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A little knowledge is dangerous
Being public on the internet means having to interact with many different sorts. Recently I’ve been having to deal with a heckler on Facebook. The heckler is actually of a particular type. I’m still trying to learn genetics at this point in my life, so I don’t propose to assert that my opinions are beyond dispute. But there is a variety of discussion which is not fruitful.
An interesting aspect of talking to people about genetics is that totally novice intelligent lay people are often very easy to communicate with. Genetics isn’t that hard, and when people want to learn new concepts and have the ability to it can be a great joy. Similarly, the numerous people who know much more genetics are easy to talk to, because they operate on a domain of fluency which makes conversation effortless (obviously this may not be reciprocated on their part in terms of their perception of your lack of knowledge!).
(pre)Historical genetics still has to be historical
Credit: Albozagros
The genetics and history of Tibet are fascinating to many. To be honest the primary reason here is elevation. The Tibetan plateau has served as a fortress for populations who have adapted biologically and culturally to the extreme conditions. Naturally this means that there has been a fair amount of population genetics on Tibetans, as hypoxia is a side effect of high altitude living which dramatically impacts fitness. I have discussed papers on this topic before. And I will probably talk more about it in the future, considering rumblings at ASHG 2012.
But to understand the character of the effect of natural selection on a population it is often very important to keep in mind the phylogenetic context. By this, I mean that evolutionary processes occur over history, and those historical events shape the course of subsequent of phenomena. Concretely, to understand how the Tibetans came to be adapted to high altitudes one must understand who they are related to, and what their long term history is. There is a paper in Molecular Biology and Evolution which attempts to do just that, Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau:
The algorithms don’t lie, but people may err
Byzantine Emperor Leo “the Khazar” with his son Constantine IV. Credit: Cplakidas
For the past year or so I’ve been getting queries about what I think about Eran Elhaik’s preprint on the genetic character of European Jews. I found some of the conclusions frankly a little weird, but I assumed that things would be cleaned up for publication. Well, it’s been out for a while now: The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses. But some reporting in The Jewish Daily Forward has brought the author and his detractors a bit into the spotlight. The reason is that as you can tell from the title of the author takes a position on the Khazarian origin model of Ashkenazi Jews (in favor). Here is a non-genetic take over at GeoCurrents, the thrust of which I basically concur with.
In any case, many of the problems with the paper remain. Really it all begins and ends here:
The eternal Aboriginal
Credit: Kwamikagami
National Geographic has an interesting article up, unoriginally titled Australia’s Aboriginals. There are lots of great data in there, though not much novel for anyone who has tread this territory before. For example, Aboriginals tend to have much lower morbidity and mortality when they are living their “traditional” lifestyle. This isn’t a particular novel or surprising outcome. Rather, it seems like a supercharged version of the same problem which occurs when immigrants move from developing to developed societies, and shift toward massive portions and processed food. This modern regime is even impacting native born segments of America’s population in a negative manner. Interesting and true.
But what concerns me is the background assumption that Aboriginals are timeless and static, arriving ~50,000 years ago from Sundaland, and remaining in a stasis. My issue isn’t normative. And I’m fascinated by the inferences some archaeologists have made about the continuity of specific motifs in Aboriginal art. Additionally, from what I understand the material culture of Aboriginals is especially changeless in relation to other populations in the world. But one thing we know about H. sapiens is that cultural forms of expression are quite protean, especially symbolic aspects which might not preserve too well. Would the Aboriginals of Australia be immune from this? I doubt it.
Saiga through the bottleneck…and back?
Credit: Tierrascott
In the 1980s I was fascinated by the pictorially oriented books on the wildlife of the world which dated to the 1960s and 1970s. One of the great conservation success stories of that era were the Saiga antelope of Eurasia. In 1920 there were only 1,000-2,0000 Saia left in the world. By the 1960s their numbers were in the millions. And so it was until the 1980s.
But the combination of the collapse of the Soviet Union, for which the Saiga was a notable conservation success, and the rise of the Chinese economy, have resulted in another crisis for the Saiga. Today their number is between 10,000-50,000, in a few fragmented regions. And yet this is still higher than their early 20th century bottleneck! The Saiga clearly have the capacity to recover from dramatic population crashes. The key, to be frank, is to keep the Saiga a viable population as China ascends up Maslow’s hierarchy of needs.
Dog and man: a 30,000 year friendship
Cite: Wang, Guo-dong, et al. “The genomics of selection in dogs and the parallel evolution between dogs and humans.” Nature Communications 4 (2013): 1860.
To the left is a figure which illustrates the phylogenetic inferences from a new paper in Nature Communications, The genomics of selection in dogs and the parallel evolution between dogs and humans (see Carl Zimmer’s coverage in The New York Times). Why is this paper important? The first thing that jumped out at me is that because they’re using whole genomes (~10X coverage) of a selection of dogs and wolves the results aren’t as subject to the bias of using “chips” of polymorphisms discovered in dogs on wolves (see: Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication). The second aspect is that the coalescence of the dog vs. wolf lineage is pushed further back in time than earlier genetic work, by a factor of three. A standard model for the origin of dogs is that they arose in the Middle East ~10,000-15,000 years ago , possibly as part of the broad shift of lifestyles which culminated in the Neolithic Revolution.
This model is now in serious question. Though there have always been claims of fossils of older domestic canids (adduced as such in terms of morphology) than the ones discovered in the Middle East ~15,000 years ago, this year there has been publication of ancient mtDNA results from ~30,000 years before the present which imply the separation of putative domestic and wolf lineages at least to that date. Over the past few years I have wondered about the specific nature of the emergence of both modern humans and modern dogs, and their co-evolutionary trajectory, over the Pleistocene and into the Holocene, in light of these results.
Human mutation unveiled
Credit: Campbell, Catarina D., and Evan E. Eichler. “Properties and rates of germline mutations in humans.” Trends in Genetics (2013).
What a great age we live in. Until recently critical parameters in population genetics such as mutation rates had to be inferred and assumed, even though they served as bases for much more complex inferences. Now with humans (and humans are only the beginning!) much of what was inferred is being assessed in a more direct fashion. Caterina Campbell and Even Eichler have a review in Trends in Genetics which surveys the field as it stands now, Properties and rates of germline mutations in humans. Notice that there’s a rough convergence using pedigree analysis of a mutation rate in the low 10-8 range. Additionally, it does seem that a disproportionate number of novel mutations come through the paternal lineage via sperm. This should increase our moderate worry about older fathers (something reiterated in the piece, with caveats). Finally, the authors suggest these results are a floor for the mutational rate, in part due to the long term conflict with the inferred ‘evolutionary rates,’ which are higher. This matters because to infer the last common ancestors between lineages the value of the mutation rate is obviously critical.
10,000 hours may gain you little if you have no talent
Mozart, born that way, trained that way
A few years ago Malcolm Gladwell made the “10,000 hour rule” famous in his book Outliers. In practice (e.g., discussions with people day to day or on this blog) the rule gets translated into the inference “practice is what matters.” When talking about genetics this often implicitly also entails that “genes don’t matter.” I’m not saying that this is necessarily what Gladwell’s own exposition taken literally would suggest, but ideas have a way of evolving once they’re outside of the pages of a book.
My own response is that this sort of rhetorical device is silly. In domains of virtuosity the intersection of innate talent and conscientiousness are often critical. That’s because for outstanding excellence gains on the extreme margin of performance are critical. There are many born with talent, and those who hone and refine that talent will have an edge over those who do not exhibit the same work ethic. But the converse is that there are those born without talent for whom 10,000 hours of invested effort is lunacy.
Please ignore mtDNA and Y chromosomal haplogroups
Guess what, we’re related! Credit: Wapondaponda
This is a public service announcement. If you are a user of direct-to-consumer personal genomics services, please do not pay any attention to your mtDNA and Y chromosomal haplogroups. Why? Because they hardly tell you anything about your individual ancestry. What do I mean by this? Your mtDNA comes down from your mother’s-mother’s-mother’s-mother… and similarly for your Y chromosomal lineage if you are a male. These few individuals are not any more likely to contribute to your ancestry than all those multitudes and multitudes who do not contribute to your mtDNA or Y lineages; also known as almost all your ancestors! What you should pay attention to are your autosomal results. Inferences made from most of your genome. These results may be more difficult to parse, but difficulty is no sin, and elegant ease is no virtue, in this case. That’s because you are interested in your ancestry, not a convenient interpretable story.
Of course I am not saying that mtDNA and Y chromosomal haplogroups are useless. They are useful for population scale phylogeography. But please don’t make inferences about yourself from one data point. At least in most cases.
Vulcans through the eye of the bottleneck
The Black Death
I noticed during Peter Ralph and Graham Coop’s Ask Me Anything about their new paper, The Geography of Recent Genetic Ancestry across Europe, someone brought up the effects of plague. Recall that ~1/3 of Europe’s population died during the Black Death. And population size reductions on the order of ~50% due to epidemics are not unknown in human history. Surely this would have a major genetic effect? Well, in fact it would have a genetic effect due to possible adaptations to disease (see CCR5). But there would be little overall impact on genetic diversity, at least in the short term. That is because for bottlenecks to produce major change in the genetic character of a population they have to be rather extreme in magnitude.
This issue came to mind for me in 2009 when I watched Stark Trek. If you haven’t watched the J. J. Abrams reboot, and are a spoilerphobe, read no more! Now, with that out of the way you may recall that during this film the Vulcans suffered a genocidal attack. Out of billions of Vulcans only ~10,000 survived. Here’s some commentary on the possible consequences, New Star Trek Movie: A Vulcan Holocaust?:
Open thread, 5/19/2013
A lot’s been happening. The human phylogenetic graph is looking curiouser and curiouser.
Why race as a biological construct matters
Credit: Characterizing the admixed African ancestry of African Americans
My own inclination has been to not get bogged down in the latest race and IQ controversy because I don’t have that much time, and the core readership here is probably not going to get any new information from me, since this is not an area of hot novel research. But that doesn’t mean the rest of the world isn’t talking, and I think perhaps it might be useful for people if I stepped a bit into this discussion between Andrew Sullivan and Ta-Nehisi Coates specifically. My primary concern is that here we have two literary intellectuals arguing about a complex topic which spans the humanities and the sciences. Ta-Nehisi, as one who studies history, feels confident that he can dismiss the utility of racial population structure categorization because as he says, “no coherent, fixed definition of race actually exists.” I am actually more of a history guy than a math guy, not because I love history more than math, but because I am not very good at math. And I’ve even read books such as The Rise and Fall of the Caucasian Race and The History of White People (as well as biographies of older racial theorists, such as Madison Grant). So I am not entirely ignorant of Ta-Nehisi’s bailiwick, but, I think it would be prudent for the hoarders of old texts to become a touch more familiar with the crisp formalities of the natural sciences.
Angelina Jolie, Myriad Genetics, & patents on genes
Because of Angelina Jolie’s revelation, the Myriad Genetics case is in the news again. If you don’t know what I’m talking about, look it up. Because of the patent Myriad can charge thousands of dollars for a test which would otherwise be much cheaper (and putting it out of reach of many without health insurance). My question here is simple: if you are a geneticist do you think Myriad’s position has any validity? The reason I ask is that I know many geneticists, and I know many geneticists read me, and I follow many geneticists on Twitter, but I’ve never encountered one who would be willing to defend Myriad’s position as plausible and passing the smell test. If you are one of those geneticists please leave a comment, because I’m honestly curious.
I went to the talks about the Myriad case at ASHG, and I have to say it was all law, and no science. The science was confused and laughable. The panelists themselves rolled their eyes and expressed resignation as to the garbled ratiocinations of the judges who reviewed the case. There is a classic “two cultures” problem.
The Kings of Minos were not Pharaohs
Credit: cavorite
A few years ago I predicted to some friends that ancient DNA would transform our understanding of the human past. The reason being that inferences of population movements via material remains were imprecise at best. We are beginning to see my prediction come to fruit (mind you, the prediction was not a bold or courageous one). A new short communication in Nature Communications, A European population in Minoan Bronze Age Crete, addresses an old and frankly somewhat outdated question: whether the first European literate civilization derived from a transplantation from Egypt, or was autochthonous.
I say that this is a somewhat outdated test because the modern proponent of this theory, Arthur Evans, lived a century ago, when our understanding of pre-Classical antiquity (i.e., the world before 600 BC and literate alphabetic Greek civilization) was sketchy at best. The reality is that ancient Crete, like the ancient Levant, does seem to have been in the greater Egyptian culture sphere of influence, just as ancient Elam (southwest Iran) was a de facto part of the Mesopotamian world. But we know the language of the Elamites, and it was not related to Mesopotamian languages. Just as the Finns have been influenced by their Nordic neighbors, so were the Elamites influenced by their Sumerian neighbors. But their linguistic difference points to fundamentally distinct origins. And so it is with the Minoans. It was already likely from the peculiar nature of Minoan writing, Linear A, that this civilization was not a simple derivation of Egypt. These genetic data just add more evidence.
GATTACA: utopia or dystopia?
Kevin Mitchell of Wiring the Brain has a very long post up inveighing against the specter of eugenics. I don’t have a great deal of time to engage Kevin right now.* But in addition to Kevin’s post I highly recommend this episode of WBUR’s On Point. It has Steve Hsu on, and he articulates many of the positions that I myself hold. Steve’s work with BGI has triggered the latest discussion of eugenics thanks to Vice‘s sensational representation of the research project and its aims. But it’s a useful discussion to engage in, even if the starting point is a little unfortunate.
I will state though Kevin’s argument seems to be predicated on the implicit assumption that his interlocutors hold to some sort of Platonic ideal of the most-perfect-human. There’s no such thing obviously, and even those who sympathized with eugenic policies such as W. D. Hamilton rejected this notion at the end of the day. Rather, human traits are evaluated in terms of how they serve the flourishing of individuals and society according to understood values. Intelligence is generally assumed to benefit individuals, and, I believe that it benefits society as well through innovation. Innovation drives the productivity growth which is the foundation of our post-Malthusian age.
Open thread, 5/12/2013
The usual.
I haven’t been able to blog much because of various other responsibilities, but I definitely do feel pent up posting energy. So when I come back I assume that I’ll have a lot of stuff to say. Meanwhile I’m chortling a bit about this bizarre attack on my friend Steve Hsu. Here’s the issue that I always have with this: Steve managed to get tenure as a theoretical physicist. When you’re talking to someone who is an academic theoretical physicist it is generally optimal to not assume a priori that they’re ignorant dullards. Unless that is you want to just engage in empty signalling rhetoric.
Though despite not having concerted time to write, I am tweeting a lot since that requires only minimal lengths of attention. Mostly it’s just repeating the functionality of my Pinboard, though I do comment and what not.
Finally, I keep hearing that the Big Five personality typology is much more scientific than Myers Briggs. So I took a bunch of tests which purport to analyze the Big Five categories.
Extraverted: Very high. Consistent. I was 90-99% on all tests.
Agreeableness: Low. Consistent. Generally in the 15-0% range.
Openness: Medium. This was not very consistent. 40-60% range.
Neuroticism: Erratic. For whatever reason I varied from 20-80% here.
Conscientiousness: Medium. But there was some variation.
Oh, and here’s a list of books I’ve rated for Good Reads.
How the sauce is made
(via The Festival of Patience)
Is the pornographic singularity real?
The above figure displays results from males in the General Social Survey who answer yes to the proposition that they’ve watched a pornographic film over the past year. This fact was cited in my post Porn, rape, and a ‘natural experiment’, to disabuse people of the notion that porn consumption has increased radically the past generation. I was aware of this finding, and so generally am careful to focus on the quantity of porn consumed, rather than the social penetration of porn consumption. No matter what the “survey says,” the IT sector is quite aware of the fact that pornographic material is a very high fraction of internet traffic (e.g., more people check Pornhub than BBC).
But I am not sure sure we should trust the GSS results any more at this point. I did some cursory poking around and last month there was a large sample size survey of Dutch youth to investigate the effects of porn consumption, Does Viewing Explain Doing? Assessing the Association Between Sexually Explicit Materials Use and Sexual Behaviors in a Large Sample of Dutch Adolescents and Young Adults:
The study found that 88% of men and 45% of women had consumed SEM ["sexually explicit material"] in the past 12 months. Using hierarchical multiple regression analyses to control for other factors, the association between SEM consumption and a variety of sexual behaviors was found to be significant, accounting for between 0.3% and 4% of the total explained variance in investigated sexual behaviors.
How the sample was collected is important for generalization, so I want to reproduce that part of the method in case you don’t have access:
Europeans share common ancestors to differing extents
Don’t forget the deep structure in Italy!
Credit: Rita Molnar
Standard apologies that I have had not the marginal time to blog much, but I thought it was important that I least note that Dr. Peter Ralph and Dr. Graham Coop’s paper on identity-by-descent segments and European populations and history is out in its final form in PLoS Biology, The Geography of Recent Genetic Ancestry across Europe. I’ve been familiar with the outlines of these results for about a year now, and to be frank I am still digesting them. The media hype will come and go, with true but to some extent trivial headlines that “all Europeans are related,” but the consequences of these sorts of genetic inquiries into the relatedness of populations are going to be long lasting. At least they should be.
But before I go on about that, if you find the paper itself a bit daunting (though the main body of the text strikes me as eminently readable for a piece of statistical genetics), see Carl Zimmer’s condensation. With this sort of result there is liable to be confusion, so note that Graham Coop has been posting comments on Carl’s blog (and elsewhere, and you can always send him a note on Twitter). Additionally he has a very readable FAQ out. Dr. Coop told me on Twitter that there would even be updates tomorrow as well! In particular one aspect of the paper which I noticed is that most relatively short, but detectable segments (~10 cM), between any two individuals in many nationalities is not going to be evidence of recent genealogical affinities, but deeper historical process.
SNL parody of Google Glass
In some quarters it is now “conventional wisdom” that Google Glass is going to seem dorky and laughable at first. But it’s probably just the pre-alpha version of the type of technology which seems inevitable (and is familiar to anyone who has read cyberpunk science fiction).
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Razib’s Pinboard
- mathbionerd: Breeder
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