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Introduction: Scott Oswald

in Chat

Hi everyone!

I am PhD student in plant biology at the University of Georgia, Savannah River Ecology Lab. The mathematics I do is part hobby and part work. I don't have much formal training (in terms of courses), but I have self-studied quite a bit (undoubtedly there are plenty of gaps in my knowledge).

I primarily got interested in category theory through John Baez' papers (and some attempts at programming in Haskell). I saw John's paper Relative entropy in biological systems linked on the /r/math subreddit of reddit. I really liked that paper because it used some interesting math to change the way I conceive of evolution and ecology. From that paper, I was led to papers on using category theory to analyze/formalize diagrams in science (e.g., A compositional framework of passive linear networks). So I started to think I might be able to find applications of category theory to the systems I already study for work.

I think compositionality will be a useful idea in studying complex biological systems, especially ones where it is difficult to measure or control phenomena of interest. By describing how systems (e.g., plant tissues) composed to form bigger systems (e.g., whole plants), we can then deduce global system properties from local ones, or vice-versa. That way data, observations, and hypotheses at different scales (e.g., observations of forests vs. observations of tissues in a lab) can be related in a systematic way.

Anyways, that's how I ended up here.

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Hi Scott! It seems like we have a similar background, and are both interested in looking at applying these ideas to practical biological problems.

Comment Source:Hi Scott! It seems like we have a similar background, and are both interested in looking at applying these ideas to practical biological problems.
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Oh cool! What area of biology do you work on? I mostly work on plant physiology and ecology, but occasionally I think about more general biological problems like ecological/evolutionary dynamics.

Comment Source:Oh cool! What area of biology do you work on? I mostly work on plant physiology and ecology, but occasionally I think about more general biological problems like ecological/evolutionary dynamics.
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Mostly computational systems biology, and synthetic biology.

Comment Source:Mostly computational systems biology, and synthetic biology.
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Hi, Scott! I'm glad you joined the course - your comments are bringing it some extra vitality. It would be great to connect category theory more firmly to biology. Right now I'm having the most luck with biochemistry: my recent series of posts on emergent conservation laws has a secret category-theoretic underpinning that I want to explain someday.

Comment Source:Hi, Scott! I'm glad you joined the course - your comments are bringing it some extra vitality. It would be great to connect category theory more firmly to biology. Right now I'm having the most luck with biochemistry: my recent series of posts on [emergent conservation laws](https://johncarlosbaez.wordpress.com/2018/06/27/coupling-through-emergent-conservation-laws-part-1/) has a secret category-theoretic underpinning that I want to explain someday.
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I would like to hear the secret category-theoretic underpinning of the emergent conservation laws as that was an interesting idea. There's a lot of utility in just the biochemistry, and not just in molecular biology. Biologists, chemists, and geologists study how elements move through ecosystems (biogeochemistry) and biochemical reactions make up a big part of how those elements move.

Where the category theoretic ideas might have serious applications is being able to link the small and large scale. Take for example photosynthesis. Photosynthesis is a big and complicated series of reactions (and differs a little bit in different plant species), but most of those reactions are only serve to characterize a simpler "pseudo reaction" CO2 + H2O + Photon --> Sugar, which is the composition of those reactions. So understanding/describing that compositionality and properties of it could lead to insights in biogeochemistry too. I think there are similar potential applications in physiology since physiology of most organisms is mostly a mixture of biochemistry and biophysics

I think it would also be interesting to revisit some of Howard Odum's ideas (unfortunately the lesser known of the Odum brothers) with ideas from category theory / networks theory. Despite having a degree in biology (with a lot of ecology too), I had never heard of his work before seeing it referenced in one of your online talks! His approach to modeling ecosystems using electric circuit analogies and diagrams suggests that category-theoretic techniques might have some application.

Comment Source:I would like to hear the secret category-theoretic underpinning of the emergent conservation laws as that was an interesting idea. There's a lot of utility in just the biochemistry, and not just in molecular biology. Biologists, chemists, and geologists study how elements move through ecosystems (biogeochemistry) and biochemical reactions make up a big part of how those elements move. Where the category theoretic ideas might have serious applications is being able to link the small and large scale. Take for example photosynthesis. Photosynthesis is a big and complicated series of reactions (and differs a little bit in different plant species), but most of those reactions are only serve to characterize a simpler "pseudo reaction" CO2 + H2O + Photon --> Sugar, which is the composition of those reactions. So understanding/describing that compositionality and properties of it could lead to insights in biogeochemistry too. I think there are similar potential applications in physiology since physiology of most organisms is mostly a mixture of biochemistry and biophysics I think it would also be interesting to revisit some of Howard Odum's ideas (unfortunately the lesser known of the Odum brothers) with ideas from category theory / networks theory. Despite having a degree in biology (with a lot of ecology too), I had never heard of his work before seeing it referenced in one of your online talks! His approach to modeling ecosystems using electric circuit analogies and diagrams suggests that category-theoretic techniques might have some application.