I've been having mail server problems.... trying anew...
>HX>What about nuclear DNA mutation rates?
SJ>It was the New Scientist article (based on a SCIENCE journal report) that
>I quoted so if Huxter has any questions about the use of mtDNA rather
>than nuclear DNA his dispute is with those journals.
[...]
HX>I have no dispute, I was just curious if any mention of nuclear DNA
mutation
>rates had been mentioned.
I posted the whole article, so if by "What about nuclear DNA mutation
rates?" Huxter was "just curious if any mention of nuclear DNA mutation
rates had been mentioned" he could have read it for himself!
======================================
Amazingly astute. Yes, I could have - and I did. I was really just curious
if you were familiar enough with what you posted to answer the question.
======================================
HX>It appears that 1) they were not and 2) you are
>unfamiliar with the concept of using nuclear DNA in molecular clock
>calculations. Do you know why mtDNA is preferentially used in such studies?
Again, I was just posting A "New Scientist article (based on a SCIENCE
journal report)". If Huxter thinks that "they" (i.e. the authors of the
New Scientist and SCIENCE articles) were "unfamiliar with the concept of
using nuclear DNA in molecular clock calculations" he should take it up
with them.
===================================
Why, Steve? I was asking YOU. They were not mentioned. I am a bit
surprised that they were not mentioned in the article, but many in the field
have preferred using mtDNA BECAUSE of its relatively rapid mutation rate and
the belief that mtDNA is inherited from only the female line. YOU presented
the material, did you not?
==================================
SJ>My understanding is that the molecular clock hypothesis is based on the
>*neutral* mutation rate. Mitochondrial DNA is therefore used instead of
>nuclear DNA because mtDNA is thought to be selectively neutral since it
>does not code for any phenotypical features.
HX>Actually, there isn't really "a" molecular clock hypothesis, at least not
>insofar as it focuses on mt or nuclear DNA. The MCH was originally aimed at
>proteins, way back in the early 1970s, and nuclear DNA has been used as far
>back as the late 1980s (if not sooner). Your understanding is apparently
>limited.
I am a layman. There is no "apparently" about it. My "understanding" *is*
"limited"!
=======================================
I know it is. It seems reasonable then that one in such a predicament should
refrain from 'siding' with anyone on technical issues.
=======================================
But OTOH, how do I know that someone who goes under the
*pseudonym* "Huxter4441" knows what *he* (or she) is talking about?
Perhaps Huxter can tell us who he/she is, and what his/her qualifications
are, so we can judge his/her ability speak authoritatively in this or any
field?
====================================
Sure. My name is Scott L. Page, Ph.D. My graduate major was Anatomy and Cell
Biology, my minor was Physical Anthropology. My undergraduate major was
Health Sciences with an emphasis in Exercise Science. I am an honorably
discharged Army veteran. While in the service, I was a paratrooper and
served as my battery's assistant Nuclear, Biological, and Chemical warfare
noncommissioned officer.
I did my graduate research under the tutelage of Morris Goodman, who is
widely recognized as the world's leading expert on the molecular evolution of
primates. My publications include:[note: the greek letters did not
translate when I pasted these - I'm sure you can get the gist]
Page, S.L., and Goodman, M. Catarrhine Phylogeny: Noncoding DNA Evidence for
a Diphyletic Origin of the Mangabeys and for a Human-Chimp Clade. Molecular
Phylogenetics and Evolution, (in press).
Page, S.L., Chiu, C-H., and Goodman, M. Molecular phylogeny of Old World
monkeys (Cercopithecidae) as inferred from a-globin DNA sequences. Molecular
Phylogenetics and Evolution, Mol. Phylogenet. & Evol. 13(2):348-359, 1999.
Chaves, R., Sampaio, I., Schneider, M. P., Schneider, H., Page, S. L., and
Goodman, M. The place of Callimico goeldii in the callitrichine phylogenetic
tree: evidence from von Willebrand factor gene (vWF) intron II sequences.
Mol. Phylogenet. & Evol., Mol. Phylogenet. & Evol. 13(2):392-404, 1999.
Goodman, M., Page, S.L., Meireles, C.M., and Czelusniak, J. Primate
phylogeny and classification elucidated at the molecular level. In:
Evolutionary Theory and Processes: Modern Perspectives, S.P. Wasser (ed.),
Kluwer Academic Publishers b.v., Dordrecht, The Netherlands, pp. 193-212,
1999.
Goodman, M., Porter, C.A., Czelusniak, J., Page, S.L., Schneider, H.,
Shoshani, J., Gunnell, G., and Groves, C.P. Toward a phylogenetic
classification of primates based on DNA evidence complemented by fossil
evidence. Mol. Phylogenet. & Evol. 9:585-598, 1998.
Meireles, C.M., Czelusniak, J., Page, S.L., Gumucio, D.L., Schneider, M.P.C.,
and Goodman, M. Testing a model of the fetal recruitment of a-globin genes
in callitrichine New World monkeys. Blood Cells, Molecules, and Diseases
24:491, 1998.
Porter, C.A., Page, S.L.,Czelusniak, J.C., Schneider, H., Schneider, M.P.C.,
Sampaio, I., and Goodman, M. Phylogeny and evolution of selected primates
as determined by sequences of the e-globin locus and 5' flanking regions.
International Journal of Primatology 18:261-295, 1997.
In addition, I have two manuscripts in preparation. I now am employed at a
small private university, where my research is limited. I have been
reluctant to use my name - anywhere on the internet - for the following
reasons:
1. I normally do not have the time to produce lengthy replies to posts, and
so usually 'resort' to short 'quip-like' posts. These are not often seen in
a favorable light. I did not want my attitude to reflect negatively on my
former advisor or my present employer. Or on my abilities and
qualifications, for that matter. For some reason, in this 'debate,'
politeness and style seem to count more than simple logic or content.
2. I liked the notion of retaining at least the semblance of anonymity for
security purposes. In the past, I have written letters to the editor and
received unpleasant mail (anonymous). I wanted to try to avoid this (getting
unsolicited email).
Is that good enough?
===================================
SJ>But if Huxter knows of any molecular clock studies based on "nuclear DNA
>mutation rates", perhaps he can post it to the List?
HX>Sure Steve. Why, doing a simple medline search produced 8 hits on
Primates
>alone. A sampling:
[...]
Thanks to Huxter, but what I mean was post the *details*, in particular
how it relates to the article I posted about mtDNA's clock.
==================================
That's funny - that is not what you asked for! Look right up there a few
lines:
"But if Huxter knows of any molecular clock studies based on "nuclear DNA
>mutation rates", perhaps he can post it to the List?"
It looked to me like you were simply asking for a few examples of using
nuclear DNA in molecular clock calculations. What details did you have in
mind? Why should it relate to your mtDNA article - which really wasn't an
article in the scientific sense, but one of those condensed 'human interest'
type articles.
===================================
HX>There are others, and I know of at least two more that will be coming out
>within a few months looking specifically at humans. There is a review paper
>that compares nuclear DNA molecular clock dates with dates inferred from the
>fossil record and there is a remarkable congruence between the two.
That is not "remarkable" at all, since the molecular clock was originally
calibrated by the fossil record!
==========================================
It was? Well, admittedly the nuclear DNA molecular clock uses a fossil date
to start from. But what rationale did you have in mind for divergence dates
corresponding to fossil data? For example, we can root the clock at 25
million years ago for the separation of Old World monkeys, apes and humans
and New World Monkeys. Why, if mutation rates are independent of speciation,
should clock calculations for subsequent lineage splits be at all congruent
with dates inferred from the fossil record?
=========================================
The interesting thing will be if there is any major differences between the
mtDNA and nuclear DNA molecular clocks. Or even between different
nuclear DNA molecular clocks.
========================================
Why would that be interesting? Would that 'disprove' Darwinian evolution
too? It should come as no surprise at all that different loci can give
slightly different results, as it is well known that different loci evolve at
different rates . The only wildly disparate dates that I know of come from
Easteal's group that used mitochondrial genomes to date some major lineage
splits. Their results are well different from those inferred from both the
fossil record and nuclear DNA dates. To me - and most observers - that
indicates that the mtDNA mutation rate has not been constant, not that
'evolution is wrong'.
=======================================
HX>I can dig up the ref if you'd like.
What does it matter what *I* "like"? If Huxter wants to post anything, let
him post it.
=======================================
Well, you seemed to be the one asking about this stuff. Just offering to
support a claim. I realize that must be foreign to you, but it is
commonplace in scientific discussions to support one's claims.
=======================================
END PART 1
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