Archive for September, 2011

All your genes belong to the tribal council!

By Razib Khan | September 28, 2011 8:51 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:

Read More

CATEGORIZED UNDER: Genetics, Genomics

The educated want more children than they have

By Razib Khan | September 27, 2011 2:30 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.

Read More

CATEGORIZED UNDER: Culture
MORE ABOUT: Culture

A college degree as contraceptive

By Razib Khan | September 27, 2011 12:57 pm

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.

Read More

CATEGORIZED UNDER: Culture
MORE ABOUT: Culture, natalism

Dodecad Ancestry Project is at ~10,000

By Razib Khan | September 26, 2011 11:35 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.

CATEGORIZED UNDER: Genomics, Personal Genomics
MORE ABOUT: Genome Blogging

Being human is important because we're human

By Razib Khan | September 26, 2011 12:29 am

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.

CATEGORIZED UNDER: Religion
MORE ABOUT: Religion

Like modestly attracts like

By Razib Khan | September 26, 2011 12:04 am

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?

CATEGORIZED UNDER: Psychology
MORE ABOUT: I.Q., marriage, Sociology

Sunday Stuff – September 25th, 2011

By Razib Khan | September 25, 2011 9:51 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:

Read More

CATEGORIZED UNDER: Blog
MORE ABOUT: Blog, Fluff, KIatz

The last 100,000 years in human history

By Razib Khan | September 25, 2011 8:02 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.

Read More

243 full human genomes sequenced per second

By Razib Khan | September 24, 2011 12:55 am

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).

CATEGORIZED UNDER: Human Genomics
MORE ABOUT: Genomics

Singularity Summit 2011

By Razib Khan | September 22, 2011 9:20 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).

CATEGORIZED UNDER: Futurism

The Australian Aborigines may not be just descendants of first settlers

By Razib Khan | September 22, 2011 5:52 pm

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

By Razib Khan | September 22, 2011 1:56 pm


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.

Read More

God is intuitive

By Razib Khan | September 20, 2011 11:15 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:

Read More

40 hits in 40 years

By Razib Khan | September 20, 2011 1:56 am

I’m not very interested in music compared to the average person. But I’m curious about changing tastes in music over time, because it’s part of our cultural fabric. Since I lack real “thick” knowledge in this domain, I started to think of crutches to allow me to get a slice of perception as a function of time. So what I did was look at all the top songs by year since 1970, and found them on YouTube. I created a “playlist” which I could listen to all at once.

Read More

CATEGORIZED UNDER: Culture
MORE ABOUT: Music

What atheism and autism may have in common

By Razib Khan | September 19, 2011 3:02 pm

My post below on atheism and autism caused some confusion. I want to quickly clear up some issues in regards to the model which I had in mind implicitly. In short I’m convinced by the work of cognitive scientists of religion (see Religion Explained and In Gods We Trust) that belief in gods and spirits is intuitively plausible to most people. It does not follow from this that when you have an intuitive belief that that belief is unshakable. This explains the variation in levels of atheism across societies as well as shifts of views across one’s lifetime. But, it also explains why in pre-modern societies acceptance of supernatural entities is the null or default position, if not necessarily universal.

But what’s the basis for the idea that belief in gods is intuitive? To reduce a lot of results down to a few sentences, humans live in a universe of other actors, agents, which we preoccupy over greatly. Additionally, we can conceive of agents which aren’t present before us. In other words, the plausibility of supernatural narratives derives from our orientation toward populating the universe with social beings and agency. There’s a lot of evolutionary psychological models for why this phenotype is adaptive, but that’s not relevant to us here. The point is that religious beliefs and systems use these intuitions and impulses as atoms with which they can build up more complex cultural ideas.

Read More

CATEGORIZED UNDER: Religion
MORE ABOUT: Atheism, Autism, Religion

The words of the father

By Razib Khan | September 18, 2011 10:01 pm

Over at A Replicated Typo they are talking about a short paper in Science, Mother Tongue and Y Chromosomes. In it Peter Forster and Colin Renfrew observe that “A correlation is emerging that suggests language change in an already-populated region may require a minimum proportion of immigrant males, as reflected in Y-chromosome DNA types.” But there’s a catch: they don’t calculate a correlation in the paper. Rather, they’re making a descriptive verbal observation. This observation seems plausible on the face of it. In addition to the examples offered, one can add the Latin American case, where mestizo populations tend to have European Y chromosomal profiles and indigenous mtDNA.

Read More

CATEGORIZED UNDER: Anthroplogy, Genetics, Human Genetics

Atheism as mental deviance

By Razib Khan | September 18, 2011 9:00 pm

Tyler Cowen points me to a PDF, Religious Belief Systems of Persons with High Functioning Autism, which has some fascinating results on the religiosity (or lack thereof) of people with high functioning autism. I’ve seen speculation about the peculiar psychological profile of atheists before in the cognitive science literature, and there’s a fair amount of social psychological data on the different personality profile of atheists (e.g., more disagreeable). But there hasn’t been a lot of systematic investigation of the possibility that autistic individuals are more likely to be atheist because they lack a fully fleshed “theory of mind,” which would make supernatural agents, gods, more plausible.

You can read the whole paper yourself, but these two figures are the most important bits:

Read More

CATEGORIZED UNDER: Religion
MORE ABOUT: Atheism, Religion

Rational optimist or scientific racist?

By Razib Khan | September 18, 2011 5:29 pm

I’m quite looking forward to Steven Pinker’s The Better Angels of Our Nature: Why Violence Has Declined. It’s coming out in three weeks, so expect to hear a lot more about it. That violence has declined is known outside of Pinker’s own work, and I try and spread this “good news” as much as I can. But I’ve always found it peculiar that some of the most pessimistic and skeptical individuals in regards to these data aren’t reactionaries pining for the ancient idyll, but self-styled progressives who seem to believe that we are fallen creatures. Many of the latter are clearly modern followers of Rousseau, previously discussed in The Blank Slate.

In any case, Jerry Coyne points me to a really strange aside in a review of Pinker’s book in The Guardian:

To be tagged as a credulous optimist is one thing, yet Pinker also risks being condemned as a scientific racist. His graphs on the incidence of murder show present-day tribal and hunter-gatherer cultures to be far more homicidal than even the most lethally armed developed nation, a fact that is bound to bring censure from those Pinker derides as the “anthropologists of peace”

If the reviewer is characterizing these “anthropologists of peace” correctly perhaps it’s a commentary on what modern anthropology has become. I’ll leave you with some charts….

Read More

CATEGORIZED UNDER: History
MORE ABOUT: History

The end of "archaic" H. sapiens

By Razib Khan | September 18, 2011 4:30 pm

The Pith: The Bushmen branch of the human family tree diverged ~130,000 years ago. The non-Africans branched off from the Africans ~50,000 years ago. The Europeans and East Asians diverged ~35,000 years ago.

One of the terms in paleoanthropology which can confuse is that of archaic Homo sapiens (AHS). This is in contrast to anatomically modern humans (AMH). A simple Out of Africa “recent-origin-with-replacement” model allowed to sidestep the semantic imprecision in tossing disparate populations into a generic category such as AHS (similarly, the term “animal” as opposed to “human” has some colloquial utility, but it’s not scientifically useful). But the possibility of admixture from archaic lineages in modern human populations forces us to grapple with the dichotomy between AHS and AMH, as modern humans may be a compound of these two categories (not to mention the idea of behaviorally modern humans, who are a subset of AMH).

I assume that fleshing out the details of a new paradigm which is both precise and accurate will be a project for the coming years. But before we move on we need to fix more sturdily our understanding of the genealogical relationships of contemporary human populations. Over the past few years there have been major strides in this domain, confirming the broad outline of a dominant African heritage for modern humans. Geneticists have moved from classical markers to SNP data, focusing on hundreds of thousands of genetic variants. But now they’re shifting to whole genome sequences, which with errors excepted encapsulate the totality of the lowest order aspect of human genetic variation.* Earlier this summer I reviewed a paper in Nature which was a foretaste, Inference of human population history from individual whole-genome sequences. Today Nature has published another, Bayesian inference of ancient human demography from individual genome sequences.

Read More

Out of Africa's end?

By Razib Khan | September 17, 2011 12:54 pm

The BBC has a news report up gathering reactions to a new PLoS ONE paper, The Later Stone Age Calvaria from Iwo Eleru, Nigeria: Morphology and Chronology. This paper reports on remains found in Nigeria which date to ~13,000 years B.P. that exhibit a very archaic morphology. In other words, they may not be anatomically modern humans. A few years ago this would have been laughed out of the room, but science moves. Here is Chris Stringer in the BBC piece:

“[The skull] has got a much more primitive appearance, even though it is only 13,000 years old,” said Chris Stringer, from London’s Natural History Museum, who was part of the team of researchers.

“This suggests that human evolution in Africa was more complex… the transition to modern humans was not a straight transition and then a cut off.”

Prof Stringer thinks that ancient humans did not die away once they had given rise to modern humans.

They may have continued to live alongside their descendants in Africa, perhaps exchanging genes with them, until more recently than had been thought.

Read More

NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
ADVERTISEMENT

See More

ADVERTISEMENT

RSS Razib’s Pinboard

Edifying books

Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »