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On Crick and Watson

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Eminent biologist Erwin Chargaff was extremely bitter about not receiving a Nobel for his important work on DNA, which contributed to Crick and Watson’s discovery of the double helix. I’ve been paging through his strange, but occasionally brilliant, memoir Heraclitean Fire: Sketches of a Life before Nature.

On meeting Crick and Watson at the Cavendish lab. Crick, 35, had already had a career in physics interrupted by the war and despaired of making his great contribution to science. Watson was a callow 23, fresh from Indiana.

It was clear to me that I was faced with a novelty: enormous ambition and aggressiveness, coupled with an almost complete ignorance of, and a contempt for, chemistry, that most real of exact sciences – a contempt that was later to have a nefarious influence on the development of “molecular biology.” Thinking of the many sweaty years of making preparations of nucleic acids and of the innumerable hours spent on analyzing them, I could not help being baffled. I am sure that, had I had more contact with, for instance, theoretical physicists, my astonishment would have been less great. In any event, there they were, speculating, pondering, angling for information. …

Thanks for digging around down there — what did you find, again? Great! I’ve got more horsepower, so I’ll just connect the dots for you now… 🙂 From Wikipedia on Crick:

Crick had to adjust from the “elegance and deep simplicity” of physics to the “elaborate chemical mechanisms that natural selection had evolved over billions of years.” He described this transition as, “almost as if one had to be born again.” According to Crick, the experience of learning physics had taught him something important—hubris—and the conviction that since physics was already a success, great advances should also be possible in other sciences such as biology. Crick felt that this attitude encouraged him to be more daring than typical biologists who tended to concern themselves with the daunting problems of biology and not the past successes of physics.

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Written by infoproc

June 12, 2008 at 2:12 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

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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

Trading on testosterone

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Take with boulder-sized grain of salt. Cause and effect? Only an eight day interval? Couldn’t that have been an exceptional period over which aggressiveness paid off?

NYTimes: MOVEMENTS in financial markets are correlated to the levels of hormones in the bodies of male traders, according to a study by two researchers from the University of Cambridge (newscientist.com).

John Coates, a research fellow in neuroscience and finance, and Joe Herbert, a professor of neuroscience, sampled the saliva of 17 traders on a stock trading floor in London two times a day for eight days. They matched the men’s levels of testosterone and cortisol with the amounts of money the men lost or won on the markets. Men with elevated levels of testosterone, a hormone associated with aggression, made more money. When the markets were more volatile, the men showed higher levels of cortisol, considered a “stress hormone.”

But, as New Scientist asked, “which is the cause and which is the effect?”

According to the researchers’ analysis, the men who began their workdays with high levels of testosterone did better than those who did not.

“The popular view is that experienced traders can control their emotions,” Mr. Coates told New Scientist. “But, in fact, their endocrine systems are on fire.”

As with anything else, when it comes to hormones, it is possible to have (from a trader’s perspective) too much of a good thing. Excessive testosterone levels can lead a trader to make irrational decisions.

New Scientist pointed out that although cortisol can help people make more rational decisions during volatile trading periods, too much of it can lead to serious health problems like heart disease and arthritis, and, over time, diminish brain functions like memory.

If individual traders are affected by their hormone levels, does the same hold true for the markets as a whole? After all, the market is nothing more than an aggregate of the individual actions of traders. Mr. Coates thinks it is possible that “bubbles and crashes are coming from these steroids,” according to New Scientist.

If so, “central banks may lower interest rates only to find that traders still refuse to buy risky assets.”

Perhaps, he told New Scientist, “if more women and older men were trading, the markets would be more stable.”

Written by infoproc

April 19, 2008 at 7:34 pm

Posted in biology, finance, hormones

Retroviruses

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The New Yorker has an amazing piece on endogenous retroviruses — retroviruses that succeeded in injecting their RNA into our DNA via germline cells such as sperm or eggs. These fragments of genetic code constitute 8 percent of our entire genome, whereas protein-producing genes are only 2 percent.

Biologists can now reconstruct these long extinct viruses from the fragments, even correcting for mutations or copy errors by comparing different versions and using statistical models to guess at the original code.

…to alter our genetic structure. That would require an organism to insinuate itself into the critical cells we need in order to reproduce: our germ cells. Only retroviruses, which reverse the usual flow of genetic code from DNA to RNA, are capable of that. A retrovirus stores its genetic information in a single-stranded molecule of RNA, instead of the more common double-stranded DNA. When it infects a cell, the virus deploys a special enzyme, called reverse transcriptase, that enables it to copy itself and then paste its own genes into the new cell’s DNA. It then becomes part of that cell forever; when the cell divides, the virus goes with it. Scientists have long suspected that if a retrovirus happens to infect a human sperm cell or egg, which is rare, and if that embryo survives—which is rarer still—the retrovirus could take its place in the blueprint of our species, passed from mother to child, and from one generation to the next, much like a gene for eye color or asthma.

When the sequence of the human genome was fully mapped, in 2003, researchers also discovered something they had not anticipated: our bodies are littered with the shards of such retroviruses, fragments of the chemical code from which all genetic material is made. It takes less than two per cent of our genome to create all the proteins necessary for us to live. Eight per cent, however, is composed of broken and disabled retroviruses, which, millions of years ago, managed to embed themselves in the DNA of our ancestors. They are called endogenous retroviruses, because once they infect the DNA of a species they become part of that species. One by one, though, after molecular battles that raged for thousands of generations, they have been defeated by evolution. Like dinosaur bones, these viral fragments are fossils. Instead of having been buried in sand, they reside within each of us, carrying a record that goes back millions of years. Because they no longer seem to serve a purpose or cause harm, these remnants have often been referred to as “junk DNA.” Many still manage to generate proteins, but scientists have never found one that functions properly in humans or that could make us sick.

Then, last year, Thierry Heidmann brought one back to life. …

…The Nobel Prize-winning biologist Joshua Lederberg once wrote that the “single biggest threat to man’s continued dominance on this planet is the virus.” Harmit Malik, an evolutionary geneticist at the Fred Hutchinson Cancer Research Center, acknowledges the threat, yet he is confident that viruses may also provide one of our greatest scientific opportunities. Exploring that fundamental paradox—that our most talented parasites may also make us stronger—has become Malik’s passion. “We have been in an evolutionary arms race with viruses for at least one hundred million years,’’ he told me recently, when I visited his laboratory. “There is genetic conflict everywhere. You see it in processes that you would never suspect; in cell division, for instance, and in the production of proteins involved in the very essence of maintaining life.

“One party is winning and the other losing all the time,” Malik went on. “That’s evolution. It’s the world’s definitive game of cat and mouse. Viruses evolve, the host adapts, proteins change, viruses evade them. It never ends.” The AIDS virus, for example, has one gene, called “vif,” that does nothing but block a protein whose sole job is to stop the virus from making copies of itself. It simply takes that protein into the cellular equivalent of a trash can; if not for that gene, H.I.V. might have been a trivial disease. “To even think about the many million-year processes that caused that sort of evolution,” Malik said, shaking his head in wonder. “It’s dazzling.” Malik grew up in Bombay and studied chemical engineering at the Indian Institute of Technology there, one of the most prestigious technical institutions in a country obsessed with producing engineers. He gave no real thought to biology, but he was wholly uninspired by his other studies. “It was fair to say I had little interest in chemical engineering, and I happened to tell that to my faculty adviser,’’ he recalled. “He asked me what I liked. Well, I was reading Richard Dawkins at the time, his book ‘The Selfish Gene’ ”—which asserts that a gene will operate in its own interest even if that means destroying an organism that it inhabits or helped create. The concept fascinated Malik. “I was thinking of becoming a philosopher,’’ he said. “I thought I would study selfishness.” …

Written by infoproc

December 4, 2007 at 9:30 pm

Dyson and Crick

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From this essay.

Also, Dyson is sceptical about global warming, but knows enough to be sceptical of his scepticism.

Bad Advice to a Young Scientist

Sixty years ago, when I was a young and arrogant physicist, I tried to predict the future of physics and biology. My prediction was an extreme example of wrongness, perhaps a world record in the category of wrong predictions. I was giving advice about future employment to Francis Crick, the great biologist who died in 2005 after a long and brilliant career. He discovered, with Jim Watson, the double helix. They discovered the double helix structure of DNA in 1953, and thereby gave birth to the new science of molecular genetics. Eight years before that, in 1945, before World War 2 came to an end, I met Francis Crick for the first time. He was in Fanum House, a dismal office building in London where the Royal Navy kept a staff of scientists. Crick had been working for the Royal Navy for a long time and was depressed and discouraged. He said he had missed his chance of ever amounting to anything as a scientist. Before World War 2, he had started a promising career as a physicist. But then the war hit him at the worst time, putting a stop to his work in physics and keeping him away from science for six years. The six best years of his life, squandered on naval intelligence, lost and gone forever. Crick was good at naval intelligence, and did important work for the navy. But military intelligence bears the same relation to intelligence as military music bears to music. After six years doing this kind of intelligence, it was far too late for Crick to start all over again as a student and relearn all the stuff he had forgotten. No wonder he was depressed. I came away from Fanum House thinking, “How sad. Such a bright chap. If it hadn’t been for the war, he would probably have been quite a good scientist”.

A year later, I met Crick again. The war was over and he was much more cheerful. He said he was thinking of giving up physics and making a completely fresh start as a biologist. He said the most exciting science for the next twenty years would be in biology and not in physics. I was then twenty-two years old and very sure of myself. I said, “No, you’re wrong. In the long run biology will be more exciting, but not yet. The next twenty years will still belong to physics. If you switch to biology now, you will be too old to do the exciting stuff when biology finally takes off”. Fortunately, he didn’t listen to me. He went to Cambridge and began thinking about DNA. It took him only seven years to prove me wrong. The moral of this story is clear. Even a smart twenty-two-year-old is not a reliable guide to the future of science. And the twenty-two-year-old has become even less reliable now that he is eighty-two.

Written by infoproc

August 11, 2007 at 3:32 pm