Tuesday, May 4, 2010

Plus c'est la même chose, plus ça change??

Nothing ever really changes, or so goes the old French saying 'plus ça change, plus c'est la même chose.' The more things change, the more they're the same thing. But is that how life really is?

An interesting new paper in Genome Research on this subject is getting some notice, but in fact the results should not be surprising, given what is known about evolution and development.

The blurb in Nature says:
The earliest stages of embryo development [as shown in the photo above, taken from the paper] seem to be almost identical among mammals. However, Sheng Zhong at the University of Illinois at Urbana-Champaign and his team have found that 40.2% of the genes shared by humans, mice and cows are expressed differently at this point.

Their analysis of gene-expression patterns in embryos at various stages early in development showed that differences result from altered gene regulation. In some cases, mutations affected the binding of regulatory proteins. In others, transposons or 'jumping genes' had hopped in front of the genes, changing their regulation.

This variation among species suggests that multiple gene networks can guide embryo development, and could be harnessed to generate embryonic stem cells.
This may have significant implications for stem cell research, but it also says a lot about evolution and development (EvoDevo). People are often surprised to learn that traits that are similar between species can have very different genetic architecture -- it's more usual to hear about homologous or orthologous genes, similar genes for similar traits (the iconic example is Hox genes, which play a major role in body patterning in fruit flies and humans, and every species in between).

Alternatively, a story in the New York Times last week described the usefulness of yeast or plants or worms for finding genes for human diseases. The genes described belong to clusters that do completely unrelated things in different organisms (one example was of a cluster of genes that repair damage to the cell wall in yeast but that is involved in blood vessel formation in humans). These clusters have been conserved through evolutionary time.

But the idea that different genes can underlay homologous traits is perhaps more counter-intuitive. Ken and his then post-doc, Malia Fullerton, published a paper in Theoretical Population Biology in 2000 describing just this. The effect is called 'phenogenetic drift' to indicate that the trait's genetic basis, the genetic effects that generate the phenotype, changes. This is not the same as genetic drift, when genetic variation that has no effect on a trait, or at least on reproductive success ('fitness') changes over the generations, nor that of phenotypic drift, when traits vary over generations to the extent that the variation doesn't affect reproductive success. Phenogenetic drift can be these things, but also, and perhaps most importantly, it occurs even when there is selection affecting the trait, even strong selection.

Thus, in the example above, the very early and hence very fundamentally important, stages in mammalian embryos are quite similar among different species, but the usage of genes to make it so is considerably different. Phenogenetic drift is easy to see all over the place -- even within species, when different people can have the same trait -- even including disease -- for different genetic reasons. Relative to each other these genotypes are equivalent in fitness terms, and their contributing alleles will change frequency over time by drift. It's no surprise to see it when we know that duplicate genes and many contributing genes together generate lots of redundancy and alternative genetic pathways to get the same trait.

However the dogma about selection and adaptive evolution has been gene- rather than trait-centered. But when many different genotypes can generate effectively the same phenotype, then perhaps genes really aren't the most important things to consider when we try to understand evolution. In this sense, perhaps because genes weren't understood at the time and perhaps because he had it right, Darwin developed his ideas about phenotypes -- the traits of organisms -- rather than genotypes. After all, he didn't need his idea of genetics to explain the historical nature of life's variation (indeed, evolution as he saw it wouldn't work under his idea of inheritance, and he knew it).

It often seems that the longer a trait is maintained, the more likely it is to have changed its genetic basis. Kazu Kawasaki in our lab, for example, has written a number of papers about the different genetic architecture for bone and tooth mineralization that has evolved in different lineages. In that case, the gene pathways share a common ancestor, a single gene that duplicated in different lineages to create gene families involved in mineralization -- he calls these the SCPP gene family. The original founding gene was apparently involved in the development of the first vertebrate mineralized skeletal tissue (probably, external skeletal protective plates or scales, even before there were calcified bones).

The final composition and structure of mineralized bone may vary, but it's the same trait, and serves essentially the same purpose (strength) in different lineages. Same trait, different genes. Whether this is usually true with conservation of form within lineages (such as the ants in amber that we wrote about last week), we can't know, because we have no way to know the original genetic basis. However, among other things, phenogenetic drift or alternative genomic pathways to the same trait, has interesting implications for notions of homology, the sharing of traits today because they have descended from the same ancestor. Traits can be homologous, but their genetic basis may not be. When selection is on the phenotype, it gets maintained however works!


Ken Weiss said...

Thanks. What about homoplasy, as well as homology--something relevant to paleontology?

Are two people with diabetes, or who share some other trait, but for different genetic reasons, instances of homologous causation? Are they homoplasies?

Homoplasy of this kind, if that's an apt term, are rife of course--that's one of the main lessons about phenogenetic complexity. And this in turn creates some questions to ponder about other uses of these terms and what should be viewed as homoplasy.

So, what about two species of baboon or gelada with long faces? Probably at least some, if not entirely, different genes. Homoplasy? Homology?

Anne Buchanan said...

Thanks, Holly! It also makes one wonder about the use of 'model' organisms and the search for genes involved in human diseases and disorders, and whether model organisms can be reliably assumed to be informative about humans. We know they often cannot be -- and phenogenetic drift is only one reason -- and yet they are often the best we have.

Holly Dunsworth said...

Exactly, Anne, another point I wanted to make in yesterday's post but skipped... the genes for x behavior/trait in mice are not necessarily the same in people and not only that but the behavior/trait is not necessarily the same in the first place. Bah!

Holly Dunsworth said...

That's the rub, Ken, what's primitive and what's derived in the fossil record? Geneticists are supposed to be helping us figure that out!

Caitlin S said...

I was debating using this Nature blurb for my summer undergraduate Sex class, but I might have them read Anne's post, instead. So glad I read it.

Anne Buchanan said...

Glad to be of interest, Caitlin!

James Goetz said...

Thank you. I always appreciate more evidence of convergent evolution whether at the molecular level or whether at the morphological level. I also like the related debate between Simon Conway Morris and the late Stephen Jay Gould concerning a restart of earth history and the inevitability or the extraordinary unlikeliness of the origin of humans capable of developing scientific theories. As many people know, Conway Morris cited the ubiquitous evidence of convergent evolution for his claim that such humans would inevitably originate in any restart of earth history while Gould pointed out many unlikely factors regardless of the increased odds from the phenomena of convergent evolution. In the context of natural history, I tend to agree with Gould. I doubt anybody could clearly quantify the debate because of the endless number of factors while I conjecture that Gould won the debate.

Ken Weiss said...

Convergence to 'human' form? What would that mean--or, rather, starting from what point? Or would it suffice that some kind of 'intelligent' beings, by our standard of the word, would eventually evolve? Or that starting 500 million years ago something looking like humans, with hair and eyebrows would evolve? In a sense, the general phenomenon of convergence can be hijacked to seem to apply to a degree of specificity a protagonist in the discussion defines, and to prove his or her point. So Gould or Conway Morris could each claim 'victory'

Holly Dunsworth said...

I end my Intro to Bio Anth course with Gould v. Morris and, at least for me, it's a fabulous thought experiment.

James Goetz said...

I could have been clearer about that. I should have put scare quotes around the word humans. Their debate focused on the origin of any species that would have intelligence including the ability to develop scientific theories. Please note the level of intelligence includes the ability to develop scientific theories and not merely, for example, the ability to use a stick as a tool.

James Goetz said...

I also want to clarify that in the follow up to the original debate, Gould clarified that intelligence at our level would unlikely descend from any lineage. That point wasn't specified in the original debate.

And Holly, that seems like a great way to end an Intro to Bio Anth course.:)

Ken Weiss said...

It's all very arbitrary. For example, what counts as 'scientific theories'? That's an ethnocentric way of describing what we ourselves consider advanced or intelligent. Still, the earth has resources and life is about getting them, surviving, proliferating and so on, and since what we call 'intelligence' is to a great extent about that at its root, it may be at least semi-safe to say that life might sooner or later have evolved organisms increasingly able to do that. We happen to be the most advanced organism in that respect. Fun to think about, at least.

James Goetz said...

Yes, it's arbitrary (personal discretion). And I suppose that some philosophers and scientists still debate about the definition of the term "scientific theory" while I suppose that any definition would do within the context of my above conjecture.

I want to defend that my arbitrary criteria isn't ethnocentric. For example, I said "the ability to develop scientific theories" while I never suggested that all ethnic groups of modern humans have developed or would develop scientific theories. But all ethnic groups have or had healthy adults who could develop scientific theories. For example, prehistoric modern humans demonstrated advanced inventiveness, which presumably correlates to the ability of developing scientific theories.

And I agree that my criteria is arbitrary and anthropocentric. Yes, on one hand, modern human inventiveness is merely another type of adaption that helps survival and reproduction. For example, Who's to say that those adaptions are any more important than antibiotic resistance adaptations in gonorrhea? On the other hand, I'm unashamedly anthropocentric. For instance, earlier today, I ate a turkey sandwich. How could I get more anthropocentric than that?:)

Per our brief comments a few days ago about Neanderthals, perhaps those builders of hearth, home, and attachable arrowheads lacked the ability to invent them while Neanderthals learned how to construct hearth, home, and attachable arrowheads from inventive anatomically modern humans. However, I know it's more complicated than that because hearths may have been developed by Homo erectus. Or did H. erectus merely take advantage of naturally occurring hearths with little or no invention? As far as I recall, this hasn't yet been resolved. (I presume Holly would know best about this in this blog.) Anyway, we don't know if Neanderthals invented or merely produced attachable arrowheads. And my conjecture leans toward saying that Neanderthals were giant pithecanthropines that were incapable of inventing attachable arrowheads.

And yes Ken, another species capable of developing scientific theories could originate on earth before the explosion of the sun, but I conjecture along with Gould that such a scenario would be extraordinarily unlikely. And it would never happen without the lineage developing some type of manual dexterity comparable to ours. That level of intelligence has little or no advantage if the species cannot manipulate the elements with dexterity. And such manual dexterity won't evolve in the descendants of any dolphins or octopuses before the sun explodes.

Ken Weiss said...

I'll only quibble a bit with what you say. 'Intelligent' beings -- let's leave it vague but stay within the general perimeters of our exchange of messages -- would not need to have manual dexterity. There could be other ways to be 'intelligent.' I agree that given life's path so far as we know it, it's not likely to happen before the sun blows up.

But if there will be a few more billion years, and you wipe us destructive humans off the earth and who knows what might happen? Even if Gould is right that they would not look or (hopefully) not act like us.

More of a problem I believe is that as long as we're here, any other creature that developed the kind of intelligence we have would be quickly killed off by us. After all, even in science fiction, the main thing we do with ETs is fight 'em. For that reason alone there isn't likely to be another branch of humanishly dexterous primates. This was called by Loring Brace an instance of the competitive exclusion principle in ecology: when it comes to other human-like beasts, there'd simply be no room at the Inn.

James Goetz said...

I agree that the extinction of humans and a couple billion life-friendly years left in our solar system would greatly increase the trivial odds of the evolutionary origination of another intelligent species. However, I don't believe this because I assume that humans would kill off an intelligent competitor. But I believe this because humans do a great job of exploiting their niche with both population size and technology while there consequently might be no advantage for another species to compete with humans.

I also agree that we could hardly imagine what could happen with a couple billion years of evolution after a hypothetical extinction of humans. And I suppose that Conway Morris would say the same with the exception that a new species with intelligence comparable to humans would inevitably originate while the new intelligent species might be a mollusk. And I assume the Gould would have said that we could hardly imagine what could happen in those couple billion years of evolution except that there would be no chance of the origination of another intelligent species. And if he were pushed, he might have said there would be a trivial chance but no practical chance. And in the context of natural history, I hold that there would be a trivial chance but no practical chance of the origination of another intelligent species.