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| | ''For a list of definitions and keywords about Theoretical biology, see [[Theoretical biology/Catalogs]].'' |
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| '''Theoretical biology''' applies [[reason]] toward the goal of explaining the [[biology|biological]] world, and aspects of it, through ideas and theories. It thereby distinguishes itself from [[observation|observational]] and [[experiment|experimental]] biology, though without the latter disciplines of biology, theoretical biologists would have no information with which to produce theories, or evaluate them. | | '''Theoretical biology''' applies [[reason]] toward the goal of explaining the [[biology|biological]] world, and aspects of it, through ideas and theories. It thereby distinguishes itself from [[observation|observational]] and [[experiment|experimental]] biology, though without the latter disciplines of biology, theoretical biologists would have no information with which to produce theories, or evaluate them. |
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| Professor [[Richard Gordon]], President of the [[Canadian Society for Theoretical Biology]], writes:
| | ==Scope of theoretical biology== |
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| <blockquote>
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| <p style="margin-left: 2%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;">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.<ref name=brochure>[http://life.biology.mcmaster.ca/~brian/biomath/careers.theo.biol.htlm Careers in Theoretical Biology.]</ref></p>
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| </blockquote>
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| Biophysicist and mathematical biologist Marc Mangel,<ref>[http://www.soe.ucsc.edu/~msmangel/bio.html Marc Mangel's Biography]</ref> in his 2006 book ''The Theoretical Biologist’s Toolbox'',<ref name=mangel2006>Mangel M. (2006) [http://books.google.com/books?id=_RW8upYq1iUC The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology.] Cambridge University Press. ISBN 0521830451, ISBN 9780521830454.
| | ==Trends in theoretical biology== |
| *'''<u>Book description:</u>''' Mathematical modelling is widely used in ecology and evolutionary biology and it is a topic that many biologists find difficult to grasp. In this new textbook Marc Mangel provides a no-nonsense introduction to the skills needed to understand the principles of theoretical and mathematical biology. Fundamental theories and applications are introduced using numerous examples from current biological research, complete with illustrations to highlight key points. Exercises are also included throughout the text to show how theory can be applied and to test knowledge gained so far. Suitable for advanced undergraduate courses in theoretical and mathematical biology, this book forms an essential resource for anyone wanting to gain an understanding of theoretical ecology and evolution.</ref> elaborates on Professor Gordon's brief description of theoretical biology:
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| <blockquote>
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| <p style="margin-left: 2.0%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;"> 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.
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| <ref name=mangel2006/></p>
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| </blockquote>
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| In describing their research program, the Biospheric Theory and Modeling group<ref name=biospheric>[http://www.bgc-jena.mpg.de/bgc-theory/index.php/Main/HomePage Biospheric Theory and Modeling]</ref> of the Max-Planck-Institut für Biogeochemie<ref name=maxbiogeo>[http://www.bgc-jena.mpg.de/ Max-Planck-Institut für Biogeochemie]</ref> highlight many of the main approaches and advantages of theoretical biology:
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| <p style="margin-left: 2.0%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;"> Our research aims to identify the general organizing principles of the [[Biosphere|biosphere]] in order to better understand and predict its interactions with [[Biogeochemical cycles|biogeochemical cycles]] and the [[Climate|climate]] system….Our view of [[Biospheric theory|biospheric theory]]….is that the development of theory goes hand in hand with observations, which serve as a reality check for the [[Theory|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 (Biology)|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 (Biology)|optimality]], multiple steady states, and pattern formation.<ref name=biospheric/></p>
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| </blockquote>
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| 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|systems biology approach]]. Most biologists will recognize themselves as theoretical biologists on some level and at some times.
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| In their 2003 book on the organization of organismal form, Gerd B. Müller and Stuart A. Newman<ref name=muller2003>Müller GB, Newman SA (2003) [http://books.google.com/books?id=8-Xm_gQgboUC Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology.] MIT Press. ISBN 0262134195, ISBN 9780262134194.
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| *'''<u>Book description:</u>''' The field of evolutionary biology arose from the desire to understand the origin and diversity of biological forms. In recent years, however, evolutionary genetics, with its focus on the modification and inheritance of presumed genetic programs, has all but overwhelmed other aspects of evolutionary biology. This has led to the neglect of the study of the generative origins of biological form. Drawing on work from developmental biology, paleontology, developmental and population genetics, cancer research, physics, and theoretical biology, this book explores the multiple factors responsible for the origination of biological form. It examines the essential problems of morphological evolution--why, for example, the basic body plans of nearly all metazoans arose within a relatively short time span, why similar morphological design motifs appear in phylogenetically independent lineages, and how new structural elements are added to the body plan of a given phylogenetic lineage. It also examines discordances between genetic and phenotypic change, the physical determinants of morphogenesis, and the role of epigenetic processes in evolution. The book discusses these and other topics within the framework of evolutionary developmental biology, a new research agenda that concerns the interaction of development and evolution in the generation of biological form. By placing epigenetic processes, rather than gene sequence and gene expression changes, at the center of morphological origination, this book points the way to a more comprehensive theory of evolution.</ref> stress the breadth of the field and its applicability beyond [[mathematical biology]]:
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| <p style="margin-left: 2.0%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;"> Theoretical 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 [[Gene|genetic]], [[Developmental biology|developmental]], and [[Evolutionary biology|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.<ref name=muller2003/></p>
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| </blockquote>
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| In describing the aims of the Dutch journal of theoretical biology, ''Acta Biotheoretica'', Thomas A. C. Reydon and Lia Hemerik<ref name=reydon>Reydon TAC, Hemerik L. (2005) [http://books.google.com/books?id=ez_JduJm2voC Current Themes in Theoretical Biology: A Dutch Perspective.] Springer. ISBN 1402029012, ISBN 9781402029011.
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| *'''<u>Table of contents: </u>'''
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| :#The History of Acta Biotheoretica and the Nature of Theoretical Biology; Thomas A.C. Reydon, Piet Dullemeijer and Lia Hemerik
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| :#Images of the Genome: From Public Debates to Biology, and Back, and Forth; Cor van der Weele
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| :#The Functional Perspective of Organismal Biology; Arno Wouters
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| :#Infectious Biology: Curse or Blessing? Reflections on Biology in Other Disciplines, with a Case Study of Migraine; Wim J. van der Steen
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| :#The Composite Species Concept: A Rigorous Basis for Cladistic Practice; D.J. Kornet and James W. McAllister
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| :#The Wonderful Crucible of Life’s Creation: An Essay on Contingency versus Inevitability of Phylogenetic Development; R. Hengeveld
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| :#The Symbiontic Nature of Metabolic Evolution; S.A.L.M. Kooijman and R. Hengeveld
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| :#The Founder and Allee Effects in the Patch Occupancy Metapopulation Model; Rampal S. Etienne and Lia Hemerik
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| :#Balancing Statistics and Ecology: Lumping Experimental Data for Model Selection; Nelly van der Hoeven, Lia Hemerik and Patrick A. Jansen
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| :#Resilience and Persistence in the Context of Stochastic Population Models; Johan Grasman, Onno A. van Herwaarden and Thomas J. Hagenaars
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| :#Evolution of Specialization and Ecological Character Displacement: Metabolic Plasticity Matters; Martijn Egas.</ref> illustrate the Dutch perspective on theoretical biology:
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| <blockquote>
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| <p style="margin-left: 2.0%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;">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.<ref name=reydon/></p>
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| </blockquote>
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| 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.<ref name=reydon/>. As theoretical biology transcends national boundaries, those topic categories qualify as representative of the field.
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| ==The Journal of Theoretical Biology== | | ==Methods in theoretical biology== |
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| The diversity of biological disciplines represented in the ''[[Journal of Theoretical Biology]]'' indicates the diversity of biologists engaged in theoretical biology.<ref name=jtb>[http://www.elsevier.com/wps/find/journaldescription.cws_home/622904/description#description Journal of Theoretical Biology: About Us]</ref> The editors of the journal emphasize the role of theory in giving insight to biological processes:
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| | ==Integration with other biological fields== |
| <p style="margin-left: 2%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;">The Journal of Theoretical Biology is the leading forum for theoretical papers that give insight into biological processes. It covers a very wide range of topics and is of interest to biologists in many areas of research. Many of the papers make use of mathematics, and an effort is made to make the papers intelligible to biologists as a whole. Experimental material bearing on theory is acceptable…. Research Areas Include: [[Cell Biology]] and Development; [[Developmental Biology]]; [[Ecology]]; [[Evolution]]; [[Immunology]]; [[Infectious Diseases]]; [[Mathematical Modeling]], [[Statistics]], and [[Database|Data Bases]]; [[Medical Sciences]] and [[Plant Pathology]]; [[Microbiology]]; [[Molecular Biology]] and [[Biochemistry]]; [[Physiology]].<ref name=jtb>[http://www.elsevier.com/wps/find/journaldescription.cws_home/622904/description#description Journal of Theoretical Biology: About Us.]</ref></p>
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| </blockquote>
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| === —Journal's ten most downloaded articles in agricultural and biological sciences, April-June 2008===
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| A listing of the ten most downloaded articles from the journal (in [[agricultural sciences|agricultural]] and biological sciences, April-June 2008) give an indication of the kinds of theoretical and conceptual approaches and topics that interest theoretical biologists:<ref>[http://top25.sciencedirect.com/subject/agricultural-and-biological-sciences/1/journal/journal-of-theoretical-biology/00225193/archive/18 Top 25 Hottest Articles, Agricultural and Biological Sciences, Journal of Theoretical Biology, April-June 2008.]</ref>
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| *[[Thermodynamics]] of [[natural selection]] I: [[Energy flow]] and the limits on organization
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| :*'''<u>From the Abstract:</u>''' This is the first of three papers analyzing the representation of information in the biosphere, and the energetic constraints limiting the imposition or maintenance of that information. Biological information is inherently a chemical property, but is equally an aspect of control flow and a result of processes equivalent to computation. The current paper develops the constraints on a theory of biological information capable of incorporating these three characterizations and their quantitative consequences….The main result of the paper is that the ''limits'' on the minimal energetic cost of information flow will be tractable and universal whereas the assembly of more literal process models into a system-level description often is not.
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| *[[Biofilms]] in the [[large bowel]] suggest an apparent function of the human vermiform [[appendix]]
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| :*'''<u>From the Abstract:</u>''' The function of the human appendix has long been a matter of debate, with the structure often considered to be a vestige of evolutionary development despite evidence to the contrary based on comparative primate anatomy. Based (a) on a recently acquired understanding of immune-mediated biofilm formation by commensal bacteria in the mammalian gut, (b) on biofilm distribution in the large bowel, (c) the association of lymphoid tissue with the appendix, (d) the potential for biofilms to protect and support colonization by commensal [living together, with some benefitting, none detrimenting] bacteria, and (e) on the architecture of the human bowel, we propose that the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.
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| *Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF [[signaling pathways]]
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| :*'''<u>From the Abstract:</u>''' The formation of somites [body segments containing the same internal structures] in the course of vertebrate segmentation is governed by an oscillator known as the segmentation clock, which is characterized by a period ranging from 30 min to a few hours depending on the organism. This oscillator permits the synchronized activation of segmentation genes in successive cohorts of cells in the presomitic mesoderm in response to a periodic signal emitted by the segmentation clock, thereby defining the future segments….A complex oscillating network of [three] signaling genes underlies the mouse segmentation clock….By means of computational modeling, we investigate the conditions in which sustained oscillations occur in these three signaling pathways. The model provides a framework for analyzing the dynamics of the segmentation clock in terms of a network of oscillating modules involving the….signaling pathways.
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| *Thermodynamics of natural selection II: Chemical Carnot cycles
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| *A [[protein]] interaction network associated with [[asthma]]
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| *[[Self-organization]] at the origin of life
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| *The timing of TNF and IFN-γ signaling affects macrophage activation strategies during Mycobacterium [[tuberculosis]] infection
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| *Thermodynamics of natural selection III: Landauer's principle in computation and chemistry
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| *Prevention of [[avian influenza]] epidemic: What policy should we choose?
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| *Evolutionary stability on graphs
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| === —Journal's ten most downloaded articles in biochemistry, genetics, and molecular biology, April-June 2008===
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| The corresponding top ten downloads in the areas of [[biochemistry]], [[genetics]] and [[molecular biology]]:<ref>[http://top25.sciencedirect.com/subject/biochemistry-genetics-and-molecular-biology/3/archive/18/ Top 25 Hottest Articles, Biochemistry, Genetics and Molecular Biology, Journal of Theoretical Biology, April-June 2008.]</ref>
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| *The Epithelial-Mesenchymal Transition Generates Cells with Properties of [[Stem Cells]]
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| *[[Induction]] of [[Pluripotency|Pluripotent]] Stem Cells from Adult Human Fibroblasts by Defined Factors
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| *Direct Reprogramming of Terminally Differentiated Mature B Lymphocytes to Pluripotency
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| *Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors
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| *SnapShot: [[Hematopoiesis]]
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| *Nuclear Receptor-Enhanced Transcription Requires Motor- and LSD1-Dependent Gene Networking in Interchromatin Granules
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| *The Hallmarks of [[Cancer]]
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| *TGF-β Primes Breast Tumors for Lung Metastasis Seeding through Angiopoietin-like 4
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| *Acetylation Is Indispensable for p53 Activation
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| *An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells
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| It appears from the titles alone that currently theoretical biology covers a widely diverse types of subject matter, not all qualifying as [[mathematical biology|mathematical]] or [[philosophical biology]].
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| ==The National Academies' National Research Council report on theoretical biology==
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| A committee of the [[National Research Council]] of the [[National Academies]] reported in 2008 on "The Role of Theory in Advancing 21st-Century Biology: Catalyzing Transformative Research"<ref name=nrctheory2008>National Research Council of the National Academies, Division of Earth and Life Studies, Board on Life Sciences, Report of the Committee on Defining and Advancing the Conceptual Basis of Biological Sciences in the 21st Century. (2008) [http://books.nap.edu/openbook.php?record_id=12026&page=R1 The Role of Theory in Advancing 21st-Century Biology: Catalyzing Transformative Research.] The National Academies Press. Washington, D.C.</ref>. In the summary of their report they discuss the nature of theoretical biology:
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| <blockquote>
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| <p style="margin-left: 2%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;">The committee was charged with examining the role of concepts and theories in biology, including how that role might differ across various subdisciplines. One facet of that examination was to consider the role of the concepts and theories in driving scientific advances and to make recommendations about the best way to encourage creative, dynamic, and innovative research in biology....The committee concluded that a more explicit focus on theory and a concerted attempt to look for cross-cutting issues would likely help stimulate future advances in biology. To illustrate this point, the committee chose seven questions to examine in detail. The list of questions is not comprehensive but rather illustrative. The questions, as shown below, were chosen to show that a focus on theory could play a role in helping to address many different types of interesting and important questions at many different levels.<ref name=nrctheory2008/></p>
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| </blockquote>
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| In the Table of Contents of the committee's report,<ref name=nrctheory2008/> they center their report around these questions:
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| *Are There Still New Life Forms to Be Discovered? The Diversity of Life - Why It Exists and Why It's Important (38-66)
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| *What Role Does Life Play in the Metabolism of Planet Earth? (67-80)
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| *How Do Cells Really Work? (81-89)
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| *What Are the Engineering Principles of [[Life|Life]]? (90-109)
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| *What Is the Information That Defines and Sustains Life? (110-129)
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| *What Determines How Organisms Behave in Their Worlds? (130-144)
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| *How Much Can We Tell About the Past - and Predict About the Future - by Studying Life on Earth Today? (145-156)
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| Achieving answers to those kinds of questions would seem to require interdisciplinary collaboration among many different biological and non-biological scientific disciples, which brings a diversity of concepts, hypotheses, and theories.
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| The NRC committee emphasized the integral role of theory in biology, in chapter so titled, and selected for the chapter's epigraph a quote from Leonardo da Vinci: He who loves practice without theory is like the sailor who boards ship without a rudder and compass and never knows where he may cast. The first chapter, broken to bullet sentences, serves to summarize their conclusion:
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| *This chapter:
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| :*describes several different ideas about scientific theories,
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| :*emphasizes the diversity of theoretical activities throughout biology, and
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| :*discusses ways in which theory is integral to each specific kind of scientific activity, including
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| :*experimentation,
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| :*observation,
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| :*exploration,
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| :*description, and
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| :*technology development as well as
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| :*hypothesis testing.
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| *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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| *Explicit recognition of the many entry points of theory into the scientific enterprise may provide greater opportunity for developing
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| :*new concepts, principles, theories, and perspectives in biology that would
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| ::*not only enhance current scientific practices
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| ::*but also facilitate the exploration of cross-cutting questions that are difficult to address by traditional means.<ref name=nrctheory2008/>
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| The committee makes a specific recommendation:
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| <blockquote>
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| <p style="margin-left: 2%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;">Theory, as an important but under appreciated component of biology, should be given a measure of attention commensurate with that given other components of biological research (such as observation and experiment). Theoretical approaches to biological problems should be explicitly recognized as an important and integral component of funding agencies’ research portfolios. Increased attention to the theoretical and conceptual components of basic biology research has the potential to leverage the results of basic biology research and should be considered as a balance to programs that focus on mission-oriented research.<ref name=nrctheory2008/></p>
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| </blockquote>
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| ==Common topic categories==
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| With the following introductory remarks, in their 1993 book, ''Thinking About Biology: An Invitation to Current Theoretical Biology'', Wilfred D. Stein and Francisco J. Varela offer a sample of then current and still topical areas of work in theoretical biology:<ref name=stein93>Stein WD, Varela FJ. (1993) [http://books.google.com/books?id=FMxxZ_8JYZgC Thinking About Biology: An Invitation to Current Theoretical Biology.] Addison-Wesley. ISBN 0201624540, ISBN 9780201624540.</ref>
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| <blockquote>
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| <p style="margin-left: 2.0%; margin-right: 6%; font-size: 1.0em; font-family: Trebuchet MS;">One the of main purposes of this book is to offer a ''sample'' of thinking about biology….one that avoids both the extremes of empiricist myopia and of theoretical aloofness. We offer this sample not as a survey of the "entire field” of theoretical biology….we see the process of thought as being an integral part of ''asking'' questions that make science both productive and more fun….Thinking about biology is done in various ways. One of the most useful approaches to this variety, we have found, is expressed in the notion of levels of theory. We distinguish between ''macro''-, ''meso''-, and ''micro''-theories…..Macotheories are the large, imaginative canvases that constitute the conceptual scaffolding of a large portion of biology, and that appear only rarely in history. One ideal example is due to Darwin….Macrotheories are usually not that interesting to most practicing biologists. As students, they absorb the major dominant macrotheories, which became second nature in their minds, and they leave it at that. The large issues, such as what is life and its origins, how can a brain secrete a mind, or can evolution be sustained on a planetary scale, are left for occasional reading at best….Mesotheories, on the other hand, are more numerous…. they attempt to cover only a selected domain of biology. A good example of classical mesotheory is the introduction of the notion of a morphogenetic gradient to account for various developmental phenomena….Microtheories are phenomenon-specific. Their purpose is to account in some conceptually clean or analytically astute manner for a given set of observations. For instance, a very famous microtheory was Hodgkin's and Huxley's equations for the action potential in nerve conduction.<ref name=stein93/></p>
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| </blockquote>
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| They offer the following ''samples'':
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| *'''<u>Table of Contents:</u>''':
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| ::*Thinking About Biology: An Introductory Essay
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| :*Section I: The Emergence of Life
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| ::*Defining the Transition to Life: Self-Replicating Bounded Structures and Chemical Autopoiesis
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| :::*"[Pier Luigi] Luisi emphasizes the fundamental operation of the life process, rather than the chemical structures that make up the living cell, but he also considers various actual model systems that point to possible paths along the road to life's origins."
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| ::*The Organism as a Dynamical System
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| :::*"['Peter T.] Saunders introduces us gently to some solutions of systems of differential equations and shows us that systems of nonlinear, but not of linear, differential equations haw sufficient complexity to be good models for embryological, and even for evolutionary, development. We learn about the "attractor," that stable set of values of the parameters of a system to which the system evolves and to which it will return if perturbed."
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| ::*Designing Bacteria
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| ::*Structural Patterns in Macromolecules
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| :*Section II: Development and the Individual: Processes of Identity
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| ::*Development as a Robust Natural Process
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| ::*Generation of Morphological Patterns: Mechanical Ways to Create Regular Structures in Embryonic ::*Development
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| ::*Gastrulation and the Evolution of Development
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| ::*Biological Organization, Coherence, and Light Emission from Living Organisms
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| ::*What is the Immune Network For?
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| ::*Randomness and Pattern Scale in the Immune Network: A Cellular Automata Approach
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| :*Section III: Species and Societies: Communication Among Multiple Agents
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| ::*Self-Organized Criticality and Gaia
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| ::*Requirements for Evolvability in Complex Systems: Orderly Dynamics and Frozen Components
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| ::*Modeling the Behavior of Ant Colonies as an Emergent Property of a System of Ant-Ant Interactions
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| ==Theoretical biology's most promising topic categories==
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| ==Theoretical biology's most hypothetical topic categories==
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| ==Trends in theoretical biology==
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| ==References== | | ==References== |
