{bio,medical} informatics
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Forbes
Genome Scientists: Gene Patents Are Bad
"Two of the scientists most instrumental in mapping the human genome, Craig Venter and Eric Lander, have often been portrayed as being at each other's throats.
"But despite their competitive streaks, there is one thing that the two men agree on: The gold rush to patent individual gene sequences will probably yield very little in the way of profits. And that is a good thing, because the development of life-saving medicine depends on genes being accessible to as many companies as possible.
redux [06.19.02]
" Since 1980 the U.S. Patent and Trademark Office has granted patents on more than 20,000 genes or gene-related molecules. This thicket of intellectual property can make it difficult to develop biotechnologies without bumping up against patents held by others. In response, a number of companies have devised ingenious technological means of getting around such IP hurdles."
redux [03.18.02]
"It's one of the toughest questions in biotechnology: Should businesses obtain patents on genetic information about plants, animals or humans? Michael Capellas, CEO of Compaq Computer Corp., surprised an audience of biotechnology specialists yesterday when he suggested that the answer should be "no.""
"In a comment that stunned the audience into several seconds of silence, Capellas responded to a question on the issue by flatly saying that companies shouldn't be able to patent genes. But he quickly backed away from the comment, pleading ignorance of all the ramifications of the issue. "If you're asking me what should be patentable," Capellas said, "I don't know.""
redux [02.07.02]
"Patents may make some genetic tests so expensive that ordinary labs cannot afford to offer them, says a team of researchers who interviewed staff at 119 US facilities.
Patents are meant to provide an incentive for companies to put their discoveries into the public domain. But some researchers wonder if prohibitive costs could in fact have the opposite effect, by keeping standard genetic tests out of the reach of all but a few laboratories. That would have far-reaching consequences not only for health care, but for clinical research and quality control, the researchers say."
redux [08.20.01]
""Like the Terrys, a rising number of patients, doctors and ethicists are questioning how the patent system handles genetic claims. Many say it awards too many patents, overly rewards their holders, and gives too little back to patients. Yet many industry voices complain the process is moving too slowly to keep up with galloping research and to yield medical care awaited by suffering patients."
"The gold rush days are about to begin,'' says Arthur Caplan, a bioethicist at the University of Pennsylvania. "There are so many targets that look so lucrative that they're falling all over one another to pursue opportunity after opportunity.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
redux [08.26.00]
"Nowhere are patents more central to the creative process than in genetic drug development, where human genes and their expressed proteins themselves are developed as therapies. The biotechnology industry in the United States has brought a handful of these crucial new products (recombinant human insulin, to name one of the most familiar) to market and is on the threshold of a bonanza of genetic drugs and vastly greater relief for ill and aging populations around the world.
Patent protection is the sine qua non of that bonanza."
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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BioMedNet
Seeing
patterns in proteins
[requires 'free' registration]
"Now that sequencing the human genome is moving off the front page, advances in understanding protein structure and function are attracting more attention. The field has a new tool in TRILOGY, a computer program designed to identify patterns in the amino acid sequences of proteins. The programmers believe that TRILOGY will aid in the prediction of protein structure, the identification of novel motifs with functional or structural significance, and the annotation of recently determined structures. For some examples, see TRILOGY's Web site.
Reference: Bradley, P., Kim, P.S., and Berger, B. 2002. TRILOGY: Discovery of sequence-structure patterns across diverse proteins. Proc. Natl. Acad. Sci. U.S.A. 99(13):8500-8505."
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BioMedNet
In
cancer, microarrays moving rapidly toward clinical use
[requires 'free' registration]
"The ability to see the whole tumor at once in a big picture of gene expression will help scientists understand the "complicated and heterogeneous" biology of cancer, he predicts. It is becoming increasingly clear that there are as many cancers as there are individuals; the same tumor from the same individual may, at different points in time, have different expression patterns."
""Although prognosis is what grabs headlines," he said, "the progress, I have always thought, is in increasing the understanding of the nature of the disease.""
redux [06.20.02]
"Patterns of genes that are active in tumor cells can predict whether patients with diffuse large B-cell lymphoma (DLBCL) are likely to be cured by chemotherapy, scientists reported today in the New England Journal of Medicine. Researchers analyzed thousands of genes in lymphoma biopsy samples from patients with DLBCL and determined that the activity of as few as 17 genes could be used to predict patients' response to treatment. "We're able to reliably predict the survival of these patients using data from a small number of genes, indicating that this technique should be entirely manageable for routine use," said National Cancer Institute (NCI) investigator Louis M. Staudt, M.D, Ph.D., the senior author on the study."
redux [05.31.01]
"Genes have fingerprints just like fingers, which got one cancer researcher thinking.
Since the FBI uses neural networks -- a type of artificial intelligence built to imitate neuron function in the brain -- to sift through masses of computerized fingerprint data to solve crimes, why not do the same for genetic fingerprint data?"
""We trained (the neural networks) to recognize this is one cancer and this is another and this is not a cancer," Kahn said. "Eventually it learned to recognize particular features that were particular for cancer.""
"We seem to forget, sometimes, that the first researchers in AI that chosen medicine as a problem domain did so, not because of an interest in medicine, but because of an interest in diagnosis as an example of intelligent behavior. Medical diagnosis was one example (perhaps a poor one given that there are much simpler and easier models in other physical systems). Automated diagnosis has rarely interested the medical community, not because of a fear of removing the human element (we've already done that with our reimbursement system) or of replacing humans with machines but, more simply, because diagnosis (as most people view it), is not really the problem. Most clinicians manage some form of diagnosis and most patients are treated appropriately. What is needed is better information on the utility of information and the means to obtain it which least stresses the system."
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Genomeweb
Linux Heavyweight Comes to Pacific Northwest National Lab
"The final version, which could be useful in protein-interaction studies, will include 1,400 next-generation Intel Itanium processors with an expected peak performance of 9.1 teraflops. It will cost $24.5 million and exceed by more than 30 times the speed of PNNL's old supercomputer, which was state of the art when it was installed in 1997."
"According to HP, the system, scheduled to begin delivery in the fall and go fully on-line next spring, will be the world's most powerful Linux-based system."
[requires 'free' registration]
"Though Q will be almost 200 times as fast, it will cost 640 times as much -- $215 million, compared with $335,000 for Green Destiny. And that does not count housing expenses -- the $93 million Metropolis center that provides the temperature-controlled, dust-free environment Q demands."
" Green Destiny belongs to a class of makeshift supercomputers called Beowulf clusters."
redux [07.13.01]
"Our solution was to construct a computing cluster using obsolete PCs that ORNL would have otherwise discarded. Dubbed the Stone SouperComputer because it was built essentially at no cost, our cluster of PCs was powerful enough to produce ecoregion maps of unprecedented detail. Other research groups have devised even more capable clusters that rival the performance of the world's best supercomputers at a mere fraction of their cost. This advantageous price-to-performance ratio has already attracted the attention of some corporations, which plan to use the clusters for such complex tasks as deciphering the human genome. In fact, the cluster concept promises to revolutionize the computing field by offering tremendous processing power to any research group, school or business that wants it."
"Above all, the Beowulf concept is an empowering force. It wrests high-level computing away from the privileged few and makes low-cost parallel-processing systems available to those with modest resources. Research groups, high schools, colleges or small businesses can build or buy their own Beowulf clusters, realizing the promise of a supercomputer in every basement. Should you decide to join the parallel-processing proletariat, please contact us through our Web site (http://extremelinux.esd.ornl.gov/) and tell us about your Beowulf-building experiences."
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BusinessWeek
A Genome Project against Disease
"In the four years she has led The Institute for Genomic Research (TIGR), Claire M. Fraser and her colleagues have decoded and analyzed the genes of bacteria that cause anthrax, Lyme disease, syphilis, tuberculosis, cholera, meningitis, pneumonia, ulcers, and many others. The work has put TIGR at the forefront of the new field of microbial genomics--the foundation for the treatment and prevention of disease in the 21st century. "In terms of microbial sequencing, the world leader is still TIGR," says Julian Parkhill, head of microbial sequencing at the other leader in the field, the Wellcome Trust Sanger Institute in Cambridge, England.
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Business Standard
Pharma sector to rise 3-fold by 2005
"Also, India's success in information technology provides excellent opportunities in the field of bioinformatics.
"Traditional IT companies are translating their strong capabilities in data mining and warehousing to business models based on biological data," says the report, citing examples of IBM's India Research Lab and Satyam's five-year agreement with the Center for Cellular and Molecular Biology, Hyderabad."
redux [02.13.02]
"India's biotech boom could even dwarf software in coming years if you trust the most optimistic projections. Much of our $2.5-billion biotech market relies on low-end products like vaccines, but experts predict that as more start-ups come up, that could change dramatically."
"The need to dive into this ocean of genetic data for hidden treasures has created a whole new discipline--bio-informatics, the science of using information technology (IT) to decipher the genomic jumble. Thanks to a flourishing IT industry, bioinformatics is today the darling of venture capitalists, drug firms, and, of course, IT majors. So, Satyam Computers has signed a five-year alliance with CCMB to create, store, and annotate genetic databases, and it is angling for contracts from global bigpharma to sequence genes and build protein catalogs. Strand Genomics, a Bangalore-based bio-informatics start-up, is designing tools to accelerate drug discovery."
redux [09.17.01]
"India has the potential to garner 8-10 per cent of the global software market in the next few years from the current levels of just 1.5 per cent, but the country?s planners need to focus on improving computer penetration and use of Indian made software in the industry.
This was the view of FC Kohli, chairman, Tata Consultancy Services, while speaking at Connect 2001, an international conference and exhibition on information technology, communication technologies and bioinformatics, which opened on Thursday. Currently, India's IT exports are about $8.7 billion."
redux [08.27.01]
"THE mood is one of caution as far as bioinformatics is concerned. The beginning of the year saw hype building up around the fledgling industry as the next big gold rush for India.
But six months after the first bioinformatics seminar in the country, with the IT industry's lesson on hype fresh in mind, things are moving at a more sedate pace."
"In India, bioinformatics training institutes have already begun to mushroom. Bangalore and Hyderabad have around five private training institutes between them. However, the industry is sceptical about the quality of manpower these centres can supply because most of them have short-term courses offering basic skills, says Dr. Sabharwal. In all fairness to them she adds, "We need to wait for a few months to see the outcome of it all.""
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GenomeWeb
With 18 Months of Market Squeeze to Go, Genomics Shops Should Weather the Doldrums (Hint: Don't Consolidate)
"To be sure, survival is a relative challenge, and not without irony: Many companies that went public during the heady past few years, and are now in disfavor with institutional investors who demand products rather than tools, had raised enough cash to weather the doldrums for at least three more years, Lien said.
"The pendulum swings back and forth," he noted."
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Science Daily
Gene Expression Profiles Predict Survival Of Lymphoma Patients
After Chemotherpy
"Patterns of genes that are active in tumor cells can predict whether patients with diffuse large B-cell lymphoma (DLBCL) are likely to be cured by chemotherapy, scientists reported today in the New England Journal of Medicine. Researchers analyzed thousands of genes in lymphoma biopsy samples from patients with DLBCL and determined that the activity of as few as 17 genes could be used to predict patients' response to treatment. "We're able to reliably predict the survival of these patients using data from a small number of genes, indicating that this technique should be entirely manageable for routine use," said National Cancer Institute (NCI) investigator Louis M. Staudt, M.D, Ph.D., the senior author on the study."
redux [05.31.01]
"Genes have fingerprints just like fingers, which got one cancer researcher thinking.
Since the FBI uses neural networks -- a type of artificial intelligence built to imitate neuron function in the brain -- to sift through masses of computerized fingerprint data to solve crimes, why not do the same for genetic fingerprint data?"
""We trained (the neural networks) to recognize this is one cancer and this is another and this is not a cancer," Kahn said. "Eventually it learned to recognize particular features that were particular for cancer.""
"We seem to forget, sometimes, that the first researchers in AI that chosen medicine as a problem domain did so, not because of an interest in medicine, but because of an interest in diagnosis as an example of intelligent behavior. Medical diagnosis was one example (perhaps a poor one given that there are much simpler and easier models in other physical systems). Automated diagnosis has rarely interested the medical community, not because of a fear of removing the human element (we've already done that with our reimbursement system) or of replacing humans with machines but, more simply, because diagnosis (as most people view it), is not really the problem. Most clinicians manage some form of diagnosis and most patients are treated appropriately. What is needed is better information on the utility of information and the means to obtain it which least stresses the system."
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Scientific American
Legal Circumvention
" Since 1980 the U.S. Patent and Trademark Office has granted patents on more than 20,000 genes or gene-related molecules. This thicket of intellectual property can make it difficult to develop biotechnologies without bumping up against patents held by others. In response, a number of companies have devised ingenious technological means of getting around such IP hurdles."
redux [03.18.02]
"It's one of the toughest questions in biotechnology: Should businesses obtain patents on genetic information about plants, animals or humans? Michael Capellas, CEO of Compaq Computer Corp., surprised an audience of biotechnology specialists yesterday when he suggested that the answer should be "no.""
"In a comment that stunned the audience into several seconds of silence, Capellas responded to a question on the issue by flatly saying that companies shouldn't be able to patent genes. But he quickly backed away from the comment, pleading ignorance of all the ramifications of the issue. "If you're asking me what should be patentable," Capellas said, "I don't know.""
redux [02.07.02]
"Patents may make some genetic tests so expensive that ordinary labs cannot afford to offer them, says a team of researchers who interviewed staff at 119 US facilities.
Patents are meant to provide an incentive for companies to put their discoveries into the public domain. But some researchers wonder if prohibitive costs could in fact have the opposite effect, by keeping standard genetic tests out of the reach of all but a few laboratories. That would have far-reaching consequences not only for health care, but for clinical research and quality control, the researchers say."
redux [08.20.01]
""Like the Terrys, a rising number of patients, doctors and ethicists are questioning how the patent system handles genetic claims. Many say it awards too many patents, overly rewards their holders, and gives too little back to patients. Yet many industry voices complain the process is moving too slowly to keep up with galloping research and to yield medical care awaited by suffering patients."
"The gold rush days are about to begin,'' says Arthur Caplan, a bioethicist at the University of Pennsylvania. "There are so many targets that look so lucrative that they're falling all over one another to pursue opportunity after opportunity.""
redux [02.27.01]
"ONCE upon a time, pure and applied science were the same. Sir Humphry Davy discovered seven chemical elements, and invented the miner's safety lamp. Louis Pasteur investigated the properties of molecules, and worked out how to stop milk spoiling. Everybody thought that was admirable. Somehow, things have changed. Today the feeling is widespread that science and commerce should not - must not - mix. There is a queasy suspicion that the process of discovery is in some way corrupted if it is driven by profit."
"Far from compromising science, profit in both these cases - the development of new medicines and the elucidation of the genome - has animated it, and directed it towards meeting pressing human needs. It is a happy marriage. Davy and Pasteur would surely have approved."
redux [08.26.00]
"Nowhere are patents more central to the creative process than in genetic drug development, where human genes and their expressed proteins themselves are developed as therapies. The biotechnology industry in the United States has brought a handful of these crucial new products (recombinant human insulin, to name one of the most familiar) to market and is on the threshold of a bonanza of genetic drugs and vastly greater relief for ill and aging populations around the world.
Patent protection is the sine qua non of that bonanza."
redux [04.26.00]
""The analogy that I would use is that of a minefield," said Bob Levy, senior VP of science and technology for American Home Products. "We are spending an incredible amount of time now, when we find exciting targets and begin to validate them, in trying to define who has rights to what. And we're finding, in almost every product that we look at, that someone has patented the protein, the gene, a fragment, a diagnostic test." Levy noted that untangling patent rights, and determining which patents are dominant, are increasingly time-consuming and expensive tasks. And patent-holders must be paid. "The royalties that will be involved soon in some of the products that we are bringing to market, they're already up into the ten, fourteen, fifteen percent [range]," said Levy. "And that may increase with time.""
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The Economist
deCODED?
"AMID the brouhaha surrounding the Human Genome Project and its commercial rivals, the fact that there is more than one way to map a genome has got rather lost."
"Linkage mapping has been somewhat neglected in recent years. The best available map was created in 1998 (a lifetime ago, in modern genetic science) by the Marshfield Medical Research Foundation, in Wisconsin, based on data collected in France. But a new one has just been published by deCODE, an Icelandic firm, in Nature Genetics. Besides being at higher resolution than the Marshfield map, it reveals some intriguing facts about human reproduction. It also reveals the whereabouts of what the company hopes might prove to be very lucrative genes."
[requires 'free' registration]
"In the year 874, Viking crews from western Norway started to drop in on Ireland, capture an allotment of young Celtic women and sail off northwest to a remote island beyond the reach of retribution.
Eleven centuries later, a direct descendant of those Icelandic pirates and their slave wives, Dr. Kari Stefansson, says he is starting to extract a tremendous prize, made possible by Iceland's tiny, isolated population and its obsessive interest in genealogy: a catalog of the deviant genes that cause the most common human diseases."
redux [06.10.02]
"Kari Stefansson and his colleagues at deCODE genetics created a new genome map by combining their extensive database of genetic data from 146 Icelandic families with the DNA sequence of the Human Genome Project (HGP). In the process, they were able to increase the accuracy of the genetic map five-fold and correct 104 mistakes in the HGP draft."
"The company plans to make the new map freely available to researchers."
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Mail and Guardian Online
Super-fast computer aids genetic research
"It may not be able to provide the answer to life, the universe and everything else, but the new million-dollar supercomputer about to arrive at the South African National Bioinformatics Institute (Sanbi) may help find why some Africans are immune to HIV.
The supercomputer, as yet unnamed, will be the first research-orientated machine on the continent. It is being handed over by United States-based company Cray, as part of a collaborative research effort with Sanbi, which is part of the University of the Western Cape."
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GenomeWeb
Pharma Financial Squeeze Bodes Ill for Genomics
"Technology duds are easy to spot in the eyes of VC types.
"Bioinformatics as a business model is "cold right now, a non-starter," said Atwood. "You can't make any money."
Then there's pharmacogenomics. "Using genetic and genomic information to guide the use of drugs is a lot harder than people thought," said Atwood."
redux [04.19.02]
[requires 'free' registration]
"This should be the golden age for pharmaceutical scientists. The deciphering of the human genome is laying bare the blueprint of human life. Medical research has increased understanding of disease. Robots and computers are turning drug discovery from a mixing of chemicals in a test tube to an industrialized, automated process."
"Instead of narrowing the list of compounds that might be useful in drugs, automation has broadened it — greatly increasing the number of formulas tested without yet delivering commensurate growth in safe and effective drugs."
redux [12.14.01]
"And although the drug industry remains the most profitable worldwide—it generated profits as a percentage of revenues four times the median rate for all Fortune 500 firms during the end of the last decade, according to a Kaiser Family Foundation report released that day—an editorial in this month’s Nature Biotechnology by David Horrobin, CEO of Laxdale Research, in Stirling, Scotland, had this to say: “With rare exceptions, most of the top 20 multinational pharmaceutical companies are not generating in-house the new products needed to sustain the rates of growth they have enjoyed in the past.
“No serious industry onlooker could dispute this depressing picture,” the commentary continues. “Although a few pharmaceutical companies may survive in their present form, most cannot…. A few brave companies are recognizing the obvious: large companies excel at sales and marketing but are hopeless at innovative research.”"
redux [05.26.00]
"Leaders in the genomics field, as in any other industry, will be companies that offer a value-added service. Large pharmaceutical companies agree on what that service should be: integration of all the genomics information available. With more information readily accessible, companies can easily decide on whether to continue investigating potential targets.
So the future of genomics companies may rest in their IT and software capabilities, a view held by Celera Genomics, a newcomer to genomics. “We are entering an era of ‘cyberpharmaceutical’ drug development,” says Samual Broder, executive VP and chief medical officer. “Pharmaceutical corporations will use genomic databases, and other relational databases involving gene expression, proteomics etc. as the foundation of their drug discovery pipelines. One of the immediate goals... is to produce appropriate databases and software to link biologic and genomic information.”"
""The data suggest that the biotechnology industry used to be more productive than Big Pharma, but not any longer," said Rebecca Henderson, a professor at MIT's Sloan School of Management whose been studying the question for six years. "The public biotechs have declining productivity… and look as if they are running into the same problems as Big Pharma."
On every metric that Henderson has studied---number of scientific papers and patents per R&D dollar, cost per new drug--she found that biotech and Pharma productivity were quickly converging, and both were getting worse. After spending six years of studying the question, Henderson says she has found "no systematic evidence that small firms are more productive.""
redux [11.29.01]
[requires 'free' registration]
"Glenn Giovanetti at Ernst & Young Life Sciences Industry Services, comments "You could really compare [today's situation] to a large degree with the first biotech boom in the late eighties and early nineties where the thought was, 'Hey, this is going to lead to better drugs faster,' and clearly that hasn't been the case." Having the genome in hand has brought about more drug targets, but, explains Ma, "People are getting more concerned that novel targets are going to have a higher rate of failures because there is less information on them." And when working in 10-year drug-development cycles, failures are costly.
Ma points to a trend of growth in clinical informatics that would effectively garner more information from expensive clinical trials instead of simply treating them as regulatory hurdles. "People are beginning to think through to how ... to take greater advantage of that information," he adds. But increasingly, the suppliers of genomic information have been looking to do the same thing.
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The New Scientist
Celera abandons gene sequencing
"But Celera's rival published its version free of charge on the internet, a move which damaged Celera's commercial prospects. "That has had an impact," says Bennett. "Any stand-alone information business will be challenged because the value of information degrades," he adds.
But he denies that the venture has been a failure. "We have 250 subscribers, both commercial and non-commercial," says Bennett. The business even makes a profit, but the company will not discuss the impact of the free genome data on profits."
redux [04.08.02]
"Jim Kent was a graduate student in biology at the University of California, Santa Cruz (UCSC), when he wrote the program that allowed the public human genome team to assemble its fragments just before Celera's private, commercial effort. His program ensured that the human genome data would remain in the public domain. Kent wrote the 10,000-line program in a month, because he didn't want to see the genome data locked up by commercial patents."
"Kent's work illustrates the need to think about more than just open source code; in the scientific community there is a growing awareness of the importance of open data."
redux [03.07.02]
"''I humbly have to admit that between only 15 to 20 percent of my requests are fulfilled. I cannot afford to do anything else,'' said Tak Mak, a leading genetics researcher at the University of Toronto.
"In fact, according to a recent study published in the Journal of the American Medical Association and led by doctors at Massachusetts General Hospital, nearly 50 percent of surveyed geneticists at major US academic institutions said that another faculty member had denied them at least one request for information in the past three years. The study also found that geneticists are vastly more likely to believe that sharing has decreased in their field over the past decade than that it has increased - a startling figure given how much easier the Internet has made the transfer of information."
redux [01.23.02]
[requires 'free' registration]
"Nearly half the academic geneticists who asked for additional information, data, or materials related to a published research report were denied their requests, a new survey reports today. Are geneticists being unfairly pilloried?"
"Because they were denied access to data, 28% of geneticists reported that they had been unable to confirm published research. Other reported consequences were delays in publications, abandonment of a promising line of research, and the collapse of collaborations."
redux [02.27.02]
"For the scientists working on the Human Genome Project, the data defining who we are is too important to be left to Celera -- or any other company. David Haussler, a team leader at the University of California at Santa Cruz who helped Kent and others put the genome online, expresses the credo of a data liberator succinctly: "Information about the human genome is better in public hands than secretly locked up somewhere."
"But it's not just the research data itself that is at the center of the tug of war between corporations and scientists. When working with data as complex and vast as the human genome, the software tools necessary to manipulate that data are as important as the genetic code itself."
"It's really clear that there are some real issues here, but there are people taking up the guerdon on behalf of openness as well as those who are working for secrecy and private advantage. So I'm hopeful that in the end, openness will win.
Especially in a field like bioinformatics, the natural advantages of open source really do outweigh the advantages of secrecy. No one controls all the data. Talk after talk at the conference focused on the way that matching up data from other researcher's databases is the key to making sense out of your own data."
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BioMedNet
Room for opposing theories
[requires 'free' registration]
"There are two theories surrounding the duplication of vertebrate genomes. The "big-bang mode" theory suggests that duplication occurred on a large-scale in the past. The "continuous mode" theory favors small-scale duplications. The accuracy of these two theories has significant implications for understanding vertebrate genome duplication. A recent extensive analysis of gene databases indicates "that large- and small-scale gene duplications both make a significant contribution during the early stage of vertebrate evolution . . ."
"Reference: Gu, X., Wang, Y., and Gu. J.. 2002. Age distribution of human gene families shows significant roles of both large- and small-scale duplications in vertebrate evolution. Nature Genet. 31(2):205-209.”
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GenomeWeb
Celera Axes 132 Jobs To Refocus On Drug Development
"Celera Genomics today announced a major restructuring that will eliminate 132 jobs and purge the company's genome sequencing and online information business.
Sixteen percent of the company's workforce will be let go, mostly in DNA sequencing, data management and analysis support, sales and general administration."
"The company indicated that it will also soon bring on new staff to pump up its efforts in drug development."
redux [04.22.02]
[requires 'free' registration]
"The Celera Genomics Group is moving out of the business of selling the database it developed by sequencing the human genome, people close to the company said."
"The move, expected to be announced this morning, is the next step in Celera's shift from being an information vendor — the "Bloomberg of biology," company officials have called it — to being a drug developer. It will partially divorce the company from what has been its core business since it was founded in 1998 and raced the publicly funded Human Genome Project to determine the three billion letters of the human genetic code."
"Terms of the intra-corporate transaction call for Celera to give ABI exclusive marketing and distribution rights to the CDS, as well as access to its content, in exchange for a royalty stream on revenues to be generated by the new knowledge business. Celera will continue to earn revenue from current CDS customers, it said.
The move was made to "free Celera's executive team to focus on therapeutic discovery and development with the same access to this genomic and biological information it has presently while maximizing the return to Celera from its CDS product," Applera said."
redux [01.28.02]
"As all that was happening, people who know him say, White, Venter's boss, was getting grumpy. He well knew that Celera, under its original business plan, could not deliver long-range earnings growth that would justify what the market was paying for Celera shares. One top genetic scientist said White snapped to him in the midst of the publicity barrage, "'This is all nice, but we need a business plan.'"
They quickly came to the same conclusion as many minds before them: In biology and medicine, the only business plan that offers the potential of extraordinary profits is drug development. All the biotechnology superstars have been companies with hit drugs."
redux [06.09.00]
"Great discoveries do not necessarily make great businesses. Businesses have to sell something. Celera Genomics doesn't sell or make anything tangible. It hawks service and information. It sells access to lists of genes and computers that can sort through those messy lists. Samuel Broder, the company's executive vice president and chief medical officer, makes Celera sound like some kind of consulting company, or perhaps a library."
"Venter's quest could be a fable, with all sorts of morals about the power of capitalism and the importance of a single, brilliant, willful individual who used the market to shake the ivory towers of science. But those morals only hold if Celera succeeds, if business and science blend to propel the company into the future with breathtaking speed without rocketing it into the realities of the marketplace. Celera could become one of the great business success stories. It could also be a financial train wreck."
Right now, that makes it a very volatile stock."
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New Scientist
Human gene map accuracy increases five-fold
"Kari Stefansson and his colleagues at deCODE genetics created a new genome map by combining their extensive database of genetic data from 146 Icelandic families with the DNA sequence of the Human Genome Project (HGP). In the process, they were able to increase the accuracy of the genetic map five-fold and correct 104 mistakes in the HGP draft."
"The company plans to make the new map freely available to researchers."
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SciNewsFactor
Researchers Deliver Supercomputing in Smaller Package
"Researchers at Los Alamos National Laboratory once again have proposed a new approach to supercomputer, focusing on efficiency and reliability rather than raw speed. The researchers believe what they have created represents a viable alternative to standard supercomputers and traditional clustered systems."
"Feng said future applications could include a global climate modeling project and bioinformatics, a new science that combines IT and biology."
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UniSci
Chromosome 21 Contains 10% More Genes Than Predicted
"Re-analyzing the same chromosome through a different technique, researchers at the University of Geneva and the Ludwig Institute for Cancer Research found that chromosome 21 contains roughly 10% more genes than were either confirmed or predicted.
“This demonstrates why we cannot rely on gene prediction alone to identify all human genes,” said the study's lead author, Dr. Stylianos Antonarakis, of the Division of Medical Genetics at the University of Geneva Medical School. “Getting the right number of genes is crucial if we hope to use this information to fight disease.”"
redux [10.11.01]
[requires 'free' registration]
"Counting human genes ought to be straightforward. Tracking telltale signs--motifs for promoters, translation start sites, splice sites, CpG islands--gene counters must by now be mopping up, finalizing chromosomal locations of every human gene already known, and predicting whereabouts of all the rest. Insert one human genome sequence, turn the bioinformatics crank, and genes gush out like a slot machine jackpot, right?
"No, no, no," says Bo Yuan, of Ohio State University, having a laugh over the idea that computation is all you need to tally genes. To the contrary, states the director of the bioinformatics group in the division of Human Cancer Genetics at Ohio State, trawling for genes is so labor-intensive that several years may pass before researchers possess a highly accurate count."
redux [08.24.01]
[requires 'free' registration]
"After a humiliating deflation this February, human dignity is on the recovery path, at least as measured by the number of genes in the human genome.
Two new estimates put the likely number of human genes at around 40,000, up by a third from the estimate of about 30,000 in February by the two teams of scientists who decoded the human genome. The low estimate still has its defenders."
"Recent estimates that the human genome consists of only about 30,000 genes may be way off the mark, according to a study published today in the journal Cell. NPR's Richard Harris has the story. (3:45)"
redux [01.18.01]
"Two rival teams that cracked the human genome may have underestimated the number of human genes, according to a new computer analysis."
Scientists in the United States claim humans are built from 66,000 genes, nearly twice as many as the current consensus."
"But the new analysis, published on the website of the journal Genome Biology, has been dismissed by the Sanger Centre, in Cambridgeshire, UK, which was responsible for about a third of the human genome sequencing effort."
""The experimental evidence actually points to 30-40,000 genes," Dr Hubbard told BBC News Online. "I don't believe the argument in this paper that there are a lot more genes. This is an entirely computational paper and I don't think it's very credible.""
redux [11.13.00]
[requires 'free' registration]
"If James Watson, co-discoverer of DNA's structure, says we don't know how many genes there are, you're inclined to believe him. So it was a great surprise to hear the legend denounced, albeit with due deference. At the last count, insisted Kay Davies, professor of anatomy at the University of Oxford, humans are reckoned to have 40,944 tiny protein factories.
She was drawing on statistics that define the proteome, the protein equivalent of the genome, as the set of all expressed proteins in humans, for which 40,944 genes are individually responsible. Not a huge figure, she noted, barely the equivalent of three flies or a couple of worms. "Apologies Jim, let's talk over tea," she added."
redux [05.13.00]
"Well, they weren't all men, but mostly. The betting in the pub continued, the lowest bet being 29,800 genes placed by Pat Tome and the highest number coming from John Quackenbush at 118,259.
The pool was organized by Erwin Birney, a team leader at the European Bioinformatics Institute. He tried to convince the bartender to oversee the betting, but was told in no uncertain terms that no gambling was allowed in the Cold Spring bar.
Guesses on the number of genes in the human genome have lowered considerably since the mapping of chromosome 21, which researchers found to contain only 225 genes, far fewer than previously predicted. The researchers on the chromosome 21 study predicted their results could mean that there are as few as 40,000 genes in the entire human genome.
"Someone from Incyte will probably show up and bet 150,000," one gambler said."
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Time
High Tech Evolves
"Software engineers will tell you that the longer they labor to solve complex problems by manually writing code, the more they respect the reasoning powers of the human brain. For years, artificial-intelligence researchers have gained some of their most useful insights from experts in brain function. And today the biological sciences are making similar contributions to all sorts of technologies useful to business, from software that "grows," "heals" and "reproduces" to tiny carbon tubes that will allow computer transistors to shrink to atomic dimensions even as they grow more powerful."
redux [03.10.02]
[requires 'free' registration]
"Biologists tolerate a level of mystery in their work that would drive your average engineer or computer programmer crazy. They've put together a complete rough draft of the human genome but they have little understanding of how those 40,000 or so genes work together to make a human. They've mapped every muscle and nerve in a fly's wings, yet still struggle to explain how it keeps from crashing into a wall. No engineer would build a DVD player without knowing what every circuit was for; no programmer would let a computer write its own code. Or at least that's how things used to be. As Peter J. Bentley demonstrates in ''Digital Biology,'' the cool, rational temple of technology is becoming infested with biology's weedy enigmas.
redux [06.29.01]
"Business leans on science the way Ginger Rogers leaned on Fred Astaire - for legitimacy and cachet. Science lent 20th-century business the aura of quantitative certainty, starting with Frederick Winslow Taylor's scientific management and Ford's assembly line. As science moves away from Newtonian notions of cause and effect to study complex systems like global climate and the human genome, which have too many variables to accurately predict, business follows. If there were a Hollywood Stock Exchange for business buzzwords, "complexity" would be trading high."
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GenomeWeb
Publish and Perish? The New Dilemma of Promotion Facing Integration Biology
"A systems approach to biology--in which a gaggle of scientists from various disciplines appears as co-authors of a study--seems to be moving beyond jargon and into labs even as it raises the thorny issue of self promotion as career advancement.
But according to Eugene Kolker, computational biology lead at the Institute for Systems Biology, researchers now have a "different systems paradigm." Instead of one leading author on a papers, he said, there are teams."
redux [04.03.02]
"When Harley McAdams was a few years shy of 60, he became a biologist. He had spent two decades of his working life as a systems engineer at AT&T’s Bell Laboratories, and four years at Lockheed Missile and Space in Sunnyvale, CA, working on data systems architecture for military satellites. In 1994, however, he took to attending biology seminars at Stanford University, where his wife, Lucy Shapiro, was chair of the developmental biology department. McAdams had his epiphany while listening to an eminent geneticist describe the complex biological circuitry that turns genes on and off in yeast. To the uninitiated, the diagram of this system was vaguely reminiscent of a plate of spaghetti, with various arrows and stop and go signs attached. To McAdams, it looked like nothing more than an electric circuit, with the kinds of feedback loops and regulatory and control mechanisms that constituted the meat and potatoes of his systems engineering work.."