Open Thread, 3/16/2014

k10181I’ve been reading reviews of The Son Also Rises, Greg Clark’s new book on the persistence of social inequality. A major problem I see in the reactions is that the idea of heritability is not one that most public intellectuals and journalists have as part of their intellectual toolkit. If, on the other hand, you understand what heritability is Clark’s formal framework is not too interesting. Rather, the empirical results are somewhat surprising, but one can after the fact understand how they might have come about.

At some point I’ll review the book, though I want to talk to Clark about it beforehand. For readers who want to know I think though, honestly you should just check out or buy a copy of Introduction to Quantitative Genetics, and absorb the section on heritability. Once that logic is under your belt you can evaluate the argument Clark lays out, and actually chew it over. Though I will say that the results in the book probably would support hereditarian maximalists, insofar as the proportion of outcomes you can control in your offspring have almost everything to do with mate choice, and nothing to do with environment (though environmental variation is huge, it’s not accounted for, so you can’t “pick” the optimal one).

Are phones an anachronism?

100px-IPhone_2G_PSD_MockRecently I was having a discussion with a friend who is a very successful businessman, and he brought up the possibility of not replacing his smartphone. His logic was that all he was paying $200 a month (family plan costs) was the number. With something like an iPad mini and 3G he could emulate almost all the functionality of the phone at a smaller recurring cost. The logic here being that most of the calls with something like Skype would be done over wi-fi anyway (so not taxing a a data plan’s bandwidth limitations for 3G). As for texting services such as WhatsApp will probably replace standard SMS over the next few years.

Which brings us to the crux of why one should keep the phone: a traditional number. Yet internet services such as Skype have numbers too. So what’s stopping us? Inertia? I’m honestly wondering why I have a phone in terms of functionality, as opposed to the fact that everyone has a phone (I actually do most of my phone calls via Skype, often on my Kindle Fire, and sometimes on my phone’s wi-fi).

Lost blonde tribes in Africa

Genseric
Genseric

Sara Tishkoff and company are leveraging their massive African data set again, with a paper out which surveys the diverse landscape of lactase persistence genetics across continent, Genetic Origins of Lactase Persistence and the Spread of Pastoralism in Africa. Many of the results were well known or could have been anticipated, selection for the trait in Africa, or even the fact that lactase persistence in the Khoikhoi derive from East Africa. So let me quote at length one section which I think is rather notable: In fact, the T-13910 variant in the Mozabite from Algeria occurred on the same haplotype background as observed in Middle Eastern populations, whereas the Fulani from Cameroon and the Bulala from Chad shared the same haplotype background with Europeans. The Fulani also shared a distinct T-13910 haplotype background with the Arabic Baggara. These patterns suggest that the distribution of observed haplotype variation might be due to gene flow that occurred over time from outside and within Africa possibly during key historical events, such as the settlement of the Roman Empire in parts of northern Africa and the expansion of the Arabs prior to and during the Ottoman empire within the last 2,000 years.67 These inferred migration events are also consistent with studies based on mtDNA, Y chromosome, and autosomal genetic variation.

The T-13910 variant is the one that is very widespread in Western Eurasia, from Northern Europe, all the way to Northwest India. Earlier analysis had suggested hat the Fulani people of the western Sahel carried the the European and South-Central Asia mutation for lactase persistence, as opposed to the ones more common in Eastern Africa or the Middle East. This was curious, but not totally incomprehensible in light of the fact that it seems that populations such as the Tuareg mediated gene flow across the Sahara, and the Berber polities extended to the northern Sahel. What is surprising is that upon closer inspection the flanking regions around T-13910 in the Fulani, but not the Mozabite Berbers, exhibit a signature which indicates a European origin. The Mozabite Berbers are a rather isolated group, probably representative of genetic variation in large part before the settlement of non-Berber populations along the coastal zone in antiquity. So it would not surprise me if T-13910 haplotypes in much of Morocco and Algeria are of the European, and not the Mozabite, flavor. But that still prompts the question, why are there two variants in the Maghreb when they are functionally the same?

A plausible model is that the European haplotype came along with the Vandals, a Germanic barbarian tribe with origins in southern Scandinavia and northern Germany which conquered North Africa in the early 5th century A.D. Of course the allele could have arrived in the centuries of earlier Roman rule, but the T-13910 mutation is generally found in low frequencies in Mediterranean populations like Italians. In contrast it is well over 50% among Northern Europeans. It is fashionable in studies of Late Antiquity to assume that the Vandals, and their Alan confederates, were ad hoc social constructs which somehow congealed out of the political compost heap of the late Roman Empire. An alternative view, championed by Peter Heather (see Empires and Barbarians), is that groups such as the Vandals were a genuine volk engaged in wholesale migration. The idea that the Vandals were social constructs of some sort, and of trivial numbers, suggests that they made only a marginal impact and disappeared in totality after the conquest by the Byzantines in the 6th century of the Maghreb. But the presence of these distinctive genetic markers indicates that the Vandal numbers may have been substantial enough to allow for the transfer of the T-13910 allele to the Berber tribes which assimilated the the rural estates they still held.

Much of this is speculation of course. We’ll know the truth of the matter when someone does extensive resequencing of the whole region of LCT in a variety of populations. At that point presumably one might be able to discern if the Fulani allele is closely related to German ones in particular. The point is that these sorts of bizarre scenarios which are more in keeping with late 19th and early 20th century adventure fiction might actually be closer to much of history than we would have thought.

Note: I should add that Greg Cochran speculated in this direction a few years ago.

Descent and selection is a bugger: black Kurgans?

Ukraine
Citation: Wilde et al.
Credit: Igor Kruglenko
Credit: Igor Kruglenko

A new paper in PNAS, Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 years, uses ancient DNA to examine the possibility of very recent natural selection in Europeans. In particular, it focuses on eastern Europeans, and roughly a region coterminous with Ukraine ~6000 to ~4000 years ago. The sample seems somewhat biased toward the low end of the age range if you look the supplemental tables. In the paper itself (which is open access) I don’t see a map to get a sense of the distribution of the sites from which the DNA was extracted. So I took the supplemental table and used the latitude and longitude information, as well as the samples from each site, and produced a density map with a bubble plot overlain upon it with specific locations (size of bubble proportional to number of samples at site). Like the earlier ancient DNA from a few European hunter-gatherers one must keep in mind the limitations of the scope of sampling so few to infer about so many. Though the number here is far larger (N >20 or >40 depending on the SNP), the set of markers examined was much smaller, a few pigmentation loci and mtDNA. Nevertheless this is not a trivial geographic example, nor is the time frame, from the Early Eneolithic down to the Bronze Age.

Figure S1
Figure S1

The clearest illustration of the topline result is found in the supplements (I prefer figures to tables obviously). What you see here is that there is a large difference in allele frequencies between ancient samples and modern ones from the equivalent geographic region at specific markers diagnostic for variation in pigmentation in modern Europeans. HERC2 is well known for being one of the two loci which span a long haplotype strongly correlated with blue eyes in Europeans. SLC452 and TRY are part of the standard suite of pigmentation genes which show up as variable across Eurasia. I am confused as to why they did not focus on SLC24A5, a locus which is nearly totally fixed in modern Europeans for the A allele, but may not have been so in hunter-gatherers. But in any case the result is rather clear: the ancient populations sampled here are statistically differentiated from modern populations in the same region, and, seem to have been darkly complected in comparison. The natural inference then is that powerful sweeps of natural selection increased the allele frequencies of lightening alleles in Europeans within the last ~4,000-6,000 years. This is not a crazy proposition; tests for recent natural selection in Europeans are often enriched around pigmentation loci, which are genomically atypical (long homogeneous blocks are common). What this study does is intersect inferences from modern variation with the distribution of variants in an ancient population presumed to be ancestral.

Read More

Evil as an irrelevancy to scientific truth

Werner Heisenberg
Werner Heisenberg

Werner Heisenberg was no Nazi. But his Nobel is obviously well deserved. But, I think it is safe to say that he, like many Germans, made his accommodation with the Nazi regime, as a patriot, if not an ideologue. In contrast Konrad Lorenz actually aligned his understanding of the nascent science of ethology rather explicitly with Nazi thought during World War II. He later disavowed this era in his intellectual life, and became sympathetic to the Green party (though it must be remembered that European right-wing thought has long had a green aspect which might confuse American conservatives). Lorenz won a Nobel for his eminence as a scientist. R. A. Fisher, one of the founders of population genetics and statistics, was famously an unpleasant and self-centered person. If you wish to be confirmed of this simply read the biography coauthored by this daughter, R. A. Fisher: Life of a Scientist. His lack of personal humanity, which his colleagues and family experienced firsthand, does not diminish his contributions to humanity as a whole. Apparently Fisher, a traditionalist Tory, had a much dimmer view of women than the man who he supplanted as the doyen of statistics in Britain, Karl Pearson. This stands to reason, as Pearson was a man of the socialist Left. He supported women’s suffrage and refused an offer of knighthood in 1935. Yet Pearson held conventional views on eugenics and race for his era, highlighting the importance of the “the struggle of race with race, and the survival of the physically and mentally fitter race.” I doubt this distasteful view will prevent readers from making recourse to the Pearson’s correlation when needed. Just as truth of the tool’s utility has no bearing on the character of the toolmaker, so the character of the toolmaker has no bearing on the utility of the tool.

This comes to mind after reading Rebecca Schuman’s Heidegger’s Hitler Problem Is Worse Than We Thought. By Heidegger, she refers to Martin Heidegger, the famously inscrutable but inexplicably influential German philosopher who wrote Being and Time. Invariably when discussing Heidegger one has to make mention of his Nazi years. As a practical matter he was marginalized rather early on in Hitler’s reign. Werner Heisenberg likely gave much more direct material aid to the Nazi regime. But Heidegger’s involvement, like Lorenz’s, does seem to involve more explicit espousal of National Socialist beliefs. Or at least in Heidegger’s case a synthesis of his own esoteric worldview and that of the Nazis. But he would be a footnote were it not for his substantial influence upon Post-War French philosophy, and Continental philosophy more generally. As an undergraduate I had to deal with somewhat lame apologia on Heidegger’s behalf by a philosophy lecturer who was clearly moved by his ideas, but shaken by the reality of his idol’s association with Nazism (for what it’s worth, the individual was of Jewish background, and also admitted a debt to Martin Buber). Schuman’s piece was triggered by the revelation of personal letters from Heidegger which indicate more longstanding and deeper anti-Semitic attitudes and such (totally unsurprising from where I stand, casual anti-Semitism was not uncommon before World War II). She finishes:

You’d have to search far and wide to find an actual Nazi sympathizer working in legitimate academia—but soon, teaching Heidegger may have people wondering. So, should academic sources be subject to the “Hitler Test”? And if they fail, does this mean responsible teaching simply includes a thorough critical contextualization—or banishment from the canon altogether?

Me, I’m a Wittgenstein fan, the Shark to Heidegger’s Jet, so it’s not a question I’m particularly fit to answer. But for those who do use his work, it’s an issue whose undeniable Dasein they must address.

It’s the part about being a fan of Wittgenstein that leaves me confused. Perhaps to the average reader this does not need further exploration, but as an Oberlin undergraduate might say, Wittgenstein is also somewhat “problematic.” To get a sense, just read Ludwig Wittgenstein on Race, Gender and Cultural Identity. I’m not saying that Wittgenstein was on Heidegger’s level, most certainly not, but he was no saint, and a close reading of his biography indicates real inner conflicts with issues such as his self-hatred as an ethnic Jew, as well as unreflective classism and sexism.

Does any of this matter? Why is that humanists have to judge their intellectual forebears by the standards of a modern Oberlin seminar? Would any of us withstand critique and deconstruction a generation down the line? Instead of grappling with the ideas, it seems that in much of the humanities there is grappling with personality’s who can no longer argue, and inveighing against ages long dead. I can compute Pearson’s correlation coefficient without being troubled by Karl Pearson’s socialism and white supremacism. Obviously it is too much to ask the humanities to be view their intellectual production in a similar manner, but it strikes me that they have gone too far down the road of putting the dead through ghostly show trials meant to solidify conformity in the ranks. As I stated on Twitter, the problem with fashionable intellectuals is that they need to be careful not to outlive the fashions of their age.

Who watches how much television?

220px-Braun_HF_1Over on Twitter the always interesting W Bradford Wilcox highlights the fact that children of more educated parents watch less television. I stumbled upon this datum via social conservative blogger Rod Dreher under the heading How Idiocracy Perpetuates Itself. If you read this blog you are aware of W Bradford Wilcox’s ouvre. It is of the nature that both Left and Right can take some comfort in it, as it serves as an informational balm upon their own particular presuppositional sores. And so here I am to suggest that the data do not declare what you fear sirs!

First, let me put into the record another piece of surprising datum, the average American watches 34 hours of television per week. That’s well near a full time job. But wait, remember that average means a large number watch more than 34 hours. Who are these people? Do you know them? By the fact that you read this weblog I suspect many of you do not. Certainly when I ask my friends they’re agog at this much television watching.

Let me try to intuit what a traditional conservative would take away from this level of watching television. “The people have lost their moral center, and lack appreciation for the edifying arts of yore, debasing themselves to partake of the passive hedonism of our fallen age.” Perhaps I stated it pompously, but I suspect you get the picture. What about a liberal? “The people lack the disposable income to avail themselves of the outdoors and finer pleasures of life, and so must make do with the accessible joys of television.” In other words, for the conservative the passive television watching public have missed the mark of their own free will, they have sinned against what their life was meant to be. For the liberal television occupies the role in the lives of the proletariat it does because they lack the economic wherewithal to enjoy all the finer things they obviously must yearn for.

New York Public Library
New York Public Library

But there may be a different answer. The people watch television because they prefer television to what the cultural elites, Left and Right, would term the “higher arts.” The soul of man is not noble, and it is not made in the image of a divine being on high. It is that of a squalid savanna ape rutting in the open and greedily thrusting sweets into its mouth until waves of satiety wash over its corpulent physique. I certainly watched television when I was a younger person, from Saturday Morning Cartoons such as The Smurfs in the 1980s to reality television in the 2000s. In 2004 as a household we stopped paying for cable, and soon enough managed to fob off our television on a friend. It was not because we disdained television, but because we found ourselves gluttons for it too often. I still remember a Saturday dissipated by a Newlyweds marathon in July of 2004.  It was indeed a temptation which we had to toss out of our house, lest we be swallowed by its demands upon our attention.

Read More

The rise of CRISPR

crispr

Google Trends Search Results for CRISPR



For God doth know that in the day ye eat thereof, then your eyes shall be opened, and ye shall be as gods, knowing good and evil.

– Genesis, 3:5

413px-Adam_na_restauratieSometimes science surprises you. Many a time science seems like a slowly sluggish river, inexorable in its progress, but languid nonetheless, beset by turns and twists which delay its progress. Over the last year though I’ve been hearing people whisper in excited tones about something new, something special. And it’s about CRISPR. This may indeed be a world-turned-upside-down moment, and CRISPR may finally cash out the promise that biological science is going to result in a flowering of engineering analogous to what occurred during physics’ ‘atomic age.’

And now the excitement is percolating into the public spaces of the middle-brow media. The New York Times has now finally put CRISPR on the radar of the broader culture, in a rather long article, A Powerful New Way to Edit DNA. As they they, “read the whole thing,” but key in on this quote:

“It just completely changes the landscape,” Dr. Doudna said. Berkeley scientists used to farm out that work to specialized laboratories or companies. Now, she said, “people are able to make mice in their own labs.”

No, it complete creates a landscape. Theory becomes concrete, and the speculations and worries of bioethicists are challenged by the real present, not some vague future. Now a biologist can state, I am become life, creator of worlds. Whereas genetic engineering up to the present has been an almost artisanal act, CRISPR opens up the window into the possibilities of scalable industrialization. No doubt there will be Neo-Luddites demanding we smash the looms, but they will fail, as they always have.

How quickly has this explosion overwhelmed us? According to Google Scholar up until the year 2012 “CRISPR” was in the title of 275 papers. For 2013-2014, 328 results.

Reanalyzing data, it does a mind good

Mindaugas
Mindaugas

There’s been a lot of talk on Twitter and the blogs about PLOS’ new data sharing policy. I don’t have much deep to say, except that I’m for it. I do think from what I can tell that there is a cultural element to the reaction, pro or con. People in genomics seem to be responding of the form “yes, of course.” On the other hand those in other fields have less positive reactions.

You can go elsewhere to hear “both sides.” I am confident that this will be the future, and the naysayers will have to deal. One of the major reasons that formalized data release is good is that in a field like genomics there is more data than people to analyze the data. By this, I mean that you can ask many different questions of data, but you may only be interested in a subset of those questions. Other people in your lab might have different questions, but ultimately you’re probably leaving avenues on the table because you don’t have the time or inclination. To give you a funny example, a few years ago I stumbled on the fact that Dan MacArthur probably has recent (>200 years) South Asian ancestry. As an academic genomicist Dan could have dug up this fact himself, but he has grants and papers to write, not to mention a non-scientific life. So it was left to me to stumble upon the fact. On the margin it’s not that useful to Dan, but it’s something. You never know what’s going to happen when you release data, because you can’t read the minds of others. And that sort of surprise is a good thing.

One of the greatest intellectual philanthropists in recent years has been Mait Metspalu. He has plenty of publications to his name, but he’s also generously released and assembled the data together in convenient form. This allows for easy reanalysis. A few days ago I noticed that he had put up a few more European populations, including understudied groups like Greeks. With the recent flair up on Ukraine I thought I would process some of the new data. I pruned the data set down to 230,000 high quality SNPs, and focused on a large and small data set respectively of 500 and 340 individuals.
Read More