Razib Khan One-stop-shopping for all of my content

September 28, 2011

All your genes belong to the tribal council!

Filed under: Australian Aboriginals,Genetics,Genomics — Razib Khan @ 7:51 pm

Dienekes has already commented on this, but I thought I would go over Ewen Callaway’s piece, Aboriginal genome analysis comes to grips with ethics. It’s not surprising that this was written. Even if you take Keith Windschuttle’s position when it comes to Aboriginal-European contact you can’t escape the reality that Aboriginals did not fare so well in the interaction. In fact, they don’t fare so well today in Australia. The life expectancy gap between Aboriginals and non-Aboriginals in Australia is most conservatively estimated at 10 years (do remember that the majority of indigenous Australians are mixed-race). In the racialized physical anthropology of the early 20th amongst the colored peoples Aboriginals occupied the lowest circle of hell. Because of the robustness of their physiques it was argued they were the most primitive exemplar of humanity. Perhaps relic H. erectus.

Here are some interesting sections of Callaway’s article:

…Researchers who work with Aboriginal Australians are now expected to obtain consent not only from the individuals concerned, but also from local and sometimes state-wide groups representing Aboriginal communities across Australia.

A Danish bioethical review board did not believe it was necessary to review the project because it viewed the hair as an archaeological specimen and not a biological one, Willerslev says. However, after his team sequenced the genome, an Australian colleague put Willerslev in touch with the Goldfields Land and Sea Council, a body based in Kalgoorlie, Western Australia, that represents the 5,000 or so Aboriginal Australians living in the region where Haddon collected the hair sample. In June, Willerslev flew to the region to describe his project to the organization’s board and to seek its approval. He says that if the board had rejected his proposal, he would have ended the project and left the genome unpublished.

Stepping away from the specific issue of Australian Aboriginals, the case of the “ownership” of genetic information is peculiar. As a “thought experiment” I have addressed the issue of whether identical twins have “rights” to each others’ genomes. For example, if one identical twin put their genotype into the public domain, would the other be within their rights to object? For that matter, people who put their genotypes in the public domain are partially exposing their whole families. Do they have to go ask for permission? Obviously I don’t think so. I didn’t ask my siblings or my parents.

So the issue of group veto or endorsement of the genotyping of individuals, living or deceased, is not a general consideration. It’s a matter of politics and sociology in very specific circumstances. In particular those groups which are labelled “indigenous” in Western societies, and so given particular distinction as the “first people.” Ultimately it reduces down to power politics. Consider for example what the Cherokee nation recently did to its black members. Just because people are indigenous, or there is a tribal council instead of a town council, does not exempt them from the common venalities of political leadership classes. Though there has been a history of “body snatching” by Western scholars in the Americas and Australia, the current respect and considerations given ancient materials which might have DNA has more to do with the possibility that those results might refute the standing of a given group as autochthons. As a practical matter DNA results probably won’t change a thing, but there is always a risk that it might introduce an element of doubt as to the legitimacy of the privileges and rights conferred on those who trace their lineages from the first settlers of a given locale.

More broadly, there is a whole world of “activists” who are themselves not indigenous who have a vested interest in ginning up controversy, and demanding that all the ethical issues be examined from every which angle (they are of course the best judges as to which issues must be tackled before science proceeds). I’ve addressed this before. In short they’re basically academic demagogues. What I’m talking about was on display during the Darkness in El Dorado controversy. Unlike indigenous people themselves these activists will always move on to a new cause to stoke the fires of their righteous indignation. In the 1990s this set was outraged over the Human Genome Diversity Project, but today that enterprise is a great success accessible to all. Did disaster and darkness ensue? Of course not. And the original critics are now fixated upon more profitable targets.

Going back to the issue about Aboriginal genetics, and the genetics of indigenous people more generally, it is in the medium run irrelevant what institutions decide. By institutions, I mean tribes, governments, NGOs, and even academics. If a scientific group avoids human genetic research for political reasons, the probability is that another group at some point in the future will take the project. And when it comes to human genetics the typing and analysis is cheap and easy enough that motivated amateurs can do it themselves. There are certainly enough white Australians with some Aboriginal ancestry that a synthetic genome could probably be reconstructed just from them at some point. Perhaps less ethically if someone wanted to they could probably obtain genetic material by surreptitious means.

Which brings me back to the question of Australian Aboriginals. One of the primary fears, implicit or explicit, about doing biological work on this group is that scientists might report results which would have a chance of dehumanizing them. Dehumanization, broadly construed, is not a problem necessarily. As I’ve noted people found that Europeans had a few percent Neandertal quite funny last year because Europeans haven’t been victims of dehumanization for the past few centuries (read the accounts of Muslim or Chinese observers from before 1800, and you do see clear dehumanization of Europeans in their perceptions). In contrast, Australian Aboriginals have been dehumanized. So how does the result that they might be ~5% admixed with a very distant human lineage change our perceptions? I don’t think it changes much at all. The problem is that people, wrongly I believe, perceive that political and social views have some deep metaphysical basis when they often do not. Scientific racism in the 19th and early 20th century did leverage science, but the racialized sentiments ascendant in the age of white supremacy were first and foremost about values. In the 16th century the partisans of the views of Bartolomé de las Casas succeeded in convincing the Iberian monarchies that the indigenous people of the New World deserved protection from predatory European settlers. But the reality is that the de jure status was flagrantly violated for centuries de facto. In the ideal the Amerindians of the New World were granted the protection of the Spanish monarchy as Christians, but in practice they were treated in a beastly manner by the American Spaniards and their Creole descendants.

Quibbling about the rights and responsibilities of scientists in a given field is not always unimportant or futile. But in the area where genetics and ethnology intersect too often people overestimate the power of genetics to totally reshape how we view ourselves, and how we view other human beings. The reality is that we are what we are, before and after we find out what we are in a more scientific and abstruse fashion. How we behave toward other human beings is less a matter of good science and more good character.

September 27, 2011

The educated want more children than they have

Filed under: Culture — Razib Khan @ 1:30 pm

 

The post below is probably going to elicit a lot of comments. Some of it will repeat chestnuts of historical wisdom which illustrate the ignorance of the typical modern. For example, it is false that the lower classes always have more children than the upper classes. In general it is the reverse, because the lower orders are more squeezed on the Malthusian margins (this explains how downward social mobility worked in early modern Europe; the less successful children of the elites drifted down to replace the masses who were not replacing themselves).

In any case, Angela M. Cable asks:

Has it not occurred to anyone that perhaps the more educated a woman is, the less she *wants* children. How do we know these women are not child-free as opposed to child-less?

If I was Angela I would go look for the literature on this. I’m not one to ask questions imperiously without taking the time out to actually do some legwork. But I’m a peculiar beast. Let’s satisfy Ms. Cable’s curiosity, which probably remains unsated by any compulsion to find out the truth of the matter. The General Social Survey has a variable which asks the ideal number of children an individual would like to have. Let’s replicate the analysis with that variable, and look at the difference between ideal and realized number of children.


 

Mean number of children of women by highest degree
attained for age cohorts surveyed after year 2000
Highest degree 1951-1960 1961-1970 1971-1980
Less than HS 2.98 2.78 2.39
HS 2.08 2.05 1.5
Junior College 2.06 1.96 1.52
Bachelor 1.49 1.47 0.85
Graduate 1.46 1.37 0.75
Mean ideal number of children of women by highest degree
attained for age cohorts surveyed after year 2000
Highest degree 1951-1960 1961-1970 1971-1980
Less than HS 2.84 3.26 3.6
HS 3.03 3 2.92
Junior College 3.72 3.17 3.11
Bachelor 3.09 3.14 3.02
Graduate 2.78 3.23 2.9
Different between mean ideal number of children and mean number of children of women by highest degree
attained for age cohorts surveyed after year 2000
Highest degree 1951-1960 1961-1970 1971-1980
Less than HS -0.14 0.48 1.21
HS 0.95 0.95 1.42
Junior College 1.66 1.21 1.59
Bachelor 1.6 1.67 2.17
Graduate 1.32 1.86 2.15

Some of the difference has to be the fact that more educated women have children later. So they’ll get closer to their “goal.” But I don’t think all of it is due to that. Interestingly the variation in the ideal number of children is smaller than that of the realized number of children. That suggests that the gap between educated and uneducated isn’t simply an ideological preference chasm.

A college degree as contraceptive

Filed under: Culture,natalism — Razib Khan @ 11:57 am

Update: The Slate piece is not accurately representing the original research:

Lerner’s article is spreading misinformation. What the Guttmacher Institute study shows is not that the educated are having fewer children vis a vis the uneducated, but that there is a growing gap in family planning: the children of the uneducated are increasingly unplanned.

Knocked Up and Knocked Down: Why America’s widening fertility class divide is a problem:

You hear about the “haves” versus the “have-nots,” but not so much about the “have-one-or-nones” versus the “have-a-fews.” This, though, is how you might characterize the stark and growing fertility class divide in the United States. Two new studies bring the contrasting reproductive profiles of rich and poor women into sharp relief. One, from the Guttmacher Institute, shows that the rates of unplanned pregnancies and births among poor women now dwarf the fertility rates of wealthier women, and finds that the gap between the two groups has widened significantly over the past five years. The other, by the Center for Work-Life Policy, documents rates of childlessness among corporate professional women that are higher than the childlessness rates of some European countries experiencing fertility crises.

Childlessness has increased across most demographic groups but is still highest among professionals. Indeed, according to an analysis of census data conducted by the Pew Research Center, about one quarter of all women with bachelor’s degrees and higher in the United States wind up childless. (As Pew notes, for women with higher degrees, that number is actually slightly lower than it was in the early 1990s—but it is still very high.) By comparison, in England, which has one of the highest percentages of women without children in the world, 22 percent of all women are childless. According to the new Center for Work-Life Policy study, 43 percent of the women in their sample of corporate professionals between the ages of 33 and 46 were childless. The rate of childlessness among the Asian American professional women in the study was a staggering 53 percent.

At the same time, the numbers of both unplanned pregnancies and births among poor women have climbed steadily in recent years. About half of all pregnancies in this country are unplanned, with poor women now five times more likely than higher-income women to have an unplanned pregnancy, and six times more likely to have an unplanned birth, according to the Guttmacher Institute’s recent analysis of government data.

It being Slate, the author does not broach what I like to term the “Idiocracy hypothesis”. I invite you to make some observations at a Walmart Supercenter as you stand behind the pregnant 16 year old holding her adorable chubby infant, and then deny the possibility of this outcome. But you don’t need to “go there.” If you have a strong environmental leaning you can still admit that the cultural traits of the middle class may be heritable through acquisition in childhood, while the dysfunctional tendencies of the underclass can also be perpetuated by modeling the behavior of parents and peers. The skewed parental origins of the next generation, and the inferred long term divergence in reproductive output, are issues of some consequence for the broader social order. Systems which shift out of equilibrium may eventually reach a new “stable state,” and one not to our liking.


In any case, here is some General Social Survey data on the mean number of children by age cohort broken down by education for women surveyed after the year 2000. Basically you’re looking at the number of children that women born in the 50s, 60s, and 70s, had by the 2000s.

Mean number of children of women by highest degree
attained for age cohorts surveyed after year 2000
Highest degree 1951-1960 1961-1970 1971-1980
Less than HS 2.98 2.78 2.39
HS 2.08 2.05 1.5
Junior College 2.06 1.96 1.52
Bachelor 1.49 1.47 0.85
Graduate 1.46 1.37 0.75

 

Solutions? One quick one made by Randall Parker is to allow for easier acceleration of education of the academically gifted. Many school districts seem to discourage skipping grades from what I have seen for practical social reasons. But currently women with professional aspirations have a difficult time having children during their peak fertility years because of the necessary demands on their time of university and graduate or professional school. It is of course true that putting 14 year old teens in classes with 18 year old young adults is going to cause problems, but if a woman can make it out of medical school and into her residency around 22, rather than 26, it is going to be a huge difference in terms of options in their early 30s (beyond the peak fertility years, but not very much).

 

September 26, 2011

Dodecad Ancestry Project is at ~10,000

Filed under: Genome Blogging,Genomics,Personal genomics — Razib Khan @ 10:35 pm

A few days ago I noticed that the Dodecad Ancestry Project had nearly nearly 10,000 individuals! ~500 are participants in the project (like myself, I’m DOD075). But most of the individuals were derived from public or shared data sets. You can see them in the Google spreadsheet with all the results. It’s quite an accomplishment, and I commend Dienekes for it. I also have to enter into the record that Dodecad prompted my own forays into genome blogging, and Dienekes also helped Zack with pointers for Harappa in the early days.

Sepia Mutiny “News” RSS

Filed under: Uncategorized — Razib Khan @ 9:06 pm

When I was still regularly contributing to Sepia Mutiny* I really, really, pushed them to move to WordPress. There’s just so much rolled into the software. For example, the News tab now has its own RSS feed! Awesome.

* I am too busy to contribute to that weblog at this point.

The axis of weasel

Filed under: Uncategorized — Razib Khan @ 6:53 pm

Pakistanis Tied to 2007 Border Ambush on Americans:

The attack, in Teri Mangal on May 14, 2007, was kept quiet by Washington, which for much of a decade has seemed to play down or ignore signals that Pakistan would pursue its own interests, or even sometimes behave as an enemy.

The reconstruction of the attack, which several officials suggested was revenge for Afghan or Pakistani deaths at American hands, takes on new relevance given the worsening rupture in relations between Washington and Islamabad, which has often been restrained by Pakistan’s strategic importance.

The details of the ambush indicate that Americans were keenly aware of Pakistan’s sometimes duplicitous role long before Adm. Mike Mullen, the chairman of the Joint Chiefs of Staff, told the Senate last week that Pakistan’s intelligence service was undermining efforts in Afghanistan and had supported insurgents who attacked the American Embassy in Kabul this month.

Terra Nova half-browns

Filed under: science fiction,Television — Razib Khan @ 5:52 pm

There’s a lot buzz on the internet for a new show called Terra Nova. Didn’t we already do this? It was called Earth 2 (Steven Spielberg also had an indirect role in that show). I’m not going to watch it. I don’t have a television, and my online television watching is very circumscribed. But I did note that the family at the center of the drama is what we would call “exotic” or “ethnic” in 1980s:

Alana Mansour, the youngest actress, probably has Middle Eastern ancestry. I don’t know. But the mother is played by Shelley Conn, an Anglo-Indian. More specifically a mix of Sri Lankan and British. And the middle child, Naomi Scott, has a ethnic Indian mother from Uganda. The father and son in contrast are fully European in appearance (and Irish and white Canadian were cast for these roles), but it is not uncommon in mixed-race families for such a variance in physical types to manifest across the set of children.

September 25, 2011

Being human is important because we’re human

Filed under: Religion — Razib Khan @ 11:29 pm

There’s a rather vanilla piece in The Philadelphia Inquirer which reviews the ideas of how humans became human. I say vanilla because the headline is somewhat more sensational than the text itself, which seems sober and accurate. But this paragraph jumped out at me:

A main source of the idea that we humans are above the rest of the living world is religion. Even religions that accept evolution espouse a kind of human exceptionalism.

It is obviously true that human religions tend to place a special importance on humans. And it is accurate as well to observe that consistent messages of human uniqueness are most prominently espoused by particular religions. Even those religions such as Neo-paganism and Hinduism which adhere to a monism which collapses the distinction between human and non-human operationally do seem to privilege the human perspective.

But I think for the purposes of analysis we need to step away from the idea that religion is the “source” of any one particular thing. Like morality it’s pretty obvious that human exceptionalism in religion is an extension of our natural intuitions, which derive from the fact that natural selection tends to shape lineages to at least a minimum level of self-absorption. I think this issue needs to be generally kept in mind when we praise religion (e.g., “there would be no charity without religion”) or condemn it (e.g., “there would be no war without religion”). Rather than an ultimate wellspring of human behavior religion is more accurately conceptualized as an intermediating phenomenon. It takes the elements of humanity and recombines them into more complex cultural units. It does does not provide the inputs, it is a function which operates upon the inputs.

Like modestly attracts like

Filed under: I.Q.,marriage,Psychology,Sociology — Razib Khan @ 11:04 pm

I saw this link posted on twitter, IQ and Human Intelligence:

An interesting finding from genetic research, which Mackintosh mentions, only in passing, as posing a problem in the estimation of the heritability of g, is that there is greater assortative mating for g than for any other behavioral trait; that is, spouse correlations are only ∼.1 for personality and only ∼.2 for height or weight, but the correlation for assortative mating for g is ∼.4. In addition to indicating that people are able to make judgments about g in real life, this finding suggests that assortative mating may contribute to the substantial additive genetic variance for g, because positive assortative mating for a character can increase its additive genetic variance.

I’ve seen these sort of results before. The review is from 1999. In general I always wonder if quantitative values for personality are not to be trusted because of issues with the measurement of personality types. But this is clearly not an issue with height or weight. And in the case of height the overwhelming causal explanation for variation in the West is genetic variation. Overall I’m rather surprised by the rather low correlations for some of these traits, such as height and intelligence. I wonder if beauty, perhaps measured by an index of facial symmetry, might exhibit higher correlation values?

Sunday Stuff – September 25th, 2011

Filed under: Blog,Fluff,KIatz — Razib Khan @ 8:51 pm

FF3

I don’t really enjoy reading past posts on this weblog (I said too much stupid stuff), and I haven’t been following comments too closely. So I’m going to skip those for now.

1) Weird search query of the week: “razib khan hiv.” Last I checked I am HIV negative.

2 Your weekly fluff fix:


The last 100,000 years in human history

Filed under: Agriculture,Anthroplogy,Human Evolution,Human Genomics — Razib Khan @ 7:02 pm

In light of the recent results in human evolutionary history some readers have appealed to me to create some sort of clearer infographic. There’s a lot to juggle in your head when it comes to the new models and the errors and uncertainties in estimates derived from statistical inference. Words are not always optimal, and there’s often something left out.

So I spent a few hours creating a series of maps which distill my own best guess as to what occurred over the past 100,000 years. I want to emphasize that this purely my own interpretation, based on what I know. This is naturally going to be biased (I don’t know as much about uniparental lineages as some of my readers, and have a weak grasp of a lot of morphological changes, etc.). But it is a place to start. I’ve put the maps into a slideshow. Please observe that in brackets I’ve put qualifies such as “high”, “medium” and “low” in regards to my assertions. That shows you how confident I am about a given assertion. I’m 100% sure that I’m wrong in a lot of the details here, but this is my best guess as to the shape of things over the past 100,000 years. Feel free to ask more in the comments. Also, take the dates with a little fudge room. If I used exact precise dates for everything there would be too many slides.

Note: You can’t see the slideshow in the RSS browser.

The enemy of my enemy

Filed under: Hinduism,Religion — Razib Khan @ 1:31 pm

Borneo Tribe Practices Its Own Kind of Hinduism:

In this village near the heart of Borneo’s great, dissolving rainforest, Udatn is regarded as a man of deep spiritual knowledge.

Of all the people in this tiny settlement, he speaks better than any other the esoteric language of the Sangiyang, the spirits and ancestors of the upper world, known simply as “Above.” His is a key role in the rituals of Kaharingan, one of a number of names for the ancestor-worshipping religion of Borneo’s indigenous forest people, the Dayak.

“In the beginning, when God separated the darkness and the light, there was Kaharingan,” said Mr. Udatn, as he sat smoking a wooden pipe on the floor of his stilt home. (Like many Indonesians Mr. Udatn uses only one name.)

The Indonesian government thinks otherwise. The world’s most populous Muslim-majority country is no Islamic state, but it is a religious one. Every citizen must subscribe to one of six official creeds: Islam, Roman Catholicism, Protestantism, Buddhism, Confucianism or Hinduism. Kaharingan, like dozens of other native faiths, does not officially exist.

Even in this village, a frontier where land clearing and mining is fast erasing ancient forest, people have long seen their faith under threat from officialdom.

“When I was in school I was a Catholic,” said Mr. Udatn. “For us, if someone wanted to keep going to school then they had to convert to another religion.”

Now, however, things are changing, and the missionaries are being held at bay. That is because villagers have seized on a strategy being used by many Dayak: They are re-branding. On paper at least, most of the people of Tumbang Saan are now followers of Hinduism, the dominant religion on the distant island of Bali. Few here could name a Hindu god or even recognize concepts, like karma, that have taken on popular meanings even in the West. But that is not the point. In a corner of the world once famed for headhunters and impenetrable remoteness, a new religion is being developed to face up to an encroaching modern world and an intrusive Indonesian state. The point, in short, is cultural survival.

In mainland Southeast Asia alignment with Christianity has also been a way that minorities can preserve their own customs and identity against assimilation into the Theravada Buddhist majority. Also, note that the Indonesian government mandates that all religious be monotheistic. So Hinduism, Confuncianism, and Buddhism, all espouse a monotheistic god in the islands nominally.

September 23, 2011

243 full human genomes sequenced per second

Filed under: Genomics,Human Genomics — Razib Khan @ 11:55 pm

MIT Technology Review has one of those articles about the exponential growth rate in the number of people who have been fully sequenced. There’s nothing too exceptional in the piece. You do have to be careful about 10 year projections, especially if they’re exponential. But this part caught my eye: ” At this exponential pace, by 2020 it may be feasible—mathematically, at least—to decode the DNA of every member of humanity in a single 12-month stretch.

What does that mean? Taking the U.N. estimate for the world’s population in 2020, and I get the following numbers:

- 874,087 genomes per hour
- 14,568 genomes per minute
- 243 genomes per second

Of course much of the sequencing would be done concurrently, so it wouldn’t be a constant rate of production. But still this would be awesome. I think being much more conservative there’ll be at least hundreds of thousands of people who are fully sequenced, if not millions. I don’t know if this is valid personally, but there’s a paper on data compression which claims it might be feasible to reduce the size of the raw sequence output to ~4 MB. That might be helpful, since even at that size you’d still have 30 million terabytes of information to store (I assume that any given genome will be replicated thousands of times in various data centers).

Expectations of Bangladesh

Filed under: Bangladesh — Razib Khan @ 7:09 pm

The New York Times has a puff piece on Sheikh Hasina up. In general I favor the Awami League despite its socialist origins because the party is less bigoted against religious minorities and would likely wink less at de facto ethnic cleansing (though of course the typical Awami League Muslim is still rather prejudiced against non-Muslims, just not nearly as so as BNP supporters I’d bet). But I worry that Bangladesh’s economic growth is a short term feature of its demographic dividend, as the nation still is near the bottom on most metrics of human capital.


September 22, 2011

How Australian Aborigines relate to Indians

Filed under: Genetics — Razib Khan @ 9:37 pm

The question has been asked. In light of recent papers, below is a stylized tree I drew up (the lengths of the branches don’t equal time!).

The indigenous population of Australia is at minimum a compound of two elements.

1) A very distinctive component which may have pushed out of Africa earlier than all other non-Africans. Term this the Ancestral Australians.

2) A second element which was a branch of the second wave of non-Africans, probably dominant across South and Southeast Asia. This branch, term then the Ancestral South Eurasians, exhibit greater similarity to East Eurasians than West Eurasians. Whether through phylogeny or just gene flow. In any case, the South Eurasians seem to have marginalized the relations of the Ancestral Australians across Southeast Asia, with the only non-Oceanian relic of the earlier inhabitants being the Negritos of the Philippines, who are also descended in part from the Ancestral Australians (the balance being Austronesian).

3) At some point the South Eurasian component become a substantial proportion of the ancestry of Near Oceanians, the peoples of Melanesia and Australia. The Peoples of Melanesia and Australia admixed with the eastern edge of the Southeast Eurasians.

4) In South Asia the western edge of the Southeast Eurasians, the Ancestral South Indians, mixed with the Ancestral North Indians.

In sum, the phenotypic and genetic connections which have been adduced between populations in the Indian subcontinent (“Australoids”) and Australian Aborigines must come via the Ancestral South Eurasians, whose range spanned both Near Oceania and South Asia. In Near Oceania they were almost certainly intrusive, an invasive layer over the Ancestral Australian substrate. In South Asia they were the indigenous population. The admixture event of the Ancestral South Eurasians and Ancestral Australians likely predates the settlement of the Americas 10-15,000 years before the present, because Native Americans seem to share particular derived mutations which span all populations with broad East Eurasian ancestry, including Aboriginals. The admixture of Ancestral North Indians and Ancestral South Indians probably dates to the Holocene, and may be as recent as 4,000 years in the past.

Singularity Summit 2011

Filed under: Futurism,Singularity Summit,Transhumanism — Razib Khan @ 8:20 pm

That time of the year for a certain type of nerd, the Singularity Summit. Here’s a a preview:

This Singularity Summit line-up this year features a mix of 25 speakers from numerous fields, with a central focus on robotics and artificial intelligence, in particular the victory of the IBM computer Watson in Jeopardy! this February. Inventor and award-winning author Ray Kurzweil will give the opening keynote on “From Eliza to Watson to Passing the Turing Test”. Registration for the Summit, which runs on October 15-16 at the 92Y in New York, is open to the public now.

The theme of the Summit this year is the Watson victory and future Watson applications, such as in medicine. Dan Cerutti, IBM’s VP of Commercialization for Watson, will give a talk on medical applications for Watson, and the closing keynote will be by Ken Jennings, who won 74 consecutiveJeopardy! matches only to lose to Watson in February. Watson won $1,000,000 in the contest and Jennings won $300,000, coming in second place. Jennings’ talk will be “The Human Brain in Jeopardy: Computers That “Think”.

I won’t be able to make it because I’m very busy right now, but that’s too bad. Ken Jennings is a great headliner, but do look at all the speakers. Tyler Cowen and Sonia Arrison will be there. I had lunch with some of the practitioners of Masonomics a few years back, but Tyler and Bryan Caplan were both out of town. No doubt the day will come. Just not this day. I haven’t had time to review 100 Plus (alas, the neglect of the Razib Khan on Books website), but it’s an excellent take on the possible implications of greater longevity (no, I don’t think longevity research is crazy as such, though I’m probably not as optimistic as many in the community).

The Australian Aborigines may not be just descendants of first settlers

Just realized. The Science paper has some interesting dates which allows us to make the above inference.

- Separation between Europeans and East Asians 25-38 thousand years before present.

- Gene flow between proto-East Asians and proto-Australians before the Native Americans diverged from the former 15 thousand years before the present.

- A conservative first landing in Australia 40-45 thousand years before the present.

The Native American result, where they share some derived variants unique to East Eurasians (mutations which emerged after the separation from West Eurasians) with Aborigines, pegs a minimum date of admixture ~15,000 years ago. But, obviously the admixture had to occur after the divergence of West and East Eurasians. Let’s say ~30,000 years ago. Even assuming that the gene flow between East Eurasians and proto-Australians occurred immediately after the separation 38,000 ago, there were anatomically modern humans in Australia for thousands of years already! The implication is that the first Australians by necessity can not have contributed in totality the ancestry of modern Aborigines. The AJHG paper gives a 50:50 estimate for the ratio of proto-Australian and the Andaman Islander/Malaysian-Negrito related population. We don’t need to be certain of the exact value to assume that numbers like this imply considerable admixture above trace levels.

Of all the dates I’m probably most confident about the archaeological ones about the settlement of Australia by anatomically modern humans. 46,000 years ago the megafauna started going extinct. That’s an immediate tell that humans have been let into the garden.

Out of Africa onward to Wallacea


There are two interesting and related papers out today which I want to review really quickly, in particular in relation to the results (as opposed to the guts of the methods). Taken together they do change our perception of how the world was settled by anatomically modern humans, and if the findings are found to be valid via replication (I think this is likely, in at least some parts) I was clearly wrong and misled others in assertions I made earlier on this weblog (more on that later). The first paper is somewhat easier to parse because it is in some ways a follow up on the paper from 2010 which documented admixture into Near Oceanian (Melanesian + Australian Aboriginal) populations from a distant hominin lineage, the Denisovans.

In this paper in The American Journal of Human Genetics they extend their geographic coverage. Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania:

It has recently been shown that ancestors of New Guineans and Bougainville Islanders have inherited a proportion of their ancestry from Denisovans, an archaic hominin group from Siberia. However, only a sparse sampling of populations from Southeast Asia and Oceania were analyzed. Here, we quantify Denisova admixture in 33 additional populations from Asia and Oceania. Aboriginal Australians, Near Oceanians, Polynesians, Fijians, east Indonesians, and Mamanwa (a “Negrito” group from the Philippines) have all inherited genetic material from Denisovans, but mainland East Asians, western Indonesians, Jehai (a Negrito group from Malaysia), and Onge (a Negrito group from the Andaman Islands) have not. These results indicate that Denisova gene flow occurred into the common ancestors of New Guineans, Australians, and Mamanwa but not into the ancestors of the Jehai and Onge and suggest that relatives of present-day East Asians were not in Southeast Asia when the Denisova gene flow occurred. Our finding that descendants of the earliest inhabitants of Southeast Asia do not all harbor Denisova admixture is inconsistent with a history in which the Denisova interbreeding occurred in mainland Asia and then spread over Southeast Asia, leading to all its earliest modern human inhabitants. Instead, the data can be most parsimoniously explained if the Denisova gene flow occurred in Southeast Asia itself. Thus, archaic Denisovans must have lived over an extraordinarily broad geographic and ecological range, from Siberia to tropical Asia.


In some ways the result is not too surprising. There’s a rather clear cline of declining Melanesian admixture as one moves west across the Indonesian archipelago. Intriguingly the Denisovan admixture seems restricted on the western boundary to Wallacea, though the story is made more complex by the existence of the Philippines. The latter archipelago was connected to Sundaland during the last Ice Age, not Sahul, or isolated such as the isles of Wallacea.

The more complex aspect of the paper is that Denisovan admixture is not just a function of admixture with Near Oceanians. Obviously the proportion for Polynesians is elegantly explained by this model, because there is a well known cline of admixture amongst various Polynesian groups with Melanesian populations. And as I noted earlier there is also a Melanesian cline in Indonesia. But the story is not neat for the Philippines due to geography and other genetic results.

A simple model would be that Philippine Negrito admixture with the Denisovans is also a function of admixture with Near Oceanians. An event which we have no record of or reason to suspect, but may have occurred. But they did not find evidence for this. To the left is a figure which shows some of the phylogenetic relationships which they report from their analysis of SNP data. First, you see the admixture of Neandertals with all non-Africans. Second, you see the admixture of Denisovans with the very distant common ancestors of the Philippine Negritos and Near Oceanians. Next, you see an admixture of what I term “Western Negritos” (Andaman Islanders + Malaysian Negritos) with the ancestral Near Oceanian population, but not with the Philippine Negritos. Then you see admixture of an East Asian element, probably Austronesian, with various Negrito groups. The distinction between Philippine and Malaysian Negritos from each other is not that surprising if you look at PanAsian Consortium SNP data. It is a nice result though that the Andaman Islanders seem to be related to the Malaysian Negritos. The geography of the Ice Age implies the origin of this group on western mainland Southeast Asia, in close proximity to the domains of the Negritos of southern Thailand and peninsular Malaysia.

Probably the most tantalizing element to me is that the ancestry and genesis of what we term Near Oceanians may be a more complex affair than we had previous thought. This brings me to the next paper, An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia:

We present an Aboriginal Australian genomic sequence obtained from a 100-year-old lock of hair donated by an Aboriginal man from southern Western Australia in the early 20th century. We detect no evidence of European admixture and estimate contamination levels to be below 0.5%. We show that Aboriginal Australians are descendants of an early human dispersal into eastern Asia, possibly 62,000 to 75,000 years ago. This dispersal is separate from the one that gave rise to modern Asians 25,000 to 38,000 years ago. We also find evidence of gene flow between populations of the two dispersal waves prior to the divergence of Native Americans from modern Asian ancestors. Our findings support the hypothesis that present-day Aboriginal Australians descend from the earliest humans to occupy Australia, likely representing one of the oldest continuous populations outside Africa.

This figure distills the model down to its essence:

The main technical issue which is straightforward when comparing the previous paper to this one is that here they sequenced a whole genome of an Australian Aboriginal man who lived 100 years ago. So while the previous paper was working with tens of thousands of markers, this paper could play with millions of SNPs (though do recall that the previous paper had a much wider set of populations covered, which isn’t trivial). The top line finding seems to be that Europeans and East Asians are closer to each other than either is to the Australian Aboriginal. I’ve seen this result before. But, a major issue which is resolved here with their methods is that Aboriginals are closer to East Asians than they are to Europeans! This is the major problem I’ve always had with the idea that there were “two waves” of migration Out of Africa. If this was so, why isn’t it that Australian Aboriginals exhibit equal distance from East Asians and Europeans? The answer here is simple: admixture between the two waves, but only amongst those going east.

In other words I was confused by excessive “tree” thinking, and neglected the possibility of admixture. The first paper also hints as a possible candidate source for the admixture event: the same source population of the Western Negritos! From what I can gather this population falls into the “eastern” branch Eurasian humanity. Not quite close to East Asians, but definitely closer to them than West Eurasians. Therefore the affinity of East Asians to Aborigines may be due to this broader global “East Eurasian” heritage, which was injected into the Aboriginal man’s genome at some point in the past. Interestingly the authors found no difference in admixture from Neandertals between the populations, in line with earlier results. This implies to me, though does not prove, that the Aboriginals are a basal outgroup to other non-Africans, who all underwent the same rough admixture dynamic with Neandertals as they pushed out of Africa. Instead of two waves Out of Africa, perhaps two pulses just outside of Africa?

Finally, the fact that the gene flow seems to pre-date the separation of Native Americans from East Eurasians serves as a “peg” on the populating of Australia. The authors conclude that at a minimum we’re talking 15-30,000 years before the present. The distinctiveness of Australian Aboriginal mtDNAs, as well the localization of Denisovan admixture amongst Near Oceanians, in addition to the archaeology, makes me credit this early founding event. The populations of Sahul may have avoided being swamped out by newcomers by and large since their arrival ~50,000 years ago. I will speculate that this may explain their relatively high quantum of “archaic” ancestry. It may be that in pre-agricultural Eurasia there were many groups with higher fractions of Neandertal ancestry on the margins of the wave of anatomically modern human advance, which were only later assimilated by the demographic swell of the farmers.

There’s a lot more one could say, but I’ll leave it to readers….

September 21, 2011

That’s Kocherlakota to you!

Filed under: Celebs,NARAYANA KOCHERLAKOTA — Razib Khan @ 3:39 pm

Fed Moves on Long-Term Interest Rates to Spur Growth:

Three members of the Fed’s 10-member policy-making committee dissented from the decision: Richard Fisher, president of the Federal Reserve Bank of Dallas; Charles Plosser, president of the Federal Reserve Bank of Philadelphia; and Narayana Kocherlakota, president of the Federal Reserve Bank of Minneapolis. The members were the same who opposed the Fed plan announced in August to hold short-term interest rates near zero until at least 2013.

I know that Naryana Kocherlakota was against an fiscal policy of the majority on the Fed Board. But I don’t know much about him. Here’s some stuff from his online biography: Narayana Kocherlakota was born Oct. 12, 1963, in Baltimore, Maryland. He earned a Ph.D. in economics from the University of Chicago in 1987 and an A.B. in mathematics from Princeton in 1983. The number of Americans of Indian background who were born before 1965 in the USA is small indeed. In case you care, apparently his name suggests Telugu Brahmin background to some. No idea if this is correct, and even I have spotted errors in Wikipedia in relation to this. I think the funniest aspect of his background is that of course his Fed website has to have a sound file as to how to pronounce his name.

September 20, 2011

God is intuitive

Filed under: Anthroplogy,atheism,Cognitive Science,Psychology,Religion — Razib Khan @ 10:15 pm

Update: An ungated version of the paper.

I used to spend a lot more time talking about cognitive science of religion on this weblog. It was an interest of mine, but I’ve come to a general resolution of what I think on this topic, and so I don’t spend much time discussing it. But in the comments below there was a lot of fast & furious accusation, often out of ignorance. I personally find that a little strange. I’ve been involved in freethought organizations in the past, and so have some acquaintance with “professional atheists.” Additionally, I’ve also been a participant and observer of the internet freethought websites since the mid-1990s (yes, I remember when alt.atheism was relevant!). In other words, I know of whom I speak (and I am not completely unsympathetic to their role in the broader ecology of ideas).

But the bigger issue is a cognitive model of how religiosity emerges. Luckily for me a paper came out which speaks to many of the points which I alluded to, Divine intuition: Cognitive style influences belief in God:

Some have argued that belief in God is intuitive, a natural (by-)product of the human mind given its cognitive structure and social context. If this is true, the extent to which one believes in God may be influenced by one’s more general tendency to rely on intuition versus reflection. Three studies support this hypothesis, linking intuitive cognitive style to belief in God. Study 1 showed that individual differences in cognitive style predict belief in God. Participants completed the Cognitive Reflection Test (CRT; Frederick, 2005), which employs math problems that, although easily solvable, have intuitively compelling incorrect answers. Participants who gave more intuitive answers on the CRT reported stronger belief in God. This effect was not mediated by education level, income, political orientation, or other demographic variables. Study 2 showed that the correlation between CRT scores and belief in God also holds when cognitive ability (IQ) and aspects of personality were controlled. Moreover, both studies demonstrated that intuitive CRT responses predicted the degree to which individuals reported having strengthened their belief in God since childhood, but not their familial religiosity during childhood, suggesting a causal relationship between cognitive style and change in belief over time. Study 3 revealed such a causal relationship over the short term: Experimentally inducing a mindset that favors intuition over reflection increases self-reported belief in God.

Recall that in many social domains where neurotypicals rely on innate, intuitive, and “fast” cognition, high functioning autistic individuals must reflect and reason. I don’t have access to the original paper, but there’s a nice piece in Harvard Gazette on the research. Here’s the last sentence: ““How people think about tricky math problems is reflected in their thinking — and ultimately their convictions — about the metaphysical order of the universe,” Shenhav said.”

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