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| | :::::::''For a compendium of perspectives on the province of theoretical biology, click this article's accompanying tab, 'Addendum', or click [[Theoretical biology/Addendum]], which serves as a continuation of the Main Article.'' |
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| | '''Theoretical biology''' applies the tools of [[reason]] toward the goal of explaining the [[Biology|biological]] world, in its manifold aspects, through the development of [[idea]]s as [[model]]s, [[Hypothesis|hypotheses] and eventually [[Theory|theories]]. It thereby distinguishes itself from [[Observation|observational]] and [[Experiment|experimental]] biology, though without those empirical disciplines, theoretical biologists would have neither inspiration nor information with which to produce their constructs, or to evaluate them. |
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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. | | [[Charles Darwin|Charles Darwin's]] and [[Alfred Russel Wallace|Alfred Russel Wallace's]] theory of [[Evolution|evolution]] by means of [[Natural selection|natural selection]], or [[survival of the fittest]], aptly illustrates the co-dependence of information and the tools of reason in producing biological theory. |
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| Professor [[Richard Gordon]], President of the [[Canadian Society for Theoretical Biology]], writes:
| | ==Scope of theoretical biology== |
| | :''See also this article's subpage'', [[Theoretical biology/Addendum]] |
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| <blockquote>
| | If one narrowly defines theoretical biology as the application of the tools of reason in the practice of the science of living systems, then every biologist qualifies as a theoretical biologist. No biologist abandons reason in pursuit of their goals. |
| <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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| 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:
| | Some biologists, however, take it as their major goal to drive themselves to apply the tools of reason to generate ideas about living systems, and consequently find themselves identified as theoreticians. Theoretical biologists aim not to produce observational data or experimental results, but to produce ideas that attempt to explain observational or experimental data, or that attempt to predict novel observational or experimental data as consequences of their ideas. Their ideas may take the form of a hypothetical construct to account for a specific natural phenomenon in living systems, of more elaborate models, or of syntheses of diverse phenomena into revolutionary concepts or theories that have insightful and powerful explanatory and predictive power. The level of formalism may range from the narrative to the mathematical and computational, depending on the nature of the question and the tools of reason employed. |
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| <blockquote>
| | Theoretical biologists emerge in every distinguishable discipline of the science of living systems, and branch beyond traditional biology into philosophy, sociology, economics, and public policy.... |
| <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.
| | ==Rewards== |
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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.
| | Frank Wilczek, a theoretical physicist at MIT and recipient of the Nobel Prize in Physics (2004), might speak for theoretical biologists: |
| *'''<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> | | <blockquote> |
| <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> | | <p style="margin-left: 2.0%; margin-right: 6%; font-size: 1.0em; font-family: Gill Sans MT, Trebuchet MS;">The most exciting thing that can happen is when theoretical dreams that started as fantasies, as desires, become projects that people work hard to build. There is nothing like it; it is the ultimate tribute. At one moment you have just a glimmer of a thought and at another moment squiggles on paper. Then one day you walk into a laboratory and there are all these pipes, and liquid helium is flowing, and currents are coming in and out with complicated wiring, and somehow all this activity is supposedly corresponds to those little thoughts that you had. When this happens, it's magic. |
| | <ref>[http://www.edge.org/3rd_culture/wilczek09/wilczek09_index.html THE NOBEL PRIZE AND AFTER (1.15.09): A Talk with Frank Wilczek.]</ref></p> |
| </blockquote> | | </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 quality as representative of the field.
| | Using that metaphor, many theoretical biologists could qualify as magicians. |
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| {{TOC-left}}
| | ==Methods in theoretical biology== |
| {{-}}
| | In general, the methods of theoretical biologists interact with those of experimental biologists in an iterative feedback process. Observational checks by experimental biologists of the concepts/hypotheses/predictions of theoretical biologists serve a central role for both groups, as the theoretical biologist must critically reevaluate her 'theory' in light of the experimental findings, perhaps finding it necessary to revise her concepts/hypotheses to accord with the experimental results, perhaps inspiring her to ask new questions that expand or redirect her thinking. In turn, the reevaluation/vision process of the theoretical biologists can lead to additional testing by the experimental biologists, requiring them to develop new technologies and enabling them to make new discoveries that enrich the the theoreticians conceptual base, the font of the theoretical biologist's inspiration. |
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| ==The Journal of Theoretical Biology==
| | In particular, the methods employed by theoretical biologists include:; |
| | conceptualization inspired and guided by... |
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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:
| | ==Trends in 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 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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| *[[Biofilms]] in the [[large bowel]] suggest an apparent function of the human vermiform [[appendix]]
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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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| *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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| <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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| <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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| ==Theoretical biology's most common topic categories==
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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== |
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| | [[Category:Suggestion Bot Tag]] |
- For a compendium of perspectives on the province of theoretical biology, click this article's accompanying tab, 'Addendum', or click Theoretical biology/Addendum, which serves as a continuation of the Main Article.
Theoretical biology applies the tools of reason toward the goal of explaining the biological world, in its manifold aspects, through the development of ideas as models, [[Hypothesis|hypotheses] and eventually theories. It thereby distinguishes itself from observational and experimental biology, though without those empirical disciplines, theoretical biologists would have neither inspiration nor information with which to produce their constructs, or to evaluate them.
Charles Darwin's and Alfred Russel Wallace's theory of evolution by means of natural selection, or survival of the fittest, aptly illustrates the co-dependence of information and the tools of reason in producing biological theory.
Scope of theoretical biology
- See also this article's subpage, Theoretical biology/Addendum
If one narrowly defines theoretical biology as the application of the tools of reason in the practice of the science of living systems, then every biologist qualifies as a theoretical biologist. No biologist abandons reason in pursuit of their goals.
Some biologists, however, take it as their major goal to drive themselves to apply the tools of reason to generate ideas about living systems, and consequently find themselves identified as theoreticians. Theoretical biologists aim not to produce observational data or experimental results, but to produce ideas that attempt to explain observational or experimental data, or that attempt to predict novel observational or experimental data as consequences of their ideas. Their ideas may take the form of a hypothetical construct to account for a specific natural phenomenon in living systems, of more elaborate models, or of syntheses of diverse phenomena into revolutionary concepts or theories that have insightful and powerful explanatory and predictive power. The level of formalism may range from the narrative to the mathematical and computational, depending on the nature of the question and the tools of reason employed.
Theoretical biologists emerge in every distinguishable discipline of the science of living systems, and branch beyond traditional biology into philosophy, sociology, economics, and public policy....
Rewards
Frank Wilczek, a theoretical physicist at MIT and recipient of the Nobel Prize in Physics (2004), might speak for theoretical biologists:
The most exciting thing that can happen is when theoretical dreams that started as fantasies, as desires, become projects that people work hard to build. There is nothing like it; it is the ultimate tribute. At one moment you have just a glimmer of a thought and at another moment squiggles on paper. Then one day you walk into a laboratory and there are all these pipes, and liquid helium is flowing, and currents are coming in and out with complicated wiring, and somehow all this activity is supposedly corresponds to those little thoughts that you had. When this happens, it's magic.
[1]
Using that metaphor, many theoretical biologists could qualify as magicians.
Methods in theoretical biology
In general, the methods of theoretical biologists interact with those of experimental biologists in an iterative feedback process. Observational checks by experimental biologists of the concepts/hypotheses/predictions of theoretical biologists serve a central role for both groups, as the theoretical biologist must critically reevaluate her 'theory' in light of the experimental findings, perhaps finding it necessary to revise her concepts/hypotheses to accord with the experimental results, perhaps inspiring her to ask new questions that expand or redirect her thinking. In turn, the reevaluation/vision process of the theoretical biologists can lead to additional testing by the experimental biologists, requiring them to develop new technologies and enabling them to make new discoveries that enrich the the theoreticians conceptual base, the font of the theoretical biologist's inspiration.
In particular, the methods employed by theoretical biologists include:;
conceptualization inspired and guided by...
Trends in theoretical biology
References
