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{bio,medical} informatics

Tuesday, April 17, 2001

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find related articles. powered by google. The American Spectator A Map to Nowhere
"Imagine that an intelligence service were to discover some unintelligible messages being sent by a spy. At first the intelligence agents naturally assume they are looking at a code. They assume the task of decoding will be straightforward. But on closer analysis it turns out that the message means one thing if the signal has been received and acted upon, another thing if it has been received and not acted upon, another thing if the receiving apparatus is not switched on, and so on. Rather than just a code the message is a bit like a set of rules for a rather complex interactive game. There are feedback loops, and circuits within circuits, and a lot of things happening inside the cell but outside the genome, in the unfashionable realm of cytogenetics. NIH-funded geneticists don't even want to think about that, because they thought that by sticking to the four nucleotide bases, they had the problem neatly "digitized." Computers would hum away unaided, 24 hours a day, and unravel the mysteries for them while they slept.

We should have known that it would not be so simple."
redux [02.20.01]
find related articles. powered by google. The New York Times Humbled by the Genome's Mysteries
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"Human complexity cannot be generated by 30,000 genes under the old view of life embodied in what geneticists literally called (admittedly with a sense of whimsy) their "central dogma": DNA makes RNA makes protein — in other words, one direction of causal flow from code to message to assembly of substance, with one item of code (a gene) ultimately making one item of substance (a protein), and the congeries of proteins making a body. Those 142,000 messages no doubt exist, as they must to build our bodies' complexity, with our previous error now exposed as the assumption that each message came from a distinct gene."

"The collapse of the doctrine of one gene for one protein, and one direction of causal flow from basic codes to elaborate totality, marks the failure of reductionism for the complex system that we call biology..."
find related articles. powered by google. 1999 Pacific Symposium on Biocomputing Gene Expression and Genetic Networks
"Biology is currently undergoing a shift from a mostly qualitative to an information rich, quantitative science. Using large-scale biological technologies, we are gaining global views of structural and dynamic information in the form of whole genome sequences and the corresponding gene activity patterns at the RNA and protein level. These data reflect the molecular workings of a complex information processing system. In many ways these systems can be effectively viewed from the perspective of genetic feedback networks, given that the fundamental step of biological information flow resides in gene activation and its control through the activity of regulatory genes."

"The following sets of nine papers deals with the modeling of molecular networks, inference of functional relationships from gene activity profiles, and networks approach to structural evolution. We begin with a review by Szallasi in which he explains shy integrative approaches have been ignored in the traditional search for "dominant" molecular genetic mechanisms, and why this is no longer tenable in light of the evidence for combinatorial molecular causes for e.g. complex human diseases."

find related articles. powered by google. On Semiotic Modeling Code-Duality and the Semiotics of Nature
"Through centuries biological theories have been molded to conform to the view of nature established in classical physics. An apparently infinite succession of deep-rooted controversies bear witness to the fact, that this was not at all an easy fit. Vitalism, teleology or finalism have perpetually been called upon to account for living systems. But the authority of physics was such, that in the end those deviations from the ideal was always defeated - to reappear, nevertheless, in new disguise in the next generation.

With the birth of molecular biology and especially molecular genetics in the fifties and sixties a strange thing happened. Suddenly a new and very foreign vocabulary was introduced into biology, that of cybernetics or information theory. Terms like 'program', 'genetic code', 'information', 'messenger-RNA', 'feedback' and the like became respectable or even indispensable notions. Such terms, however, clearly played no role in the world view of classical physics.

This contradiction disappears when it is recognized that these new terms did not mean the same thing in biology as they did in general language. Facilitated by a widespread indifference to epistemological problems among biologists the concept of genetic information became for all practical purposes identified as the sum of the genes which carried it."

"We highly suspect the fruitfulness of this paradigm."
redux [02.13.00]
find related articles. powered by google. The New York Times Genome's Riddle: Few Genes, Much Complexity
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"As the modest number of human genes became apparent, biologists in both teams were forced to think how to account for the greater complexity of people, given that they seem to possess only 50 percent more genes than the roundworm. It is not foolish pride to suppose there is something more to Homo sapiens than Caenorhabditis elegans. The roundworm is a little tube of a creature with a body of 959 cells, of which 302 are neurons in what passes for its brain. Humans have 100 trillion cells in their body, including 100 billion brain cells.

Several explanations are emerging for how to generate extra complexity other than by adding more genes."

redux [10.17.00]
find related articles. powered by google. The Scientist N.Y. Panel Explores Genomics Issues
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"What can people expect from biotechnology and genomics? Ten luminaries from the biomedical arena, law, and journalism grappled with issues related to that question at the City University of New York's Graduate Center on Sept. 20. In attendance was an audience of 350 whose research, medical, and counseling careers could hinge on how such issues are resolved. Syracuse University's Gene Media Forum ( sponsored the event.

The recurring theme was biological predictability. Eric Lander, director of the Whitehead Institute Center for Genome Research, in Cambridge, Mass., noted that in the past century, biologists "worked out a disease by being clever enough to figure out what was wrong." The systematic approach of genomics, he continued, would render research largely predictable.

Panelists stressed, nevertheless, that genomics would not yield answers easily. Harold Varmus, president of Memorial Sloan-Kettering Cancer Center in New York, said that biologists were used to studying one gene at a time. Now, he added, "you've got all the parts of the clock dumped on the table, and you can look at them. But, you know, it's a lot harder to put back together, too."

A consensus emerged that much of the public--including many journalists, behavioral scientists, and physicians--either were unaware of this newfound complexity or twisted it into misguided support for genetic determinism. "

[ rhetoric ]

Bioinformatics will be at the core of biology in the 21st century. In fields ranging from structural biology to genomics to biomedical imaging, ready access to data and analytical tools are fundamentally changing the way investigators in the life sciences conduct research and approach problems. Complex, computationally intensive biological problems are now being addressed and promise to significantly advance our understanding of biology and medicine. No biological discipline will be unaffected by these technological breakthroughs.


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