Re: Final Solution of the Aquatic Question


Pauline M Ross wrote:
> On 16 Aug 2005 10:11:01 -0700, "JAE" <jae@xxxxxxxxxxx> wrote:
>
> >Yes, there are theoretically other possibilities,
> >> in the real world those other possibilities are highly unlikely.
> >
> >That's simply your own projection. In the real world, there are
> >several possibilities. The authors enumerate a few of them. I'm not
> >sure how it is that you are assigning probabilites to make all but one
> >highly unlikely. Care to explain?
>
> The authors dismiss as "unlikely" and "highly unlikely" the
> possibility of descent of the retrovirus marker from a common
> ancestor, and the possibility of an error in currently accepted
> primate phylogeny, respectively.

I would agree. That is highly unlikely.

> The authors discuss the possibility of high susceptibility in the
> African apes or high resistance in humans and Asian apes, but this
> would require convergent evolution (which is possible but not likely:
> my interpretation).

Your interpretation differs from that of the authors, who did note that
resistance has occurred independently in parallel in other closely
related lines. Do note that in assigning this probability in support
of your initial claim that "in the real world those other possibilities
are highly unlikely" that you have anointed yourself arbiter of
probabilities for the real world. (I don't recall voting for you in
such a capacity.)

> The authors discuss the possibility that the differences are due to
> population size differences, but produce evidence against that option.

This is some of their weaker interpretations as I see them. It would
not take a dramatic crash in the chimp and gorilla populations if
infections didn't hit all members of the species. The authors discount
several factors: one is that a population crash in the human line,
followed by a rapid expansion could eliminate traces if virus
'infection' wasn't complete. They also possibly present contradictory
evidence to their own claim. They say that %5 of the insertions could
have been deadly in homozygous conditions. If the human population was
ever drastically smaller, this creates a situation where effective
inbreeding due to a limited gene pool could produce a greater than
expected number of homozygous individuals, thus exposing the trait to
more intense selection against carriers. Large populations are in
many cases able to carry deleterious alleles longer than small
populations. The *effective* neutrality of a deleterious allele is a
factor of population size.

> That leaves the possibility that human ancestors were not occupying
> the same habitat as chimp and gorilla ancestors at the time the
> infection occurred.
>
> >Essentially, the study tested three four primate genera known to have
> >lived in Africa and it was present in three, absent in one.
>
> Well, the 'one' here is humans, and their location at the time of the
> retrovirus marker is precisely what is under discussion, so let's set
> them on one side.
>
> Also, the paper says that "similar infections with a related
> retrovirus appear commonplace among the Old World monkeys", which
> implies that it occurs in a number of other species not mentioned
> explicitly in the paper.

This passage isn't as clear as it could be, but out of context as
you've presented it here, it's meaningless. In context the previous
line discusses their estimated date of diversification of the gorilla
and chimp elements. "Similar infections with a related
retrovirus...among the Old World monkeys" appears to me to refer to
similar PTERV1 insertions in baboons and macaques, the only old world
monkeys in their study or mentioned in their study. Since the end of
the particular sentence you quote implores the reader to refer to a
figure that mentions several species of macaque and baboon but no other
monkeys, I do not think that the authors were implying that other
monkeys had been tested. Nothing else in the paper suggests that other
species were tested that they might be referring to any other unnamed
species. There are no citations in that line to suggest that there is
any other work done elsewhere and no other hints from the paper that
anything other than the baboons and macaques have been studied.
Further, in the unlikely event, old world monkeys does not define only
an African geography.

> So it may be more like N:0 rather than 3:1 (but the paper isn't very
> clear on this).

It is a rather biases stretch to use a single line out of context to
imply that there's unknown data favoring an interpretation of
widespread fixed in Africa and similarly discount that it could be
widespread in Asia. I do not think that the authors imply at all that
they know anything of its distribution outside of the species tested,
but certainly, nothing in their paper implies that they know it's not
found in other Asian old world monkeys beyond the macaques tested.

> >The study
> >also tested four genera known to have lived in Asia and found it absent
> >in three, present in one. Is this significant? If there's a fifty
> >fifty chance of any primate showing the trait, this particular
> >distribution isn't all that strange.
>
> Yes, the macaques are intriguing, certainly, but the paper suggests
> that their infection might be from a later date (2Mya), which would
> make it irrelevant for this discussion. But the dates are not
> discussed very clearly, so maybe this is not what the authors mean.
>
> >Honestly, it seems like you've got a favored
> >interpretation and base your probability estimates on a very limited
> >consideration of what is involved.
>
> Honestly, I don't have a favoured interpretation. But I don't see
> anything very convincing in the alternatives. These results are just -
> well, odd, and not consistent with the standard assumption that human
> ancestors were in Africa 3-4Mya.

*You* do not see anything else as very convincing. This is not the
same thing as "...in the real world those other possibilities are
highly unlikely," unless while I wasn't looking, Pauline Ross was
appointed arbiter of all that the "real world" thinks and judges.

.

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