{bio,medical} informatics
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NPR: Science Friday
J.
Craig Venter
"J. Craig Venter's company, Celera Genomics, decoded the human genome faster and more cheaply than a large federally-funded effort. Join host Iraq Flatow and Venter for a discussion about his philosophy and vision for genomics. Who should own the human genome?"
redux [11.26.02]
[requires 'free' registration]
"Craig Venter's "minimal genome" project announced Wednesday is not about creating a new life form and probably doesn't pose much of a biowarfare threat, researchers say. The high-profile project was just funded by the US Department of Energy (DOE) with $3 million going to the Institute for Biological Energy Alternatives (IBEA), one of the non-profit research institutes Venter founded after leaving the newly profit-minded Celera Genomics early this year.
According to some scientists, the new project won't even define the minimal genomethe basic gene set required for lifebecause there can be no single minimal genome."
redux [10.15.02]
"But we're asking the philanthropic community to say, 'How about funding 100 genomes for patients with these diseases? Diseases that you care about or ethnogeographic groups to make sure there's sufficient diversity in the population or in some cases you yourself or your family as part of a legacy,' and everybody would have their data be part of a database that would be used for genome analysis in comparing clinical records, genotype/phenotype correlations, obviously in an anonymous fashion."
"It was misrepresented the first time in the press that this was the millionaires' genome project. Hopefully, it would not just be millionaires' genomes, although I think that would be an interesting study. I think we would find them to be remarkably similar to all the other genomes, but I think what we'd expect to happen is that there would be groups that support diseases that they really care about getting solved that they know are not going to get solved with the current paradigm..."
redux [10.03.02]
"Mapping and reading J. Craig Venter's genome took 15 years, $5 billion and some of the world's most sophisticated computers.
Wouldn't you, too, like your genome decoded?
Venter says he plans to offer the service, with the goal of burning individual human's entire DNA sequences onto shiny compact discs."
"Tonight's plenary panel discussion at GSAC, "The Future of DNA Sequencing: Advancing Toward the $1,000 Genome," hosted by Craig Venter and Gerald Rubin, quickly turned into a genomics version of the game show "The Price is Right."
"I had to do a little better than the thousand-dollar genome," said VisiGen Biotechnologies CEO Susan Hardin, one of the panelists, about her company's efforts to develop a single-molecule sequencing method using both a modified polymerase and nucleotides. "So we're going for the $995 genome.""
redux [05.03.02]
"Coming from a man whose life revolves around the study of genes, this might sound surprising: People are not the sum total of their genes.
But J. Craig Venter, former president of Celera Genomics and genome mapper extraordinaire, wants the American public to know that genes are not fate and he's launched a nonprofit organization to prove it. "
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The Boston Globe
Putting patents in their place
"''The land grab is over,'' said Kate Murashige, a partner at Morrison & Foerster LLP specializing in intellectual property for pharmaceuticals. ''It was a game that was bound to fail.''"
"''Filing huge patent applications containing thousands of gene sequences is now considered a really useless strategy,'' said Kathleen Williams, cochair of the patent practice at Palmer & Dodge LLP in Boston. ''Gene and protein patent filings are down for a number of reasons, but the biggest is the publication of the human genome sequence two years ago.''"
redux [07.23.02]
"Patents on DNA sequences "inhibit innovation and development" and should be the exception rather than the norm, says a panel of leading UK bioethicists. In the past, biotech companies have said that without such patent protection they would not have the economic incentive to invest in expensive research towards new drugs.
A discussion paper, produced by the Nuffield Council on Bioethics (NCB), says that too many patents are of doubtful validity because they are being issued for genetic discoveries that are not adequately inventive. It recommends a number of significant changes to the way patents in the field are granted in the future and to limit possible adverse effects of those already issued."
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 Chronicle
The
Mythical Threat of Genetic Determinism
"The issue is not about determinism, either genetic or environmental or both together; the issue is about what we can change whether or not our world is deterministic. A fascinating perspective on the misguided issue of genetic determinism is provided by Jared Diamond in his magnificent book Guns, Germs, and Steel (1997). The question Diamond poses, and largely answers, is why it is that "Western" people (Europeans or Eurasians) have conquered, colonized, and otherwise dominated "Third World" people instead of vice versa. Why didn't the human populations of the Americas or Africa, for instance, create worldwide empires by invading, killing, and enslaving Europeans? Is the answer ... genetic? Is science showing us that the ultimate source of Western dominance is in our genes? On first encountering this question, many people -- even highly sophisticated scientists -- jump to the conclusion that Diamond, by merely addressing this question, must be entertaining some awful racist hypothesis about European genetic superiority. So rattled are they by this suspicion that they have a hard time taking in the fact (which he must labor mightily to drive home) that he is saying just about the opposite: The secret explanation lies not in our genes, not in human genes, but it does lie to a very large extent in genes -- the genes of the plants and animals that were the wild ancestors of all the domesticated species of human agriculture."
redux [11.19.02]
"The idea that we are a mix of nature and nurture would seem to be common sense by now. But as Pinker demonstrates, the nature deniers continue to argue that beyond the basic support systems--breathing, excreting--our personalities are the product of our social existence, arriving courtesy of our parents, teachers, peer groups, media, dominant ideologies and cultural norms: the product, in other words, of our history, both personal and public. This is what Pinker calls the hypothesis of the "blank slate." It is a strange sort of human exceptionalism. Unlike all the other organisms on earth, which clearly arrive with a sophisticated set of instincts designed to exploit the parameters of their environment, human minds are merely abstract learning machines, born with no innate proclivities other than to soak up information along the way. The blank slate has turned out to be a way of drawing a line in the sand against the last 150 years of Darwinian encroachments. Sure, we share a basic body plan with all the vertebrates and a respiratory system with our fellow mammals, and perhaps even 98 percent of DNA with our chimpanzee cousins. But the human mind is another matter."
redux [10.04.02]
"Evolutionary psychology is addressing age-old questions about human nature. Are people inherently good? Are they social animals? Are they rational, utility-maximizing individuals? If both nature and nurture shape our characters and determine our destinies, what is the precise contribution of each? Do we have free will? These questions lie at the heart of centuries-long political, philosophical, and religious conflicts. And the answers inform how we think social, political, and economic life should be organized.
Evolutionary psychology discomfits many intellectuals and scientists and Pinker has been savagely attacked by both the left and the right. Marxists such as Harvard's Richard Lewontin and the late Stephen Jay Gould assert that evolutionary psychology is little more than fatuous cocktail party speculation, while conservative commentators in The Weekly Standard and First Things charge Pinker with trying to undermine the religious basis of morality."
"The third fear is a fear of determinism: that we will no longer be able to hold people responsible for their behavior because they can they can always blame it on their brain or their genes or their evolutionary history--the evolutionary-urge or killer-gene defense. The fear is misplaced for two reasons. One is that the silliest excuses for bad behavior have in fact invoked the environment, rather than biology, anyway--such as the abuse excuse that got the Menendez brothers off the hook in their first trial, the "black rage" defense that was used to try to exonerate the Long Island Railroad gunman, the "pornography made me to it" defense that some rapists have tried. If there's a threat to responsibility it doesn't come from biological determinism but from any determinism, including childhood upbringing, mass media, social conditioning, and so on.
redux [08.30.00]
"Are blacks programmed by their genes to be promiscuous? Can we read any morality off our genes at all? Is religion pernicious nonsense? The field of evolutionary psychology attempts to illuminate such inquiries into human nature with the insights of modern Darwinism. It raises questions that have a prickly, intense and scary quality. To get inside them is like putting on a hair shirt with explosives strapped to it. Even in sober academic journals, the discussion can rapidly become a screaming match. On the Internet, home of the flame, any attempt at a reasonable discussion seems completely futile."
"Given the volatility of online debate, the existence, then, of the Evolutionary Psychology mailing list seems like a miracle. All these unspeakable things and more are debated there, yet it is actually possible to learn new things -- and the arguments, however ruthless, are always polite."
"The 'implication' that seems to worry people most of all is so-called 'genetic determinism'. It's the notion that, if human nature was shaped by evolution, then it's fixed and so we're simply stuck with it -- there's nothing we can do about it. We can never change the world to be the way we want, we can never institute fairer societies; policy-making and politics are pointless.
Now, that's a complete misunderstanding. It doesn't distinguish between human nature -- our evolved psychology -- and the behavior that results from it. Certainly, human nature is fixed. It's universal and unchanging -- common to every baby that's born, down through the history of our species. But human behavior -- which is generated by that nature -- is endlessly variable and diverse. After all, fixed rules can give rise to an inexhaustible range of outcomes. Natural selection equipped us with the fixed rules -- the rules that constitute our human nature. And it designed those rules to generate behavior that's sensitive to the environment. So, the answer to 'genetic determinism' is simple. If you want to change behavior, just change the environment. And, of course, to know which changes would be appropriate and effective, you have to know those Darwinian rules. You need only to understand human nature, not to change it."
"In the late 1970s I attended meetings at which sociobiologists E. O. Wilson and David Barash, critic Stephen J. Gould, and others were on a panel. Standing blocked by the crowd in the hall outside the doorway to the packed hall I was unable hear the speakers. I spied a little door near the stage, and figured that if I could get to that door, I could get next to the stage and the front row. I sneaked through the hotel kitchen and found the door. Just as I opened it I was passed by a number of African American students who ran up on stage and poured water on Wilson's head. Wilson responded by saying to the audience that he felt like he had been speared by an aborigine. The crowd applauded the martyred Wilson (on crutches at the time--from a skiing accident) and some in the front row muttered epithets at the disrupters and at me, who appeared to have held the door for the demonstrators. The water pitcher story has been repeated scores of times in journalistic accounts, but none of these mention Wilson's racially tinged response. Two decades later the debate concerning the genetic determination of human behavior has been reanimated in the general intellectual and middle-brow media with a somewhat more restrained tone. The study of evolutionary accounts of human behavior is now called "evolutionary psychology" to avoid some of the justifiably bad connotations that were associated with sociobiology. During the last few years the linguist Steve Pinker, (1997) philosopher Daniel Dennett, (1995) New Republic editor and science popularizer Robert Wright,(1994) and science writer Matt Ridley (1994, 1997) have produced feisty, polemical expositions of evolutionary psychology for a broad audience. Stephen J. Gould has returned to the breach to criticize evolutionary psychology, but several writers considered to be on the left have defended sociobiological approaches and criticized postmodern rejection of biologism.
The core theories of evolutionary psychology are the same as those of sociobiology. Several of the commonly made distinctions between evolutionary psychology and sociobiology turn out not to distinguish the two. So what has changed and what is new?"
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Santa Fe New Mexican
Genomics Revolution Costs Investors Billions
"Government-backed scientists will fete themselves in April during a monthlong celebration of the marvels of the human genetic code. They'll toast the much-hyped map of life, which genome researchers believe will lead to cures for diseases and greatly enrich biotech firms."
"But all of this is small potatoes.
The big payoff -- powerful disease-fighting medicines -- has yet to materialize."
redux [11.08.02]
""Until the pharmaceutical industry writ large adopts as a central tenet of their activity the best and highest use of these new technologies -- i.e. the discovery of new protein and antibody drugs -- you will not see productivity pick up," he said.
"We view as an industry with great alarm what appears to be the floundering of our best (big pharma) partners. It is time for them to realise that beating the same dead horse of small molecule discovery should change.""
redux [09.20.02]
"In a so-called Masterminds Panel here this morning, four life sciences-industry execs pondered the question, "When and how will '-omic' technologies have a positive impact on pharma's output?" They were generally optimistic, and agreed that genomics and proteomics have had a significant effect on the drug-discovery trade--albeit a different one from what investors desired.
Genomic technologies have generated "lots of target ideas, but the bottleneck [exists] in understanding which target is for which disease," said Mark Crockett, executive director of functional genomics for Bristol Myers Squibb. The effect so far from genomic technologies has been to create more work for pharmas, Crockett said. "New targets have no literature associated with them. There are an average of seven publications on any given protein, which means that pharmas have to do a lot more basic biology.""
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.
redux [05.26.00]
""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 Scientist
How Did I Get That Job? | Sidetracked to Bioinformatics -
Lincoln Stein
[requires 'free' registration]
" Early Indications: My original plan was to be a science journalist. At Johns Hopkins University I started taking science courses along with my writing classes to be a better journalist, but got sidetracked. I became interested in the life sciences and never got back to my original plan. Also, I've always enjoyed computers, even since high school. In graduate school at Harvard I became the resident computer whiz of the pathology department."
" Best lesson: It's OK to not know what you want to do. Just follow your heart; good things happen when you continue to pursue what you enjoy. I liked computers but didn't know how they fit into my plan. I kept looking for ways to use computers in biology, and conveniently, bioinformatics emerged."
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Scientific American
The Reality of Race
"Race doesn't exist, the mantra went. The DNA inside people with different complexions and hair textures is 99.9 percent alike, so the notion of race had no meaning in science. At a National Human Genome Research Institute (NHGRI) meeting five years ago, geneticists were all nodding in agreement. Then sociologist Troy Duster pulled a forensics paper out of his briefcase. It claimed that criminologists could find out whether a suspect was Caucasian, Afro-Caribbean or Asian Indian merely by analyzing three sections of DNA.
"It was chilling," recalls Francis S. Collins, director of the institute. He had not been aware of DNA sequences that could identify race, and it shocked him that the information can be used to investigate crimes. "It stopped the conversation in its tracks.""
redux [12.20.02]
"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]
"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]
"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]
[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]
"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]
[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."
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O'Reilly Network
Stephen Wolfram on Bioinformatics
"Bioinformatics has traditionally concentrated on handling genomic data---mostly in the form of strings. What's now starting in computational biology is the study of actual processes that operate in biological systems. The things I've discovered in writing A New Kind of Science suggest a framework for thinking about such processes. The key idea is to think in terms of simple programs---and to use those to capture the essential mechanisms in biological systems. From genomics we know the lowest level code for biological organisms; now we have to have models for how that code actually runs."
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News.Com
IBM joins
genetics firm in drug search
"IBM and Icelandic company Decode Genetics will announce on Thursday a partnership to offer technology and services for applying genetic information to the hunt for new drugs."
"IDC ranks IBM near the top of the heap when it comes to outfitting life sciences organizations with information technology. IBM pulled in $1.36 billion in life sciences sales in 2001, according to IDC, while Hewlett-Packard and Compaq Computer--now merged--combined for $1.77 billion. Dell Computer ranked third with $821 million."
redux [12.10.02]
"Gateway Inc., the PC maker best known for its consumer systems and talking cow, is linking thousands of display PCs in its nationwide chain of stores to create a grid computing environment capable of scaling to 14 teraflops of performance."
In a pilot test, Inpharmatica Ltd. reproduced the results of a bioinformatics job run on the Processing on Demand system and its own computer farm, said CIO Pat Leach. The London-based company turned to Gateway because it wants to cut the amount of time it spends managing its 2,300-processor computer farm. "We are a drug discovery company, not an IT shop," Leach said. "We would much rather employ people to do innovative analysis of the data than spend time building computers.""
redux [11.15.02]
"The Santa Clara, Calif.-based chipmaker said this week that it is working with universities, software developers and server manufacturers to come up with supercomputer-class systems, built around Intel technology, for pharmaceutical engineering, genetic research and other biotech projects, said Rick Herrmann, Intel's manager for worldwide high-performance computing.
"There seems to be a rush toward building out the infrastructure around life sciences," Hermann said. "Every country in the world is looking for bioinformatics to be the next technology pillar: Singapore...Taiwan...the U.S. Even Ireland is looking at it.""
redux [09.04.02]
"Billionaire Michael Dell is in the Buffalo area today to help the University at Buffalo unveil a powerful new computer cluster provided by the company that he founded and continues to run."
""We've installed hundreds of these clusters. (But UB's) would be one of the larger ones, not only for us but in the world," Dell said. "And the amazing thing is we got this up and running in 60 days.""
redux [12.05.01]
"The world's largest computer makers, faced with sagging consumer demand, are betting that the huge data crunching needs of nascent biotechnology firms will grow into a multi-billion dollar market for their equipment and consulting services over the next decade."
""The average individual can't comprehend what has happened in the last half dozen years, where the two greatest medical discoveries, the genome and the microchip, have converged," said Cal Stiller, chief executive of the $250 million Canadian Medical Discoveries Fund."
"We need companies that are on the informatics side that say 'holy cow', we have just stumbled onto the mother lode! We know nothing about mining that area, but we can build the best drilling equipment out there," added Stiller."
redux [06.26.01]
"In 1998, biotech upstart Celera Genomics needed a supercomputer to help it map the human genome. It didn't turn to IBM , which built 204 of the 500 fastest supercomputers. Both Celera and its academic competition, the Human Genome Project, used machines built by Compaq Computer. Two years later, Compaq is the leading seller of supercomputers to biological researchers.
But IBM noticed that biologists now need microprocessors as much as microscopes. A year ago, it used $100 million to start a division that sells computers, software and services to biotechnology and drug companies. This life sciences division has had some success; pulling into second place behind Compaq, it must do better."
redux [08.14.01]
"For years, technologists have dreamed that information technology and biotechnology would someday converge into one seamless superscience that could crack the molecular code of disease and yield a gold mine of new treatments and cures. It always seemed so logical, even if it never quite seemed to happen. Some very big names in tech -- Bill Gates ( MSFT ), Paul Allen, and Jim Clark, among others -- for years have been placing bets on so-called convergence companies that promised to exploit the merging of computing and biotech. Allen alone has investments in more than 50 of them, mostly obscure companies that use words like "genomics," "bioinformatics," and "proteomics" to describe what they do. This industry is so new it hasn't settled on a single name yet."
"Now, like a middle-age actor who has just been discovered, convergence has hit the big time. Corporate giants such as IBM ( IBM ) and Compaq ( CPQ ) are pouring $100 million dollops of cash into "life science" projects that mesh computers and biotech."
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The New York Times
U.S. Is Deploying a Monitor System for Germ Attacks
[requires 'free' registration]
"To help protect against the threat of bioterrorism, the Bush administration on Wednesday will start deploying a national system of environmental monitors that is intended to tell within 24 hours whether anthrax, smallpox and other deadly germs have been released into the air, senior administration officials said today.
The system uses advanced data analysis that officials said had been quietly adapted since the Sept. 11 attacks and tested over the past nine months. It will adapt many of the Environmental Protection Agency's 3,000 air quality monitoring stations throughout the country to register unusual quantities of a wide range of pathogens that cause diseases that incapacitate and kill."
redux [11.25.02]
"The Albuquerque physician-turned-researcher just returned from a trip to the NATO Summit in Prague, where he hoped to persuade President Bush and the other 19 member nations that a global health surveillance network is the best way to protect people from manufactured disease."
""The current system is exquisitely designed to fail," Zelicoff said."
redux [10.31.02]
"An epidemic resulting from an act of bioterrorism could be catastrophic. However, if an epidemic can be detected and characterized early on, prompt public health intervention may mitigate its impact. Current surveillance approaches do not perform well in terms of rapid epidemic detection or epidemic monitoring. One reason for this shortcoming is their failure to bring existing knowledge and data to bear on the problem in a coherent manner. Knowledge-based methods can integrate surveillance data and knowledge, and allow for careful evaluation of problem-solving methods. This paper presents an argument for knowledge-based surveillance, describes a prototype of BioSTORM, a system for real-time epidemic surveillance, and shows an initial evaluation of this system applied to a simulated epidemic from a bioterrorism attack."
redux [02.18.02]
"President George W. Bush, the National Homeland Defense Secretary, Tom Ridge, and Health and Human Services Secretary, Tommy Thompson visited the University of Pittsburgh (UP) yesterday to review one of the advanced developments in medical informatics - a collaboration of the University's Center for Biomedical Informatics and Carnegie Mellon University. The project, known as the Real-Time Outbreak and Disease Surveillance system (RODS), is an early warning system for outbreaks of disease designed to obtain and analyze existing sources of data in real time."
"The Real-time Outbreak and Disease Surveillance (RODS) system is a prototype public health surveillance system. RODS collects and analyzes relevant data automatically and in real-time, including emergency room registration data, microbiology culture results, reports of radiographs, and laboratory orders. RODS provides tools that (1) help detect the presence of a disease outbreak, and (2) support the characterization of that outbreak by a public health official. These tools include case definitions, automatic detection algorithms that can be attached to specific data streams, and data analytic tools that support temporal and spatial data analysis and visualization."
redux [06.29.01]
"The merits of linking two fields seemingly as disparate as geographic information systems (GIS) and bioinformatics might not seem obvious, but Virginia Tech's recent symposium linking the twoaeand its roster of renowned participants from both fieldsaehas raised expectations "Applications of GIS to Bioinformatics" was the first major public forum to cross-pollinate the disciplines, helping to fortify a relatively new, yet highly promising investigative area."
""As a result of new dialog between the fields, as we've had at this conference, we are gaining an important mechanistic link between individual-level processes tracked by genomics and proteomics and population-level outcomes tracked by GIS and epidemiology. This will allow us to do a far better job of monitoring, quantifying, and predicting human-health consequences associated with the environment. The potential payoff in related fields such as those looking at climate change, emerging and resurgent infectious diseases, and environmental health is enormous.""
"The meeting brings together researchers in two of the most dynamic analytical technologies-GIS and bioinformatics. The value of GIS analytical systems and data structures to bioinformatics are only now being recognized. Similarly, the methodologies used in bioinformatics can inform GIS scholars of new approaches to pattern recognition and analysis. The purpose of the symposium is to explore the potentials for using GIS as an analytical methodology in bioinformatics and to understand the opportunities bioinformatics presents to the GIS research community. The symposium, the first to focus on the interface between these two research areas, will afford scholars the opportunity to establish new research directions in both fields of investigation."
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The Washington Post
Celera Aims to Crack The Code to Success
"On a bitter-cold morning in New York City last month, Tony L. White, chief executive of Celera Genomics Corp.'s parent company, told investors that its wrenching transformation from a business that sells genetic data to one that develops drugs was "essentially complete." In what was expected to be a one-two punch that day, Celera also announced the appointment of a new head of development, pharmaceutical-industry heavyweight James P. Yee.
Investors' response? The next day, the company's stock price fell 21 cents, or about 2 percent."
redux [06.11.02]
"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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The New York Times
RNA Trades Bit Part for Starring Role in the Cell
[requires 'free' registration]
"In the family of genetic material, RNA has long been the poor cousin of DNA. DNA makes up the genes, the master instructions of life, while RNA merely conveys those instructions to other parts of the cell.
But surprising new discoveries are showing that cells contain an army of RNA snippets that do much more than act as DNA's messenger. The discoveries are helping to refine the prevailing theories of genetics -- or even upend them."
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BioMedNet
Double-helix jubilee takes a turn
[requires 'free' registration]
"The star exhibit is a full-size reconstruction of the very first spidery model that Watson and Crick famously used to solve the puzzle. The model was moved to the Cambridge Laboratory of Molecular Biology (LMB) in 1962, but the original pieces have long since gone astray.
"The model itself was absolutely the center of their philosophy," said Richard Henderson, director of the LMB. "The essence of their approach was to integrate all the available information and use a model-building approach to come up with a hypothesis," he told BioMedNet News at the private launch of the exhibition."
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Bio-IT World
KARI STEFANSSON: The Icelandic Man Cometh
"I have no interest in discussing software systems with you. If you want to see it, just come to Iceland. Don't ask me silly questions like this. I am not going to describe to you [expletive] software systems!"
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Infoworld
Now playing: The human genome
"LIFE SCIENCE TECHNOLOGY is about as cutting-edge as it gets, but now it's apparently also hip. At least that's the image projected by University of New Hampshire researcher Will Gilbert, who has taken to carrying around the human genome on his Apple Computer iPod."
"Gilbert recalls the story of Nobel Prize winner Walter Gilbert -- no relation -- who, during a speech at Harvard in the late '80s, held up a CD-ROM and said, "One day you will be carrying the genome around on this." Actually, the iPod-touting Gilbert notes, it turned out to be an MP3 player."
redux [11.06.02]
"While it sounds neat to put the human genome on a hip-looking device people more commonly use to crank out Mos Def tunes, some researchers say using it to store the blueprint for humankind is not entirely practical."
""If you're walking back and forth (to transfer data) that's not good," said Richard Gibbs, director of the human genome sequencing center at Baylor College of Medicine. "It's often tempting to do that because of bandwidth, but the smart thing to do is make sure you have the proper infrastructure to (transfer data).""
redux [10.29.02]
"Dr. Will Gilbert likes to carry the human genome around on his iPod. It's the easiest way, he says, to transfer the genome -- 3 billion chemical "letters" that make up a person's genetic code, or DNA -- to the computers of other researchers at the Hubbard Center for Genome Studies at the University of New Hampshire.
Gilbert had set up a research project involving the human genome on his Power Mac, using the Apple/Genentech version of BLAST. A breakthrough implementation of the popular bioinformatics tool from the National Center for Biotechnology Information (NCBI), A/G BLAST conducts high-speed DNA searches in biomedical research and drug discovery. "But," says Gilbert, "I wanted to run the project down the hall on another Mac. Rather than copy it across the network, I'd pull out my iPod. Plug it in, drag, drop, zip, boom, bang and walk it down the hall.""
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Genomeweb
Should Bioterror Fear Make Sequences Secret? For TIGR's Fraser
It's a Qualified No
"Despite fears that bioterrorists will use DNA sequence data to create 21st century superpathogens, genomic science should remain public, The Institute for Genomic Research head Claire Fraser said at a special National Academies meeting on national security and the life sciences last week.
Her explanation: genomics just isn't good enough yet to provide the kind of tools terrorists need."
redux [12.01.02]
[requires 'free' registration]
"Scientific information that the US government wants to keep mum, but which can't officially be labeled "classified," has been designated "sensitive but unclassified." One example is the National Academy of Science's recent report on agricultural bioterrorism. Its chapter on bioterror case studies is available only on a need-to-know basis. Other professional groups may find themselves in the same boat, but the rules governing the category are anything but clear.
Reference: Enserink, M. 2002. Entering the twilight zone of what material to censor. Science 298(5598):1548."
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The Scientist
Metaphors and Dreams
[requires 'free' registration]
"To reread James Watson's The Double Helix is to see once again the power of the scientific method: Reduce the problem to little solvable bits and attack them serially. The book shares the exhilaration of the discovery of why DNA must be the secret of life.
But "must be" is a prediction, not an explanation. The secrets are still there. How could DNA inside the cell make trillions of cells behave as one? What is it about DNA and the cell that makes a protein, that triggers a process, that ends in a firing of electrical signals and discharge of transmitters that assembles a thought, like this one, in these 40 words? What flickering community of a spin doctor's genes set in motion the thought expressed by President Clinton upon the completion of the first drafts of the human genome, on June 26, 2000? He said (and compared to some other things people said, it seemed quite modest), "This is the most important, the most wondrous map ever produced by mankind. It will revolutionize the diagnosis, prevention, and treatment of most, if not all, human diseases." And could there have been a genetic basis for the response of 100,000 clinicians, biomedical researchers, health managers, and patients: "Yes, but how? And when?""
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Genomeweb
Systems Biology at MIT: It's All Over the Place
"At last count, 103 of the 341 faculty in MIT's engineering school-and we're talking aeronautic, astronautic, chemical, civil, electrical, environmental, materials science, mechanical, and nuclear engineering--were using the term "bio" to describe the nature of their research.
At a luncheon for 175 invited guests in the MIT faculty club here today, Vest gave a plug for the institute's nascent Computational and Systems Biology Initiative, an interdisciplinary program that will facilitate cross-fertilization among all of MIT's bio-interested faculty and students, whether they be engineers or in the departments of biology, chemistry, computer science, or physics."
redux [03.08.02]
[ summary can be viewed for free once registered ]
"To understand biology at the system level, we must examine the structure and dynamics of cellular and organismal function, rather than the characteristics of isolated parts of a cell or organism. Properties of systems, such as robustness, emerge as central issues, and understanding these properties may have an impact on the future of medicine. However, many breakthroughs in experimental devices, advanced software, and analytical methods are required before the ach