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Steak, It's What's for Publication

Citation: Decker, Jared E., et al. "Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle." arXiv preprint arXiv:1309.5118 (2013).

Citation: Decker JE, McKay SD, Rolf MM, Kim J, Molina Alcalá A, et al. (2014) Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle. PLoS Genet 10(3): e1004254. doi:10.1371/journal.pgen.1004254

 

440px-Steak_03_bg_040306I am a man of a particular age, old enough to remember when the idea of thousands of what were then quaintly termed ‘molecular markers’ would have left one aghast as the surfeit of data. Today the term “post-genomic” almost strikes me as anachronistic as the “information superhighway.” This is not the post-genomic era, it just is, the wildest dreams that were are. But the glorious present of data abundance is not without its limitations and pitfalls. As a friend explained once, bioinformaticians just “do stuff,” sometimes without understanding why they do stuff. Somewhere along the way the bio part seems to have been forgotten in the hurry to assemble the next organism as the machine demands more and more for its hungry maw. But the mechanical monster slurping through the fire hose of data with a hacked together chimera of a regular expression isn’t without some purpose. Many biologists with an interest in evolution have a dream of dense marker painting vast swaths of the tree of life, an empire of phyolgenetic information to be conquered.

But these vistas need some context, a horizon of information about the organism. This came to mind when I read Jared Decker’s new paper on the phylogenetics of domestic cattle, Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle. In many ways it is a straightforward paper. You can see discussions on the earlier iterations over at Haldane’s Sieve (the preprint process seems to have worked to make it a more robust and clear publication from what I can tell!). Decker utilizes some straightforward methods (at least straightforward in 2014) on a very large SNP marker data set with expansive geographic coverage. In particular, TreeMix, Admixture, and PCA. With about ~40,000 SNPs these packages should blast through the data rather quickly (I’ve used all of them with this marker density, and sample sizes of approximately the size of the one Decker has).

You can read the whole paper yourself since it is open access. To me it seems to reiterate that cattle truly are cattle, to be pulled and prodded and traded at the whim of human beings. The fact that many East African cattle have predominantly Indian heritage (one of the two major clades) illustrates the fact that domestic animals exhibit the protean tendencies of human culture, rather than biological organisms which are governed by standard geographical and morphological diversification through conventional population genetic pressures. But I have to still admit that much of the narrative force of this paper escapes me because I lack understanding of the cattle at a level beyond the plainly statistical genetic. In other words, the organism matters. Cattle geneticists who may “hum through” the plots may still be able to grasp the force of argument with a greater clarity because their understanding of the topic is fundamentally thicker than that of outsiders. Many of the paper’s inferences from genetic data clearly draw their plausibility from elements of natural history which bovine biologists would take for granted.

And this is just the beginning. Over the next decade it seems inevitable that the clusters at the heart of “genomics cores” across the world will be gorging on whole sequences of thousands of individuals for many organisms. It will be a “flood the zone” era for attempting to understand the tree of life. An army of bioinformaticists will be thrown at the data in human waves, absorbing shock after shock, slowly transforming the ad hoc kludge pipelines of the pre-Model T era of genomics into simpler turnkey solutions. And then the biology will come back to the fore, and the deep wellspring of knowledge by those who focus on specific organisms and is going to be the essence of the enterprise once more.

• Category: Science • Tags: Admixture, Cattle Genomics, Genomics, PCA, TreeMix     

It Takes a Village More Than Parents

Trait-scale-linear

The New York Times has a piece up, Raising a Moral Child, which does a run through on the various orthodoxies and heresies about child-rearing and inculcating values floating around the upper middle class Zeitgeist of modern America. There are plenty of references to research and the like. Literature reviews or not, it always helps to know some history, and realize that many ‘orthodox’ opinions seem to be a manner of fashion, not science (in fact, this is clear when you look at cross-cultural mores; France is today different from the USA when it comes to views on how to raise a good child). But there are things I think that are known, and should be reiterated. So, the author states that:

Genetic twin studies suggest that anywhere from a quarter to more than half of our propensity to be giving and caring is inherited. That leaves a lot of room for nurture, and the evidence on how parents raise kind and compassionate children flies in the face of what many of even the most well-intentioned parents do in praising good behavior, responding to bad behavior, and communicating their values.

The-Nurture-Assumption-Harris-Judith-Rich-9780684857077Two insights from behavior genetics can shed light here. First, shared-environmental effects are often the smallest proportion of the variation in behavior. This is the part which is due to the family home and the parental influence. Second, the proportion of variance explained by shared-environment tends to go down as people get older. So parental influence tends to diminish.

Obviously part of the reason you behave as you do can be put down to genes. Or more precisely genetic dispositions which express themselves. And another portion can be chalked up to what your parents teach you. But a large proportion, in fact in many cases the largest proportion, is accounted for by factors which we don’t have a good grasp of. We don’t know, and term this “non-shared environment.”* In The Nurture Assumption Judith Rich Harris posited that much of non-shared environment was one’s peer group. This is still a speculative hypothesis, but I do think it is part of a broader set of models which emphasize culture and society, and how it shapes your mores and behaviors, as opposed to the nuclear family.

The research cited in the piece shows how modeling by parents or people in positions of authority can affect short-term changes in the behavior of children. I am sure that these effects are real, what I am skeptical about is that these effects maintain themselves in a non-congenial social environment. To illustrate what I am getting at, imagine two children who are given up for adoption, and whose biological parents are alcoholics. Imagine that you know the biological parents are both carrying genes which are strongly correlated with alcoholism. Both these hypothetical children are adopted into conservative white upper middle class families, one in Orange county California, and another in an affluent suburb of Salt Lake City. Both families are socially conservative, and do not tolerate drinking among their children. My prediction is that the child adopted into a Mormon culture which is far less tolerant of individual choice on the issue of alcohol consumption will have lower risks of being an alcoholic simply because the whole landscape of decisions is going to be altered throughout their whole life. An adopted child with a family history of alcoholism is still going to have a higher risk within their population, but the nature of the population is likely to shift the baseline odds.

Contemporary child-rearing advice and literature has a focus on the nuclear family because parents are the ones buying the books, reading the magazines, and attending the workshops. They want to believe that they have control on the outcomes of their offspring decades after they their leave home. Reality is not congenial to this. Parents do have control, but it is far more a case of establishing frameworks through choice in nationality and cultural identification, and loading the die with genetic dispositions.

* This might actually be genetic or more broadly biological; epigenetics, epistasis, and developmental stochasticity.

• Category: Science • Tags: Behavior Genetics     

The Edges of the Genotype-Phenotype Map

correlation

Claes, Peter, et al. “Modeling 3D Facial Shape from DNA.” PLoS genetics 10.3 (2014): e1004224.

A few weeks ago a paper came out in PLoS GENETICS, Modeling 3D Facial Shape from DNA, which attempts to push the ball forward when it comes to mapping complex traits like facial morphology from genetic data. The long term goal here is clear: to forensically infer one’s phenotype purely from genetic information. For simple quasi-Mendelian traits like blue vs. brown eye color difference this is already possible with a high degree of certainty (or at least far higher than eyewitness reports) because much of the trait variation is controlled by one or a few genes. But for complex traits like height where variance is distributed across thousands of loci this is not feasible because the understanding of the genetic architecture is far more primitive and incomplete. The most explanatory height loci are on the order of ~1 percent of the variance of the trait in a population. In contrast blue vs. brown eye color variance within Europeans has a ~75 percent explanatory proportion at the HERC2-OCA2 locus.

The technical details of how they modeled facial morphology is rather interesting, but I’m not going to focus on that (they zeroed in on a mixed-race population to maximize phenotypic and genotypic variance). Rather, note that the authors can now relate phenotype and genotype very precisely on a population wide basis. In the past you would have to look at someone and assess their racial background or sex status. But today genetics can give you a very precise estimate of their racial ancestry, or an accurate prediction of their biological sex. The correlations are good, but observe that there are deviations from a strict association. These are perhaps just as interesting over the long term.

When it come to the domain of sociology and culture there are many models of how your physical appearance impacts how others perceive you, and how you develop as a person. You can see in the chart that there are many people who have more African ancestry, but less African features, than other sets of people (Rashida Jones and Joakim Noah likely fall into this class of pairs; Rashida Jones’ father is 66% African in ancestry, while Noah’s is 50%, so she is likely to have more African ancestry, despite having more European facial features by most accounts). By looking at these deviations from expectation you can actually test the power of genetics vs. sociology. In the case of the Duffy antigen trait clearly genetics will be determinative. On the other hand there are all sorts of medical (e.g., hypertension) and behavioral (e.g., intelligence test scores) differences between the socially understood black and white American populations where looking at individuals who vary in genotype and phenotype might illuminate the weight of the variables.

And I’m not talking rocket science here. Within 10 years surely much research will have been done in this area simply by looking at numerous genetic data sets, and combining them with phenotypic information. If scientists don’t do it, I suspect marketing and credit rating firms will, because they already have huge piles of data on most Americans (i.e., phenotypes, or instrumental variables to infer phenotypes). And this does not apply to just race. Though the difference between male and female faces is striking, there is some overlap there as well. Questions could be asked about the outcomes of men and women conditional on their facial morphology. The existence of AIS individuals would be another dimension to explore.

• Category: Race/Ethnicity, Science • Tags: Complex Traits, Facial Morphology     

Open Thread, 4/13/2014

What’s going on in the world? I’m still trying to finish writing a draft of a paper, so you know how it is….

• Category: Miscellaneous • Tags: Open Thread     

Little Lord Khan and the PCA

I’ve been busy with a very personal genomic project over the past month or so. Needing to make sure that the SNP calls make sense I plotted him on a PCA with his sister. The results are straightforward, and reassuring in their expected nature.
LordKhan

• Category: Science • Tags: Fetal Genomics, Little Lord Khan     

Open Thread, 4/7/2014

Obviously been busy. Still comment on Twitter, but hard to free up time to write something substantive here. But this too shall pass. It always has.

I should mention I am almost done with A Concise History of Russia. Nothing revolutionary, but worthwhile as a refresher.

• Category: Miscellaneous • Tags: Open Thread     

Open Thread, 3/30/2014

What’s going on?

• Category: Miscellaneous • Tags: Open Thread     

BaneCat

• Category: Miscellaneous     

Saying Crazy Things Makes You Less Credible

440px-Desembarque_de_Pedro_Álvares_Cabral_em_Porto_Seguro_em_1500I pay a subscription to The New York Times because it’s America’s premier middle-brow journal. Its science pages are decent, so my interest was piqued when I saw the the bold headline, Discoveries Challenge Beliefs on Humans’ Arrival in the Americas. But the article is a total mishmash, alternating between spotlighting paradigm challenging scholars, and crazy. Here’s the crazy:

Having their findings disputed is nothing new for the archaeologists working at Serra da Capivara. Dr. Guidon, the Brazilian archaeologist who pioneered the excavations, asserted more than two decades ago that her team had found evidence in the form of charcoal from hearth fires that humans had lived here about 48,000 years ago.

Dr. Guidon remains defiant about her findings. At her home on the grounds of a museum she founded to focus on the discoveries in Serra da Capivara, she said she believed that humans had reached these plateaus even earlier, around 100,000 years ago, and might have come not overland from Asia but by boat from Africa.

These are changing times in human evolutionary biology. But if humans couldn’t make it by boat to Madagascar until 1,000 to 2,000 years ago, there’s no way they made it to Brazil.

• Category: Science • Tags: Archaeology, Brazil     

Not by Cline Alone

Citation: Moreno-Estrada, Andrés, et al. "Reconstructing the Population Genetic History of the Caribbean." PLoS genetics 9.11 (2013): e1003925.

Citation: Moreno-Estrada, Andrés, et al. “Reconstructing the Population Genetic History of the Caribbean.” PLoS genetics 9.11 (2013): e1003925.

The Chronicle of Higher Education has an article up on the intersection of genomics and sociology, In Research Involving Genome Analysis, Some See a ‘New Racism’. Most of the quotes are from sociologists, which is a problem, because whenever I try and delve into the topic it seems that sociologists don’t actually engage with the latest genomic research, but simply rehash older models which refute naive essentialism which biologists would never find plausible in the first place. But there was an intriguing quote in the piece from Jiannbin Shiao: …The social sciences should replace their biology-based rejection of race “with a version of the feminist distinction between biological sex and socially constructed gender,” he writes. With several co-authors, he has developed a concept called “clines,” adapted from how economists talk about social class, which reflects the continuous nature of human variation while allowing loose clusters to develop, depending on how you zoom into the data.

The paper is The Genomic Challenge to the Social Construction of Race. It is admirable in its attempt to engage in the recent literature. Unlike other sociologists the authors seem to have read publications from the 21st century. I do think it’s strange that they are talking about clines as if it is a new idea, seeing as they cite its long-standing usage in biology. But perhaps it is somehow a novel concept in sociology? That says something about sociology I suppose.

But in an area of research such as genomics citations that are six years old may be out of date. The authors published in the summer of 2012, and no doubt had been working on the paper for a few years before that. I’m pretty sure that Steve Hsu, a former colleague of the first author at the University of Oregon, actually told me about the genesis of this paper in the spring of 2011 when I had coffee with him at Berkeley. The authors state:

The primary tools for identifying population structure have been, in order of emergence, (1) comparisons of predefined populations, (2) the Bayesian clustering approach of the program STRUCTURE developed by Pritchard, Stephens, and Donnelly (2000), and (3) new variations on the classical technique of principal components analysis (Paschou et al. 2007). Although social studies of science continue to criticize the circular research design of the first method (Bolnick 2008; Duster 2006b; Marks 2006), the second and third methods have been preferred among academic researchers for over a decade (Risch et al. 2002; Rosenberg et al. 2002).

• Category: Science • Tags: Race     

Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"