Measuring games in the Petri dish

For the next couple of months, Jeffrey Peacock is visiting Moffitt. He’s a 4th year medical student at the University of Central Florida with a background in microbiology and genetic engineering of bacteria and yeast. Together with Andriy Marusyk and Jacob Scott, he will move to human cells and run some in vitro experiments with non-small cell lung cancer — you can read more about this on Connecting the Dots. Robert Vander Velde is also in the process of designing some experiments of his own. Both Jeff and Robert are interested in evolutionary game theory, so this is great opportunity for me to put my ideas on operationalization of replicator dynamics into practice.

In this post, I want to outline the basic process for measuring a game from in vitro experiments. Games in the Petri-dish. It won’t be as action packed as Agar.io — that’s an actual MMO cells-in-Petri-dish game; play here — but hopefully it will be more grounded in reality. I will introduce the gain function, show how to measure it, and stress the importance of quantifying the error on this measurement. Since this is part of the theoretical preliminaries for my collaborations, we don’t have our own data to share yet, so I will provide an illustrative cartoon with data from Archetti et al. (2015). Finally, I will show what sort of data would rule-out the theoretician’s favourite matrix games and discuss the ego-centric representation of two-strategy matrix games. The hope is that we can use this work to go from heuristic guesses at what sort of games microbes or cancer cells might play to actually measuring those games.
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A year in books: Neanderthals to the National Cancer Act to now

A tradition I started a couple of years ago is to read at least one non-fiction book per month and then to share my thoughts on the reading at the start of the following year. Last year, my dozen books were mostly on philosophy, psychology, and political economy. My brief comments on them ended up running a long 3.2 thousand words. This time the list had expanded to around 19 books. So I will divide the summaries into thematic sets. For the first theme, I will start with a subject that is new for my idle reading: cancer.

As a new researcher in mathematical oncology — and even though I am located in a cancer hospital — my experience with cancer has been mostly confined to the remote distance of replicator dynamics. So above all else these three books — Nelson’s (2013) Anarchy in the Organism, Mukherjee’s (2010) The Emperor of All Maladies, and Leaf’s (2014) The Truth in Small Doses — have provided me with insights into the personal experiences of the patient and doctor.

I hope that based on these reviews and the ones to follow, you can suggest more books for me to read in 2016. Better yet, maybe my comments will help you choose your next book. Much of what I read in 2015 came from suggestions made by my friends and readers, as well as articles, blogs, and reviews I’ve stumbled across.[1] In fact, each of these cancer books was picked for me by someone else.

If you’ve been to a restaurant with me then you know that I hate choosing between close-to-equivalent options. To avoid such discomfort, I outsourced the choosing of my February book to G+ and Nelson’s Anarchy in the Organism beat out Problems of the Self by a narrow margin to claim a spot on the reading list. As I was finishing up Nelson’s book — which I will review last in this post — David Basanta dropped off The Emperor of All Maladies on my desk. So I continued my reading on cancer. Finally, Leaf’s book came towards the end of the year based on a recommendation from Jacob Scott. It helped reinvigorate me after a summer away from the Moffitt Cancer Center.
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Cataloging a year of blogging

Happy Old New Year.

January 2016 is the the start of the 6th calendar year and the 41st month with updates to TheEGG. The reason for the large discrepancy between these two numbers is occasional months without activity. The past year was exceptional in this regard with the longest single silence on the blog between April 4th and October 26th. This means that the year saw only 29 new entries, 2 indexes cataloging 2014, a report on the EGT reading group, and an update on readership. This post is meant to organize the last year of activity for future reference, and to try to uncover common themes.

If you like lists and TL;DRs then this is for you.
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