Saturday, April 30, 2011

A first lecture on primate taxonomy (with obvious debts to Robert Benchley and Will Cuppy)

               To begin with, In 1987 there were about 170 species of primates.  Today there are over 400.  Go Primates! 
               For the sake of argument, let us say that there about 400 species of primates, ±75%.
               The first kind of primates are called prosimians.  Actually, however, they are not really a kind of primate, but two kinds of primate: lemurids of Madagascar, and lorisids of Asia and Africa.  To be absolutely fair, however, we have to acknowledge that there are two kinds of lorisids – fast-moving galagos and slow-moving lorises, although at the speed of light they may seem identical – so the first kind of primate is really three kinds of primates.
               But we should also include the fourth kind of primate in this first kind of primate, because the tarsier isn’t quite a monkey, and that’s what prosimians are – “not quite monkeys”.  According to cladists, the tarsier should be reclassified with the monkeys because phylogenetically it is almost one of them.
               The first four kinds of one kind of primates share an arbitrary property: namely, that they are still alive, and have not gone extinct.  Yet.   Consequently we need to expand our first kind of primates to incorporate the adapids and omomyids, two other kinds of the first kind of primates, now extinct.  The most interesting feature of the adapids and omomyids is that we don’t know what they evolved from and we don’t know what they evolved into, but we’re pretty sure that they evolved.  Don’t tell the creationists. 
               And before the adapids and omomyids were the plesiadapids, who only had a few of the primatey features by which we identify primates as primates and not as colugos, or flying lemurs, which are not actually even lemurs, so it’s hardly even worth asking whether they really fly.  But they do seem to be transitional forms between other mammals and primates, and you can tell the creationists that for me. 
               Fortunately, the diversity of the second group of primates is more precise.  The group we contrast with the prosimians is not, as you might think, the antisimians, but rather the simians themselves, although only Europeans really call them that.   We officially call them anthropoids, which means “sort of like people” from the Greek, and they should most definitely not be confused with the hominoids, which means “sort of like people” from the Latin, and comprise only a subset of the ones from the Greek.
               There are two kinds of anthropoids, and we distinguish them on the basis of geography and their noses.  There are other things we could focus on, like the form of their skull sutures, or the number of premolar teeth they have, but no, we focus on their noses.  The kind of monkey found in the Americas is really two or five kinds of monkey.  One or more of them is the marmosets, also known as the marmosets and tamarins.  Their principal distinction is how small they are. 
               How small are they?  They are so small that they never grow wisdom teeth.  Marmosets are also widely regarded as the stupidest anthropoids.  That is probably just a coincidence, however.  
               The pygmy marmoset is actually smaller than the dwarf marmoset, but it is the other way around for people.
               The other kind of New World monkey is known as everything else.  They include monkeys that hang by their tails, monkeys that hang out at night, monkeys that resemble The Phantom of the Opera, and even monkeys that resemble monks, which sounds more reasonable than it should.
               The other kind of anthropoid is actually two kinds of monkeys and one or several kinds of apes.  They all have the same number of teeth as us, or at least they would if we didn’t have our teeth pulled.  They are called Catarrhini, on the basis of their noses, from the Greek “flowing downward”.  You probably don’t want to know what that’s referring to, but suffice it to say, if you were a New World monkey, you would go through Kleenexes twice as fast.
               The Catarrhini consequently include the vervet monkey, known to biomedical research as The Monkey; and the rhesus macaque, known to neurobehavioral research as The Monkey.   Nobody remembers Jimmy Durante anymore, so the future of the proboscis monkey is in doubt.   Baboons should never be described as polygamous, since they do not have marriage.  They should be called polygynous instead.  In addition to the monkeys of the Old World are the Hominoidea or apes.  They lack a tail, unlike the Old World Monkeys, which all have a tail, except for some of the macaques. 
               The apes are all adapted for hanging from the trees, including humans, who do not hang from trees.  Extinct apes were very diverse, but that didn’t help them.  Today there are two or more kinds of apes.  The lesser apes are gibbons, who are very speciose, but probably not for long.  If they were smart enough to know about The Great Ape Project, they would probably get really upset.  The gibbons are monogamous, because there is no such word as “monogynous”. 
               The hominids come from the Latin for “even more like people”.  They may or may not include the great apes.  The great apes include the orangutan; the gorilla, known to evolutionary psychology as Koko; and the chimpanzee, known to evolutionary psychology as the human.
               The hominins are the Tribe Hominini.  Chimpanzees are the Tribe Panini.  When chimps  cannibalize the dead infants of their species, they may be confusing them with sandwiches.  To cladists, australopithecines never existed.  Australopiths existed.  But it makes them seem kind of naked without a Latin-sounding suffix.
               Hominin evolution, also known as hominid evolution, includes those hominids, also known as hominoids, who became bipedal, or at least had their canine teeth shrunk.  Stone tools, also known as culture, coincide with the origin of the genus Homo.  Some experts believe that there are 12 species recognizable within the genus Homo, of which 11 are now extinct.  I guess culture wasn’t such a great adaptation, after all.

I know it’s a stretch, but George S. Kaufman and Robert Benchley were both members of the Algonquin Round Table.

Tuesday, April 26, 2011

Clades versus Rhizomes

Cladistic analysis is certainly a powerful, logically rigorous tool for the determination of relatedness among species.  In the simplest case you have three species and want to know which two are most closely related.  You look at features shared by two of the three.  But since evolutionary rates can vary widely in different lineages, two of the three might look similar because the third one changed a lot, not because those two are actually closest relatives.  So you look for a subset of shared features, the shared derived features, (or synapomorphies, from the Early Hittite), which you determine by finding a species slightly more distantly related from the three that you are really interested in. Then you tally up the traits shared by two of the three, and not by the outgroup. Those are your synapomorphies and, in principle, they should tell you which two of any three species are closest relatives. 
It’s quite straightforward, actually.  Trust me.
[In fact, aside from the Hittite vocabulary, much of the philosophy of phylogenetic reconstruction is articulated in William King Gregory’s 1910 monograph on The Orders of Mammals, which was thrust into my hand back in 1983, when I attempted to raise the subject with Dr. Simpson.  Some history-of-science graduate student really ought to “do” Will Gregory, BTW.]
But a cladistic analysis contains a number of important assumptions.  First, it presumes that the species only get their features vertically, through a process of what Darwin called “descent with modification”.  The goal of the method is to establish relatedness by descent.  If traits are acquired some other way, such as horizontally, by airborne viruses, by Lamarckian inheritance, or by dirty toilet seats, then the system breaks down, for then there is no way to establish synapomorphy, which is what the method is predicated on.  Shared derived features might be there either by virtue of proximity of descent, or by virtue of infection, or perhaps even by sheer force of will in different animals. 
Second, it only works on species.  After all, if the taxa in question could receive their similarities via gene flow, the system would likewise break down.
There are also other constraints.  The outgroup can’t be too distant, and the rate  of convergent evolution can’t be very high.  One simply assumes that a single character distributed across three taxa in two states, is the result of a single evolutionary change from one form to another, inherited in the two species that share it, from their common ancestor.  Not from parallel mutations, or miasmas.
So I just don’t get how people can build research programs based on the application of cladistics to cultural traits, where the method logically fails.  Worse yet, that’s why paleoanthropological systematics will never get cleared up.  To do cladistics, you need species, and the surest way to get species in paleoanthropology is to “split” fossil samples, and pretend that the groups you name correspond to some biological reality.  Yet a cladistic analysis is the most straightforward paper in the field.  One measures a bunch of things and throws the mess into PAUP (for a phylogenetic analysis using parsimony).
But suppose the taxa you are making nested phylogenetic clusters out of, aren’t phylogenetically nested in the first place?   Suppose, for example, they were linked bio-historically like a rhizome, or a trellis, or a capillary system (as indeed, generations of physical anthropologists have thought)? 
Hooton, E. A. (1946) Up From the Ape, 2d edition, New York: Macmillan.

Holliday, T. (2003) 'Species Concepts, Reticulation, and Human Evolution ', Current Anthropology, 44: 653-673.

Possibly because they were actually members of rather few  real biological lineages. 
The point is, that if you impose four species on Homo (as the authors of The Human Lineage seem to, although they do some mighty fancy tap dancing around that issue) or if you impose 12 species on Homo (as the authors of The Last Human do – ridiculously, but at least clearly), you are not just having a sterile disagreement about a sterile issue of classification.  You are actually disagreeing over what you can fundamentally do methodologically. 
Cartmill, M. and Smith, F. H. (2009) The Human Lineage, New York: Wiley-Blackwell

Sawyer, G. and Deak, V. (2007) The Last Human: A Guide to Twenty-Two Species of Extinct Humans, New Haven, CT: Yale University Press.

A cladistic analysis is done on species, not specimens, and is meaningless below the level of the species.  The best you can do is a “numerical taxonomy” analysis – the kind of thing that Chris Stringer was doing back in the 1970s – and that will (if you’re lucky) tell you what is most similar to what else.  But it won’t make false assumptions about how they got that similar, which the cladistic analysis probably does. 
I confess, I’m an just ol’ country anthropologist, but you know what?  I think human evolution is strongly rhizotic, just like the post-modernists might-or-might-not have said. 
Deleuze, G. and Guattari, F. (1987) A Thousand Plateaus: Capitalism and Schizophrenia, St. Paul, MN: University of Minnesota Press.

[For the love of God, please don’t give me a quiz on this one, but I know it says something about the rhizome as a powerful metaphor.]

But here’s the scary (i.e., challenging) thought:  What if it’s rhizomes all the way down?
Arnold, M. (2009) Reticulate Evolution and Humans: Origins and Ecology, New York: Oxford University Press.

Friday, April 22, 2011

Simpson story #1

Back in Tucson in 1983-4, I worked as G. G. Simpson’s secretary, during the last couple of years of his life.  But I was also inspired by the emerging analytical tools of cladistics, and drew particular intellectual inspiration from Niles Eldredge and Joel Cracraft’s Phylogenetic Patterns and the Evolutionary Process.  So inspired was I, in fact, that I even named my adopted cat Willi, after the godfather of phylogenetic systematics, Willi Hennig.
               Unfortunately, I didn’t know much about caring for cats, and I overfed Willi, and he became a fat blob, and one day he just exploded.  Well, he didn’t explode actually, but he died, in my shower stall.  I was quite broken up about it.
               So that afternoon I went in to do some typing for Dr. Simpson, and as we sat in his study he could tell I was a little upset, and I told him that my cat had died earlier in the day.   “Too bad.  What was his name?” asked Dr. Simpson.
               I told him.  “Willi”.
               “Mm,” said Dr. Simpson, without even looking up.  “Who’d you name him after?”
               Um....  Holy Shit!  I couldn’t tell Simpson that I had named my cat after Hennig.  That would be like saying I had named my cat after Charles Manson or Josef Stalin, he’d never talk to me again.
               Um... Um...  Um...  “Mays,” I finally said. 
               “Oh,” said  Dr. Simpson.  “Good ballplayer.”  And he continued his work.

It’s mildly interesting that chimps are born facing in the same direction as humans are (toward the westward sky?) as a recent report has it.
But whatever merit the observation may have is more than negated by the authors’ articulation of  its meaning.
Although the study does not tackle that question, it certainly helps to quash the outmoded idea that humans are distinct from the rest of the animal kingdom. "In a broad sense I think humans tend to believe we are unique," says Hirata, "but that belief is not based on facts."
The fact that a chimp couldn’t possibly articulate that thought as he did, is, ironically, too obvious to be noted by the scientist.  GGS, in The Meaning of Evolution (1949) followed Julian Huxley in ridiculing this pseudo-scientific attitude as “nothing-butism”. 
After all, since they understood evolution to refer to the production of difference, the statement that "we are not unique" could reasonably be construed to mean "we have not evolved," could it not?

Tuesday, April 19, 2011

Why Anthropomics?

Because anthropology isn’t science.  Everybody knows that.  Anthropology wasn’t science at the University of Arizona, when I was a graduate student, nor was it a science at Yale when I taught there.  It always amused me that the students couldn’t get science credit for Primate Functional Anatomy – a dissection course! – or Primate Ecology, or Human Paleontology, much less for my own classes, like the only undergraduate course focusing on human genetics offered in Yale College, or even my course like Human Biology and Culture, which (the biology department actually told me) couldn’t possibly be science because it had the word “culture” in it.
Their course in Tissue Culture notwithstanding...
Anthropology is scholarly, and as such it is bigger than science, but isn't science.  At any rate, if you can't even convince your dean what it is, don't try and convince me.  And between us both, the people who insist the most loudly that anthropology really is a science, tend to do the crappiest fucking science themselves.
Which reminds me that I should probably warn you that my appreciation for, and invocation of, the English language not uncommonly extends beyond the decorous.  I was in fact indignantly chastized only last week for using the word “moron” in a podium paper at a scholarly meeting.
No kidding.
No names, of course, or name-calling, such as “douchebag retard,” but just an observation that my interlocutor was adopting an age-old sleight of hand to avoid discussing the substantive issues, more about which some other time.
The point is that since anthropology isn’t science, we need a word to signify a sciencey engagement of anthropology.  The kind of work that maybe involves expensive machines with flashing multicolored lights, and somber people with greasy hair in white lab coats.  You know, science.  Drawing authoritative-sounding conclusions about the state of being human from ridiculously thin bits of data.
But that’s evolutionary psychology, and we need a word to distinguish ourselves from that, don’t we?
Hence, “anthropomics”.  It jettisons the scholarly implications of “-ology” (from Greek logos, word/knowledge) in favor of the trendily scientistic “-omics” (from an obscure homage to Tom Mix, silent screen cowboy). 
Seriously, though, Robert Proctor had a very interesting article on naming processes in science a few years ago. 
Proctor, R. (2007) “‐Logos,”“‐Ismos,” and “‐Ikos” The Political Iconicity of Denominative Suffixes in Science (or, Phonesthemic Tints and Taints in the Coining of Science Domain Names).  Isis, 98(2): 290-309.
All right, get back to work.

First post

“Those who can, do; those who can’t do, teach; those who can’t teach, write nasty book reviews; those who can’t write nasty book reviews, submit indignant letters to the editor; and those who can’t submit indignant letters to the editor, blog.”