Replicator dynamics and the simplex as a vector space

Over the years of TheEGG, I’ve chronicled a number of nice properties of the replicator equation and its wide range of applications. From a theoretical perspective, I showed how the differential version can serve as the generator for the action that is the finite difference version of replicator dynamics. And how measurements of replicator dynamics can correspond to log-odds. From an application perspective, I talked about how replicator dynamics can be realized in many different ways. This includes a correspondance to idealized replating experiments and a representation of populations growing toward carrying capacity via fictitious free-space strategies. These fictitious strategies are made apparent by using a trick to factor and nest the replicator dynamics. The same trick can also help us to use the symmetries of the fitness functions for dimensionality reduction and to prove closed orbits in the dynamics. And, of course, I discussed countless heuristic models and some abductions that use replicator dynamics.

But whenever some object becomes so familiar and easy to handle, I get worried that I am missing out on some more foundational and simple structure underlying it. In the case of replicator dynamics, Tom Leinster’s post last year on the n-Category Cafe pointed me to the simple structure that I was missing: the vector space structure of the simplex. This allows us to use linear algebra — the friendliest tool in the mathematician’s toolbox — in a new way to better understand evolutionary dynamics.

A 2-simplex with some of its 1-dimensional linear subspaces drawn by Greg Egan.

Given my interest in operationalization of replicator dynamics, I will use some of the terminology and order of presentation from Aitchison’s (1986) statistical analysis of compositional data. We will see that a number of operations that we define will have clear experimental and evolutionary interpretations.

I can’t draw any real conclusions from this, but I found it worth jotting down for later reference. If you can think of a way to make these observations useful then please let me know.

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Ontology of player & evolutionary game in reductive vs effective theory

In my views of game theory, I largely follow Ariel Rubinstein: game theory is a set of fables. A collection of heuristic models that helps us structure how we make sense of and communicate about the world. Evolutionary game theory was born of classic game theory theory through a series of analogies. These analogies are either generalizations or restrictions of the theory depending on if you’re thinking about the stories or the mathematics. Given this heuristic genealogy of the field — and my enjoyment of heuristic models — I usually do not worry too much about what exactly certain ontic terms like strategy, player, or game really mean or refer to. I am usually happy to leave these terms ambiguous so that they can motivate different readers to have different interpretations and subsequently push for different models of different experiments. I think it is essential for heuristic theories to foster this diverse creativity. Anything goes.

However, not everyone agrees with Ariel Rubinstein and me; some people think that EGT isn’t “just” heuristics. In fact, more recently, I have also shifted some of my uses of EGT from heuristics to abductions. When this happens, it is no longer acceptable for researchers to be willy-nilly with fundamental objects of the theory: strategies, players, and games.

The biggest culprit is the player. In particular, a lot of confusion stems from saying that “cells are players”. In this post, I’d like to explore two of the possible positions on what constitutes players and evolutionary games.

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Spatializing the Go-vs-Grow game with the Ohtsuki-Nowak transform

Recently, I’ve been thinking a lot about small projects to get students started with evolutionary game theory. One idea that came to mind is to look at games that have been analyzed in the inviscid regime then ‘spatialize’ them and reanalyze them. This is usually not difficult to do and provides some motivation to solving for and making sense of the dynamic regimes of a game. And it is not always pointless, for example, our edge effects paper (Kaznatcheev et al, 2015) is mostly just a spatialization of Basanta et al.’s (2008a) Go-vs-Grow game together with some discussion.

Technically, TheEGG together with that paper have everything that one would need to learn this spatializing technique. However, I realized that my earlier posts on spatializing with the Ohtsuki-Nowak transform might a bit too abstract and the paper a bit too terse for a student who just started with EGT. As such, in this post, I want to go more slowly through a concrete example of spatializing an evolutionary game. Hopefully, it will be useful to students. If you are a beginner to EGT that is reading this post, and something doesn’t make sense then please ask for clarification in the comments.

I’ll use the Go-vs-Grow game as the example. I will focus on the mathematics, and if you want to read about the biological or oncological significance then I encourage you to read Kaznatcheev et al. (2015) in full.
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Cataloging a year of cancer blogging: double goods, measuring games & resistance

Happy year of the Rooster and 2017,

This month marks the start of the 7th calendar year of updates on TheEGG. Time to celebrate and summarize the posts of the year past. In 2016 there was the same number of posts as 2015, but instead of being clustered in a period of <7 months, they were more uniformly distributed across the calendar. Every month had at least one new post, although not necessarily written by me (in the case of the single post by Abel Molina in October). There were 29 entries, one linkdex cataloging 2015, and two updates on EGT reading group 51 – 55 & 56 – 60.

In September, as part of my relocation from Tampa to Oxford, I attended the 4th Heidelberg Laureate Forum. I wrote two pieces for their blog: Alan Turing and science through the algorithmic lens and a spotlight on Jan Poleszczuk: from HLF2013 to mathematical oncology. You can read those (and more posts coming this year) on their blog. I won’t go into more detail here.

As before, this post is meant to serve as an organizing reference and a way to uncover common themes on TheEGG. A list of TL;DRs from 2016. The year was split up into four major categories: cancer, complexity & evolution, other models, and philosophy. The cancer posts make up almost half the articles from last year, and are further subdivided into three subsections: double goods game, experimental game theory, and therapy resistance. I want to focus on these cancer posts for this linkdex, and the other three categories in the next installment.

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Chemical games and the origin of life from prebiotic RNA

From bacteria to vertebrates, life — as we know it today — relies on complex molecular interactions, the intricacies of which science has not fully untangled. But for all its complexity, life always requires two essential abilities. Organisms need to preserve their genetic information and reproduce.

In our own cells, these tasks are assigned to specialized molecules. DNA, of course, is the memory store. The information it encodes is expressed into proteins via messenger RNAs.Transcription (the synthesis of mRNAs from DNA) and translation (the synthesis of proteins from mRNAs) are catalyzed by polymerases necessary to speed up the chemical reactions.

It is unlikely that life started that way, with such a refined division of labor. A popular theory for the origin of life, known as the RNA world, posits that life emerged from just one type of molecule: RNAs. Because RNA is made up of base-complementary nucleotides, it can be used as a template for its own reproduction, just like DNA. Since the 1980s, we also know that RNA can act as a self-catalyst. These two superpowers – information storage and self-catalysis – make it a good candidate for the title of the first spark of life on earth.

The RNA-world theory has yet to meet with empirical evidence, but laboratory experiments have shown that self-preserving and self-reproducing RNA systems can be created in vitro. Little is known, however, about the dynamics that governed pre- and early life. In a recent paper, Yeates et al. (2016) attempt to shed light on this problem by (1) examining how small sets of different RNA sequences can compete for survival and reproduction in the lab and (2) offering a game-theoretical interpretation of the results.

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Drug holidays and losing resistance with replicator dynamics

A couple of weeks ago, before we all left Tampa, Pranav Warman, David Basanta and I frantically worked on refinements of our model of prostate cancer in the bone. One of the things that David and Pranav hoped to see from the model was conditions under which adaptive therapy (or just treatment interrupted with non-treatment holidays) performs better than solid blocks of treatment. As we struggled to find parameters that might achieve this result, my frustration drove me to embrace the advice of George Pólya: “If you can’t solve a problem, then there is an easier problem you can solve: find it.”

IMO6 LogoIn this case, I opted to remove all mentions of the bone and cancer. Instead, I asked a simpler but more abstract question: what qualitative features must a minimal model of the evolution of resistance have in order for drug holidays to be superior to a single treatment block? In this post, I want to set up this question precisely, show why drug holidays are difficult in evolutionary models, and propose a feature that makes drug holidays viable. If you find this topic exciting then you should consider registering for the 6th annual Integrated Mathematical Oncology workshop at the Moffitt Cancer Center.[1] This year’s theme is drug resistance.
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Multiplicative versus additive fitness and the limit of weak selection

Previously, I have discussed the importance of understanding how fitness is defined in a given model. So far, I’ve focused on how mathematically equivalent formulations can have different ontological commitments. In this post, I want to touch briefly on another concern: two different types of mathematical definitions of fitness. In particular, I will discuss additive fitness versus multiplicative fitness.[1] You often see the former in continuous time replicator dynamics and the latter in discrete time models.

In some ways, these versions are equivalent: there is a natural bijection between them through the exponential map or by taking the limit of infinitesimally small time-steps. A special case of more general Lie theory. But in practice, they are used differently in models. Implicitly changing which definition one uses throughout a model — without running back and forth through the isomorphism — can lead to silly mistakes. Thankfully, there is usually a quick fix for this in the limit of weak selection.

I suspect that this post is common knowledge. However, I didn’t have a quick reference to give to Pranav Warman, so I am writing this.
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Evolutionary dynamics of acid and VEGF production in tumours

Today was my presentation day at ECMTB/SMB 2016. I spoke in David Basanta’s mini-symposium on the games that cancer cells play and postered during the poster session. The mini-symposium started with a brief intro from David, and had 25 minute talks from Jacob Scott, myself, Alexander Anderson, and John Nagy. David, Jake, Sandy, and John are some of the top mathematical oncologists and really drew a crowd, so I felt privileged at the opportunity to address that crowd. It was also just fun to see lots of familiar faces in the same place.

A crowded room by the end of Sandy's presentation.

A crowded room by the end of Sandy’s presentation.

My talk was focused on two projects. The first part was the advertised “Evolutionary dynamics of acid and VEGF production in tumours” that I’ve been working on with Robert Vander Velde, Jake, and David. The second part — and my poster later in the day — was the additional “(+ measuring games in non-small cell lung cancer)” based on work with Jeffrey Peacock, Andriy Marusyk, and Jake. You can download my slides here (also the poster), but they are probably hard to make sense of without a presentation. I had intended to have a preprint out on this prior to today, but it will follow next week instead. Since there are already many blog posts about the double goods project on TheEGG, in this post I will organize them into a single annotated linkdex.

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Hamiltonian systems and closed orbits in replicator dynamics of cancer

Last month, I classified the possible dynamic regimes of our model of acidity and vasculature as linear goods in cancer. In one of those dynamic regimes, there is an internal fixed point and I claimed closed orbits around that point. However, I did not justify or illustrate this claim. In this post, I will sketch how to prove that those orbits are indeed closed, and show some examples. In the process, we’ll see how to transform our replicator dynamics into a Hamiltonian system and use standard tricks from classical mechanics to our advantage. As before, my tricks will draw heavily from Hauert et al. (2002) analysis of the optional public good game. Studying this classic paper closely is useful for us because of an analogy that Robert Vander Velde found between the linear version of our double goods model for the Warburg effect and the optional public good game.

The post will mostly be about the mathematics. However, at the end, I will consider an example of how these sort of cyclic dynamics can matter for treatment. In particular, I will consider what happens if we target aerobic glycolysis with a drug like lonidamine but stop the treatment too early.

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Multiple realizability of replicator dynamics

Abstraction is my favorite part of mathematics. I find a certain beauty in seeing structures without their implementations, or structures that are preserved across various implementations. And although it seems possible to reason through analogy without (explicit) abstraction, I would not enjoy being restricted in such a way. In biology and medicine, however, I often find that one can get caught up in the concrete and particular. This makes it harder to remember that certain macro-dynamical properties can be abstracted and made independent of particular micro-dynamical implementations. In this post, I want to focus on a particular pet-peeve of mine: accounts of the replicator equation.

I will start with a brief philosophical detour through multiple realizability, and discuss the popular analogy of temperature. Then I will move on to the phenomenological definition of the replicator equation, and a few realizations. A particular target will be the statement I’ve been hearing too often recently: replicator dynamics are only true for a very large but fixed-size well-mixed population.

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