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# Introduction: Patrick O'Neill

Hi all, I'm Pat.

I'm very much looking forward to getting started. Much thanks to John for organizing the seminar, and to Brendan and David for writing the text!

As for a bit about myself, I studied math and philosophy as an undergrad and then jumped ship to computational biology for grad school where I really came to miss having crisp definitions and theorems. I studied information processing in bacterial gene expression for my Ph.D., trying to understand how transcription factors work over the cellular and evolutionary timescales. Now I work in industry as a data scientist.

I'd been curious about category theory since I got hooked on Haskell as an undergraduate. I'd studied from a few other texts like Pierce and Awodey, along with some of the very weird papers of Robert Rosen. I always felt, though, that I was somehow missing the point of it. It was puzzling to me because it seemed that category theory should be right up my alley.

Studying category theory felt kind of like raking a zen rock garden: it was soothing and pleasing for its own sake, but I struggled to understand what it was actually good for! I trust that there's a good answer to this question, and believe people when they tell me that category theory is now indispensable in some areas of math and physics. So that's what I most hope to get out of this course: a sense of what you can do with category theory that would be difficult or impossible without it. I'd be especially interested in working through the implications for biology.

Anyway, can't wait to dive in and get to know everyone. Thanks again to everyone who's making it possible.

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1.

Robert Rosen was a great thinker, pointing out the obvious two categories of biological life: structure and behavior.

Comment Source:Robert Rosen was a great thinker, pointing out the obvious two categories of biological life: structure and behavior.
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2.
edited March 2018

It's tough, though-- the average biologist is uncomfortable with calculus, compared to which category theory is practically a slap in the face :/ It might be an interesting challenge to translate Rosen's central results out of the language of category theory and see what remains. A few reviews have already attempted this, and Rosen's continuing obscurity perhaps speaks to the difficulty of the task.

Comment Source:It's tough, though-- the average biologist is uncomfortable with calculus, compared to which category theory is practically a slap in the face :/ It might be an interesting challenge to translate Rosen's central results out of the language of category theory and see what remains. A few reviews have already attempted this, and Rosen's continuing obscurity perhaps speaks to the difficulty of the task.
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Patrick, you are living proof that biology is an important subject for applied mathematics. As far as Robert Rosen, I developed a personal relationship with him and admired him greatly. Unfortunately his work, although groundbreaking was not always mathematically solid. I am hoping people like John and David can help us remedy this problem.

As far as what category theory can allow us to do that you can't do otherwise I would like to suggest you ask a different question. When tackling really hard problems one can quickly get lost in tactical issues losing track of the "big picture". Category theory in my view is about organizing how you think about problems that allows you to keep track of the details while maintaining a clear picture how those details fit into a larger conceptual framework. I think this will become clearer in the later chapters of Brendon and David's book.

So in principle, I have not yet seen anything that you couldn't do without category theory. Of course the extent of my ignorance is vast so there may be examples of such problems. Practically I think really difficult problems requiring that you think about the problem at different levels of resolution will benefit immensely from using category theory. You can think of learning category theory as a capital investment. Every problem you tackle will now be easier. If you have to dig a big ditch you want to have a backhoe.

Comment Source:Patrick, you are living proof that biology is an important subject for applied mathematics. As far as Robert Rosen, I developed a personal relationship with him and admired him greatly. Unfortunately his work, although groundbreaking was not always mathematically solid. I am hoping people like John and David can help us remedy this problem. As far as what category theory can allow us to do that you can't do otherwise I would like to suggest you ask a different question. When tackling really hard problems one can quickly get lost in tactical issues losing track of the "big picture". Category theory in my view is about organizing how you think about problems that allows you to keep track of the details while maintaining a clear picture how those details fit into a larger conceptual framework. I think this will become clearer in the later chapters of Brendon and David's book. So in principle, I have not yet seen anything that you couldn't do without category theory. Of course the extent of my ignorance is vast so there may be examples of such problems. Practically I think really difficult problems requiring that you think about the problem at different levels of resolution will benefit immensely from using category theory. You can think of learning category theory as a capital investment. Every problem you tackle will now be easier. If you have to dig a big ditch you want to have a backhoe.
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4.

If I want to get an intro to Robert Rosen's thinking, what should read? (Hopefully accessible to somebody with no academic connections...)

Comment Source:If I want to get an intro to Robert Rosen's thinking, what should read? (Hopefully accessible to somebody with no academic connections...)