The Role of Theory in Advancing 21st-Century Biology Catalyzing Transformative Research (2008) / Chapter Skim
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2 The Integral Role of Theory in Biology
2 The Integral Role of Theory in Biology
Pages 25-37
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From page 25... ...
This chapter describes several different ideas about scientific theories, emphasizes the diversity of theoretical activities throughout biology, and discusses ways in which theory is integral to each specific kind of scientific activity, including experimentation, observation, exploration, description, and technology development as well as hypothesis testing. Biologists use a theoretical and conceptual framework to inform the entire scientific process, and they frequently advance theory even when their work is not explicitly recognized as theoretical.
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From page 26... ...
Scientific observation is likewise complex, although it is often thought of as no more than merely "looking." To count as observation in science, "looking" usually requires a sophisticated approach, involving instruments and elaborate protocols embedded in technical practices that frame and shape both the observations and the reports of the results (Hacking, 1983)
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From page 27... ...
Theory seems to be different and abstract, the product of purely conceptual work to formalize empirical knowledge achieved by science, rather than a living part of the material practice and process of science. Indeed, theory is often described in opposition to practice.
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From page 28... ...
However, from a scientific point of view, the two theories have equivalent goals in the sense that both seek to explain and interpret a set of facts. As Stephen Jay Gould memorably wrote (see Box 2-1)
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From page 29... ...
, while the scientific credentials of Darwin's theory continue to be doubted despite its continuing success in guiding empirical research in a wide variety of biological sciences. It is interesting that at least some physicists no longer describe physical theories in terms of "laws of nature," noting that even such a "well-tested and well-established understanding of an underlying mechanism or process," as the standard model in physics unifying strong and electroweak interactions among fundamental particles, "can never be proved to be complete and final -- that is why we no longer call it a ‘law'" (Stanford Linear Accelerator Center, 2007)
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From page 30... ...
This alternative understanding of the word captures the diverse relationships among theories, laws, hypotheses, and models in modern biology and makes it easier to see that biology is a deeply theoretical enterprise, but not one in which theory is understood in opposition to practice, experiment, or observation or focused narrowly on developing a set of master equations. Theory as Speculation The view that theory is untested speculation is often accompanied by the view that once "proved," theories turn into facts.
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From page 31... ...
Examples of important qualitative theories in biology include the circulation theory of the vascular system, the cell theory of living organization, theories of ecological succession, the impact theory of the extinction of dinosaurs, and the theory of evolution by natural selection. Whether qualitative theories such as these win silver or bronze rather than the gold of quantitative theories like Newton's or Einstein's is a matter for debate.
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From page 32... ...
Many molecular biologists and neurobiologists use diagrams to depict causal structure in their models, for example, of how transcription factors regulate gene expression or how neurons interact in brain circuits. Prior to computers, chemists often built elaborate physical models of molecular structures (for more information on modes of model representation, see de Chadarevian and Hopwood, 2004)
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From page 33... ...
Increasingly, videography is used to capture dynamic aspects of natural phenomena visually and animation can be used to display dynamic aspects of structural models. At a minimum, mathematical tools are needed to develop and use these visual display technologies, since most are computer based, and to depict empirical data stored in databases.
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From page 34... ...
. Computer models of interacting molecular networks that are being developed to understand gene regulation represent a spectrum of approximation methods: from binary state, to Boolean models, to systems of differential equations, to stochastic random models of molecular interactions, and hybrids of all these types.
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From page 35... ...
In many situations, for example, formal mathematical models can be crucial in helping investigators determine when their qualitative models actually are adequate. Biologists often come up with "word models" about processes which then are shown to be inadequate when one tries to actually implement a formal mathematical model or construct a computer algorithm.
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From page 36... ...
Quantitative approaches, from formal mathematical models, to simulations, to pattern recognition algorithms, have another very important value: By requiring logical discipline and a formal methodology, they can be a powerful tool in hypothesis development and prediction. In some instances, large data sets can themselves serve as experimental resources.
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From page 37... ...
Support for theoretical work in science, because of theory's many entry points into biological practice, may require investment in both low-risk traditional as well as high-risk radically transformative approaches, since the robustness of empirical results to the idealizing assumptions of conventional models cannot properly be evaluated without worthy alternatives to compare. This report frames a series of questions about life that cut across established disciplinary perspectives while drawing on shared principles or theories that are central to all biological subdisciplines, including basic principles of evolution (life is descended from a common ancestor and natural selection is a key mechanism of change)
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