{bio,medical} informatics
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New Scientist
Biologists in Norway use a computer program to "read" the scientific literature and successfully predict gene interactions"Biologists in Norway have used a computer program to "read" the scientific literature and successfully predict gene interactions.
This data-mining of the "biobibliome" provides a way of dealing with the ever-increasing torrent of biological data - millions of papers a year. But even more impressively, the completely automated process can make new genetic discoveries - essentially free research."
"Annotating the tremendous amount of sequence information being generated requires accurate automated methods for recognizing homology. Although sequence similarity is only one of many indicators of evolutionary homology, it is often the only one used. Here we find that supplementing sequence similarity with information from biomedical literature is successful in increasing the accuracy of homology search results. We modified the PSI-BLAST algorithm to use literature similarity in each iteration of its database search. The modified algorithm is evaluated and compared to standard PSI-BLAST in searching for homologous proteins. The performance of the modified algorithm achieved 32% recall with 95% precision, while the original one achieved 33% recall with 84% precision; the literature similarity requirement preserved the sensitive characteristic of the PSI-BLAST algorithm while improving the precision."
"And the future of data-mining technology? Wide open, says Fayyad—especially as researchers begin to move beyond the field's original focus on highly structured, relational databases. One very hot area is "text data mining": extracting unexpected relationships from huge collections of free-form text documents. The results are still preliminary, as various labs experiment with natural-language processing, statistical word counts and other techniques. But the University of California at Berkeley's LINDI system, to take one example, has already been used to help geneticists search the biomedical literature and produce plausible hypotheses for the function of newly discovered genes."
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GenomeWeb
Experts Question Value of Myriad's Proteome Mapping Strategy "Myriad Genetics made a splash earlier this month when it announced a collaboration with Hitachi and Oracle to "map the human proteome" by 2004.
The scope of this ambitious task could vary widely, depending on how the companies want to define "map" and how thorough they want to be. But regardless of how Myriad and its collaborators define the outer limits of the project, proteomics experts are questioning how much scientific value there is Myriad's basic approach.
These scientists say Myriad's two pronged attack on the proteome, an automated yeast two-hybrid strategy combined with MALDI-TOF mass mass spectroscopy analysis of protein complexes, won' t provide Myriad and its partners with a thorough understanding of how proteins play a role in disease."
redux [03.31.01]
[requires 'free' registration]
"A commonly expressed opinion is that a single Human Proteome Project can never match HGP's success. Eric S. Lander , director of the Whitehead Center for Genome Research in Cambridge, Mass., notes that biologists simply don't know how to characterize the proteome "from end to end, nailing every protein. The tools are not ready. And it's not clear that [such a project] makes sense." He contrasts proteomics to HGP where "there is a certain fixed number of base pairs--about three billion--and we were going to get them all. And so it had a beginning and an end to it."
redux [01.31.01]
"Can sequencing do for the proteome what it did for the genome?
On Wednesday, a number of world-renowned researchers in the field of proteomics issued a resounding " no."
Instead of devoting their efforts to decoding the human proteome, proteomics researchers should focus on developing a larger picture of protein structure, function, and pathways within cells and organisms, panelists said at a New York Academy of Sciences briefing entitled "The Promise of Proteomics."
"When a company has phenomenal success with strategy A, you want to do strategy A on the next subject," said John Richards, a professor of organic and biochemistry at California Institute of Technology, referring to current corporate attempts to map the proteome.
"This doesn't work," he said."
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The Boston Globe
Celera Has Mouse Map Monopoly" Celera Genomics Corp. will announce this morning that it has compiled a virtually complete gene map for the laboratory mouse -- but the company has decided against full scientific publication of the feat in order to preserve the data as a commercial product."
" The announcement means Venter's company is likely far ahead of publicly financed researchers in analyzing the genome of the laboratory mouse, an organism of vital import in research by drug companies, biotechnology companies and academic scientists. All these groups are prime markets for Celera, which sells access to genetic databases. Celera is "the only place to get the mouse genome," Venter said."
"Growing doubts about the importance of genomics in drug discovery are holding sales of Celera Genomics' database in check, chief executive Craig Venter said on Thursday.
The new scepticism is limiting Celera's sales to the pharmaceutical industry, even as its sales to academic institutions thrive.
The discovery that the human body has far fewer genes than once believed has thrown into question the "one gene, one protein, one drug" model, Mr Venter explained."
redux [03.10.01]
"With information on the genome now rapidly becoming available, the business models for companies that sell information about the genome, such as Celera and Incyte, may soon be outmoded. Biotech companies will then have to earn their stripes the old-fashioned way: by developing blockbuster drugs. Of course, proteomics companies could arise to sell information about proteins to other drug companies, but Strosberg thinks this is a flawed approach. Given his history, he should know. "Incyte's business model," he recalls, "was originally to be an information provider. That period is over. People will not pay as much for information as they used to because so much of it is now publicly available. Information is becoming a commodity." Instead of selling information about proteins, he is focusing Hybrigenics on using its proteomics information to develop drugs, either alone or in partnership with larger pharmaceutical companies."
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BioMedNet
Scientists frequently fail to divulge industry ties, study shows[requires 'free' registration]
"According to the first thorough investigation of scholarly journals published in 1997, only one-half of one percent of the authors revealed personal financial interests relating to their research. The study, lead by Tufts University's Sheldon Krimsky, appears in this month's Science and Engineering Ethics. A likely explanation, according Krimsky, is that journal editors do not compel uncooperative authors to report financial conflicts of interest. Many are not surprised at the findings. David Blumenthal, director of the Institute for Health Policy at Massachusetts General Hospital, said that researchers who fail to disclose the potential conflicts often "believe that they are people of integrity, and they feel they can separate their work from their financial interests."
But studies suggest otherwise, he said. For example, last year the editors of The New England Journal of Medicine wrote an apology for publishing reviews of drug therapies in spite of the reviewers' ties with the manufacturers. Scientists with ties to companies tend to write more favorable about those products, he said.
Reference: The New York Times, 25 April 2001"
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The Boston Globe
Battle lines drawn on genetic frontier"The question of how to patent proteins, the human body's workhorses, is creating a fierce and far-reaching debate in government and industry over a field seen as one of the hottest arenas on the genetic frontier.
The science of structural genomics is as complex as it is promising, and the stakes are potentially huge - pitting scientist against scientist, start-up against start-up, and drawing in some of the mightiest of agencies and charities in Britain, Germany, Japan, and the United States.
The consensus being sought may help determine the future of one of today's emerging fields of biotechnology research."
[requires 'free' registration]
"GeneProt, a new Swiss proteomics company, will open its first facility in Geneva this week and is building a second one in Princeton, New Jersey. Founder Denis Hochstrasser has said that the company's data on proteins without commercial value, such as housekeeping proteins, will be available for free. The company is seeking proteins that either make good targets for drug development and diagnostics, or proteins that provide therapeutic benefit themselves.
Reference: Abbot, A. 2001. Swiss proteomics company aims to make big impact. Nature 410(6831):856."
redux [02.27.01]
"Let me be frank here: my view is, and always has been, that the information in the genome is our genetic heritage and should not be profited from directly. It is not for sale. This is a pro partnership, not an anti-business, stance. We want to ensure that the entire world has equal access to the data, so that the potential health benefits are reaped by the many, rather than the few.
As Prime Minister Blair said: "The knowledge contained in the map of the human genome has the power to touch the lives of everyone on the planet." It is for precisely this reason that our commitment should be for the entire world to use this data so the benefits can be realised by all, and major killers such as malaria, tuberculosis, river blindness and leprosy will not be neglected."
"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."
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Scientific American
Publish Free or Perish"When a molecular biologist or a biochemist has made a discovery–often after many months or even years of tedious experiments—they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot—but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
[requires 'free' registration]
"The war between scientists and science journal publishers shows no sign of abating. Two journals, Science and the Journal of Cell Biology , last week said that they would make their contents free on the Web a year after publication. Since both are prestigious journals, their move puts pressure on the major publishing houses that have thus far refused to make content free, contending that it would be financial suicide. In March, more than 12,000 scientists signed a petition call for the establishment of a proposed Public Library of Science, which would contain articles six months after publication, and threatened to boycott journals that did not agree to participate.
Reference: Wadman, M. 2001. Publishers challenged over access to papers. Nature 419(6828):502."
redux [10.19.00]
[requires 'free' registration]
"A grass-roots movement is gaining momentum among life scientists, who are pressing for the creation of a permanent, public Internet archive of life science research, provided free of charge. The "Public Library of Science" inititative, begun last November by Stanford University biochemist Patrick Brown, has picked up the support of some 1,600 scientists to date."
redux [11.13.00]
"A group of leading American scientists is promising to boycott scientific journals that refuse to make research articles available free of charge. The scientists have joined a campaign to promote the unfettered exchange of scientific information and establish a web-based public library for science."
"The supporters of the initiative believe that it will "vastly increase the accessibility and utility of the scientific literature, enhance scientific productivity, and catalyze integration of the disparate communities of knowledge and ideas in biomedical sciences." Campaigners aim to prevent the published record of scientific research, much of it paid for with public funds amounting to tens of billions of dollars a year, from being "permanently controlled and monopolized by publishers."redux [11.03.00]
"publiclibraryofscience.org was established to promote the unfettered exchange of scientific information and to organize community support for an international online public library of science. We are asking all scientists of all nations to sign the following letter, which we plan to publish as an open letter in May 2001. Your support will help us to persuade the publishers of scientific journals to commit to giving their archival material to the public domain for distribution through online public libraries. More information about this effort, and a list of journals that are currently compliant is available in our FAQ. Click here if you would like to sign the open letter. We welcome your questions and comments at feedback@publiclibraryofscience.org.
This website is intended to provide information about the open letter and the "public library" initiative to interested scientists, and to provide a convenient mechanism for scientists to sign the letter. Because the open letter is not intended to be "published" until May 2001, we ask that neither the letter nor the list of scientists who have signed the letter be reported elsewhere before May 2001."
[requires 'free' registration]
"Research librarians will meet with the US Justice Department next week to discuss their concerns over publishing monopolies and increasing costs. They've asked the US government to block the merger of two of the largest scientific publishing companies in the world."
"Elsevier owns about 300 biomedical journals and Harcourt owns about 200 biomedical titles. Combining the two publishing houses will give Elsevier 33 to 45% of the market share within biomedical publishing, he says. There's no hard and fast threshold to determine anti-trust monopolies, but this number is clearly above the line, McCabe says."
redux [10.19.00]
""Publishers are reluctant to give away content because they are concerned that advertisers may go away," said Jerome Kassirer, former editor-in-chief of the New England Journal of Medicine. "Advertisers pay more attention to the number of subscriptions to paper journals than to the number of eyeballs on any given website."
"There's a lot of anxiety that if (print journals) have an electronic offering, people will migrate online and they will lose their paper subscription revenues," agreed Tony Delamothe, editor of BMJ Online, a medical association journal that, unlike most journals, does not charge to access its electronic content.
Some insist that simply publishing electronically is not enough --and that open, free access is necessary to disseminate global research."
redux [09.20.00]
"How should biomedical research be communicated? How should research be assessed and validated?"
"Below are abstracts, transcripts, and biographies from the conference. Some presentations did not lend themselves to transcription. Where possible we have supplemented them with editorials from the speakers.
We have also commissioned editorial articles from several speakers and delagates at the meeting.
All thoughts, comments, and suggestions are welcome on our email discussion list"
"What if you could wave a wand, in this very Harry Potter decade, and make libraries - at least digital libraries - more open, more easy to manage, cheaper, and even more eclectic and democratic? What if content contributors could submit, catalog, index, manage, rate and rank materials in large collections themselves? I believe that, thanks to the innovations from the Open Source community and perhaps more importantly the Free Software community, that we can have a contributor-run library at this very moment.
In fact, there are several very successful examples from which we can draw not only best practices, but also - that grail of the programmer - working code. But better still, these projects are also examples of vibrant, lively, noisy, democratic communities. "
"Librarians are increasingly called upon not only to collect information in electronic form but also to organize it into digital libraries. The materials may be created and held locally, or they may be created and accessed in a distributed fashion as a virtual library. Digital libraries can provide material on a variety of topics, from children's games to high-energy physics. Their scope may be local, national, or even international; the audience may be a small group with specialized interests or the broader public. Essential to the successful implementation and use of any digital library is the organization of that library, either directly or indirectly, by one or more knowledge organization systems (KOS).
The term knowledge organization systems is intended to encompass all types of schemes for organizing information and promoting knowledge management. Knowledge organization systems include classification and categorization schemes that organize materials at a general level, subject headings that provide more detailed access, and authority files that control variant versions of key information such as geographic names and personal names. Knowledge organization systems also include highly structured vocabularies, such as thesauri, and less traditional schemes, such as semantic networks and ontologies. Because knowledge organization systems are mechanisms for organizing information, they are at the heart of every library, museum, and archive. "
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MSNBC
Wanted: Hot Industry Seeks Supergeeks"Craig Benham has a problem. As a professor at Mount Sinai School of Medicine in New York, he trains students in the exploding new field of bioinformatics—the fusion of high-powered computing and biology that is aimed at revolutionizing the health-care industry. But Benham can’t keep a postdoctorate researcher for more than a year. They keep leaving for jobs that pay up to $100,000 at bioinformatics start-ups, giant pharmaceutical companies or technology giants like Motorola and IBM that are targeting the rapidly growing life-sciences field. “These companies need a whole new class of biologists who have training in the computational and mathematical methods,” Benham says."
"It can take up to six months to fill a business development position in a genomics or similar company, and a director of marketing and sales realistically takes 60 to 90 days, Takahashi said.
University bioinformatics programs have just begun to address the other key need in this personnel-strapped sector: people with both computer and biology experience. Until these graduates start flooding the market, companies may have to resort to finding qualified computer people, as Perlegen did.
"There's been an explosion of biotech companies that's created the demand, but the supply isn't there, so companies have to find computer scientists who are willing to understand the biology," said Herbert Hess, a Toronto-based recruiter of IT and bioinformatics professionals."
redux [09.01.00]
[requires paid registration]
"Since Next Wave last covered bioinformatics, in our July 1996 Profiles of Bioinformaticians and February 1997 Bioinformatics Skills features, the prominence of the bioinformatician's role in modern biology has only increased. This month, Next Wave provides a comprehensive picture of the current state of bioinformatics, from the funding situation in Europe and the U.S. to the new bioinformatics degree programs and the immediate hiring needs of industrial and academic labs around the world.”
redux [07.25.00]
"Are you a hacker? Do you yearn for something more important to work on than yet-another-gnome-applet? Are you annoyed that you can't find a problem that is fun to code and stretches your brain in new ways... bioinformatics might be the answer."
"The amount of data is growing faster than anyone expected and only a handful of people can both remain with academic ideals and coding potential. We need hackers to join any number of projects out there. And there are a host to join. If you just liking hacking perl or you prefer compiler technology, there is something to suit you. "
redux [06.27.00]
"A fast-growing field known as bioinformatics uses computing to analyze the vast amount of biological, genomic, and related research to make sense of things too complex for the human brain to fathom.
But bioinformatics is also a bottleneck for many drug and biotech companies that can't find enough talented software engineers who combine sophisticated analysis tools with an understanding of genomics.
''We resolve the bioinformatics issue [by hiring] two people: one who understands computer science and the biologist or researcher,'' said Kenneth Fasman, vice president and global head of informatics of AstraZeneca LLC in Waltham."
"...according to Dr. Donald Johnson, a pathologist at the Nebraska University Medical Center. He estimated there are about 60,000 jobs available to scientists and managers versed in bioinformatics."
redux [05.10.00]
"As expected, salaries for the most part climb as the level of training rises, starting in the $40,000-$50,000 range for BAs and reaching over $100,000 for one post doc. But there are exceptions. For example, two of the three undergraduates who were placed received salaries between $50,0000 to $60,000. This is higher than that earned by seven of the masters students, although ten of the nineteen masters students for whom we have salary information earn more than $60,000. One masters student received a starting salary of over $100,000. Reported salaries for five hires at the doctorate level are over $70,000. One is between $80,000 to $90,000; another is over $100,000; yet another is between $60,000 to $70,000. Three post docs received placements with a salary between $80,000 to $90,000. One post doc was placed at a salary of over $100,000. One institution reported that one or more masters student(s) received a signing bonus.""The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs—who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised."
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USNews.Com
Bytes and bits meet biotech"Life science is the fastest-growing sector in the market for high-performance supercomputers already, and the real boom is yet to come. "DNA is digital information," says James Pierce, a professor at Philadelphia's University of the Sciences. "Life is an expression of information; that's why it's so beautifully adaptable to computers." The computer industry is adaptable, too. IBM is rushing to sell life-sciences companies everything from supercomputers to E-commerce tools, while the burgeoning market for biochips, tiny silicon wafers embedded with genetic material, has attracted high-tech powerhouses such as Motorola, Corning, and Agilent. In the new merger of infotech and biotech, biologists and drug companies will spur advances in computing power while computer geeks will play a pivotal role in the drive to treat disease."
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OReilly.Com
Computers + Biology = Bioinformatics"Since Developing Bioinformatics Computer Skills first appeared on Amazon, I've received dozens of emails from computer professionals asking, "How do I retrain myself to get into bioinformatics?" Across the country, colleges and universities are asking a similar question: "How do we design a training program in bioinformatics?" Many computer professionals, however, are probably still asking themselves the more basic question: "What the heck is bioinformatics?"
In a research environment, where many biologists are still asking basic questions, such as "What's the best way to organize my data files on the computer?", and with a lot of computer professionals probably thinking about protein mainly as a component of lunch, "What is bioinformatics?" is a very valid question."
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The New York Times
Approaching Biology From a Different Angle[requires 'free' registration]
" Systems biology is a loosely defined term, but the main idea is that biology is an information science, with genes a sort of digital code. Moreover, while much of molecular biology has involved studying a single gene or protein in depth, systems biology looks at the bigger picture, how all the genes and proteins interact. Ultimately the goal is to develop computer models that can predict the behavior of cells or organisms, much as Boeing can simulate how a plane will fly before it is built.
But such a task requires biologists to team up with computer scientists, engineers, physicists and mathematicians. The structure of universities makes that difficult, Dr. Hood said.
"To do this kind of thing you have to have them shoulder to shoulder and next door," he said at his new institute, near the University of Washington campus."
redux [02.16.01]
"Computers capable of mimicking life have long been the stuff of sci-fi nightmares—think The Terminator or 2001's HAL 9000. But for researchers struggling to make sense of vast amounts of new biological data, and for drug companies anxious to cut costs and speed development, having accurate computer simulations of living systems is still a dream. To make that dream come true, they are turning to "in silico biology," building computer models of the intricate processes that take place inside cells, organs, and even people. The ultimate goal: an entire organism modeled in silicon, allowing researchers to test new therapies much as engineers "fly" new airplane designs on supercomputers."
redux [07.13.00]
"A new mathematical biology is emerging. Building on experimental data from developing organisms, it uses the power of computational methods to explore the properties of real gene networks."
"Our understanding of gene networks is at an early stage. We perceive their complexity only after it has been filtered by the limitations of the techniques used to study them. Genome databases and DNA-chip technology, which enables huge numbers of genes to be screened for activity, will undoubtedly provide more, and much more complicated, data than anything produced by Drosophila genetics. If a relatively simple gene network such as the segment-polarity system is hard to understand intuitively, we can be certain that modelling will be essential to make sense of the flood of new data.
But this will not be elegant theoretical modelling: rather, it will be rooted in the arbitrary complexity of evolved organisms. The task will require a breed of biologist–mathematician as familiar with handling differential equations as with the limitations of messy experimental data. There will be plenty of vacancies, and, on present showing, not many qualified applicants."
redux [04.05.00]
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."
"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."
redux [02.24.00]
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”
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The American Spectator
A Map to Nowhere"Imagine that an intelligence service were to discover some unintelligible messages being sent by a spy. At first the intelligence agents naturally assume they are looking at a code. They assume the task of decoding will be straightforward. But on closer analysis it turns out that the message means one thing if the signal has been received and acted upon, another thing if it has been received and not acted upon, another thing if the receiving apparatus is not switched on, and so on. Rather than just a code the message is a bit like a set of rules for a rather complex interactive game. There are feedback loops, and circuits within circuits, and a lot of things happening inside the cell but outside the genome, in the unfashionable realm of cytogenetics. NIH-funded geneticists don't even want to think about that, because they thought that by sticking to the four nucleotide bases, they had the problem neatly "digitized." Computers would hum away unaided, 24 hours a day, and unravel the mysteries for them while they slept.
We should have known that it would not be so simple."
redux [02.20.01]
[requires 'free' registration]
"Human complexity cannot be generated by 30,000 genes under the old view of life embodied in what geneticists literally called (admittedly with a sense of whimsy) their "central dogma": DNA makes RNA makes protein — in other words, one direction of causal flow from code to message to assembly of substance, with one item of code (a gene) ultimately making one item of substance (a protein), and the congeries of proteins making a body. Those 142,000 messages no doubt exist, as they must to build our bodies' complexity, with our previous error now exposed as the assumption that each message came from a distinct gene."
"The collapse of the doctrine of one gene for one protein, and one direction of causal flow from basic codes to elaborate totality, marks the failure of reductionism for the complex system that we call biology..."redux [02.13.00]
"Biology is currently undergoing a shift from a mostly qualitative to an information rich, quantitative science. Using large-scale biological technologies, we are gaining global views of structural and dynamic information in the form of whole genome sequences and the corresponding gene activity patterns at the RNA and protein level. These data reflect the molecular workings of a complex information processing system. In many ways these systems can be effectively viewed from the perspective of genetic feedback networks, given that the fundamental step of biological information flow resides in gene activation and its control through the activity of regulatory genes."
"The following sets of nine papers deals with the modeling of molecular networks, inference of functional relationships from gene activity profiles, and networks approach to structural evolution. We begin with a review by Szallasi in which he explains shy integrative approaches have been ignored in the traditional search for "dominant" molecular genetic mechanisms, and why this is no longer tenable in light of the evidence for combinatorial molecular causes for e.g. complex human diseases."
"Through centuries biological theories have been molded to conform to the view of nature established in classical physics. An apparently infinite succession of deep-rooted controversies bear witness to the fact, that this was not at all an easy fit. Vitalism, teleology or finalism have perpetually been called upon to account for living systems. But the authority of physics was such, that in the end those deviations from the ideal was always defeated - to reappear, nevertheless, in new disguise in the next generation.
With the birth of molecular biology and especially molecular genetics in the fifties and sixties a strange thing happened. Suddenly a new and very foreign vocabulary was introduced into biology, that of cybernetics or information theory. Terms like 'program', 'genetic code', 'information', 'messenger-RNA', 'feedback' and the like became respectable or even indispensable notions. Such terms, however, clearly played no role in the world view of classical physics.
This contradiction disappears when it is recognized that these new terms did not mean the same thing in biology as they did in general language. Facilitated by a widespread indifference to epistemological problems among biologists the concept of genetic information became for all practical purposes identified as the sum of the genes which carried it."
"We highly suspect the fruitfulness of this paradigm."
[requires 'free' registration]
"As the modest number of human genes became apparent, biologists in both teams were forced to think how to account for the greater complexity of people, given that they seem to possess only 50 percent more genes than the roundworm. It is not foolish pride to suppose there is something more to Homo sapiens than Caenorhabditis elegans. The roundworm is a little tube of a creature with a body of 959 cells, of which 302 are neurons in what passes for its brain. Humans have 100 trillion cells in their body, including 100 billion brain cells.
Several explanations are emerging for how to generate extra complexity other than by adding more genes."
redux [10.17.00]
[requires 'free' registration]
"What can people expect from biotechnology and genomics? Ten luminaries from the biomedical arena, law, and journalism grappled with issues related to that question at the City University of New York's Graduate Center on Sept. 20. In attendance was an audience of 350 whose research, medical, and counseling careers could hinge on how such issues are resolved. Syracuse University's Gene Media Forum (www.genemedia.org) sponsored the event.
The recurring theme was biological predictability. Eric Lander, director of the Whitehead Institute Center for Genome Research, in Cambridge, Mass., noted that in the past century, biologists "worked out a disease by being clever enough to figure out what was wrong." The systematic approach of genomics, he continued, would render research largely predictable.
Panelists stressed, nevertheless, that genomics would not yield answers easily. Harold Varmus, president of Memorial Sloan-Kettering Cancer Center in New York, said that biologists were used to studying one gene at a time. Now, he added, "you've got all the parts of the clock dumped on the table, and you can look at them. But, you know, it's a lot harder to put back together, too."
A consensus emerged that much of the public--including many journalists, behavioral scientists, and physicians--either were unaware of this newfound complexity or twisted it into misguided support for genetic determinism. "
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The Economist
Array of hope"FIRST, the genome. Then the proteome. Now, it seems, the “metabolome”. The range of biochemicals that can be analysed systematically will expand yet again if Ronald Breaker, a biologist at Yale, is right. In this month’s Nature Biotechnology Dr Breaker and his colleagues describe a chip-based technique that is able to distinguish and identify the molecular maids-of-all-work that support genes and proteins in the task of keeping a cell’s metabolism up and running."
redux [11.09.00]
"Traditionally, cancer treatments have been selected on the basis of tumor type, pathological features, clinical stage, the patient's age and performance status, and other nonmolecular considerations. We have generally accepted with a certain fatalism that some patients pigeonholed into a given category will have a response to a particular therapy, whereas others will not. The difference is often viewed as a matter of luck, like the result of a coin toss, but in fact, treatment response can be predicted in some cases, whereas it is close to impossible to predict the results of a coin toss. The field of pharmacogenomics, through the study of large numbers of genes that influence drug activity, toxicity, and metabolism, provides the opportunity to tailor drug treatments and to eliminate many of the uncertainties of current therapy for cancer. "
"In this issue of the Journal, Esteller and colleagues (2) provide clinical evidence of an intriguingly different sort of mechanism -- an epigenetic one that does not involve any change in DNA sequence -- to explain the resistance of some gliomas to nitrosourea alkylating agents."
"Such comprehensive approaches to biology can be characterized as "omic" research (6) -- that is, research in which one generates large resources of information on biologic molecules in aggregate without necessarily knowing in advance which pieces of information and which correlations will prove most important. (7) "Omic" research is hypothesis-driven, but the hypothesis relates to information and its usefulness, rather than to particular molecules or processes. "Omics" began with genomics and the Human Genome Project. Then, as coined by various researchers, there came proteomics, kinomics (for the kinases in aggregate), CHOmics (for the carbohydrates), metabolomics, immunomics, toxicomics, and clinomics -- as well as compound forms, such as functional genomics, structural genomics, and pharmacogenomics. In view of the study by Esteller et al., (2) and as we search for other clinically relevant instances in which promoter methylation affects therapy, can "pharmacomethylomics" be far behind?"
redux [07.11.00]
"Genes are tricksters. They can be turned on or off -- and whether they're on or off decides whether the gene-owner will develop disease.
Gene researchers have embarked on a new field of research, called epigenomics, to determine whether genes are in the on or off position. This type of marker could prove an important diagnostic or therapeutic tool for all types of cancer.
"At Johns Hopkins, researchers are performing clinical trials on about 15 patients with leukemia and other cancers to find out if epigenomics might give pharmaceutical companies a lead for developing cancer drugs.
The research, like all epigenomics research, is studying a chemical found in everyone's DNA called cytosine. Cytosine is the only chemical of the four that make up human DNA (the others are adenine, thymine, and guanine) that is prone to a phenomenon called methylation. When cytosine is methylated, it tuns off its gene. "
"For most of us, formal biology education begins with complex systems--the traditional dissection of a frog in high school biology class is virtually a rite of passage in the U.S.
But the way many people learn about and invest in biotechnology is at the smallest end of the spectrum--the genome, now often described as the "periodic table" of biology. Genomics and all its related buzzwords have been responsible for much of the media attention, government grants, and investment capital heaped on the biotech industry over the past decade.
But just as there is a whole lot of chemistry that happens in between the periodic table and a birthday cake, there is a lot of biology in between the genome and a living organism. With the completion of biology's periodic table within sight, academics and industry players alike are pondering the best way to apply our hard won knowledge.
The only problem is, the path from genome to system seems to get harder the more we learn."
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Financial Times
Slow-acting medicine""There has been no revolution in medicine in the past 25 years," says Arthur Levinson, chairman and chief executive of Genentech.''
"It should not have been this way. In theory, a greater understanding of the biology of disease should make it easier to design drugs."
""Those waiting for a so-called genomics revolution will be disappointed," argues Mr Levinson at Genentech.
"Sequencing of the human genome is a very important scientific development. But it's difficult to say what will come out of it," warns Mr Sharer at Amgen. "It takes 10 years to develop a new medicine, so don't expect any overnight results. The project provides a parts list of the cellular mechanism of the body but it doesn't explain how those parts work together. We are not on the cusp of a discontinuity."
"If you were going to build a drug discovery company from scratch now, you'd start with informatics. The pharmaceutical industry has not yet had the sea change in productivity it requires. Information generated through each drug discovery project needs to be recycled and re-used, whereas usually data is not re-interpreted and reapplied to new projects. The attrition from gene to drug is currently much too high. If the car industry threw away many, many automobiles to get one that works, that wouldn't be acceptable."
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.""
"First came germ theory with antibiotics. Then came replacement theory with insulin and growth factors. Now the paradigm for drug development has shifted once again: We have entered the era of genomics-based medicine.
In less than a decade a new genomics industry has taken hold. Gemomics companies now ferret through miles of genetic code to identify the genetic causes of disease, select potential target genes, and help big pharma find the next blockbuster.
But the face of genomics—or at least its role in drug discovery—is about to change, due largely to its own success. “We’re knee deep in potential targets,” says Nicholas Dracopoli, executive director of pharmacogenomics with Bristol-Myers Squibb. “Prioritising the targets is the rate limiting step.”"
"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.”"
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Boston Globe
Biotech CEO says map missed much of genome"Somewhere within the vast microprocessors that hum in the Maryland offices of biotech firm Human Genome Sciences Inc. are the sequences of 60,000 never-before-seen human genes."
"Or so says Dr. William Haseltine, the CEO of Human Genome Sciences. He wants a recount. And he is not alone."
"Haseltine, one of the most respected - and wealthiest - geneticists of his generation, has a guess: 120,000. He said the world's best genetic minds missed tens of thousands of genes in their haste to produce the completed map.
''We believe they have missed as many as two-thirds of the genes that exist,'' said Haseltine in an interview. ''I think they are guilty of sloppy science and sloppy conclusions.''
redux [02.11.01]
"The first close reading of the "The Book of Life" —the 3 billion letters that make up the human genetic code — reveals that it's packed with more mysteries and surprises than a pulp thriller. Perhaps the biggest surprise since the code was deciphered in June is that it takes just 30,000 to 40,000 genes to make, maintain and repair a human. That's far fewer than the 140,000 genes some had predicted and not many more than an earthworm or a common weed. "If you're judging the complexity of an organism by the number of genes it has, we've just taken a big hit in the pride department," says National Genome Research Institute's director Francis Collins, who also heads the U.S. arm of the international Human Genome Project (HGP)."redux [11.13.00]
"The human genome project has revealed that our genetic make-up is far less complicated than first thought.
Researchers have worked out that as few as 30,000 genes are needed to produce a human, only twice as many as the humble fruitfly.
One of the scientists behind the project, Dr Craig Venter says this would suggest our behaviour is not determined by our genes, with environmental factors playing a large part in shaping our thoughts and actions."
[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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Conference
WEB01: Workshop on Education in Bioinformatics 2001"In response to the worldwide shortage of trained bioinformaticians, several universities and institutes have spearheaded Bioinformatics teaching and research. This workshop will bring together Bioinformatics educators for the first time to meet, discuss and exchange ideas and suggestions. WEB01 will address fundamental issues that will determine the nature, extent, content and delivery tools available for Bioinformatics programs embarked upon, as well as provide valuable lessons for focus and improvement of nascent Bioinformatics programs.
Besides oral presentation sessions, the workshop will feature a tutorial on how to set up a Bioinformatics teaching program."
redux [09.01.00]
[requires paid registration]
"Since Next Wave last covered bioinformatics, in our July 1996 Profiles of Bioinformaticians and February 1997 Bioinformatics Skills features, the prominence of the bioinformatician's role in modern biology has only increased. This month, Next Wave provides a comprehensive picture of the current state of bioinformatics, from the funding situation in Europe and the U.S. to the new bioinformatics degree programs and the immediate hiring needs of industrial and academic labs around the world.”
redux [06.27.00]
"A fast-growing field known as bioinformatics uses computing to analyze the vast amount of biological, genomic, and related research to make sense of things too complex for the human brain to fathom.
But bioinformatics is also a bottleneck for many drug and biotech companies that can't find enough talented software engineers who combine sophisticated analysis tools with an understanding of genomics.
''We resolve the bioinformatics issue [by hiring] two people: one who understands computer science and the biologist or researcher,'' said Kenneth Fasman, vice president and global head of informatics of AstraZeneca LLC in Waltham."
"...according to Dr. Donald Johnson, a pathologist at the Nebraska University Medical Center. He estimated there are about 60,000 jobs available to scientists and managers versed in bioinformatics."
redux [05.10.00]
"As expected, salaries for the most part climb as the level of training rises, starting in the $40,000-$50,000 range for BAs and reaching over $100,000 for one post doc. But there are exceptions. For example, two of the three undergraduates who were placed received salaries between $50,0000 to $60,000. This is higher than that earned by seven of the masters students, although ten of the nineteen masters students for whom we have salary information earn more than $60,000. One masters student received a starting salary of over $100,000. Reported salaries for five hires at the doctorate level are over $70,000. One is between $80,000 to $90,000; another is over $100,000; yet another is between $60,000 to $70,000. Three post docs received placements with a salary between $80,000 to $90,000. One post doc was placed at a salary of over $100,000. One institution reported that one or more masters student(s) received a signing bonus.""The results of our current survey make it clear that the majority of these jobs are not being filled by graduates of formal programs—who by our count represent about 15 percent of the positions advertised in 1997. And, we believe the 15 percent figure to be an overestimate given that ads have been growing over time and our most recent ad count is for 1997, a year earlier than our hiring data. This leads us to infer that most of the advertised positions are being filled by individuals trained in informal programs and by individuals who change jobs. The distinct possibility exists that a number of these jobs remain vacant for a period of time, an issue not studied here. Furthermore, our pipeline estimates (see Table 2) lead us to conclude that the number of individuals currently enrolled in formal programs falls far short of the number of positions that have recently been advertised."
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HMS Beagle
Bioinformatics: Key to 21st Century Biology[requires 'free' registration]
"Bioinformatics, which straddles the interface between traditional biology and computer science, has emerged as a new discipline that promises to transform research in fields from genomics to pharmacology, and may well reverse the life sciences' longstanding reductionist paradigm. More and more universities are establishing bioinformatics programs to meet the growing demand for training."
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New Scientist
Screen test"There's never been a better reason to ditch the flying windows or gyrating text drifting across your computer screen. Cancer researchers are offering a new computer screen saver that will use spare processor time on your computer to look for drugs to fight the disease.
Pinching the idea from the search for extraterrestrial intelligence (SETI), the researchers hope that drafting in PC users across the globe will speed up drugs discovery. "We're going to need perhaps three or four million hours of computing time," says Graham Richards of Oxford University. "Using our own computers, we'd be dead before we finished."
To look for new drugs, the team takes 3D computer models of four key proteins that seem to promote cancer - by encouraging the growth of blood vessels to supply tumours, for example. The models include all the active binding sites of the proteins. "We'd like to design little molecules that would get into these sites and block them," says Richards."
redux [02.18.01]
"A new distributed computing project is comparing gene data with protein structures to determine their genome sequences.
"Genome@home is the second project from Stanford University's chemistry department, which also runs the Folding@Home project.
"Whereas Folding@Home is designed to learn how genomes fold into proteins, Genome@Home was launched this week to try and reverse engineer known proteins by guessing the genome sequence of their structures."
redux [02.02.01]
"Facing shrinking ad revenues, ISP Juno Online is jumping into a new field that to date has enjoyed its greatest fame from the search for extraterrestrial life.
The New York-based company announced Thursday the creation of Juno Virtual Supercomputer Project, a distributed computing effort that would tap the computing power of Juno's 4 million subscribers. Juno hopes to sell that vast power to large-scale research projects, initially focusing on bioinformatics and pharmaceutical work, said Juno President and CEO Charles E. Ardai."
redux [10.09.00]
"The SETI@Home problem can be thought of as a special case of the distributed computation verification problem: "given a large amount of computation divided among many computers, how can malicious participating computers be prevented from doing damage?" This is not a new problem. Distributed computation is a venerable research topic, and the idea of "selling spare CPU cycles" has been a science fiction fixture for years.
In real life, distributed computation has been used since at least the late 1980's to create "farms" of machines for rendering 3-D images. Farms allow graphic artists to create large images without needing to buy a supercomputer. More recently, the needs of scientific computation have led to the creation of frameworks such as Parallel Virtual Machine (PVM) and Beowulf, which make it easier to distribute computations across many machines. The machines involved are usually owned by the same entity and a machine is either "good" or "bad" if it is operating or malfunctioning. There are no blatantly malicious machines.
The Internet makes it possible for computation to be distributed to many more machines. However, distributing computing around the internet requires developers to consider the possibility of malicious clients."
"The general study of secure multiparty computation has produced much interesting work over the last two decades. Less well studied, unfortunately, are the tools and techniques required to move the theoretical results to the real world. The old dream of massively distributed computations is finally coming true, and yet our tools for building and analysing real systems still seem primitive. The challenge of the next few years will be to bridge this gap."
redux [08.09.00]
BBC Screensavers could save lives
"Your computer could be helping to save lives when you are not using it to play games or surf the internet.
Instead of it sitting idle, it could be taking part in scientific experiments being distributed across thousands of computers on the internet.
Drugs to beat cancer and flu are starting to be tested in simulations split up and run on personal computers that would otherwise be doing nothing useful." [via slashdot.org]PC Magazine New Apps Exploit Connectivity
"A natural complement to distributed f