Reflectorites
On Mon, 23 Oct 2000 07:35:33 EDT, Huxter4441@aol.com wrote:
[...]
>HX>I have no dispute, I was just curious if any mention of nuclear DNA
>>mutation rates had been mentioned.
SJ>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!
HX>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.
Huxter should make up his mind what he is "curious" about! First he says
he "was just curious if any mention of nuclear DNA mutation rates had
been mentioned". Then he says he "was really just curious if you were
familiar enough with what you posted to answer the question"?
Once again, I freely admit that I am a *layman* and my knowledge in any
particular field is *limited*. I post scientific articles to *learn*.
If this is Huxter's field I would appreciate him imparting some genuine
scientific knowledge, rather than trying to score cheap points by trying to
put-down laymen.
I would remind Huxter what a *real* scientist said about the right scientific
*attitude* in dealing with laymen:
"I would like to add something that's not essential to the science,
but something I kind of believe, which is that you should not fool
the layman when you're talking as a scientist. ... I'm talking about
a specific, extra type of integrity that is not lying, out bending
over backwards to show how you're maybe wrong, that you ought t
o have when acting as a scientist. And this is our responsibility as
scientists, certainly to other scientists, and I think to laymen."
(Feynman R.P., "Surely You're Joking, Mr Feynman!", 1990,
p.343)
>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?
SJ>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.
HX>Why, Steve? I was asking YOU. They were not mentioned.
Huxter said: "1) they were not ...". So "They were" in fact "mentioned."
And what is Huxter's point trying to see if I am "unfamiliar with the
concept of using nuclear DNA in molecular clock calculations" and if I
"know why mtDNA is preferentially used in such studies"? I had already
said (twice from memory) that my understanding was it was because
mtDNA are selectively neutral, not coding for any bodily parts.
If this is not correct I would appreciate Huxter saying so and why,
preferably with a quote from the literature I can check up on.
HX>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?
I did, but my understanding was that both are less important to the
molecular clock hypothesis than the assumption that mtDNA is selectively
neutral.
>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.
SJ>I am a layman. There is no "apparently" about it. My "understanding" *is*
>"limited"!
HX>I know it is.
So do I! So what is Huxter's point?
Mind you, so is Huxter's. Even in his own field, his "understanding" would
be "limited". And once out of his specialty, Huxter is just another layman:
"Being a scientist is not necessarily an advantage when dealing with
a very broad topic like evolution, which cuts across many scientific
disciplines and also involves issues of philosophy. Practicing
scientists are of necessity highly specialized, and a scientist outside
his field of expertise is just another layman." (Johnson P.E.,
"Darwin on Trial," 1993, p.13).
HX>It seems reasonable then that one in such a predicament should
>refrain from 'siding' with anyone on technical issues.
There is no "predicament" and I am not "'siding' with anyone"? I quoted a
New Scientist article, and expressed a *tentative* view. Here it is again.
================================================
On Sun, 01 Oct 2000 06:37:35 +0800, Stephen E. Jones wrote:
>Here is a New Scientist article, based on a SCIENCE report, which says
>that molecular clocks, the rate of neutral mtDNA mutation, is possibly 100
>times faster than previously thought.
>
>If this turns out to be really the case, it would bring any "Mitochondrial
>Eve", the last common female genetic ancestor, which has been variously
>dated from ~ 400-60 kya, into closer contact with Biblical time-frames.
>
>I have also attached another New Scientist article from the same issue,
>which claims that the maximum human life-span might be much longer than the
>current estimate of around 120 years.
>
>If this holds up, it could not be ruled out that the ages of the antediluvians
>in Genesis 5 (e.g. "Methuselah lived 969 years" -Gn 5:27); were literally
>true.
>
>I would imagine that Hugh Ross and the ICR will *love* these!
>
>Whatever happens, this shows that scientific `fact', especially in the field of
>human origins, is only as good as the next discovery.
================================================
Note "If this turns out to be really the case..."; :"If this holds up..." and
"Whatever happens...".
SJ>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?
HX>Sure. My name is Scott L. Page, Ph.D.
Thanks to Scott for this. I will still call him "Huxter" and "HX" to avoid
confusion.
HX>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 respect Huxter's qualifications in the above fields.
HX>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.
Again I respect Huxter's experience here.
HX>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.
As *the* world's leading expert on the molecular evolution of primates?
Leakey & Lewin say that Goodman is-he started the field of molecular
phylogeny in anthropology, but Wilson and Sarich eclipsed him:
"In the early 1960s Morris Goodman, at Wayne State University,
introduced this kind of molecular evidence into anthropology when
he demonstrated the close genetic relationship between humans and
African apes, the chimpanzee ant gorilla, and the distance between
humans and the Asian great ape, the orangutan. But it was the
Berkeley biochemists Allan Wilson and Vincent Sarich who really
caught the anthropological community's attention by suggesting, in
1967, that molecular evidence showed humans and apes to have
diverged from each other some five million years ago. At the time,
anthropologists believed that this divergence took place much
earlier, at least fifteen and possibly as much as thirty million years
ago." (Leakey R. & Lewin R., "Origins Reconsidered," 1993, p.76
The anthropology text I have does not even mention Goodman but it does
mention Walker and Sarich:
"Another method used to contrast proteins in different species is
not as precise as a detailed protein analysis but is less time-
consuming and less costly. By measuring the strength of reaction to
specially prepared antisera, similarities in proteins are calibrated on
a relative scale, indicating antigenic distance. This approach,
developed by Vincent Sarich and Allan Wilson at the University of
California, Berkeley, has enabled many more proteins to be
compared among a wide variety of different primate species. The
results again generally tally favorably with traditional
classifications." (Nelson H. & Jurmain R., "Introduction to Physical
Anthropology," 1991, p.255).
HX>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.
Thanks to Huxter for these. I must say I am disappointed though that
someone with Huxter's expertise, rather than posting helpful information
from his field, tried to use his expert status to put down a layman.
HX>I now am employed at a
>small private university, where my research is limited.
Which tends to dilute Huxter's jibes at Wells for no longer doing
"research"!
HX>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.
I cannot see why short replies cannot be helpful and informative rather than
nasty, as most of Huxter's posts are.
Besides, Huxter's posts *are* often "lengthy" so this does not seem to hold
much water.
HX>These are not often seen in a favorable light.
It is the *nastiness* of Huxter's posts that might not be "seen in a favorable
light" by an employer. This is one of the problems with pseudonyms-one
can post what one likes without the normal social moderating influences
(witness the revolting posts by Huxter's alter ego Pantrog and the other
name that is too obscene to repeat).
HX>I did not want my attitude to reflect negatively on my
>former advisor or my present employer.
I am not surprised Huxter felt this way, bearing in mind the content of his
posts!
May I suggest that Huxter drops the pseudonyms and starts posting under
his real name, but not putting anything in his posts that he would be
ashamed for his employer to know about?
HX>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.
It is Huxter's *lack* of "politeness and style" that get in the way of "logic
or content"!
HX>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).
If Huxter's "letters to the editor" were anything like his posts, I am not
surprised!
But even if not, so what? We all have received "unpleasant mail" and it is
the price one sometimes pays for stating publicly what one believes to be
the truth in this `culture war'. Think of the "unpleasant mail" IDers like
Jonathan Wells, Johnson and Dembski must get, yet they have the courage
of their convictions to use their real names, and even where they work.
HX>Is that good enough?
Personally I don't think the above are "good enough" reasons for Huxter
not to use his real name. But then Huxter is not accountable to me.
>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:
[...]
SJ>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.
HX>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?"
I did not say *titles* - I said "studies". Since we are having a debate about
the molecular clock in general and mtDNA vs nuclear DNA mutation rates
in particular, I would have expected some helpful *information*, especially
now that it is Huxter's specialty.
HX>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?
Huxter seemed to be making claims about "DNA mutation rates" in the
context of the molecular clock and mtDNA mutation rates. I would have
expected him to actually post some *information* rather than all this
`dancing around the ring'!
HX>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.
It is *Huxter* who asked the original question What about nuclear DNA
mutation rates?" in response to my posting of the New Scientist article
about "mtDNA". If he has anything to contribute then let him do so.
>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.
SJ>That is not "remarkable" at all, since the molecular clock was originally
>calibrated by the fossil record!
HX>It was? Well, admittedly the nuclear DNA molecular clock uses a fossil date
>to start from.
Then what was Huxter's point?
HX>But what rationale did you have in mind for divergence dates
>corresponding to fossil data?
I said nothing about "divergence dates corresponding to fossil data" and me
having any particular "rationale" for it.
Huxter is the expert, I am sure everyone (including me) would be more
interested in hearing what *his* views are.
HX>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?
I said nothing about "speciation".
SJ>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.
HX>Why would that be interesting?
Wouldn't Huxter think that "would that be interesting"? I would have
thought that "any major differences between the mtDNA and nuclear DNA
molecular clocks" would mean that either: 1) one is wrong; or 2) the whole
molecular clock hypothesis might be wrong.
HX>Would that 'disprove' Darwinian evolution too?
I tend not to use the word "disprove". But I see the very existence of
neutral mutations as yet more weakening of the central role of natural
selection and hence "Darwinian evolution":
"Yet it has become a widely held view, particularly among certain
American and Japanese geneticists that much of the variation serves
little purpose in the survival of creatures, and that it may represent
neutral 'noise' in the system. This is not necessarily to deny that
selection exists, nor that selection can cause adaptation, but to
emphasize that selection may be a much weaker force than has
previously been thought, and that a large proportion of the genetic
variability observed in nature may serve no useful function. Motoo
Kimura is a Japanese population geneticist and the most ardent
proponent of this 'neutralism'. For Kimura, the majority of genetic
variants are neutral in their effect, bestowing neither advantage nor
disadvantage on the bearer and capable of drifting through
populations unhindered by selection. Variation arises by mutation
and may survive because it causes no harm. Kimura certainly has
little time for those who see selection as the omnipotent force in
evolution, the 'naive pan-selectionists'" (Leith B., "The Descent of
Darwin," 1982, p.49)
HX>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.
Who would dispute that? I presume the overall molecular clock estimate is
an average?
Besides, how *would* one compare "loci" between mtDNA and nuclear
DNA? They are on totally different chromosomes.
HX>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,
And/or the dates of the "major lineage splits" are wrong?
HX>not that 'evolution is wrong'.
Who said that this would show that "'evolution is wrong'"? Huxter said that
above that "it is well known that different loci evolve at different rates" so
presumably just one "loci" changing is "evolution" to him?
>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.
HX>Well, you seemed to be the one asking about this stuff.
*Huxter* was "the one asking" the original question "about this stuff"
namely "What about nuclear DNA mutation rates?" in response to my post
about mtDNA mutation rates. His question implies there is something there
is something different about "nuclear DNA mutation rates" (otherwise what
was his point?) If Huxter wants to support is argument (assuming he even
has one) let him do it if he wants to.
HX>Just offering to support a claim.
Why "offer"? It is *Huxter's* "claim". If he wants to support it, he is free
to do so.
HX>I realize that must be foreign to you, but it is
>commonplace in scientific discussions to support one's claims.
Why "must" this "be foreign to" me?
I *expect* "in scientific discussions" for one "to support one's claims" and
in fact it is *me* encouraging Huxter to "support" his "claim" (whatever it
is).
Huxter's `dancing around the ring' is extraordinary, especially since this is
his field.
Maybe Huxter doesn't actually *have* a "claim" but hoped to get by on
bluff and put-downs?
HX>END PART 1
I await Part 2 with bated breath! :-)
Steve
--------------------------------------------------------------------------
"Biology is the study of complicated things that give the appearance of
having been designed for a purpose." (Dawkins R., "The Blind
Watchmaker," [1986], Penguin: London, 1991, reprint, p.1)
Stephen E. Jones | Ph. +61 8 9448 7439 | http://www.iinet.net.au/~sejones
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