Monday, March 21, 2011

Honoring Masatoshi Nei

There was a special meeting here at Penn State this weekend.  It was a gathering to honor the distinguished, perhaps nearly legendary, Masatoshi Nei on his recent 80th birthday.  Nei's work has been on molecular evolutionary genetics as it applies in particular to the evolution of DNA sequence.  A rather incredible array of distinguished people, including Prof. Nei's many distinguished former students, and other distinguished population geneticists were in attendance.

Many interesting papers were given, but in particular we wanted to mention some work presented by Michael Lynch.  He has been stressing the role of chance (drift) in the assembly of genomes by evolutionary processes.  In particular, he has shown that much of our genome has not been the result of strong, highly focused natural selection as is the widespread mythology about evolution.  Instead, or in addition to natural selection, many variants that are not the most 'fit' in their time, can still advance even to fixation, replacing other variants at their respective locus. This can happen, for example, if their fitness 'deficit' is quite small relative to the most fit variant in the population. 

Mike Lynch's talk here concerned the way in which the mutation rate was molded in the ancestry of species living today.  The main idea is that if mutations, or mutation rates, are only slightly deleterious, then selection is rather powerless to mold them.  Much that happens again depends on drift.  There are regular relationships between mutational rates, the amount of genetic variation, and genome and population sizes (the latter affects the power of drift--chance--in determining what survives or raises in frequency and what doesn't).  If you're interested in this, his book ("The Origins of Genome Architecture") and a recent paper in Trends in Genetics (2010) are very much worth reading.

The point of mentioning this here on Mermaid's Tale is that the idea that fine-tuning by natural selection is the, or even the major, factor in evolution is exaggerated, as we've often said.  Every species here today is the result of a 4-billion-year successful ancestry, so we're all 'adapted' to what we do (if not, we're headed for extinction).  Selection removes what really doesn't work.  But evolution is very slow generally and the evidence strongly suggests that there are many ways to be successful enough, and that is good enough to proliferate.  While there are many instances of what appear to be finely selected, exotically specialized adaptations (and Darwin wrote about  many of them!), that is not the whole story  (and perhaps not the main story?) of evolution.


Holly Dunsworth said...

I'm thinking that instead of pleading my students to think "survival of the fitter" (rather than "fittest"), that maybe I should suggest "survival of the fit enough." Perhaps that would resonate better for them and also be more scientifically sound.

Holly Dunsworth said...

And we're back to the point that there are many ways to evolve and to adapt.

Holly Dunsworth said...

(Don't mind me! Just riffing further and further away from your stimulating post...)

Another technique I've used (to combat the limitations to assuming that fossil hominins were stupid knuckle-draggers): "Were proto-bears stupid? Were proto-kangaroos knuckle-draggers? Did proto-elephants suck at being proto-elephants?"

Holly Dunsworth said...

And of course, there's the problem with "proto" as well.

Ken Weiss said...

Yes, it's like saying Heracotherium (Eohippus) had too many toes to be a good horse, and we really didn't have 'adapted' horses until not so long ago. And of course, horses are now (finally!) adapted so they're now just going nowhere fast (just round and round the track).

occamseraser said...

Sadly, too many folks, pro and am alike, still think evolution necessarily implies "progress". I think trying to explain human evolution in "grades" or stages promotes the same kind of fuzzy, teleological thinking. I guess Ardi gets a lower grade than Lucy and has to repeat the Miocene ;)
I still think there's heuristic value in models of fitness/adaptive landscapes, with various local optima that are "fit enough" to persist.

Ken Weiss said...

Occam, Michael Ruse's book Monad to Man deals with the persistent history of the view of 'progress' in evolution. Progress is so ingrained in our culture, along with self-pride and human exceptionalism, that it's like kudzu: unkillable.

At the I wads a graduate student, it was so ingrained, as Loring Brace used to say, that text books showed all fossils to be on side branches--after all, we wouldn't want one of those savage-looking brutes to be our ancestor!

The problem with 'heuristic' values in fitness landscape notions is if they are unrealistic, because then their 'heurism' (if that's a word) is misleading. I am simulating drift-only scenarios in which it _seems_ nonetheless quite clear that there are fitness peaks and valleys if one looks at phenotypes--but of course there aren't any. How and when it can actually happen in evolution is a legitimate question.

Likewise, personally I think ideas of 'optima', local or otherwise, make many assumptions about both genotypic and environmental stability relative to mutation rates and population size and so on, that I think they may also be convenience concepts that are only apt some of the time.

These at least are the real questions we should be trying to address, rather than the usual practice of assuming them and then constructing scenarios that are too easily accepted as being true rather than just speculation.

That's my own view, anyway....even if it's a deeply minority view!

Holly Dunsworth said...

I'm thinking that fashion trends through time may be a good way to explore fitness without progress.

Also, looking across space but not time...examples of where similar animals make it work in different environments or different animals make it work in different ways but in similar environments. Could potentially weaken the notion of every perfect thing in its perfect place.

Ken Weiss said...

Did you know about the famous study of fashion cycles in the classic book Anthropology by Krober? It may provide some useful thoughts.

It is, I think, well known that birds, and baboons (if not probably many other primates) change their social structure or even their diet based on circumstances.

Of course, if all of this were so programmed, one would expect rigid ways-to-be, but one primate, called Homo sapiens, shows how false that idea is. Yet, even in our case, every day one reads claims about how were are genetically programmed for this or that or anything else. And some of this even stated with a serious face by scientists whose job it is to know better.

Holly Dunsworth said...

They can't help it... it's programmed in their genes.

Ken Weiss said...

Science progresses incrementally most of the time, and then with a leap. We all hunger to make the leap, perhaps, but the pressures are to work the increments (but claim the leap!). Striving for a leap doesn't get you tenure or grants, as a rule.

Here, we have had about 200 years of real evolutionary thinking (since Lamarck, say), with accelerating work, using an industrial system (called 'the scientific method'), that normally would have take a millennium. So we press more quickly up against the limits to which the current approach can go.

At least, questioning our deep assumptions or, perhaps more appropriately, our _reflex_, institutionalized assumptions, can't be harmful and might be salubrious.

G Greene said...

From a layperson's standpoint, to the extent that they could ponder it at all, 'lower' life forms would hardly look upon us 'evolved', but rather as a destructive mutation, growing rapidly out of control, consuming everything and (if we keep at it) leading to the death of the 'organism' or ecosystem (Gaia) - much the same way we view cancer. I don't know who coined the term, but it often appears we few, we unreasonably proud, we homo sapiens, taken as a species, aren't much more than a 'virus in shoes'.

Ken Weiss said...

Whether we are worse than other species, from the point of view of those other species, is debatable. We're very good for many species (corn, cows, chickens, lab mice), but from a Gaia point of view we're clearly temporary. Either we set up some sort of equilibrium that's stable, with other species,or we become extinct, leaving the stage after our sound and fury, to our successors.

Keeping in mind that this is a clockwork rather than divinely staged play, if science is right, then no species is better or worse than any other. All species, except perhaps mushrooms, are predators on other life, and most lineages become extinct.

The view of humans as the strutting tragedy, to continue the thespian metaphor, is one from humans themselves as the audience, stepping aside from ourselves as it were, but giving us a 'review' based on our own cultural views of good and bad.

Anyway, we are advanced in terms of our type of resource meddling, certainly, and from many points of view, we're a scourge.