Ohio HOPE

A few days ago we mentioned a new group in Ohio that will be helping promote pro-science candidates for the Ohio Board of Ed, and especially helping to bust "Ohio's answer to Connie Morris." Well, HOPE has webpage now, so you can click over there and help support their important work.

How western Kansas became K-State country, and how we can make it evolution country

KU Country? | LJWorld.com:

Craig Miner’s latest book, “Next Year Country: Dust to Dust in Western Kansas, 1890-1940,” was featured in Monday’s Journal-World. In the book, Miner, a history professor at Wichita State University, chronicles the peaks and valleys of western Kansas, where harsh weather often spelled the difference between success and failure for the agricultural economy.

While compiling the history, Miner turned up several clues about why residents of the western two-thirds of the state have a good feeling about K-State. The school set up experiment stations across the area to test crop varieties and develop new hybrids that were resistant to pests and drought.

K-State, the railroads and the local Farm Bureaus took information on the road, traveling to different cities giving lectures and sharing information about better agriculture techniques for men and home economics for women.

I see nothing to suggest that a similar strategy, reaching out to the more distant communities and showing the value of science and evolutionary biology to people in rural Kansas couldn't bring the western part of the state as firmly onto the side of Darwin as they are of the Wildcats.

Request for help

I haven't had the time to deal with TEP lately, but I hate to see it languish. Would anyone like to help me out?

678: The Living Worlds Hypothesis

In this interview David Grinspoon posits a hypothesis about the way life could have evolved on Titan. It's a testable hypothesis.

677: A Prize Bug

A Prize Bug:

As scientists got to know the global variation of Helicobacter better, they began to discover a remarkable pattern. They mapped out an evolutionary tree of the strains of the bacteria and found that it lined up very well with the migrations of humans over the past 50,000 years. One study looked at the Ladakh province of northern India. Muslims and Buddhists have coexisted there for 1000 but remain isolated from one another. It turns out that Muslim Ladakhs only carry a European strain of Helicobacter, while Buddhists carry a mix of European and East Asian bugs. In Peru, Indians who have lived in relative isolation from European colonists carry Helicobacter that is akin to the bugs in East Asia, a major source of migration into the New World. Peruvians from the cities, on the other hand, carried European Helicobacter. It appears that Helicobacter existed in our species before humans began to move beyond Africa, and was then carried around the world as our ancestors traveled the globe. But exactly how long ago this parasite first made its home in us remains to be discovered.

Scientists have a long way to go in order to understand the full evolutionary story of Helicobacter. Many ethnic groups have yet to be sampled, and the evolutionary contortions of their bacteria have yet to be documented. This work promises to offer some guidance about what we should do about this remarkable bug. Antibiotics can wipe it out, but that doesn't necessarily mean we should eradicate it from our species. It produces some proteins that kill other microbes, and one study suggested that it reduces the chances of children getting diarrhoea. Other studies have suggested that while Helicobacter causes some kinds of cancer, not having it increases the chances of other kinds. It's possible that a long coevolution has made Helicobacter part parasite, part mutualist--much the same as intestinal worms may have prevented our ancestors from getting allergies. It's even possible that Helicobacter's high-speed evolution allowed it to become more parasitic in some parts of the world and more mutualistic in others. Before we decide on its future, it will serve us well to understand Helicobacter's past.

This is the bacterium that won Marshall and Warren this year's Nobel Prize. Understanding its evolution gives insight into the diseases it causes and prevents, and our own species' history.

676: Fitting in: Newly evolved genes adopt a variety of strategies to remain in the gene pool

The Panda's Thumb: Fitting in: Newly evolved genes adopt a variety of strategies to remain in the gene pool:

To determine the basis for the persistence of functional gene duplicates in the genome, three scientists at the Institute of Molecular Systems Biology at the Swiss Federal Institute of Technology in Zürich have collaborated on the largest systematic analysis of duplicated gene function to date. Using an integrative combination of computational and experimental approaches, they classified duplicate pairs of genes involved in yeast metabolism into four functional categories: (1) back-up, where a duplicate gene copy has acquired the ability to compensate in the absence of the other copy, (2) subfunctionalization, where a duplicate copy has evolved a completely new, non-overlapping function, (3) regulation, where the differential regulation of duplicates fine-tunes pathway usage, and (4) gene dosage, where the increased expression provided by the duplicate gene copy augments production of the corresponding protein.

Their results, which appear in the October issue of the journal Genome Research, indicate that no single role prevails but that all four of the mechanisms play a substantial role in maintaining duplicate genes in the genome.

Gene duplication is a major source of novel material for evolution.

675: The words of the world

The Panda's Thumb: The words of the world:

A study in Science has returned biological methods to linguistic evolution in a reversal of history, and concluded that one can, within limits, reconstruct the history of language.

Charles Darwin was not the first person to suppose that historical evolution could be recognised by homologies and represented by tree diagrams. That honour goes to Sir William Jones in 1797, although the tree idea was later.

Jones argued that one could compare cognate terms and infer a historical relationship between languages and this has become the foundation of modern philology. For example, words that are based on the idea of “knowing” (including, as it happens, “idea”) generate a tree of Indo-European languages. [And like biological evolution, there are “creationists” who think that all language was created in Sanskrit.]

Now, a study in Science has returned biological methods to linguistic evolution in a reversal of history, and come up with some interesting conclusions.

Evolution gives insight into linguistics.

674: New dolphin species discovered

New dolphin species in Australia.

673: How A Zebra Lost Its Stripes: Rapid Evolution Of The Quagga

How A Zebra Lost Its Stripes: Rapid Evolution Of The Quagga:

In the past, the quagga has alternatively been described as a species and a subspecies of the Plains zebra.These researchers asked how and when the quagga diverged from all the remaining related horses, zebras, and asses. They compared the genetics, coat color and habitats of existing zebras with related extinct species.

The mitochondrial DNA markers from 13 museum specimens, including the only skeleton in museum collections, which is at Yale's Peabody Museum of Natural History, showed that quagga likely diverged from Plains zebra about 120,000 to 290,000 years ago during the Ice Age. These results suggest that the quagga descended from a population of plains zebras that became isolated and the distinct quagga body type and coloring evolved rapidly.

This study reveals that the Ice Age was important not just in Europe and North America, but also in Africa.

"The rapid evolution of coat color in the quagga could be explained by disrupted gene flow because of geographical isolation, an adaptive response to a drier habitat, or a combination of both of the two forces," said Caccone.

Thanks to afarensis for the tip.

672: Autoimmune overload may damage HIV-infected brain | Science Blog

Autoimmune overload may damage HIV-infected brain | Science Blog:

Researchers studying the evolution of the human immunodeficiency virus (HIV) in the brain have found that the body's own defenses may cause HIV-related dementia.

Publishing in the Sept. 2005 issue of the Journal of Virology, the researchers show that HIV in the temporal lobe mutates at a rate 100 times faster than in other parts of the body, triggering white blood cells to continually swarm to attack the infection. The associated overcrowding and inflammation appear to cause the dementia.

Earlier studies had suggested that the build-up of white blood cells could lead to HIV-related dementia, but this is the first study to track the probable mechanism.

The findings could lead to new treatments that target HIV-infected white blood cells, perhaps one day countering the brain wasting that will affect as many as 15 percent of the nearly 40 million people around the world who are infected with the virus.

Evolution, saving lives.

671: Save the Flowers

Save the Flowers: Science News Online, Sept. 24, 2005:

No one knows what's responsible for this waning of fragrance by roses and other ornamental-flower varieties, including carnations and chrysanthemums, but scientists who investigate floral scent suspect that the flower breeding that's led to an estimated 18,000 rose cultivars in an ever-widening spectrum has run roughshod over fragrance.

"Pigment compounds are derived from the same biochemical precursors [as scent compounds are], so it makes sense that if you make more of one you get less of the other," notes floral-scent biochemist and geneticist Eran Pichersky of the University of Michigan in Ann Arbor.

Floral scent may be dwindling because breeders for the $30 billion ornamental-flower industry pay scant attention to this most emblematic attribute of flowers.

Evolution is a story of trade-offs. This is a testable evolutionary hypothesis.

Thanks to BoingBoing for the tip.

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.

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.