RE: [asa] Two questions...Ayala's article

David wrote:

-- do you accept the evidence for an old universe and earth?

Yes, absolutely.

If so, aren't you being inconsistent in rejecting the conclusions population
geneticists draw from the MHC data based on the presumption you've drawn
from the Bible that there must have been only one pair from whom all present
humans directly are genetically descended? The YEC's, after all, make
exactly the same argument about the "days" of creation, the age of the
earth, and the nature of Noah's flood.

No, I don’t think so, not at all. First, and as I said, I don’t think MHC
data should be used much, if at any, for this kind of thing. I am also not
sure how that ties into the next part of your statement. But the evidence
for the Big Bang, the age of the universe, the age of the earth, that’s all
“hard” science – physics and cosmology. It is much more defined and clear
than the biological sciences. It’s very hard to argue with mathematical
equations like those that define our universe. However, the math used in
Ayala’s paper is *much* less clear, and the math used in the entire field of
population genetics isn’t nailed down yet…just look at some of the
references. We don’t understand this field well enough in general, and I
don’t accept or understand the science well enough to take a position that
it is impossible to have an n=2. I think that some very good evidence for
their being an n=2 is that is what the Bible tells us, and it seems
reasonably clear that an n of 2 is what is indicated – I don’t see a way
around that. The strongest argument I see for there being some other answer
to this is Dick Fischer’s argument that it was an n=2, but they were the
first ancient Hebrews, not the first man. However, I have to state that I
don’t accept that position (although I haven’t read his book yet, it’s on
order Dick). The Bible seems generally clear that it refers to the origins
of mankind – all of mankind.

The essential foundation of my argument is that in general, what the Bible
says and what science says agree. YOM doesn’t mean a literal day. The
Hebrews didn’t mean a global flood. How Genesis is interpreted is obviously
not easy, and not clear, or we wouldn’t be here talking about it.

-- you say, ". . . we see the emergence of man in the correct *general*
location, from (at least) a small population, sometime in the past." I used
to find this kind of argument from RTB et al. somewhat persuasive.

However, let's be honest: central Africa is not the same "general location"
as Mesopotamia,

Yes, it is. First off, I think it’ East Africa. But I’m not going to split
hairs. And even if you draw that circle down to Tanzania and Ethiopia, it’s
still in the same general location. We do not understand mans origins well
enough to put him in anything other than Africa. That’s fine. It’s not
Europe, it’s not Australia, it’s not America, it’s not Russia, it’s not
China, or India. God said he created man west of Eden. Africa is west of
Eden. Sure, most of it is also south…but it’s still west. I don’t really
think that’s worth belaboring…it agrees well enough. Science puts the
origins of man in Africa, and the first civilizations in Mesopotamia. The
Bible put’s the creation of man west of Eden, and Eden in Mesopotamia. That
agrees well enough for me. Here’s the map again, since it wasn’t in this
email. http://www.pattersonhistory.net/map01.jpg

and "sometime in the past" -- if that is 150 kya or so even for
Mitochondrial Eve -- doesn't fit with the Bible's description of the culture
into which Adam's immediate descendants were placed.

I am working on that presently…and answering this thread is detracting me
from that work…

Moreover, "(at least) a small population" isn't two individuals. I am no
expert either, but my sense is that for the MHC data to be accounted for by
a single pair, you'd either have to have (a) diversification of the MHC at a
truly astonishing (not just 'fast') rate; or (b) a whole set of miracles not
mentioned in scripture.

Not mentioned???? God creates man and woman, breaths their spiritual nature
into them, and you tell me that’s not mentioned? Come now. He doesn’t give
out details on how He did it…or what He did. If so the world would be a much
simpler place. But I think it’s clear – He did something.

Isn't it more parsimonious to suggest, as John Stott did in his Romans
commentary, that the "image of God" and "original sin" are essentially
spiritual qualities rather than genetic ones? It seems to me that this
removes much of the burden of trying to tie Adam to the genetic record.

That’s not a bad point, but parsimony can be taken only so far. Occam’s
razor can slice down to the bone of metaphysical naturalism, if you let it.

Perhaps Adam lived in (or was removed from the "garden" into) a context
where there were other "humans," but this says nothing of the spiritual
aspects of those other homo sapiens who shared the physical world with Adam
and his descendants for a time.

Well, I don't like that either, but I haven't been able to conceive of a way
to pull these threads together more tightly without resorting to
presuppositional logic that ultimately leads to YECism.

I don’t deny that PC is a tough position. The one thing that brought me here
to this position is the strong Biblical foundation, and the thing that keeps
me here is that there is a model. Models can be revised based on new data,
and other opinions and interpretations can be incorporated. This is not true
of YEC – the entire foundation of their position is based on a unbalanced
premise that only the Bible is true, and not science (at least not anyone’s
science but their own). The PC position is balanced: both Bible and science.
The TE position is (in my opinion) a bit unbalanced the other way – too much
reliance on only natural explanations. I know most of you don’t agree with
that, but hey if I wasn’t here testing your positions, you wouldn’t be
having so much fun. J

God bless, JP

---
David W. Opderbeck
Associate Professor of Law
Seton Hall University Law School
Gibbons Institute of Law, Science & Technology
On Sat, Feb 21, 2009 at 2:47 PM, James Patterson <james000777@bellsouth.net>
wrote:
All,
 
I've finally been able to get back to this thread (and sub-threads) and read
them. I wanted to go read the Ayala manuscript first. I have read it as well
as the comments on the article, and a few other related articles.
 
I must also classify myself as "not an expert" in this field. However, I
find it quite interesting to look at how often the words "presume" and
"presumption" are used in the Ayala article. If you look at this article
specifically and the field as a whole, there is significant controversy over
the various models and how to interpret the results…more so than I am
comfortable with. This is reflected in the comment in reply to the Ayala
article, as well as several other articles (see below).
 
All that as an aside. The main issue is the size of the "n" required to pass
thru a bottleneck. Ayala argues there wasn't even a bottleneck, but I think
most would agree there is plenty of evidence that there was at least one if
not more bottlenecks. So I am not going to belabor that issue.
 
Ayala's point is that, for a given chunk of DNA, including mtDNA chunks, you
may be able to trace that chunk back to a common ancestor. However, the next
chunk of DNA will be from a *different* ancestor, not the same one, implying
not one, but a population of "Eves". I am NOT familiar enough to state for
certainty, but I thought that the mtDNA was looked at more as a whole than
other DNA? It's size is about 15-17 kbp, and codes for 37 genes.  
 
When we get to the point of whether there was a n=2 vs an n=X, Ayala puts X
at ~100,000. He describes how it would be impossible for all the alleles of
the MHC to survive a population smaller than (I think) about 10,000 sexually
active humans, which equates to a total population that is of course larger.
The issue here of course is the MHC region. If one is going to look at
comparative regions and molecular clocks, it seems to me that the MHC has
got to be the *worst* possible choice to use. Within the field of
immunology, this region of the genetic code is sometimes called the G.O.D.
(interesting, yes?) region, for Generator (or Generation) Of Diversity.
Mutation rates here can be quite rapid. See the Hogstrand or Carrington
articles below.
 
Given that, Ayala's work does not seem to distinguish itself any greater
than other studies on this topic. And that gets to the heart of the matter:
From a strict, naturalistic, population genetics viewpoint, a bottleneck of
an n=2 is unacceptable. The only way to have an n=2 bottleneck is if this
couple were quite special in some way or ways, and that isn't "natural".
 
Thank God, I am not a strict naturalist. J
 
The integration of science and faith is why we are here. You may want to
find a strict natural explanation of everything, because you think that's
the way God works at all times. If you extrapolate this to the extreme, the
TE viewpoint becomes the DE viewpoint. I think I mentioned this in another
thread recently. At the very least, I think you should at least consider
this to be a prime example of Russell's OSP hard at work. You may be able to
track the lineage of the descent of man genetically, but tracking the hand
of God is another matter.
 
It becomes very difficult, very quickly, to reconcile God's creation of our
spiritual selves (as well as original sin) with a (large) population of
humans that evolved slowly. No matter how you slice it, God's handiwork is
present. And if we are going to presume the hand of God being involved, then
strict naturalistic explanations will ultimately fail. 
 
However, if you *presume* that God was involved, and that God created Adam
and Eve (as the Bible tells us), and look at what the natural sciences show
us, we see the emergence of man in the correct *general* location, from (at
least) a small population, sometime in the past. How exactly, may remain
unclear. We will have to save the time question for later, tho.  J
 
If you choose not to believe that God was intimately involved with the
creation of man through Adam and Eve, then that's your choice. As for me and
my family, we choose God.
 
God bless,
James P
 
A few interesting references: 
 
Gibbons A, (1993). Mitochondrial Eve refuses to die. Science,
259(5099):1249-1250. 
 
Ayala F, (1995). The Myth of Eve: Molecular Biology and Human Origins.
Science, 270(5244):1930-1936.
 
Erlich HA, Bergstrom TF, Stoneking M, and Gyllensten U (1996). HLA Sequence
Polymorphism and the Origin of Humans (in reply to Ayala's article).
Science, 274(5292):1552-1554.
 
Watson E, Forster P, Richards M, Bandelt HJ, (1997). Mitochondrial
footprints of human expansions in Africa. Am J Hum Genet, 61(3):691-704.
 
Carrington M, (1999). Recombination within the human MHC. Immunological
Reviews, 167(1):245-256.
 
Gray M, Burger G, Lang BF, (1999). Mitochondrial Evolution. Science,
283(5407):1476-1481.
 
Högstrand K, Böhme J, (1999). Gene conversion can create new MHC alleles.
Immunological Reviews, 167(1):305-317.
 
Cann R, (2001). Genetic Clues to Dispersal in Human Populations: Retracing
the Past from the Present. Science, 291(5509): 1742-1748.
 
Stumpf M and Goldstein D, (2001). Genealogical and Evolutionary Inference
with the Human Y Chromosome. Science, 291(5509):1738-1742.
 
Zimmerman S, (2001). Population size at the time of mitochondrial eve. Human
Evolution, 16(2):117-124.
 
Curnoe D, Thorne A, (2003) Number of ancestral human species: a molecular
perspective. Homo, 53(3):201-224. 
 
Hagelberg E, (2003). Recombination or mutation rate heterogeneity?
Implications for Mitochondrial Eve. Trends Genet,  19(2):84-90.
 
http://en.wikipedia.org/wiki/Major_histocompatibility_complex#MHC_evolution_
and_allelic_diversity
 
 
 
 
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