, had a pachinko machine, and we played on it a lot (while we were putatively studying for our physics or chemistry exams).

Ken Weiss said...

On a quick look, even before there were much relevant 'genetics' (in 1960), this mechanical model showed the nature of complexity, and the author seems to have been clear about that. If the machine exists, and you can find it, let me know as I'd be curious to see what you can do with it.