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{bio,medical} informatics

Monday, July 31, 2000

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HMS Beagle Adding up mutations
[requires 'free' registration]
"A new mathematical model shows that competition for food among a small group of animals can lead to “synergistic epistasis.” This is a genetic interaction in which the negative effects of a deleterious mutation are more pronounced in a genome that has other harmful mutations. The authors note that similar models could demonstrate synergy stemming from competition for other resources besides food. Territory is one example. Furthermore, the approach might be applied to other sources of fitness variation aside from mutations.

Reference: Peck, J.R. and Waxman, D. 2000. Mutation and sex in a competitive world. Nature 406(6794):399-404."
redux [04.25.00]
UniSci Selfish Gene Theory Of Evolution Called Fatally Flawed
"In the current issue of Advances in Complex Systems (February-April), Dr. Yaneer Bar-Yam, president of the New England Complex Systems Institute and an expert on the application of mathematical analysis to complex systems, contends that the selfish-gene theory of evolution is fatally flawed.

If his mathematical proof gains general acceptance, it will shut the door on controversial "gene-centered" views of evolution.

Bar-Yam, in the upcoming article, proves that the "selfish gene" approach is not valid in the general case. He demonstrates that the gene-centered view, expressed in mathematical form, is only an approximation of the dynamics actually at work."

"The key to Bar-Yam's analysis lies in recognizing three levels of structure in nature: the gene, the organism and the group (or network) of organisms."

redux [04.05.00]
HMS Beagle Are Computers Evolving in Biology?
[requires 'free' registration]
"I suspect that although the new enthusiasm for computers in biology is genuine, it overlooks some basic problems in implementation. The basic difficulty, as I see it, is that although biologists use computers, they do not trust everything that comes out of them. It is one thing to use them to print up nice-looking graphs, but it is an entirely different matter to use them to think better."

"Francis Crick was once quoted as saying that no biologist had ever made a discovery using a mathematical model. I would reply that no biologist has ever made a discovery by running an electrophoretic gel. They make discoveries by using their brains. Computers, like all scientific tools, are only as good as the person who uses them. If biologists don't understand how computer models are constructed, they won't know their strengths and limitations. Without some foundation of trust, biologists will be unlikely to utilize or accept this powerful method of data analysis."

redux [02.24.00]
Science Revealing Uncertainties in Computer Models
[summary - can be viewed for free once registered]
"Computer simulations give the impression of precision, but they are founded on a raft of assumptions, simplifications, and outright errors. New tools are needed, scientists say, to quantify the uncertainties inherent in calculations and to evaluate the validity of the models. But making uncertainties evident is a tough challenge, as evidenced by several recent workshops.”

[ 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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