R1a1a conquers the world…in a few pulses?

As many of you know around the year 2000 the analyses of Y chromosomal human lineages became a pretty big deal. The reason these lineages are important and useful is that they record the uninterrupted ancestry of males, from father to son, along the Y chromosome. Instead of the complexities of the whole genome, as with mtDNA you have a simple and elegant phylogenetic tree to interpret. The clusters along this tree are defined as broad haplogroups, united by derived states from a common ancestor. One of the largest haplogroups is R1a1a. It happens to be my paternal lineage, as well as Dr. Daniel MacArthur’s and Dr. Zack Ajmal’s.

The map above illustrates the peculiarity of R1a1a: it is geographically enormously expansive. How to explain this distribution? A naive response might be that this distribution is surprising similar to that of the Indo-European languages. Unfortunately this runs up against the conundrum that low caste South Indian groups, relatively untouched by Indo-Aryan culture (at least until the past few hundred years), also manifest high frequencies of R1a1a.

To make a long story short it seems that R1a1a is an old haplogroup with a lot of structure across Eurasia. Maju points me to a paper in American Journal of Physical Anthropology which simply & elegantly brings home to us some obvious insights, New Y-chromosome binary markers improve phylogenetic resolution within haplogroup R1a1:

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Which results from cognitive psychology are robust & real?

A paper on the psychology of religious belief, Paranormal and Religious Believers Are More Prone to Illusory Face Perception than Skeptics and Non-believers, came onto my radar recently. I used to talk a lot about the theory of religious cognitive psychology years ago, but the interest kind of faded when it seemed that empirical results were relatively thin in relation to the system building (Ara Norenzayan’s work being an exception to this generality). The theory is rather straightforward: religious belief is a naturally evoked consequence of the general architecture of our minds. For example, gods are simply extensions of persons, and make natural sense in light of our tendency to anthromorphize the world around us (this may have had evolutionary benefit, in that false positives for detection of other agents was far less costly than false negatives; think an ambush by a rival clan).*


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Humans are at least 8% virus

In the comments below there is a lot of talk about the worry of transferring gene X from organism 1 to organism 2, where the two organisms are very far apart on the tree of life. I’m a little sanguine about this, but that’s because there is already much of this going on through natural processes.

Carl Zimmer for example points out that 8 percent of the human genome seems to derive from endogenous retroviruses (the post draws on material from his book A Planet of Viruses). This is probably a low bound number, as he notes in the comments. Additionally, this isn’t just limited to viruses. See: Horizontal gene transfer between bacteria and animals.

I think on of the chasms between geneticists and the public is that a lot of things that seem creepy and strange to the public are part & parcel of the geneticist’s professional toolkit. For example, to my knowledge no transgenic mice have turned into the Brain. I have friends that order weird mouse varieties, and then do weirder things to them, every week.

Prop 37 and the right to have the government enforce your right to know

With the election coming up, California Proposition 37, Mandatory Labeling of Genetically Engineered Food, is on my mind. From Ballotpedia:

If Proposition 37 is approved by voters, it will:

* Require labeling on raw or processed food offered for sale to consumers if the food is made from plants or animals with genetic material changed in specified ways.

* Prohibit labeling or advertising such food as “natural.”

* Exempt from this requirement foods that are “certified organic; unintentionally produced with genetically engineered material; made from animals fed or injected with genetically engineered material but not genetically engineered themselves; processed with or containing only small amounts of genetically engineered ingredients; administered for treatment of medical conditions; sold for immediate consumption such as in a restaurant; or alcoholic beverages.”

James Wheaton, who filed the ballot language for the initiative, refers to it as “The California Right to Know Genetically Engineered Food Act.”

Michael Eisen has two posts up on this which get the meat of the issue for me. I disagree with Prop 37, though on first blush I think the idea of transparency is radically empowering. Before I get to my reasoning, I want to set aside some ancillary considerations. Some are voting for the measure because they oppose agribusiness in general, or have a particular bone to pick with the way that some firms enforce their intellectual property on seed lines. These are fine critiques, but I’m not going to address them, because I think they’re separate from the science.

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I, for one welcome our yellow overlords!

The above infographic from The New York Times article For Asians, School Tests Are Vital Steppingstones, was titled “1027-asians” when I tried to save it. No idea why, but I think that’s an amusing file name. My offensively titled post is inspired by the cliche reference to Confucianism in the piece. As my previous posts on “Tiger Mom’s” indicate I am not a big fan of the “Asian” way of obtaining academic laurels through brute force alone. In places like South Korea a cram-school bidding war has distorted the culture. The single-minded focus on a specific test means that the whole society has to shift to keep up with the innovators in the educational “arms race.” Think of it as the analog to the doping scandal in cycling. And it’s an irony that the term innovation is being used here by me, because this sort of “education” destroys the creativity, flexibility, and originality which is the engine which motors modern civilization. Sufficient for producing engineers, but I doubt fruitful as the seedbed for an individualistic scientific culture which aims to shift paradigms.

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Doctors are apparently gods, get used to it

Here’s a caption from a Time article, What Your Doctor Isn’t Telling You About Your DNA:

Nice to know that two physicians in Philadelphia not only have medical degrees, but specialize in mind-reading the parents of this nation! Above the caption is a photo of  the two concerned and worried looking professionals in question. Let me quote the first two paragraphs of the article:

The test results were crystal clear, and still the doctors didn’t know what to do. A sick baby whose genome was analyzed at the Children’s Hospital of Philadelphia turned out to possess a genetic mutation that indicated dementia would likely take root around age 40. But that lab result was completely unrelated to the reason the baby’s DNA was being tested, leaving the doctors to debate: Should they share the bad news?

When it comes to scanning DNA or sequencing the genome — reading the entire genetic code — what to do with unanticipated results is one of the thorniest issues confronting the medical community. Many conflicted discussions followed the dementia discovery at the Children’s Hospital of Philadelphia (CHOP) before a decision was reached: the parents would not be told that this fatal memory-sapping disease likely lurks in their child’s future. Given the hopelessness of the situation, with no treatment and no cure, the doctors said forwarding such information along felt pointless. We came around to the realization that we could not divulge that information,” says Nancy Spinner, who directs the hospital laboratory that tested the infant. “One of the basic principles of medicine is to do no harm.”

The fourth in a five-part series exploring the promise and pitfalls of sequencing children’s genomes

Around the same time, Spinner’s lab also tested another child — an unusually short 2-year-old referred for kidney disease — and discovered the toddler had a gene linked to a rare form of colon cancer. In some cases, polyps arising from this kind of cancer have been known to develop as early as age 7. This time, the decision to inform the parents was easier: We feel good about that one,” says Spinner. “Proper screening can make a huge difference.”


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A golden age of sibling comparisons

Image credit: Assumption-Free Estimation of Heritability from Genome-Wide Identity-by-Descent Sharing between Full Siblings

I really love the paper Assumption-Free Estimation of Heritability from Genome-Wide Identity-by-Descent Sharing between Full Siblings. I first read it about six years ago. The result is rather straightforward, but the problem is empirically a moderately deep one. Modern analytic genetics as the fusion between Mendelism and biometrics began with R. A. Fisher’s The Correlation between Relatives on the Supposition of Mendelian Inheritance in 1918. But note, that paper assumed particular relatedness between relatives. As highlighted in the above paper the expected values for most categories of relatedness always had a variance component which was unaccounted for, and so reduced the power of the methodology to ascertain the extent of heritability. The relatedness you can expect between any two siblings is ~0.50, and that is also the average across all siblings. But the reality is that in most cases two given siblings will not share half their genes identical by descent.

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Putting a stop on the biological clock

Egg freezing enters clinical mainstream:

Egg freezing is no longer an experimental procedure, according to the American Society for Reproductive Medicine (ASRM), which on 22 October issued new guidelines on the controversial practice. The change in policy is expected to accelerate the growth of clinics that offer egg freezing to women who face fertility-damaging treatment for cancer or other conditions, and to women wishing to delay having a baby — although the society stopped short of endorsing the procedure for that purpose

You can read the full guidelines, with caveats, online. Last I checked this costs on the order of $10,000. Nothing to sneeze at, but definitely not insane when you consider how much money many couples spend on fertility technologies when women are between 35 and 40.

And of course I recommend freezing sperm too. That’s far less costly.