Gene Expression

John Noble Wilford in The New York Times has a piece titled The Human Family Tree Has Become a Bush With Many Branches, which reflects the current consensus thinking that the hominid lineage was until recently relatively diversified, with a host of species extant contemporaneously (the other view is that many of the “species” we conjecture are just the extant morphological variation of one species across varied local ecological conditions). To be honest the piece seemed to just be throwing a lot of genus and species names at you all the while stirring up the tempest in the tea pot between paleoanthropologists and biologists. Consider:

Now paleoanthropologists say they accept the biologists as allies triangulating the search for human origins from different angles. As much as anything, a rapid succession of fossil discoveries since the early 1990s has restored the confidence of paleoanthropologists in the relevance of their approach to the study of early hominids, those fossil ancestors and related species in human evolution.

“All biology can tell you is that my nearest relative is a chimpanzee and about when we had a common ancestor,” he said. “But biology can’t tell us what the common ancestor looked like, what shaped that evolutionary change or at what rate that change took place.

I tend to agree that the various disciplines are now triangulating. Genetic methods do need supplements and complements. The original Mitochondrial Eve paper had some serious technical errors. A geneticist working at Berkeley at the time told me about how some people were shocked that those in Allan Wilson’s were in such a hurry to get the work out there that they made some elementary errors in even interpreting the phylogenetic tree in their discussion section (a more serious error was in the way they generated their trees). Lab biologists and computational researchers aren’t gods, and the guys in the field offer critical morphological context which scaffolds the evolutionary story. That being said, the quote above suggests that the paleoanthropologist is conflating phylogenetics with the whole of evolutionary biology. Certainly until recently much of the work was focused on reconstructions of evolutionary history using molecular clock assumptions, but the work with ancient Neandertal DNA suggests that one might be able query functionally salient regions of the genome to generate inferences about phenotype. Now, it seems implausible that in the near future we’ll be able retrieve large amounts of erectine genetic material from 1 million years before the present, but if they could extract protein from 68 million year old dinosaur remains don’t count the geneticists out! Additionally, the “pruning” of the bush did not truly begin occurring until around 50,000 years ago. Not only are we likely to get get a more fully fleshed out picture of the Neandertal genome, but erectine descendant species were extant on Java at least within the last 50,000 years, while Flores opens up the possibility of even more recent remains. As for the tempo of evolution genetic studies can of course compare humans (and the future paleo-DNA) to outgroups such as chimpanzees. Inferences about the hominid lineages along the intermediary branches are then derived. Finally, geneticists can detect evidence of past selective events or pressures, and quite often (though not always or most of the time) genomic regions are known to be associated with particular functions.

In short, all respect to the paleoanthropologists. Good data is always necessary data, but the impression that the researcher in the article gives is that molecular and genetic techniques are past the point of diminishing returns. This certainly is not the reality; hominid phylogeny might be bare of low hanging fruit, but only because of its past success. And the study of molecular evolution does not restrict itself purely to the clock.


  1. #1 David B
    June 27, 2007

    John Hawks has an interesting post about this.

  2. #2 P. S. Spence
    July 6, 2007

    Hurricanes and Tsunami predicted through dna and synchronicity
    The smallest of points overlooked changes everything

  3. #3 J. V.
    July 12, 2007

    1. Your paternal grandmother may look like you, act like
    you, and love you, but she has absolutely nothing
    similar about her Mitochondrial DNA. Yet she
    contributes every bit as much DNA as your maternal
    grandmother to you.
    2. The Mitochondrial Eve contributed no more DNA to you
    than millions of other ancestors except for
    mitochondrial DNA.
    3. Mitochondrial DNA is not human DNA!!!!!!
    4. Mitochondria are bugs; proto bacteria or proto viruses
    or something else, but they are not human, and may or
    may not be alive (much controversy).
    5. Mitochondrial Eve is a fluke; one woman’s line was
    never extinguished.
    6. You have 2 biological parents; they have 2 also, so you
    have 4 biological grandparents. 8 great-grandparents.
    16 great-great, then 32, 64, 128, 256, 512, 1,024
    (round off to 1,000), 2,000, 4K, 8K, 16K, 32K, 64K, 128K
    256, 512, 1 million, 2,4,8,16,32,64,128,256,512,
    1 billion, …………1 trillion after 40 generations
    That’s a trillion people on your ancestral tree about
    1,000 years ago.

    You have numerous common ancestors with every human being on the planet only 1,000 years ago, and the same name appears millions of time at the top levels making every person on earth your cousin hundreds of times over!!!!!

    Mitochondrial Eve theory is the most misleading, least
    reasoned concept I have ever seen even though it may
    very well be technically correct!!!!!
    That one female, Eve, has no more genetic significance to
    anyone than billions of other individuals, and is no
    more closely related.
    All she contributed was Mitochondrial DNA, the genetics of
    “bugs” that that help process chemicals in human cells.
    Think about it. There is no trick; no flaw; you are
    related to everyone within 1,000 years, and look up
    mitochondria and read it.