Natural Adaptation vs Natural Selection

It is obvious that adaptation is a far better explanation for the evolutionary process than natural selection ever was. This functions on the basis of the organism making choices.

I anticipated this in my manuscript ‘paradigms shift. It is good to see others coming to the same conclusion. All organisms can make choices, and they respond to the environment by adaptation. The tool set is already in place to grab from and this shows that the grabbing mechanism is not overly precise.

This is not the directed evolution that fundamentalists are calling for but it is directed nonetheless. Those folks pointed out an alternative to natural selection for all the wrong reasons. Their real error was to attempt faith based science, an oxymoron if there ever was one.

Been able to make adaptive choices on behalf of your offspring is such a powerful tool in your clan’s ability to survive, that natural selection demands it. This paper confirms it or at least begins the process.

If you feel up to it, you are now licensed to tell those who argue for directed evolution or whatever they call it, that science has discovered that it is true. Only the directing is coming from the organisms as part of our wiring.

http://www.terradaily.com/reports/Adaptation_Plays_A_Significant_Role_In_Human_Evolution_999.html

Adaptation Plays A Significant Role In Human Evolution

by Staff Writers
Stanford CA (SPX) Jan 22, 2009

For years researchers have puzzled over whether adaptation plays a major role in human evolution or whether most changes are due to neutral, random selection of genes and traits.

Geneticists at Stanford now have laid this question to rest. Their results, scheduled to be published Jan. 16 online in Public Library of Science Genetics, show adaptation-the process by which organisms change to better fit their environment-is indeed a large part of human genomic evolution.

"Others have looked for the signal of widespread adaptation and couldn't find it. Now we've used a lot more data and did a lot of work cleaning it up," said Dmitri Petrov, associate professor of biology at Stanford University and one of two senior authors of the paper.

"We were able to detect the adaptation signatures quite clearly, and they have the characteristic shape we anticipated."

All genetic mutations start out random, but those that are beneficial to an organism's success in their environment are directly selected for and quickly perpetuate throughout the population, providing a uniform, traceable signature.

With the help of post-doctoral researcher James Cai and recent graduate student Michael Macpherson, Petrov and co-senior author Guy Sella, a biologist at the Hebrew University of Jerusalem, used different methodology from what's been used before to look for signatures of adaptation left in the human genome.

"We detected a number of signatures that suggest adaptation is quite pervasive and common," Petrov said.

Humans have a very complex history from traveling around the globe, and the human genome is also highly structured, making it complicated and difficult to work with, he said.

To find the adaptation signal, Petrov and his colleagues looked for regions of the genome that "hitchhiked" along with an adaptation. When a genetic adaptation occurs and is passed on to offspring, other genes on both sides of the adaptation typically accompany it.

The result is a whole region of the genome where all humans are unusually similar to each other, referred to as a "selective sweep," that researchers can identify and trace through human genetic history.

"Adaptation becomes widespread in the population very quickly," Petrov said. "Whereas neutral random mutation doesn't and would not have the selective sweep signature."

"We tried to see if these regions of unusual similarity among all humans tended to be in particular places in the genome as the theory predicts they should be, and indeed we find them there," Petrov said. "The work suggests human beings have undergone rampant adaptation to their environment in the last 200,000 years of history."

In the past, these sweeps were difficult to discern because the data were not sufficiently abundant and were filled with noise. Depending on the methodology, estimates of the degree of adaptation in humans ranged from as high as 30 percent down to zero. Signatures were impossible to interpret with confidence.

"People would find changes in specific genes suggesting that recent adaptations in humans might be common but could not find genome-wide signatures of pervasive adaptation. That was unsettling," Petrov said. "I'm hoping that people will react with relief that things are starting to make sense."

Petrov hopes that researchers can now do a much better job of finding the regions within the genome responsible for specific human adaptations and relate them to changes in human history or past environments.

For example, one could trace the arrival of lactose tolerance to the domestication of cattle and the introduction of milk into our adult diet.

"As the data are going to grow, we should be able to locate specific adaptive events quite well," Petrov said. "By identifying specific genes, we can unravel this evolutionary history of adaptive change."

Another possibility is tracing the origin of skin pigmentation genes, which give people their different skin-color types. Many of these genes are linked to skin cancer. Researchers may be able to recreate past environments while better understanding how adaptation comes into play.

"We see signatures of possibly hundreds of recent adaptive events, and now we can ask what are they doing there," he said. "It's both exiting and puzzling."

This paper follows similar work in bacteria and fruit flies indicating adaptation is a significant contribution to evolution as a whole.

"We are on a crest of a wave showing that adaptation is a lot more prevalent than we thought," Petrov said

Scott Strobel finds Rainforest Fungus Converting Celluose to Diesel

This piece is amazing and unexpected and certainly worth following up with. Of course it will take decades to really see the light of day in practical applications but we at least know it is possible and other protocols are out there just as promising.

At least it is an interesting bit of unusual science that could well add to our growing biological palette. Enjoy the article.

Rainforest Fungus Makes Diesel Compounds From Cellulose

BOZEMAN, Montana, November 4, 2008 (ENS) - A unique fungus that makes diesel compounds directly from cellulose has been discovered living in trees in the Patagonian rainforest.

"These are the first organisms that have been found that make many of the ingredients of diesel," said Professor Gary Strobel from Montana State University. "This is a major discovery."

The discovery may offer an alternative to fossil fuels, said Strobel, MSU professor of plant sciences and plant pathology, who travels the world looking for exotic plants that may contain beneficial microbes. The find is even bigger, he said, than his 1993 discovery of fungus that contained the anticancer drug taxol.

Strobel's paper, published in the November issue of the journal "Microbiology," is based on his discovery of the unique properties of the Patagonian fungus, called Gliocladium roseum.

"Gliocladium roseum lives inside the Ulmo tree in the Patagonian rainforest," Strobel begins, telling the story of how he and his team learned that they had found an entirely new source of fuel.

"We were trying to discover totally novel fungi in this tree by exposing its tissues to the volatile antibiotics of the fungus Muscodor albus," Strobel recounts. "Quite unexpectedly, G. roseum grew in the presence of these gases when almost all other fungi were killed. It was also making volatile antibiotics."

"Then when we examined the gas composition of G. roseum, we were totally surprised to learn that it was making a plethora of hydrocarbons and hydrocarbon derivatives. The results were totally unexpected and very exciting and almost every hair on my arms stood on end!"

Strobel calls the fuel produced by the fungus "myco-diesel," from the Greek-derived root word for the study of fungi - mycology.

"This is the only organism that has ever been shown to produce such an important combination of fuel substances," said Strobel. "The fungus can even make these diesel compounds from cellulose, which would make it a better source of biofuel than anything we use at the moment."

Intense research into ways of making ethanol fuel directly from cellulose now is taking place in public, private and university labs, and several companies are producing demonstration scale cellulosic ethanol from wood waste, from municipal solid waste and from agricultural residue.

Nearly 430 million tons of plant waste are produced from U.S. farmland alone every year, material that scientists are learning to convert to biofuel.

In current biofuel production, this waste is treated with enzymes called cellulases that turn the cellulose into sugar. Microbes then ferment the sugar into ethanol that can be used as a fuel.

"We were very excited to discover that G. roseum can digest cellulose," Strobel said. "Although the fungus makes less myco-diesel when it feeds on cellulose compared to sugars, new developments in fermentation technology and genetic manipulation could help improve the yield."

"When crops are used to make biofuel they have to be processed before they can be turned into useful compounds by microbes," said Strobel. "G. roseum can make myco-diesel directly from cellulose, the main compound found in plants and paper."

In the rainforest, G. roseum produces lots of long chain hydrocarbons and other biological molecules. When the researchers grew it in the lab, it produced fuel that is even more similar to the diesel we put in our cars.

The majority of hydrocarbons found naturally occur in crude oil, where decomposed organic matter provides carbon and hydrogen. When bonded, these elements can form seemingly limitless chains of molecules.

Professor Strobel, who travels the world looking for exotic plants that may contain beneficial microbes, says his discovery brings into question our knowledge of the way fossil fuels are made.

The accepted theory is that crude oil, which is used to make diesel, is formed from the remains of dead plants and animals that have been exposed to heat and pressure for millions of years.

Strobel speculates, "If fungi like this are producing myco-diesel all over the rainforest, they may have contributed to the formation of fossil fuels."

Strobel is the lead author of the paper published in "Microbiology." His MSU co-authors are Berk Knighton and Tom Livinghouse in the Department of Chemistry/Biochemistry, and Katreena Kluck and Yuhao Ren in the Department of Plant Sciences and Plant Pathology.

Other co-authors are Meghan Griffin and Daniel Spakowicz from Yale University and Joe Sears from the Center for Lab Services in Pasco, Washington.

Researchers in government agencies and private industry have already shown interest in the fungi. A team to conduct further research has been established between MSU's College of Engineering and researchers at Yale University.

One member of the team is Strobel's son, Scott, who is chairman of molecular biophysics and biochemistry at Yale and a Howard Hughes Medical Institute Professor. The MSU-Yale team will investigate a variety of questions, including the genetic makeup of Gliocladium roseum.

Scott Strobel said his team is already screening the fungus' genome. Besides determining the complete genetic makeup of the fungus, they will run a series of genetic and biochemical tests to identify the genes responsible for its diesel-making properties.

"The broader question is, what is responsible for the production of these compounds," Scott Strobel said. "If you can identify that, you can hopefully scale it up so you end up with better efficiency of production."

Scientists in a variety of disciplines may be able to combine their talents to optimize production and find a way to turn what is essentially a vapor into a burnable, liquid fuel.