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Turtles all the way down!
Nature Genetics (2013) doi:10.1038/ng.2615
No time to comment extensively, but check out The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan (open access). The paper and the ScienceDaily press release allude to some phylogenetic confusion as to the relationship of turtles to other reptilian lineages, but my own superficial knowledge of this area left me rather unsurprised by this tree. What am I missing? Though reading the Wikipedia entry it seems that spotty marker coverage has produced a lot of controversy. What’s more striking to me is that so many terrestrial vertebrate lineage seem to have emerged over a relatively short period of time. Though presumably this may simply be an artifact of the reality that most lineages go extinct so we’re only left with relatively deep branching patterns. Someone who knows fossils can chime in.
Against the seriousness of theology
Over at The American Conservative Noah Millman and Rod Dreher are having a discussion over the basic premise that founding texts (e.g., Bible, Koran) and individuals (e.g., Jesus, Muhammad) have a deep influence upon the nature of a religion. Long time readers will be aware that I side much more with Millman on this. In fact I recall that years ago in the comments of Ross Douthat’s old blog at The Atlantic (alas, comments are gone from their archives) I took the more maximalist position that theology and logical coherency are not particularly relevant toward understanding religious phenomena in an exchange with Noah (he made an analogy with law, and I responded that that proved my point about the pliability of religious ideas).
The end of demic diffusion
German woman, product of Mid-Neolithic?
Source: Siebbi
Yesterday I pointed to a paper which was interesting enough, but didn’t pass the smell test in relation to other evidence we have (at least in my opinion!). A primary concern was the fact that uniparental (male and female lineages) show a peculiar distribution of variation in comparison to autosomal genetic variation (i.e., the vast majority of the genome) in the case of Europe (genome-wide analysis suggest more of Europe’s variation is partitioned north-south, but Y and mtDNA results often imply an east-west split). But a secondary concern I had was that I felt the models were a bit too stylized. In particular following Cavalli-Sforza and Ammerman the authors concluded that demic diffusion better fits their results of genetic variation in Europe (as opposed to continuity of Paleolithic hunter-gatherers). This is likely correct, but these are not the only two models.
A paper out in Nature Communications, using analysis of the phylogenetics of whole ancient mitchondrial genomes, outlines my primary concern when it comes to the models being tested, Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans:
Haplogroup H dominates present-day Western European mitochondrial DNA variability (>40%), yet was less common (~19%) among Early Neolithic farmers (~5450 BC) and virtually absent in Mesolithic hunter-gatherers. Here we investigate this major component of the maternal population history of modern Europeans and sequence 39 complete haplogroup H mitochondrial genomes from ancient human remains. We then compare this ‘real-time’ genetic data with cultural changes taking place between the Early Neolithic (~5450 BC) and Bronze Age (~2200 BC) in Central Europe. Our results reveal that the current diversity and distribution of haplogroup H were largely established by the Mid Neolithic (~4000 BC), but with substantial genetic contributions from subsequent pan-European cultures such as the Bell Beakers expanding out of Iberia in the Late Neolithic (~2800 BC). Dated haplogroup H genomes allow us to reconstruct the recent evolutionary history of haplogroup H and reveal a mutation rate 45% higher than current estimates for human mitochondria.
Models are great, because rejection is easy
There’s a new paper in PLoS ONE, Female and Male Perspectives on the Neolithic Transition in Europe: Clues from Ancient and Modern Genetic Data, which uses a combination of contemporary and ancient (that is, from subfossils) Y and mitochondrial DNA to understand the demographic past of Europe. Recall that the Y traces the direct male lineage, and the mtDNA the direct female lineage. Because they don’t recombine and generate clean converges back to a last common ancestor (there is no reticulation because there is no sex on these loci; they’re inherited from one of the two parents), they’re amenable to a lot of nifty demographic inference generation. In this paper they test specific models, and produce probability distributions of those models. Since it is open access I invite you to read the paper. The problem with these sorts of papers is I have a hard time trusting them until I replicate the results or have a sense of how cranky the software/code is!
The End of War is not inevitable
I read John Horgan’s The End of War a few month ago now, but I haven’t gotten around to saying much about it. Part of the problem is that I don’t know what to think. It’s a small book which manages to wander in many different directions, and the primary focus is Horgan’s mantra that war is not an inevitable fact of the human condition. Since I agree with that proposition much of the argumentation was lost on me.
And yet there is one aspect of the book which was notable: a disputation of the Richard Wrangham’s work in Demonic Males. I’m still quite a fan of Wrangham’s thesis, but over the years I’ve become much more skeptical of one of the primary methods he employs: extrapolation from another ape (in his case, chimpanzees). Similarly, I’m also skeptical of those who claim that we’re more more like bonobos (here’s looking at you Frans de Waal). No, we’re human beings, and our common ancestor with other apes may have been very different from all the descendant lineages. Our cousins are informative and interesting, but we shouldn’t confuse ourselves for our cousins.
Why atheists can speak in the West
Recently Bill Maher ripped into CSU San Bernadino professor Brian Levin for making the ridiculous equivalence between Christian extremism and Islamic extremism. The problem, which Maher pinpoints, is that Islamic extremism is not that extreme. By this, I mean that Islamic extremism (e.g., Muslim Brotherhood) has much greater broad based support than Christian extremism (e.g., Christian Reconstruction). The difference here is that you’ve heard of the Muslim Brotherhood, while far fewer have heard of Christian Reconstructionists. That’s because the former have democratic support in a populous Muslim country as the ruling party.
The sex gap
I was recently reading Sexual Behavior in the United States: Results from a National Probability Sample of Men and Women Ages 14–94. At N ~ 6,000 it’s a large sample of American sexual behavior around 2010. There was one descriptive result which I thought was interesting, though not surprising. Before the age of 25 it seems that women are more likely to have sex in a given year than an equivalent age man. After the age of 25 this starts to reverse, and men are more likely to be having sexual intercourse in a given year. The dynamics underlying this phenomenon seem to be easily subject to various speculations, so I’ll leave that to readers. Rather, I offer the graph (data drawn from the paper linked above):
Open thread, 4/21/2013
Haven’t been posting much because I’ve busy with a lot of things right now. So tell me what’s been happening the past week?
Don’t forget parents share genes with their offspring
In 2002 I read The Blank Slate. With all due respect to Steven Pinker one of the most fascinating aspects of this book was actually a review of the work of another psychologist, Judith Richard Harris. Harris’ own views are explicated crisply in The Nurture Assumption. In it she reviews and expands on a major insight from behavior genetics: over the long term parental influence seems to be a relatively marginal predictor in terms of many behavioral traits. To be explicit, one can imagine a personality trait which varies in the population. The variation of genes may explain 40% of the variation of the trait. The variation in parental child-rearing techniques, “shared home environment,” may explain 10% of the variation of the trait. The remaining 50% of the variation may be “non-shared environment.” That basically means we don’t have a definitive explanation of what the 50% remainder is, though Harris posits that this consists to a great extent of peer groups.*
Ancient Ainu mariners!
Ainu man from 1870 (colorized)
Well, not really. But a new paper in PLOS GENETICS has a really weird speculation nested into the discussion of what seems a relatively banal paper on the phylogeography of South Americans. It’s a Y chromosomal survey of the populations of the New World, so it’s tracing the male lineage only. Because Amerindian populations likely went through at least one (more if you accept multiple migrations) bottleneck the variation on the Y chromosome is low. Ideally you’d be looking at tens of thousands of markers on the autosome, the non-sex inherited genome. But this group had a very good population coverage. Over 1,000 men from 50 tribal populations, with a focus on South America. Additionally, non-recombining markers are more manageable in terms of reconstructing demographic histories.
The spice, it burns (a bit)
A few days ago I came across this four year old article in The Wall Street Journal on the Naga Bhut Jolokia “ghost” pepper, which is reportedly hotter than Habanero. Since none of the local grocers carry the ghost pepper, I went online. I purchased some seeds. But I also ordered Dave’s Ghost Pepper Naga Jolokia Hot Sauce and Volcano Dust Bhut Jolokia Powder. The latter was spicy, but it actually wasn’t too potent. I’d expected a lot more. Think cayenne powder on steroids. On the other hand, the hot sauce was hot. And unlike Dave’s Insanity Sauce there were flavors besides the heat which one could discern. Unlike Dave’s Insanity the Dave’s Ghost Pepper doesn’t taste like it came out of a chemical plant. I heartily recommend it.
Why are taller people more intelligent?
Credit: Keith Ellison
Update: First, people coming to this weblog for the first time should know that I moderate comments. So if you leave an obnoxious one it’s basically like an email to me (no one will see it). Second, the correlation between height and intelligence is not that high. This association is probably not going to be intuitively visible to anyone, but rather only shows up in large data sets. So please stop offering yourself as a counter-example of the trend (also, the key is to look within families, because the signal here is going to be swamped by other factors when you compare across populations). Third, a friend has sent me another paper which does confirm that even within sibling cohorts there does seem to be a correlation between height and I.Q. The problem is that it is a very small one, so you need large data sets with a lot of power to see it.
End Update
One moderately interesting social science finding is that there is a positive correlation between height and measured intelligence (e.g., on an I.Q. test). Setting aside the possibility that I.Q. tests designs are culturally biased against shorter people, one wonders why this is so. Height is a highly heritable trait where most of the variation within the population is due to variation as numerous genes. In other words, there isn’t a “tall” or “short” gene, but thousands and thousands of variants which shape the variation of the trait across the population. When I say it is highly heritable, I mean to imply that most of the variation in height in developed societies is due to genes (80-90%). As it happens intelligence is somewhat similar in its genetic architecture, heritable due to small effects across many genes. In general estimates for the heritability of intelligence tend to be somewhat lower, on the order of ~50% rather than 80-90%.
It is due to the highly polygenic nature that both of these traits have been posited as candidates for a “good genes” model of sexual selection. Presumably individuals with a higher mutational load will have lower intelligence and be shorter, all things equal, because these traits have extensive genome-wide coverage and are big targets. Geoffrey Miller’s The Mating Mind: How Sexual Choice Shaped the Evolution of Human Nature, was predicated on this logic. If the mutational load argument holds then the reduced I.Q. of shorter individuals may simply be due to the same cause: “bad genes.”
Managing the sea of data: Mendeley and PubChase
Every few months someone asks me what I use to manage my papers. Stupidly, I don’t use anything. Or I haven’t. Over the past few weeks I’ve been playing around with PubChase and Mendeley. You probably know of the latter, and the fact that it’s been purchased Elsevier. Elsevier is what it is. Mendeley on the other hand is a firm that I have a positive view of, in part because of their culture of openness and support for the free flow of information, but also due to the fact that I’ve known their head of outreach for ten years. You trust people, not things. Mendeley‘s not a charity, and I don’t begrudge them their new resources now that they are under the corporate wing of Elsevier. Whether you’re pessimistic or optimistic about their future, I think caution is warranted.
Genes are not just rhetoric
Remember that genetics (in the Mendelian sense) predates the understanding of what a genes was in a material sense (a segment of DNA) by 50 years.
Pedigree + Personal Genomics = More Insight
Update: Feature was always there. Just hard to find.
23andMe did a site redesign. Most of it is user interface clean up, but there one particular cool function: if you have an individual’s pedigree up to grandparents you can see which allele they inherited. Just select “Family Traits” under “Family & Friends.”
Why a foolish instinct?
I remember the specific moment when I was 13 that I became aware of the 1950s hit “Why Do Fools Fall in Love” by Frankie Lymon & The Teenagers. I’m rather sure I heard it before, but it didn’t penetrate my consciousness. But as we all know puberty changes things, and the idea of love becomes more comprehensible. As I’ve grown older I’ve also started to ponder the lyrics a bit more. Not out of any sense of sensitivity toward music criticism, but because of the evolutionary implications. Here are some relevant sections:
Some macrohistorical context about Myanmar
For whatever reason The New York Times has been putting out many articles on Myanmar recently. For example, Buddhist-Muslim Tensions Spread as 8 Detainees Die in Indonesia. Second, Ethnic Rifts Strain Myanmar as It Moves Toward Democracy. I’m a subscriber to The New York Times, so I think the paper of record is worthwhile. But quite often its international pieces lack historical and cultural context, and don’t impart the heart of the matter to readers. (see: The New York Times flubs basic facts about Islam) First, the simple part. The “religious conflict” in Myanmar is really just an ethnic-racial conflict. Demographic statistics from Myanmar are pretty woolly, so one can’t say anything with any great confidence, but it seems likely that the majority of Muslims in that nation are ethnic Rohingya. These Rohingya derive from agriculturalists who emigrated at some point in the last few centuries from eastern Bengal, and, that is the region which has always been predominantly Muslim. There are two giveaways as to their origin. First, their language (from Wikipedia):
Does one need math for a career in science?
E. O. Wilson has a op-ed in WSJ which I find quite interesting, Great Scientist ≠ Good at Math:
For many young people who aspire to be scientists, the great bugbear is mathematics. Without advanced math, how can you do serious work in the sciences? Well, I have a professional secret to share: Many of the most successful scientists in the world today are mathematically no more than semiliterate.
…
This imbalance is especially the case in biology, where factors in a real-life phenomenon are often misunderstood or never noticed in the first place. The annals of theoretical biology are clogged with mathematical models that either can be safely ignored or, when tested, fail. Possibly no more than 10% have any lasting value. Only those linked solidly to knowledge of real living systems have much chance of being used.
Wilson has been on this for a bit now, to the bewilderment of some of the scientists I follow on Twitter (granted, the people I follow tend to be quantitative genomics types whose backgrounds may have been in math, physics, or statistics). Two immediate things come to mind reading this. First, a disproportionate number of the famous and successful scientists alive today are old, like E. O. Wilson. Just because you could get by with a certain level of mathematical fluency as an enfant terrible in the 1970s does not mean that that will cut it in the 2010s. Great scientists who are mathematically weak often have collaborators, post-docs, and graduate students, who do their bidding. It might be a different matter if you aren’t one of the Great Ones of the earth. From what I can tell scientists who are doing the hiring who don’t have mathematical skills prefer candidates who do have mathematical skills.
A plethora of beats
In the recent past the standard model of information distribution was one that had a few top-down nodes. There was print, television, and radio. Journalists collected a salary from the institution (obviously there were prominent exceptions in the form of famous columnists, but these were numerically not significant), which tasked them with specific beats. This traditional model is coming under great pressure, and to some extent dissolving. I don’t keep track of journalism, as such, because I’m not a professional journalist.* But it’s hard to avoid the headlines which chronicle layoffs, as well as the reality that professional journalist’s are being undercut by high quantity and (often) low quality content. Combining this with the fact that the null model of a free internet in terms of media access is likely to be undermined quite rapidly in the near future, and we’re in for some restructuring and updating of expectations.
One change has been the rise of subscription only emails by several young journalists. I subscribe to Conor Friedersdorf’s The Best of Journalism. Now in a recent conversation with Michael Brendan Dougherty Friedersdorf describes the former’s baseball newsletter, The Slurve.
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Razib’s Pinboard
- High Plains Aquifer Dwindles, Hurting Farmers - NYTimes.com
- Roots of future tropical rainfall: Sea level influenced tropical climate during the last ice age
- About That Dissertation | National Review Online
- Study: Kids Are Prejudiced Against Fat People by Age 4 - Lindsay Abrams - The Atlantic
- Portland fluoride vote: Will medical science trump fear and doubt? - Slate Magazine
- Investigative Genetics | Abstract | Clinal distribution of human genomic diversity across the Netherlands despite archaeological evidence for genetic discontinuities in Dutch population history
- Archaeological genetics: It's not all as old as it at first seems
- Trends in Genetics - Properties and rates of germline mutations in humans
- www.culturalcognition.net - Cultural Cognition Blog - Annual "new study" finds 97% of climate scientists believe in man-made climate change; public consensus sure to follow once news gets out
- Will Google Glass finally make doing this gauche? - Quartz
- For Gay Men, a Fear That Feels Familiar - NYTimes.com
- Daniel Dennett's seven tools for thinking | Books | The Observer
- Insect repellents’ EPA approval: Evaluating DEET, picaridin, lemon eucalyptus oil and all-natural ingredients. - Slate Magazine
- Gymnophobia - Wikipedia, the free encyclopedia
- Viral star Kai the hatchet-wielding hitchhiker wanted for murder - latimes.com
- Economic Recovery, Made in Bangladesh? - NYTimes.com
- Amazon's never-gonna-happen monopoly.
- Google Glass review: These goofy spectacles aren’t lame. They might even replace the smartphone some day. - Slate Magazine
- Liberals for Low Wages | The American Conservative
- Snoop Dawged Gene Expression
