>(1) Is the identity being claimed a base-pair-level identity, or
>something broader?
Base pair identity, across the entire genome. By that, I mean that's
what people *think* when they say "we're such and such a percentage
similar." See Jim Behnke's post however for some relevant caveats.
>(2) Given that I'm a bit disappointed that these estimates are
>apparently somewhat rough (which would account for the variety of
>precise numbers I've heard, 95-99%, usually 98 or 99%), have there been
>any representative (or random), small-scale base-pair comparisons to
>confirm or disconfirm the general reliability of the extrapolation? If
>so, what are the results of such tests?
I think it's accurate to say that any *individual* gene sequence
(e.g., globins, cytochrome c, and so on) comparison between chimps
and humans will yield a percentage identity in the 90%+ range.
Certainly off the top of my head I don't know of any exceptions to that.
>(3) Is there a strong consensus in the scientific community that these
>estimates are very reliable? If so, is this confidence the result of
>strong conviction that the methodology is sound (realistic/alethic
>conviction), or simple a result of there being no competing, clearly
>superior method of estimating (pragmatic conviction)?
Hard question to answer. Many evolutionary biologists, or those most directly
concerned with these data, take Jared Diamond's view. Humans really are "the
third chimpanzee."
Others however are vastly more skeptical. At the 1993 AAAS annual meeting
in Boston, Jon Marks, a physical anthropologist and geneticist at Yale, made
a remark in his talk (co-written with Laurie Godfrey, but delivered by Marks)
that I'll never forget. "If the overall biology of the animals tells you they
are very different," he said, "and the genetics tells you that they are nearly
identical, it follows that the genetic comparison is telling you something
relatively trivial about the overall biology." [That's an exact quote, taken from
the AAAS tape.] This view reflects what King and Wilson argued in 1975: if
human and chimp structural genes are 99% identical -- closer than sibling species
of Drosophila -- then *something else*, elsewhere in their genomes, must account
for their obvious organismal differences. I'll cite King and Wilson again.
Chimps and humans, they argue
differ far more than sibling species in anatomy and way of life.
Although humans and chimpanzees are rather similar in the structure
of thorax and arms, they differ substantially not only in brain
size but also in the anatomy of the pelvis, foor, and jaws,
as well as in relative lengths of limbs and digits. Humans and
chimpanzees also differ significantly in many other anatomical
respects, to the extent that nearly every bone in the body of a
chimpanzee is readily distinguishable in shape and size from its
human counterpart. Associated with these anatomical differences
there are, of course, major differences in posture..., mode of
locomotion, methods of procuring food, and means of communication.
Because of these major differences in anatomy and way of life,
biologists place the two species not just in seperate genera but
in separate families. So it appears that molecular and organismal
methods of evaluating the chimpanzee-human difference yield quite
different conclusions.
M.C. King and A.C. Wilson, "Evolution at Two Levels in Humans and
Chimpanzees," _Science_ 188 (1975): 107-116; p. 113.
This raises all kinds of questions that we don't know how to answer. (Incidentally
I should mention that DNA-DNA hybridization has fallen on hard times, in part
because of uncertainties about the method raised by Marks, Sarich, and others,
but mainly because it's just a lot easier now to sequence genes directly. If you
can go straight to the nucleotides why bother with a distance method that's only
an estimate?) The Big Question is what do these genetic similarities really signify.
Here's a thought experiment.
1. "That was a thoughtful post to the reflector," he said with sarcasm.
2. "That was a thoughtful post to the reflector," he said with empathy.
There are 67 "sites" in each sentence, i.e., locations along the string
which may be occupied by a letter, space, or punctuation. A straightfoward
alignment yields a sequence identity of nearly 90 percent (.895), or 60/67.
Yet the sentences have exactly opposite meanings. Despite their apparent
similarity, one sentence could not be lifted out of a story, and the other
inserted, without changing the meaning of the paragraph (or larger unit) into
which they are placed.
And one can complicate this even further. Exactly the *same* sentence, depending
on its larger context, can mean different things. The Berkeley molecular geneticist
Gunther Stent calls this the difference between the "explicit" and "semantic"
content of a gene sequence. He writes:
The implicit [semantic] meaning...is not really contained in the structure
itself and arises secondarily from the explicit meaning by virtue of the
*context* in which the structure has been produced. For instance, the
explicit meaning of the sentence "John Smith is traveling to New York",
is that a particular individual is on his way to a particular geographical
location. However, depending on the context in which the sentence is
produced, it can also have a large number and variety of implicit meanings.
To take the analogy into biology:
When we apply this distinction to the semantic relation between genotype
and phenotype it becomes evident that the explicit meaning of the genetic
information consists of the protein amino acid sequences encoded in the
genes, and of the nucleotide sequences of the ribosomal and transfer RNA
molecules encoded in other non-genic DNA sectors.
But protein folding, physiological function, and all higher-order "meanings" (if you
will) are, Stent argues, *implicit*, and highly context-dependent. "This procedure
of identifying implicit meanings of the genetic information," he writes, "can be
continued almost indefinitely to higher and higher levels of the contextual hierarchy."
It is those higher-order levels that are likeliest to matter in understanding the
organismal differences between any two species -- and those are the levels
we least understand. See Stent's paper, "Explicit and Implicit Semantic
Content of the Genetic Information," in _The Centrality of Science and
Absolute Values_, vol. 1, Fourth International Conference on the Unity of the
Sciences (New York: International Cultural Foundation, 1975), pp. 261-277.
Let me give this a science fiction spin. Take the entire genome of a human,
and the entire genome of a chimp, and swap their single-copy DNA sequences
gene by gene: chimp cytochrome into the human, human cytochrome into the
chimp, etc., until all their DNA has been exchanged. At what point does
the chimp become a human, or vice versa? I don't think anyone has a clue,
because -- it seems to me, anyway -- what makes us distinct as organisms
are the higher-level interactions of genetic differences (and other differences! --
I'm no worshipper of nucleic acid), in development, whose complexity lies
well beyond our horizon of understand right now.
[I'm bracketing my own theological convictions, of course, and am also sparing
the list my usual rant against poorly-supported theories of macroevolution. But
one of the reasons I have a low regard for neo-Darwinism stems from its complete
inability to answer questions like those sketched above, which are properly its
bailiwick, and which it claims to be able to answer.]
Well, that's a long-winded answer. Sorry! Here's a paper by Jon Marks that I'd
recommend, on all this: "Blood Will Tell (Won't It?): A Century of Molecular
Discourse in Anthropological Systematics," _American Jl of Physical Anthropology_
94 (1994): 59-79. The abstract:
Being derived from hereditary material, molecular genetic data are often
assumed to be a source of sounder inferences about evolution that data
from other kinds of investigations. This, however, tends to be taken in
the absence of a clear knowledge of the evolutionary processes at work,
the technical shortcomings, and the manner of deriving the specific
conclusions. The history of biological anthropology shows that, from the
beginning of the 20th century, grossly naive conclusions have been promoted
simply on the basis that they are derived from genetics, without having been
fully thought-out. A balanced consideration of the shortcomings as well as
the advantages of genetic data are necessary for its proper integration into
the field. When molecular and morphological data disagree, both must be
re-examined carefully, for genetics has been used irresponsibly as a form
of scientific validation, both in American society and in American science.
Contemporary data bearing on the molecular relationships of the apes are
noteworthy for their diversity in quality, and need to be evaluated in the
light of molecular and microevolutionary theory.
This paper is a good introduction to many of the relevant issues.
Paul Nelson