Re: Chimps had more positively selected genes than humans

Jim,

Sorry for the confusion. I didn't mean to suggest that Varki is a theist,
or that he belongs to a church. I don't know Varki. I was attributing a
mindset to him that reminds me of the defensive "reasoning" often asserted
by religious folks who maintain their beliefs in phenomena in the face of
scientific evidence. The text I responded to suggested to me that Varki's
response to this article was to argue in favor of a traditional and
cherished viewpoint without empirical support over an alternative that has
empirical support, and that his tactic was to defensively tear down the
alternative as imperfect. If this was the norm in science, none of us would
every have our minds changed for the right reasons.

Guy


in article f0c68n$2vu9$1@xxxxxxxxxxxxxxxxxxx, Perplexed in Peoria at
jimmenegay@xxxxxxxxxxxxx wrote on 4/20/07 10:08 PM:


"Guy A Hoelzer" <hoelzer@xxxxxxx> wrote in message
news:f0asov$2c9s$1@xxxxxxxxxxxxxxxxxxxxxx
I love it. We humans are incredibly defensive about how special (perfect,
even) and best adapted we are, and we are highly skilled at making arguments
to defend this sort of self-image in the face of evidence to the contrary.
We generally do this in a religious sort of way, as I think is done by Varki
below. "The data don't PROVE that our evolution is ordinary, so you can't
make me stop believing that it was."

I had never heard of Varki, but your comment sent me Googling to learn more
about his POV. Based on some very cursory research, I don't see much to
indicate that he is religiously motivated, except maybe an animal-rights
stance regarding captive chimpanzee research:
http://cmm.ucsd.edu/Lab_Pages/varki/varkilab/B104.pdf

Varki was also co-author of an interesting article on chimp human differences
and what the genome comparisons are likely to show.
http://cmm.ucsd.edu/Lab_Pages/varki/varkilab/B096%20copy.pdf

I'm curious as to what ReMine's take would be on the suggestion in the Zhang
paper that only 154 selective changes separate us from our common ancestor
with
the chimp. Wasn't there some kind of argument from incredulity involving
the number 1667?

Incidentally, the Zhang article is now available online here
http://www.pnas.org/cgi/content/abstract/0701705104v1
but unfortunately I can only read the abstract and supporting materials.
I think I understand that they are not claiming that the 154 identified
changes constitute the totality of the selective changes. These are only
the ones they can be 95% confident of. Perhaps someone who understands the
pop-gen math better than I do can tell me what the selection coefficient for
the cutoff point would be, approximately.

I am not saying that we don't belong
on a pedestal; that would be a different argument. I am saying that
evidence to the contrary is a healthy thing promoting open mindedness in the
science of human evolution.

Cheers,

Guy


in article f08kl9$1973$1@xxxxxxxxxxxxxxxxxxx, Danniel Soares at
dannielsc@xxxxxxxxxxxx wrote on 4/19/07 1:49 PM:

[...]

Jianzhi Zhang, a population geneticist, and his colleagues compared
nearly 14,000 protein-coding genes in humans and chimpanzees, which
have about the same size genome. Using a statistical analysis, they
identified 154 human genes that have been positively selected. In
contrast, they found 233 such genes in chimpanzees, a 51% increase,

I wish she had written "51% greater" rather than "a 51% increase"!

they report online this week in the Proceedings of the National
Academy of Sciences.

[...]

The study "challenges the idea that there was a great burst of
adaptive change in humans, one that was more profound than in other
primates or mammals," says Morris Goodman, an evolutionary biologist
at Wayne State University School of Medicine in Detroit, Michigan.

But that's not the whole story, argues Ajit Varki, a physician-
scientist at the University of California, San Diego. "It's a terrific
paper, but they're only looking at one mechanism, the changing amino
acids in proteins. Other mechanisms in gene evolution--such as gene
expression, duplication, conversion, and inactivation--are likely to
be equally important." Further, Varki adds, these types of genomewide
analyses are limited, because they do not address the issue of gene
function. "It could be that the deletion of a specific gene or a
single amino acid change could have more biological significance than
a large number of genes that seem to have undergone many changes." And
that means we're still a long way from explaining what makes us human--
or them chimpanzee, he says.


http://sciencenow.sciencemag.org/cgi/content/full/2007/416/1?rss=1








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