Theoretical biology/Bibliography

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Journals focusing on aspects of theoretical biology

• Journal of Theoretical Biology

• See Journal of Theoretical Biology section of the Addendum to the Main Article for description of this journal.

• Computational and Mathematical Methods in Medicine: An Interdisciplinary Journal of Mathematical, Theoretical and Clinical Aspects of Medicine

• Aims & Scope: Computational & Mathematical Methods in Medicine (formerly Journal of Theoretical Medicine) seeks to promote genuine interdisciplinary collaboration between those interested in the theoretical and clinical aspects of medicine and to foster and encourage the application of mathematics to problems arising from the biomedical sciences. Areas of interest include gene therapy, cell kinetics, pharmacokinetics, chemotherapy, oncology, developmental biology, wound healing, physiology, heart modelling, cardiovascular and lung dynamics, neurobiology, computational neuroscience, biomechanics, biomedical statistics, image analysis, epidemiology, immunology, time series analysis, extracellular matrix properties and signalling, and tissue engineering. This list is not exclusive and papers in other biomedical disciplines are encouraged, particularly in the emerging areas of multiscale modelling in medicine, systems biology and translational research.

• Theoretical Population Biology

• Description: An interdisciplinary journal, Theoretical Population Biology 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.
• Five most downloaded articles, April-June 2008:

• On analytical approaches to epidemics on networks
• Game theory and human evolution: A critique of some recent interpretations of experimental games
• The ideal free distribution: A review and synthesis of the game-theoretic perspective
• Effects of predation on host-pathogen dynamics in SIR models [SIR model: an epidemiological model, computes theoretically the number of individuals infected contagiously by an illness over time in a closed population]
• The evolution of strong reciprocity: cooperation in heterogeneous populations

• Biological Theory: Integrating Development, Evolution, and Cognition

• Description: Biological Theory: Integrating Development, Evolution, and Cognition is devoted to theoretical advances in the biological and cognitive sciences, with an emphasis on the conceptual integration afforded by evolutionary and developmental approaches. The journal appeals to a wide audience of scientists, social scientists, philosophers and historians of biology.
• Titles of the ten most downloaded articles (as of November 2008):

• Do Molecular Clocks Run at All? A Critique of Molecular Systematics (2661 times)
• Movement Matters: The Contributions of Esther Thelen (732 times)
• Karl Popper and Lamarckism (494 times)
• Theoretical Integration, Cooperation, and Theories as Tracking Devices (467 times)
• Self-Extending Symbiosis: A Mechanism for Increasing Robustness Through Evolution (430 times)
• Ontogeny, Genetics, and Evolution: A Perspective from Developmental Cognitive Neuroscience (392 times)
• The Essence of Scientific Theories (368 times)
• The Heterochronic Evolution of Primate Cognitive Development (363 times)
• The Developmental-Genetic Toolkit and the Molecular Homology–Analogy Paradox (328 times)
• Modest Evolutionary Naturalism (316 times)

• Theoretical Biology and Medical Modelling

• Description: An Open access journal focusing on all aspects of biology and the conceptual modeling required to understand its complexity.
• Titles of the ten most downloaded articles (as of November 2008):

• Inflammation: a way to understanding the evolution of portal hypertension (733 times)
• Analysis of novel geometry-independent method for dialysis access pressure-flow monitoring (555 times)
• Extracting key information from historical data to quantify the transmission dynamics of smallpox (390 times)
• Transient antiretroviral therapy selecting for common HIV-1 mutations substantially accelerates the appearance of rare mutations (375 times)
• Mitochondrial concept of leukemogenesis: key role of oxygen-peroxide effects (372 times)
• Moderate exercise and chronic stress produce counteractive effects on different areas of the brain by acting through various neurotransmitter receptor subtypes: A hypothesis (350 times)
• Common angiotensin receptor blockers may directly modulate the immune system via VDR, PPAR and CCR2b (333 times)
• Vasculature deprivation – induced osteonecrosis of the rat femoral head as a model for therapeutic trials (327 times)
• A mathematical model of glutathione metabolism(324 times)
• Activation instead of blocking mesolimbic dopaminergic reward circuitry is a preferred modality in the long term treatment of reward deficiency syndrome (RDS): a commentary (310 times)

• Theory in Biosciences

• Description: "....formerly Biologisches Zentralblatt, focuses on new concepts in theoretical biology. It likewise deals with analytical and modeling approaches as well as the biophilosophy and history of ideas....Coverage in the journal includes systems theory/dynamics, theoretical ecology/neurobiology, evolution, cognition, visual computation, simulation strategies and bioethics, and more.
• Aims and scope: "Theory in Biosciences" focuses on new concepts in theoretical biology. It also includes analytical and modelling approaches as well as philosophical and historical issues. Central topics are: Artificial Life; Bioinformatics; Bioinspired Modeling; Complexity; Evolutionary Biology; Genetics; History of Biology; Mathematical Biology; hilosophy of Biology; Population Biology; Theoretical Ecology; Theoretical Molecular Biology; Theoretical Neuroscience & Cognition."

Selected journal articles relating to theoretical biology

• Laubichler MD, Rheinberger HJ. (2006) August Weismann and Theoretical Biology. Biological Theory 1:195-198.

• Excerpt: Weismann's concept of the germ plasm, its constitution, and its role in the transmission, the ontogenetic development and the subsequent evolution of traits is prime example of the analytical tradition within theoretical biology. [italics added]

• Brenner S. (2006) Theoretical biology in the third millennium. Phil. Trans. R. Soc. Lond. B 354:1963-1965.

• Abstract: During the 20th century our understanding of genetics and the processes of gene expression have undergone revolutionary change. Improved technology has identified the components of the living cell, and knowledge of the genetic code allows us to visualize the pathway from genotype to phenotype. We can now sequence entire genes, and improved cloning techniques enable us to transfer genes between organisms, giving a better understanding of their function. Due to the improved power of analytical tools databases of sequence information are growing at an exponential rate. Soon complete sequences of genomes and the three-dimensional structure of all proteins may be known. The question we face in the new millennium is how to apply this data in a meaningful way. Since the genes carry the specification of an organism, and because they also record evolutionary changes, we need to design a theoretical framework that can take account of the flow of information through biological systems.

• Perelson AS. (2002) Modelling viral and immune system dynamics. Nature Reviews Immunology 2:28-36.

• Abstract: During the past 6 years, there have been substantial advances in our understanding of human immunodeficiency virus 1 and other viruses, such as hepatitis B virus and hepatitis C virus, that cause chronic infection. The use of mathematical modelling to interpret experimental results has made a significant contribution to this field. Mathematical modelling is also improving our understanding of T-cell dynamics and the quantitative events that underlie the immune response to pathogens.

• Emmeche C. (2000) Closure, function, emergence, semiosis, and life: the same idea? Reflections on the concrete and the abstract in theoretical biology. Ann.N.Y.Acad.Sci. 901:187-197. PMID 10818570.

• Abstract: In this note epistemological problems in general theories about living systems are considered; in particular, the question of hidden connections between different areas of experience, such as folk biology and scientific biology, and hidden connections between central concepts of theoretical biology, such as function, semiosis, closure, and life.
• Introduction: The aim of this brief note is to consider partly hidden ideas about theoretical biology and its subject matter, living beings, organisms in their ecosystems—whichmeans beetles, cows, worms, bacteria cells, green algae, and dinosaurs, their history and interactions, their development and evolution, their structure and function, their origin, self-organization, the extinction of individuals as well as species, and the genesis of higher modes of life. In other words, an extremely multifaceted subject. First, however, recall an observation on the fate of general systems theory, which in the 1960s and 1970s had the ambitious goal of synthesizing the general fields of cybernetics, information theory, operation analysis, and specific fields, such as evolutionary theory and thermodynamics. That goal was not achieved and various reasons may be given for the failure, but an important factor might have been a too high level of theoretical generality in accounting for the highly different types of systems included in the ambitions of systems theory. With this in mind, we could ask for the possibility of facing a similar situation with respect to the current trends in systems thinking.