Epigenetics News on 'epigenetics'

Trevor at Epigenetics News follows up on our recent discussions about the term’s increasing popularity. He’s cites several good reasons why we might expect to see the term more often, and one reason that may not be all that good:

With all of these high profile and highly funded areas becoming closely associated with epigenetics, is it any surprise that more researchers are finding ways to include their focus as part of “epigenetics”?

If a large enough portion of researchers stretch the word to apply to their topic of interest eventually ‘epigenetics’ will just mean ‘biology’.

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Round-eyed Chinese?

Via Dienekes, a new possible historical genetic story on the horizon: the extent of “European”-origin settlers in pre-modern China. The biography of the individual sequenced:

Yu Hong (d. 592 [C.E.]) was a high-ranking member of a community of Sogdians who had settled on the northern border of China at the beginning of the fourth century. While barely in his teens, Yu Hong began his career in the service of the most powerful nomadic tribe at the time, known as the Ruru, and was posted as an emissary to several countries, including Iran.

Now, the genetics:

…we discuss our analysis of the mitochondrial DNA of human remains excavated from the Yu Hong tomb in Taiyuan, China, dated 1400 years ago. The burial style of this tomb is characteristic of Central Asia at that time. Our analysis shows that Yu Hong belonged to the haplogroup U5, one of the oldest western Eurasian-specific haplogroups, while his wife can be classified as haplogroup G, the type prevalent in East Asia. Our findings show that this man with European lineage arrived in Taiyuan approximately 1400 years ago, and most probably married a local woman. Haplogroup U5 was the first west Eurasian-specific lineage to be found in the central part of ancient China

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Hitchens on religion

I haven’t read any of the books carrying the torch for the “New Atheism”, but I dig Christopher Hitchens’s style, maybe I’ll make an exception. Slate has published an excerpt from his forthcoming book, God is Not Great.

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Why is so much biological research centered on genes and DNA?

You’ll find one professional’s answer below the fold. What’s missing is a discussion of genes as replicators.

from the SEP – Molecular genetics:

In official and public contexts, scientists appeal to the fundamental theory associated with molecular genetics to justify centering research on genes and DNA (e.g., see the websites of funding agencies such as National Center for Biotechnology Information). Genes are typically referred to as “the fundamental units” that are responsible for guiding all basic life processes. Usually a combination of causal and information metaphors are invoked to explain the role of genes. Genes are said to produce RNA and polypeptides, to provide instructions, or direct processes. But philosophical investigation has shown that these kind of sweeping claims cannot withstand careful scrutiny. Why, then, is so much research centered on genes and DNA? One answer to this question is that biologists are blinded by an ideology of genetic determinism. But Wagner’s defense of gene centrism suggests another answer, an answer that resonates with Keller’s explanation (2000) of why gene talk is useful.

It has been proposed that the real reason biologists center attention on genes and DNA is that genes are difference makers that can be used to trace and manipulate a broad range of biological processes (Waters 2004a and 2006). This scientific practice makes sense independently of any fundamental theory associated with molecular genetics. In the case of molecular genetics, it is investigative pragmatics, not fundamental theorizing, that drives scientific research. The basic theory suffices to explain the investigative utility and results of gene-centered approaches. The fundamental theory is, in an important sense, epiphenomenal with respect to the design and implementation of gene-centered research. On this view, the role of the fundamental theory should be understood in Latourian terms (1987, 1988), as a platform for rallying the troops and bringing resources to research endeavors. The design of the laboratory experiments and the reason why the experiments work, can be explained in terms of broad investigative strategies, the basic causal theory of molecular genetics, and the details of the experimental contexts.

Earwax and breast milk

Miura, Yoshiura, Miura, Shimada, Yamasaki, Yoshida, et al. A strong association between human earwax-type and apocrine colostrum secretion from the mammary gland. Human Genetics.

Here we provided the first genetic evidence for an association between the degree of apocrine colostrum secretion and human earwax type. Genotyping at the earwax-type locus, rs17822931 within the ABCC11 gene, revealed that 155 of 225 Japanese women were dry-type and 70 wet-type. Frequency of women without colostrum among dry-type women was significantly higher than that among wet-type women (P < 0.0002), and the measurable colostrum volume in dry-type women was significantly smaller than in wet-type women (P = 0.0341).

Related from Razib: Here are two posts from me on earwax distributions worldwide.

PKM Zeta on This American Life

The new Showtime version of This American Life has a segment featuring Todd Sacktor and Andre Fenton. They published a remarkable paper (discussed on gnxp) last year showing that specific inhibition of PKM Zeta (a consitutively active version of protein kinase C) can erase memories. This is all in rats of course. So if you have Showtime, it’ll air tomorrow night, Thursday the 26th.

ScienceBlogger threatend with legal action

Final Update: Victory Day! In response to Shelley’s request I’ve removed the text of the original email.

A fellow ScienceBlogger has been threatened with legal action for reproduction of figures. Obviously we post figures here on this weblog pretty frequently. It isn’t to screw over the companies doing the publishing from making profits, we just want to talk science. We don’t repost whole papers. It seems highly likely no one who sees the figures on our weblog is going be disinclined then to buy the article if it piques their interest (more likely they’ll go to the local university library). Instead, we’re giving free publicity to the journal in question. So is what was done fair use or not? Honestly, I don’t care too much, it seems that they just wanted the bad publicity/review to go away. So I say give them more! Here is the text of the email:

[removed]

Addendum: Thinking about it more, I wonder what percentage of sales massive academic publishers make via the “buy this article” option which pops up when your institution doesn’t have access? My own hunch is that very few people go this route, but rather will simply ask the researcher in question for a reprint/PDF if it is of particular academic interest. From a sales perspective I can’t believe that reproduction of figures would in any way diminish the interest of an individual in a paper or article. Rather, it is more likely to increase interest (i.e., whetting appetite). So even assuming that the email Lisa Richards sent was defensible on legal grounds it doesn’t seem to make much business sense to take up time doing something like this. Unless of course, as I noted above, the main motive was just to squelch some negative publicity.

Finally, I don’t want to give the impression that bloggers have a carte blanche to say or do whatever they want to on the web. But, that being said, when someone to whips out the law as a cudgel against discussion of a topic, they should know that if the cause is unjust they’ll be blog-mobbed.

Breaking: People are different

Heredity has a summary of a study on the genetics of gene expression differences between European and Asian populations (which I summarized here). The opening lines are a striking glimpse into the academic world:

It has often been observed that people are different. Indeed, some observers have gone further to suggest that this diversity exists between people from different parts of the world, or of different ethnic groups, and it is hereditary. This latter observation has led to a certain amount of contention over time. As a result, many geneticists have been wary about asserting that such differences exist.

That’s right, it’s contentious to say that the “diversity” we are all so fond of might have some relation to genetic diversity, something that is patently obvious given a basic knowledge of evolutionary processes and a pair of eyes.

But whatever, it’s a good summary of the research, though I must take issue with the argument that gene expression variation between individuals may have no effect on phenotype:

[W]hile the exact numbers of differences could be debated, the data at least suggest that there should be considerable variation in actual humans. But, does this matter? One problem with establishing the importance of microarray results is that they only tell about gene expression, not about the physiological effects of the gene. Earlier studies on the dynamics of metabolic pathways have shown that fluxes through the pathways may be relatively insensitive to changes in the concentration of many of the enzymes in a pathway

Overall, it is not clear how the variation in gene expression relates to phenotype, and fitness

This shows a striking lack of familiarity with studies on the evolution of gene expression. Where it has been well-studied, it’s clear that gene expression levels are under strict control– they are under strong negative selection and do not vary neutrally[1]. This implies, of course, that changes in gene expression have an effect on fitness (though it’s true the precise effects of individual genes are mainly unknown). Changes in gene expression levels are very likely to have some sort of phenotypic consequence.

[1] Citations: For a meta-analysis of gene expression evolution in a number of organisms, see this paper, which concludes “Our analyses used a number of metrics to show that most mRNA levels are evolutionary stable, changing little across the range of taxonomic distances compared. This implies that, overall, widespread stabilizing selection on transcription levels has prevented greater evolutionary changes in mRNA levels.”

A more rigorous look at changes in gene expression in Drosophila concludes, “Although spontaneous mutations have the potential to generate abundant variation in gene expression, natural variation is relatively constrained“. In C. elegans, as well, a similar study to that done in Drosophila concludes, “We directly compared observed transcriptional variation patterns in the mutation-accumulation and natural isolate lines to a neutral model of transcriptome evolution to show that strong stabilizing selection dominates the evolution of transcriptional change for thousands of C. elegans expressed sequences.”

These studies have all looked at broad evolutionary patterns; some researchers are now able to look at the evolution of gene expression globally while making inferences about individual genes. For example, this study in humans identifies a number of genes whose expression has evolved rapidly in humans, as well as a number whose expression levels appear to be stable.

Overall, to imply that genetic differences between populations, which then translate into gene expression differences between populations, have no effect on phenotype or fitness is naive at best.