Within biological systems, degeneracy refers to circumstances where structurally dissimilar components/modules/pathways can perform similar functions (i.e. are effectively interchangeable) under certain conditions, but perform distinct functions in other conditions. Degeneracy is thus a relational property that requires comparing the behaviour of two or more components. In particular, if degeneracy is present in a pair of components then there will exist conditions where the pair will appear functionally redundant but other conditions where they will appear functionally distinct.

Biological Examples

Examples of degeneracy are found in the genetic code

Genetic code

The genetic code is the set of rules by which information encoded in genetic material is translated into proteins by living cells....

, when many different nucleotide sequences encode the same polypeptide; in protein folding

Protein folding

Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....

, when different polypeptides fold to be structurally and functionally equivalent; in protein functions, when overlapping binding functions and similar catalytic specificities are observed; in metabolism

Metabolism

Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...

, when multiple, parallel biosynthetic and catabolic pathways may coexist.
More generally, degeneracy is observed in proteins of every functional class (e.g. enzymatic, structural, or regulatory), protein complex assemblies, ontogenesis (see page 14 in), the nervous system, cell signalling (crosstalk) and numerous other biological contexts reviewed in.

Contribution to Robustness

Degeneracy contributes to the robustness of biological traits through several mechanisms. Degenerate components compensate for one another under conditions where they are functionally redundant, thus providing robustness against component or pathway failure. Because degenerate components are somewhat different, they tend to harbour unique sensitivities so that a targeted attack such as a specific inhibitor

Inhibitor

Something that restrains, blocks, or suppresses.Inhibitor or inhibition may refer to:* Corrosion inhibitor, a substance that decreases the rate of metal oxidation...

 is less likely to present a risk to all components at once. There are numerous biological examples where degeneracy contributes to robustness in this way. For instance, gene families can encode for diverse proteins with many distinctive roles yet sometimes these proteins can compensate for each other during lost or suppressed gene expression, as seen in the developmental roles of the adhesins gene family in Saccharomyces. Nutrients can be metabolized by distinct metabolic pathways that are effectively interchangeable for certain metabolites even though the total effects of each pathway are not identical. In cancer, therapies targeting the EGF receptor are thwarted by the co-activation of alternate receptor tyrosine kinases (RTK) that have partial functional overlap with the EGF receptor (and are therefore degenerate), but are not targeted by the same specific EGF receptor inhibitor. Other examples from various levels of biological organization can be found in.

Theory

Several theoretical developments have outlined links between degeneracy and important biological measurements related to robustness, complexity, and evolvability. These include:

• Theoretical arguments supported by simulations have proposed that degeneracy can lead to distributed forms of robustness in protein interaction networks. Those authors suggest that similar phenomena is likely to arise in other biological networks and potentially may contribute to the resilience of ecosystems as well.
• Tononi et al. have found evidence that degeneracy is inseparable from the existence of hierarchical complexity in neural populations. They argue that the link between degeneracy and complexity is likely to be much more general.
• Fairly abstract simulations have supported the hypothesis that degeneracy fundamentally alters the propensity for a genetic system to access novel heritable phenotypes and that degeneracy could therefore be a precondition for open-ended evolution.
• The three hypotheses above have been integrated in where they propose that degeneracy plays a central role in the open-ended evolution of biological complexity. In the same article, it was argued that the absence of degeneracy within many designed (abiotic) complex systems may help to explain why robustness appears to be in conflict with flexibility and adaptability, as seen in software, systems engineering, and artificial life.

Further reading

Because there are many distinct types of systems that undergo heritable variation and selection (see Universal Darwinism

Universal darwinism

Universal Darwinism refers to a variety of approaches that extend the theory of Darwinism beyond its original domain of biological evolution on Earth...

), degeneracy has become a highly interdisciplinary topic. The following provides a brief roadmap to the application and study of degeneracy within different disciplines.

Ecosystems

• Atamas, S. and J. Bell, Degeneracy-Driven Self-Structuring Dynamics in Selective Repertoires. Bulletin of Mathematical Biology, 2009. 71(6): p. 1349-1365.

History and Philosophy

• Mason, P.H., Degeneracy at Multiple Levels of Complexity. Biological Theory, 2010. 5(3): p. 277-288.

Systems Biology

Systems biology

Systems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...

• Solé, R.V., R. Ferrer-Cancho, J.M. Montoya, and S. Valverde, Selection, tinkering, and emergence in complex networks. Complexity, 2002. 8(1): p. 20-33.
• Whitacre, J.M. and A. Bender, Networked buffering: a basic mechanism for distributed robustness in complex adaptive systems. Theoretical Biology and Medical Modelling 2010. 7(20).

Evolution

Evolution

Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...

• Edelman, G.M. and J.A. Gally, Degeneracy and complexity in biological systems. Proceedings of the National Academy of Sciences, USA, 2001. 98(24): p. 13763-13768.
• Whitacre, J.M., Degeneracy: a link between evolvability, robustness and complexity in biological systems. Theoretical Biology and Medical Modelling, 2010. 7(6).
• Whitacre, J.M. and A. Bender, Degeneracy: a design principle for achieving robustness and evolvability. Journal of Theoretical Biology, 2010. 263(1): p. 143-53.
• Whitacre, J.M. and S.P. Atamas, The Diversity Paradox: How Nature Resolves an Evolutionary Dilemma. Biology Direct, (in press).

Immunology

Immunology

Immunology is a broad branch of biomedical science that covers the study of all aspects of the immune system in all organisms. It deals with the physiological functioning of the immune system in states of both health and diseases; malfunctions of the immune system in immunological disorders ; the...

• Cohn, M., Degeneracy, mimicry and crossreactivity in immune recognition. Molecular immunology, 2005. 42(5): p. 651-655.
• Cohen, I.R., U. Hershberg, and S. Solomon, Antigen-receptor degeneracy and immunological paradigms. Molecular immunology, 2004. 40(14-15): p. 993-996.
• Tieri, P., G.C. Castellani, D. Remondini, S. Valensin, J. Loroni, S. Salvioli, and C. Franceschi, Capturing degeneracy of the immune system. In Silico Immunology. Springer, 2007.
• Tieri, P., A. Grignolio, A. Zaikin, M. Mishto, D. Remondini, G.C. Castellani, and C. Franceschi, Network, degeneracy and bow tie integrating paradigms and architectures to grasp the complexity of the immune system. Theor Biol Med Model, 2010. 7: p. 32.

Artificial Life

Artificial life

Artificial life is a field of study and an associated art form which examine systems related to life, its processes, and its evolution through simulations using computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American computer scientist, in 1986...

, Computational Intelligence

Computational Intelligence

Computational Intelligence is an international, peer-reviewed journal, published by Wiley-Blackwell.The editors for 2009 are Ali Ghorbani, and Evangelos Milios.- External links :* — official website...

• Andrews, P.S. and J. Timmis, A Computational Model of Degeneracy in a Lymph Node. Lecture Notes in Computer Science, 2006. 4163: p. 164.
• Mendao, M., J. Timmis, P.S. Andrews, and M. Davies. The Immune System in Pieces: Computational Lessons from Degeneracy in the Immune System. in Foundations of Computational Intelligence (FOCI). 2007.
• Whitacre, J.M. and A. Bender. Degenerate neutrality creates evolvable fitness landscapes. in WorldComp-2009. 2009. Las Vegas, Nevada, USA.
• Whitacre, J.M., P. Rohlfshagen, X. Yao, and A. Bender. The role of degenerate robustness in the evolvability of multi-agent systems in dynamic environments. in PPSN XI. 2010. Krakow, Poland.
• Macia, J. and R. Solé, Distributed robustness in cellular networks: insights from synthetic evolved circuits. Royal Society Interface, 2009 6: p. 393-400.
• Fernandez-Leon, J.A. (2011). Evolving cognitive-behavioural dependencies in situated agents for behavioural robustness. BioSystems 106, pp. 94-110 .
• Fernandez-Leon, J.A. (2011). Behavioural robustness: a link between distributed mechanisms and coupled transient dynamics. BioSystems 105 , Elsevier, pp. 49-61 .
• Fernandez-Leon, J.A. (2010). Evolving experience-dependent robust behaviour in embodied agents. BioSystems 103:1, Elsevier, pp. 45-56 .

Brain

Brain

The brain is the center of the nervous system in all vertebrate and most invertebrate animals—only a few primitive invertebrates such as sponges, jellyfish, sea squirts and starfishes do not have one. It is located in the head, usually close to primary sensory apparatus such as vision, hearing,...

• Price, C. and K. Friston, Degeneracy and cognitive anatomy. Trends in Cognitive Sciences, 2002. 6(10): p. 416-421.
• Tononi, G., O. Sporns, and G.M. Edelman, Measures of degeneracy and redundancy in biological networks. Proceedings of the National Academy of Sciences, USA, 1999. 96(6): p. 3257-3262.

Oncology

Oncology

Oncology is a branch of medicine that deals with cancer...

• Tian, T., S. Olson, J.M. Whitacre, and A. Harding, The origins of cancer robustness and evolvability. Integrative Biology, 2011. 3: p. 17-30.

Peer Review

Peer review

Peer review is a process of self-regulation by a profession or a process of evaluation involving qualified individuals within the relevant field. Peer review methods are employed to maintain standards, improve performance and provide credibility...

• Lehky, S., Peer Evaluation and Selection Systems: Adaptation and Maladaptation of Individuals and Groups through Peer Review. 2011: BioBitField Press.

Researchers

• Sergei Atamas
• Gerald Edelman
  Gerald Edelman
  Gerald Maurice Edelman is an American biologist who shared the 1972 Nobel Prize in Physiology or Medicine for work with Rodney Robert Porter on the immune system. Edelman's Nobel Prize-winning research concerned discovery of the structure of antibody molecules...
  
  
• Ricard Sole
• Giulio Tononi
  Giulio Tononi
  Giulio Tononi is a professor of psychiatry at the University of Wisconsin. He is an authority on sleep, and in particular the genetics and etiology of sleep.He is also interested in the nature of consciousness,...
  
  
• James Whitacre