Gene Expression

The neuroscience prosopagnosia

Sun, 30 Nov 2008 22:23:27 -0500

A few years ago I blogged about prosopagnosia, "face blindness." Nature Neuroscience now has a new paper finding some correlates with brain architecture, Reduced structural connectivity in ventral visual cortex in congenital prosopagnosia:

Using diffusion tensor imaging and tractography, we found that a disruption in structural connectivity in ventral occipito-temporal cortex may be the neurobiological basis for the lifelong impairment in face recognition that is experienced by individuals who suffer from congenital prosopagnosia. Our findings suggest that white-matter fibers in ventral occipito-temporal cortex support the integrated function of a distributed cortical network that subserves normal face processing.

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Racial hygiene 2008?

Sun, 30 Nov 2008 19:11:03 -0500

FuturePundit points me to a research paper, Impact of a new national screening policy for Down's syndrome in Denmark: population based cohort study:

Results The number of infants born with Down's syndrome decreased from 55-65 per year during 2000-4 to 31 in 2005 and 32 in 2006. The total number of chorionic villus samplings and amniocenteses carried out decreased from 7524 in 2000 to 3510 in 2006. The detection rate in the screened population in 2005 was 86% (95% confidence interval 79% to 92%) and in 2006 was 93% (87% to 97%). The corresponding false positive rates were 3.9% (3.7% to 4.1%) and 3.3% (3.1% to 3.4%).

Conclusion The introduction of a combined risk assessment during the first trimester at a national level in Denmark halved the number of infants born with Down's syndrome. The strategy also resulted in a sharp decline in the number of chorionic villus samplings and amniocenteses carried out, even before full implementation of the policy.

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ACTN3 sports gene test is a con!

Sun, 30 Nov 2008 13:03:27 -0500

I was waiting for Dan MacArthur to comment on the "ACTN3 sports gene" story because I knew he had done research on this very locus. As usual, he's rather diplomatic, with a post titled The ACTN3 sports gene test: what can it really tell you?. He says:

Kevin Fischer has already noted that from a pure cost-benefit point of view the ATLAS test doesn't compete with the offerings of personal genomics companies. ATLAS will charge you $150 for testing ACTN3; for just $250 more, you get genetic information pertaining to more than 90 different conditions and traits from 23andMe. Neither test is likely to change your life (the predictive power of most current genetic tests using common markers is extremely low), but if you're interested enough in recreational genetics to fork out for an ACTN3 test you might as well spend a little extra to get information on a bunch of other traits at the same time.

Remember those astrology infomercials on TV? "For entertainment purposes only!" Over the next few years many firms will piggy-back on the cultural prestige of science to make a quick buck. It seems the banal CW that new technology is oversold in the short term but underappreciated over the long term applies here. The new applied genetics (i.e., "personal genomics) will be seamlessly integrated into our lives in 10-20 years, but right now there's not much value-add for purchasing kits which tell people that they are European or have blue eyes.

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What's new in life science research?

Tue, 25 Nov 2008 21:09:43 -0500

If the title piques your interest, check out a new ScienceBlog of that name. The contributors are familiar faces....

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The Secular Right & prayers for H. L. Mencken.

Tue, 25 Nov 2008 10:29:58 -0500

Since the Right is roiling with faction, I thought I'd point you to a new weblog, Secular Right. No need to explain what it's about, the title says it all. John Derbyshire recounts an interesting experience at the H. L. Mencken Club:

Well, so there I was sitting down to dinner on the first evening of this Menckenfest. Seeing a plate of salad in front of me, I applied some condiments and started eating. In between the second and third mouthfuls I heard an amplified voice coming from the speakers' tables: "All right, everybody, we shall now say Grace. Bless us O Lord and these thy gifts ..." I felt as if I'd been caught picking my nose on live TV.

Somewhat later I got into conversation with the lady who had given out the Grace. She was very charming and friendly, and had been instrumental in getting the conference organized, so is obviously very capable. It emerged, however, in the course of our conversation, that she is a Young Earth Creationist!

In case you don't know, H. L. Mencken was the basis for the skeptical reporter in Inherit the Wind. Aside from being an infamous atheist, Mencken was also a lion of the Old Right, explaining the fondness many conservatives have for him today.

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Woolly Mammoth best left dead?

Mon, 24 Nov 2008 00:24:16 -0500

An editorial in The New York Times, Bring Back the Woolly Mammoth?:

No one is quite sure why the woolly mammoths died out toward the end of the last ice age, some 10,000 years ago. Theories include warmer temperatures that gradually displaced the plants on which they fed, overhunting by primitive man, an accumulation of harmful genetic mutations, widespread disease, or an asteroid or comet colliding with Earth and disrupting the climate.

If scientists do bring back a few mammoths, we suspect our warming world won't look any more hospitable than the one that did them in.

A meta-point here is that it's great that the chattering classes devote time to scientific issues; we're on the cusp of the age of applied biology. But a question I have is the presupposition that a warmer world would be inimical to the existence of the mammoth. After all, there is tundra, and there is glacier. It seems that some tundra would remain as the glacier retreated, following its march..

But I also decided to figure out when Woolly Mammoths speciated. From what I can tell it seems that they diverged from the Steppe Mammoth about 150,000 years ago. Fossil people can clarify or correct. I was curious about this fact because of this chart:

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Andrew Gelman on Bloggingheads.tv

Sun, 23 Nov 2008 04:26:38 -0500

Andrew Gelman has commented on his interview performance....

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Similarities & differences: American Indians & Real Indians

Sat, 22 Nov 2008 13:46:08 -0500

After reading American Colonies: The Settling of North America, I was struck by the incredible similarities in British modus operandi in North America and India the 17th and 18th centuries. These two imperial domains seem very different, but recall that Lord Cornwallis plays a prominent role in both Colonial and Indian history. This was a world-wide empire, the French and Indian War in North America was just a piece of the broader Seven Years' War, which also played out in India.

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Myers-Briggs & this blog

Sat, 22 Nov 2008 00:04:21 -0500

The Elf pointed me to Typealyzer where it supposedly analyzes the personality of the weblog. Well, this blog is....

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Opinions on evolution, intelligence & religion

Fri, 21 Nov 2008 21:24:34 -0500

In my post yesterday where I compared Catholics & Protestants in New England with Southerners in the McCain Belt, I was struck on the evolution question that in New England Protestants exhibited much more variance than Catholics. More Protestants rejected evolution or definitely believed it was true than Roman Catholics, who tended to agree that it was probably true. To me, this indicates the fissiparous tendencies of Protestantism, whereby new sects emerge from schisms within denominations, in contrast to the "broad church" philosophy of Roman Catholicism as well as the due deference to clerical elites. Though acceptance of some sort of evolutionary theory is not demanded by the Roman Catholic church, there is a general acceptance among the clerical caste as to the validity of general evolutionary processes. In contrast, liberal Protestants have arguably taken much more enthusiastically to evolutionary theory (e.g., Barack Obama, a member of the United Church of Christ, admits to believing in evolution with more certitude than angels), while conservative Protestants make its rejection a touchstone of their distinctiveness.

So I decided to go into the GSS, and see how the SCITEST4 variable relates to WORDSUM.

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More genetic maps of Europe

Fri, 21 Nov 2008 14:45:17 -0500

Another paper on European phyogeography, Investigation of the fine structure of European populations with applications to disease association studies:

An investigation into fine-scale European population structure was carried out using high-density genetic variation on nearly 6000 individuals originating from across Europe. The individuals were collected as control samples and were genotyped with more than 300 000 SNPs in genome-wide association studies using the Illumina Infinium platform. A major East-West gradient from Russian (Moscow) samples to Spanish samples was identified as the first principal component (PC) of the genetic diversity. The second PC identified a North-South gradient from Norway and Sweden to Romania and Spain...The next 18 PCs also accounted for a significant proportion of genetic diversity observed in the sample. We present a method to predict the ethnic origin of samples by comparing the sample genotypes with those from a reference set of samples of known origin. These predictions can be performed using just summary information on the known samples, and individual genotype data are not required. We discuss issues raised by these data and analyses for association studies including the matching of case-only cohorts to appropriate pre-collected control samples for genome-wide association studies.

Below the fold is a PC map where I've added clarifying labels.

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Evolution of Primate Regulation

Fri, 21 Nov 2008 12:30:57 -0500

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures:

Regulatory changes have long been hypothesized to play an important role in primate evolution. To identify adaptive regulatory changes in humans, we performed a genome-wide survey for genes in which regulation has likely evolved under natural selection. To do so, we used a multi-species microarray to measure gene expression levels in livers, kidneys, and hearts from six humans, chimpanzees, and rhesus macaques. This comparative gene expression data allowed us to identify a large number of genes, as well as specific pathways, whose inter-species expression profiles are consistent with the action of stabilizing or directional selection on gene regulation. Among the latter set, we found an enrichment of genes involved in metabolic pathways, consistent with the hypothesis that shifts in diet underlie many regulatory adaptations in humans. In addition, we found evidence for tissue-specific selection pressures, as well as lower rates of protein evolution for genes in which regulation evolves under natural selection. These observations are consistent with the notion that adaptive circumscribed changes in gene regulation have fewer deleterious pleiotropic effects compared with changes at the protein sequence level.

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In Defense of Monogamy!

Fri, 21 Nov 2008 00:16:44 -0500

OK, not really, but I have a new piece in The Guardian's Comment Is Free on polygamy.

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Yankees, Catholics and Southerners

Thu, 20 Nov 2008 22:55:57 -0500

At my other weblog I have a post which presents dozens of charts gleaned from the GSS. The intent was to compare Catholics and Protestants of New England origin to whites from the McCain Belt, and adduce whether the various Catholic immigrant groups such as the Irish and Italians in New England absorbed the values of the Yankee natives.

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We have the technology; we can resurrect them!

Thu, 20 Nov 2008 13:18:02 -0500

Regenerating a Mammoth for $10 Million:

If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant's egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.

The same would be technically possible with Neanderthals, whose full genome is expected to be recovered shortly, but there would be several ethical issues in modifying modern human DNA to that of another human species.

In the age of $700 billion dollar bailouts, what's $10 million to bring back megafauna? By the way, a pygmy mammoth survived on Wrangel Island until 3,650 years ago, as late as the end of the Egyptian Middle Kingdom

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