11.1: Simulating evolution
- Page ID
- 46667
\( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)
\( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)
\( \newcommand{\dsum}{\displaystyle\sum\limits} \)
\( \newcommand{\dint}{\displaystyle\int\limits} \)
\( \newcommand{\dlim}{\displaystyle\lim\limits} \)
\( \newcommand{\id}{\mathrm{id}}\) \( \newcommand{\Span}{\mathrm{span}}\)
( \newcommand{\kernel}{\mathrm{null}\,}\) \( \newcommand{\range}{\mathrm{range}\,}\)
\( \newcommand{\RealPart}{\mathrm{Re}}\) \( \newcommand{\ImaginaryPart}{\mathrm{Im}}\)
\( \newcommand{\Argument}{\mathrm{Arg}}\) \( \newcommand{\norm}[1]{\| #1 \|}\)
\( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\)
\( \newcommand{\Span}{\mathrm{span}}\)
\( \newcommand{\id}{\mathrm{id}}\)
\( \newcommand{\Span}{\mathrm{span}}\)
\( \newcommand{\kernel}{\mathrm{null}\,}\)
\( \newcommand{\range}{\mathrm{range}\,}\)
\( \newcommand{\RealPart}{\mathrm{Re}}\)
\( \newcommand{\ImaginaryPart}{\mathrm{Im}}\)
\( \newcommand{\Argument}{\mathrm{Arg}}\)
\( \newcommand{\norm}[1]{\| #1 \|}\)
\( \newcommand{\inner}[2]{\langle #1, #2 \rangle}\)
\( \newcommand{\Span}{\mathrm{span}}\) \( \newcommand{\AA}{\unicode[.8,0]{x212B}}\)
\( \newcommand{\vectorA}[1]{\vec{#1}} % arrow\)
\( \newcommand{\vectorAt}[1]{\vec{\text{#1}}} % arrow\)
\( \newcommand{\vectorB}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)
\( \newcommand{\vectorC}[1]{\textbf{#1}} \)
\( \newcommand{\vectorD}[1]{\overrightarrow{#1}} \)
\( \newcommand{\vectorDt}[1]{\overrightarrow{\text{#1}}} \)
\( \newcommand{\vectE}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash{\mathbf {#1}}}} \)
\( \newcommand{\vecs}[1]{\overset { \scriptstyle \rightharpoonup} {\mathbf{#1}} } \)
\(\newcommand{\longvect}{\overrightarrow}\)
\( \newcommand{\vecd}[1]{\overset{-\!-\!\rightharpoonup}{\vphantom{a}\smash {#1}}} \)
\(\newcommand{\ket}[1]{\left| #1 \right>}\)
\(\newcommand{\bra}[1]{\left< #1 \right|}\)
\(\newcommand{\braket}[2]{\left< #1 \vphantom{#2} \right| \left. #2 \vphantom{#1} \right>}\)
\(\newcommand{\braopket}[3]{\left< #1 \vphantom{#2}\vphantom{#3} \right| #2 \vphantom{#1}\vphantom{#3} \left| #3 \vphantom{#1}\vphantom{#2} \right>}\)
\(\newcommand{\qmvec}[1]{\mathbf{\vec{#1}}}\)
\(\newcommand{\op}[1]{\hat{\mathbf{#1}}}\)
\(\newcommand{\expect}[1]{\langle #1 \rangle}\)
\(\newcommand{\dfn}[1]{\emph{\textbf{#1}}}\)
I start with a simple model that demonstrates a basic form of evolution. According to the theory, the following features are sufficient to produce evolution:
- Replicators: We need a population of agents that can reproduce in some way. We’ll start with replicators that make perfect copies of themselves. Later we’ll add imperfect copying, that is, mutation.
- Variation: We need variability in the population, that is, differences between individuals.
- Differential survival or reproduction: The differences between individuals have to affect their ability to survive or reproduce.
To simulate these features, we’ll define a population of agents that represent individual organisms. Each agent has genetic information, called its genotype, which is the information that gets copied when the agent replicates. In our model1, a genotype is represented by a sequence of N binary digits (zeros and ones), where N is a parameter we choose.
To generate variation, we create a population with a variety of genotypes; later we will explore mechanisms that create or increase variation.
Finally, to generate differential survival and reproduction, we define a function that maps from each genotype to a fitness, where fitness is a quantity related to the ability of an agent to survive or reproduce.
1This model is a variant of the NK model developed primarily by Stuart Kauffman (see http://thinkcomplex.com/nk).