ScienceBlogs is shutting down at the end of the month

The people, whoever they are, at ScienceBlogs have announced that they’ll be shutting down at the end of the month. I actually should have all my archives, so there’s no worry on that end for me.

The first few years for Seed were pretty flush for a small operation. There were a couple of blogger meet-ups in New York City (and a fair number of ad hoc meet-ups in the San Francisco Bay area, as several of us lived there and many people traveled there). But the Great Recession hit media hard, and that included Seed. Some attrition of bloggers started to occur in 2008 and 2010, and then presumably in an attempt to get more revenue they started a Pepsi sponsored blog, and that caused a further set of defections.

But there are some great blogs still there. Respectful Insolence and Uncertain Principles I’ve followed on and off since the beginning. The latter blog has had some continuity as a science blog since the spring of 2003, so along with Gene Expression it’s been around for 15 years or so.

Here is an article in The New York Times from January 20th of 2006, Science Blogs as a Vehicle for Upscale Ads. I remember where I was then, chilling out in Prospect Heights at my friend’s apartment in New York City. Honestly, a nearly 12-year run is not that bad. Some great journalists started at or grew their careers at ScienceBlogs.

ScienceBlogs’ wiping away of the whole site illustrates the major problem with relying on someone else’s platform to gain scale and synergy. It might be a short-term strategy. Unfortunately, I think the areas of science twitter I’m familiar with are already in steep decline from the vibrant and spirited by collegial conversations dominant between 2010-2015. It’s not quite as far gone as ScienceBlogs’ neglect.

Open Thread, 10/22/2017

Reading The Turks in World History and confused how any state whose elite were non-nomads held out before the gunpowder revolution. Also, the persistent defection of Chinese generals and soldiers to the side of the barbarians is interesting light of other conversations we’ve had.

Are there any (post-)Roman examples of this? I know that an early Dark Age a major Slavic warlord was actually a Frankish merchant (Samo). But did whole units “go native”? Seems likely in Francia and Britain.

ASHG in Orlando is over. Much more excited by ASHG in San Diego next year, because it’s in San Diego. That being said the conference seems to be moving into a strong clinical genomic direction.

Lots of stuff going on. Still recuperating. My company released a Metabolism app.

A paper from a few years ago argues that we could sequence the whole world by 2025 (capacity).

This paper argues 60 million will be sequenced in healthcare context by 2025. Seems conservative.

Went to a Broad Institute presentation where they said they had 300,000 exomes and 85,000 whole genomes sequenced.

Now that researchers are converging in the likelihood that  modern humans spend the vast majority of their time in Africa, it looks like evolutionary population genomics in the next 10 years will really focus on that continent.


Selection swimming against the genomic tide

One of the major issues that confuses people is that the distribution of a trait or gene is often only weakly correlated with overall phylogeny and the rest of the genome.

To give a strange but classic example, the MHC loci are subject to strong balancing selection. This means that novel alleles do not substitute and replace ancestral alleles. Substitution of this sort results in “lineage sorting,” so that when you look at chimpanzees and humans you can see many polymorphic loci where all humans carry one variant and all chimpanzees the other. In contrast at the MHC loci there is frequency-dependent selection for rare variants, so the normal cycling process does not occur. Humans and chimpanzees overlap quite a bit on MHC, and any given human may have a more similar profile to a given chimpanzee than another human.

There are 19,000 human genes. At 3 billion base pairs only about ~100 million are polymorphic on a worldwide scale (using some liberal definitions). There are lots of unique stories to tell here.

A new preprint, Inferring adaptive gene-flow in recent African history, illustrates how certain genes with functional significance may differ from genome-wide background. The authors find that among the Fula (Fulani) people of West Africa there has been introgression from a Eurasian mutation that confers lactase persistence. The area of the genome around this gene is much more Eurasian than the rest of the genome. In contrast, the area around the Duffy allele is much less Eurasian. The variation in this locus is related to malaria resistance. Finally, in other African populations, they found gene flow of MHC variants.

None of this is entirely surprising, though the authors apply novel haplotype-based methods which should have wider utility.

Machine learning swallowing population genetics = understanding patterns in population genomics

Dan Schriber and Andy Kern have a new review preprint out, Machine Learning for Population Genetics: A New Paradigm. On Twitter there has already been a little snark to the effect of “oh, you mean regression?” That’s fair enough, and the preprint would probably benefit from a lower key title, though that’s really the sort of titles journals seem to love.

I would recommend this preprint to two large groups of my readers. There are those with strong computational skills who are curious about biology. It makes it clear why population genomics benefits from machine learning methods. Second, those who are interested or trained in genetics with less of a computational and pop gen background.

Yes, all models are wrong. But some give insight, and some are just not salvageable. In population genomics some of the model-building is obviously starting to yield really fragile results.

The backlash against social psychology was pent up demand

Both Slate and The New York Times, have pieces deconstructing the fall from grace of  “power posing.”

This is all obviously wrapped up in the “replication crisis”, which is impacting most sciences which use some statistics and are characterized by modest and complex causal effects (social and biological sciences in particular).

Obviously, I am no social psychologist, but can I just say that everyone knew there was a problem in the field a long time ago. By everyone, I mean psychologists. I had friends who worked in related fields who told me as early as 2006 not to trust anything coming out of social psychology. Others described how p-hacking and “unconscious” data manipulation was relatively common in psychological experimentation, and the personal stands they had to take to avoid engaging in the practices which were ubiquitous.

When everyone knows that something is wrong, but no one says anything, you have a coordination problem. But once the snowball starts rolling down the hill…everyone decides to speak their mind.

Finally, there’s the demand-side problem: ideas like power posing, implicit bias, and stereotype threat, offer neat, clean, and powerful explanations and oftentimes solutions for social problems. Wonkish Left-liberal publications and pundits in particular literally mine the literature to “show what the science says” (don’t worry, it overwhelmingly confirms prior beliefs).

As a testament to the power of the likely wrong (not robust) viewpoints, consider that John Bargh has a book out published this month, Before You Know It: The Unconscious Reasons We Do What We Do. Bargh’s work was one of the first research programs to be critiqued in the early 2010s. Of course, he doesn’t agree with the critics, but it does strike me that the field as a whole (e.g., people like Daniel Kahneman) believe that these subliminal effects are much weaker than originally claimed, at best. Nevertheless, Bargh is going to sell his books, and people in coffee shops and airports all over the country are going to eat it up. The reality is that subliminal effects are probably not that different than Freudianism; there may be something there, but it isn’t nearly the deal that the practitioners claimed it was.

Addendum: Arguably, the candidate gene studies of the 1990s and early 2000s and under-powered GWAS of the mid to late 2000s, fall into the same category. But I don’t know any geneticists who defend these results or engage in that analytic paradigm in 2017.

Addendum II: Since some have asked, The Invisible Gorilla is a very good book. It helped crystallize many of my skepticisms of the psychology to pop social science conveyer belt.

The rise of the word “weaponized”

The gratuitous use of the word “weaponized” really annoys me.

Why farming was inevitable and miserable

There are many theories for the origin of farming. A classic explanation is that farming was simply a reaction to Malthusian pressures. Another, implied in Big Gods: How Religion Transformed Cooperation and Conflict, is that ideological factors may also have played a role in the emergence of sedentary lifestyles and so eventually farming.

I don’t have a strong opinion about the trigger for farming. What we know is that forms of farming seem to have emerged in very disparate locales after the last Ice Age. This is a curious contrast with the Eemian Interglacial 130 to 115 thousand years ago when to our knowledge farming did not emerge. Why didn’t farming become a common lifestyle then? One explanation is that behavioral modernity wasn’t a feature of our species, though at this point I think there’s a circularity in this to explain farming.

It seems plausible that biological and cultural factors over time made humans much more adaptable, protean, and innovative. We can leave it at that, and assume that the time was ripe by the Holocene.

Also, we need to be careful about assuming that modern hunter-gatherers, who occupy marginal lands, are representative of ancient hunter-gatherers. Ancient hunter-gatherers occupied the best and worst territory in terms of productivity. If territory is extremely rich in resources, such as the salmon fisheries of the Pacific Northwest, then a hunting and gathering lifestyle can coexist with dense sedentary lifestyles. But the fact is that in most cases hunting and gathering can support fewer humans per unit of land than agriculture.

The future belongs to the fecund, and if farming could support larger families, then the future would belong to farmers. Though I don’t think it was just a matter of fertility; I suspect farmer’s brought their numbers to bear when it comes to conflicts with hunter-gatherers.

Of course, farming is rather miserable. Why would anyone submit to this? One issue that I suspect needs to be considered is that when farming is initially applied to virgin land returns on labor are enormous. The early United States is a case of an agricultural society where yeoman farmers, what elsewhere would be called peasants, were large and robust. They gave rise to huge families, and never experienced famine. By the time the frontier closed in the late 19th century the American economy was already transitioning to industry, and the Malthusian trap was being avoided through gains in productivity and declining birthrates.

The very first generations of farmers would have experienced land surplus and been able to make recourse to extensive as opposed to intensive techniques. Their descendants would have to experience the immiseration on the Malthusian margin and recall the Golden Age of plenty in the past.

And obviously once a society transitioned to farming, there was no going back to a lower productivity lifestyle. Not only would starvation ensue, as there wouldn’t be sufficient game or wild grain to support the population, but farmers likely had lost many of the skills to harvest from the wild.

Finally, there is the question of whether farming or hunting and gathering is preferable in a pre-modern world. I believe it is definitely the latter. The ethnography and history that I have seen suggest that hunters and gatherers are coerced into settling down as farmers. It is never their ideal preference. This is a contrast with pastoralism, which hunting and gathering populations do shift to without coercion. The American frontier had many records of settlers “going native.” Hunting was the traditional pastime of European elites. Not the farming which supported their lavish lifestyles.

Many of the institutional features of “traditional” civilized life, from the tight control of kinship groups of domineering male figures, to the transformation of religion into a tool for mass mobilization, emerged I believe as cultural adaptations and instruments to deal with the stress of constraining individuals to the farming lifestyle. Now that we’re not all peasants we’re seeing the dimishment of the power of these ancient institutions.

Open Thread, 10/15/2017

E. O. Wilson has a new book out, The Origins of Creativity. Did you know about it? Honestly totally surprised. Wilson’s been retired for a while now, so his profile isn’t as high as it was. He’s 88, so you got to give it to him that he can keep cranking this stuff out.

The New Yorker introduced me to Against the Grain: A Deep History of the Earliest States. This is a topic that I’m interested in, but I’m not sure I disagree with the author at all, so I doubt I’d get much out of it for the time invested.

Basically, I agree with the proposition that for the average human being quality of life was probably somewhat better before agriculture, until the past few hundred years when innovation increased productivity and the demographic transition kicked in.

Will be at ASHG meeting Tuesday night until Saturday morning. Going to be at the Helix session on Wednesday and probably man their booth for an hour.

This year seems a little light on evolutionary genomics. Perhaps the methods posters will be good though.

Wolf Puppies Are Adorable. Then Comes the Call of the Wild. Basically, it looks like there are some genetically based behavioral differences which makes dogs amenable to being pets and wolves not so much.

Na-Dene populations descend from the Paleo-Eskimo migration into America. Not entirely surprised, but kind of nails it down for good. One thing to remember is that New World and Old World were not totally isolated before the arrival of the Norse and later Iberians. For example, the Asian War Complex shows up in northwest North America 1,300 years ago.

The Decline of the Midwest’s Public Universities Threatens to Wreck Its Most Vibrant Economies. I think it is important to remember that economics is a means, not an ends. There is plenty of evidence that conservatives in the USA see academia as hostile to them and inimical to its values. On a thread where Alice Dreger asserted the importance of truth as the ultimate goal of an academic, one scientist unironically wondered how they could make their research further social justice goals.

So yes, many people who are going to try and defund academia understand that might not be optimal for economic growth. But if they believe that they’re funding their own cultural and political elimination, they don’t care.

An Alternate Universe of Shopping, in Ohio. Another story about the transformation of retail. One thing that is curious and strange to me is the evolution of the idea and perception of the mall over the past 25 years. Back in the 1980s malls were modernist shrines to the apogee of American capitalism. Today they seem mass-market and declasse. Part of it is that you don’t want to be a member of a club that everyone can join.

California Fires Leave Many Homeless Where Housing Was Already Scarce. This is horrible on so many levels.

An Unexpectedly Complex Architecture for Skin Pigmentation in Africans.

Over at Brown Pundits I wrote Race is not just skin color. I didn’t post it here because frankly it just seemed a silly thing to even have to explain.

Variation and functional impact of Neanderthal ancestry in Western Asia .

A few weeks ago over at Secular Right I wrote Why Trump could murder someone and people would still support him.

1977–2017: A Retrospective. Peter Turchin reminds us that for Russians the 1990s were horrible.

This graph from Planet Money blew up for me a bit on sci-twitter. The thing is that it’s easy to talk about racial and sexual diversity (or lack thereof) because it’s visible. On the other hand, people from less affluent backgrounds may not want to advertise that, so many are unaware of the implicit class assumptions that many people make:

Another great-great-great…great-uncle in Asia

The paper which surveys the relationship of the 40,000 year old Tianyuan sample is finally out in Current Biology, 40,000-Year-Old Individual from Asia Provides Insight into Early Population Structure in Eurasia. There isn’t anything too surprising here. Here is the part of the abstract that presents new finding:

…we generated genome-wide data from a 40,000-year-old individual from Tianyuan Cave, China…We find that he is more related to present-day and ancient Asians than he is to Europeans, but he shares more alleles with a 35,000-year-old European individual than he shares with other ancient Europeans, indicating that the separation between early Europeans and early Asians was not a single population split. We also find that the Tianyuan individual shares more alleles with some Native American groups in South America than with Native Americans elsewhere, providing further support for population substructure in Asia [8] and suggesting that this persisted from 40,000 years ago until the colonization of the Americas. Our study of the Tianyuan individual highlights the complex migration and subdivision of early human populations in Eurasia.

The Tianyuan sample lived about ~40,000 years ago in China, and it does not seem to have been the direct ancestor of modern East Eurasians. It also seems to have had some relationship to the Australo-Melanesian affiliated population which contributed ancestry to the indigenous peoples of South America. Additionally, it also shares ancestry above what you’d expect with a 35,000 year old Paleolithic European, the GoyetQ116-1 sample, which is found in an Aurignacian context.

There are some direct conclusions that one can infer from this paper. First, as known beforehand the divergence between East Eurasians and West Eurasians has to predate 40,000 years before the present since this sample already shares drift with East Eurasians far more than West Eurasians. In the paper, the authors give an interval of 40,000 to 80,000 years before the present, which seems advised. Remember that “Basal Eurasians” separated before the divergence of East and West Eurasians.

Second, “ghost” populations were common. There are at minimum two ancient Eurasian populations, represented by the Oase1 sample in Romania from 40,000 years ago, and the 45,000 year old Ust’-Ishim from Siberia, who were not closely related to any populations which left descendants today.

Third, the human “family tree” looks more like a human “family bramble.” One of the interesting points in this paper is that Tianyuan shares drift with Goyet, but does not share drift with El-Miron, which seems to be descended in large from a population like Goyet. The key here is to note that Goyet is the closest proxy to some of the ancestors of El-Miron, but it may not be the ancestor at all. So if Goyet-like populations were heterogeneous in relation to East Eurasian, then El-Miron may descend from a group which never mixed with East Eurasians.

This is clear when you read many of these ancient DNA papers closely. The Mal’ta boy was representative of a population which contributed to both Northern Europeans (via Eastern Hunter-Gatherers) and Amerindians, but the deeper results also indicated that the common contributor to these populations was not the Mal’ta population, but related to them. That is, there is no expectation that the sparse sampling of ancient DNA in many regions and epochs will find the ancestral populations, as opposed to groups related to the ancestral populations.

This is a looking-through-the-glass-darkly situation. The true pattern of population relationships of the past needed to be inferred from a finite set of individuals randomly drawn from those populations. If most of those populations left no descendants due to common and repeated local extinction events, then it may be that most of the time we’re going to have to triangulate to the “true” ancestral groups, who left descendants simply due to luck.

Finally, this should really put the nail in the coffin of the idea that we can think of ancient populations are algebraic recombinations of modern populations. Modern groups almost certainly sample only a small part of the distribution of ancient populations.