{bio,medical} informatics
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Bio-IT World
The Business of Bioinformatics
"Bioinformatics as a business, not to be confused with bioinformatics as a field of study, is at an interesting crossroads. As an academic branch of learning, bioinformatics remains mostly what it always was -- a cross-disciplinary endeavor between computer science and molecular biology. But bioinformatics as a money-making proposition has different criteria for success, and it has received a lot of bad press lately, some of it deserved."
"During this golden age, bioinformaticists developed software that computational biologists could use to make biological discoveries based on genomic data. But the industry swerved off course by selling expensive systems that focused on the individual pieces of a solution, without heeding downstream processes that were the actual bread-and-butter of our customers. Bioinformatics has always been about integrating data and converting it into information. When it loses that focus, it loses its value to the customer."
redux [11.05.02]
[requires 'free' registration]
"The biotechnology industry is facing one of its worst financial squeezes ever. The prices of many biotechnology stocks have plummeted, and Wall Street's vaults have snapped nearly shut, making it almost impossible for capital-hungry companies to finance themselves."
"Another sector that has suffered is bioinformatics, which uses computers to analyze masses of genetic data. Several young companies have gone out of business or been acquired for a pittance after sales did not meet expectations."
"R&D spending among some of the biggest biotech and pharma consumers will grow at a much slower clip as Wall Street applies pressure to curb losses and bolster earnings, according to the report by the investment bank Stephens. Plus, what little cash that is allotted for new drug-discovery technology will likely go to later-stage tools.
"What is disturbing regarding the tools companies, is that not only are you having an absolute slowing in the growth rate of R&D spending, you're also having within that spending more emphasis on molecules already in clinical trials," study author John Sullivan told GenomeWeb in a recent interview. "If something's in clinical trials, there's not more tool spending.""
redux [03.14.01]
"The story proclaimed in its lead, "Move over Information Age. Make room for the age of bioinformation." You could picture bleary eyes opening all over the Bay Area. The story went on to note that a San Jose consulting firm was predicting a 10 percent annual growth in the bioinformatics market for years to come; and that the National Science Foundation estimated that 20,000 new jobs in the field would be created in the field in just the next four years.
If that wasn't enough, the rest of the section was filled with page after page of biotech firms listing job openings - in powerful juxtaposition to the endless lists of dot-com layoffs just a few pages earlier. Picture Starbucks spit-takes from Marin to Santa Cruz.
Wow! Rewrite that resum to emphasize that biology course you took in college. Roll your Aeron chair down to the nearest lab. Trade that black turtleneck for a white lab coat..."
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The O'Reilly Network
Relational Modeling of Biological Data: Trees and Graphs
"While these projects have rich public Web sites for browsing and downloading the data, none of them provide the means to compute on the data, to relate your own data to theirs, or to query across the disparate resources. Fortunately, all of these data sources can be freely obtained by ftp or anonymous cvs for integration into a local, custom-made relational database. But how does one represent hierarchical data in a relational database? And, more importantly, how can one make efficient use of such data?"
"The lesson here is that often the obvious way to model data (such as adjacency lists of tree or graph edges) is not the most efficient data model with which to query or compute. Alternatives such as the nested-set implicit representation of a tree-like hierarchy, or the transitive closure of a graph structure costs very little to create, and provides one-step mechanisms to extract informative subsets of the data. Commercial relational database products that advertise native support for hierarchical data are often simply transparently building and managing these same representations. Now you know how to it yourself."
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The Scientist
Minimal controversy
[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."
"Several years ago, Venter first looked at this mycoplasma as the best such model, because the organism is a record-holder of sorts: the self-replicating life form with the smallest known complement of genetic material. Unlike the human genome with its 30,000 to 50,000 genes, M. genitalium gets by with only 517. But remarkably, nearly half of even that minimal set is extra baggage. Under some laboratory conditions, as few as 300 of the genes can fulfill its definition as a lifeform that feeds and divides.
As it turns out, what is the definition of life itself? and also exactly what is its minimal genetic set? have been hotly contested. Gene size is one of the main limits to what could be the final and minimal cell size, and thus may set a limit on possible targets for creating life from scratch.
But what structures are too small or too simple to be considered "life"?"
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Wired News
Global Network Battles Bioterror
"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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Nature: Insight
Computational biology
"This Insight presented us with a difficult problem, not in its content -- a collection of reviews showing how sophisticated mathematical concepts have illuminated and continue to illuminate the principles underlying biology at a genetic, molecular, cellular and even organismal level. The problem was what to call it.
In the end we concluded that the unifying strand that runs through all the work described in this Insight was computation, whether it be the production of sophisticated models against which reality is compared, or the subtle analyses that derive patterns and trends from vast and noisy data sets. There are other themes running through the reviews in this Insight, more than you might expect from the titles alone, but 'Computational Biology' it has become."
redux [09.09.02]
"Consistent with his lifelong reputation as a visionary and provocateur, Brenner challenged a crowd of over 250 bioinformaticists gathered at the Wellcome Trust Genome Campus in Hinxton, UK, to "forget the genome."
"The more you annotate the genome, the more you make it opaque," he warned in a keynote speech delivered at the joint Cold Spring Harbor Laboratory/Wellcome Trust Genome Informatics conference on Saturday. "We need to focus on our cells."
Brenner questioned the ability of computational approaches to derive functional knowledge from genomic sequence alone--a "hideously difficult task," he said--because some problems are simply "not soluble or computable." The future, according to Brenner, requires going back to the bench. Old-fashioned data on the biochemistry of the cell would then be used to flesh out the cell map, which would serve as "a framework to think of genomes and their products.""
redux [07.29.02]
"Colin Hill, president and CEO of GNS, said the adoption of modeling will be slow, but even the largest and most stubborn pharmas will soon realize they have to adopt it if they want to compete.
He has seen more success selling pharmas the baby steps toward modeling: tools, such as its Diagrammatic Cell Language, software and database information, rather than actual models."
redux [11.27.00]
"What do a Boeing 777 and the human body have in common? Both are complex systems, dependent on millions of complex parts, whether they be a jet-propelled engine or a pumping organ such as the heart. The big difference: Engineers can design and build highly accurate computer models of the way a Boeing 777 will behave in flight. The human heart? Its complexity has long stymied efforts by researchers intent on turning drug development into a predictive science, much like building airplanes.
But that's changing. A handful of companies are developing software that can model single cells, whole organs, cellular metabolism and toxicology, diseases throughout a patient's body, and even an entire clinical trial."
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 [12.17.01]
""We used to look at several data points for each experiment," says Louis Renzetti, senior director of discovery pharmacology. "Now there are dozens and dozens." Simply dump all of that data on a scientist's desk, and one of two tragicomic things will happen: Either the scientist will want to pursue every promising lead and will end up like a frazzled amusement-park visitor, or the scientists will refuse to touch the report at all, for fear that she will never be able to make sense of it.
It has taken a while to find the right approach, says James Rosinski, one of Roche's experts in the new field of bioinformatics, which covers the management of genomic data. The key, he says, is for biologists and statisticians to start talking early about how to use data from a GeneChip experiment. "It's iterative," he explains. "We can't just take a one-shot approach and tell the biologists what they ought to be interested in. We have to interact.""
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."
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BioMedNet
The human proteome - a global challenge
[requires 'free' registration]
"The Human Proteome Organization (HUPO), which will tomorrow launch its first world congress, faces the unique challenge of bringing together the public and private sectors in a coordinated global research effort aimed at mining the human proteome, says HUPO president Sam Hanash.
Contributing to that effort are researchers in Europe, Asia-Oceania, and North America. "We are witnessing a tremendous interest in proteomics on the part of countries that a decade ago were not active in genomics and that may well become leaders in proteomics in a short time," said Hanash, an oncologist at the University of Michigan in Ann Arbor."
redux [10.10.02]
"The Institute for Systems Biology, a Seattle nonprofit research center led by gene-sequencing pioneer Dr. Leroy Hood, said yesterday it has landed a $19.8 million contract from the National Institutes of Health to advance understanding of proteomics, the study of how proteins interact in the body."
In the wake of recent breakthroughs unraveling the human genetic code, proteomics is increasingly being viewed by scientists as the next step. Scientists say genes provide the instructions for making proteins, and proteins carry out the real action inside the cell."
redux [12.20.01]
[requires 'free' registration]
""Just because you use a protein doesn't make you a proteomics researcher," Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School, told BioMedNet News.
After the success of genomics, "everyone wants to think of proteomics as the next great science," but calling themselves proteomics researchers "is not really fair," LaBaer said. "A lot of people who claim to do genomics aren't genomic researchers either," he added. "They are just studying gene sequences.""
redux [12.12.01]
[ summary can be viewed for free once registered ]
"Proteomics aims to chart the ebb and flow of tens of thousands of proteins at once to produce snapshots of life inside cells. The technology to pull it off doesn't exist yet, however, and the competition is stiff for those proteins that can be nabbed using current methods. But this young field is growing up fast. This special News Focus looks at the promise and roadblocks of biology's latest wellspring. The package includes profiles of GeneProt, the biggest proteomics test-bed to date, and Stephen Burley , a crystallographer who is leaving academia to direct research at a small start-up company. Other stories discuss the potential of protein chips for new diagnostics and research tools and the problems faced by companies attempting to patent proteins."
redux [08.15.01]
"A new study of the proteomics market forecast that the proteomics market would grow nearly six-fold to $5.6 billion by 2006 from $963 million in 2000.
In its report, consultancy firm Frost & Sullivan said the increase would be driven by a shift towards the analysis of proteomes following the discovery that the human genome contains fewer genes than originally predicted.
"Proteomics adds value to drug discovery by charting the distribution of proteins, identifying and characterizing proteins of interest, and elucidating the participation of proteins in biochemical pathways boosting the number of potential targets around which lead compounds can be designed and screened," Eric Gay, a Frost & Sullivan analyst, said in a statement."
redux [07.11.01]
"Their bold proclamation has raised a few eyebrows in the scientific community. "It's easy to say that you'll complete a comprehensive proteome map," notes Marc Vidal of the Dana-Farber Cancer Institute in Boston. "But none of us knows what that means." There may be only one genome, but when it comes to the proteome, different proteins can be more or less active in different cells at different times during development, under different physiological conditions or in different disease states. The proteome's nature "makes it hard to define what we're doing--not just Myriad, but all of us," remarks Joshua LaBaer, director of the Institute of Proteomics at Harvard Medical School. "There's no such thing as a human proteome," adds Keith L. Williams, CEO of Proteome Systems, headquartered in Sydney, Australia. Look at the liver, for example, he says: "After a glass of red wine, you'll have a different proteome."
redux [06.20.01]
"Scientists thought about trying to catalogue all the proteins in the body a decade ago.
But it seemed impossible, and was therefore impossible to fund. Researchers moved on to the much simpler job of sequencing the human genome.
They were right to do so. Cataloguing proteins turns out to be downright confusing. Lately, more and more biotech companies are entering a field they call "proteomics," an ugly word searching for a focus group."
redux [03.13.01]
[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."
"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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SFGate
Junk DNA Revisited
"In a provisional patent application filed July 31, Pellionisz claims to have unlocked a key to the hidden role junk DNA plays in growth -- and in life itself.
Rather than being useless evolutionary debris, he says, the mysteriously repetitive but not identical strands of genetic material are in reality building instructions organized in a special type of pattern known as a fractal. It's this pattern of fractal instructions, he says, that tells genes what they must do in order to form living tissue, everything from the wings of a fly to the entire body of a full-grown human."
redux [08.28.02]
"In a new study in the August 29 issue of Nature, researchers at The Wistar Institute identify a cohesin-containing protein complex that reshapes chromatin to allow cohesins to bind to DNA. In doing so, they also identified the locations on the human genome where the cohesins bind. Somewhat to their surprise, the binding sites were found to be a repetitive DNA sequence found throughout the human genome for which no previous role had ever been identified. These bits of DNA, known as Alu sequences, are liberally represented along those vast stretches of the human genome not known to directly control genetic activity, sometimes referred to as junk DNA."
redux [08.09.02]
"Results of a new University of Michigan study suggest that junk DNA - dismissed by many scientists as mere strings of meaningless genetic code - could have a darker side.
In a paper published in the Aug. 9 issue of Cell, scientists from the U-M Medical School report that, in cultured human cancer cells, segments of junk DNA called LINE-1 elements can delete DNA when they jump to a new location - possibly knocking out genes or creating devastating mutations in the process."
"Scientists in the past decade have discovered that remnants of ancient germ line infections called human endogenous retroviruses make up a substantial part of the human genome. Once thought to be merely "junk" DNA and inactive, many of these elements, in fact, perform functions in human cells.
Now, a new study by John McDonald of the University of Georgia and King Jordan at the National Center for Biotechnology Information at the National Institutes of Health, suggests for the first time that a burst of transpositional activity occurred at the same time humans and chimps are believed to have diverged from a common ancestor - 6 million years ago."
redux [01.20.01]
[requires 'free' registration]
"Speaking at a National Institutes of Health conference on ethical and social issues in genetics, Dr. Francis Collins said that a "spate of papers in public journals'' due out within a month will signify the incredibly rapid pace of scientific discovery seen since the announcement of the nearly complete sequencing of the human genome last summer.
The first, Collins said, will be a paper that puts the total count of human genes at between 30,000 and 35,000. "That's less than half the number most people have been predicting.'' The second is a study ascribing previously unknown biological missions to genes scientists thought were inactive, or so-called "junk genes."
"There is now clear evidence that (the junk genes) have been performing a number of functions for tens or hundreds of thousands of years,'' he said."
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IBM developerworks
Open source in the biosciences
"Until recently, open source has often appeared to bioscientists as some sort of novelty, or, worse, a threat to IP protection. In the last few years, though, solid achievements in clustering, genomic data management, Web publication, and scores of specific "vertical" applications have established open source as a serious technical alternative.
Big Pharma and other biosciences are just starting to realize how open source can systematically cut costs, improve security, allow their own workers to shift attention back to their "core competences" from proprietary IT expertise, and even promote better science. We're in the midst of a dramatic evangelical movement that teaches better ways for open source IT to support bioscientific goals. Perhaps the most consequential shift is that participants have begun to understand that standards-based open source can enhance biosciences' fundamental values. These are exciting times for open source bioinformatics."
redux [09.30.02]
"Brenner, for example, stressed that while open sourcing "has potential in a generic sort of way," success depends on the operational and business models of specific companies.
Even considering a move to open sourcing can meet with resistance. "All of the instrument companies were brought up in closed-source shops, so they would have to change this fundamental attitude," explained Hood."
"THE OPEN SOURCE MOVEMENT has gained significant momentum of late, particularly within the bioinformatics field. While open source licenses vary widely, distribution of open source software typically requires delivery of both the object code and the source code. Most commercial software is delivered only in object code form, which is not easily read and modified by programmers.
The decision of whether to use open source software requires a careful analysis of various factors. In the right situations, open source software can be an excellent choice. In other cases, it can be disastrous."
redux [08.21.02]
"Want to make money from open-source bioinformatics? As long as it's not too much you might be OK.
This was the verdict of a panel of academics and business executives who had convened last week to talk broadly about open-source bioinformatics. But the discussion, which took place at the IEEE Computer Society bioinformatics conference at Stanford University, frequently veered to whether one could, or even should, make money from it.
The answer was a resounding maybe."
redux [01.16.02]
"A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.
Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site, OpenInformatics.org, to further this cause.
Here we present two opposing viewpoints on this issue."
redux [01.07.01]
"The Open Source movement is infectious, it seems. It has bubbled up in the field of bioinformatics - gene research software. Gene research is already a burgeoning area of activity, which is predicted to deliver numerous benefits to the health industry. It is also an area where software counts and where universities have managed to prosper from their activities. US universities lodge about 2000 patents each year, many in bioinformatics, and these patents contribute a good deal of revenue - an amount estimated at about $5 billion per annum, or ten percent of their total budgets. Thus Open Source activities in this area are not universally welcomed."
"Over the past several years, open-source software development has won high-profile adherents in the business world -- including the likes of IBM and Sun Microsystems. But it has always had its strongest fans in the academic world, where open-source software is seen as a natural extension of the idea that the fruits of academic research should be shared with everyone.
But now some academic programmers on the cutting edge have found that the licensing office is proving a more formidable obstacle to progress than the limits of their imagination and skill."
redux [11.26.01]
"Before computer whiz Steven E. Brenner accepted his tenure-track research post at the University of California-Berkeley last year, he demanded that the school's intellectual property police leave him alone.
Brenner prevailed. He's now one of the few experts in the emerging field of bioinformatics with the freedom to distribute his work, software used in gene research.
``It's vital to what we do,'' says Brenner, who supports a movement to force universities to allow ``open source'' publishing of gene research software code."
redux [08.18.01]
"Steve Brenner, assistant professor and leader of a computational genomics research group at the University of California, Berkeley, said he fears that many academic bioinformaticists are unaware of a legal risk they face on a daily basis: contributing to open source software projects without explicit permission from their institutions.
While many employers have clauses in their employment contracts that restrict the creation and use of open source software, bioinformatics programmers at universities are often not as attuned to copyright issues as their industry counterparts. This fact, Brenner said, raises the possibility that a good portion of biological open source software is currently being produced illegally."
"The issue seems to be coming to a head in the academic world now, as more universities are exploiting the revenue stream made possible by their copyright and patent holdings. ?If you?re a software developer, the university holds rights to your software, but if you?re an English professor or Law professor and publish a book, they?re not the least bit interested in copyright,? said Thomas Field, an attorney at the Franklin Pierce Law Center affiliated with the Association of University Technology Managers."
redux [11.05.01]
"Computers are supposed to help biotechnology, right? Isn't bioinformatics all the rage right now? Well, it is, but with popularity comes legal questions that many companies don't address until it's too late."
"It seems that many biotech companies don't realize that a computer vendor may have the rights to the software, and ultimately, the work that the biotech companies do.
For example, if a biotech company orders a computer network to help it sequence the genome of yeast, the company may ask the vendor to customize the software it will use to do the sequencing. However, the question is, who owns the right to that customized software--the biotech company or the software programmer?"
redux [08.23.01]
"This report outlines recent activity in open source software development within the discipline of bioinformatics. I present the relevant highlights of two bioinformatics meetings held in July 2001 in Copenhagen, Denmark: the Bioinformatics Open Source Conference and the Intelligent Systems for Molecular Biology Conference. The report also describes a large number of projects and groups important to bioinformatics open source software development. The appendices include meeting programs, the currently accepted definition of open source software, and descriptions of important online biological data sources."
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The Nation
Sociobiology and You
"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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BioMedNet
Paying
the price for drug company profits
[requires 'free' registration]
"It has never been a secret that the pharmaceutical industry is a profit-making industry. It is also a well-known fact that the citizens of poorer nations, for the most part, don't benefit from pharmaceutical advances, because they can't afford to them. This is still the case, according to David Henry and Joel Lexchin, writing in the Lancet. The pair claims that although the industry does provide notable and charitable contributions of its products to poorer nations, it has begun stressing marketing to rich nations to maximize profits. The authors also doubt industry claims that high drug prices are needed to earn a return on high research and development costs.
Reference: Henry, D. and Lexchin, J. 2002. The pharmaceutical industry as a medicines provider. Lancet 360(9435):1590-1595."
"But given the sheer numbers involved and its still-evolving nature, the Purple Pill may be our best case study of the forces driving up prescription drug costs. It's the story of a wondrous medical advance that brought relief to millions and significantly reduced the need for surgery. But it's also the story of the steroid-injected marketing muscle that has ensnared, among others, Boston's most respected hospitals and the exhaustive legal maneuvers that have delayed competition, helping to drive up costs for you, me, and Gertrude.
"This is a locomotive that's barreling down the tracks, and you either get out of the way, get on board, or get squished," says Dr. James Richter, a Boston gastroenterologist."
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Federal Computer Week
More sites targeted for shutdown
"Having persuaded the Energy Department to pull the plug on PubScience, a Web site that offered free access to scientific and technical articles, commercial publishers are taking aim at government-funded information services offering free legal and agricultural data.
"We're delighted with the decision [to shut down PubScience]," LeDuc said. "The administration has done a tremendous job of hearing our concerns and responding to what we've always considered to be our legitimate concern."
redux [09.24.02]
[requires 'free' registration]
"The UK's Office of Fair Trading says that the prices for scientific, technical, and medical (STM) journals are too high because normal competitive forces have been suspended. Libraries are paying too much. The prices of STMs are rising faster than inflation, and the disparity between for-profit and not-for-profit journals is obvious. Part of the problem is that the journals compete on quality, not price, so libraries are prone to skip the cheaper journals for the better, more expensive ones. Bundling journals also skews the market.
Goodman, S. 2002. "Unusual forces" are pushing journal market off course. Nature 419(6904):239.
redux [09.05.01]
[requires 'free' registration]
"Publishers of established scientific journals have thus far resisted demands for freer access. In its campaign to make biomedical research literature available free online, Public Library of Science is now taking a new tack: It hopes to publish peer-reviewed, electronic journals.
"If we really want to change the publication of scientific research, we must do the publishing ourselves," says an announcement posted Sept. 1 on the group's Web site. "It is time for us to work together to create the journals we have called for."
redux [04.24.01]
"When a molecular biologist or a biochemist has made a discovery - often after many months or even years of tedious experiments - they tell the rest of the world by publishing their results in a scientific journal. So far, these journals have controlled who can read them and who cannot - but maybe not for much longer.
E-mail, Internet discussion groups, electronic databases and pre- or e-print servers have already transformed the way scientists openly exchange their results. And in the life sciences, researchers are now demanding that their work be included in at least one free central electronic archive of published literature, challenging the traditional ownership of publishers. The demand has sparked widespread discussions among scientists, publishers, scientific societies and librarians about the future of scientific publishing. The outcome may be nothing short of a revolution in the scientific publishing world."
redux [09.20.00]
"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."
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News.Com
Intel delves into life sciences
"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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Bio-IT World
Computer model predicts disease variant based on genetic
defect
"University of California, San Diego (UCSD) bioengineers have for the first time used a computer model to relate specific genetic mutations to exact variations of a disease. This is the first model-based system for predicting phenotype (function of the cell or organism) based on genotype (an individual's DNA).
In the study, published in Genome Research (Vol. 12, Issue 11, 1687-1692, November 2002), Bernhard Palsson and his team at UCSD's Jacobs School of Engineering reviewed genetic information from patients who have an enzyme deficiency that causes hemolytic anemia. Physicians have recorded some 150 DNA sequence variations that could be involved in this type of anemia. By inserting the specific DNA sequences into a computer model for red blood cell metabolism, Palsson accurately predicted which mutations would result in chronic hemolytic anemia and which would cause a less severe version of the disease."
redux [06.26.02]
[requires 'free' registration]
"The ability to see the whole tumor at once in a big picture of gene expression will help scientists understand the "complicated and heterogeneous" biology of cancer, he predicts. It is becoming increasingly clear that there are as many cancers as there are individuals; the same tumor from the same individual may, at different points in time, have different expression patterns."
""Although prognosis is what grabs headlines," he said, "the progress, I have always thought, is in increasing the understanding of the nature of the disease.""
redux [06.20.02]
"Patterns of genes that are active in tumor cells can predict whether patients with diffuse large B-cell lymphoma (DLBCL) are likely to be cured by chemotherapy, scientists reported today in the New England Journal of Medicine. Researchers analyzed thousands of genes in lymphoma biopsy samples from patients with DLBCL and determined that the activity of as few as 17 genes could be used to predict patients' response to treatment. "We're able to reliably predict the survival of these patients using data from a small number of genes, indicating that this technique should be entirely manageable for routine use," said National Cancer Institute (NCI) investigator Louis M. Staudt, M.D, Ph.D., the senior author on the study."
redux [05.31.01]
"Genes have fingerprints just like fingers, which got one cancer researcher thinking.
Since the FBI uses neural networks -- a type of artificial intelligence built to imitate neuron function in the brain -- to sift through masses of computerized fingerprint data to solve crimes, why not do the same for genetic fingerprint data?"
""We trained (the neural networks) to recognize this is one cancer and this is another and this is not a cancer," Kahn said. "Eventually it learned to recognize particular features that were particular for cancer.""
"We seem to forget, sometimes, that the first researchers in AI that chosen medicine as a problem domain did so, not because of an interest in medicine, but because of an interest in diagnosis as an example of intelligent behavior. Medical diagnosis was one example (perhaps a poor one given that there are much simpler and easier models in other physical systems). Automated diagnosis has rarely interested the medical community, not because of a fear of removing the human element (we've already done that with our reimbursement system) or of replacing humans with machines but, more simply, because diagnosis (as most people view it), is not really the problem. Most clinicians manage some form of diagnosis and most patients are treated appropriately. What is needed is better information on the utility of information and the means to obtain it which least stresses the system."