cont'd.....
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).
=====================================
Employer? What does that have to do with anything? I am so nasty, aren't I?
My 'revolting' posts were in response to DNAunions 'revolting' posts. So
sue me for responding in kind. My 'other name that is too obscene to repeat'
was of course in response to how DNAunion referred to me in the post of his
that I replied to. I'm sure that HIS revolting words were not quite as
revolting to you, being fellow creationists and all... I think some take
these discussion fora a bit too seriously....
====================================
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!
======================================
Oh boy!
=====================================
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?
=======================================
No, you may not. I think you misread what I meant about my employer and so
on. I am ashamed of nothing I have written. I would not be ashamed if my
employer read them. My point was that I did not want what *I* wrote to bear
on the positions of my employers. In other words, I did not want to make
them 'guilty by association'.
=======================================
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"!
=========================================
Just what I meant. Creationists always seem more concerned about how 'nice'
someone is than what they bring to the discussion. I, frankly, don't care
how 'nasty' someone is as long as what they say makes sense. One of the most
knowledgible people I knew while in the military was an ex-Marine Corp
gunnery sergeant who literally could not finish a sentence without at least
one F-word in it. He made an art out of cursing and I will forever be amazed
at how he could utilize profanity. It puts 'gangsta rappers' to shame. Of
course, none of that impacted his ability to successfully do his job and earn
the trust and admiration of his colleagues and subordinates.
=========================================
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!
========================================
They were not, of course, as a newspaper is quite a different medium from
this.
========================================
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.
======================================
Perhaps because they *work* at institution dedicated to 'destroying
Darwinism'? Of course, Baylor does not fit that bill, but the now defunct
Polyani center certainly had an agenda, and it wasn't 'supporting' ID!
=====================================
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.
=====================================
That is right. As I already stated, there are legitimate reasons for not
using one's real name on the internet. And it has little to do with the
courage of anyone's convictions.
=====================================
>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.
======================================
You asked if I *knew of any*, not if I would lay out the content of the
articles in detail. What 'debate' are we having? I tried to ask a few
questions, tried to disseminate information, you refused. I guess what I
consider 'information' and what you consider 'information' differs.
======================================
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'!
======================================
What 'dancing' are you talking about? Where is YOUR *information* about
these topics? In reality, I have made no claims about mutation rates, I
mentioned that nuclear DNA molecular clock calculations are generally
congruent with fossil data. I offered to dig up the ref and my offer was
rebuffed. Shall I simply cut and paste a lenghty section of the article I
had in mind with a fleeting commentary about how it minimizes any problems?
Please tell me what type of information you might like. I will do what I can
to provide it. What I will not do is take the time to write a lengthy
exposition only to have it not be exactly what you looking for and so of no
use.
=======================================
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.
========================================
That is what I am asking! WHAT shall I contribute? What did you want to
know?
========================================
>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?
=======================================
There is a difference between using a 'known' fossil date to start from and,
as you seem to be implying, that fossil dates are used to adjust each date
inferred using clock calculations. That is my 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.
======================================
But you did! In reply to this:
"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."
you replied:
"That is not "remarkable" at all, since the molecular clock was originally
calibrated by the fossil record! "
You made an implicit charge that dates inferred from molecular data should
correspond to dates inferred from fossil data because the molecular dates are
calibrated to fossil dates.
=========================================
Huxter is the expert, I am sure everyone (including me) would be more
interested in hearing what *his* views are.
=======================================
Fine. There is no ratonale whatsoever for there to be conguence between
divergence dates inferred via nuclear DNA local molecular clock calculations
and those inferred from fossil evidence if the congruence is not due to
common descent. Here is what I mean: The 'starting point' for, say, the
divergence of Old World monkeys from New World monkeys is 25 million years.
This date is the 'agreed' upon date inferred from fossil evidence. It is not
an exact date. Using this time, and the information provided by analyses of
DNA sequence data, we can set up simple proportions to determine the time of
the next divergence. Using this step-wise procedure, estimates of divergence
times are calculated all the way to the most recent. The dates inferred using
this method - the so-called local molecular clock (local because a uniform
mutation rate is NOT assumed) - are fairly congruent (less than +/-10% for
most) with dates inferred by dating fossils. Since the only calibration in
the whole exercise is the oldest, there is no alternative - certainly none
has been presented anywhere in the literature - reason for there to be a
correlation between fossil dates and dates inferred by the above method
except for descent. If we exclude descent as the viable explanation, we have
to conjure up spectacular amounts of coincidence. And since the studies that
I have done involve non-coding, non-regulatory DNA, 'common design' is moot.
====================================
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".
====================================
What do you think the molecular clock clocks? If we are not estimating
divergence times (speciation), what do you propose the molecular clock
studies actually look at?
===================================
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.
=================
Explained elsewhere. I guess my explanation wasn't exactly what you wanted.
===================
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":
============================
Please explain. I can see no scientific basis for that position. If
mutations occur in noncoding DNA, how exactly shall that be anything but
neutral?
=============================
"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)
==================================
Your point?
==================================
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?
===================================
More or less. If you do not dispute that, I fail to see why you wrote:
"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. "
===================================
Besides, how *would* one compare "loci" between mtDNA and nuclear
DNA? They are on totally different chromosomes.
==================================
mtDNA is not on any chromosome. It is contained inside the mitochondria.
One would not directly compare mtDNA and nuclear loci at all; there is no
reason to do so. At best one can compare mutation rates. There was an
interesting article in Science a few weeks ago that I keep forgetting to
refer to (and I don't have it with me now, either) that showed how selection
significantly reduces the effective mutation rate.
===================================
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?
================================
Actually, even Easteals (or maybe it was Arneson....) work shows congruent
dates until we get well back into the area of mammal/reptile splits and such.
As for being wrong, that is always a possibility, as *true* science is
tentative, not set in stone. However, if we have 10 studies saying one thing
and one study saying another, I think it safe to side with the majority until
such time as the majority can be shown to be in error.
================================
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?
====================================
In a sense, yes. I know that the 'popular' definition of evolution is fish
changing into frogs or some such nonsense. But at the most basic level,
evolution is change at the molecular level. Not necessarily body parts.
=====================================
>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.
======================================
I wasn't aware that simply offering to supply information would be so
aggressively attacked by you. My 'argument' was that one should not take a
single article on the mtDNA molecular clock and extrapolate it into some
evolution-wide catastrophe (let me guess - you never said 'catastrophe',
right?) and at the same time some sort of OEC friendly science.
=====================================
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.
=====================================
I offered because I did not have the ref handy and thought you might want to
verify it for yourself.
=====================================
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?
=====================================
Well, I asked more than once for you to provide a rationale for some of your
points; you have yet to do so.
=====================================
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).
======================================
It is? Funny - I offer to do so and I am rebuffed! It doesn't sound much
like you are asking anything.
======================================
Huxter's `dancing around the ring' is extraordinary, especially since this
is
his field.
=====================================
Amazing.
=====================================
Maybe Huxter doesn't actually *have* a "claim" but hoped to get by on
bluff and put-downs?
======================================
What bluff? What put-downs? I'm still trying to figure out what you would
like me to address. I do not want to waste my time writing something only to
have it not exactly address the question in your head (which I have no way of
knowing).
Maybe if you had the *attitude* of a *true* layman, I would not get so
frustrated! :)
end part 2
Steve
>>
This archive was generated by hypermail 2b29 : Mon Oct 30 2000 - 17:18:06 EST