Uncertainty in Nature's Protein and Cellular Dance of Life (Arnold Goodman, organizer)
Arnold F. Goodman (UC Irvine)
BioInformatics of DNA-RNA-Protein Processes: Uncertainty, a Flow Model and Collaborations
Friday 4:00-5:30, Fountain III
Abstract:
Elizabeth Pennisi [1] posed four essential question areas within Science's 125th Anniversary Issue, and we introduce novel contributions toward resolving the first, second and fourth question areas. "Why Do Humans Have So Few Genes?" "What Determines Species Diversity?" "How Did Cooperative Behavior Evolve?" "How Will Big Pictures Emerge from a Sea of Biological Data?
Paul H. Silverman had raised similar questions in "Rethinking Genetic Determinism" [2]. He not only questioned the biological dogma of molecular determinism, but also described the need for it to be expanded into a much more valid and reliable representations of reality. In addition, he strongly believed scientific progress would depend on exploring those uncertainties in molecular differences that influence organismal variability, and on a "wide-angled view" of cell behavior.
"The Uncertain Future for Central Dogma" [3] then proposed uncertainty as an influential partner of determinism and reductionism (another faulty dogma) in representing behavior of the cell, as well as understanding its cascading and complex processes. It also introduced our new process-flow model for the cellular life-cycle from DNA through RNAs to proteins, and beyond to regulation.
Molecular biology is at a crossroads similar to the one faced by quantum physics in 1925-1926. The existing dogmas, "that waves are particles and that particles are waves", could no longer be reconciled with experimental reality, despite a "miracle" of "beautiful mathematical formalism" [4].
Max Born and Werner Heisenberg, his student, creatively proposed uncertainty as the missing link between these dogmas and experimental reality [5]. No less physicists than Einstein, Planck and Schrdinger were on the wrong side of science, opposing uncertainty to the end of their lives.
According to Born and Heisenberg, the best physics can do at the subatomic level is to specify a given outcome's probability distribution, which is determined by its governing physical laws. Is it realistic for us to anticipate biological processes differing significantly at the molecular level?
Both molecular biology and subatomic physics are driven by natural processes which are repeated an enormous number of times. Even a process outcome having miniscule probability will occur with a meaningful likelihood, when its process is repeated over and over continually. Democritus observed centuries ago, "Everything existing in the universe is the fruit of chance and necessity."
This complex problem was solved by successful collaboration across both nations and disciplines. Collaboration will be critical to solving most significant and complex multidisciplinary problems. The "what to do" and "how to do it" essentials of collaboration are described in substantial detail.
References:
[1] Elizabeth Penissi, "Why Do Humans Have So Few Genes?", "What Determines Species Diversity?", "How Did Cooperative Behavior Evolve?" and "How Will Big Pictures Emerge from a Sea of Biological Data?", Science 309 (5731): 80, 90, 93 and 94, July 1, 2005.
[2] Paul H. Silverman, "Rethinking Genetic Determinism", The Scientist 18(10): 32-33, May 24, 2004.
[3] Arnold F. Goodman, Claudia. M. Bellato and Lily Khidr, "The Uncertain Future for Central Dogma", The Scientist 19(12): 20-21, June 20, 2005.
[4] Roger Penrose, The Road to Reality, Alfred Knopf, 2005.
[5] Nancy Thorndike Greenspan, The End of the Certain World, Basic Books, 2005.