Wednesday, March 10, 2010

“Leroy Hood Sizes Up South Lake Union as Institute for Systems Biology ... - Xconomy” plus 3 more

“Leroy Hood Sizes Up South Lake Union as Institute for Systems Biology ... - Xconomy” plus 3 more


Leroy Hood Sizes Up South Lake Union as Institute for Systems Biology ... - Xconomy

Posted: 10 Mar 2010 04:19 AM PST

Biotech, people, Genomics

Luke Timmerman 3/10/10

Leroy Hood's eye is turning from the north to the south side of Seattle's Lake Union. The biotechnology pioneer and his colleagues at the Institute for Systems Biology are looking for new digs that are twice as big as their 65,000 square foot facility on the north side of the lake, Hood says.

"We just don't have enough space. It's an ideal building, we love the location, and the view of the city is terrific," Hood says. "But we need twice as much space."

He added: "We are thinking seriously about moving to South Lake Union. In all probability, it will be the old Rosetta building there."

He's talking about the fancy facility developed in 2004 by Paul Allen's Vulcan Real Estate to house the Rosetta Inpharmatics unit of Merck. That cutting-edge biology and computing facility had room for about 300 employees, but it has been much quieter since the fall of 2008 when Merck said it was shutting down that operation as part of global cost cuts. Hood never worked there, but he was partly responsible for its creation, since he was a co-founder of Rosetta back in the mid-90s with Stephen Friend and Lee Hartwell.

Few people in Seattle know much about Hood's nonprofit research center, and it puzzles more than a few biologists, but it has definitely been on a roll the past couple years. The basic idea for the Institute, which Hood co-founded with Alan Aderem and Reudi Aebersold in 2000, is to use high-powered computers to study complex networks of genes and how they interact, rather than the traditional ways of biology that Hood says are too narrow, looking at one gene, or one protein in isolation. He says the holistic approach of studying entire biological systems will lead science down the path to a historic attitude shift from reactively treating disease to what he calls "P4 medicine," or predictive, preventive, personalized, and participatory medicine.isblogo3

The Institute is known as a hotbed of entrepreneurial activity, having spawned the Accelerator, Seattle-based NanoString Technologies, Integrated Diagnostics, and an intriguing partnership with Mountain View, CA-based Complete Genomics to sequence 100 entire human genomes. But none of those for-profit efforts have generated windfall profits that could provide the comfort, of, say, an endowment to support the nonprofit institute for decades to come.

One of the watershed moments for the Institute came in June 2008 when it scored a five-year, $100 million commitment from the government of Luxembourg. In January, an independent review of research institutes around the world said the Institute for Systems Biology produced the highest impact scientific publications of any U.S. research center from 2003 through 2007. And just this week, the Institute said it received a $6 million gift from an unnamed California venture capitalist to further its research in personalized medicine, biofuels, and global health.

It's all starting to add up to a growth curve that few biotech companies in town can match. The Institute had 230 employees, and an annual budget of $35 million, when Hood gave a talk about it in February 2009 at a Technology Alliance event. One year later, it has 300 employees, and an annual budget of $45 million, Hood says. The Institute's strategic plan over the coming five to eight years is to add eight to 10 new faculty members, bringing the faculty roster to 20, with a staff of 400 to 450 people, operating with a "substantially" bigger budget, Hood says.

Luke Timmerman is the National Biotechnology Editor for Xconomy. You can e-mail him at ltimmerman@xconomy.com, call 206-624-2374, or follow him on Twitter at http://twitter.com/ldtimmerman.

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Creationists: Museum ‘makes up’ facts about evolution - Raw Story

Posted: 10 Mar 2010 08:30 AM PST

libertyuniversity Creationists: Museum makes up facts about evolutionThey plan to become doctors, researchers and professors, but these students from Liberty University, an evangelical school, also believe God created the Earth in a week, some 6,000 years ago.

Each year, a group of biology students at the Christian university based in Lynchburg, Virginia, travels to the Natural History Museum in Washington to learn about a theory they dismiss as incorrect -- Darwin's theory of evolution.

The young "creationists" examined a model of the Morganucodon rat, believed to be the first and common ancestor of mammals that appeared some 210 million years ago.

Lauren Dunn, 19, a second-year biology student, was unimpressed.

"210 million years, that's arbitrary. They put that time to make up for what they don't know," she said.

Nathan Hubbard, a 20-year-old from Michigan and a first-year biology major who plans to become a doctor, regarded the model with suspicion.

"There is no scientific, biological genetic way that this, this rat, could become you," he said, seemingly scandalized by the proposition.

Liberty University is the most prominent evangelical university in the United States, with some 12,000 students who adhere to strict rules and regulations regarding moral conduct.

Its biology curriculum includes a course on "Young Earth Creationism", which juxtaposes Charles Darwin's "Origin of the Species" with the Book of Genesis.

"In order to be the best creationist, you have to be the best evolutionist you can be," said Marcus Ross, who teaches paleontology and says of Adam and Eve: "I feel they were real people, they were the first people."

David DeWitt, a Liberty University biology professor, opens his classes with a prayer, asking God to help him teach his students.

"I pray that you help me to teach effectively and help the students to learn and defend their faith," he says.

Strongly-expressed faith is not unusual in the United States, a country where 80 percent of the population claim to believe in God and ascribe to established religions.

Polls taken in the last two years found that between 44 and 46 percent of Americans believe that the Earth was created in a week, somewhere between 6,000 and 10,000 years ago.

Creationism, an increasingly popular theory in the United States and elsewhere in the world, rejects Darwin's theory that all living species evolved over the course of billions of years via the process of natural selection.

The school of thought has adherents among Jehovah's Witnesses and some fundamentalist Muslims, but in the United States it has won most converts in the evangelical Christian community.

Former president George W. Bush, a born-again Christian, is among those who say evolutionary theory does not fully explain the Earth's creation, though the ex-president also noted he is not a "literalist" when it comes to the Bible.

Creationist belief has implications for the way people understand a variety of fields, including biology, paleontology and astronomy, but also impacts questions about climate change and educational debates.

At the Smithsonian Institute, among crowds of weekend visitors, the Liberty University students visited the evolution exhibition,.

But Darwin's explanation for why giraffes have long necks -- that they evolved over time so they could reach higher foliage -- and displays of fossil evidence failed to sway them.

"Creationism and evolutionism have different ways of explaining the evidence. The creationist way recognizes the importance of Biblical records," said Ross.

He teaches his students that dinosaurs were wiped from the face of the Earth some 4,000 to 5,000 years ago during the Biblical flood that Noah survived by building an ark.

He says carbon-dating techniques that have been used to suggest the Earth is in fact billions of years old are simply not reliable.

He doesn't reject one prominent theory that dinosaurs were wiped out by a massive asteroid that collided into Earth, but suggests the collision coincided with the Biblical flood.

Though Ross acknowledges that the United States is among the most welcoming environments in the world for creationists, he said it can be difficult to convince people to take him and his beliefs seriously.

"The attitude is when you are a creationist you are ignorant of the facts," he said.

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Genomatix gives a hand in the analysis of Wayne State's sequencing ... - Genetic Engineering News

Posted: 10 Mar 2010 06:57 AM PST

Mar 10 2010, 10:00 AM EST

Genomatix gives a hand in the analysis of Wayne State's sequencing projects

EUREKALERT

Contact: Dr. Martin Seifert
seifert@genomatix.de
49-895-997-660
Genomatix Software GmbH

The Department of Obstetrics and Gynecology in collaboration with the Applied Genomics Technology Core have generated a considerable amount of data about cis and epigenetic elements that control many reproductive events, including cell-fate

Munich (Germany), Ann Arbor, MI (USA) March 10, 2010 - The C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, at the Wayne State University School of Medicine, in collaboration with the Center for Molecular Medicine and Genetics, the Karmanos Cancer Institute and the Institute for Environmental Health Sciences, installed a Genomatix Mining Station (GMS) and a Genomatix Genome Analyzer (GGA) last year at their labs in Detroit, MI in order to support the analysis of Next Generation Sequencing (NGS) data. The GMS and GGA together represent the only complete, integrated analysis solution for NGS data analysis, starting with the raw data generated by the sequencer and leading to a molecular level understanding of the biology being studied.

Within the Department of Obstetrics and Gynecology, Professor Stephen Krawetz is the Director of Translational Reproductive Systems. His lab is utilizing the Genomatix systems to help analyze the cis and epigenetic elements that control many reproductive events, including cell-fate. "After a year of routine use we have found the comprehensive, open, and integrated nature of the Genomatix systems to be very helpful in the analysis of our sequencing projects. One of our current projects is to provide a comprehensive description of both spermatozoal mRNAs and small non-coding RNAs. In collaboration with Susan Land, Director of the Applied Genomics Technology Core, we have generated a considerable amount of data using the Illumina NGS platforms," said Dr. Krawetz, "Access to the integrated analysis core is helping us to get from data to the biology."

Peter Grant, Chief Executive Officer at Genomatix, USA commented: "We are very happy that these systems have now proven their practical value after almost a year in this very successful lab at the Wayne State University. This is confirming that Genomatix' technology provides a stable analysis platform for this important new genomic technology."

About Genomatix:

Genomatix Software GmbH is a computational biology company headquartered in Munich, Germany with a wholly owned subsidiary in Ann Arbor, MI, U.S.A. Founded in 1997, Genomatix pioneered the analysis and understanding of eukaryotic gene regulation. Over a decade of developments in computational and systems biology has put Genomatix into position to have a complete analysis pipeline in place at the arrival of next generation sequencing technology. Genomatix has published more than 180 peer reviewed scientific papers with more than 5,000 citations. Over 35,000 researchers worldwide currently apply Genomatix tools and databases.


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UAH shooting suspect Amy Bishop's lawyers seek preliminary hearing - Everything Alabama Blog

Posted: 10 Mar 2010 05:24 AM PST

By Brian Lawson

March 10, 2010, 6:30AM

Dr. Amy Bishop arrested.jpgDr. Amy Bishop being taken into custody outside the Shelby Center for Science and Technology on the UAH campus Feb. 12. Three biology faculty members were shot to death in a third floor conference room and three others were wounded.HUNTSVILLE, AL - Lawyers for accused UAH shooter Amy Bishop have asked for a preliminary hearing where the prosecution will outline the basic facts of the case against her, but she is not scheduled to appear in court before then.

Bishop, 45,  is charged with capital murder and attempted murder for a Feb. 12 shooting rampage that left three fellow University of Alabama in Huntsville biology faculty members dead and three others wounded.

She originally had a court date today for a felony examination where the court finds out if a defendant needs an attorney. But Bishop was given two court-appointed lawyers last month, Roy Miller and Barry Abston, both of Huntsville, so there was no need for an appearance today.

The defense's preliminary hearing motion was filed with District Judge Ruth Ann Hall, but a date has not been set, Abston said. The hearings are typically scheduled within 30 to 60 days of the request, he said, and Bishop will attend.

"It's the first opportunity an attorney will normally have to attain information in a criminal case," Abston said.

Abston said he has spoken several times with Bishop but declined to comment on the case or what steps the defense may be taking in establishing a defense related to mental illness or impairment.

Miller said at a press conference last month that Bishop doesn't remember shooting her colleagues. He said her history, which includes the fatal shooting of her brother in Braintree, Mass., in 1986, shows something is wrong with Bishop.

Madison County District Attorney Rob Broussard said he will lead the prosecution of  Bishop along with Bob Becher, chief trial attorney in the district attorney's office.

Broussard said he has not yet received the investigation report of the shooting from the Huntsville Police Department, and his office is still in the information-gathering stage.

"With the comments heard from defense counsel, we'll be doing it with that possible mental defense in mind," Broussard said. "In other words, we will be gathering lots of background information."

Bishop is accused of killing Dr. Gopi Podila, biology department chair, Dr. Maria Ragland Davis and Dr. Adriel Johnson.

Three others were shot that day. Dr. Luis Cruz-Vera is back at work. Stephanie Monticciolo, a biology department staff assistant, is continuing her recovery. Dr. Joseph Leahy was released from Huntsville Hospital last week and is undergoing extensive rehabilitation at a center in Atlanta.

 


 

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