{bio,medical} informatics
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The Scotsman
Gene for nurture reasserts itself in who humans are
"Increasingly, scientists are now unravelling the full extent of the influence of our genes and breakthroughs seem to come thick and fast: a gene for fear, one for depression, another for creativity.
But those who believe these headline-making discoveries are triumphs for supporters of the nature side of the argument should think again.
What makes us who we are is far more complex and the study of "epigenetics" - the way genes are expressed - has thrown up evidence that being cuddled as a young child, what you eat, what the weather is like and even who are your friends can change the way your genes behave.
And it would appear some of these altered genes are passed on to future generations with a range of studies emerging to support the idea.
"What we eat may influence our health by changing specific genes, researchers believe.
Several studies in rodents have shown that nutrients and supplements can change the genetics of animals by switching on or off certain genes."
redux [08.18.05]
"The more we learn about the human genome, the less DNA looks like destiny.
As scientists discover more about the "epigenome," a layer of biochemical reactions that turns genes on and off, they're finding that it plays a big part in health and heredity.
By mapping the epigenome and linking it with genomic and health information, scientists believe they can develop better ways to predict, diagnose and treat disease."
redux [07.02.04]
[requires 'free' registration]
"In a written commentary, evolutionary biologist Massimo Pigliucci said that Ruden's experiment was "one of the most convincing pieces of evidence that epigenetic variation is far from being a curious nuisance to evolutionary biologists." Pigluicci doesn't go so far as to say that the heritable changes caused by Hsp90 alterations are Lamarckian, but Ruden does. "Epigenetics has always been Lamarckian. I really don't think there's any controversy," he says.
Not that Mendelian genetics is wrong; far from it. The increased understanding of epigenetic change and the recent evidence indicating its role in inheritance and development doesn't give epigenetics greater importance than DNA. Genetics and epigenetics go "hand in hand," says Ohlsson. In the case of disease, says Reik, "there are clearly genetic factors involved, but there are also other factors involved. My suspicion is that it will be a combination of genetic and epigenetic factors, as well as environmental factors, that determine all these diseases.""
redux [10.07.03]
"The Human Epigenome Project will look for patterns in our "life code" that are associated with gene regulation but are also implicated in causing disease."
"Researchers at Epigenomics AG in Berlin and the Sanger Institute in Cambridge will take part in the five-year study."
"The announcement follows the completion of an HEP pilot project that studied methylation patterns within the Major Histocompatibility Complex in chromosome 6 to determine the methylation status of over 100,000 sites. Data from the pilot study, which was funded by the European Union, was released today on the HEP's website."
"The methylation data will be integrated with the human genome sequence using the Ensembl interface and publicly released at www.epigenome.org and at www.sanger.ac.uk/epigenome."
redux [10.06.03]
[requires 'free' registration]
"With the help of some fat yellow mice, scientists have discovered exactly how a mother's diet can permanently alter the functioning of genes in her offspring without changing the genes themselves."
"The research is a milestone in the relatively new science of epigenetics, the study of how environmental factors like diet, stress and maternal nutrition can change gene function without altering the DNA sequence in any way."
redux [09.13.01]
[requires 'free' registration]
"The term was introduced by Conrad H. Waddington in 1942.1 To paraphrase an erudite epistolary exchange in Science, he is said to contrast genetics with epigenetics , the study of the processes by which genotype gives rise to phenotype. In 1942 we had barely any clue as to what those processes are, so "epigenetic" had no connotation of the underlying chemical mechanism, whatever it was that modulated cell differentiation.
In 1994, as cited in the same issue of Science, Robin Holliday voiced a commonly apprehended drift in meaning, and redefined epigenetic as "Nuclear inheritance which is not based on differences in DNA sequence." These two memes are freely circulating and can cause muddle or mischief mainly when they recombine, namely when epigenetic-H is automatically applied to epigenetic-W."
"This neology of nucleic, epinucleic, extranucleic, has attracted few followers, I think largely because so few people had really thought through the distinctions. There is much merit in Ben Johnson's caution about unbridled proliferation of terms: "A man coins not a new word without some peril, and less fruit; for if it happen to be received, the praise is but moderate; if refus'd, the scorn is assur'd." But is a polysemy to be preferred, with thought-muddling as a further peril?"
redux [08.16.01]
[ summary can be viewed for free once registered ]
"Some of the weirdest genetic phenomena have very little to do with the genes themselves. True, as the units of DNA that define the proteins needed for life, genes have played biology's center stage for decades. But whereas the genes always seem to get star billing, work over the past few years suggests that they are little more than puppets. An assortment of proteins and, sometimes, RNAs, pull the strings, telling the genes when and where to turn on or off."
""The unit of inheritance, i.e., a gene, [now] extends beyond the sequence to epigenetic modifications of that sequence," explains Emma Whitelaw, a biochemist at the University of Sydney, Australia."
""[Epigenetic effects] give you a mechanism by which the environment can very stably change things," says Rudolph Jaenisch, a developmental biologist at the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts. Researchers are hoping to harness these effects to design drugs that correct cancer and other diseases brought on by gene misregulation."
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."
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The Sunday Times
Google turns its search power to the hunt for genetic drugs
"SERGEY BRIN and Larry Page have ambitious long-term plans for Google’s expansion into biology and genetics through the fusion of science, medicine and technology."
"Over dinner and plenty of wine in February, Brin discussed the prospects for genetics with Craig Venter, the maverick biologist who decoded the human genome.
Despite millions of dollars in funding and thousands of hours of computing time from America’s federal Department of Energy, Venter needed more help to unlock the molecular mysteries of life. It seemed to him that Google’s mathematicians, scientists, technologists, and computing power had the potential to vault his research forward. He pressed Brin hard to get Google involved."
"Not long after the dinner, Brin and Page teamed up with Venter."
redux [11.08.05]
"By the end of next year, Google intends to open an engineering center in the Valley that will employ 600. The company has said it wants to be in a place with a strong quality of life for its employees, with access to public transportation and amenities."
"Downtown Phoenix offers perfect geography, housing and the public transit amenities that Google wants, said John Chan, deputy director of the downtown development office."
"Downtown is the Valley’s financial center and it also has a growing cluster of biotechnology companies. That may interest Google, since the company is said to be intrigued by bioinformatics, the use of computers to characterize the molecular components of living things."
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PLoS Computational Biology
Bioinformatics Education—Perspectives and Challenges
"Education in bioinformatics has undergone a sea change, from informal workshops and training courses to structured certificate, diploma, and degree programs—spanning casual self-enriching courses all the way to doctorate programs. The evolution of curriculum, instructional methodologies, and initiatives supporting the dissemination of bioinformatics is presented here.
Building on the early applications of informatics (computer science) to the field of biology, bioinformatics research entails input from the diverse disciplines of mathematics and statistics, physics and chemistry, and medicine and pharmacology. Providing education in bioinformatics is challenging from this multidisciplinary perspective, and represents short- and long-term efforts directed at casual and dedicated learners in academic and industrial environments. This is an NP-hard problem."
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Guardian Unlimited
Keep science off web, says Royal Society
"The Royal Society, Britain's national academy of science, yesterday joined the debate about so-called open access to scientific research, warning that making research freely available on the internet as it is published in scientific journals could harm scientific debate.
The Royal Society fears it could lead to the demise of journals published by not-for-profit societies, which put out about a third of all journals. "Funders should remember that the primary aims should be to improve the exchange of knowledge between researchers and wider society," The Royal Society said."
"A spokesman for the Royal Society said: "We think it conceivable that the journals in some disciplines might suffer. Why would you pay to subscribe to a journal if the papers appear free of charge?""
redux [10.18.05]
"PLoS Clinical Trials, a new online journal, will be launched next spring to report results of all randomized controlled clinical trials on humans in all medical and public-health disciplines, its sponsor said Monday."
"PLoS will charge a publication fee to authors to offset the journal's costs, but the fee will be waived for authors with insufficient funds, the library said in a statement."
"Dr. Catherine DeAngelis, editor-in-chief of the Journal of the American Medical Association, said the entire scientific community is concerned about getting research information into the public domain.
"I think the idea of getting things out there is fine," DeAngelis told UPI, "but I'd like to see the (journal's) business plan. I think they will find this is a more expensive proposition than they thought.""
redux [09.28.05]
"IT USED to be so straightforward. A team of researchers working together in the laboratory would submit the results of their research to a journal. A journal editor would then remove the authors' names and affiliations from the paper and send it to their peers for review. Depending on the comments received, the editor would accept the paper for publication or decline it. Copyright rested with the journal publisher, and researchers seeking knowledge of the results would have to subscribe to the journal.
No longer. The internet—and pressure from funding agencies, who are questioning why commercial publishers are making money from government-funded research by restricting access to it—is making free access to scientific results a reality. This week, the Organisation for Economic Co-operation and Development (OECD) issued a report describing the far-reaching consequences of this. The report, by John Houghton of Victoria University in Australia and Graham Vickery of the OECD, makes heavy reading for publishers who have, so far, made handsome profits. But it goes further than that. It signals a change in what has, until now, been a key element of scientific endeavour."
redux [08.15.05]
"Now, after a study that sent reverberations through the medical profession by finding that almost one-third of top research articles have been either contradicted or seriously questioned, some specialists are calling for radical changes in the system."
In advance of a world congress on peer review next month in Chicago, these specialists are suggesting that reviewers drop their anonymity and allow comments to be published."
""It would be lovely to start anew and to set up a trial of peer review against no peer review," Rennie said. "But no journal is willing to risk it.""
redux [06.25.04]
[requires 'free' registration]
"More than money and success is at stake. Free and widespread distribution of new research has the potential to redefine the way scientific and intellectual developments are recorded, circulated and preserved for years to come.
"Society pays for science," said Dr. Nicolelis, whose article in the October issue of PLoS got worldwide attention. "We have the technology, we have the expertise. Why is it that the only thing that has remained the same for 50 years is the way we publish our results? The whole system needs overhaul.""
redux [11.22.03]
"Science's Rocky-style publishing battle starts its second round Monday when a groundbreaking journal releases its latest issue.
The challenger, the upstart Public Library of Science: Biology, packed a strong punch last month with its first issue, which featured a headline-grabbing report of monkeys getting brain implants to control robot arms. The upcoming issue spotlights newly discovered genes for obesity and osteoporosis."
redux [10.14.03]
"There are lots of scientific journals, and the debut of another one normally would not raise many eyebrows.
But yesterday's online launch of Public Library of Science Biology drew so many curious browsers -- half-a-million Web hits in the first eight hours -- that the swamped site had to divert many to a backup site."
"Led by heavyweights such as Nobel laureate Harold Varmus, former director of the National Institutes of Health, the PLoS project aims to shake up the world of scholarly publishing by freely sharing its monthly contents."
redux [10.10.03]
"In the highly lucrative world of cutting-edge scientific research, it is nothing short of a revolution. A group of leading scientists are to mount an unprecedented challenge to the publishers that lock away the valuable findings of research in expensive, subscription-only electronic databases by launching their own journal to give away results for free.
The control of information on everything from new cancer treatments to space exploration is at stake, while caught in the crossfire are the world's publicly funded scientists, some of whom will soon face a choice between their career and their conscience."
redux [08.22.03]
[requires 'free' registration]
"Debate over open access to scientific articles is steadily moving into the mainstream, with the publication this month of an editorial in The New York Times, a recently introduced Congressional bill to promote open access publishing, and a television commercial sponsored by the Public Library of Science (PLoS), a California-based group that plans to launch an open-access journal in October.
As enthusiasm grows, however, some skeptics wonder whether open-access journals will succeed financially, since they charge relatively small "article processing fees," paid upfront by the researcher, instead of substantial fees for institutional library subscriptions."
redux [07.01.03]
""It's ridiculous," Eisen said in this voice during a recent phone interview from Washington. "All these things we're so used to doing with information on the Internet, we're preventing clever entrepreneurial people from doing with works of science. The idea that a narrow profit motive would prevent the dissemination of this information -- it's insane!"
Eisen was in Washington to lend his support to a congressional effort he believes will make scientific publishing less insane and less ridiculous. Most scientific journals -- such as Science, Nature or the New England Journal of Medicine -- require researchers to turn over all rights to the reports selected for publication; the publications then charge institutions and individuals subscription fees to view these reports, a model that Eisen believes inhibits scientific progress. The approach is especially galling, Eisen says, when you consider that a great deal of the money that funds the research published in these journals comes from the federal government. The public is paying for science that it never gets to see, he says."
redux [12.16.02]
[requires 'free' registration]
"A group of prominent scientists is mounting an electronic challenge to the leading scientific journals, accusing them of holding back the progress of science by restricting online access to their articles so they can reap higher profits.
Supported by a $9 million grant from the Gordon and Betty Moore Foundation, the scientists say that this week they will announce the creation of two peer-reviewed online journals on biology and medicine, with the goal of cornering the best scientific papers and immediately depositing them in the public domain."
redux [11.15.02]
"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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Guardian Unlimited
Don uses DNA to trace Christmas past
"The world's leading genetic expert is conducting research to try to find England's own "Father Christmas".
Professor Bryan Sykes, professor of human genetics at Oxford University, is appealing to men with the "Christmas" surname to come forward to take part in his unique study."
""Perhaps we will find our original Father Christmas did have a white beard and give presents to children."
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News.Com
Grid to take on AIDS
"The World Community Grid, counted among the top 10 supercomputers in the world, will work with the La Jolla, Calif.-based Scripps Research Institute in designing new therapeutic tools to counter HIV, the fast-mutating virus that causes AIDS, IBM said Monday.
The initiative, dubbed FightAIDS@Home, will draw idle computing power from more than 170,000 computers.
"The computational challenges in approaching this problem are the vast number of possible mutations that may occur, and the huge number of possible chemical compounds that might be tested against them," Dr. Arthur J. Olson, Anderson Research Chair Professor of the Scripps Department of Molecular Biology said in a statement. "The new World Community Grid project will run millions upon millions of docking computations to evaluate potential interactions between compounds and mutant viral proteins.""
redux [09.14.03]
[requires 'free' registration]
"This fall, distributed computing will take a step forward when its largest project, SETI@home (short for Search for Extraterrestrial Intelligence), introduces a software program named for its University of California origins: Berkeley Open Infrastructure for Network Computing, or Boinc."
"The University of Maryland's Center for Bioinformatics and Computational Biology plans to use Boinc next spring for a project analyzing DNA sequence data to investigate molecular evolution, particularly of bacteria that cause tuberculosis and leprosy. The project provides opportunities for many people to contribute to scientific research in ways other than through their taxes," said Michael P. Cummings, a visiting associate professor at the center."
redux [10.23.02]
"Scientists at Stanford University have demonstrated tangible proof that scientific experiments can be conducted using thousands of low-end PCs wrangled together into loosely linked networks.
A group of chemists, including Stanford assistant professor Vijay Pande, said they successfully predicted the folding rate of a protein using calculations worked out on a so-called distributed computing network. Their research, conducted last year, was published this week in the science journal Nature."
redux [04.04.01]
[requires 'free' registration]
"Intel is providing equipment and software downloads for a project in which volunteers are donating spare home computer cycles to a Stanford University project studying the protein-folding process. The project, Folding@Home, was the first to model successfully a complete protein fold - a task not even achieved by supercomputers."
""We want to increase the value of the PC," said Scott Griffin, Intel's program manager. "The PC is there when people aren't at it, like when they are in meetings. A great thing about this is you get every day users involved in research that they care about. Not only do they get to help out, but they get to help cure these terrible diseases.""
redux [09.23.01]
"IBM is spending $100 million building the world's fastest supercomputer to do cutting-edge medical research, but a distributed computing effort running on ordinary PCs may have beaten Big Blue to the punch.
IBM's proposed Blue Gene , a massively parallel supercomputer, in hopes to help diagnose and treat disease by simulating the ultra-complex process of protein folding.
"But Folding@Home , a modest distributed computing project run by Dr. Vijay Pande and a group of graduate students at Stanford University, has already managed to simulate how proteins self-assemble, something that computers, until now, have not been able to do."
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."
"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."
"Eighty-eight percent of American households were food secure throughout the entire year in 2004, meaning that they had access, at all times, to enough food for an active, healthy life for all household members. The remaining households were food insecure at least some time during that year. The prevalence of food insecurity rose from 11.2 percent of households in 2003 to 11.9 percent in 2004 and the prevalence of food insecurity with hunger rose from 3.5 percent to 3.9 percent. This report, based on data from the December 2004 food security survey, provides the most recent statistics on the food security of U.S. households, as well as on how much they spent for food and the extent to which food-insecure households participated in Federal and community food assistance programs."
"Hunger and food insecurity have been called America’s “hidden crisis.” At the same time, and apparently paradoxically, obesity has been declared an epidemic. Both obesity and hunger (and, more broadly, food insecurity) are serious public health problems, sometimes co-existing in the same families and the same individuals. Their existence sounds contradictory, but those with insufficient resources to purchase adequate food can still be overweight, for reasons that researchers now are beginning to understand. Policymakers and the public need to better grasp this apparent paradox if our nation is to grapple with these parallel threats to the well-being of many children and adults, and avoid potentially damaging policy prescriptions arising from a mistaken belief that food insecurity and obesity cannot co-exist."
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Portland Business Journal
OSU research center undergoes change
"The Center for Gene Research and Biotechnology at Oregon State University has changed its name and its emphasis.
The center in Corvallis, which was formed in 1983, is now the Center for Genome Research and Biocomputing.
The new name reflects an ongoing revolution in the biological sciences -- the merger of biology with advanced computational science, said Jim Carrington, professor and director of the center.
"The conversion of biology into an information-based science allows much bigger and more difficult questions to be addressed," Carrington said. "In addition to research focusing on single genes and proteins, we're now studying entire genomes and populations of genomes, enabled by powerful advances in technology and computational systems. This represents a major forefront in biological research, and the center is a key part of how OSU is building leadership in this area.""
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Bio-IT World
W3C Forms Life Science Semantic Web Group
"Specifically, the Semantic Web Health Care and Life Sciences Interest Group (HCLSIG) aims to help life scientists tap the potential benefits of using Semantic Web technology by developing use cases and applying standard Semantic Web specifications to healthcare and life sciences problems."
"One area where the group will likely apply its efforts is to finding ways to make existing life science and healthcare vocabularies and ontologies work within a Semantic Web context. Making existing data Semantic Web-aware will make it easier to access, find, and share that information. And once the information is in a Semantic Web format, “people will start seeing the benefits as they will be able to stitch together data,” said Miller."
redux [05.28.02]
"The genetics revolution is generating such a gigantic glut of information that artificial intelligence may be the only way scientists will ever put it to practical use.
Inspired by an AI effort to record all of the common-sense knowledge shared among humans called Cyc, scientists have come up with a technology that can gather all of the information scientists know about an organism."
redux [09.19.01]
"Future understanding of genomic data may be severely limited unless bioinformaticists gain a better understanding of knowledge representation, according to Peter Karp, director of SRI International's Bioinformatics Research Group."
"As biological research grows more and more dependent on information technology to make sense of increasing amounts of genomic data, Karp wrote, it will be crucial for bioinformaticists to keep up with new developments in symbolic computing. "The genome revolution is increasing the need for pathway databases in the biological sciences, and similar developments will occur in other sciences. However, effective implementation of this paradigm is hampered because most biologists (and most other scientists) receive essentially no education in databases or knowledge representation."
redux [08.19.01]
"Biomedical researchers are decoding the human genome with astonishing speed, but the clinical significance of the massive volumes of data collected remains largely undiscovered. Progress requires communication and data sharing among scientists. These data may be in the form of (1) raw data, derived data, and inferences that result from computational analyses, or (2) text documents published by experts who present their conclusions in natural language. The World Wide Web provides a valuable infrastructure for enabling researchers to share the rapidly growing knowledge about biology and medicine, and a fully functional Semantic Web is necessary to support data submission and retrieval, the sharing of knowledge, and interoperation of related resources."
redux [05.10.00]
"We may rehearse this fundamental axiom of descriptive markup in terms of a classical SGML polemic: the doubly-delimited information objects in an SGML/XML document are described by markup in a meaningful, self-documenting way through the use of names which are carefully selected by domain experts for element type names, attribute names, and attribute values. This is true of XML in 1998, was true of SGML in 1986, and was true of Brian Reid's Scribe system in 1976. However, of itself, descriptive markup proves to be of limited relevance as a mechanism to enable information interchange at the level of the machine.
As enchanting as it is to contemplate the apparent 'semantic' clarity, flexibility, and extensibility of XML vis--vis HTML (e.g., how wonderfully perspicuous XML <bookTitle> seems when compared to HTML <i>), we must reckon with the cold fact that XML does not of itself enable blind interchange or information reuse. XML may help humans predict what information might lie "between the tags" in the case of <trunk> </trunk>, but XML can only help. For an XML processor, <trunk> and <i> and <booktitle> are all equally (and totally) meaningless. Yes, meaningless .
Just like its parent metalanguage (SGML), XML has no formal mechanism to support the declaration of semantic integrity constraints, and XML processors have no means of validating object semantics even if these are declared informally in an XML DTD. XML processors will have no inherent understanding of document object semantics because XML (meta-)markup languages have no predefined application-level processing semantics. XML thus formally governs syntax only - not semantics."
"With XML has come a proliferation of consortia from every industry imagineable to populate structured material with standard terms (see Appendix B). By one estimate, a new industry consortium is founded every week, perhaps one in four of which can collect serious membership dues. Rising in concert are intermediary groups to provide a consistent dictionary in cyberspace, in which each consortium's words are registered and catalogued.
Having come so far with a syntactic standard, XML, will E-commerce and knowledge organization stall out in semantic confusion?"
"How are semantic standards to come about?"
"There is an increasing demand for formalized knowledge on the Web. Several communities (e.g. in bioinformatics and educational media) are getting ready to offer semiformal or formal Web content. XML-based markup languages provide a 'universal' storage and interchange format for such Web-distributed knowledge representation. This tutorial introduces techniques for knowledge markup: we show how to map AI representations (e.g., logics and frames) to XML (incl. RDF and RDF Schema), discuss how to specify XML DTDs and RDF (Schema) descriptions for various representations, survey existing XML extensions for knowledge bases/ontologies, deal with the acquisition and processing of such representations, and detail selected applications. After the tutorial, participants will have absorbed the theoretical foundation and practical use of knowledge markup and will be able to assess XML applications and extensions for AI. Besides bringing to bear existing AI techniques for a Web-based knowledge markup scenario, the tutorial will identify new AI research directions for further developing this scenario."
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EurekAlert
'Perception' gene tracked humanity's evolution, scientists say
"A gene thought to influence perception and susceptibility to drug dependence is expressed more readily in human beings than in other primates, and this difference coincides with the evolution of our species, say scientists at Indiana University Bloomington and three other academic institutions. Their report appears in the December issue of Public Library of Science Biology."
"This report supports a growing consensus among evolutionary anthropologists that hominid divergence from the other great apes was fueled not by the origin of new genes, but by the quickening (or slowing) of the expression of existing genes."
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The New York Times
Genetic Find Stirs Debate on Race-Based Medicine
[requires 'free' registration]
"In a finding that is likely to sharpen discussion about the merits of race-based medicine, an Icelandic company says it has detected a version of a gene that raises the risk of heart attack in African-Americans by more than 250 percent."
"Dr. Kari Stefansson, the company's chief executive, said he would consult with the Association of Black Cardiologists and others as to whether to test a new heart attack drug specifically in a population of African-Americans."
"Last year a drug called BiDil evoked mixed reactions after it was shown to sharply reduce heart attacks among African-Americans, first in a general study and then in a targeted study, after it failed to show efficacy in the general population. The drug, invented by Dr. Jay N. Cohn, a cardiologist at the University of Minnesota, prompted objections that race-based medicine was the wrong approach."
redux [10.26.05]
"Gattaca, a science-fiction movie released in 1997, portrays a dystopian future in which a person's place in society is determined by an analysis of his or her DNA, and the likelihood of disease is ascertained at birth. The movie would seem to have little connection with reality -- except that an international consortium has just completed the groundwork for a version of this future. Ultimately, an individual's DNA could be decoded at an early age to spot a predisposition to illness. And here's where life improves on art: The goal will be to counter the risk of disease, not pigeonhole the person."
"And HapMap shows how differences between ethnic groups can be very subtle."
"But although the absolute differences between the various ethnic backgrounds are tiny, there are genetic trends that differ between ethnic groups. A given set of SNPs may be linked in one way in Asian populations for example, but in a different way in Europeans. Over the whole genome there are more differences between individuals than there are between ethnic groups, but such trends are still thought to be useful for targeting drugs.
Hudson stresses that not all people within an ethnic group share the same SNP pattern, so pharmaceutical companies should bear this in mind. "We would want to give a drug not based on the colour of someone's skin but based on the presence or absence of the genetic markers," he says."
redux [07.27.05]
"So, what's in it for me? That question probably crossed many minds five years ago following the news that scientists had successfully assembled the first draft of the human genome -- the genetic blueprint of a human being. The answer for most of us was ''not much."
What a difference five years can make. Today, we are witnessing a revolution in the understanding of health and disease, spurred on by the sequencing of the human genome and the subsequent creation of a map of human genetic variation. And, like most historic movements, this revolution has been given a name: personalized medicine."
"Will access to genomic technologies be equitable? Will knowledge of human genetic variation reduce prejudice or increase it? What boundaries will need to be placed on this technology, particularly when applied to enhancement of traits rather than prevention or treatment of disease? Will we succumb to genetic determinism, neglecting the role of the environment and undervaluing the power of the human spirit?"
redux [07.12.03]
[requires 'free' registration]
"Genetics increasingly shows that racial and ethnic distinctions are real -- but often fuzzy and greatly exaggerated. Genetics will increasingly show that most humans are mongrels, and it will make a mockery of racism.
"There are meaningful distinctions among groups that may have implications for disease susceptibility," said Harry Ostrer, a genetics expert at the New York University School of Medicine. "The right-wing version of this is `The Bell Curve,' and that's pseudoscience -- that's not real. But there can be a middle ground between left-wing political correctness and right-wing meanness.""
redux [05.28.03]
"Howard University officials yesterday announced plans to create the first large-scale collection of genetic profiles of African Americans, an endeavor they described as a bid for a "place at the table in genetic research" and a pathway to improved medical care for blacks."
"However, other genetics experts question the premise that the program can help as much as Howard officials say."
redux [05.13.03]
"The use--and often misuse--of genetics to explain racial and ethnic differences is, of course, nothing new. But the HapMap, together with a series of powerful genomic tools developed over the last several years, will make it possible to spell out in great detail the genetic differences between peoples from different parts of the world. Sociologists, bioethicists, and anthropologists worry that the genetic data could be manipulated to give an air of biological credence to ethnic stereotypes, to revive discredited racial classifications, and even to fuel bogus claims of fundamental genetic differences between groups."
redux [01.25.03]
"Race doesn't exist, the mantra went. The DNA inside people with different complexions and hair textures is 99.9 percent alike, so the notion of race had no meaning in science. At a National Human Genome Research Institute (NHGRI) meeting five years ago, geneticists were all nodding in agreement. Then sociologist Troy Duster pulled a forensics paper out of his briefcase. It claimed that criminologists could find out whether a suspect was Caucasian, Afro-Caribbean or Asian Indian merely by analyzing three sections of DNA.
"It was chilling," recalls Francis S. Collins, director of the institute. He had not been aware of DNA sequences that could identify race, and it shocked him that the information can be used to investigate crimes. "It stopped the conversation in its tracks.""
redux [12.20.02]
"Inuit or Basque, Laotian or Pashtun: we're much more similar than we are different, says the most detailed analysis of human genetic variation to date.
When it comes to sensitivity to drugs or diseases, the analysis also suggests that a person's account of their ethnic origin is almost as reliable an indicator as intrusive genetic tests.""
redux [11.01.02]
"In response to early concerns about racial profiling, scientists at the Human Genome Project went out of their way to downplay ethnic variations. Humans are 99.9 per cent alike, the sequencing showed, a figure that was leveraged into a call for global harmony. "The concept of race has no genetic or scientific basis," said Francis Collins, head of the Human Genome Project, at the White House ceremony to celebrate the genome completion.
Yet a great deal of controversy is now brewing over that 0.1 per cent. A growing number of scientists want to use such information as a way to find cures for devastating diseases. If we know more about the genes that cause susceptibility to cystic fibrosis in whites, or sickle cell anaemia in blacks, they argue, we will move closer to a solution for these illnesses. "Ancestry is imperative to biomedical research," says Mark Shriver, an anthropologist at Pennsylvania State University."
redux [10.30.01]
"Race should not influence drug prescriptions, warn geneticists. Genetic differences between individuals give a better indication of who will respond well to a medicine, a new study shows."
Geneticists have known this for a while. "It's no surprise that skin pigment is a lousy predictor of physiology," says Howard McLeod of Washington University School of Medicine in St Louis, Missouri. This study is the first to prove it."
redux [07.20.01]
[requires 'free' registration]
"Scientists planning the next phase of the human genome project are being forced to confront a treacherous issue: the genetic differences between human races."
"With the decoding of the human genome largely complete, government scientists are beginning to construct a special kind of genetic map that would provide a shortcut to locating the variant human genes that predispose people to common diseases."
"The question the scientists face is whether that map should chart possible differences that may emerge among the principal population groups, those of Africans, Asians and Europeans."
redux [03.18.01]
"Genetics research is demonstrating that the differences in appearance among groups are profoundly incidental, but these differences do have a genetic basis. And although it's true that all people have inherited the same genetic legacy, the genetic differences among groups have important implications for our understanding of history and for biomedical research. These complications in an otherwise reassuring story have thoroughly spooked the leaders of the public and private genome efforts. The NIH has been collecting information about genetic variants from different ethnic groups in the United States, but it has refused to link specific variants with ethnicity. Celera has been sequencing DNA from an Asian, a Hispanic, a Caucasian, and an African-American, but it, too, declines to say which DNA is which.
This strategy of avoiding the issue is almost sure to backfire. It seems to imply that geneticists have something to hide. But the message emerging from laboratories around the world should be hailed, not muzzled. It is one of great hope and promise for our species."
redux [06.11.01]
[requires 'free' registration]
"Scientists have long suspected that the racial categories recognized by society are not reflected on the genetic level.
But the more closely that researchers examine the human genome -- the complement of genetic material encased in the heart of almost every cell of the body -- the more most of them are convinced that the standard labels used to distinguish people by "race" have little or no biological meaning.""
""Ethnicity is a broad concept that encompasses both genetics and culture," Dr. Anand said. "Thinking about ethnicity is a way to bring together questions of a person's biology, lifestyle, diet, rather than just focusing on race. Ethnicity is about phenotype and genotype, and, if you define the terms of your study, it allows you to look at differences between groups in a valid way."
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Bio-IT World
What's 'Post' About Postgenomic?
"We've heard the term "postgenomic era" quite a bit over the past half-decade. Despite this, it seems that each week we hear about the publication of the genome of a new species -- a pathogenic microbe, an agricultural staple, or an obscure new species of mammal -- making it hard to imagine finding ourselves in such an era anytime soon. Nevertheless, the technology of sequencing genomes is very late '90s. What is the postgenomic era about? Bioinformatics."
"Bioinformatics has quickly become an integral part of the drug discovery process. While many algorithms and tools remain open-source and public-domain, it seems only a matter of time before we see a greater number of proprietary services. This will help define the so-called postgenomic era."
redux [05.13.04]
"Typical open source project development strategies work well for free software but don't flourish in commercial settings, according to one expert."
"Specifically, [Professor Jim Herbsleb of Carnegie Mellon University's International School of Computer Science] looked at cases where many developers from all over the world would successfully collaborate and coordinate to work on one piece of software. While looking at this, he also examined why this distributed development model has not thrived in industry. In fact, Herbsleb found that it takes companies more than twice as long to develop software in disparate locations than in one location."
redux [03.31.04]
"Australia's bioinformatics industry will increasingly rely on open source software as researchers look for inexpensive point solutions that are not just a "black box", according to delegates at an Australian Technology Park Innovations bioinformatics symposium in Sydney.
Sydney University senior lecturer in bioinformatics, Dr Bret Church, said open source is undoubtedly the founding stone of bioinformatics.
"We love it," Dr Church said. "It is made for research, and there was plenty out there when bioinformatics came along. On the way to solutions, and while exploring possibilities and avenues, open source code tends to play a leading role.""
redux [12.18.03]
"3rd Millennium wants to cash in on the software it spent seven years developing for various government and commercial clients - by giving it away free.
The Waltham, Mass.-based informatics consultancy and services firm has released its Data Centric Knowledge Management System for biotech and drug R&D under a GNU general public license (GPL)."
"The company is betting that, of those life science organizations deploying the software, some will want to buy support and maintenance contracts."
redux [11.20.02]
"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."