The blood of the first men runs thin in our kind


According to a new paper in Nature, Ancient gene flow from early modern humans into Eastern Neanderthals, a basal population of anatomically modern humans mixed with eastern Neanderthal populations on the order of ~100,000 years ago. The figure above is from the paper, and shows (on the left)  the proportions and direction of gene flow across the phylogenetic tree, and (on the right) the dates of divergences and effective population sizes of the various groups. In The New York Times Carl Zimmer has a write-up, Ancient Humans May Have Left a Genetic Mark on Neanderthals (also, see Ewen Callaway in Nature, Evidence mounts for interbreeding bonanza in ancient human species). It’s useful to read, because he reports that some of the researchers assumed their results were in error, so they double-checked, and, other prominent researchers believe that the results are broadly credible. This doesn’t mean the results are correct…though the team that came out with this has people I trust to attend to details, and the results are not implausible on a priori grounds.

51t3ZeiK+vL._SX331_BO1,204,203,200_Where does this lead us? As observed on Twitter there are some curious results in this paper in terms of the phylogenetic relationships and demographic history of human populations. The modern human lineage which contributed to the Altai individual seems to have done so ~100,000 years ago. This is 40,000 to 50,000 years before the “Out of Africa” event which we know of, and which seems to have resulted in the patterns of human genetic variation outside of Africa, excepting archaic admixture, that we see today. As noted in the paper there have been recent finds in locations such as China of very ancient pre-“Out of Africa” modern human remains, and there has always been the Skhul and Qafzeh hominids in the Near East. So that’s not too much of a problem necessarily. But, if you look closely at the phylogenetic tree above San diverge from other modern lineages ~200,000 years ago, well before the admixture event, but the modern human ancestry in the Altai Neanderthal looks equally related to all modern humans. That seems peculiar, since in the 100,000 intervening years there should have been significant structure to sample. There are a variety of ways to “resolve” this…though as one of the authors stated, there are many reasons why the date of the divergence of the various groups and admixture differ so much (e.g., archaic admixture into the San might push back their divergence from other groups). I need to think about this more and read the supplements. The picture in the details is getting cloudier, not clearer….

But the overall result does clarify and highlight some big picture inferences we can make in generating a framework toward understanding new results. Mait Metspalu’s group is going to publish a paper on low levels of pre-“Out of Africa” modern admixture in Sahul populations (that is, a earlier movement of modern people than the canonical one), and I now judge that their result is a true positive to a higher degree than earlier. These Altai Neanderthals likely did not contribute to modern human Neanderthal ancestry, as the Neanderthal ancestry in modern humans is closer to that of European Neanderthals (who did not have modern human ancestry like the Altai individual). Follow that?

The upshot is that these results should change our prior expectations about the nature of ancient human population structure. Yes, it was complicated, but there’s a pattern. The genetic patterns indicate that there was selection in the genome against the introgressed variants, so Neanderthals and modern humans exhibited hybrid breakdown. In light of no such genomic evidence for admixture of Eurasian ancestry into KhoeSan (I’ve asked, people have looked), that suggests we know that for hominins hybrid incompabilities seem to arise on the scale of between 200,000 and 600,000 years.  It also seems that due meta-population dynamics lineage extinctions were very common in hominins. The genetic relatedness of Neanderthals across human swaths of territory indicate that they were subject to this dynamic, where there were massive lineage pruning events over the 600,000 years that this group was a distinct population. With modern humans, we now know that first settlers do not always leave a genetic impact later on because of extinction events. With these facts under our belt it is less surprising if there were “false dawns” of the “triumph of humanity.”

mmXlVoUaP2In-yXZPl_WuZgWhat these results do warrant though is the final expiration of a particular narrative of the explosion of humanity ~50,000 years ago due to singular biological changes that cascaded themselves into a cultural explosion, where the hominin-made-man swept all before them. Probably the best illustration of this thesis can be found in Richard Klein’s 2002 book, The Dawn of Human Culture. In it he proposes that 50,000 years ago there was a single mutation which resulted in a pleiotropic cascade, and allowed for the emergence of full elaborated language and ergo the package of features which we associate with behavioral modernity. This model was presaged in the earlier decade with popularizations of “mitochondrial Eve” which implied that all humans were descended from a very small tribe resident in East Africa on the order of ~100,000 years ago. (the date varied as a function of the vicissitudes of mutational rate estimates)

Here’s what we know now that changes this. First, there are populations within Africa, in particular the the San of the far south, who diverged much earlier than 50,000 years ago. The most recent genomic estimates are suggesting divergence dates as early as ~200,000 years before the present. Second, the effective population size of humans outside of Africa is incredibly small, suggesting expansion from a very small founding population, but one should be cautious about generalizing to groups within Africa. That is, the blitzkrieg sweep model of modern human expansion does not hold to within Africa, and there is both archaeological and genomic inference to indicate the persistence of highly diverged hominin lineages in that continent until relatively recently. And, these lineages may have admixed with modern humans just as they have outside of Africa.

Finally, the emergence of H. sapiens sapiens supremacy seems to have been a process, not a singular event which emerged de novo like a supernovae in the hominin firmament. The Omo remains in Ethiopia were anatomically modern humans. The people who gave rise to Omo lived ~200,000 years ago. The encephalization of the human lineage increased gradually up until around ~200,000 years ago, and Neanderthals were famously the most encephalized of all. Therefore, some form of modern humans were present within Africa for 150,000 years while other lineages were dominant elsewhere. Remains from places like China suggest though that offshoots of African humanity did push into the rest of the world…but they may not have left much of a genetic trace. This may have been part of movements due to climate change during the Pleistocene, or one of the natural migrations which a consequence of Malthusian pressures and inter-deme competition which afflicted humans. But they clearly did not conquer all before them. Why? We don’t know. And we don’t know why the situation was different 50,000 years ago. As a null hypothesis one might entertain the possibility that it was random. That periodically turnovers occur, and it just so happened that an African lineage lucked out in a massive extinction event. But that’s hard to credit when you consider that these modern humans crossed into Sahul and Siberia after sweeping aside other groups, and then eventually crossed over into the New World. There was something different about us. Additionally, the modern humans eventually absorbed or extirpated other lineages within Africa too.

A generation ago many people thought they had the answer. That man was born 50,000 years ago on the East African plain, and the gods gave him the world. Only he was endowed with a soul. Today we know that that’s wrong. We just don’t know what’s right.

Addendum: We need to start thinking about Eurasian gene-flow into Africa over the Pleistocene.

Thou shalt love thy neighbour as thyself

41V-vYSuQrL._SY344_BO1,204,203,200_Everyone seems to have a “theory” of religion. About 20 years ago Rodney Stark and William Bainbridge published A Theory of Religion, which utilizes a “rational choice” framework, and engages in deduction to make some predictions. As it happens, I believe many of the predictions have not been born out exactly (to be precise, it seems that the supply-side model of religion works best in only a particular type of society, of which the United States may be the best case). A little over 10 years ago David Sloan Wilson published Darwin’s Cathedral: Evolution, Religion, and the Nature of Society, which attempted to resurrect an organismic metaphor for human societies and a functionalist rationale for the emergence of religious institutions. That is, religion emerges and persists because it maintains and allows for particular functions essential for a society. Wilson’s book was heavy on description because the field was nascent, at least in its newest iteration. Though it is true that intuitively the idea is appealing, scientifically for various reasons it had gone into some disrepute, with evolutionary theories of society in general.

41I42XDmNfL._SX335_BO1,204,203,200_In Theological Incorrectness: Why Religious People Believe What They Shouldn’t, the author reports on the relatively robust cognitive research which suggests that there is a disjunction between reported beliefs of people of the gods they believe in, and the mental models that people hold in their heads about the gods that they can conceive. Humans may ascribe omniscience to gods, but their behaviors and narratives when pushed off any script suggest that they don’t take this at face value in any deep manner. Or, more accurately, they can’t really construct a plausible model of the universe where gods are omniscient. Similarly, though there is a wide range of high-level religious ideas across denominations, from the spare monotheism of Islam, the de facto* polytheism of Hinduism, to the marginalization of gods in Theravada Buddhism, the author’s field work in Sri Lanka suggests that in fact the average peasants’ conception of supernatural agents was surprisingly uniform across religious groups.

Religion_Explained_by_Pascal_Boyer_book_coverThis is unsurprising. Both Scott Atran in In Gods We Trust and Pascal Boyer in Religion Explained develop in detail the evolutionary anthropological raw material from which religious phenomenon seems to be constructed. The abstruse and arcane manner of theological and metaphysical speculation which elite religious practitioners engage in is to a great extent a function of the reality that prosaic human cognition is highly limited and constrained. Perhaps the most surprising revelation of this body of research for me is that ofttimes believers in a particular creed are not quite clear on the details of their own religious profession. As I am an atheist who has never really had any belief in gods in any deep manner this took me by total surprise, but then, I had no intuition to go on. But, after realizing this fact I became much more skeptical of the idea that “Christians are x because the Bible says….” or “Islam is x because the Koran says….” As per Kahneman’s scheme in Thinking, Fast and Slow, much of religious phenomena probably bubbles up from system 1, but the preoccupation of elite institutional religion is geared toward system 2 (not to go off on a current events tangent, but this might explain why so many notionally conservative Christians are willing to put their orthodoxy to the side and support Donald Trump, he appeals to their system 1 instincts).

Around 2007 I basically stopped reading much about the anthropology of religion. Despite this my internet footprint in this area was large enough that I got a review copy of Marketplace of the Gods: How Economics Explains Religion (answer: it doesn’t). But I stopped paying much attention because it didn’t seem like much was changing on the margin. The cognitive and evolutionary anthropologists had laid the ground-work  for understanding the basic individual foundations of religious belief. Some thinkers were attempting to develop a model of religion which was more high-level, where religious identity serves as “meta-ethnic” markers (e.g., Peter Turchin). And, theorists in cultural evolution and human behavioral ecology were attempting to push forward models where religious identity served as drivers of inter-group competition.

k10063But for me the essential element has always been individual scale empirical results. Some of Arya Norzenzayan’s research projects that I’ve seen, reported in Big Gods: How Religion Transformed Cooperation and Conflict, goes in the right direction, though I was still not sure as to the generality or robustness of some the results of his group (a lot of one-off psychological research does need to be put under a high level of scrutiny). But now with a new paper in Nature I am starting to be convinced.

It’s titled Moralistic gods, supernatural punishment and the expansion of human sociality:

…Here we focus on one key hypothesis: cognitive representations of gods as increasingly knowledgeable and punitive, and who sanction violators of interpersonal social norms, foster and sustain the expansion of cooperation, trust and fairness towards co-religionist strangers…We tested this hypothesis using extensive ethnographic interviews and two behavioural games designed to measure impartial rule-following among people (n = 591, observations = 35,400) from eight diverse communities from around the world: (1) inland Tanna, Vanuatu; (2) coastal Tanna, Vanuatu; (3) Yasawa, Fiji; (4) Lovu, Fiji; (5) Pesqueiro, Brazil; (6) Pointe aux Piments, Mauritius; (7) the Tyva Republic (Siberia), Russia; and (8) Hadzaland, Tanzania. Participants reported adherence to a wide array of world religious traditions including Christianity, Hinduism and Buddhism, as well as notably diverse local traditions, including animism and ancestor worship. Holding a range of relevant variables constant, the higher participants rated their moralistic gods as punitive and knowledgeable about human thoughts and actions, the more coins they allocated to geographically distant co-religionist strangers relative to both themselves and local co-religionists. Our results support the hypothesis that beliefs in moralistic, punitive and knowing gods increase impartial behaviour towards distant co-religionists, and therefore can contribute to the expansion of prosociality.

The top-line result is displayed in the figure above. In short those who held beliefs about moralistic gods were more altruistic, more ethical, toward co-religionists. This confirms a deep human intuition. Recall that historically atheists were held in suspicion because they were perceived to be unethical, and even today in the United States most Americans view atheists unfavorably. Though these results don’t say anything about atheism (it seems unlikely any of the respondents were atheists!), it does suggest that moralistic gods do nudge many people toward particular behaviors, so they logically infer that removing the god from the equation would result in the converse.

This is only a letter, so quite short. You really need to read the supplements to get a good feel. Additionally, their data and code are online.

Some of you may take from these findings deep and wide-ranging conclusions as to the utility of religion in the modern world. Or, you may rebel against accepting that moralistic gods really could make people more altruistic. I would suggest that people not draw too much from one single study, but rather see this as one of the first empirical steps toward understanding the relationship between religion and prosocial behavior in a cross-cultural and controlled context. Too many of the economic analyses of religion have focused on data sets amenable to econometric analysis, while detailed ethnographic studies were often too qualitative and theory poor. This research programs combines empirical richness with theoretical rigor.

Many “new atheists” and religiously convinced will continue to ignore this research, because it will (possibly) challenge their deeply held notions. Basically, they believe they know all their needs to be known about religion. In contrast, there are those of us who believe that there’s a lot we don’t know, for we haven’t bitten of the apple and are not as the gods.

* I make the qualification because I am aware that many Hindus would vociferously assert their religion is monotheistic fundamentally. I’m not interested in technical details, but rather wish to emphasize that Hinduism has traditionally been more accepting of a multiplicity of god-heads, even if the ultimate source is unitary in a monistic understanding of the universe.

Open Thread, 2/15/2016

31-UGeAXYVL._SY300_I went back to the gym for the first time since I got my pull-up and chin-up stand. Mostly I was just waiting until the people who show up around New Years finally dissipate. I got a sense that I was getting stronger just from how much easier it was to do a greater number of pull ups recently, but I was shocked to see that I could do about 20 pounds more on a lat pull-down and maintain form! I noticed a similar effect on the chest machines (fly and press). As most readers know I got serious about my health in about the spring of 2014 and began running and hitting the gym about then, but I’m a little surprised at how much gain I’ve had from just doing pull ups at home. My own suspicion is it has less to do with the better quality of the exercise, than the reduction in activation energy of actually working out when the stand is right there in my home office. (a long-time reader has also started doing pull ups, and reports that he’s seeing immediate results)

s106325072993223414_p3_i2_w1240In other news, I got some mealsquares. I like them much better than soylent. They’re 400 calories a serving at $3 a pop. Basically like very dense banana bread. Often if I haven’t had much of a breakfast I’ll eat two.

The convenience is good, but one thing I’ve started to question is the whole idea of a “nutritionally complete meal” that can work for everyone. Much of the extra cost in these sorts of ‘scientific’ foods is getting to nutritional completeness, but what if you’re just optimizing for outmoded government recommendations? Consider that the reference daily intake you see on nutritional labels are “level of a nutrient that is considered to be sufficient to meet the requirements of 97–98% of healthy individuals in every demographic in the United States.” That means that the majority of people do fine without getting the recommended dosages of lots of nutrients. That’s why vitamin deficiency isn’t a major problem and supplements are mostly useless.

Meritocracy: Harvard PR vs. Factual Reality. Ron & company got the signatures needed. Meanwhile, Harvard wants to revolutionize college admissions. Will it work? No.

12715644_10153469513932984_8201782310467061513_nCalifornia gets a lot of hate. It’s expensive, and the taxes are high. But I really don’t get the people who say that they “like seasons”. Why exactly? It’s as if you have a climatic fetish or something. Yesterday it was in the 70s and I decided to go pick some kumquats form the tree next to my house. I wore a t-shirt and shorts. Today I went into the office with sandals on. Meanwhile I’m seeing friends in the Northeast posting images on Facebook like they were taken from The Road.

Someone asked me about a book on evolution (as in, what should they read). There are plenty out there. Mayr’s What evolution is is decent, but I noticed that the Charlesworths came out with something in the early 2000’s, Evolution: A Very Short Introduction. I got a copy, though I don’t know when I’ll get to it. The main issue though is that I have a lacunae at this point for stuff outside of evolutionary genetics, and Charlesworth & Charlesworth probably isn’t a way to fix that. Prothero’s Evolution: What The Fossils Say and Why It Matters fills in that hole a bit, but it’s been around six years and I don’t recall much.

We’ve had debates about Amy Chua’s Battle Hymn of the Tiger Mother on this weblog before. Overall I like Chua’s oeuvre, but she’s a bit superficial and over-hyped. It probably has to do with the fact that she’s trained as a lawyer, and so can nail the style but doesn’t have enough of the cognitive toolkit to process large amounts of empirical data (as opposed to selectively marshaling her “case”). Chua is persuasive if you are primed to believe her. Well, Joshua Hart and Chris Chabris have a paper out, Does a “Triple Package” of traits predict success? In short, no. So don’t abuse your children!

zyZ & Y is as good as advertised. Definitely the best Szechuan in San Francisco that I’ve encountered. But I still will give the nod to Mala bistro, where the flavors are stronger and have more of a kick. Then again, I’m probably biased, since I can barely taste mild flavors.

Yes, I think long but fixed terms for Supreme Court Justices would be a good thing. I also think our courts have too much of a role in the governance of this country…but looking at the world-wide trends, it strikes me the United States might be ahead of the curve on that.

I’ve put the reader survey up in CSV format. Recently I was having dinner with a few friends. One of them (a recent college grad) mentioned he’d been reading me since 7th grade. This prompted my other friend, who is less aware of my blog history, to express surprise and ask how many years I’d been blogging. She was taken aback when I said since 2002. The median number of years people have read me is 4 years, with a mean of 4.8. The standard deviation is 3.3 years, and the third quantile goes back 7 years. That means that at least 25% or so of the readers date to the ScienceBlogs years, which sounds about right.readersThe density plot to the left makes it clear that many people are anchoring to values like 5 or 10. Several people claim to have been reading me since 2002, though those of you claiming that you’ve been reading me for 16 years are off (I changed the values to 14). The drop off in the last few years is simply a function of the fact that the people most likely to actually fill out a survey like this are regular readers, and those who are only recently sampling probably don’t have any incentive (this sort of distribution where there’s a drop off at 1-2 years has been pretty consistent over all the years I’ve posted a survey).

Jerry Coyne has a post up where he comments on Stephen Fry leaving Twitter. He ends:

Do readers here use Tw**er? If so, do you use it to get information, enjoy drama, or to simply communicate with others in a non-rancorous way? My own view, which is mine, is that if you have a website on which to write at length, there’s simply no need for Twi**er to communicate anything other than articles that you wish others to see. And Fry does have his own website.

I have my own website, and I’m very active on Twitter. For the first few years I did as Jerry does, mostly using Twitter to push my own content out there passively. What changed? First, Twitter became the locus for a lot of scientific conversation. This is especially true in genomics, where lots of people are on the computer facing a terminal, but have a browser open somewhere. At Jerry’s stage in his career and his prominence there’s no need for him to be consuming on Twitter, as he is mostly in production-phase. But a lot of conversations that might have occurred on blogs have now moved to Twitter (a very prominent blog like Jerry’s is exceptional). At least in genomics. If you want the latest responses to a big splashy paper, look to Twitter.

Second, if you don’t really care too much about being “problematic” it’s not that big of a deal being on Twitter. When the whole issue with The New York Times happened some progressive people on Twitter demanded that I justify my previous opinions and explain myself. I ignored them, because I didn’t really care about being validated by their opinions, since I’m not a member of their tribe in the first place.* Twitter be scary if you worried that you’ll be up next on the docket of cyber-show-trials. But if you aren’t invested in the idea of being part of a movement/group with particular shared norms then it isn’t as much of an issue since you don’t care too much whose toes you step on inadvertently if you can’t keep up with the treadmill-of-social-justice. The same goes in real life, when people who try to correct or educate me on social justice, they are surprised when I brush them off and tell them I’m conservative and I couldn’t care less (their prior assumption is that I share their values since I’m currently in academia). I don’t know what the equivalent for conservative deviationism would be…I have a fair number of high profile conservative Twitter followers, and my acerbic atheism, pretty clear isolationism, and periodic sympathy for positions more in keeping with left-wing populism haven’t triggered a “call out.” But I don’t care. Most of the people I follow on Twitter are scientists.

Two papers submitted for your approval: A Genealogical Interpretation of Principal Components Analysis and Population Structure and Eigenanalysis.

The latest on the GCTA wars in reverse order:

Response to Commentary on “Limitations of GCTA as a solution to the missing heritability problem”

Commentary on “Limitations of GCTA as a solution to the missing heritability problem”

Limitations of GCTA as a solution to the missing heritability problem

GCTA: A Tool for Genome-wide Complex Trait Analysis

These need serious digesting. For various reasons I lean toward the GCTA camp.

Who killed Nokia? Nokia Did. One can quibble on the details, but the phenomenon outlined is well known in the corporate world. Organizations evolve, and over time feedback loops snowball. I had a friend who worked at Sun during the tail end of its pre-Oracle days, and he said it was very depressing, as the only people left were those who either at the end of their careers or had no other options.

Is anyone reading anything interesting?

* A few prominent public intellectuals did contact me and suggest I explain myself in long-form because they thought my voice was important to have in the public arena. But I don’t see myself as a journalist, and frankly my experience last spring convinced me that there’s no way I should ever devote most of my energy to this sort of stuff (some of my less socially intelligent readers actually thought that it was a big deal for me personally that The New York Times dropped my contract, but the reality is that it fell into my lap without any expectation, and most of my time is allocated to and income derived from things that don’t get any mention on this weblog, which is more a hobby about my intellectual interests). I don’t plan on “explaining” myself ever, because I try to say what I think is true. That’s just a major problem for anyone trying to be a public intellectual today, unless they are independently wealthy. But the truth is kind of a much bigger deal than any ephemeral exposure via mainstream media for me. It’s what I began with as a child, and it’s what I plan to die with as an old man.

Three admixture recipes for Razib Khan

ancestryJust got my results back from AncestryDNA. I’ve done autosomal ancestry tests with 23andMe and Family Tree DNA, in addition to analyzing the raw data myself. When I first got the results the Y and mtDNA results were totally expected; R1a1a and U2b respectively. Those are typical South Asian lineages. But what surprised me was how East Asian I turned out to be. This is really obviously in ADMIXTURE and PCA, but curiously 23andMe, even in speculative mode above, gives a relatively low fraction. Below 10%. You can see in the AncestryDNA results that in fact I’m a lot more East Asian than that, as well as a Melanesian-like element. I suspect that the latter is due to Austro-Asiatic admixture, in particular from my mother. ftdna Family Tree DNA gives similar proportions.

The differences don’t invalidate the robustness of admixture analyses. It’s just that these results are always carved around the joints and reifications which are human-digestible, and humans are the ones who pick the specific parameter values and data inputs around which the models are constructed. The companies have different reference populations, and these reference populations are the data inputs around which individuals are constructed as linear combinations. 23andMe uses a sophisticated system that looks at haplotype blocks, but it seems quite clear that finely admixed people are sometimes difficult for them to resolve (because of the uniqueness of their blocks in comparison to their reference populations).

And you shall be as gods, knowing additive and independent….

9780582243026_lPeter Visscher has an essay in Genetics, Human Complex Trait Genetics in the 21st Century. I believe it’s open access, so I encourage you to read it. It strikes me that he’s conflating genetics with all of biology when he states that “Genomics will become synonymous with biology.” But that’s my main area of skepticism. Visscher’s influence is in part due to the fact that he leverages a background in quantitative genetics with genomics. If there is anything I think Visscher will be remembered for, I suspect it’s his association with the revolution triggered by GCTA. Many complex traits which seemed intractable are now coming down to earth. The ground is changing underneath us, and the public and even many biologists don’t feel the tremors.

Here some important selections form Visscher’s piece:

With gigantic sample sizes, it will be possible to explain most, if not all, additive genetic variation for a range of traits and to tackle old questions about the nature of mutational variance, the maintenance of genetic variation, the genetic control of variability, and the elusive quantification of variation due to nonadditive and genotype-by-environment (G × E) interactions.

Model organisms such as fruit flies, mice, and worms have been at the forefront of major discoveries in genetics over the last century. Many if not most of these discoveries were about mechanisms, e.g., mechanisms of natural selection, speciation, recombination, imprinting, response to selection, and gene function. Experimental organisms have been less successful in modeling human disease (in the sense of leading to successful prevention or treatment), even, for example, when engineered mutations in mice are identical to those discovered in human patients. My prediction for future research into human disease causes and drug discovery is that humans will become a “model organism” through exploiting new technologies such as tissue-specific cell lines and gene editing.\

One major application of studying complex traits in humans is in medicine. Indeed, most of the public funding to study complex traits in human populations has come from medical research funding bodies such as the National Institutes of Health, the Wellcome Trust, and the Medical Research Council. Genetic technologies, including genome sequencing, have already led to changes in clinical practice, for example by personalizing drug advice for cancer depending on the tumor’s genomes. I believe the very near future will see this extended to diagnosis of Mendelian disease and to providing more refined personalized treatment advice for cancer.

Happy Darwin Day! Now read some Fisher….

41L69h9XdRL._SX331_BO1,204,203,200_It’s Darwin Day. I’m a little ambivalent about the sort of cultishness that sometimes accrues to Charles Darwin. But it is probably a phenomenon that only makes sense in light of the culture war started by evolution-rejectionists. But there is reason to be optimistic on this; according to the GSS young people tend to be more accepting of evolutionary theory. And I was intrigued by these Pew data which indicate that a substantial minority of religious people accept a naturalistic evolutionary model! (Muslims have a high fraction of this element, and, of Creationists, indicating that this is a particularly heterogeneous group)

I’m gratified that ~40 percent of my readers have read The Origin of Species. But, I’m a bit concerned that only ~8 percent have read The Genetical Theory of Natural Selection (though one more than The Structure of Evolutionary Theory). Darwin is important, but for the stuff that is more the bread & butter of this weblog, I think R. A. Fisher is probably more relevant. That is, an analytical and formal understanding of evolutionary process. With that in mind I would recommend that if you can afford it, get a hardcover The Genetical Theory of Natural Selection with the forward by J. H. Bennett. Otherwise, read the original version online. Focus on the first half, and understand that Fisher was not God, so it’s how he conceived of a problem, not his particular solution, that’s useful (he was wrong on dominance it seems for example).

2016 Gene Expression Reader Survey

I’ve been doing reader surveys for a while, so I figured now was about time. For the demographic questions I tried to mimic the GSS more than usual. It’s two pages and 40 questions, but it should be pretty quick (it’s not a quiz, you shouldn’t have to think).

Here is the link to the survey.

There will be instant result updates, but after a few days I will post a link to the raw results on this blog post (I’ve turned off IP collecting by the way). Usually I get 300-400 responses, so I assume that’s the “core” readership. It’s been stable for a long while now.

You can use this as an “unlurk” thread if you want.

Update: You can check the results as they get updated. I will put the raw results link up when there are more people who submit….

The technology and science of “gene drive”

41eQOJU5FBL._SX331_BO1,204,203,200_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

Over at MIT Tech Review my friend Antonio Regalado has an article up, We Have the Technology to Destroy All Zika Mosquitoes, which seems to promise almost god-like powers in the hands of bio-engineers. But, one thing that I did suggest was that these sorts of articles which focus on technological element of developing story don’t inform the public that there has long been an understanding that there are selfish genetic elements which violate Mendel’s law of segregation. In other words, the technology is leveraging a natural phenomenon. These forces may be pervasive, but they do not seem to ultimately upend the balance which allows for the persistence of Mendelian transmission, especially for salient morphological (a lot of the eukaryotic genome may be shaped by intragenomic dynamics though). This was at the heart of Mark Ridley’s book The Cooperative Gene: How Mendel’s Demon Explains the Evolution of Complex Beings.

Second, it probably is useful for people to review some of the science. Here is a paper which seems open access, A CRISPR-Cas9 gene drive system targeting female reproduction in the malaria mosquito vector Anopheles gambiae. 267858Anyone who is more interested in the topic needs to read Austin Burt and Robert Trivers’ Genes in Conflict: The Biology of Selfish Genetic Elements. And, as I pointed out to Antonio meiotic drive has been on the minds of population geneticists’ for decades.

Personally I haven’t given deep thought to the utilization of gene drive in public health campaigns, though it seems to be one of the favorite tools for those arguing for mosquito extermination. One the one hand the potential for ecological disturbance is not trivial, though perhaps more in a case where gene drive methods are executed badly and other species’ are inadvertently effected (my understanding is that conventional mosquito eradication has not led to ecosystem collapse anywhere). And on the other hand there is the fact that humans constantly disturb the ecology of many organisms. Genetics, even gene drive, is not magic. At least in the sense that Arthur C. Clarke would have defined magic. A lot of the fear is just fear of the unknown.

Update: Kevin Esvelt leaves a comment I’m going to reproduce below the fold. Note the emphasized section. I’m pretty shocked:
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