Archive for November, 2007


By Razib Khan | November 30, 2007 12:56 pm

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Mixed-race but homogeneous appearance?

By Razib Khan | November 26, 2007 8:19 am

tiger-woods-picture-1.jpgSeveral years ago Oprah Winfrey asked Tiger Woods what he would say to people who say that when they look him they see a black man. The issue was that some African Americans objected to Woods’ contention that he was multiracial, Cablinasian, which reflected the fact that he was ancestrally 1/2 Asian, 1/4 African, 1/8 European and 1/8 Native American. Woods is also a Therevada Buddhist by religion, taking after his Thai nationality (though mixed-race) mother, so one can argue he is quite Asian culturally. I know many people who frankly disagree with Winfrey’s assessment, that is, that Woods looks “like a black man.” Some Asian Americans have stated that “from the eyes down” he looks Asian, and frankly I can see that. Tiger Woods’ hair reflects his mixed ancestry, and it is neither straight nor kinky, but curly (he cuts it short enough that this doesn’t manifest normally, but I know people who played golf with him when he was a teenager and they attest to this). Some of my friends in college who were Asian American activists quite loudly would proclaim that Tiger Woods “looks Asian” when the topic came up.
Does Tiger Woods look Asian? Does he look like a “black man”? I am posting on this because of some responses below which asked how it was that mixed-race children can so favor one race. But to start out with I need to offer that perceptions of race are as much a matter of psychology and culture as they are of genetics. I bring up Tiger Woods because black Americans and Asian Americans might have radically different viewpoints about what race he looks like, showing that where you start from shapes where you end up at.

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The Islamic race

By Razib Khan | November 26, 2007 5:10 am

Ali Eteraz has an article titled Mistaken identity in The Guardian which is a long rambling reflection on Islamic identity, and specifically his Islamic identity. He is somewhat confused by the conflation of Islam with a quasi-ethnic identity.

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This is faith!

By Razib Khan | November 26, 2007 3:42 am

Rock of Ages, Ages of Rock:

. To the young-earth creationists, this is both unscientific and dubiously religious. “We don’t subscribe to this idea of the ‘God of gaps,’ meaning if you can’t explain something, then blame God,” Whitmore told me before describing a method that hardly seemed more scientific. “Instead, we think: ‘Here’s what the Bible says. Now let’s go to the rocks and see if we find the evidence for it.’ ”

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Evolution: What the Fossils Say and Why It Matters

By Razib Khan | November 25, 2007 11:10 pm

evolutionwhatfossils.jpgEvolution: What the Fossils Say and Why It Matters is an expansive new book authored by vertebrate paleontologist Donald Prothero and lushly illustrated by Carl Buell. The quality of the plates and illustrations, the binding as well as the texture of the pages, screams out “Coffee Table Book.” That’s not an insult, but it just reinforces that this isn’t a monograph aimed at specialists, rather, it is in large part a manifesto aimed toward the general public. And its high production quality testifies to the fact that it wants to be taken seriously by marrying style with substance.
Though the subtitle places the emphasis on fossils, Prothero covers a lot of ground early on in the book which examines evolution from various angles outside of his core field of expertise. There is a quick overview of the ideas of evolution before Charles Darwin, as well as the necessary geological context which made an evolutionary model of biology plausible. Biogeography, Mendelian genetics and molecular biology are all brought into the discussion and shown to converge upon the validity of evolutionary theory and its assumptions of common descent with modification. Additionally, the book also tackles the topic of abiogenesis, since it often gets thrown in with the arguments about the validity of evolutionary theory by Creationists and other assorted skeptics. The number of topics which the author addresses before moving onto the paleontological meat of the book is rather mind-boggling, and the economy of the prose is impressive.

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Kindling the future

By Razib Khan | November 24, 2007 2:43 am

kindlephoto.jpgThe Future of Reading:

All these ideas are anathema to traditionalists. In May 2006, novelist John Updike, appalled at reading Kelly’s article (“a pretty grisly scenario”), decided to speak for them. Addressing a convention of booksellers, he cited “the printed, bound and paid-for book” as an ideal, and worried that book readers and writers were “approaching the condition of holdouts, surly hermits who refuse to come out and play in the electric sunshine of the post-Gutenberg village.” (Actually, studies show that heavy Internet users read many more books than do those not on the Net.) He declared that the “edges” of the traditional book should not be breached. In his view, the stiff boards that bound the pages were not just covers but ramparts, and like-minded people should “defend the fort.”

Jeremiads such as Updike’s are pretty amusing after you read a book like Ancient Literacy, which notes the suspicion that many traditionalists had toward literacy due to its presumed encouragement of intellectual laziness. And of course there have been presentation revolutions in the past, the introduction of the papyrus scroll and its eventual replacement by the codex. Perhaps those of who love books should remember that it’s the content which matters in the end. The onerous distribution restrictions upon that content are probably the main issues that many of us are going to have with the Kindle, not some mystical attachment to paper and ink.



By Razib Khan | November 23, 2007 11:17 pm

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Firefox 3.0 beta

By Razib Khan | November 23, 2007 12:45 am

I downloaded and installed Firefox 3.0 beta. It might have some bugs, but it resolved all the problems I’d been having earlier with Firefox crashing in gmail.


Happy Thanksgiving!

By Razib Khan | November 22, 2007 5:26 am

Just wishing readers who live in the USA a good holiday.


More genes please!

By Razib Khan | November 21, 2007 4:00 am

Targeted discovery of novel human exons by comparative genomics:

Here we describe a genome-wide effort, carried out as part of the Mammalian Gene Collection (MGC) project, to identify human genes not yet in the gene catalogs. Our approach was to produce gene predictions by algorithms that rely on comparative sequence data but do not require direct cDNA evidence, then to test predicted novel genes by RT-PCR. We have identified 734 novel gene fragments (NGFs) containing 2188 exons with, at most, weak prior cDNA support. These NGFs correspond to an estimated 563 distinct genes, of which >160 are completely absent from the major gene catalogs, while hundreds of others represent significant extensions of known genes. The NGFs appear to be predominantly protein-coding genes rather than noncoding RNAs, unlike novel transcribed sequences identified by technologies such as tiling arrays and CAGE. They tend to be expressed at low levels and in a tissue-specific manner, and they are enriched for roles in motor activity, cell adhesion, connective tissue, and central nervous system development. Our results demonstrate that many important genes and gene fragments have been missed by traditional approaches to gene discovery but can be identified by their evolutionary signatures using comparative sequence data. However, they suggest that hundreds–not thousands–of protein-coding genes are completely missing from the current gene catalogs.

ScienceDaily makes it intelligible.


Brown out!

By Razib Khan | November 20, 2007 4:37 am

IMG_2953.jpgThe most common emails I receive are about hair and eye color, and of these the most frequent source seems to be from individuals in interracial relationships. Quite often they are curious as to the possible outcome of their offspring’s phenotype. Sometimes they wonder why their offspring looks the way he or she does. On one disturbing occasion someone was appealing to me to clear up the suspicion of non-paternity because of the unexpected outcome of the offspring’s appearance! Today I received this email:

I have a 19 month old son who is very light skinned, blond hair and blue eyes. My husband (American) is bi-racial. His mother is white and his father is black.
Myself (German), I’m white, same with both of my parents and grandparents. I’m a redhead with greenish brown eyes, my husband has black hair and brown eyes.
What are the odds for this to happen, for us to have a white baby with blond hair and blue eyes?

This question is very common: why does my baby look so white? Succinctly the child’s ancestors are mostly white (American blacks are on average 20% white, so it is likely that the child is more than 75% European in terms of recent ancestors). I’ve offered more detailed expositions on black white twin pairs. The underlying logic is that genetics is discrete, not blending. This is the the insight and power which Mendelian principles introduced to our understanding of evolutionary process. All that being said the above posts and these sorts of jargon-laden assertions really don’t mean much to many people. So I’m going to answer the email above in some more detail below.

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The genomic future is almost here?

By Razib Khan | November 19, 2007 1:35 am

Technology dramatically speeds gene mapping. A short little piece which repeats the standard mantras; faster, cheaper and better. The Human Genome Project was proof of principle. Right now, with all the stuff that is starting to bubble up around personal genomics it looks like we’re at a technological and social point of no return, the second derivative is positive, the the rate of change is increasing. Hsien-Hsien is going to have to start getting a bit more selective about what she blogs about since the sample space of upon which the commentary is based will start to rapidly increase in size.
Though I do have to say stuff like this gets a bit old:

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Sidr hearsay blogging

By Razib Khan | November 19, 2007 12:27 am

Just talked to my mother today and she phoned relatives in Dhaka. Everything is OK, electricity is coming back online. She seemed dismissive of the idea when I asked if it was all well in the rural areas where some of my distant relatives live; it wasn’t that big of a deal. On the other hand a cousin married a man whose family is from Barisal. Her husband went to check out the situation (family has estates and properties around the Sundbarbans) which was in the path of the storm, and it wasn’t as pretty there as everything had been blasted away and tossed around. The main aim of my call was that I wanted to know if I should send money to dispossessed relatives, and my mother stated there was really no one to send money to. So to the Red Cross it goes.


Glimpse of the future?

By Razib Khan | November 18, 2007 3:01 am

My Genome, Myself: Seeking Clues in DNA:

For as little as $1,000 and a saliva sample, customers will be able to learn what is known so far about how the billions of bits in their biological code shape who they are. Three companies have already announced plans to market such services, one yesterday.
Offered the chance to be among the early testers, I agreed, but not without reservations. What if I learned I was likely to die young? Or that I might have passed on a rogue gene to my daughter? And more pragmatically, what if an insurance company or an employer used such information against me in the future?
But three weeks later, I was already somewhat addicted to the daily communion with my genes. (Recurring note to self: was this addiction genetic?)

Update: Hsien-Hsien Lei has much more.


Sidr update

By Razib Khan | November 18, 2007 2:05 am

Update: OK, not to be morbid, but the confirmed death tolls is now greater than 3,000, and there is a tentative projected death toll on the order of 10,000. That’s in line with my comments below. End Update
The death toll is pushing 2,000. I think I might be safe in saying that the fatalities are going to be one order of magnitude lower than the 1991 and 1970 typhoons. Chris Mooney considers whether Sidr was as bad as hurricane Mitch in 1998. Mitch caused 11,000 fatalities. Sidr might cause as many. But the combined population for Nicaragua and Honduras is about 13 million today (one assumes it was a bit smaller back then). The population of Bangladesh today is in the range of 150 million. In 1970 East Pakistan (what became Bangladesh) had less than half the population of Bangladesh today, so that puts the fatality contrast in some perspective as well. The numbers here lead me to suggest that the impact of Mitch in relative terms was more comparable to the typhoons of ’91 or ’70 which hit Bangladesh rather than Sidr. Some of this might be chalked up to better preparedness, though much of it surely has to be that Sidr made landfall in a relatively underpopulated region, the Sundarbans. It might have been a different story if the bull’s-eye had been on the mouth of the Meghna, one of the most densely populated regions of country (which combines the flow of the Ganges and Brahmaputra as well as several other local rivers).
Here’s a donation page for the International Red Cross/Crescent.


Questioning the breastfeeding & IQ link

By Razib Khan | November 18, 2007 12:39 am

A few weeks ago I reported some research that seemed to show a relationship between a gain in IQ due to breastfeeding and a particular genetic variant. Looks like I spoke too soon. p-ter has the goods:

The fact that they have a measure of maternal IQ but don’t directly include it in the published multiple regression suggests that they tried it, but didn’t like the results. They didn’t include parental phenotype in any of their previous studies, but there, at least, there was some functional evidence linking the polymorphism and the phenotype. Here, there’s nothing. Considering the fact mentioned in a previous post that other researchers find absolutely no evidence for link between IQ and breastfeeding (the entire basis for this study), this has to be classified as highly questionable. And regardless of the veracity of any gene-environment interactions here, the huge effects of breastfeeding on IQ shown by the authors are clearly artefacts of the heritability of IQ, and it’s unfortunate that they are being propagated.

This is the classic problem that Judith Rich Harris points on in her work, many researchers just don’t control for the correlation between parents and offspring genetically.


The evolving male

By Razib Khan | November 16, 2007 10:05 am

Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster:

Sexual selection drives faster evolution in males. The X chromosome is potentially an important target for sexual selection, because hemizygosity in males permits accumulation of alleles, causing tradeoffs in fitness between sexes. Hemizygosity of the X could cause fundamentally different modes of inheritance between the sexes, with more additive variation in males and more nonadditive variation in females. Indeed, we find that genetic variation for the transcriptome is primarily additive in males but nonadditive in females. As expected, these differences are more pronounced on the X chromosome than the autosomes, but autosomal loci are also affected, possibly because of X-linked transcription factors. These differences may be of evolutionary significance because additive variation responds quickly to selection, whereas nonadditive genetic variation does not. Thus, hemizygosity of the X may underlie much of the faster male evolution of the transcriptome and potentially other phenotypes. Consistent with this prediction, genes that are additive in males and nonadditive in females are overrepresented among genes responding to selection for increased mating speed.

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By Razib Khan | November 16, 2007 3:36 am

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Is Sidr a sign of progress?

By Razib Khan | November 16, 2007 2:39 am

It’s almost Friday here in the United States. The latest update I can find is that 200 people have died due to typhoon Sidr. These are almost certainly “early returns,” and the numbers will keep going up. Like pre-modern battles most of the fatalities won’t be directly due to the cyclone. Social disturbances, and likely outbreaks of disease (cholera) are going to take their their toll. That being said, at this point I think it is important to have a sense of perspective. A cyclone in 1991 killed 138,000 people and left 10 million homeless (I heard from relatives who told of how they had to set up shelters on their roofs and boil water for months). The 1970 cyclone was even worse, some estimates say that 500,000 people were killed (though a more usual number is around 300,000). In non-cyclone related natural disasters, a 1974 famine resulted in 26,000 deaths. The Bengal famine of 1943 left 1.5-3 million dead in its wake. Though a 1770 famine wiped out 1/3 of the region’s population.
I repeat this litany to offer optimistic note: things are getting better! Bangladesh is a depressing kleptocracy, but it muddles along, and the arrow of progress is in a positive direction. There was a definite improvement in public facilities & transportation networks between 1990 and 2004, the two times I’ve been back. A proliferation of NGOs means that some of my cousins are now opting to stay home instead of looking for jobs with multinational corporations abroad or relocating for decades to the Persian Gulf. And, it is a good thing when my uncle complains that he had to drive 100 miles out into the country to find an appropriate servant for his family (most of the socioeconomic stratum which would have satisfied this niche is now being absorbed by the textile industry).
I’m hoping I won’t have to change the tone of this post with an update when I get up tomorrow morning. As usual, check in on Rezwanul & Intersection for updates.
Update: 600 dead. Rezwanul has a post up very similar to mine.


Radio Open Source almost back?

By Razib Khan | November 15, 2007 1:46 am

Read about it.


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