Theoretical biology/Addendum

Biologists' comments on the province of theoretical biology

Professor Richard Gordon, President of the Canadian Society for Theoretical Biology, writes:

The theoretical biologist delves deeply into all the data available, comes up with unexpected relationships, tries to quantify them using all the tools of reason (math, logic, computers, etc.), and makes specific predictions about the outcome of future experiments and observations. Sometimes a critical experiment would never have been done without the inspiration of your theory in the first place.

Biophysicist and mathematical biologist Marc Mangel, in his 2006 book The Theoretical Biologist’s Toolbox, elaborates on Professor Gordon's brief description of theoretical biology:

Theoretical biology begins with the natural world, which we want to understand. By thinking about observations of the world, we begin to conceive an idea about how it works. This is theory, and may already lead to predictions, which can then flow back into our observations ot the world. The idea about how the world works can also be formalized using mathematical models that describe appropriate variables and processes. The analysis of such models then provides another level of predictions which we can take back to the world (from which new observations may flow). In some cases, analysis may be insufficient and we choose to implement our models using computers through programming (software engineering). These programs then provide another level of prediction, which can also flow back to the models or to the natural world.

In describing their research program, the Biospheric Theory and Modeling group of the Max-Planck-Institut für Biogeochemie highlight many of the main approaches and advantages of theoretical biology:

Our research aims to identify the general organizing principles of the biosphere in order to better understand and predict its interactions with biogeochemical cycles and the climate system….Our view of biospheric theory….is that the development of theory goes hand in hand with observations, which serve as a reality check for the theory, as well as inspiration for more precise research questions. The precise research questions in return can be used to streamline the experiments and measurement campaigns to allow new insights. As the theory develops, models become helpful for understanding the implications of the theory and for rejecting unrealistic assumptions or formulating new research questions. Conceptual models are particularly helpful for determining similarities or incompatibilities between different theories. Emergence-based models are useful for linking small-scale processes with large-scale effects, while Optimality-based models are useful for making reproducible predictions directly at the scale of interest.... Theoretical concepts help us to formulate hypotheses how the biosphere should function and respond to change. We work on several concepts, such as optimality, multiple steady states, and pattern formation.

In summary, observational checks of theory, inspiring more precise questions, leading to better experiments, with modeling to test assumptions, leading to new questions and revised theories: a systems biology approach. Most biologists will recognize themselves as theoretical biologists on some level and at some times.

In their 2003 book on the organization of organismal form, Gerd B. Müller and Stuart A. Newman stress the breadth of the field and its applicability beyond mathematical biology:

heoretical biology is firmly rooted in the experimental biology movement of early twentieth-century Vienna. Paul Weiss and Ludwig von Bertalanffy were among the first to use the term theoretical biology in a modern scientific context. In their understanding the subject was not limited to mathematical formalization, as is often the case today, but extended to the general theoretical foundations of biology. Their synthetic endeavors aimed at connecting the laws underlying the organization, metabolism, development, and evolution of organisms….A successful integrative theoretical biology must encompass not only genetic, developmental, and evolutionary components, the major connective concepts in modem biology, but also relevant aspects of computational biology, semiotics, and cognition, and should have continuities with a modern philosophy of the sciences of natural systems.

Geneticist and Nobel laureate, Sydney Brenner, discusses his views of theoretical biology in the 21st century, emphasizing the need for a theoretic framework based on living systems as “information processing machines”:

The databases of [genome] sequence information are now growing at an immense rate and the number and productivity of biological researchers has also vastly increased. There seems to be no limit to the amount of information that we can accumulate, and today, at the end of the millennium, we face the question of what is to be done with all of this information….Writing in the last months of this millennium, it is clear that the prime intellectual task of the future lies in constructing an appropriate theoretical framework for biology….Unfortunately, theoretical biology has a bad name because of its past. Physicists were concerned with questions such as whether biological systems are compatible with the second law of thermodynamics and whether they could be explained by quantum mechanics….There have also been attempts to seek general mathematical theories of de¬velopment and of the brain: the application of catastrophe theory is but one example. Even though alternatives have been suggested, such as computational biology, biological systems theory and integrative biology, I have decided to forget and forgive the past and call it theoretical biology….But none of [physics and chemistry] captures the novel feature of biological systems: that, in addition to flows of matter and energy, there is also the flow of information. Biological systems are information-processing machines and this must be an essential part of any theory we may construct….I believe that this is what we should be trying to do in the next century. It will require theoretical biology.[italics added]

In describing the aims of the Dutch journal of theoretical biology, Acta Biotheoretica, Thomas A. C. Reydon and Lia Hemerik illustrate the Dutch perspective on theoretical biology:

In this understanding, theoretical biology is seen as encompassing the entire spectrum of theoretical investigation of the living world, ranging from philosophy of biology to mathematical biology. Consequently, the process of biological theory formation in the journal is allowed to range from purely verbal argumentation to the mathematical analysis of biological theory.

One can appreciate to some extent the broad range of topic categories published by theoretical biologists in Acta Biotheoretica from the Table of Contents shown in the cited reference to the Current Themes book by Reydon and Hemerik.. As theoretical biology transcends national boundaries, those topic categories qualify as representative of the field.

Encyclopedia summaries of theoretical biology

The Encyclopedia Britannica has no entry for theoretical biology, but NationMaster Encyclopedia, emphasizing that the theoretical biologist’s product is a model or theory, whether reached through the use of mathematical or computational tools, or through other means, and listing many of the biological areas of study in which theoretical biologists contribute:

The ultimate goal of the theoretical biologist is to explain the biological world using mainly mathematical and computational tools, though not necessarily. Though it is ultimately based on observations and experimental results, the theoretical biologist's product is a model or theory, and it is this that chiefly distinguishes the theoretical biologist from other biologists….Theoretical biology is an Interdisciplinary work is that which integrates concepts across different disciplines. New disciplines have arisen as a result of such syntheses…Many separate areas of biology fall under the concept of theoretical biology, according to the way they are studied. Some of these areas include:

-animal behavior –biorhythms –cell biology –complexity of biological system –ecology –enzyme kinetics –evolutionary biology –genetics –immunology –membrane transport –microbiology –molecular structure –morphogenesis –physiological mechanisms –systems biology –origin of life –neurobiology -computational neuroscience

References and notes cited in text

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