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

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Written by infoproc

October 1, 2008 at 3:22 pm

Fast times in Jamaica

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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.

Written by infoproc

June 30, 2008 at 5:26 pm

Brainpower ain’t free

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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.”

Written by infoproc

May 6, 2008 at 11:52 am

Brainpower ain’t free

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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.”

Written by infoproc

May 6, 2008 at 11:52 am

Brainpower ain’t free

leave a comment »

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.”

Written by infoproc

May 6, 2008 at 11:52 am

Happiness: all in da gene?

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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.

Written by infoproc

March 16, 2008 at 4:13 pm

The exponential curve for genome sequencing

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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. …

Written by infoproc

February 10, 2008 at 12:29 am