Archive for November, 2006

States of Islam

By Razib Khan | November 16, 2006 11:37 pm

“Ali Eteraz” has started a new site, States of Islam. My friend Aziz Poonawalla has a post up offering his thoughts on the Israel-Palestine conflict. I am aware of two of the headline contributors, Haroon Moghul and Thabet. Though I disagree with them, they’re both smart, so I indulge them in their error. Being a SCOOP based site I’ve set up an account and might post a diary or two flagrantly exhibiting my ridda. I hope Ali indulges me.


Example of an ecotype

By Razib Khan | November 16, 2006 11:34 am

polar.jpgFrom here: “Cronin et al. (1991) then discovered that mtDNA of brown bears is paraphyletic with respect to polar bears. That is, the mtDNA of brown bears of the Alexander Archipelago in southeastern Alaska is more closely related to the mtDNA of polar bears than it is to the mtDNA of other brown bears. Cronin et al. (1991) reported that mtDNA sequence divergence between Alexander Archipelago brown bears and polar bears is only about 1%, whereas a divergence of about 2.6% separates polar bears from brown bears occurring elsewhere…Following the discovery of Cronin et al. (1991), others corroborated the finding of paraphyletic mtDNA in brown bears and polar bears. Talbot and Shields (1996a, 1996b) suggested that the Alexander Archipelago brown bears represent descendents of ancestral stock that gave rise to polar bears.”
Caution!!! Caution!!! Appropriate consideration given to the overuse of mtDNA in phylogeography, etc. The idea is that marker phylogeny has in general reflected our gestalt perception of taxonomical relationships, but there’s a reason that people test the hypotheses.


Neandertals: Episode II

By Razib Khan | November 16, 2006 10:54 am

More Neandertal news, as promised!
John Hawks is getting so much traffic that his site is getting bogged down. Anyway, he posts on the two studies that came out on Neandertal genomic sequencing. No big news, Neandertals are very different, and there isn’t a great deal of evidence for mixing resulting in a large load of Neandertal derived genes in modern populations. RPM has more. At my other blog p-ter excises an important point:

[T]his high level of derived alleles in the Neanderthal is incompatible with the simple population split model estimated in the previous section, given split times inferred from the fossil record. This may suggest gene flow between modern humans and Neanderthals. Given that the Neanderthal X chromosome shows a higher level of divergence than the autosomes (R.E.G., unpublished observation), gene flow may have occurred predominantly from modern human males into Neanderthals. More extensive sequencing of the Neanderthal genome is necessary to address this possibility.

In related news, Afarensis and Kambiz are both approaching the problem from a more physical anthropological perspective. This being a historical science all the various angles are necessary in attaining the most crisp perception of the past as it was.
Related: Round up of this topic from last week.


Multi-regionalism vs. Ecotype Persistence

By Razib Khan | November 16, 2006 2:29 am

This comment made me aware that I should probably be more precise about how I view the “new model,” which I will provisionally label “Ecotype Persistence” (EP), as being different from Multi-regionalism in the old school. Consider two variables:
Full genome content
Phenotypically salient characters (controlled by a few selected loci)

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Human evolutionary models in pictures

By Razib Khan | November 16, 2006 1:35 am
The Out of Africa Replacement Model

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By Razib Khan | November 16, 2006 12:41 am

The Lord Our God is One! Check out my results from the Belief-O-Matic below….

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MAC vs. PC

By Razib Khan | November 15, 2006 11:34 pm

Genetic draft

By Razib Khan | November 15, 2006 10:23 pm

My next post on Gillespie’s chapter in Evolutionary Genetics: Concepts & Case Studies is going to cover “genetic draft.” I don’t know when I’ll get to it, so I’ll point to Robert Skipper’s post on the topic from six months ago. Yes, selection is proximately stochastic. Like this.


The stochasticity of genetic drift

By Razib Khan | November 15, 2006 11:00 am

I have spoken of the probability of extinction and the rate of substitution once past extinction, but now to something more prosaic, genetic drift. My post is based on John Gillespie’s treatment in Evolutionary Genetics: Concepts & Case Studies. Like R.A. Fisher he does not think much of this process in evolutionary dynamics, and deemphasizes its salience. The easiest way to think of drift is simply as sample variance over generations, the expected deviation from the mean as one moves through time. In a diallelic model the deviation between generation n and generation n + 1 is:
σ = √(pq)/(2N), where
p = allele 1
q = allele 2 (and is 1 – p)
N = population size

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Post-genomic era = socialized medicine?

By Razib Khan | November 15, 2006 2:32 am

Over at my other weblog there is a post up, Genomics and socialized health care, which asks if the new DNA era might not explode the acturial edifice that is modern health insurance in the United States. I suspect in this case many will welcome a “broken” system which needs to be replaced by a universal single-payer system, at least on the basal level. But, with privilege comes responsibilities. I suspect that the overturning the old system of health insurance, which was predicated on imperfect knowledge, will be correlated with the rise of a new system where particular values common within the society will shape the extent and relevance of genetic “screening.”


Ask a ScienceBlogger

By Razib Khan | November 15, 2006 2:12 am


What are the best pickup lines for scientists and science-savvy folk?…

I’ll go narrow-church: low mutational load baby, look beyond the proximate and focus on the ultimate.

CATEGORIZED UNDER: Ask a ScienceBlogger

The Family That Walks on All Fours – on PBS

By Razib Khan | November 14, 2006 11:31 pm

It seems that The Family That Walks on All Fours is now on NOVA. I don’t have a television so I won’t be seeing it, but some of you might catch a re-run. Years ago I remember a slogan: “If PBS doesn’t do it, who will?” Hm.


Brass Crescent Awards

By Razib Khan | November 14, 2006 9:56 pm

The Brass Crescent Awards are up again this year:


Super-tsunami 4,800 years ago?

By Razib Khan | November 14, 2006 12:19 pm

Ancient Crash, Epic Wave is a story in The New York Times about an enormous impact 4,800 years which might have had world-wide repercussions:

At the southern end of Madagascar lie four enormous wedge-shaped sediment deposits, called chevrons, that are composed of material from the ocean floor. Each covers twice the area of Manhattan with sediment as deep as the Chrysler Building is high.

The explanation is obvious to some scientists. A large asteroid or comet, the kind that could kill a quarter of the world’s population, smashed into the Indian Ocean 4,800 years ago, producing a tsunami at least 600 feet high, about 13 times as big as the one that inundated Indonesia nearly two years ago. The wave carried the huge deposits of sediment to land.

If it killed 1/4 of the world’s population, and probably a disproportionate number around the rim of the Indian Ocean, we would probably be able to see a concurrent population bottleneck, and subsequent demographic expansion, in the genetic record. The Toba Catastrophe Theory after all is predicated on population genetic signatures correlated with a volcanic explosion 75,000 years ago.


Neandertals & introgression – the past week….

By Razib Khan | November 14, 2006 10:20 am

This is more for google, but if you missed anything, you should check it out. Here is a replay of the introgression & Neandertal related posts….
Neandertal & H. sapiens sapiens interbreeding
Neandertal-“modern” mixing
Introgression related posts over the past 6 months
Main course:
Did Modern Humans Get a Brain Gene from Neandertals? (link to Lahn. et. al.)
Neandertal & humans – introgression (this has the nice graphic that people seem to think illustrates the concept pretty well)
The Neandertal child (a face to it all)
Introgression vs. gene flow (illustration of introgression and verbal exposition)
2s-a little interbreeding goes a long way (a bit more quantitative exposition of why a little interbreeding is all that’s needed)
Neanderthal introgression & microcephalin (Greg Cochran’s thoughts, he is co-author of a paper with John Hawks on this topic)
Neandertals in our midst (this is from Seed Magazine, and probably the most thorough of the popular press pieces)
Your Great * 1800 Grandmother Was a Neanderthal
The following are posts by John Hawks
Neandertal introgression, anatomically
Neandertal introgression, genetic
Introgression and microcephalin FAQ
Why introgression
What about species?


Scientific American link round up on Bruce Lahn

By Razib Khan | November 14, 2006 1:39 am

Scientific American has a nice link round up on l’affaire Lahn & Neandertals.


PLOS redesign

By Razib Khan | November 14, 2006 1:14 am

PLOS Biology and PLOS Genetics have a slick brand new look. Go check ’em out!


The Netherlands & Islam

By Razib Khan | November 13, 2006 11:27 pm

Aziz points me to this article over at alt.muslim which reviews Murder in Amsterdam by Ian Buruma. It is a fair review, but this caught my attention:

…Buruma’s parallelisation of the careers of both Fortuyn and Van Gogh and their capitalisation on Islamophobia begs the question of how the Enlightenment virtues of freedom and reason could have been politically perverted to justify hatred for a racial underclass. This crucial question, posed repeatedly, if not directly, by Buruma through his coinage of the term “Enlightenment fundamentalist” represents the most intellectually fascinating aspect of the book.

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Species and introgression

By Razib Khan | November 11, 2006 5:41 pm

John Hawks has a long post on introgression in the context of the Species Concept problem.


Spirituality among American ethnic groups

By Razib Khan | November 11, 2006 12:18 pm

The Inductivist cranked the GSS to figure which American ethnic groups are spiritual and which are not, and this is what he found:
Spirituality Ethnic Group
1.92 East Asians
2.78 Scandanavians
2.8 Italians
2.9 Irish
2.9 Germans
2.91 Mexicans
2.95 English/Welsh
3.12 American Indians
3.26 Blacks
3.29 Scots


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