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.”

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
Intogression^-1
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.

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

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

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.

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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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.”

Later 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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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.

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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I 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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Check the comments interspersed….

A 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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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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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.