Wednesday, September 28, 2005

644-670: Evolutionary Game Theory

A few words on Evolutionary Game Theory:

About a month ago, Michael asked me to give my opinion on an article on cheating viruses and game theory. Coincidentally, I had to write a referee report on a paper about evolutionary game theory (EGT) only recently, so I have collected further material and ideas about this topic which I would like to share with you:

Jörgen Weibull's paper "What have we learned from Evolutionary Game Theory so far?" provides a great non-technical introduction to EGT. It gives a first idea of what EGT is all about. I very much appreciated the reference list of this paper as well. In Evolutionary game dynamic, Josef Hofbauer and Karl Sigmund dig a little deeper and provide some interesting insights into the relationship between systems of differential equations (inclusions) and special equilibrium refinements (notable ESS and ES). Finally, I would like to draw your attention to Daniel Friedman's paper "On economic applications of evolutionary game theory". This paper is also non-technical and its objective is to make the general ideas behind an evolutionary game theoretic model more tranparent. As the title suggests, Friedman gives a nice outline of how these ideas can be incorporated into economic models.
Links are omitted, but click through and check out the ways that evolutionary logic is used by economists.

Monday, September 26, 2005

643: Insight into our sight: A new view on the evolution of the eye lens

Via Stranger Fruit, Insight into our sight: A new view on the evolution of the eye lens:

Fish, frogs, birds and mammals all experience image-forming vision, thanks to the fact that their eyes all express crystallins and form a lens; however, the vertebrates' nearest invertebrate relatives, such as sea squirts, have only simple eyes that detect light but are incapable of forming an image. This has lead to the view that the lens evolved within the vertebrates early in vertebrate evolution, and it raises a long-standing question in evolutionary biology: How could a complex organ with such special physical properties have evolved?

In their new work, Shimeld and colleagues approached this question by examining the evolutionary origin of one crystallin protein family, known as the ß?-crystallins. Focusing on sea squirts, invertebrate cousins of the vertebrate lineage, the researchers found that these creatures possess a single crystallin gene, which is expressed in its primitive light-sensing system. The identification of the sea squirt's crystallin strongly suggests that it is the single gene from which the vertebrate ß?-crystallins evolved.

The researchers also found that, remarkably, expression of the sea squirt crystallin gene is controlled by genetic elements that also respond to the factors that control lens development in vertebrates: The researchers showed that when regulatory regions of the sea squirt gene are transferred to frog embryos, these regulatory elements drive gene expression in the tadpoles' own visual system, including the lens. This strongly suggests that prior to the evolution of the lens, there was a regulatory link between two tiers of genes: those that would later become responsible for controlling lens development, and those that would help give the lens its special physical properties. This combination of genes appears to have then been co-opted in an early vertebrate during the evolution of its visual system, giving rise to the lens.
Common descent, testable evolutionary predictions and evaluating evolutionary hypotheses. Cool.

642: Evolving modularity

John Hawks explains Why organisms are modular. Very neat simulations by Kashtan and Alon on the evolution of circuits in varying environment.

Monday, September 19, 2005

641: Researchers Find How Malaria Parasite Disperses From Red Blood Cells | Science Blog

Researchers Find How Malaria Parasite Disperses From Red Blood Cells | Science Blog:

Researchers at the National Institute of Child Health and Human Development have determined the sequence in which the malaria parasite disperses from the red blood cells it infects. The National Institute of Child Health and Human Development is one of the National Institutes of Health.

“It’s extremely important to learn about all aspects of the malaria parasite’s life cycle, ” said Duane Alexander, M.D., Director of the NICHD. “The parasite is growing resistant to the drugs used to treat it, and new information is essential for developing strategies to protect against the disease.”
Evolution is at work in the resistance to drugs, but also explains how the parasite is so well adapted to parasitism.

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Sunday, September 18, 2005

640: Stressed Cells Spark DNA Repair Missteps And Speed Evolution

Thanks to afarensis for point out Stressed Cells Spark DNA Repair Missteps And Speed Evolution:

When Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine, first published her finding that the mutation rate increased in bacteria stressed by starvation, sometimes resulting in a rare change that benefited the bacteria, it was controversial.

In a report in the current issue of the journal Molecular Cell, she and her colleagues describe not only how it happens but also show that this only occurs at a special time and place in the stressed cells.
Research on evolution that reveals how cancer works, how the body fights it, and how new mutations arise.

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639: Mitochondrial DNA adaptations in living human populations

Mitochondrial DNA adaptations in living human populations:

populations in northern latitudes today are enriched for a number of mtDNA haplogroups that are likely adaptive to cold. Today, these haplogroups (as a class) are largely protective against degenerative diseases of aging, possibly because they reduce oxygen free radical production. But they are also more susceptible to disorders of energy metabolism, because they reduce ATP production.

Needless to say, this says some interesting things about the relationship of longevity and energy metabolism in recent human populations.
Human evolution and the trade-offs between longevity and energy efficiency.

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638: Part Human, Part Virus

Part Human, Part Virus: Corante > The Loom >:

Here’s the history as they now see it: the free-living, oxygen-breathing ancestors of mitochondria were infected with some nasty T3/T7 viruses. Most of the time the viruses were fatal. But some mutant tried to replicate itself inside a proto-mitochondrion and failed. Its genes were trapped in the genome of its host. Its host was able to reproduce, and one of its descendants took up residence inside the cell of a eukaryote. At some point after this merger, a mutation caused the virus’s DNA and RNA copying genes to come back online. They took over the job of making these molecules, and the mitochondria’s own genes for this job were later stripped out of its genome.
Viruses, endosymbionts, and the evolution of eukaryotes.

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Wednesday, September 14, 2005

637: For Fossil Hunters, Gobi Is No Desert - New York Times

For Fossil Hunters, Gobi Is No Desert - New York Times:

It has been the paleontologists' boast, never disputed, that this particular forbidding stretch of the Gobi holds the world's richest and most diverse deposits of dinosaur and early mammal remains from 80 million years ago, a critical time for life in the Cretaceous geologic period.

Four years had passed since paleontologists of the American-Mongolian expedition last pitched camp at Ukhaa Tolgod ("brown hills" in Mongolian), scene of their greatest triumphs. They were lured back last month, as surely as gold prospectors to the mother lode, by the expectation that the site has more to yield.
Hunting early fossils. Evolution at work.

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636: Immune system has evolved to prevent autoimmune disease | Science Blog

Immune system has evolved to prevent autoimmune disease | Science Blog:

New research finds the human immune system has foregone evolutionary changes that would allow it to produce better antibodies in less time because the improved antibodies would be far more likely to attack the body's own tissues. The Rice University study finds the immune system has evolved a near-perfect balance for producing antibodies that are both effective against pathogens and unlikely to cause autoimmune disease.

The findings will be published in the journal Physical Review Letters. They are based on a new model of the immune system that is the first to simulate the hierarchical nature of the body's immune response. The model predicts that chronic infections may lead to autoimmune diseases, a scenario that has been proposed as a cause of some rheumatic diseases like arthritis.
Mmmm, evolution. There are constraints on evolution and our immune system is (clearly) not perfect.

635: How bodies and plants repair UV damaged DNA | Science Blog

How bodies and plants repair UV damaged DNA | Science Blog:

For the first time, researchers have observed exactly how some cells are able to repair DNA damage caused by the sun's ultraviolet (UV) radiation.

The Ohio State University study revealed how the enzyme photolyase uses energy from visible light to repair UV damage.

This enzyme is missing in all mammals, including humans, although all plants and all other animals have it. Greater understanding of how photolyase works could one day lead to drugs that help repair UV damage in human DNA.

Scientists believe that all placental mammals lost the ability to make this enzyme some 170 million years ago, said Zhong, an assistant professor of physics and adjunct assistant professor of chemistry and biochemistry at Ohio State.

That's why humans, mice, and all other mammals are particularly vulnerable to cancer-causing UV rays from the sun. But the rest of the animal kingdom – insects, fish, birds, amphibians, marsupials, and even bacteria, viruses and yeast – retained a greater ability to repair such damage.
Common descent!

634: In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times

In Chimpanzee DNA, Signs of Y Chromosome's Evolution - New York Times:

Scientists have decoded the chimp genome and compared it with that of humans, a major step toward defining what makes people human and developing a deep insight into the evolution of human sexual behavior.

Scientists sequenced the DNA of a chimpanzee named Clint and compared it with that of humans.

The comparison pinpoints the genetic differences that have arisen in the two species since they split from a common ancestor some six million years ago.

The realization that chimpanzees hold a trove of information about human evolution and nature comes at a time when they and other great apes are under harsh pressures in their native habitat. Their populations are dwindling fast as forests are cut down and people shoot them for meat. They may soon disappear from the wild altogether, primatologists fear, except in the few sanctuaries that have been established.

Chimpanzees and people possess almost identical sets of genes, so the genes that have changed down the human lineage should hold the key to what makes people human.
Common descent and human evolution!

633: Brain May Still Be Evolving, Studies Hint - New York Times

Brain May Still Be Evolving, Studies Hint - New York Times:

Two genes involved in determining the size of the human brain have undergone substantial evolution in the last 60,000 years, researchers say, leading to the surprising suggestion that the brain is still undergoing rapid evolution.

The discovery adds weight to the view that human evolution is still a work in progress, since previous instances of recent genetic change have come to light in genes that defend against disease and confer the ability to digest milk in adulthood.

It had been widely assumed until recently that human evolution more or less stopped 50,000 years ago.
This surprises no one, in fact. I've got a stack of cases where humans are evolving, ranging from lactose intolerance to mutations which conferred protection against the Plague and now protect some people against HIV.

Don't read this to mean that particular alleles necessarily are "genetically smarter" or anything like that. It may mean that or it may not, all they are showing is change, another name for evolution.