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Evolution as a pachinko history: what is 'random'?

We discussed a Japanese pachinko machine in an earlier post, a pinball machine, as an example of the difference between randomness and determinism, in an evolutionary context.   Here we want to use pachinko machine imagery in a different way.

The prevailing, often unstated but just-under-the-surface assumption is that every trait in life is here because of natural selection.  Of course, for a trait to be here at all, bearers of its ancestral states up to the present (or, at least, the recent past) were successful enough to have reproduced.  It would not be here if it were otherwise, unless, for example, it's itself harmful, or without function but connected to a much better, related trait since genes are usually used in many different bodily contexts and may be associated with both beneficial and harmful traits.  Most sensible evolutionary geneticists know that many or even most sites in genomes tolerate variation that has either no effect or effects so small that in realistic population sizes they change in frequency essentially by chance.





However, the widespread default assumption that there must be an adaptive explanation for every trait usually also tacitly assumes that probabilism doesn't make much difference.  Some alert evolutionary biologists will acknowledge that one version among contemporary but equivalent versions of a trait can evolve by chance relative to other versions.  But the insistence, tacit or expressed, is that natural selection, treated essentially as a force, is responsible.  The very typical view is that the trait arose because of selection 'for' it, and that's why it's here.  And speaking of 'here', here's where a pachinko analogy may be informative.

If a bevy of metal balls tumbles through the machine, each bouncing off the many pins, they will end up scattered across the bottom ledge of the machine (the gambling idea is to have them end up in a particular place, but that's not our point here).  So let's take a given ball and ask 'Why did it end up where it did?"





The obvious and clearly true answer is 'Gravity is responsible'.  That is the analogue of 'selection is responsible'.   But it is rather an empty answer.  One can always say that what's here must be here because it was favored (that is, not excluded) by fitness considerations: its ancestral bearers obviously reproduced!  We can define that as 'adaptation' and indeed in a sense that is what is done every day, almost thoughtlessly.

Gravity is, like the typical if tacit assumption about natural selection, a deterministic force for all practical purposes here.  But why did this ball end up in this particular place?  One obvious answer is that each starts out in a slightly different place at the top, and no two balls are absolutely identical. However, each ball makes a different path from the top to the bottom of the obstacle course it faces. Yes, it is gravity that determines that they go down (adapt), but not how they go down.

In fact, each ball takes a different path, zigging and zagging at each point based on what happens, essentially by chance, at that point.   This one might think of as local ecosystems on the evolutionary path of any organism, that are beyond its control.  So, in the end, even if the entire journey is deterministic, in the sense that every collision is, the result is not one that can, in practice, be understood except by following the path of each ball (each trait, in the biological analogy).  And this means that the trajectory cannot be predicted ahead of time. And in turn, this means that our interpretation of what a trait we see today was selected 'for' is often if not usually either basically just a guess or, more often, equates what the trait does today to what it was selected to be, expressed as if it were an express train from then to now.

And this doesn't consider another aspect of the chaotic and chance-affected nature of evolutionary adaptation: the interaction with the other balls bouncing around at the same time in such an obstacle course.  Collisions are in every meaningful sense in the game of life, if not pachinko, chance events that affect selective ones, even were we to assume that selection is simple, straightforward, and deterministic.

The famous argument by Gould and Lewontin that things useful for one purpose, such as 'spandrels' in cathedral roofs, are incidental traits that provide the options for future adaptations--life exploits today with what yesterday produced for whatever reason even if just by chance.  The analogy or metaphor has been questioned, but that is not important here.  What is important is that contingencies of this nature are chance events, relative to what builds on them.  Selectionism as a riposte to creationism is fine but hyper-selectionism becomes just another often thought-free dogma.  Darwin gave us inspiration and insight, but we should think for ourselves, not in 19th century terms.

A far humbler, and far less 'Darwinian' (but not anti-Darwinian!), explanation of life is called for if we really want to understand evolution as a subtle often noisy process, rather than as a faith.  Instead, even serious biologists freely invent--and that's an apt word for it--selective accounts, as if true explanations, for almost any trait one might mention. It's invented because some reason is imagined without any direct evidence other than present-day function, but then treated as if directly observed, which is rarely possible. Here is an interview that I just came across that in a different way makes some of the same points we are trying to make here.

Everything here today is 'adaptive' in the sense that it has worked up to now.  Everything here today is also a 4 billion year successful lineage, that all made its way through the pachinko pins.  But these are almost vacuous tautologies.  Understanding life requires understanding one's biases in trying to force simple solutions on complicated reality.

Causal complexity in life

Evolution is the process that generates the relationships between genomes and traits in organisms.  Although we have written extensively and repeatedly about the issues raised by causal complexity,  we were led to write this post by a recent paper, in the 21 October 2016 issue of Science, which discusses molecular pathways to hemoglobin (Hb) gene function.  Although one might expect this to be rather simple and genomically direct, it is in fact complex and there are many different ways to achieve comparable function.

The authors, C Nataragan et al.,  looked at the genetic basis of adaptation to habitats at different altitude, focusing on genes coding for Hb molecules, that transport oxygen in the blood to provide the body's tissues with this vital fuel.  As a basic aspect of our atmosphere, oxygen concentrations differ at different altitudes, being low in mountainous regions compared to lowlands.  Species must somehow adapt to their localities, and at least one way to to this is for oxygen transport efficiency mechanisms to differ at different elevations.  Bird species have moved into and among these various environments on many independent occasions.

The affinity of Hb molecules for, that is, ability to bind oxygen, depends on their amino acid sequence, and the authors found that this varies by altitude.  The efficiency is similar among species at similar altitudes, even if due to independent population expansions. But when they looked at the Hb coding sequences in different species, they found a variety of species-specific changes.  That is, there are multiple ways to achieve similar function, so that parallel evolution at the functional level, which is what Nature detects, is achieved by many different mutational pathways.  In that sense, while an adaptation can be predicted, a specific genetic reason cannot be.

The authors looked only at coding regions, but of course evolution also involves regulatory sequences (among other functional regions in DNA), so there is every reason to expect that there is even more complexity to the adaptive paths taken.

Important specific documentation....but not conceptually new, though unappreciated
The authors also looked at what they call 'resurrected ancestral' proteins, by experimentally testing the efficacy of some specific Hb mutations, and they found that genomic background made a major difference in how, or whether, a specific change would affect oxygen binding.  This shows that evolution is contingent on local conditions, and that a given genomic change depends on the genomic background.  The ad hoc, locally contingent nature of evolution is (or should be) a central aspect of evolutionary world views, but there is a widespread tendency to think in classical Mendelian terms, of a gene for this and a gene for that, so that one would expect similar results in similar, if independent areas or contexts.  This is a common, if often tacit, view underlying much of genome mapping to find genes 'for' some human trait, like important diseases.  But it is quite misleading, or more accurately, is very wrong.

In 2008 we wrote about this in Genetics, as we've done before and since here on MT and in other papers.  In the 2008 article we used the following image to suggest metaphorically the nature of this complex causation, with its alternative pathways and the like, where the 'trait' is the amount of water passing New Orleans on the Mississippi River.  The figure suggests how difficult it would be to determine 'the' causal source of the water, how many different ways there are to get the same river level.

Drainage complexity as a metaphor for genomic causal complexity.  Map by Richard Weiss and ArcInfo
One can go even further, and note that this is exactly the kind of findings that are to be expected from and documented by the huge list of association studies done of human traits.  These typically find a great many genome regions whose variation contributes to the trait, usually each with a small individual effect, and mainly at low frequency in the population.  That means that individuals with similar trait values (say, diabetes, obesity, tall, or short stature, etc.) have different genotypes, that overlap in incomplete and individually unique ways.

We have written about aspects of this aspect of life, in what we called evolution by phenotype, in various places.  Nature screens on traits directly and only on genes very indirectly in most situations in complex organisms.  This means that many genotypes yield the same phenotype, and these will be equivalent in the face of natural selection and will experience genetic drift among them even in the fact of natural selection, again because selection screens the phenotype.  This is the process we called phenogenetic drift.  These papers were not 'discoveries' of ours but just statements of what is pretty obvious even if inconvenient for those seeking simple genetic causation.

The Science paper on altitude adaptation shows this by stereotypical sequences from one individual each from a variety of different species, rather than different individuals within each species, but that one can expect must also exist.  The point is that a priori prediction of how hemoglobin adaptation will occur is problematic, except that each species must have some adaptation to available oxygen.  Parallel phenotype evolution need not be matched by parallel genotypic evolution because selection 'sees' phenotypes and doesn't 'care' about how they are achieved.

The reason for this complexity is simple: it is that this is how evolution working via phenotypes rather than genotypes molds the genetic aspects of causation.

They were all my future specimens. And they died.

Without skeletal collections we'd struggle to do much evolutionary biology, especially when it comes to studying fossils.

We'd hate to let all those specimens go to waste, just languishing there in museum drawers. Sciencing them brings honor to their death. (Thanks for the new verb, Andy Weir.) But while we're learning from skeletons we can never forget that they're dead.

So although many of our samples are animals that were hunted by President Theodore Roosevelt (thanks Smithsonian!) or Major Powell-Cotton (thanks Powell-Cotton museum!), many of them, especially when it comes to human skeletons, are ones that died of "natural" causes.

You're thinking, well, duh. Well, yeah. Duh. But sometimes what's obvious still isn't so obviously important until someone goes to the trouble to very carefully consider it.

If the "osteological paradox" has already come to mind, that's probably because you're familiar with the classic paper "The Osteological Paradox" co-authored by a certain Mermaid and other former graduate school professors of mine.  Although the paper discusses issues that are more complicated and more specific than we need to hash out here, "osteological paradox" is a great term for the conundrum that scientists face when reconstructing things like health, fitness, and adaptation in past populations from the remains of the individuals who died.

Naturally, if you've been raised on "osteological paradox" thinking, it's one of the first things that comes to mind when you see a visually stunning study by my colleagues that analyzes pelvic morphology of dead individuals to reveal differing adaptive morphologies in the pelves of males vs. females.

Sexual dimorphism in the human pelvis has been known for quite some time, and it's already well-understood that the differences are largely located in the dimensions of a woman's birth canal. But this new study shows that differences are observable from birth and that women at post-reproductive ages do not retain the obstetrically-beneficial dimensions that younger women do during their fertile years. One of the arguments this new paper makes is that human female pelves are adapted to be most accommodating for childbirth during the child-bearing years. And that very well may be the case. However, these claims for adaptation, like most based on human skeletal samples, were based on women who were dead and, thus, not adapted.

In this context, the concluding paragraph of "The Osteological Paradox" is worth quoting:

"...choosing among competing interpretations of the osteological evidence requires tight control over cultural context as well as a deeper understanding of the biology of frailty and death. These problems deserve far more attention than they have received to date if we are to make sense of the biomedical consequences of the major social and environmental changes that have occurred during the course of cultural evolution."

And that could be extended to "biological evolution" as well. Maybe it has been in a later paper.

Anyway, when we're looking at dead humans with an evolutionary mindset, it's probably good to ask whether we can know if selective pressures were the same across the timespan covered by the sample. It's also probably good to ask whether environmental conditions were the same across the timespan covered by the sample. It's also probably good to sing this to ourselves as we design our evolutionary study of the human skeleton:



Rare Disease Day and the promises of personalized medicine

O ur daughter Ellen wrote the post that I republish below 3 years ago, and we've reposted it in commemoration of Rare Disease Day, Febru...