Trends in social science

More interesting graphs from GNXP, based on searches of JSTOR in the following journal categories: anthropology, economics, education, political science, psychology and sociology. Progress!

Fast times in Jamaica

Ever wonder how Jamaica, a country of 3 million people, can compete with the US and totally dominate all of Europe and Asia when it comes to the sprints? China has spent billions on a Soviet-style sports program that selects promising athletes at a young age and sends them to special sports schools. When Liu Xiang won the 110 hurdles at the last Olympics, Chinese officials referred to his gold as the “heaviest” of all medals won by Chinese in Athens. There is no lack of Chinese desire to win sprint gold — Liu Xiang is the biggest sports star in China after Yao Ming! Similarly, the US and Europe have far more money than Jamaica for training facilities, coaches, scholarships, stipends, etc. World class athletes in Jamaica train on a grass track and in weight rooms with rusty barbells. Most US high schools have superior facilities. (See video here.)

The times below are phenomenal — they rival the times put up this weekend in Eugene at the US Olympic trials, and totally surpass the performance of any European or Asian nation.

World record-holder Usain Bolt beat former record-holder Asafa Powell in the 100-meter final in Jamaica’s Olympic trials, finishing in 9.85 seconds in Kingston.

Powell was second in 9.97. Last month in New York, Bolt ran a 9.72 to break Powell’s world record of 9.74.

Kerron Stewart won the women’s 100 in 10.80, the second-fastest time by a Jamaican woman ever. Shelly-Ann Fraster was second in 10.85, Sherone Simpson followed in 10.87 and world champion Veronica Campbell-Brown was fourth in 10.87.

Brainpower ain’t free

This NYTimes article describes research on the fitness costs and benefits of increased intelligence (learning ability). The specific results are for fruit flies, C. Elegans (worms) and E. Coli (bacteria), but the theoretical basis is well understood already. Evolutionary equilibrium occurs at a local fitness maximum, which means that further increases in brainpower come with negative fitness costs in some other area (e.g., disease resistance, physical capability). If brainpower could continue to increase without negative side effects, it would have. The fact that it hasn’t suggests that genes with beneficial effects on intelligence may also come with negative consequences.

Note that equilibrium is only an approximate condition — there may be directions in gene space in which overall fitness can still increase (even substantially), but it takes time for the random mutational process of evolution to find them. In most directions one would expect to find either only a very small positive (or zero) fitness gradient or a negative gradient, assuming a population that has been genotypically stable for a long time. Recent studies suggest that humans may have experienced rapid evolution in the last 10-50 thousand years due to the advent of agriculture, population growth, etc.

At the end of the article, one of the biologists seems ready to rediscover the Cochran-Harpending hypothesis 🙂 See also here.

NYTimes: … It takes just 15 generations under these conditions for the flies to become genetically programmed to learn better. At the beginning of the experiment, the flies take many hours to learn the difference between the normal and quinine-spiked jellies. The fast-learning strain of flies needs less than an hour.

But the flies pay a price for fast learning. Dr. Kawecki and his colleagues pitted smart fly larvae against a different strain of flies, mixing the insects and giving them a meager supply of yeast to see who would survive. The scientists then ran the same experiment, but with the ordinary relatives of the smart flies competing against the new strain. About half the smart flies survived; 80 percent of the ordinary flies did.

Reversing the experiment showed that being smart does not ensure survival. “We took some population of flies and kept them over 30 generations on really poor food so they adapted so they could develop better on it,” Dr. Kawecki said. “And then we asked what happened to the learning ability. It went down.”

The ability to learn does not just harm the flies in their youth, though. In a paper to be published in the journal Evolution, Dr. Kawecki and his colleagues report that their fast-learning flies live on average 15 percent shorter lives than flies that had not experienced selection on the quinine-spiked jelly. Flies that have undergone selection for long life were up to 40 percent worse at learning than ordinary flies.

… “Humans have gone to the extreme,” said Dr. Dukas, both in the ability of our species to learn and in the cost for that ability.

Humans’ oversize brains require 20 percent of all the calories burned at rest. A newborn’s brain is so big that it can create serious risks for mother and child at birth. Yet newborns know so little that they are entirely helpless. It takes many years for humans to learn enough to live on their own.

Dr. Kawecki says it is worth investigating whether humans also pay hidden costs for extreme learning. “We could speculate that some diseases are a byproduct of intelligence,” he said.

The benefits of learning must have been enormous for evolution to have overcome those costs, Dr. Kawecki argues. For many animals, learning mainly offers a benefit in finding food or a mate. But humans also live in complex societies where learning has benefits, as well.

“If you’re using your intelligence to outsmart your group, then there’s an arms race,” Dr. Kawecki said. “So there’s no absolute optimal level. You just have to be smarter than the others.”

Brainpower ain’t free

This NYTimes article describes research on the fitness costs and benefits of increased intelligence (learning ability). The specific results are for fruit flies, C. Elegans (worms) and E. Coli (bacteria), but the theoretical basis is well understood already. Evolutionary equilibrium occurs at a local fitness maximum, which means that further increases in brainpower come with negative fitness costs in some other area (e.g., disease resistance, physical capability). If brainpower could continue to increase without negative side effects, it would have. The fact that it hasn’t suggests that genes with beneficial effects on intelligence may also come with negative consequences.

Note that equilibrium is only an approximate condition — there may be directions in gene space in which overall fitness can still increase (even substantially), but it takes time for the random mutational process of evolution to find them. In most directions one would expect to find either only a very small positive (or zero) fitness gradient or a negative gradient, assuming a population that has been genotypically stable for a long time. Recent studies suggest that humans may have experienced rapid evolution in the last 10-50 thousand years due to the advent of agriculture, population growth, etc.

At the end of the article, one of the biologists seems ready to rediscover the Cochran-Harpending hypothesis 🙂 See also here.

NYTimes: … It takes just 15 generations under these conditions for the flies to become genetically programmed to learn better. At the beginning of the experiment, the flies take many hours to learn the difference between the normal and quinine-spiked jellies. The fast-learning strain of flies needs less than an hour.

But the flies pay a price for fast learning. Dr. Kawecki and his colleagues pitted smart fly larvae against a different strain of flies, mixing the insects and giving them a meager supply of yeast to see who would survive. The scientists then ran the same experiment, but with the ordinary relatives of the smart flies competing against the new strain. About half the smart flies survived; 80 percent of the ordinary flies did.

Reversing the experiment showed that being smart does not ensure survival. “We took some population of flies and kept them over 30 generations on really poor food so they adapted so they could develop better on it,” Dr. Kawecki said. “And then we asked what happened to the learning ability. It went down.”

The ability to learn does not just harm the flies in their youth, though. In a paper to be published in the journal Evolution, Dr. Kawecki and his colleagues report that their fast-learning flies live on average 15 percent shorter lives than flies that had not experienced selection on the quinine-spiked jelly. Flies that have undergone selection for long life were up to 40 percent worse at learning than ordinary flies.

… “Humans have gone to the extreme,” said Dr. Dukas, both in the ability of our species to learn and in the cost for that ability.

Humans’ oversize brains require 20 percent of all the calories burned at rest. A newborn’s brain is so big that it can create serious risks for mother and child at birth. Yet newborns know so little that they are entirely helpless. It takes many years for humans to learn enough to live on their own.

Dr. Kawecki says it is worth investigating whether humans also pay hidden costs for extreme learning. “We could speculate that some diseases are a byproduct of intelligence,” he said.

The benefits of learning must have been enormous for evolution to have overcome those costs, Dr. Kawecki argues. For many animals, learning mainly offers a benefit in finding food or a mate. But humans also live in complex societies where learning has benefits, as well.

“If you’re using your intelligence to outsmart your group, then there’s an arms race,” Dr. Kawecki said. “So there’s no absolute optimal level. You just have to be smarter than the others.”

Brainpower ain’t free

This NYTimes article describes research on the fitness costs and benefits of increased intelligence (learning ability). The specific results are for fruit flies, C. Elegans (worms) and E. Coli (bacteria), but the theoretical basis is well understood already. Evolutionary equilibrium occurs at a local fitness maximum, which means that further increases in brainpower come with negative fitness costs in some other area (e.g., disease resistance, physical capability). If brainpower could continue to increase without negative side effects, it would have. The fact that it hasn’t suggests that genes with beneficial effects on intelligence may also come with negative consequences.

Note that equilibrium is only an approximate condition — there may be directions in gene space in which overall fitness can still increase (even substantially), but it takes time for the random mutational process of evolution to find them. In most directions one would expect to find either only a very small positive (or zero) fitness gradient or a negative gradient, assuming a population that has been genotypically stable for a long time. Recent studies suggest that humans may have experienced rapid evolution in the last 10-50 thousand years due to the advent of agriculture, population growth, etc.

At the end of the article, one of the biologists seems ready to rediscover the Cochran-Harpending hypothesis 🙂 See also here.

NYTimes: … It takes just 15 generations under these conditions for the flies to become genetically programmed to learn better. At the beginning of the experiment, the flies take many hours to learn the difference between the normal and quinine-spiked jellies. The fast-learning strain of flies needs less than an hour.

But the flies pay a price for fast learning. Dr. Kawecki and his colleagues pitted smart fly larvae against a different strain of flies, mixing the insects and giving them a meager supply of yeast to see who would survive. The scientists then ran the same experiment, but with the ordinary relatives of the smart flies competing against the new strain. About half the smart flies survived; 80 percent of the ordinary flies did.

Reversing the experiment showed that being smart does not ensure survival. “We took some population of flies and kept them over 30 generations on really poor food so they adapted so they could develop better on it,” Dr. Kawecki said. “And then we asked what happened to the learning ability. It went down.”

The ability to learn does not just harm the flies in their youth, though. In a paper to be published in the journal Evolution, Dr. Kawecki and his colleagues report that their fast-learning flies live on average 15 percent shorter lives than flies that had not experienced selection on the quinine-spiked jelly. Flies that have undergone selection for long life were up to 40 percent worse at learning than ordinary flies.

… “Humans have gone to the extreme,” said Dr. Dukas, both in the ability of our species to learn and in the cost for that ability.

Humans’ oversize brains require 20 percent of all the calories burned at rest. A newborn’s brain is so big that it can create serious risks for mother and child at birth. Yet newborns know so little that they are entirely helpless. It takes many years for humans to learn enough to live on their own.

Dr. Kawecki says it is worth investigating whether humans also pay hidden costs for extreme learning. “We could speculate that some diseases are a byproduct of intelligence,” he said.

The benefits of learning must have been enormous for evolution to have overcome those costs, Dr. Kawecki argues. For many animals, learning mainly offers a benefit in finding food or a mate. But humans also live in complex societies where learning has benefits, as well.

“If you’re using your intelligence to outsmart your group, then there’s an arms race,” Dr. Kawecki said. “So there’s no absolute optimal level. You just have to be smarter than the others.”

Happiness: all in da gene?

shared environment = no effect
monozygotic twins = big effect

An overview of recent books on happiness, in the New York Review of Books.

…Beginning in the 1980s, Lykken and his colleagues surveyed 2,310 pairs of identical and fraternal twins, some reared together, others brought up apart, looking to see how closely mood, affect, temperament, and other traits tracked with shared genes and/or a shared environment.

What they found (from a smaller subset of the original group) was that the “reported well-being of one’s identical twin, either now or 10 years earlier, is a far better predictor of one’s self-rated happiness than one’s own educational achievement, income, or status.” This held not only for identical twins raised together but for those brought up apart, while for fraternal twins raised in the same household, the likelihood that one’s sense of well-being matched one’s twin’s was, statistically speaking, not much greater than chance.

Original research by the Lykken group.

Happiness Is a Stochastic Phenomenon

David Lykken and Auke Tellegen
University of Minnesota
Psychological Science Vol.7, No. 3, May 1996

Happiness or subjective wellbeing was measured on a birth-record based sample of several thousand middle-aged twins using the Well Being (WB) scale of the Multidimensional Personality Questionnaire (MPQ). Neither socioeconomic status (SES), educational attainment, family income, marital status, nor an indicant of religious commitment could account for more than about 3% of the variance in WB. From 44% to 53% of the variance in WB, however, is associated with genetic variation. Based on the retest of smaller samples of twins after intervals of 4.5 and 10 years, we estimate that the heritability of the stable component of subjective wellbeing approaches 80%.

Lykken’s book.

The exponential curve for genome sequencing

Below is an update on progress towards less expensive gene sequencing. At the moment you can have your genome sequenced for $350k, but we might hit the $1k mark within just a few years. This progress is funded by a combination of taxpayer and venture capital dollars. The rate of technological advance would slow to a snail’s pace without sophisticated capital markets, intellectual property rights and plain old human greed and ambition.

For a cost per base pair curve extending up to 2005, see here. As the cost nears $1k per genome we will see a tremendous explosion in detailed genetic data across all major population groups.

NYTimes: A person wanting to know his or her complete genetic blueprint can already have it done — for $350,000.

But whether a personal genome readout becomes affordable to the rest of us could depend on efforts like the one taking place secretly in a nondescript Silicon Valley industrial park. There, Pacific Biosciences has been developing a DNA sequencing machine that within a few years might be able to unravel an individual’s entire genome in minutes, for less than $1,000. The company plans to make its first public presentation about the technology on Saturday.

Pacific Biosciences, or PacBio, is just one entrant in a heated race for the “$1,000 genome” — a gold rush of activity whose various contestants threaten to shake up the current $1-billion-a-year market for machines that sequence, or read, genomes. But the company has attracted some influential investors. And some outside experts say that if the technology works — still a big if — it would represent a significant advance.

“They’re the technology that’s going to really rip things apart in being that much better than anyone else,” predicted Elaine R. Mardis, the co-director of the genome center at Washington University in St. Louis.

If the cost of sequencing a human genome can drop to $1,000 or below, experts say it would start to become feasible to document people’s DNA makeup to tell what diseases they might be at risk for, or what medicines would work best for them. A DNA genome sequence might become part of each newborn’s medical work-up, while sequencing of cancer patients’ tumors might help doctors look for ways to attack them.

To spur such advances, the federal government has awarded about 35 grants totaling $56 million to companies and universities for development of technology that could put the $1,000 genome sequence within reach. PacBio has received $6.6 million from that program.

The nonprofit X Prize Foundation, meanwhile, is offering $10 million to the first group that can sequence 100 human genomes in 10 days, for $10,000 or less per genome. Six companies or academic groups — although not PacBio — have signed up for the competition so far.

Computerized sequencing machines use various techniques to determine the order of the chemical units in DNA, which are usually represented by the letters A, C, G and T. Humans have three billion such units, or six billion if one counts the second copy of each chromosome pair.

The industry has long been dominated by Applied Biosystems, which sold hundreds of its $300,000 sequencers to the publicly financed Human Genome Project and to Celera Genomics for their sequencing of the first two human genomes, which were announced in 2000. But two newcomers — Solexa and 454 Life Sciences — have already started to cut into Applied Biosystems’ sales with machines that are faster and less costly per unit of DNA sequenced. Solexa is now owned by Illumina and 454 Life Sciences by Roche.

Applied Biosystems, which is a unit of Applera, recently started selling its own new type of sequencer, which it obtained by buying Agencourt Personal Genomics for $120 million in 2006. Helicos BioSciences, a newly public company, announced its first order on Friday. It has said its machine might be able to sequence a human genome for $72,000, with further improvements to come.

“We can look somebody in the eye and say, ‘This instrument is going to get you to the $1,000 genome,’ ” said Steve Lombardi, the president of Helicos, which is based in Cambridge, Mass.

Intelligent Bio-Systems, a privately held company in Waltham, Mass., says it will introduce a machine by the end of the year that might reduce the cost of a genome to $10,000. Other contenders include the privately held companies NABsys of Providence, R.I., VisiGen Biotechnologies of Houston and Complete Genomics of Mountain View, Calif.

Some contestants say that they might try for the X Prize as early as next year and that the $1,000 genome is as little as three years away. But other experts are more conservative. …

"No scientific basis for race"

Ha ha ha — “it’s just a social construction” — a picture (and some real science) is worth a million ignorant words…

Caption: Each point is an individual, and the axes are two principal components in the space of genetic variation. Colors correspond to individuals of different European ancestry. (Via gnxp.)

The figure is from the following paper (first author is at Harvard medical school and the Harvard/MIT Broad Institute), reporting on a study of over 4000 individuals. The researchers can group most Europeans into a geographical cline (NW vs SE, that’s the red band in the lower right of the figure; there are two clusters but also individuals who are in-between) + Ashkenazim (the pink isolated cluster in the upper left) using a few hundred markers. I’m sure even better resolution can be obtained with more loci.

Discerning the Ancestry of European Americans in Genetic Association Studies

Abstract: European Americans are often treated as a homogeneous group, but in fact form a structured population due to historical immigration of diverse source populations. Discerning the ancestry of European Americans genotyped in association studies is important in order to prevent false-positive or false-negative associations due to population stratification and to identify genetic variants whose contribution to disease risk differs across European ancestries. Here, we investigate empirical patterns of population structure in European Americans, analyzing 4,198 samples from four genome-wide association studies to show that components roughly corresponding to northwest European, southeast European, and Ashkenazi Jewish ancestry are the main sources of European American population structure. Building on this insight, we constructed a panel of 300 validated markers that are highly informative for distinguishing these ancestries. We demonstrate that this panel of markers can be used to correct for stratification in association studies that do not generate dense genotype data.

The money paragraph: “…Here we mine much larger datasets (more markers and more samples) to identify a panel of 300 highly ancestry-informative markers which accurately distinguish not just northwest and southeast European, but also Ashkenazi Jewish ancestry. This panel of markers is likely to be useful in targeted disease studies involving European Americans.”

For previous discussion of genetic clustering of human populations, see here and here. It has been known for some time that major continental groups (“races”) form distinct clusters. Improved data allow for much finer exploration of clusters within clusters.

This post is getting a lot of traffic from metafilter, and judging from the comments people are confused. I offer the following from the second link in the paragraph above:

…no matter what genetic markers you choose: SNPs, STRs, no matter how you choose them: randomly or based on their “informativeness”, it is relatively easy to classify DNA into the correct continental origin. Depending on the marker types (e.g., indel vs. microsatellite), and their informativeness (roughly the distribution differences between populations), one may require more or less markers to achieve a high degree of accuracy. But, the conclusion is the same: after a certain number of markers, you always succeed in classifying individuals according to continental origin.

Thus, the emergent pattern of variation is not at all subjectively constructed: it does not deal specifically with visible traits (randomly chosen markers could influence any trait, or none at all), nor does it privilege markers exhibiting large population differences. The structuring of humanity into more or less disjoint groups is not a subjective choice: it emerges naturally from the genomic composition of humans, irrespective of how you study this composition. Rather than proving that race is skin-deep, non-existent, or unimportant, modern genetic science is both proving that it is in fact existent, but also sets the foundation for the study of its true importance, which is probably somewhere in between the indifference of the sociologists and the hyperbole of the racists.

One thing commenters seem particularly confused about is the difference between phenotypic and genetic variation. The clustering data show very clearly that the genetic variation within a particular population cluster is less than between clusters. That is, the genetic “distance” between two individuals within a cluster is typically much less than the distance between clusters. (Technical comment: this depends on the number of loci or markers used. As the number gets large the distance between clusters becomes much larger than the individual cluster radius. For continental clusters, if hundreds or thousands of markers are used the intercluster distance dominates the intracluster size. Further technical comment: you may have read the misleading statistic, spread by the intellectually dishonest Lewontin, that 85% percent of all human genetic variation occurs within groups and only 15% between groups. This neglects the correlations in the genetic data that are revealed in a cluster analysis. See here for a simple example which shows that there can be dramatic group differences in phenotypes even if every version of every gene is found in two groups (i.e., 100% of the variation is found within each group) — as long as the frequency or probability distributions are distinct. Sadly, understanding this point requires just enough mathematical ability that it has eluded all but a small number of experts.)

On the other hand, for most phenotypes (examples: height or IQ, which are both fairly heritable, except in cases of extreme environmental deprivation), there is significant overlap between different population distributions. That is, Swedes might be taller than Vietnamese on average, but the range of heights within each group is larger than the difference in the averages. Nevertheless, at the tails of the distribution one would find very large discrepancies: for example the percentage of the Swedish population that is over 2 meters tall (6″7) might be 5 or 10 times as large as the percentage of the Vietnamese population. If two groups differed by, say, 10 points in average IQ (2/3 of a standard deviation), the respective distributions would overlap quite a bit (more in-group than between-group variation), but the fraction of people with IQ above some threshold (e.g., >140) would be radically different. It has been claimed that 20% of all Americans with IQ > 140 are Jewish, even though Jews comprise only 3% of the total population.

…The imbalance continues to increase for still higher IQ’s. New York City’s public-school system used to administer a pencil-and-paper IQ test to its entire school population. In 1954, a psychologist used those test results to identify all 28 children in the New York public-school system with measured IQ’s of 170 or higher. Of those 28, 24 were Jews.

There is no strong evidence yet for specific gene variants (alleles) that lead to group differences (differences between clusters) in behavior or intelligence, but progress on the genomic side of this question will be rapid in coming years, as the price to sequence a genome is dropping at an exponential rate.

What seems to be true (from preliminary studies) is that the gene variants that were under strong selection (reached fixation) over the last 10k years are different in different clusters. That is, the way that modern people in each cluster differ, due to natural selection, from their own ancestors 10k years ago is not the same in each cluster — we have been, at least at the genetic level, experiencing divergent evolution.

In fact, recent research suggests that 7% or more of all our genes are mutant versions that replaced earlier variants through natural selection over the last tens of thousands of years. There was little gene flow between continental clusters (“races”) during that period, so there is circumstantial evidence for group differences beyond the already established ones (superficial appearance, disease resistance).

More mutants

From the Economist, a nice summary of the Hawks et al. paper on a possible recent speedup in human evolution.

Economist: …Dr Moyzis’s paper suggests is a wider phenomenon—that Homo sapiens is continuing to undergo local evolution. He and his colleagues reckon they can both estimate the rate of evolution and identify many of the evolving genes, by using a trick with the clumsy name of linkage disequilibrium.

Genes are linked together in cell nuclei on structures called chromosomes. These come in pairs, one from each parent. However, when sperm and egg cells are formed, the maternal and paternal chromosomes swap bits of DNA to create a new mixture. The pieces of DNA swapped are complementary—that is, they contain the same types of gene. But they may contain different versions of the genes in question, and these different versions can have different biological effects.

Over the generations this process of swapping mixes the genes up thoroughly, and an equilibrium emerges. If a new mutation appears, however, it will take quite a while for that thorough mixing to happen. This means recent mutations can be spotted because they are still linked to the same neighbouring bits of DNA as they were when they first appeared. Moreover, the size of these neighbouring blocks gives an indication of how long ago the mutation in question emerged; long blocks suggest a recent mutation because the mixing process has not had time to break them up.

All this has been known for decades, but it is only recently that enough human DNA sequences have become available for the technique to be used to compare people from different parts of the world. And this is what Dr Moyzis and his colleagues have now done.

What they have found is that about 1,800 protein-coding genes, some 7% of the total known, show signs of having been subject to recent natural selection. By recent, they mean within the past 80,000 years. Moreover, as the chart shows, the rate of change has speeded up over the course of that period. (The sudden fall-off at the end is caused because the linkage-disequilibrium method cannot easily detect very recent mutations, rather than by a sudden reduction in the rate of evolution.) The researchers put this acceleration down to two things. First, the human population has expanded rapidly during that period, which increases the size of the gene pool in which mutations can occur. Second, the environment in which people find themselves has also changed rapidly, creating new contexts in which those mutations might have beneficial effects.

That environmental change itself has two causes. The past 80,000 years is the period in which humanity has spread out of Africa to the rest of the world, and each new place brings its own challenges. It has also been a period of enormous cultural change, and that, too, creates evolutionary pressures. In acknowledgment of these diverse circumstances, the researchers looked in detail at the DNA of four groups of people from around the planet: Yoruba from Africa, Han Chinese and Japanese from Asia, and Europeans.

Various themes emerged. An important one was protection from disease, suspected to be a consequence of the increased risk of infection that living in settlements brings. In this context, for example, various mutations of a gene called G6PD that are thought to offer protection from malaria sprang up independently in different places.

A second theme is response to changes in diet caused by the domestication of plants and animals. One example of this is variation in LCT, a gene involved in the metabolism of lactose, a sugar found in milk. All human babies can metabolise lactose, but only some adults can manage the trick. That fact, and the gene involved, have been known for some time. But Dr Moyzis’s team have worked out the details of the evolution of LCT. They suspect that it was responsible for the sudden spread of the Indo-European group of humanity about 4,000 years ago, and also for the more recent spread of the Tutsis in Africa, whose ancestors independently evolved a tolerant version of the gene.

The pressures behind other changes are less obvious. In the past 2,000-3,000 years, for example, Europeans have undergone changes in the gene for a protein that moves potassium ions in and out of nerve cells and taste buds. There have also been European changes in genes linked to cancer and Alzheimer’s disease. Chinese, Japanese and Europeans, meanwhile, have all seen changes in a serotonin transporter. Serotonin is one of the brain’s messenger molecules, and is particularly involved in establishing mood.

The finding that may cause most controversy, however, is that in the Asian groups there has been strong selection for one variant of a gene that, in a different form, is responsible for Gaucher’s disease. A few years ago two of the paper’s other authors, Gregory Cochran and Henry Harpending, suggested that the Gaucher’s form of the gene might be connected with the higher than average intelligence notable among Ashkenazi Jews. The unstated inference is that something similar might be true in Asians, too.

The Ashkenazim paper caused quite a stir at the time. It was merely a hypothesis, but it did suggest a programme of research that could be conducted to test the hypothesis. So far, no one—daring or foolish—has tried. Eventually, however, such questions will have to be faced. The paper Dr Moyzis and his colleagues have just published is a ranging shot, but the amount of recent human evolution it has exposed is surprising. Others will no doubt follow, and the genetic meaning of the term “race”, if it has one, will be exposed for all to see.

We are all mutants now

Some interesting new science suggests that human evolution has accelerated in the last tens of thousands of years. The study by Hawks, Wang, Cochran, Harpending and Moyzis (of UW Madison, Affymetrix, U Utah and UC Irvine) uses linkage disequilibrium tests on hapmap SNP data to determine that roughly 7% of all genes have undergone strong selection recently. The method looks for regions of DNA with similar SNP patterns. If an advantageous gene swept through a population in a relatively short time, replacing other variants, then the pattern of nucleotide polymorphisms in that area of the chromosome will be particularly uniform throughout the group. The results imply that we are all descended from mutants who, relatively recently, out-competed and replaced their contemporaries. The distribution of mutations is not uniform in different geographical populations (i.e., races). Recent evolution is causing genetic divergence, not convergence.

There is a good theoretical argument for why evolution may speed up due to population growth. Given a particular probability distribution for producing beneficial mutations, a large population implies a faster rate of incidence of such mutations. Because reproductive dynamics leads to exponential solutions (i.e., a slight increase in expected number of offspring compounds rapidly), the time required for an advantageous allele to sweep through a population only grows logarithmically with the population, while the rate of incidence grows linearly.

Note Cochran is a physicist who does evolutionary biology as a hobby 🙂 For some reason, this seldom happens in the opposite direction…

(original graphic from the Times; PNAS paper; University of Utah press release.)

NYTimes: Researchers analyzing variation in the human genome have concluded that human evolution accelerated enormously in the last 40,000 years under the force of natural selection.

The finding contradicts a widely held assumption that human evolution came to a halt 10,000 years ago or even 50,000 years ago. Some evolutionary psychologists, for example, assume that the mind has not evolved since the Ice Age ended 10,000 years ago.

But other experts expressed reservations about the new report, saying it is interesting but more work needs to be done.

The new survey — led by Robert K. Moyzis of the University of California, Irvine, and Henry C. Harpending of the University of Utah — developed a method of spotting human genes that have become more common through being favored by natural selection. They say that some 7 percent of human genes bear the signature of natural selection.

By dating the time that each of the genes came under selection, they have found that the rate of human evolution was fairly steady until about 50,000 years ago and then accelerated up until 10,000 years ago, they report in the current issue of The Proceedings of the National Academy of Sciences. The high rate of selection has probably continued to the present day, Dr. Moyzis said, but current data are not adequate to pick up recent selection.

The brisk rate of human selection occurred for two reasons, Dr. Moyzis’ team says. One was that the population started to grow, first in Africa and then in the rest of the world after the first modern humans left Africa. The larger size of the population meant that there were more mutations for natural selection to work on. The second reason for the accelerated evolution was that the expanding human populations in Africa and Eurasia were encountering climates and diseases to which they had to adapt genetically. The extra mutations in their growing populations allowed them to do so.

Dr. Moyzis said it was widely assumed that once people developed culture, they protected themselves from the environment and from the forces of natural selection. But people also had to adapt to the environments that their culture created, and the new analysis shows that evolution continued even faster than before.

The researchers took their data from the HapMap project, a survey designed by the National Institutes of Health to look at sites of common variation in the human genome and to help identify the genes responsible for common diseases. The HapMap data, generated by analyzing the genomes of people from Africa, East Asia and Europe, has also been a trove for people studying human evolutionary history.

David Reich, a population geneticist at the Harvard Medical School, said the new report was “a very interesting and exciting hypothesis” but that the authors had not ruled out other explanations of the data. The power of their test for selected genes falls off in looking both at more ancient and more recent events, he said, so the overall picture might not be correct.

Similar reservations were expressed by Jonathan Pritchard, a population geneticist at the University of Chicago.

“My feeling is that they haven’t been cautious enough,” he said. “This paper will probably stimulate others to study this question.”

University of Utah press release:

ARE HUMANS EVOLVING FASTER?

FINDINGS SUGGEST WE ARE BECOMING MORE DIFFERENT, NOT ALIKE

Media Contacts

Dec. 10, 2007 – Researchers discovered genetic evidence that human evolution is speeding up – and has not halted or proceeded at a constant rate, as had been thought – indicating that humans on different continents are becoming increasingly different.

“We used a new genomic technology to show that humans are evolving rapidly, and that the pace of change has accelerated a lot in the last 40,000 years, especially since the end of the Ice Age roughly 10,000 years ago,” says research team leader Henry Harpending, a distinguished professor of anthropology at the University of Utah.

Harpending says there are provocative implications from the study, published online Monday, Dec. 10 in the journal Proceedings of the National Academy of Sciences:

“We aren’t the same as people even 1,000 or 2,000 years ago,” he says, which may explain, for example, part of the difference between Viking invaders and their peaceful Swedish descendants. “The dogma has been these are cultural fluctuations, but almost any Temperament trait you look at is under strong genetic influence.”

“Human races are evolving away from each other,” Harpending says. “Genes are evolving fast in Europe, Asia and Africa, but almost all of these are unique to their continent of origin. We are getting less alike, not merging into a single, mixed humanity.” He says that is happening because humans dispersed from Africa to other regions 40,000 years ago, “and there has not been much flow of genes between the regions since then.”
“Our study denies the widely held assumption or belief that modern humans [those who widely adopted advanced tools and art] appeared 40,000 years ago, have not changed since and that we are all pretty much the same. We show that humans are changing relatively rapidly on a scale of centuries to millennia, and that these changes are different in different continental groups.”

The increase in human population from millions to billions in the last 10,000 years accelerated the rate of evolution because “we were in new environments to which we needed to adapt,” Harpending adds. “And with a larger population, more mutations occurred.”

Study co-author Gregory M. Cochran says: “History looks more and more like a science fiction novel in which mutants repeatedly arose and displaced normal humans – sometimes quietly, by surviving starvation and disease better, sometimes as a conquering horde. And we are those mutants.”

Harpending conducted the study with Cochran, a New Mexico physicist, self-taught evolutionary biologist and adjunct professor of anthropology at the University of Utah; anthropologist John Hawks, a former Utah postdoctoral researcher now at the University of Wisconsin, Madison; geneticist Eric Wang of Affymetrix, Inc. in Santa Clara, Calif.; and biochemist Robert Moyzis of the University of California, Irvine.

No Justification for Discrimination

The new study comes from two of the same University of Utah scientists – Harpending and Cochran – who created a stir in 2005 when they published a study arguing that above-average intelligence in Ashkenazi Jews – those of northern European heritage – resulted from natural selection in medieval Europe, where they were pressured into jobs as financiers, traders, managers and tax collectors. Those who were smarter succeeded, grew wealthy and had bigger families to pass on their genes. Yet that intelligence also is linked to genetic diseases such as Tay-Sachs and Gaucher in Jews.

That study and others dealing with genetic differences among humans – whose DNA is more than 99 percent identical – generated fears such research will undermine the principle of human equality and justify racism and discrimination. Other critics question the quality of the science and argue culture plays a bigger role than genetics.

Harpending says genetic differences among different human populations “cannot be used to justify discrimination. Rights in the Constitution aren’t predicated on utter equality. People have rights and should have opportunities whatever their group.”

Analyzing SNPs of Evolutionary Acceleration

The study looked for genetic evidence of natural selection – the evolution of favorable gene mutations – during the past 80,000 years by analyzing DNA from 270 individuals in the International HapMap Project, an effort to identify variations in human genes that cause disease and can serve as targets for new medicines.

The new study looked specifically at genetic variations called “single nucleotide polymorphisms,” or SNPs (pronounced “snips”) which are single-point mutations in chromosomes that are spreading through a significant proportion of the population.

Imagine walking along two chromosomes – the same chromosome from two different people. Chromosomes are made of DNA, a twisting, ladder-like structure in which each rung is made of a “base pair” of amino acids, either G-C or A-T. Harpending says that about every 1,000 base pairs, there will be a difference between the two chromosomes. That is known as a SNP.

Data examined in the study included 3.9 million SNPs from the 270 people in four populations: Han Chinese, Japanese, Africa’s Yoruba tribe and northern Europeans, represented largely by data from Utah Mormons, says Harpending.

Over time, chromosomes randomly break and recombine to create new versions or variants of the chromosome. “If a favorable mutation appears, then the number of copies of that chromosome will increase rapidly” in the population because people with the mutation are more likely to survive and reproduce, Harpending says.

“And if it increases rapidly, it becomes common in the population in a short time,” he adds.

The researchers took advantage of that to determine if genes on chromosomes had evolved recently. Humans have 23 pairs of chromosomes, with each parent providing one copy of each of the 23. If the same chromosome from numerous people has a segment with an identical pattern of SNPs, that indicates that segment of the chromosome has not broken up and recombined recently.

That means a gene on that segment of chromosome must have evolved recently and fast; if it had evolved long ago, the chromosome would have broken and recombined.

Harpending and colleagues used a computer to scan the data for chromosome segments that had identical SNP patterns and thus had not broken and recombined, meaning they evolved recently. They also calculated how recently the genes evolved.

A key finding: 7 percent of human genes are undergoing rapid, recent evolution.

The researchers built a case that human evolution has accelerated by comparing genetic data with what the data should look like if human evolution had been constant:

The study found much more genetic diversity in the SNPs than would be expected if human evolution had remained constant.

If the rate at which new genes evolve in Africans was extrapolated back to 6 million years ago when humans and chimpanzees diverged, the genetic difference between modern chimps and humans would be 160 times greater than it really is. So the evolution rate of Africans represents a recent speedup in evolution.

If evolution had been fast and constant for a long time, there should be many recently evolved genes that have spread to everyone. Yet, the study revealed many genes still becoming more frequent in the population, indicating a recent evolutionary speedup.
Next, the researchers examined the history of human population size on each continent. They found that mutation patterns seen in the genome data were consistent with the hypothesis that evolution is faster in larger populations.

Evolutionary Change and Human History: Got Milk?

“Rapid population growth has been coupled with vast changes in cultures and ecology, creating new opportunities for adaptation,” the study says. “The past 10,000 years have seen rapid skeletal and dental evolution in human populations, as well as the appearance of many new genetic responses to diet and disease.”

The researchers note that human migrations into new Eurasian environments created selective pressures favoring less skin pigmentation (so more sunlight could be absorbed by skin to make vitamin D), adaptation to cold weather and dietary changes.

Because human population grew from several million at the end of the Ice Age to 6 billion now, more favored new genes have emerged and evolution has speeded up, both globally and among continental groups of people, Harpending says.

“We have to understand genetic change in order to understand history,” he adds.

For example, in China and most of Africa, few people can digest fresh milk into adulthood. Yet in Sweden and Denmark, the gene that makes the milk-digesting enzyme lactase remains active, so “almost everyone can drink fresh milk,” explaining why dairying is more common in Europe than in the Mediterranean and Africa, Harpending says.

He now is studying if the mutation that allowed lactose tolerance spurred some of history’s great population expansions, including when speakers of Indo-European languages settled all the way from northwest India and central Asia through Persia and across Europe 4,000 to 5,000 years ago. He suspects milk drinking gave lactose-tolerant Indo-European speakers more energy, allowing them to conquer a large area.

But Harpending believes the speedup in human evolution “is a temporary state of affairs because of our new environments since the dispersal of modern humans 40,000 years ago and especially since the invention of agriculture 12,000 years ago. That changed our diet and changed our social systems. If you suddenly take hunter-gatherers and give them a diet of corn, they frequently get diabetes. We’re still adapting to that. Several new genes we see spreading through the population are involved with helping us prosper with high-carbohydrate diet.”