Tuesday, January 26, 2010

“Success in the DREAM3 Signaling Response Challenge Using Simple ... - Elites TV” plus 4 more

“Success in the DREAM3 Signaling Response Challenge Using Simple ... - Elites TV” plus 4 more

Success in the DREAM3 Signaling Response Challenge Using Simple ... - Elites TV

Posted: 25 Jan 2010 10:58 PM PST

Our group produced the best predictions overall in the DREAM3 signaling response challenge, being tops by a substantial margin in the cytokine sub-challenge and nearly tied for best in the phosphoprotein sub-challenge. We achieved this success using a simple interpolation strategy. For each combination of a stimulus and inhibitor for which predictions were required, we had noted there were six other datasets using the same stimulus (but different inhibitor treatments) and six other datasets using the same inhibitor (but different stimuli). Therefore, for each treatment combination for which values were to be predicted, we calculated rank correlations for the data that were in common between the treatment combination and each of the 12 related combinations. The data from the 12 related combinations were then used to calculate missing values, weighting the contributions from each experiment based on the rank correlation coefficients. The success of this simple method suggests that the missing data were largely over-determined by similarities in the treatments. We offer some thoughts on the current state and future development of DREAM that are based on our success in this challenge, our success in the earlier DREAM2 transcription factor target challenge, and our experience as the data provider for the gene expression challenge in DREAM3.

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Success in the DREAM3 Signaling Response Challenge Using Simple Weighted-Average Imputation: Lessons for Community-Wide Experiments in Systems Biology
Syndicated from:PLoS ONE

Article is licensed under a Creative Commons Attribution License.

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Horizontal and vertical: The evolution of evolution - New Scientist

Posted: 26 Jan 2010 01:36 AM PST

JUST suppose that Darwin's ideas were only a part of the story of evolution. Suppose that a process he never wrote about, and never even imagined, has been controlling the evolution of life throughout most of the Earth's history. It may sound preposterous, but this is exactly what microbiologist Carl Woese and physicist Nigel Goldenfeld, both at the University of Illinois at Urbana-Champaign, believe. Darwin's explanation of evolution, they argue, even in its sophisticated modern form, applies only to a recent phase of life on Earth.

At the root of this idea is overwhelming recent evidence for horizontal gene transfer - in which organisms acquire genetic material "horizontally" from other organisms around them, rather than vertically from their parents or ancestors. The donor organisms may not even be the same species. This mechanism is already known to play a huge role in the evolution of microbial genomes, but its consequences have hardly been explored. According to Woese and Goldenfeld, they are profound, and horizontal gene transfer alters the evolutionary process itself. Since micro-organisms represented most of life on Earth for most of the time that life has existed - billions of years, in fact - the most ancient and prevalent form of evolution probably wasn't Darwinian at all, Woese and Goldenfeld say.

Strong claims, but others are taking them seriously. "Their arguments make sense and their conclusion is very important," says biologist Jan Sapp of York University in Toronto, Canada. "The process of evolution just isn't what most evolutionary biologists think it is."

Vertical hegemony

How could modern biology have gone so badly off track? According to Woese, it is a simple tale of scientific complacency. Evolutionary biology took its modern form in the early 20th century with the establishment of the genetic basis of inheritance: Mendel's genetics combined with Darwin's theory of evolution by natural selection. Biologists refer to this as the "modern synthesis", and it has been the basis for all subsequent developments in molecular biology and genetics. Woese believes that along the way biologists were seduced by their own success into thinking they had found the final truth about all evolution. "Biology built up a facade of mathematics around the juxtaposition of Mendelian genetics with Darwinism," he says. "And as a result it neglected to study the most important problem in science - the nature of the evolutionary process."

In particular, he argues, nothing in the modern synthesis explains the most fundamental steps in early life: how evolution could have produced the genetic code and the basic genetic machinery used by all organisms, especially the enzymes and structures involved in translating genetic information into proteins. Most biologists, following Francis Crick, simply supposed that these were uninformative "accidents of history". That was a big mistake, says Woese, who has made his academic reputation proving the point.

In 1977, Woese stunned biologists when his analysis of the genetic machinery involved in gene expression revealed an entirely new limb of the tree of life. Biologists knew of two major domains: eukaryotes - organisms with cell nuclei, such as animals and plants - and bacteria, which lack cell nuclei. Woese documented a third major domain, the Archaea. These are microbes too, but as distinct from bacteria genetically as both Archaea and bacteria are from eukaryotes. "This was a enormous discovery," says biologist Norman Pace of the University of Colorado in Boulder. Woese himself sees it as a first step in getting evolutionary biology back on track. Coming to terms with horizontal gene transfer is the next big step.

In the past few years, a host of genome studies have demonstrated that DNA flows readily between the chromosomes of microbes and the external world. Typically around 10 per cent of the genes in many bacterial genomes seem to have been acquired from other organisms in this way, though the proportion can be several times that (New Scientist, 24 January 2009, p 34). So an individual microbe may have access to the genes found in the entire microbial population around it, including those of other microbe species. "It's natural to wonder if the very concept of an organism in isolation is still valid at this level," says Goldenfeld.

Lateral thinking

This is all very different from evolution as described by Darwin. Evolution will always be about change as a result of some organisms being more successful at surviving than others. In the Darwinian model, evolutionary change occurs because individuals with genes associated with successful traits are more likely to pass these on to the next generation. In horizontal gene transfer, by contrast, change is not a function of the individual or of changes from generation to generation, but of all the microbes able to share genetic material. Evolution takes place within a complex, dynamic system of many interacting parts, say Woese and Goldenfeld, and understanding it demands a detailed exploration of the self-organising potential of such a system. On the basis of their studies, they argue that horizontal gene transfer had to be a dominant factor in the original form of evolution.

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'Bye Bye' high school - Delmarva Now

Posted: 26 Jan 2010 12:38 AM PST

SALISBURY -- In the musical "Bye Bye Birdie," singer Conrad Birdie plans to give a fan a "good-bye kiss" on The Ed Sullivan Show.

Kim MacAfee of Sweet Apple, Ohio, wins the honor.

"I had to do a lot of screaming," said Emily Leonard, who played Birdie's lucky fan, Kim MacAfee, in Pocomoke High School's production of the musical.

The senior says acting forces her to step out of her comfort zone. Behind the curtains, Leonard has butterflies in her stomach. But that feeling fades once the senior takes the stage.

"It's such a great feeling," said the 17-year-old, who also performed in the school's production of the musical "Grease." "It's so cool."

Of course, acting isn't Leonard's only talent. She also thrives in biology class.

"The stuff that grosses everybody out (in biology), I enjoy," Leonard said laughing.

In college, Leonard plans to major in her favorite subject with the hopes of becoming an athletic trainer in the future.

"Emily is truly a dedicated, motivated, funny, and caring young lady," said Kathy Baker, Pocomoke's athletic trainer.

Baker had a chance to work with Leonard, who has played varsity tennis and field hockey since her freshman year. Leonard says Baker inspired her to choose a career path in sports medicine.

"Emily sustained an injury in her sophomore year that sidelined her most of the season," Baker said. "During that time in the training room and during rehabilitation, I saw how dedicated she was to her team, family and her education."

This year, Leonard set a goal to "not have any regrets" after she graduates from Pocomoke High. In the coming months, the senior will have some big decisions to make for her future.

Leonard hasn't picked a college yet. She is considering either University of Maryland College Park or St. Mary's College of Maryland.

"I'm ready to find out what else is out there," she said. "But I don't want to go that far away."

cevans@dmg.gannett.com

410-845-4639

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UW-Madison opens institute for evolution - Daily Cardinal

Posted: 25 Jan 2010 11:27 PM PST

By Kelsey Gunderson

Published: Tuesday, January 26, 2010

Updated: Tuesday, January 26, 2010

The University Academic Planning Council approved the opening of a new UW-Madison institute for evolutionary studies last week.

The institute, called the J.F. Crow Institute for the Study of Evolution, will consist of evolutionary research, teaching and outreach programs, according to David Baum, a UW-Madison professor of botany who is the director of the new center.

Baum said the institute began as a small group at UW-Madison called the Evolution Coordinating Committee about six years ago. He said it wasn't until last year that the group decided to become an institute.

According to Baum, the institute plans to hold a weekly research seminar series, review evolutionary curriculum offered on campus and push for a graduate program in evolutionary biology.

Baum said he feels it is important for all UW-Madison students to learn something about evolution, especially those interested in studying biology.

"Evolution is such an essential part of biology," he said. "If you want to understand biology you have to understand where biological diversity came from."

According to Baum, religious opposition has prevented evolution from being taught properly at some high schools, making it even more important to be provided at UW-Madison.

"At a university like this with great research in evolution, we've got to make sure that we provide students with every opportunity to learn about it," he said.

Baum said the institute receives a small amount of funding from the UW-Madison College of Letters and Science as well as the College of Agricultural and Life Sciences, and is open for all students, faculty and staff members to join.

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Trooper recalled as 'tough,' 'unselfish' - Daily Star

Posted: 26 Jan 2010 01:00 AM PST

{"DS | Byline name"/}By Mark Boshnack

{"DS | Byline title"/}Staff Writer

{"DS | Body text"/}CHEEKTOWAGA "" "We want you to know how proud we are of the person you have become, and that you will always be our Little Angel.'"

Those words by the parents of the late state police at Oneonta Trooper Jill E. Mattice are from the dedication in their daughter's yearbook when she graduated from Cleveland Hill High School in Cheektowaga in 1996.

Her parents, Jeff and Karen Farrar, requested privacy for the family as they hold a funeral for their daughter today at 11 a.m. at Eastern Hills Wesleyan Church at 8445 Greiner Road in Williamsville.

Mattice's family includes brother Nate, also from the Cheektowaga area, and her husband, Troy Mattice, of Oneonta. The couple had no children.

Interment will follow at White Chapel Memorial Park at 3210 Niagara Falls Blvd. in Amherst.

Mattice was the first woman to die in the line of duty with state police. Her patrol car drifted into oncoming traffic while heading east on state Route 23 about two miles from the village of Morris. Her vehicle sideswiped a tractor-trailer, and she died instantly, troopers said.

The cause of the accident still is under investigation. Mattice was with the state police for 61/2 years.

Mattice's high school basketball coach and biology teacher Glen Graham said the words in the yearbook were "poignant" for teachers to read after learning about her death.

She was also his student in honors biology as a sophomore and Advanced Placement biology in her senior year, he said, adding that getting the news "was really tough."

In hindsight, he said inscription only confirmed his impression of her parents as "good and well-balanced people.

"They never would have overlooked the fact that they were given a blessing," Graham said. When they wrote the dedication, "they may have realized you never know what is going to happen in life."

Mattice was an outstanding student, and "she was very aggressive on the court," he said.

"She was a good defender who was very unselfish," Graham said. "She was tough as nails and always showed leadership."

He wrote a letter of recommendation for her application to the state police.

When she told him about her chosen career, "It sounded like a great combination for her and the state police," he said. "She always loved to serve her community."

Patricia Krzesinski, a former school history teacher of Mattice, agreed that Mattice was "an ideal student" with "so many wonderful qualities."

Although she set high standards for herself, "she had fun at whatever she did," Krzesinski said.

She was also "one of our outstanding athletes," playing on the school's basketball, volleyball and softball teams.

"She had an outgoing, friendly personality" that students and staff enjoyed being around, Krzesinski said.

Mattice was returning to the Oneonta barracks _where she was stationed _ from her assignment as school resource officer at Unadilla Valley Central when the accident occurred. She divided her time between Unadilla Valley and Franklin Central School districts, where officials previously said she was a friend and mentor to students. Both schools will be represented at the funeral where thousands are expected, officials said.

Thousands attended the wakes held Sunday and Monday at Amigone Funeral Home in Tonawanda, funeral director Ed McGrew Jr. said.

There will be delegations from all 10 troops that are part of the state police, Troop C public information officer Nelson Torres previously said.

There will also be members of police agencies from many states in the country and Canada, McGrew said, adding that he was planning for more than 5,000 people at the church.

"They do it out of respect for a fallen comrade," he said. "She touched a lot of people's lives."

Among those attending is Oneonta Police Chief Joseph Redmond.

There will be at least seven firefighters and nine police officers at the funeral from Oneonta, Redmond said. In these types of situations, people from uniformed services nationwide attend, he said, not only out of respect for the fallen, but also in support of the family and department for which he or she worked.

Redmond said he knew Mattice through her work as a trooper helping the Oneonta police on different details throughout her time in the area.

"She was genuinely a nice person," he said.

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