Category: Genetics
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Lactose intolerant when you shouldn’t be
Milk, it does a body good (or not): I’ve discussed this before earlier this year, when we got our results back (my husband, children, in-laws, parents, siblings… etc have all done genomic scans), two results came back that surprised us but proved true. My mother-in-law and husband were likely lactose intolerant. When I pointed that…
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How to reconstruct the Indo-Europeans
As must be obvious, I think now that the spread of Indo-European languages had some demographic impact. It wasn’t analogous to the spread of English to Jamaica, or the existence of French as an official language in Congo-Brazzaville. Because of this, I now believe it is possible in the near future that scientists will reconstruct…
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The history and geography of genomes
A new paper in PloS Genetics sheds some light on issues which we were already familiar with through conventional history, Ancestral Components of Admixed Genomes in a Mexican Cohort. What we already know: Mexicans and people of Mexican descent predominantly derive from an admixture event(s) between Europeans and Amerindians, with a minor African component. The…
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Out of the agricultural hearths
Dienekes has an important post up, The womb of nations: how West Eurasians came to be. He outlines a scenario where a rapid expansion of a farming population has overlain much of Western Eurasia, atop aboriginal substrata. A few years ago you’d have laughed at such a model, mostly due to the authority of archaeologists…
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Peeling the population genetic Indian onion
There’s a new paper in The American Journal of Human Genetics, Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia. It’s free, so go read it. I don’t have time to comment in detail, but I did read the paper, and I want to mention a few…
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Introducing “genoeconomics”
A new paper (open access) in The Journal of Economic Perspectives, Molecular Genetics and Economics. The authors introduce the term “genoecomics.” They start out with the proposition that the intersection of genomics and behavioral economics suffers from 1) the study samples are way too small, 2) there’s a publication bias toward false results. It’s a…
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Thoughts on the $1,000 genome, circa 2007
You’ve probably read Andrew Pollack’s DNA Sequencing Caught in Deluge of Data, by now. This section caught my eye: “The cost of sequencing a human genome — all three billion bases of DNA in a set of human chromosomes — plunged to $10,500 last July from $8.9 million in July 2007, according to the National…
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But it still adapts!
Dienekes and Maju recently pointed to a paper, Contrasting signals of positive selection in genes involved in human skin color variation from tests based on SNP scans and resequencing, in Investigative Genetics. Skin color is an interesting trait because it’s one of the big “wins” in human genomics over the past 10 years. To a great…
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Modern humans in Arabia >100,000 years ago
The genetic model of the “Out of Africa” scenario is getting more complex. There may be two waves, as well as the likelihood of admixture between the Neo-Africans and “archaic” hominins, such the Neandertals and Denisovans. From what I can gather the genetic evidence is now converging upon the sequence of events where African populations…
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On structure, variation, and race
I noticed yesterday that Andrew Sullivan, Ta-Nehisi Coates, and a cast of others were having a roiling debate on race and I.Q. My name came up in several comment threads on various issues. I’m aware of this because I have Google Alerts set for my name. I don’t have the time or energy to get immersed…
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Genetic Creationism
Carl Zimmer points me to a piece in a publication called GeneWatch, The Crumbling Pillars of Behavior Genetics. I won’t quote from it because it’s kind of a tired rehash of the confusions and misrepresentations found in The Great DNA Data Deficit: Are Genes for Disease a Mirage?, thoroughly refuted by Luke Jostins and Dan…
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More than models
Slate recently had a series up on the use of mice as “model organisms.” In particular, it put the spotlight of some limitations of extrapolating from a mouse to a man (or other species). This is in some ways biology’s “WEIRD” problem. There are always going to be obvious reasons why we’d want to use…
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When trees turn into brambles
Genetics is powerful. The origins of the field predate Gregor Mendel, and go further back to plain human common sense. Crude theories of inheritance in the 19th century gave way in the early 20th to Mendelism, which happens to be a very powerful formal system for predicting the patterns of transmission of information from generation…
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On the real possibility of human differences
I have discussed the reality that many areas of psychology are susceptible enough to false positives that the ideological preferences of the researchers come to the fore. CBC Radio contacted me after that post, and I asked them to consider that in 1960 psychologists discussed the behavior of homosexuality as if it was a pathology.…
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How the worm turns the genic world
In the middle years of the last decade there were many papers which came out which reported many ‘hard’ selective sweeps reshaping the human genome. By this, I mean that you had a novel mutation arise against the genetic background, and positive selection rapidly increased the frequency of that mutation. Because of the power and…
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Bulldogs, inbreeding, and correlated response
Last of the Spanish Habsburgs The New York Times has a long piece out, Can the Bulldog Be Saved? To a great extent it is a parable of the problems with purebred dogs. Domestic dogs are much more homozygous than humans. That is, for their two gene copies they are much more likely to exhibit…
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Don’t hate the hybrid!
There is a specter haunting the intersection of conservation biology and public policy, the specter of the biological species concept. Coyote-Wolf Hybrids Have Spread Across U.S. East: Scientists already knew that some coyotes, which have been gradually expanding their range eastward, mated with wolves in the Great Lakes (map) region. The pairings created viable hybrid…
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Genomes made real
Things we said today: But change is afoot. Numerous teams of clinicians and genomicists (including two at my own institution) have come together to sequence patients’ genomes and/or exomes to identify disease-causing mutations. Of course, doctors and researchers and genetic counselors are still bickering about when to sequence, whom to sequence, return of results, institutional…
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How many human genomes have been sequenced?
That query doesn’t seem to have an easy answer on Google, so I’m trying to enter it here. A prominent genomicist asserted a ballpark figure of ~30,000 human genomes in the year 2011. Most of that is in the year 2011 itself. Also, in regards to the “$1,000 genome” question, it seems that some labs…
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The hunter-gatherers within us
Lesley-Ann Brandt One of the reasons that the HGDP populations are weighted toward indigenous groups is that there was the understanding that these populations may not be long for the world in their current form. But the Taino genome reconstruction illustrates that even if populations are no longer with us…they are still within us. With…