Friday, December 20, 2002

Nature: Science Update Humans more similar than different

"Inuit or Basque, Laotian or Pashtun: we're much more similar than we are different, says the most detailed analysis of human genetic variation to date.

When it comes to sensitivity to drugs or diseases, the analysis also suggests that a person's account of their ethnic origin is almost as reliable an indicator as intrusive genetic tests.""

redux [11.01.02]
Financial Times Wires cross over genes

"In response to early concerns about racial profiling, scientists at the Human Genome Project went out of their way to downplay ethnic variations. Humans are 99.9 per cent alike, the sequencing showed, a figure that was leveraged into a call for global harmony. "The concept of race has no genetic or scientific basis," said Francis Collins, head of the Human Genome Project, at the White House ceremony to celebrate the genome completion.

Yet a great deal of controversy is now brewing over that 0.1 per cent. A growing number of scientists want to use such information as a way to find cures for devastating diseases. If we know more about the genes that cause susceptibility to cystic fibrosis in whites, or sickle cell anaemia in blacks, they argue, we will move closer to a solution for these illnesses. "Ancestry is imperative to biomedical research," says Mark Shriver, an anthropologist at Pennsylvania State University."

redux [10.30.01]
Nature: Science Update Race is a poor prescription

"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."

Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."

redux [07.20.01]
The New York Times Genome Mappers Navigate the Tricky Terrain of Race
[requires 'free' registration]

"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."

"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."

"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."

redux [03.18.01]
The Atlantic Online The Genetic Archaeology of Race

"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.

This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."

redux [06.11.01]
The New York Times Do Races Differ? Not Really, DNA Shows
[requires 'free' registration]

"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.

But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""

""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."

Thursday, December 19, 2002

Genomeweb International Collaboration Announces Draft Sequence of Rice Genome

Scientists today announced the completion of a draft of the rice genome Oryza sativa japonica ."

""The rice genome's sequence is crucial to our scientific understanding of the staples of life," Rita Colwell, director of the National Science Foundation, said in a statement. "With this data we open new doors at all levels of research [including] universities, private industry and government.""

redux [09.06.02]
BBC News Rice code is 'greatest achievement'

"Unravelling the blueprint of rice may be the most important breakthrough genetic science has achieved."

"Because rice is mankind's most important food crop - the staple diet for half of humanity - the researchers say reading its genome is of more importance than decoding mankind's own genetic code."

redux [04.06.02]
The New York Times Experts Say They Have Key to Rice Genes
[requires 'free' registration]

"Rice is "the Rosetta stone of the cereals," Dr. Wing said. Once researchers have found an important gene in rice, they can look for its counterpart in other crop plants, or insert the rice gene itself since the genes of all these crops are thought to be largely interchangeable."

"Syngenta has already developed a microchip holding an array of DNA fragments that recognizes some 24,000 rice genes and can tell which genes are switched on at each stage of the plant's development. Because of corn's genetic similarity to rice, the rice gene chip can also recognize 90 percent of the genes in corn.""

redux [03.28.02]
The Washington Post Swiss Firm Plans to Share Rice Genome

"One of the world's largest agricultural companies is putting finishing touches on a plan to make public huge amounts of genetic information about the rice plant, an effort to accelerate research aimed at improving one of mankind's most important crops."

"The plan Syngenta is working on is, in part, an effort to stave off an incipient controversy."

GenomeWeb Science to Print Part of Syngenta's Rice Genome; Consortium May Get Data-Sharing Deall

"Syngenta's decision to share some data with the International Rice Genome Sequencing Project may help to quiet a growing controversy about public access to data gathered through privately funded sequence projects. But the decision by Science to allow Syngenta to publish without making its data available in Genbank will undoubtedly spur further debate."

redux [03.19.02]
New Scientist Fears over rice genome access

"Prominent gene researchers fear that access to the complete DNA sequence of rice, the world's most important food crop, will be restricted when it is published in a scientific journal."

"Science says the issue is complex. "We have to weigh the benefit of publishing some data so that it is in the public domain or having it all deposited as privately held trade secrets," says Science spokesperson Ginger Pinholster. "In the case of the human genome it was felt that publishing was the best option - for rice, the case is even stronger.""

Independent News Geneticists protest at DNA of rice becoming a trade secret

"Twenty leading geneticists are protesting against a deal that will allow a multinational company to control who has access to the complete DNA sequence of the rice genome - the most important food crop in the developing world.

The scientists, who include British Nobel laureates Sir Paul Nurse and Sir Aaron Klug, are up in arms against a plan to lock away the entire rice sequence on a company database rather than having it published in the open scientific literature."

Wednesday, December 18, 2002

The Mercury News Margaret Steen: Be realistic about shifting to biotech

"If you do decide to go back to school, consider what area of biotech will make the best use of the skills you already have.

For example, bioinformatics -- the intersection of biology and computer science -- needs people with a background in computer science who also understand biology enough to help companies handle the data that their research generates. If you find an area where you can build on your previous experience, rather than trying to start from scratch, you'll have a better chance of success."

redux [08.26.02]
Genomeweb School of Informatics moving into its envisioned role at IU

"Three years after Indiana University launched its School of Informatics, the school is growing into the role that officials envisioned."

"Perhaps most significantly, the number of IU informatics majors topped 1,100 this year, almost triple what it was a year earlier."

"The Bloomington campus had its first informatics classes in 2000 and offers master's degrees in bioinformatics, chemical informatics and human-computer interaction. Undergraduate majors study informatics along with a "cognate area" such as computer science, economics and telecommunications."

redux [08.06.02]
Genomeweb New University Degree Programs Fuel Surge in Bioinformatics Grads in '02

"The number of card-carrying bioinformaticists entering the job market more than tripled in 2002, according to a recent survey of US university degree programs."

"This new wave of graduates -- not to mention their prospective employers -- are the first beneficiaries of the remarkable growth seen over the last few years in the number of degree programs: While only six dedicated bioinformatics-degree programs existed before 1997, 13 universities added new programs in 2001, and seven schools are adding bioinformatics-related degrees in 2002."

redux [10.05.01]
The Washington Post Bio-Help Wanted And Wooed

"Almost all companies say they're having trouble finding people with expertise in bioinformatics, the use of computers to solve complex biological problems. The human genome's mapping has ushered in a new era of genetic medicine, but to capitalize on this knowledge, researchers need to know how to use powerful computers to translate raw biological data into information useful for developing new therapies.

"There's a struggle to have people that are well educated in both computer science as well as biology," said David Pot , InforMax's director of application sciences. "We recognize we need super scientists, but those super scientists don't have the training to write super software.""

redux [03.05.01]
SFGate Why Bioinformatics Is Hot Career

"Move over Information Age. Make room for the age of bioinformation.

Experts have already dubbed bioinformatics - a hybrid profession pairing biology and computer science - the career choice of the decade.

"There is a crying need for experts in bioinformatics and this is not something that will just fade away," said Dr. Leena Peltonen, chairwoman of the Department of Human Genetics at UCLA."

redux [05.10.00]
Alfred P. Sloan Foundation Hiring Patterns Experienced by Students Enrolled in Bioinformatics/Computational Biology Programs

" "The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs - who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised." "

Tuesday, December 17, 2002

Forbes Genomics Revolution Actually Happens

"Investors may have stopped watching, but drug companies are finally beginning to wrench tangible benefits from the human genome. Two years after a boom fed by hype, a revolution finally is starting to take hold not in how drugs are invented, but in how they are tested.

Merck (nyse: MRK - news - people ), the world's third-largest drug company, is using gene expression arrays, also known as DNA chips, to keep clinical duds from reaching expensive animal or human trials. Separately, Millennium Pharmaceuticals (nasdaq: MLNM - news - people ) used similar chips in its late-stage clinical studies of its cancer drug, Velcade. Millennium's work is a big step toward so-called personalized medicine, in which treatment would be tailored toward individual patients based on genetic makeup."

redux [10.07.02]
SFGate Proofreading the human genome

"Perlegen has spent upwards of $50 million on the chemistry, instruments, computers and brain power needed to pull off this hellish job of proofreading.

Yet there was only a muted celebration a few weeks ago, when Perlegen's scientists decided they'd found the last of the 1,717,015 SNPs that biotech firms have been seeking since the human genome was sequenced in 2000.

The Scientist In Style, but... Out of Reach
[requires 'free' registration]

"Pharmacogenomics holds the promise of delivering safer, better designer drugs--and profits--to pharmaceutical manufacturers. But the technology also poses a challenge to the industry's current, highly successful business model that relies on one-size-fits-all blockbuster drugs.

For small biotech companies and large drug manufacturers alike, pharmacogenomics remains only one component of genome-based research and consumes only a small part of the $30 billion (US) in annual pharmaceutical research and development funding, according to the Pharmaceutical Research and Manufacturers of America (PhRMA). "It's an area where we are seeing movement, but it's not there yet," says Gillian Woollett, associate vice president for biologics and biotechnology at PhRMA."

redux [09.10.02]
Bio-IT World The New, New Pharmacogenomics

"Collins is unimpressed by the hubbub that has shaken the industry lately. "In some quarters there was a misunderstanding, or naivete, about how having the sequence was going to solve everything. And there were some business models built solely upon the notion of quick profits, particularly selling subscription databases."

He dismisses talk about a foundering industry. "I think that every pharmaceutical company is still expecting that genomics will be the platform upon which they will build the next generation of drugs," says Collins. Others echo Collins' perspective. "We will change the treatment of cancer," says Variagenics' Adams. And there is no hint of doubt in his voice."

redux [08.08.01]
Stanford Medical Informatics Preprint Archive Challenges for Biomedical Informatics and Pharmacogenomics

"Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and thus offers a remarkable set of challenges to biomedical informatics. These include infrastructural challenges such as the creation of data models and data bases for storing this data, the integration of these data with external databases, the extraction of information from natural language text, and the protection of databases with sensitive information. There are also scientific challenge in creating tools to support gene expression analysis, three-dimensional structural analysis, and comparative genomic analysis. In this review, we summarize the current uses of informatics within pharmacogenomics, and show how the technical challenges that remain for biomedical informatics are typical of those that will be confronted in the post-genomic era."

Monday, December 16, 2002

The New York Times New Premise in Science: Get the Word Out Quickly, Online
[requires 'free' registration]

"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.

Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."

redux [11.15.02]
Federal Computer Week More sites targeted for shutdown

"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.

"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."

redux [09.24.02]
BioMedNet Adam Smith and science journals
[requires 'free' registration]

"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.

Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.

redux [09.05.01]
BioMedNet Profit vs. Public access
[requires 'free' registration]

"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.

"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."

redux [04.24.01]
Scientific American Publish Free or Perish

"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.

E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."

redux [09.20.00]
BioMedCentral Freedom of Information Conference: The impact of open access on biomedical research

"How should biomedical research be communicated? How should research be assessed and validated?"

"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.

We have also commissioned editorial articles from several speakers and delagates at the meeting."