Category Theory originated in the applied mathematics community, particularly the "General Theory of Natural Equivalence" [2]. In many ways, category theory is familiar to those with conceptual knowledge of set theory. Uniquely, category theory deals with the classification of objects and their transformations between mappings. However, category theory is far more powerful than set theory, and serves as a bridge to formal logic, systems theory, and classification.
A category is defined by two basic components: objects and morphisms. An example of objects are a collection of interrelated variables or discrete states. Morphisms are things that link objects together, either structurally or functionally. This provides us with a network of paths between objects that can be analyzed using categorical logic. This allows us to define a composition (or path) by tracing through the set of objects and morphisms (so-called diagram chasing) to find a solution.
In this example, a pie recipe is represented as a category with objects (action steps) and morphisms (ingredients and results). This monoidal preorder can be added to as the recipe changes. From [3]. Click to enlarge.
Animal taxonomy according to category theory. This example focuses on exploring existing classifications, from species to kingdom. The formation of a tree from a single set of objects and morphisms is called a preorder. From [3]. Click to enlarge.
One potential application of this theory to evolution by natural selection is to establish an alternate view of phylogenetic relationships. By combining category theory with feature selection techniques, it may be possible to detect natural classes that correspond to common ancestry. Related to the discovery of evolutionary-salient features is the problem of phylogenetic scale [5], or hard-to-interpret changes occurring over multiple evolutionary timescales. Category theory might allow us to clarify these trends, particularly as they relate to evolving life embedded in ecosystems [6] or shaped by autopoiesis [7].
More relevant to physiological systems that are shaped by evolution are gene regulatory networks (GRNs). While GRNs can be characterized without the use of category theory, they also present an opportunity to produce an evolutionarily-relevant heteromorphic mapping [8]. While a single GRN structure can have multiple types of outputs, multiple GRN structures can also give rise to the same or similar output [8, 9]. As with previous examples, category theory might help us characterize these otherwise super-complex phenomena (and "wicked" problems) into well-composed systems-level representations.
NOTES:
[1] Spivak, D.I. (2014). Category theory for the sciences. MIT Press, Cambridge, MA.
[2] Eilenberg, S. and MacLane, S. (1945). General theory of natural equivalences. Transactions of the American Mathematical Society, 58, 231-294. doi:10.1090/S0002-9947-1945-0013131-6
[1] Spivak, D.I. (2014). Category theory for the sciences. MIT Press, Cambridge, MA.
[3] Fong, B. and Spivak, D.I. (2018). Seven Sketches in Compositionality: an invitation to applied category theory. arXiv, 1803:05316.
[4] Stepanov, A. and McJones, P. (2009). Elements of Programming. Addison-Wesley Professional.
[5] Graham, C.H., Storch, D., and Machac, A. (2018). Phylogenetic scale in ecology and
evolution. Global Ecology and Biogeography, doi:10.1111/geb.12686.
[6] Kalmykov, V.L. (2012). Generalized Theory of Life. Nature Precedings, 10101/npre.2012.7108.1.
[7] Letelier, J.C., Marin, G., and Mpodozis, J. (2003). Autopoietic and (M,R) systems. Journal of Theoretical Biology, 222(2), 261-272. doi:10.1016/S0022-5193(03)00034-1.
[8] Payne, J.L. and Wagner, A. (2013). Constraint and contingency in multifunctional gene regulatory circuits. PLoS Computational Biology, 9(6), e1003071. doi:10.1371/journal.pcbi.1003071.
[4] Stepanov, A. and McJones, P. (2009). Elements of Programming. Addison-Wesley Professional.
[5] Graham, C.H., Storch, D., and Machac, A. (2018). Phylogenetic scale in ecology and
evolution. Global Ecology and Biogeography, doi:10.1111/geb.12686.
[6] Kalmykov, V.L. (2012). Generalized Theory of Life. Nature Precedings, 10101/npre.2012.7108.1.
[7] Letelier, J.C., Marin, G., and Mpodozis, J. (2003). Autopoietic and (M,R) systems. Journal of Theoretical Biology, 222(2), 261-272. doi:10.1016/S0022-5193(03)00034-1.
[8] Payne, J.L. and Wagner, A. (2013). Constraint and contingency in multifunctional gene regulatory circuits. PLoS Computational Biology, 9(6), e1003071. doi:10.1371/journal.pcbi.1003071.
[9] Ahnert, S.E. and Fink, T.M.A. (2016). Form and function in gene regulatory networks: the structure of network motifs determines fundamental properties of their dynamical state space. Journal of the Royal Society Interface, 13(120), 20160179. doi:10.1098/rsif.2016.0179.
Darwinism has recently been criticized - people cannot understand how undefined genetic changes (and even more so random point mutations of the genome) can give rise to extremely complex and at the same time harmonious and efficient living systems. But even in this problem, category theory makes a hint, demonstrating examples of super-complex structures of algebraic geometry and category theory that "naturally" arise on a combinatorial basis. Well, we must not forget that the evolution is mainly not so much by random point mutations of DNA, but as a result of the combinatorial process known as “chromosomal crossing over”. It is the fundamental need of evolution in "chromosomal crossing over" that forces living organisms to reproduce sexually (and to give this occupation such great and priority importance).
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