The following HTML text is provided to enhance online
readability. Many aspects of typography translate only awkwardly to HTML.
Please use the page image
as the authoritative form to ensure accuracy.
Catalyzing Inquiry at the Interface of Computing and Biology
catalog the characteristics, behaviors, and variations of individual biological organisms or populations through the direct observation of organisms in their environments, rather than trying to identify general principles through mathematical or abstract modeling. For this reason, the culture of biology is both strongly visual and specific. Identifying a new species, and adequately describing its physical appearance, environment, and life cycle, remains a highly considered contribution to biological knowledge.
It is revealing to contrast this philosophy with that of modern physics, where the menagerie of new subatomic particles discovered in the 1960s and 1970s was a source of faint embarrassment and discomfort for physicists. Only with the introduction of quarks, and the subsequent reduction in the number of fundamental particles, did physicists again feel comfortable with the state of their field. Biology, in strong contrast, not only prizes and embraces the enormous diversity of life, but also considers such diversity a prime focus of study.
Second, biology is an ontological science, concerned with taxonomy and classification. From the time of Linnaeus, biologists have attempted to place their observations into a larger framework of knowledge, relating individual species to the identified span of life. The methodology and basis for this catalog is itself a matter of study and controversy, and so research activity of this type occurs at two levels: specific species are placed into the tree of life (or larger taxa are relocated), still a publishable event, and the science of taxonomy itself is refined.
Biology is a historical science. Life on Earth apparently arose just once, and all life today is derived from that single instance. A complete history of life on Earth—which lineage arose from which, and when—is one of the great, albeit possibly unachievable, goals of biology. Coupled to this inquiry, but separate, are the questions, How? and Why? What are the forces that cause species to evolve in certain ways? Are there secular trends in evolution, for example, as is often claimed, toward increasing complexity? Does evolution proceed smoothly or in bursts? If we were to “replay the tape” of evolution, would similar forms arise? Just as with taxonomy (and closely related to it), there are two levels here: what precisely happened and what the forces are that cause things to happen.
These three strands—empirical observations of a multitude of life forms, the historical facts of evolution, and the ordering of biological knowledge into an overarching taxonomy of life—served to define the central practices of biology until the 1950s and still in many ways affect the attitudes, training, philosophy, and values of the biological sciences. Although biology has expanded considerably with the advent of molecular biology, these three strands continue as vital areas of biological research and interest.
These three intellectual strands have been reflected in biological research that has been qualitative and descriptive throughout much of its early history. For example, empirical and ontological researchers have sought to catalog the characteristics, behaviors, and variations of individual biological organisms or populations through the direct observation of organisms in their environments.
Yet as important and valuable as these approaches have been for biology, they have not provided—and cannot provide—very much detail about underlying mechanisms. However, in the last half-century, an intellectual perspective provided by molecular biology and biochemistry has served as the basis for enormous leaps forward.
2.1.2Molecular Biology and the Biochemical Basis of Life
In the past 50 years, biochemical approaches to analyzing biological questions and the overall approaches now known as molecular biology have led to the increased awareness, identification, and knowledge of the central role of certain mechanisms, such as the digital code of DNA as the mechanism underlying heredity, the use of adenosine triphospate (ATP) for energy storage, common protein signaling protocols, and many conserved genetic sequences, some shared by species as distinct as humans, sponges, and even single-cell organisms such as yeast.
This new knowledge both shaped and was shaped by changes in the practice of biology. Two important threads of biological inquiry, both existing long before the advent of molecular biology, came