evolgen

Excuse Me While I Repeat Myself

As I mentioned before, you should definitely check out the Tangled Bank. This bi-week’s issue is quite diverse (and all the astronomers seem to be talking about the “earth-like” planet). One entry comes from an extremely opinionated anthropologist who calls out quantitative geneticists:

Chimps More Like Humans Than Apes??? What does it mean to be human? And why quantitative geneticists should stick to their jobs.
Retarded Geneticists With No Understanding of the Word ‘Phenotype’ Mouth Off
[link]

More after the jump…

Well, I gotta say something about this, right?? I mean, I’m a retarded geneticists (quantitative at that), and I like my job. I’ll stick to it, but, first, I need to set a few things straight. The author (the Indian Cowboy) was writing in response to an article about the recent ape molecular clock paper. Soojin Yi, lead scientist on the paper, claimed that humans and chimps belong in a single genus. I guess this is a sensitive issue with anthropologists, as the Cowboy makes quite clear:

If we were to do a Sesame Street bit with a chimp, gorilla, and a human, singing “one of these things is not like the other…”, almost all of us would say the human sticks out like a sore thumb. In my professional capacity as bioanthropologist (MSc from University College of London in ’05), I’d have to agree.

For the sake of monophyly, I hope we all agree that humans are apes. Where we draw the line between genera is arbitrary (what is called a genus in one taxon, may contain the evolutionary equivalent of an order or family in another taxon), but I think it’s pretty standard to make all extant taxa monophyletic.

I don’t want to squabble about taxonomic classifications within apes (I have written about it here, so I won’t repeat myself). I did notice some larger differences in how we each approach evolutionary biology. I have broken them into three areas in which the Cowboy (an anthropologist) and I (a quantitative geneticist) disagree. These come down to how we value different types of data and how we interpret and understand that data.

  • Lumpers versus splitters: I won’t generalize across all taxa, but amongst hominids and primates, he appears to be a splitter, whereas I am a lumper. I think that the hominid bias we have leads us to over split hominids relative to other apes, over split apes relative to other primates, over split primates relative to other mammals, over split mammals relative to other vertebrates/chordates, over split vertebrates/chordates relative to other animals, and, possibly, over split animals relative to other eukaryotes (dare I even bring up over splitting of eukaryotes relative to archae and eubacteria?). This is not a very big deal, but still a difference, none the less.

  • Genetic versus phenotypic data: Once again, I have written about this before, so I won’t linger on it for too long. Long story short, molecular data is far more objective than morphological/phenotypic data. You may not like the molecular clock, but genetic divergence is an excellent indicator of the relative order and time in which lineages diverged (Note: I said relative; we are not talking about calibrating the molecular clock so that it can be used to estimate absolute time in years).

    We can see the subjective nature of phenotypic data in how the Cowboy frames his argument. He points out to several morphological characteristics that distinguish Homo from all other apes (bipedality and body proportions, brain size, maturation patterns, and teeth). Are there other morphological characters that would group chimps with humans, excluding other apes? Here is where my knowledge of anatomy (or lack thereof) gets the best of me, and my argument reaches its end. Any help from a more informed reader would be greatly appreciated (let’s look at all phenotypes, not just morphology). Am I right in my understanding that chimps and humans are both carnivorous and kill members of their own species, whereas other apes do not practice this behavior?

  • Reductionist versus holistic: This touches on the subjective nature of phenotypic data. What level of organization (subcellular, cellular, tissue level, organ level, organism) are we using to determine phenotypic differences? There is, however, an appropriate level for the comparison being made (there are no homologous tissues to compare between plants and animals). But the reductionist in me thinks that we can construct the whole from its parts, but we cannot determine the parts by looking at their end result. The reason I point out this divide is because of the following from the Cowboy:

    A lot of people will run around saying “Chimps are 99% human” or “Humans are 99% chimp.” But, based on the same logic, we are 47% cabbage. I am not making this up. You and I share 47% of our genes with cabbage. Do you feel like you’re half leafy green vegetable? Because I certainly don’t. I don’t look, act, or behave like it either except at the cellular level where commonalities such as cell membranes, mitochondria, ribosomes and other aspects of our shared eukaryotic heritage reveal themselves.

    I don’t like the idea of saying I’m any percentage like anything else. What we should be saying is, “Humans and chimps are 99% identical at the DNA sequence level.” This statistic is somewhat biased, as it depends on whether we are looking at coding sequences, alignable nucleotide, indels, or large scale chromosomal rearrangements. Setting that aside, I wonder why the Cowboy does not want to look at cellular level commonalities. There are some important similarities between humans and cabbage — we both have cells that contain nuclei, mitochondria, ribosomes, endoplasmic reticula, etc — which we have inherited from our single celled eukaryotic common ancestor. There are also important differences that accumulated since our divergence (plants cells have a cell wall, chloroplasts, and larger vacuoles). Just because we don’t look like a cabbage to the naked eye, does not mean we are not similar to a cabbage; we are more similar to cabbage than we are to an E. coli.

    This illustrates the subjective nature of categorizing phenotypic divergence, but also the divide between molecular and phenotypic data. The geneticist is a reductionist — not for the sake of reductionism, but because that is where the most objective data lies. The holistic interpretation is motivated by the idea that the reductionist’s data has been stripped of its meaning in the process of being reduced to a more objective framework. That is why the Cowboy says things like:

    You see, out here in the physical world, genes only matter in terms of their expression in phenotype. When I see a chimp, I see a somewhat intelligent African ape that walks on the knuckles of its front limbs, has significantly more robust dentition than humans, shorter legs, opposable toes, and a ribcage shaped more like a funnel than the human-type barrel chest. This is remarkably similar to what I see in a Gorilla, and only slightly different from what I see in an Orang.

    He feels that genetic differences that do not manifest themselves in some sort of observable phenotype are not important in categorizing taxa. This stands in stark contrast to the geneticists, who prefers neutral changes when determining evolutionary relationships. This preference is strictly dictated by the data — there are far more neutral changes between taxa than changes that affect the observable phenotype. Additionally, if we would like to use the phenotypic changes, we must be extremely careful to avoid any subjectivity (ie, “When I see a chimp . . .”). It’s just a lot safer and easier to use the molecular data, when available, than the phenotypic — it’s good to avoid bias whenever possible in taxonomy.

This post is long enough for now. Next time, I will outline a neat little research project that I would like to see someone carry out to quantify the hominid/primate/mammalian/vertebrate/eukaryote bias in taxonomy.

Comments

  1. #1 Gerardo Camilo
    February 1, 2006

    That kid should learn say Congenital Hypertrichosis.

  2. #2 IndianCowboy
    February 1, 2006

    Gerardo, my last girlfriend insisted I had congenital hypertrichosis.

    RPM, it’s apparent that I did not spend enough time talking about the highly useful nature of genetic data in systematics. I’m working on a post about clade, grade, and taxonomy for the next tangled bank that’ll address these issues in more depth, but here’s the short version:

    Genetic versus phenotypic
    Genetic data is the best for drawing phylogenetic trees. From a cladistic perspective, it offers the most objective data with the least chance of bias in selection of character traits to be based upon; it basically makes other methods obsolete. In fact, I used that argument in my dissertation for why the only phylogenies I used were the somewhat controversial genetic ones.

    The problem comes when dealing not with the tree or even with species names (for the most part), but rather with higher taxonomic categories, especially the genus. Above the species level (which can be determined from genetics in extant species), taxonomic categories become essentially gradistic.

    Quantitative genetics is silent on gradistic classification, again in my opinion, since for the most part it relies on introns and other aspects of the genome that aren’t necessarily reflected in appearance and behavior of an animal. Rather, when determining higher level taxonomic affinities, I think the only consistent way to do so is to rely on the unfortunately subjective matter of what Wood termed the adaptive zone.

    Draw the tree with genetic information, label it with phenotypic. That’s my basic stance.

    Lumpers/Splitters:
    Yeah, I’m a splitter. But I’d like to think that I’m a fairly consistent splitter. My area of interest is actually neotropical primates, where I’m inclined to split up genera again, dependent on morphology and behavior. I am far more likely to split at the genus level than below, however.

    The reason I’m a splitter is because, since I study whole animals interacting in their natural environment, I tend to think in terms of the selection pressures that led to the differences between related taxa. If I see a different trend within two branches in a single lineage, i think that those two trends need to be reflected in their classification; as I see it, that’s the point of classification.

    reductionist versus holistic
    It all depends on what you’re studying doesn’t it? I study the evolution of paternal care. There’s not a whole lot that quantitative genetics can tell me there about ultimate causation as it doesn’t illustrate how aspects of population density, interspecies feeding competition, resource distribution, and mate access might have made monogamy more favorable than promiscuity.

    Genetics was a boon to my thesis (and hopefully eventual publication) as it allowed me to draw these phylogenies, to test for phylogenetic inertia, and to estimate the times of divergence and thus when changes might have taken place in these lineages. But if I didn’t have the ability to look at ‘softer’ data like intestinal length and paternal-infant attachment, I coudln’t have said a darn thing.

    I can’t do my job without genetics, but it bothers me when geneticists insist I don’t need to work at all.

  3. #3 RPM
    February 1, 2006

    The reason we’re not interested in gradist (and prefer cladistic) classifications is that the only evolutionary meaningful classifications are those that are monophyletic. We must first determine monophyletic clades (this is best done using molecular data) before we can compare taxa. Once the clades have been determined, we can then perform any type of analysis that interests us (whether it be phenotypic or molecular).

    Also, it’s important to differentiate phenotypic similarities that arise due to common ancestry versus those that arise due to convergent evolultion. Only through a cladistic approach towards systematics/taxonomy can this analysis be performed.

    We have no problem with the analysis performed by non-geneticists — it’s essential — unless they refuse to change historical precedents in the face of uncontroversial molecular data that conflicts.

  4. #4 IndianCowboy
    February 1, 2006

    I guess maybe hte tone of my first post made you think I dismiss genetics entirely. I agree with your last comment entirely and in fact as I said in my last comment, that’s how I see the process working.

    In fact, in my thesis, and in the papers i’m preparing, I supported genetic data over historical precedent, using the reasoning you presented. My position is at odds with many if not most of the people studying neotropical primates. In fact, one guy argued that despite the fact that molecular data overturned an old convention, he refused to stop using his wholly gradistic taxonomic scheme.

    All I’m saying is that genetic similarity is silent on which level of classification to use for a given monophyletic clade.

  5. #5 razib
    February 2, 2006

    u guyz are talking past each other! btw, i had lunch with a friend recently whose an insect systematist and she had some harsh words to say about the hennigian cladists. their obsession with popperian parsimony is religious. not that their’s anything wrong with that, but sometimes pragmatism is human.

  6. #6 RPM
    February 2, 2006

    Razib,

    We’re harmonically converging to a similar point of view.

  7. #7 bob
    February 6, 2006

    How many chloroplasts are found in one cell?

  8. #8 RPM
    February 9, 2006

    Bob,

    I think it depends on if you are talking about leafy tissues (chloroplast rich) or root/stem tissue (chloroplast poor). I think leafy tissue can have tens of cholorplasts per cell. It may also depend on the amount of light/water the plants are exposed to. Someone who knows anything about plant physiology can correct me.

  9. #9 Automated Blog Posting
    January 2, 2007

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