Principles of biological computation: from circadian clock to evolution
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
For the final — third — day of the Santa Fe Institute workshop on “What is Biological Computation?” (11 – 13 September) organized by Albert Kao, Jessica Flack, and David Wolpert, we opened the floor to short impormptu talks from all the participants. The result was 21 presentations organized in 4 sessions. As with my posts on the previous two days of this workshop (Day 1: Elements of biological computation & stochastic thermodynamics of life; Day 2: The science and engineering of biological computation: from process to software to DNA-based neural networks), I want to briefly touch on all ..read more
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The science and engineering of biological computation: from process to software to DNA-based neural networks
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
In the earlier days of TheEGG, I used to write extensively about the themes of some of the smaller conferences and workshops that I attended. One of the first such workshops I blogged about in detail was the 2nd workshop on Natural Algorithms and the Sciences in May 2013. That spawned an eight post series that I closed with a vision for a path toward an algorithmic theory of biology. In the six years since, I’ve been following that path. But I have fallen out of the habit of writing summary posts about the workshops that I attend. Since my recent trip to the Santa Fe Institute for the “What is ..read more
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Elements of biological computation & stochastic thermodynamics of life
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
This week, I was visiting the Santa Fe Institute for a workshop organized by Albert Kao, Jessica Flack, and David Wolpert on “What is biological computation?” (11 – 13 September 2019). It was an ambitious question and I don’t think that we were able to answer it in just three days of discussion, but I think that we all certainly learnt a lot. At least, I know that I learned a lot of new things. The workshop had around 34 attendees from across the world, but from the reaction on twitter it seems like many more would have been eager to attend also. Hence, both to help synchronize the memory net ..read more
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Rationality, the Bayesian mind and their limits
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
Bayesianism is one of the more popular frameworks in cognitive science. Alongside other similar probalistic models of cognition, it is highly encouraged in the cognitive sciences (Chater, Tenenbaum, & Yuille, 2006). To summarize Bayesianism far too succinctly: it views the human mind as full of beliefs that we view as true with some subjective probability. We then act on these beliefs to maximize expected return (or maybe just satisfice) and update the beliefs according to Bayes’ law. For a better overview, I would recommend the foundations work of Tom Griffiths (in particular, see Griffit ..read more
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Web of C-lief: conjectures vs. model assumptions vs. scientific beliefs
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
In his 1951 paper on the “Two Dogmas of Empiricism”, W.V.O Quine introduced the Web of Belief as a metaphor for his holistic epistemology of scientific knowledge. With this metaphor, Quine aimed to give an alternative to the reductive atomising epistemology of the logical empiricists. For Quine, no “fact” is an island and no experiment can be focused in to resole just one hypothesis. Instead, each of our beliefs forms part of an interconnected web and when a new belief conflicts with an existing one then this is a signal for us to refine some belief. But this signal does not unambiguously sing ..read more
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Idealization vs abstraction for mathematical models of evolution
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
This week I was in Turku, Finland for the annual congress of the European Society for Evolutionary Biology. I presented in the symposium on mathematical models in evolutionary biology organized by Guy Cooper, Matishalin Patel, Tom Scott, and Asher Leeks. It was a fun. It was also a big challenge given the short ten minute format. I decided to use my ten minutes to try to convince the audience that we should consider not just idealized models but also abstractions. So after my typical introduction of computational vs algorithmic biology, I switched to talking about triangles. If you would like ..read more
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Allegory of the replication crisis in algorithmic trading
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
One of the most interesting ongoing problems in metascience right now is the replication crisis. This a methodological crisis around the difficulty of reproducing or replicating past studies. If we cannot repeat or recreate the results of a previous study then it casts doubt on if those ‘results’ were real or just artefacts of flawed methodology, bad statistics, or publication bias. If we view science as a collection of facts or empirical truths than this can shake the foundations of science. The replication crisis is most often associated with psychology — a field that seems to be having the ..read more
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Process over state: Math is about proofs, not theorems.
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
A couple of days ago, Maylin and I went to pick blackberries along some trails near our house. We spent a number of hours doing it and eventually I turned all those berries into one half-litre jar of jam. On the way to the blackberry trails, we passed a perfectly fine Waitrose — a supermarket that sells (among countless other things) jam. A supermarket I had to go to later anyways to get jamming sugar. Why didn’t we just buy the blackberries or the jam itself? It wasn’t a matter of money: several hours of our time picking berries and cooking them cost much more than a half-litre of jam, even f ..read more
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Generating random power-law graphs
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
‘Power-law’ is one of the biggest buzzwords in complexology. Almost everything is a power-law. I’ve even used it to sell my own work. But most work that deals in power-laws tends to lack rigour. And just establishing that something is a power-law shouldn’t make us feel that it is more connected to something else that is a power-law. Cosma Shalizi — the great critic of sloppy thinking in complexology — has an insightful passage on power-laws: [T]here turn out to be nine and sixty ways of constructing power laws, and every single one of them is right, in that it does indeed produce a power law ..read more
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Blogging community of computational and mathematical oncologists
Theory, Evolution, and Games Group
by Artem Kaznatcheev
3y ago
A few weeks ago, David Basanta reached out to me (and many other members of the mathematical oncology community) about building a community blog together. This week, to coincide with the Society for Mathematical Biology meeting in Montreal, we launched the blog. In keeping with the community focus, we have an editorial board of 8 people that includes (in addition to David and me): Christina Curtis, Elana Fertig, Stacey Finley, Jakob Nikolas Kather, Jacob G. Scott, and Jeffrey West. The theme is computational and mathematical oncology, but we welcome contributions from all nearby disciplines. T ..read more
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