Category Archives: Essays

The End of the Beginning

In the late 1800’s, physicists thought that the problems of physics had been mostly solved. After all, Newton’s laws described the motion of ordinary objects, Maxwell’s equations explained electricity and magnetism, and thermodynamics detailed the relationship between forms of energy. But that view of the world soon changed as special and general relativity altered our views of space, time, and gravitation; statistical mechanics provided a stochastic basis for understanding bulk properties of matter; and quantum mechanics blurred the lines between particles and waves, matter and energy. The biological sciences are entering a similar phase of transition between what was and what will be our view of the world and the way it operates. The Human Genome Project has been long heralded as the means to understanding how we as beings carry on the biological processes we need to survive. Sure, if you read the papers you know that the genome sequencing has been declared finished—but we have a long way to go before the promise of the genome project is complete.
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Systems Biology

Systems Biology1
Over a half-century ago, the renowned (and eccentric)2 mathematician, Norbert Wiener, suggested that living organisms be viewed as systems governed by feedback control.3 Wiener attempted to found a new discipline—“cybernetics�—for the study of such systems. In spite of Wiener’s impassioned proselytization on behalf of the new discipline, cybernetics didn’t amount to much. It generated some excitement in the social sciences in the 1950s4 and then fizzled out. Engineers occasionally referred to cybernetic concepts (especially feedback) but that’s about it. In biology, especially in the emerging field of molecular biology, cybernetics proved to be a disaster.5 Strangely, at the beginning of the twenty-first century, Wiener’s vision has returned with a vengeance.
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Metabolomics

The central achievement of the genomics revolution in biology arguably lies in the mapping and sequencing of the human genome and the generation of the fine haplotype maps that are being used to study human diversity. While this is an amazing accomplishment that will likely pay dividends for years, the genome’s sequence itself has taught us little that has immediate applicability in human health. This was clearly anticipated by some, who reflected that knowing the sequence of a 10 kB virus did little to immediately curb the AIDS epidemic, nor did identification of the gene for Huntington’s disease lead immediately to a cure for that disease. In both cases, however, great strides have been made, and these great strides have followed from the integration of genomics data with data from other areas, including studies of gene expression (mRNA and protein) and general biochemistry and cell biology studies.
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Applying Hypothesis-Driven Science to Post-Genomics

We are living in the era of ‘data dumps’ in the post-genomic era. How does one go about sorting out the massive amount of scientific information, extracting what is useful and putting it to work to benefit our health, our environment and the food we eat to keep us healthy?

Imagine all this data as construction material for building a bridge to the answers of many of the questions we have been asking about physiology and metabolism for decades. The data is varied and diverse and in many instances in a code that we have to unravel. There is no biometrics for many of the tools in the toolbox in the post-genomic era; how do we keep up with the ever-accelerating technology being developed as state-of-the-art when within two years the technology might already be primitive or have shown to be unreliable?
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