Re: [asa] Humanity and the Fall: Questions and a Survey

Rich, this is very impressive, and apparently unassailable on its own
merits, at least by someone like me, who really doesn't have the ability to
study the primary literature and data intesively. Nevertheless, it
conflicts with scripture, at least seemingly so, and many theologians of
various stripes see it is a serious theological problem, much more serious
than geocentrism or the days of creation. Is this not a place where we say,
"thus far shall you go and no further?" Have we not reached here a place
where the scientific method, which properly cannot admit miracles, is
incompetent to deliver to us the Truth?

On Sun, May 4, 2008 at 8:53 PM, Rich Blinne <rich.blinne@gmail.com> wrote:

>
> On May 2, 2008, at 5:02 PM, Gregory Arago wrote:
>
> "The current view is not a founder pair but a founder small population in
> the 10K range." - TG
> Is this consistent with the idea of 'polygenism,' even if it doesn't
> address the 'multiregional hypothesis'? Does it not contradict the idea of
> 'monogenism'?
>
> Can you forgive my SoS question: whose view is the 'current view' and the
> 'present notion'? Is this what 'normal science' says? (And for a non-NS)
> Which fields does the 'current view' mainly draw upon?
>
> It seems to me that David C.'s post carefully left open more than one
> option, which I quite appreciate, not being a 'scientist' in a field that
> speaks about bottlenecks (though 'probka' means 'bottleneck/traffic jam' in
> Russian) or near extinction events. The consequences of a 'founder small
> population' instead of a 'founder pair' in sociology is significant, though
> not commonly discussed in the literature.
>
>
>
> All of this goes back to a very simple observation. The genetic diversity
> of people of African descent have greater genetic diversity than those who
> aren't. It gets a lot more complicated than this but there are basically two
> ways you can get this, bottlenecks and founder effects. When a population
> suddenly gets smaller in a bottleneck its genetic diversity also goes down.
> Likewise, when there is colonization the same happens. Out-of-Africa holds
> to a multiple founder effects and Multi-Regional-Evolution to bottlenecks.
> Another difference between the two approaches is MRE claims there is
> admixture of "modern" humans with Neanderthal, the evidence being some
> commonalities in the microcephalin gene in MtDNA found in fossilized
> Neanderthal. OOA says there is little or no admixture but that the Eurasia
> population were replaced by African ones. Both approaches give you dates and
> population sizes. *NONE of the options or suboptions give you monogenism*.
> That's why I prefer Adam and Eve in the ANE because both it and its
> alternative have the same theological problems. Note: *the theological
> problems caused by evolution are still there even when you restrict yourself
> to genetics and so-called microevolution*. David C's point was there are
> problems with uncalibrated molecular clocks giving accurate dates. Both
> sides agree with the size of the original population Terry quoted. More on
> this later.
>
> What we have here is a classic stage two science with two conflicting
> theories fighting for dominance. We are, however, on the cusp of stage three
> here and that is a very interesting story. Note what does not happen where
> both sides don't talk to each other, just publish in the popular literature
> and produce no falsifiable hypotheses like ID. Given the time frame is
> roughly the same as ID, this will give us a good comparison/contrast between
> the scientific approach and the ID approach. David C. mentioned the issue
> with molecular clocks and this reflects the battle between the
> paleontologists and the molecular biologists on how things are dated. This
> is also moving from stage two to stage three. The answer is to do both
> mirroring the massive success of the neo-darwinian synthesis. This has of
> late produced some very fruitful results. For example, we are getting the
> same answer out of both fields of the what and when concerning the
> speciation of mammals. We are even getting confirming evidence from ancient
> biological materials. Collagen from T Rex confirmed what the paleontologists
> have been telling us that dinosaurs are birds. The other thing that makes it
> much easier is since the human genome was produced five years ago the
> technology has taken off like a rocket -- and ID still produces no research.
> I would submit the fundamental difference between science now and fifty
> years ago is not a difference in the *philosophy* of science but rather
> the *technology* of science.
>
> Paul Harvey voice: "And now for the resssst of the story. Page two." In
> 2004, Osbjorn M. Pearson wrote "Has the Combination of Genetic and Fossil
> Evidence Solved the Riddle of Modern Human Origins?" [Evolutionary
> Anthropology 13:145-159 (2004)]. This was when the debate between OOA and
> MRE was in the second stage, trench warfare stage. By combining the genetic
> and archeological data the balance was tipping to the OOA side. Pearson
> said:
>
>
> Debate over the origin of modern humans continues without a clear end in
> sight. Currently, the genetic and fossil evidence is still used to support
> two different interpretations of the origin of modern humans. Some
> researchers claim that the genetic evidence is compatible with either an
> Out-of-Africa or a Multiregional model, while other scientists argue that
> the evidence supports only a Multiregional model of evolution. I argue that
> the fossil record and archeological evidence constrain interpretation of the
> genetic evidence and imply that very little, if any, admixture with Eurasian
> archaic hominins such as the Neanderthals occurred during the spread of
> modern humans out of Africa.
>
>
> ...
>
> First, the effective population size of [approximately] 10,000
> individuals for our species would have to have arisen from a bottleneck or
> series of bottlenecks long before the origin of modern humans ... [RDB Note:
> *this is what Terry quoted. This will come back again so keep your eye on
> the ball.*]
>
> ...
>
> Future discoveries in genetic patterns or the genetic basis of "modern"
> traits should help to narrow down even further the possibilities with
> respect to exactly what happened with the origin of modern humans. There is
> reason for optimism that these discoveries will be made soon. [RDB Note: He
> was right.]
>
>
> Fast forward to 2008.
>
> Weaver and Roseman, New Developments in the Genetic Evidence for Modern
> Human Origins, Evolutionary Anthropology 17:69–80 (2008)
>
> The genetic evidence for modern human origins was reviewed recently in
> Evolutionary Anthropology by Pearson, so our goal is to highlight new
> developments rather than attempt a comprehensive review. For years,
> polarized Multiregional and Out-of-Africa models for modern human origins
> were debated vigorously, but today there is substantial agreement among
> specialists. One area of broad consensus is that Africa or, more accurately,
> sub-Saharan Africa, played a predominant role in the origins of modern
> humans. This view is found even among researchers who argue against complete
> replacement of nonmodern Eurasians. The importance of Africa is clear not
> only from genetics, but also from the fossil record. On the other hand, most
> researchers also agree that, at least in principle, modern humans and
> nonmodern Eurasians, such as Neandertals, could have interbred with each
> other. The fossil record suggests that Neandertals and modern humans
> constituted independent evolutionary lineages, but their recent common
> ancestry leaves open the possibility of admixture. The open question is
> whether there is any evidence of admixture.
>
>
> What brought about the consensus? A better technique using short tandem
> repeat analysis (STR) rather than single nucleotide polymorphisms (SNP) was
> done. This produces much less ascertainment bias and thus allows us to do
> within-population variation on the global STR dataset. If you look at just
> the difference in genetic diversity between African and other locations this
> can be explained via multiregionalism with isolation by distance which is an
> equilibrium model. But, looking at in-population gives us greater precision.
> When looking at this there is a straight line relationship for every
> population with the diversity with distance from East Africa. In other
> words, we have a smoking gun for OOA. The farther you are from Africa the
> later the founder arrives and the further you are away from equilibrium.
> Isolation by distance has no such preference to the direction of the
> distance.
>
> Late last year a Bayesian analysis was done on 50 independent autosomal
> noncoding loci with six different models (African Replacement, Assimilation,
> Multiregional with instantaneous (bottleneck) and exponential growth).
> [Fagundes et al, Statistical evaluation of alternative models of human
> evolution, PNAS 104:45, 17614-17619 (2007)] The winning model based on
> posterior probabilities was the African Replacement Model with Exponential
> Growth (AFREG). After the model was determined, 5,000,000 different
> simulations under an approximate Bayesian computation (ABC) framework were
> done to get the parameters. *Did you keep your eye on the ball and
> remember Terry's population size number? Note what came out as the ancient
> African population (12722)*. Also note that census populations (what we
> normally think of populations) can and often are quite larger than the
> effective number of diploid individuals.
>
> Table 1. Demographic and historical parameters estimated under the
> favored AFREG model
> Parameters† Median‡ 95%
> HPD§
> Speciation time for modern human, yr (TMH) 141,455 103,535–185,642
> Exit out of Africa, yr (TAS) 51,102
> 40,135–70,937
> Colonization of the Americas, yr (TAM) 10,280 7,647–15,945
> Size of archaic African population (NA-AF) 12,772 6,604–20,211
> Bottleneck size during speciation (NbMH) 600 76–1,620
> Bottleneck size when leaving Africa (NbAS) 462 64–1,224
> Bottleneck size when leaving Asia (NbAM) 452 71–1,280
>
>
> † Population sizes are given in effective number of diploid individuals.
> ‡ Median value of the marginal posterior density.
> § The 95% highest posterior density interval.
>
> What about the admixture of humans and Neanderthal? Currently there isn't
> enough information to prove or exclude it. We are still in stage 2 there.
> Given the speed at which the genetic technology is moving I would not be
> surprised to be at stage 3 soon. This is a rather easy prediction to make.
> (Just don't force me to pick which one is right. :-)
>
> Rich Blinne
> Member ASA
>
> P.S. I am including the glossary from the 2008 Evolutionary Anthropology
> article to explain the terms used in this post:
>
> Admixture—transfer of genes between two populations that had previously
> been isolated from each other.
>
> Ancient DNA—a DNA sequence retrieved from a biological sample of a dead
> organism, often coming from an extinct taxon.
>
> Ascertainment bias—genetic loci are usually discovered by finding
> differences among individuals in a small sample, then typed for a
> larger sample. This nonrandom discovery process often biases estimates of
> population genetic parameters such as measures of
> within-population genetic diversity, among-population
> differentiation, linkage disequilibrium, and tests for departures from
> mutation-drift-equilibrium. The only way to eliminate ascertainment bias is
> to completely resequence all the individuals in the study; that is, the
> discovery sample is the same as the study sample.
>
> Autosomal locus—a position on one of the paired (non-sex) chromosomes.
>
> Bottleneck—a sharp contraction followed by a recovery in population size.
>
> Census population size—the actual number of individuals in a population.
>
> Coalescence time—the time in the past when all DNA sequences in a sample
> shared a last common ancestor (time to the most recent common ancestor).
>
> Directional natural selection— when natural selection favors a phenotype
> that differs from the population mean, resulting in a shift
> of the mean.
>
> Effective population size—a population genetics parameter that equals the
> number of breeding individuals in an idealized population
> that would have as much genetic drift as is in the actual population.
>
> Founder effect—when a small subset of a population moves to a new
> geographic region, its genetic diversity is lower than and is
> often unrepresentative of the original population. A founder effect produces
> a genetic signature similar to a bottleneck.
>
> Gene flow—transfer of genes between populations by migration of individuals
> between the populations and subsequent mating.
>
> Gene tree—a tree that shows the evolutionary relationships among a sample
> of DNA sequences.
>
> Genetic distance—a statistic that reflects some aspect of genetic variation
> between two populations, sometimes standardized by the variation found
> within them.
>
> Genetic drift—chance genetic changes in a population due to finite size.
>
> Genetic locus—a particular position in the genome.
>
> Haplotype—the presence of particular nucleotides over a stretch of DNA
> that tend to be inherited together.
>
> Isolation by distance—an equilibrium model that predicts a positive
> relationship between genetic and geographic distance. This relationship
> occurs because individuals tend to migrate short distances to find mates and
> because long-range migrations are rare.
>
> Linkage disequilibrium—deviation from a random association of the
> nucleotides present at a set of genetic loci.
>
> Microsatellite—a rapidly evolving block of DNA in which a simple DNA
> sequence is repeated multiple
> times and individuals vary in their number of repeats.
>
> Mitochondrial DNA—a short DNA molecule that is found outside of the cell
> nucleus. It traces maternal lines of descent because it is inherited only
> from the mother.
>
> Mutation-drift-equilibrium—a population is said to be at
> mutation-drift-equilibrium when a balance (equilibrium) has been reached
> between the genetic variation introduced by mutation and that lost by
> genetic drift.
>
> Negative natural selection— when natural selection acts to remove
> low-frequency novel genotypes from a population.
>
> Nuclear DNA—the bulk of an individual's DNA, which is found within the
> cell nucleus.
>
> Population subdivision or structure—a population is said to be subdivided
> or structured when it is divided into a set of local groups
> and there is nonrandom mating across groups.
>
> Population tree—a tree that shows the evolutionary relationships among a
> set of populations.
>
> Positive natural selection— when natural selection acts to
> shift low-frequency novel genotypes to high frequency or fixation within a
> population.
>
> Purifying natural selection— another term for negative natural selection.
>
> Range expansion—an increase in the geographic range occupied by a
> population or species. Range expansions are often linked with
> increases in population size.
>
> Short tandem repeat (STR)— another term for a microsatellite.
>
> Single nucleotide polymorphism (SNP)—a position in the genome where
> individuals differ with regard to which nucleotide is pre-
> sent.
>
> Stabilizing natural selection— when natural selection favors the mean
> phenotype, preventing a shift of the mean.
>
> Y-chromosome—a sex chromosome that is paired with the X chromosome in
> males, whereas females have two X chromosomes. The
> nonrecombining portion traces paternal lines of descent.
>
>

-- 
David W. Opderbeck
Associate Professor of Law
Seton Hall University Law School
Gibbons Institute of Law, Science & Technology
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