Space-time maps & tracking colony size with OpenCV in Python

One of the things that the Department of Integrated Mathematical Oncology at the Moffitt Cancer Center is doing very well, is creating an atmosphere that combines mathematics and experiment in cancer. Fellow TheEGG blogger, Robert Vander Velde is one of the new generation of cancer researchers who are combining mathematics and experiment. Since I left Tampa, I’ve had less opportunity to keep up with the work at the IMO, but occasionally I catch up on…

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Four stages in the relationship of computer science to other fields

This weekend, Oliver Schneider — an old high-school friend — is visiting me in the UK. He is a computer scientist working on human-computer interaction and was recently appointed as an assistant professor at the Department of Management Sciences, University of Waterloo. Back in high-school, Oliver and I would occasionally sneak out of class and head to the University of Saskatchewan to play counter strike in the campus internet cafe. Now, Oliver builds haptic interfaces…

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On Frankfurt’s Truth and Bullshit

In 2015 and 2016, as part of my new year reflections on the year prior, I wrote a post about the ‘year in books’. The first was about philosophy, psychology and political economy and it was unreasonably long and sprawling as post. The second time, I decided to divide into several posts, but only wrote the first one on cancer: Neanderthals to the National Cancer Act to now. In this post, I want to return…

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Coarse-graining vs abstraction and building theory without a grounding

Back in September 2017, Sandy Anderson was tweeting about the mathematical oncology revolution. To which Noel Aherne replied with a thorny observation that “we have been curing cancers for decades with radiation without a full understanding of all the mechanisms”. This lead to a wide-ranging discussion and clarification of what is meant by terms like mechanism. I had meant to blog about these conversations when they were happening, but the post fell through the cracks…

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Game landscapes: from fitness scalars to fitness functions

My biology writing focuses heavily on fitness landscapes and evolutionary games. On the surface, these might seem fundamentally different from each other, with their only common feature being that they are both about evolution. But there are many ways that we can interconnect these two approaches. The most popular connection is to view these models as two different extremes in terms of time-scale. When we are looking at evolution on short time-scales, we are primarily…

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Colour, psychophysics, and the scientific vs. manifest image of reality

Recently on TheEGG, I’ve been writing a lot about the differences between effective (or phenomenological) and reductive theories. Usually, I’ve confined this writing to evolutionary biology; especially the tension between effective and reductive theories in the biology of microscopic systems. For why this matters to evolutionary game theory, see Kaznatcheev (2017, 2018). But I don’t think that microscopic systems are the funnest place to see this interplay. The funnest place to see this is in…

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Constant-sum games as a way from non-cell autonomous processes to constant tumour growth rate

A lot of thinking in cancer biology seems to be focused on cell-autonomous processes. This is the (overly) reductive view that key properties of cells, such as fitness, are intrinsic to the cells themselves and not a function of their interaction with other cells in the tumour. As far as starting points go, this is reasonable. But in many cases, we can start to go beyond this cell-autonomous starting point and consider non-cell-autonomous processes. This…

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Local maxima and the fallacy of jumping to fixed-points

An economist and a computer scientist are walking through the University of Chicago campus discussing the efficient markets hypothesis. The computer scientist spots something on the pavement and exclaims: “look at that $20 on the ground — seems we’ll be getting a free lunch today!” The economist turns to her without looking down and replies: “Don’t be silly, that’s impossible. If there was a $20 bill there then it would have been picked up already.”…

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Quick introduction: the algorithmic lens

Computers are a ubiquitous tool in modern research. We use them for everything from running simulation experiments and controlling physical experiments to analyzing and visualizing data. For almost any field ‘X’ there is probably a subfield of ‘computational X’ that uses and refines these computational tools to further research in X. This is very important work and I think it should be an integral part of all modern research. But this is not the algorithmic…

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Danger of motivatiogenesis in interdisciplinary work

Randall Munroe has a nice old xkcd on citogenesis: the way factoids get created from bad checking of sources. You can see the comic at right. But let me summarize the process without direct reference to Wikipedia: 1. Somebody makes up a factoid and writes it somewhere without citation. 2. Another person then uses the factoid in passing in a more authoritative work, maybe sighting the point in 1 or not. 3. Further work inherits…

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