Catalyzing Inquiry at the Interface of Computing and Biology (2005) / Chapter Skim
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2 21st Century Biology
2 21st Century Biology
Pages 23-34
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From page 23... ...
Biological researchers have long sought to 23
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From page 24... ...
However, in the last half-century, an intellectual perspective provided by molecular biology and biochemistry has served as the basis for enormous leaps forward. 2.1.2 Molecular 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)
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From page 25... ...
With molecular biology, some of the underlying mechanisms of life have been identified and analyzed quantitatively. The effort to uncover the basic chemical features of biological processes and to ascertain all aspects of the components by way of experimental design will continue to be a major aspect of basic biological research, and much of modern biology has sought to reduce biological phenomena to the behavior of molecules.
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From page 26... ...
In short, knowing the complete sequence of base pairs in a genome is like knowing the complete sequence of 1s and 0s that make up a computer program: by itself, that information does not necessarily yield insight into what the program does or how it may be organized into functional units such as subroutines.4 A third illustration of biological complexity is that few, if any, biological functions can be assigned to a single gene or a single protein. Indeed, the unique association between the hemoglobin molecule and the function of oxygen transport in the bloodstream is by far the exception rather than the rule.
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From page 27... ...
Complexity, then, appears to be an essential aspect of biological phenomena. Accordingly, the development of a coherent intellectual approach to biological complexity is required to understand systems-level interactions -- of molecules, genes, cells, organisms, populations, and even ecosystems.
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Although deciphering the various cellular regulatory networks is a huge challenge in itself, systems biology ultimately has to deal as well with how cells organize themselves into tissues, organs, and the whole organism. One group that is trying to lay the groundwork for such an effort is the Physiome Project at the University of Auckland in New Zealand.
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From page 29... ...
, systems biology aims to understand the mechanisms of a living organism across all relevant levels of hierarchy.8 These different foci -- a focus on components of biological systems versus a focus on interactions among these components -- are complementary, and both will be essential for intellectual progress in the future. Twenty-first century biology will bring together many distinct strands of biological research: taxonomic studies of many species, the enormous progress in molecular genetics, steps towards understanding the molecular mechanisms of life, and an emerging systems biology that will consider biological entities in relationship to their larger environment.
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From page 30... ...
All told, 21st century biology will entail a broad spectrum of research, from laboratory work directed by individual principal investigators, to projects on the scale of the human genome that generate large amounts of primary data, to the "mesoscience" in between that involves analytical or synthetic work conducted by multiple collaborating laboratories. For the most part, these newer research strategies involving discovery science and analytical work will complement rather than replace the traditional, relatively small laboratory focusing on complementary empirical and experimental methods.
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From page 31... ...
For life sciences ranging from ecology, botany, zoology, and developmental biology to cellular and molecular biology -- all of which can be characterized as science with diverse data types and high degrees of data heterogeneity and hierarchy -- IT is essential to collect key information and organize biological data in methodical ways in order to draw meaningful observations. Massive computing power, novel modeling approaches, new algorithms and mathematical or statistical techniques, and systematic engineering approaches will provide biologists with vital and essential tools for managing the heterogeneity and volume of the data and for extracting meaning from those data.
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Furthermore, the uniqueness and historical contingency of life means that for population-scale problems, the potential state space that the population actually inhabits is huge.13 As an information science, the life sciences use computing and information technology as a language and a medium in which to manage the discrete, asymmetric, largely irreducible, unique nature of biological systems and observations. In the words above, those even marginally familiar with the history of biology will recognize hints of what was once called theoretical biology or mathematical biology, which in earlier days meant models and computer simulations based on such then-fashionable ideas as cybernetics and general systems theory.14 The initial burst of enthusiasm waned fairly quickly, as it became clear that the available experimental data were not sufficient to keep the mathematical abstractions tethered to reality.
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2.3.4 A Computational Perspective on Biology Coming to grips with the complexity of biological phenomena demands an array of intellectual tools to help manage complexity and facilitate understanding in the face of such complexity. In recent years, it has become increasingly clear that many biological phenomena can be understood as performing information processing in varying degrees; thus, a computational perspective that focuses on information abstractions and functional behavior has potentially large benefit for this endeavor.
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From page 34... ...
Just as the invention of the microscope extended biological inquiry into new arenas and enlarged the scope of questions that were reasonable to ask in the conduct of biological research, so will the computer. Computing and information technology will enable biological researchers to consider heretofore inaccessible questions, and as the capabilities of the underlying information technologies increase, such opportunities will continue to open up.
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