TB

THEORETICAL BIOLOGY

Introduction

Books

Journals

Newsletter

Societies

Departments and Institutes

Schools

Personal websites

Other resources

It must be emphasised that theoretical biology differs from theoretical physics in that (i) it emphasises the rational treatment of diversity and complexity; (ii) it tries to combine holistic ideas with the modelling approach; and (iii) the number of relevant facts that must be taken into account is very large. Its main role can be summarized in the words of the Nobel laureate Sir Peter Medawar: "No new principle will declare itself from beneath a heap of facts." (A good recent example of this is the need to interpret the results to be expected from the Human Genome Project.) It is timely to distil from the avalanche of observations whatever general principles can be discerned.

— Eörs Szathmáry

UNDER CONSTRUCTION

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Introductory Readings

• Lewontin, The Triple Helix, 1998

• Maynard Smith, The Problems of Biology, 1986

• Williams, Adaptation and Natural Selection, 1966

Anthologies

• Goodwin/Saunders, Theoretical Biology, 1989

• Kull/Tiivel, Lectures in Theoretical Biology, 1988 [TOC]

• Ho/Saunders, Beyond Neo-Darwinism, 1984

• Waddington, Towards a Theoretical Biology (4 vols.), 1968-1972

• Waterman/Morowitz, Theoretical and Mathematical Biology, 1965

Selected monographs

• Barbieri, The Organic Codes, 2001

• Israel, La mathématisation du réel, 1996

• Williams, Natural Selection, 1992

• Thom, Apologie du Logos, 1990

• Bertalanffy, Modern Theories of Development, (1928) 1961

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• Acta Biotheoretica

[TOCs and article information]

A publication of the Prof. Dr. Jan van der Hoeven Foundation for Theoretical Biology, attached to Leiden University, the Dutch Society of Theoretical Biology, and the French Society of Theoretical Biology.

• Adaptive Behavior

• BioSystems: Journal of Biological and Information Processing Sciences

(Elsevier.) Encourages experimental, computational, and theoretical articles that link biology, evolutionary thinking, and the informationprocessing sciences. The link areas form a circle that encompasses the fundamental nature of biological information processing, computational modeling of complex biological systems, evolutionary models of computation, the application of biological principles to the design of novel computing systems, and the use of biomolecular materials to synthesize artificial systems that capture essential principles of natural biological information processing. Examples of categories and topics: molecular evolution (self-organizing and self-replicating systems; origin and evolution of the genetic mechanism); biological information processing (molecular recognition; cellular control; neuromuscular computing; biological adaptability; molecular computing technologies); evolutionary systems (stochastic evolutionary algorithms; evolutionary optimization; simulation of genetic and ecological systems; applications (neural nets, machine learning, robotics).

• Bulletin of Mathematical Biology

(Academic Press.) Devoted to research at the junction of computational, theoretical and experimental biology. With its high scientific standards and stress on clear exposition, the Bulletin is of interest to theorists and experimentalists alike. In addition to original research papers and survey articles, the Bulletin publishes extended book reviews. Every article has a biological message.

• Comments® on Theoretical Biology

A Journal of Critical Discussion of the Current Literature

(Gordon and Breach.) With the increasing amount of highly sophisticated data now being generated in almost all areas of biology, the need to organize such data into realistic mathematical models has correspondingly increased. Such models should ideally provide quantitative insight into the mode of operation of the system under investigation and serve as a guide to further experimentation. Comments® on Theoretical Biology is a journal devoted to critical discussion of areas where significant theoretical investigations are occurring. It is expected that the journal will facilitate dissemination and critical evaluation of recent theoretical analyses of biological systems ranging from the population to the subcellular level. A "Comment" is an expert guide to a particular field. Editions may contain articles on individual topics, a single topic, or reports on conferences. Contributors are by invitation of the editor, but suggestions for topics are solicited.

• Folia Baeriana

An international serial publication of Baer House (Tartu, Estonia), published by the Estonian Naturalists' Society and the Institute of Zoology and Botany.

• Journal of Biological Systems (JBS)

(Quarterly.) Promotes interdisciplinary approaches in biology and medicine. Mathematical methods and general systems theory should be brought into the study of biological situations. Solicits original research papers and survey articles in areas that include (but are not limited to):

• General systems theory: Complex systems studies; isomorphies; nonlinear dynamics; entropy; mathematical tools and systems theories with applications in biology and medicine.

• Interdisciplinary approaches: Transfer of methods from one discipline to another; integration of biological levels, from atomic to molecular, macromolecular, cellular, and organic levels; animal biology; plant biology.

• Environmental studies: Relationships between individuals, populations, communities and ecosystems; bioeconomics, management of renewable resources; hierarchy theory; integration of spatial and time scales.

• Evolutionary biology: Co-evolutions; genetics and evolution.

• Medical systems: Physiology; cardiac modeling; computer models in Medicine.

• Numerical simulations and computations: Numerical study and analysis of biological data.

• Epistemology: Interdisciplinary transfers of concepts; knowledge; education; history of science.

The journal will also publish book reviews.

• Journal of Theoretical Biology (JTB)

[TOCs]

Publishes theoretical papers which give insight into biological processes. The biological significance should be clearly stated. Highly speculative papers not based on current biological knowledge will not be acceptable. Papers may include new experimental results which bear on the theory being presented. Every effort should be made to make the main points of the paper intelligible to biologists as a whole. Authors should thus make it clear how any mathematical models relate to the biological problems they address; detailed mathematical technicalities and experimental procedures may usually be best presented in appendices so as not to impede the exposition of the central ideas.

• Systema Naturae (1998— )

Annali di Biologia Teorica

• Theoretical Population Biology (TPC)

[TOCs (February 1993— )]

(Academic Press.) Interdisciplinary; presents articles on the theoretical aspects of the biology of populations, particularly in the areas of ecology, genetics, demography, and epidemiology. Primary emphasis is on development of theory, but the journal also presents experimental results directly impinging on theoretical descriptions of populations and the dynamics of populations.

• Theory in Biosciences

Theory in Biosciences, formerly: Biologisches Zentralblatt, focuses on new concepts in theoretical biology. It is likewise interested in analytical or modelling approaches and in biophilosophy or history of ideas. Central topics are systems theory, systems dynamics, theoretical ecology, evolution, cognition, theoretical neurobiology, visual computation, simulation strategies, and bioethics. Manuscripts present original work with a strong conceptual background. In addition, each issue provides a literature review that comments on recent developments of a selected topic.

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• European Communication of Mathematical and Theoretical Biology

formerly Biomathematics Newsletter

A European forum for the exchange of information, ideas and requests between biomathematicians and theoretical biologists. Also the official journal of communication of the European Society for Mathematical and Theoretical Biology.

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• Associazione Italiana di Biologia Teorica (ABT) (1997— )

Fosters discussions and publication of ideas, hypotheses, and theories concerning all problems of biology.

• Canadian Society for Theoretical Biology / Société canadienne de biologie théorique

• Centro Linceo Interdisciplinare di Scienze Matematiche e Loro Applicazioni (Italy)

• European Society for Mathematical and Theoretical Biology

• International Society for Adaptive Behavior (ISAB)

• Israeli Society for Theoretical and Mathematical Biology (ISTMB) (1996— )

Fosters interdisciplinary research in Israel and provides a forum for Israeli scientists to discuss research in theoretical biology, mathematical-biology, and mathematics applied to or motivated by biology. We also see interdisciplinary research, such as computational biology or biophysics, as part of our mandate.

• Netherlands Society for Theoretical Biology

• Société Française de Biologie Théorique (SFTB) (1985— )

Promotes the development of methods and theoretical formalisms that are useful to fundamental research and its practical applications (Journal Officiel du 15 novembre 1981, p. 9999).

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• Innovationskolleg Theoretische Biologie (ITB), Humboldt Universität zu Berlin(Germany)

• Biological Cybernetics / Theoretical Biology, Universität Bielefeld (Germany)

• Institute for Neuroinformatics, Ruhr-Universität Bochum (Germany)

• Division of Theoretical Biology at the University of Bonn (1986— ) (Germany)

• Department of Integrative Biology, University of California, Berkeley (USA)

• Institute for Theoretical Dynamics, University of California, Davis (USA)

• The Complex Systems Research Group (Barcelona, Spain)

An interdisciplinary group of researchers working on complex adaptive systems, located at the Departament de Fisica i Enginyeria Nuclear, Universitat Politècnica de Catalunya.

• Center for the Philosophy of Nature and Science Studies (Copenhagen, Denmark)

Involves a small group of scientists, philosophers of science and researchers engaged in the interdisciplinary field denominated here as philosophy of nature and science studies, including history, philosophy and sociology of science.

• Institute of Evolutionary and Ecological Sciences, Theoretical Biology and Phylogenetics Section (Leiden, Netherlands)

Studies patterns and processes involved in evolutionary change. Speciation (macroevolution) is major area of interest. Evolutionary and ecological issues are investigated by use of theoretical and experimental research. Gastropods are used as model system in the experimental research. The theoretical research ranges from exploring the consequences of established biological theories to the construction of models for specific biological systems. In addition the section investigates the nature of key biological concepts.

• Kieckhefer Center for Theoretical Biology, The Salk Institute (La Jolla, CA, USA)

• Max Planck Institute for Mathematics in the Sciences

The Max-Planck-Institute for Mathematics in the Sciences, founded in 1995, is concerned with mathematical challenges which arise through theoretical questions in the natural sciences. The common denominator of all teams in the institute is the field of partial differential equations and the calculus of variations.

• Santa Fe Institute (SFI) (USA)

Draws scientists from universities and research institutions world-wide to pursue broad research problems. Much of the work focuses on the science of complexity (emergence), which examines underlying patterns and regularities behind a wide assortment of real-world phenomena. Projects range from the communication patterns of ants to the way information spreads across economic markets.

• The Center for Theoretical Study (CTS)

CTS is an institute of advanced studies, jointly administered by Charles University and the Academy of Sciences of the Czech Republic. CTS was established in June 1990 with the primary aim of supporting high quality theoretical research in diverse fields ranging from the humanities to the exact sciences.

• Theoretical Biology and Biophysics (T-10) at Los Alamos National Laboratory (USA)

Modeling of biological systems and analysis and informatics of molecular and cellular biological data.

• Theoretical Biology Program, Institute for Advanced Study, Princeton University (1998— ) (USA)

[Press release]

• Theoretical Biology / Bioinformatics Group, Utrecht University (Netherlands)

Performs fundamental research in biology by means of formal models. Examples of the biological areas covered are ecology, spatial pattern formation, (molecular) evolution, immunology, and ethology. Formalisms range from mathematical models, cellular automata, genetic algorithms, to discrete-event individual-oriented simulation models.

• Theoretical Biology at Virginia Tech (USA)

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• Mathematical and Theoretical Biology Institute (MTBI), Cornell University (USA)

Summer School.

• Estonian Spring Schools in Theoretical Biology

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• Claus Emmeche

A theoretical biologist with general interests in philosophy of nature, philosophy of science, and science studies, and research interests in artificial life and theoretical biology. Links to online papers, other resources, and to the Center for the Philosophy of Nature and Science Studies.

• Mike Levin's TB Page

Links and books on TB, in particular those that relate to process-oriented definitions of life, complexity theory, studies of embryonic development as a context for evolution, and the constructionist approaches of Artificial Life.

• Luis Rocha's Cyber Corner

• Eörs Szathmáry

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• Biological Information Theory and Chowder Society FAQ

• Exobiological Aspects of Comets and Meteorites

Annotated bibliography by Norman Redington and Karen Ræ Keck. The Net Advance of Physics: Annotated Bibliographies, No. 1. First edition, 1996.

• Molecular Information Theory

The theory of molecular machines from the NIH Laboratory of Computational and Experimental Biology (USA).

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