Archive for October, 2006

I endorse Shelly Batts for the blog scholarship

By Razib Khan | October 31, 2006 6:08 pm

Vote early and vote often for Shelley Batts. Shelley makes her pitch here. Shelley is a hard working graduate student with moral fiber.
Q: Is it permissable for believers to aid a kuffar in amassing riches?
A: It is permissable if the kuffar adds to the body of knowledge so that the believers may benefit. The prophet Muhammad, P.B.U.H., said, “Seek knowledge even unto Michigan.”


Introgression redux

By Razib Khan | October 31, 2006 10:35 am

I was going to continue with my review of chapter 5 of Evolutionary Genetics: Concepts & Case Studies today, but time does not permit. This section was to focus on the orgination of advantageous mutations from the stochastic cauldron of generation 1 (which, as we’ve seen exhibits a 1/3 probability of immediate extinction in th subsequent generation assuming Poisson distribution of reproductive variance and fixed population size), so I will point to my older posts on introgression (of advantageous alleles):
The baby model
My fixations
Archaic-modern hybridization
Introgression in wolves & dogs
Introgression related papers
Bumping uglies with the Neandertal
These will come in handy in the near future because papers are pending which make the general conceptual framework extremely relevant.


Promiscuous Girl

By Razib Khan | October 30, 2006 11:32 pm

O believers!
If kuffar flesh is beauteous it is permissable for the faithful to partake of it without nikah….

Q: Is a beauteous kuffar female permissable or unclean?
A: Lo! A beauteous kuffar female is both permissable and unclean! If the kuffar women entreat the believers, let it be known that that the faithful are commanded to hit them hard and hit them often so long as the believers are sufficiently freaky! As the kuffar woman is unclean let it be stated that it is enjoined upon the believers that they wash themselves thoroughly and redouble their salat.
-Ibn Hanbal


John Derbyshire "leaves" Christianity

By Razib Khan | October 30, 2006 3:04 pm

My friend John Derbyshire chronicles his spiritual devolution over the past few years….


A resolution to the molecular clock debates?

By Razib Khan | October 30, 2006 10:05 am

Heterogeneous Genomic Molecular Clocks in Primates:

The rate at which mutations accumulate in a genome, referred as a “molecular clock,” is an instrumental tool in molecular evolution and phylogenetics. Different types of mutations occur via distinctive molecular pathways. In particular, while most mutations occur from errors in DNA replication, spontaneous deamination of methylated CpG dinucleotides is another important source of mutation in mammalian genomes. Molecular clock studies typically combined all types of mutations together. In this paper, the authors analyze molecular clocks of replication-origin and methylation-origin mutations separately. By utilizing high-quality sequence data from several primate species and fossil calibration, the authors demonstrate that the two types of mutations follow statistically different molecular clocks. Methylation-origin mutations accumulate relatively constantly over time, while replication-origin mutations scale with generation-times. Therefore, the genomic molecular clock, as a whole, is shaped by the molecular origins of mutations that have accumulated over time. The authors’ results have direct implications on phylogenetic analyses, estimation of species divergence dates, and studies of the mechanisms and processes of evolution, where molecular clocks are imperative.

I really don’t have much to add, their own summary covers all the bases. Molecular clocks are critical in reconstructing phylogenies, and in human evolution their utility is so great that they have arguably revolutionized paleoanthropology. Obviously the great “rate debate” within phylogenetics matters here, as a million years here and there is essential in framing and generating hypotheses about the environment in which our hominid ancestors evolved and speciated.


You only go extinct once….

By Razib Khan | October 29, 2006 2:51 am

Assume that you have a new mutation, totally novel. What’s its probability of going extinct in one generation? That is, it doesn’t get passed on….
Consider, you have a population of N individuals. Fix the population size across nonoverlapping generations. So, in generation t you have N individuals and in t + 1 you have N individuals. In the first generation of the mutation the proportion in the population is 1/N, that is, there is one mutant amongst N individuals (ergo, N – 1 other copies). The probability that the mutant is never “drawn” (copied) to the next generation in this fixed population is (1 – 1/N)N. 1 – 1/N represents the non-mutants, and there are N draws since the population across generations is fixed. For example, if there are 100 individuals (haploid) and 99 are non-mutants, and the next generation will also have 100 individuals, there are 100 opportunities for the 99 out of 100 instead of the 1 out of 100 to be drawn, i.e., (1 – 0.01)100.
This equation converges upon ~ 0.37 as N approaches ∞. Here are some values generated for a given N:
10 → 0.34867844
100 → 0.366032341
1000 → 0.367695425
10000 → 0.367861046

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True unbeliever

By Razib Khan | October 29, 2006 1:23 am

The Washington Post has a fun profile of Sam Harris. This part cracked me up:

“If the Koran were exactly the same,” he said, toward the end of the night, “and there were just one line added to it, and the line said, ‘If you see a red-haired woman on your lawn at sunset, kill her,’ I can tell you what kind of world we’d live in. We’d live in a world where red-haired women would be killed often. We’d live in a world where people like yourself” — and here Harris gestures to his opponent, Oliver McTernan — “would say, ‘That’s not the true Islam.’ Twenty women in Baghdad would have their heads cut off and someone would come forward and say, ‘This has nothing to do with Islam. Some of them were strawberry blond. Some of them were strangled.”

sam_harris_200.jpgLater on religious scholars chide Harris for his simplistic reading of religion. The bloggers are Get Religion dismiss Harris’ arguments as shallow. If by “shallow” they mean that Harris takes religion at its word and interprets its own axioms in a straightforward and guileless manner, then shallow he is. Once I was talking to an evangelical Christian who was attempting to convince me of the power of prophecy in the New Testament. I pointed out that Jesus himself said, “Verily I say unto you, This generation shall not pass, till all these things [the wonders of the Second Coming] be fulfilled.” To this my friend responded, “Ah, but you see, generation means the Jewish people in this context! And the Jewish people remain, so of course Christ has not returned.” And there you have it, my understanding was “shallow” and superficial, a closer look at scripture and religious practice fleshes out the nuance and richness.

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Ask a ScienceBlogger – Underfunded?

By Razib Khan | October 28, 2006 4:32 am

This week’s Ask a ScienceBlogger:

What’s the most underfunded scientific field that shouldn’t be underfunded?…

I’ll say old fashioned biological anthropology. There’s a reason that a pall was cast over thsi field after World War II, but we need to start pushing an analysis of man the animal on all levels again, as the post-genomic era is starting with an explosion centered on the most important animal of all, and the moment is ripe for the re-emergence of complementary fields.


Godless professors?

By Razib Khan | October 28, 2006 3:44 am

There is a working paper out which reports on the nature of the religiousness of the professoriate. Some data of interest….
* Proportion of professors with “No religion” – 31% (vs. ~10% for the general public)
“I don’t believe in God” – 10% (vs. 2.8% for the general public)
“I don’t know whether there is a God, and I don’t believe there is a way to find out” – 13.4% (vs. 4.1% for the general public)
“I don’t believe in a personal God, but I do believe in a Higher Power of some kind” – 19.6%
“I find myself believing in God some of the time, but not at others” – 4.4%
“While I have my doubts, I feel that I do believe in God” – 16.9%
“I know God really exists and I have no doubts about it” – 35.7%

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By Razib Khan | October 27, 2006 12:41 pm

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Ivory & ebony, twins again…and again…

By Razib Khan | October 27, 2006 10:05 am

twinsagain.jpgI noticed today that I was receiving a lot of search engine queries for black and white twins. Well, I have posted on it several times, but I thought it was a bit much, so I checked the news, and lo & behold, another case just popped up. Like the Australian twins the mother here was biracial (Nigerian and English) while the father was white (in contrast to the earlier British case where the parents were both biracial). I’m sure you’re getting tired of this, but I have to comment when I see headlines this: Mum defies million-to-one odds to give birth to black and white boys. I’ve posted on it, and the odds in this particular case are not “a million to one,” and since you’ve had three recent cases in the public eye within the past 6 months you would figure that we would re-evalute our priors here in regards to the expectation of probability.
But in any case, I did think it was worth posting on this specifically because this pair of “black” and white twins were male and not female.1 What if they mated??? Let’s focus on skin color here, since that is what people are focusing on:
Dark + Light = ?
Dark + Dark = ?
Light + Light = ?

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Decomposition of the RNC Harold Ford Jr. ad

By Razib Khan | October 26, 2006 10:58 pm

Check the comments interspersed….


Genetics of hair color

By Razib Khan | October 26, 2006 10:51 am

blondeblack-725852.jpgA reader emailed me asking about the genetics of hair color. Since I’ve discussed the topic before I simply pointed them to the query of the topic on my other blog. But, I thought it might be good to directly answer two specific questions:
Why do many people have much lighter hair during childhood?
The same reason that European babies are often with blue eyes or dark skinned babies are born with light skin, we get darker as we age (with the partial exception of females during puberty). The darkening of hair is simply a symptom of a general trend toward increased melanin as we age (or as women go through pregnancies). Proximately in an individual’s life history it probably has hormonal upstream causes, e.g., the increased level of testosterone vs. estrogen levels in females after menopause (and pregnancies), or the elevation testosterone in males after puberty. Our ancestral state was probably “pink,” but after we lost our fur humans developed dark skin (a “consensus sequence” is found among tropical peoples). Light skinned peoples are a response to the relaxation of this particular selection pressure, but the darkness is something that we develop (some of us more than others) over our lifetime as genes express proteins which lead to the phenotype.
Also discuss the dependency and independency between hair and eye color, and hair and skin color.

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Religion, good and bad and all that

By Razib Khan | October 26, 2006 1:05 am

John Wilkins has a good post on religion, I tend to agree with its general thrust though I might quibble with details. Not being gifted with much marginal time right now, a few quick thoughts:
1) I believe that institutional organized religion, e.g., Christianity, Islam, etc., can increase the magnitude of a social vector, but has little influence on its direction. For example in relation to slavery religion was a force for inflaming both abolitionist enthusiasm and justifying the holding of other humans in bondage. Religion doesn’t do good or evil, humans do, religion is simply a ‘virus of the mind’ which hitch-hikes and surfs on cultural waves.
2) There is a distinction between basal religion, psychological propensities toward supernatural belief, and formalized systematic “higher religions” which exist on top of the basal layer and channel sociological dynamics and psychological biases toward the perpetuation of their particular “meme-complexes” (i.e., higher religions are constrained toward being cognitively optimal).
Second, Chad has two posts on The God Delusion. In reality Chad was commenting on this review in The New York Times. I was also pointed to this thrashing of Dawkins’ book. A few points:

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John Maynard Smith

By Razib Khan | October 25, 2006 11:51 am

One of the things I regret during my tenure blogging is that I started doing “10 questions” too late to get in touch with John Maynard Smith. If you haven’t, I highly recommend this interview by Robert Wright from a few years ago. Also, Smith wrote one of the more readable introductory texts on Evolutionary Genetics, as well as pioneering the use of game theory in evolutionary biology, introducing the concept of the ESS.


Four Stone Hearth

By Razib Khan | October 25, 2006 2:44 am

Four Stone Hearth, the Anthropology Carnival, starts at today.


Vedic Creationism

By Razib Khan | October 24, 2006 11:11 pm

US author offers ‘Vedic alternative’ to evolution theory:

Offering a “Vedic alternative” to Darwin’s Theory of Evolution, an American author has claimed that human beings devolved from the “realm of pure consciousness”, as testified by archaeological evidence discovered over the past 150 years.
We did not evolve up from matter. Instead, we devolved, or came down, from the realm of pure consciousness, spirit,” author Michael A Cremo, said, citing many archaeological, psychological and genetic examples.

I have stated before that Creationism might be most prominent in American fundamentalist Christianity, but it is not limited to it. The reality is that I suspect that a “Creationist” bent is the default human mode, ready to kick in sans science. Note that this “theorist” uses similar talking points to convential Christian Creationists, replace “matter” with “monkeys,” and instead of coming down from a “realm of spirit” we are endowed with souls.


Blue eyed devil!

By Razib Khan | October 24, 2006 11:35 am

Note: Download file here (it has more precise percentages on blue eyes in Norway, someone could try their hand at some game theoretic modeling if they were inclined, I lack the time right now).
Ruchira Paul brought this article to my attention:

Before you request a paternity test, spend a few minutes looking at your child’s eye color. It may just give you the answer you’re looking for…Their studies…show that blue-eyed men find blue-eyed women more attractive than brown-eyed women. According to the researchers, it is because there could be an unconscious male adaptation for the detection of paternity, based on eye color.
Both blue-eyed and brown-eyed women showed no difference in their preferences for male models of either eye color. Similarly, brown-eyed men showed no preference for either blue-eyed or brown-eyed female models. However, blue-eyed men rated blue-eyed female models as more attractive than brown-eyed models.

First, it is debatable whether a single locus Mendelian model of one biallelic gene is appropriate for eye color (see this review [PDF], or this introduction). Though it does seem that the majority of the population level variance in eye color is due to OCA2, there is a residual and non-trivial affect from other loci, some of which act independently. This is obviously clear insofar as blue and brown eye colors are typologies which compress a range of shades which span greens and hazels, the latter of which reflect quantitative variation in melanin within the iris. The short of it is that it is genetically possible without mutation for two blue eyed parents to have brown eyed offspring, and there is quantitative variance between siblings in many families in regards to eye color because more than one locus is at work here.
That being said, there is a difference between skin color and eye color in that the latter is dominated by one locus which seems to be responsible for 0.7 – 0.8 of the variance across populations, so as a first approximation one may hold to a simple Mendelian model without too much distortion of the nature of the system. So, from this moment on I will neglect the reality that the inheritance of eye color is not as simple as the authors of the paper seem to present it, and look at some other issues. The authors use the one-locus Mendelian model to posit that the recessive character of blue eyes serve as paternity confidence markers. Fair enough. But there is a problem with this narrative: large swaths of Europe have very low frequencies of individuals with dark eyes. In other words, the potential lovers are likely to have blue eyes as well, making this trait useless as a distinctive marker! Consider a population where 90% of the individuals have blue eyes (e.g., Estonia or Finland might be good candidates). Assume a Hardy-Weinberg system, so

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Brains are expensive

By Razib Khan | October 24, 2006 3:38 am

One of the many hypotheses in palaeoanthropology is homonids shifted to meat eating because it was metabolically rich and allowed the increase in our brain sizes. Well, there might now be some support from primate analogs finally, Study suggests evolutionary link between diet, brain size in orangutans:

In a study of orangutans living on the Indonesian islands of Borneo and Sumatra, scientists from Duke University and the University of Zurich have found what they say is the first demonstration in primates of an evolutionary connection between available food supplies and brain size.
Based on their comparative study, the scientists say orangutans confined to part of Borneo where food supplies are frequently depleted may have evolved through the process of natural selection comparatively smaller brains than orangs inhabiting the more bounteous Sumatra.

cranial.jpgI’m sure by now you’ve seen Nick Matzke’s chart of fossil hominid cranial capacities. Between 3 million and 200,000 years BP there was consistent long term growth in our brains (with a few possible spurts within the general trend). Brain genes have also been selected for. 25% of our caloric intake is reserved just for our expensive grey and white matter, so not only do we service it, it better serve us!


"Black" & white twins again

By Razib Khan | October 22, 2006 2:05 pm

twins.jpgHsien-Hsien Lei points me to another story about black and white twins. First, the “black” twin is clearly mixed race, her skin color is between the modal complexion of Europeans and sub-Saharan Africans on the von Luschan scale. The “white” twin on the other hand does seem to exhibit the color of someone of European descent. What’s going on here? This is somewhat different than the other case of black and white twins, in that case both parents were mixed-race, in this case the father is white (German) and the mother is mixed-race (Jamaican & English). The two cases are different even though the outcome is pretty much the same in appearence, which goes to show that there are many ways to skin the cat.

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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