Saturday, March 17, 2012

Gorilla my dreams, I adore you

What to do about geneticists?  On one hand, they are so smart that we should accept whatever they say, no matter how absurd, inaccurate, or even racist it may be.  (See Nicholas Wade’s Before the Dawn).[1]   On the other hand, they’re ignorant and arrogant assholes and they should be thrown in jail (See Trofim Lysenko).[2]  There has got to be a middle ground.

The gorilla genome is now out, and when combined with human, chimpanzee, and orangutan, it allows us to do a phylogenetic comparison.[3]  We have known since the 1980s that human-chimp-gorilla genetically is a very close call, with DNA tending to place humans and chimps a little closer, but only with a lot of discordance or statistical noise.  (That is in fact exactly what the ill-fated DNA hybridization showed, although it was infamously misrepresented.)  When the mtDNA data first came out [4] they linked human to chimp pairwise, but only if you ignored the fact that over half of the phylogenetically informative DNA sites did not in fact show it to be human-chimp.   Those data showed it to be chimp-gorilla and human-gorilla.  The only way to extract human-chimp from those data was to treat the question like a Republican primary, where whoever gets the plurality of the votes wins the state.  So human-chimp was Mitt Romney, winning the nomination, but with barely 45% of the phylogenetically informative sites.

It then becomes a trivial task to explain away the discordant data, that is to say, the 55% of your data that you have decided is giving you the “wrong” answers.   You say it is “incomplete lineage sorting” or the result of ancestral polymorphisms, which have segregated into descendant taxa in a pattern different from the sequence of speciation.  Geneticists illustrate this with images that always seem to remind me of maps of the London Underground, with chimpanzees being Bakerloo and humans Victoria Station.

But I digress. It might also be parallel mutation or even backcrossing.  The problem, though, is that you have a lot of  homoplasy, and one of the assumptions of cladistic/phylogenetic analysis is that homoplasy (i.e., observed as discordance) is very, very low compared to synapomorphy (i.e., the shared derived characters that you think are tracking the actual branching history of the species).

This is the equivalent of simply choosing the most parsimonious solution to the phylogenetic problem.  Most of the data that give a pairwise resolution give this pairwise resolution, therefore it must be the right one.  But there is an inherent contradiction in this logic.  You are choosing the most parsimonious solution in a system that is not obviously very parsimonious.  In other words, if you are willing to accept the possibility that 55% of your phylogenetically informative sites are homoplasies (that is to say, are giving you the “wrong” answer), then how can you reject the idea that 70% of your sites might be giving you the “wrong” answer?  I talked about this many years ago in the American Journal of Physical Anthropology.[5] 

The model that fits the data best is not a model of two successive bifurcations, but what we called at the time a “trichotomy” and now would call “reticulate” or even “rhizotic” evolution.[6] [7]

The geneticists working on this problem have been hampered by the cladistic necessity of regarding speciation as events, rather than as processes – when their ape data are showing speciation as processes, not as events.  The new paper on the gorilla genome says that 30% of their phylogenetically informative sites are discordant.  This is how the new paper imagines the genomic relationships of humans, chimps, and gorillas – as indicating two temporally isolated speciation “events” and whatever the hell is going on in the middle there.

The creationists jumped all over this inconsistency, and it really is just the result of sloppy thinking by the scientists.

In trying to plug the genomic data into sequential speciation events, we are committing the square-peg-round-hole fallacy. There are historical and ideological reasons for depicting it as two successive, temporally distinct “events,” but that certainly misrepresents the evidence, and most likely misrepresents the biological history.  One of the most bizarre illustrations was in a recent introductory textbook, which showed this to students:

It’s trying to say that there were two speciation events, 7 mya and 6 mya, but has located the 7 mya event incorrectly.  If you look at the scale, you’ll see that it’s actually drawn at 8 million, to put a separation between them that shouldn’t be there.  The same text draws it this way a bit later. with very little (vertical) time separating the two “events” at 7-8 mya and 5-7 mya, but a lot of (horizontal) space.  That ought to learn ‘em!

Obviously, that’s not the text I use. 

The new paper on the gorilla genome, I might add, sets the “speciation events” at 6.0 and 3.7 mya.  The 3.7 mya date for the divergence of human and chimpanzee is simply, to the extent that anything can be falsified in the fossil record, false - although it is oddly congruent with some of Vince Sarich and Allan Wilson’s early writings on the subject in the 1960s.[8]  The (myriad) authors of the new paper go on to argue that they can juggle some of the parameters in their computer program to make the dates come out to about 6 and 10 million years ago – as if that is supposed to give us confidence!

For the Alternative Introduction, I drew this figure to illustrate the problem.

Rather than prurient talk about cross-species buggery on the part of early hominids, how about speciation here as a temporal process, and populations through time as anastemosing capillary systems (Earnest Hooton’s metaphor, expressing the same point as rhizomatic and reticulate evolution).  It is also noteworthy that we tend to model and depict the gene pools of all three species as equivalent, when we’ve known for years that chimps and gorillas, even as relict populations, have gene pools that are considerably more extensive than that of our own species.  That is to say, Homo sapiens is relatively depauperate in genetic diversity.  The only study to try and incorporate that information into a phylogenetic analysis, many years ago, found that it completely obscured the phylogenetic “signal” and that it was therefore a fool’s errand to try and extract two successive bifurcations from a genomic analysis of human, chimpanzee, and gorilla.[9] 

Interestingly, the new paper actually did look at diversity in gorilla genomes, but didn’t incorporate that into their phylogenetic analysis.  Bottom line:  Human evolution is probably more interesting than the geneticists realize.

[1] Wade N. 2006. Before the Dawn: Recovering the Lost History of Our Ancestors. New York: Penguin.

[2] Medvedev Z, and Lerner I. 1969. The Rise and Fall of TD Lysenko. New York: Columbia University Press.

[3] Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T et al. . 2012. Insights into hominid evolution from the gorilla genome sequence. Nature 483(7388):169-175.

[4] Horai S, Satta Y, Hayasaka K, Kondo R, Inoue T, Ishida T, Hayashi S, and Takahata N. 1992. Man's place in hominoidea revealed by mitochondrial DNA genealogy. Journal of Molecular Evolution 35(1):32-43.

[5] Marks J. 1994. Blood will tell (won't it?)? A century of molecular discourse in anthropological systematics. American Journal of Physical Anthropology 94:59-79.

[6] Marks J. 1995. Learning to live with a trichotomy. American Journal of Physical Anthropology 98:211-213.

[7] Arnold M. 2009. Reticulate Evolution and Humans: Origins and Ecology. New York: Oxford University Press.

[8] Sarich VM. 1968. The origin of the hominids: An immunological approach. In: Washburn SL, and Jay PC, editors. Perspectives on Human Evolution I. New York: Holt, Rinehart, and Winston. p 94-121.

[9] Ruano G, Rogers, Jeffrey A., Ferguson-Smith, Anne C., Kidd, Kenneth K. 1992. DNA sequence polymorphism within hominoid species exceeds the number of phylogenetically informative characters for a HOX2 locus Molecular Biology and Evolution 9(4):575-586.

Friday, March 2, 2012

A rant on race and genetics

I have really had it with anti-intellectualism masquerading as biological science.  What really set me off is a blog post by the distinguished evolutionary geneticist Jerry Coyne ( 

               Unlike the great fruitfly geneticist Theodosius Dobzhansky, who was a member of various anthropological associations and had personal and professional relationships with anthropologists who worked on human diversity (notably Sherry Washburn, Ashley Montagu, and Margaret Mead) – and even let his daughter marry one, archaeologist Michael Coe  – Coyne writes in abject ignorance of anthropology.  Freed from the constrains of actual knowledge, then, Coyne is able to present his own commonsensical views as if they were based on science. 

               He quotes historian of biology Jan Sapp, reviewing two new books on the subject which both come to the same conclusion – that human races are biocultural constructs, not natural facts – and dismisses the conclusion of the books and the reviewer: “Well, if that’s the consensus, I am an outlier.”   

               The irony is that Coyne is not self-aware enough to appreciate that that is precisely parallel to the position of the creationists.   His idea of race is the existence of between-group variation in the human species, and the discovery that groups of people are different from one another.  Anthropologists have been studying the nature of that difference for around a century and a half, but Coyne isn’t interested in what they’ve learned.  Since there exist “morphologically different groups of people who live in different areas” then there are, ipso facto, human races, regardless of what anthropologists think they have learned about the subject.

               Of course the discovery that people in different places are different is a trivial one.  At issue is the pattern of those differences and its relation to the classification of the human species.  To equate the existence of between-group variation to the existence of human races  is to miss the point of race entirely.  Race is not difference; race is meaningful difference.  It’s the “meaningful” that takes the question of human races out of the geneticist’s domain and places it into the anthropologist’s domain (which is where it has always been – although occasionally opposed by reactionary geneticists like Charles Davenport and Ruggles Gates, whom Coyne would do well to read).  At issue is the (cultural) decision about how much difference and what kinds of difference “count” in deciding that this kind of a person is categorically different from that kind of a person.  The merest familiarity with the modern literature on race would have made that clear to Coyne.  Coyne echoes right-wing ignoramuses with the sentiment that “the subject of human races, or even the idea that they exist, has become taboo.”  Jon Entine made the same claim in his stupid 2000 book on the imaginary genetic superiority of black athletes; and the segregationists made the same argument in the early 1960s. 

               But of course, race is only taboo in the same sense that creationism has become taboo, as being a false theory about  the world, from which scholars have moved on.  In fact, Coyne’s anti-intellectualism here is the equivalent of the creationist’s claim that “We obviously did not evolve from apes, since apes still exist”.  It reveals such an abject ignorance of the topic that all you can do is suggest a return to kindergarten.

               Coyne’s post, as it turns out, was inspired by a review (in American Scientist by Jan Sapp) of two books on race.  He explains, “I haven’t talked much about Sapp’s review, as I find it tendentious; nor have I read the books he’s reviewing.”  The books he’s reviewing are: 
Race and the Genetic Revolution: Science, Myth, and Culture, edited by Sheldon Krimsky and Kathleen Sloan.

               I haven’t read that one, but I can vouch that many of the contributors – including Troy Duster, Duana Fullwiley, Jonathan Kahn, Joe Graves, and Pilar Ossorio - have written insightfully and at considerable length on the subject, and know a heck of a lot more about it than Jerry Coyne does.  

               The other book is called Race?: Debunking a Scientific Myth and is actually by a biological anthropologist and an evolutionary geneticist – Ian Tattersall and Rob DeSalle.  If Coyne ever gets around to handling a copy of the book that inspired the review that inspired his ignorant blog post, he’ll discover that the jacket blurb says,

a prominent anthropologist and a prominent evolutionary geneticist have teamed up to give us a powerful scientific critique of the commonsensical idea of race.  Distinguished scholars and skilled communicators, Ian Tattersall and Rob DeSalle show clearly how “race” simply cannot be used as a synonym for “human biological diversity”.  In the age of genomics, this partnership of intellectual specialties is particularly valuable, and the result is a splendid testament to the merits of trans-disciplinary collaborations.

The good news is that there are evolutionary geneticists like Rob DeSalle out there.  But the scholarly boat seems to have sailed away without Jerry Coyne on board.   Ironically, the last time I gave a talk at the University of Chicago, about three years ago, it was on this very subject.  My title was, “Some More Things I’m Pissed Off About”.  Coyne wasn’t in attendance. 

               And yes, I wrote that blurb.