It’s time to continue this information geometry series, because I’ve promised to give the following talk at a conference on the mathematics of biodiversity in early July… and I still need to do some of the research!

## Diversity, information geometry and learning

As is well known, some measures of biodiversity are formally identical to measures of information developed by Shannon and others. Furthermore, Marc Harper has shown that the replicator equation in evolutionary game theory is formally identical to a process of Bayesian inference, which is studied in the field of machine learning using ideas from information geometry. Thus, in this simple model, a population of organisms can be thought of as a ‘hypothesis’ about how to survive, and natural selection acts to update this hypothesis according to Bayes’ rule. The question thus arises to what extent natural changes in biodiversity can be usefully seen as analogous to a form of learning. However, some of the same mathematical structures arise in the study of chemical reaction networks, where the increase of entropy, or more precisely decrease of free energy, is not usually considered a form of ‘learning’. We report on some preliminary work on these issues.

So, let’s dive in! To some extent I’ll be explaining these two papers:

• Marc Harper, Information geometry and evolutionary game theory.

• Marc Harper, The replicator equation as an inference dynamic.

However, I hope to bring in some more ideas from physics, the study of biodiversity, and the theory of stochastic Petri nets, also known as chemical reaction networks. So, this series may start to overlap with my network theory posts. We’ll see. We won’t get far today: for now, I just want to review and expand on what we did last time.

### The replicator equation

The **replicator equation** is a simplified model of how populations change. Suppose we have types of self-replicating entity. I’ll call these entities **replicators**. I’ll call the types of replicators **species**, but they don’t need to be species in the biological sense. For example, the replicators could be genes, and the types could be alleles. Or the replicators could be restaurants, and the types could be restaurant chains.

Let or just for short, be the population of the th species at time Then the replicator equation says

So, the population changes at a rate proportional to but the ‘constant of proportionality’ need not be constant: it can be any smooth function of the populations of all the species. We call the **fitness** of the th species.

Of course this model is absurdly general, while still leaving out lots of important effects, like the spatial variation of populations, or the ability for the population of some species to start at zero and become nonzero—which happens thanks to mutation. Nonetheless this model is worth taking a good look at.

Using the magic of vectors we can write

and

This lets us write the replicator equation a wee bit more tersely as

where on the right I’m multiplying vectors componentwise, the way your teachers tried to brainwash you into never doing:

In other words, I’m thinking of and as functions on the set and multiplying them pointwise. This will be a nice way of thinking if we want to replace this finite set by some more general space.

Why would we want to do that? Well, we might be studying lizards with different length tails, and we might find it convenient to think of the set of possible tail lengths as the half-line instead of a finite set.

Or, just to get started, we might want to study the pathetically simple case where doesn’t depend on Then we just have a fixed function and a time-dependent function obeying

If we’re physicists, we might write more suggestively as and write the operator multiplying by as Then our equation becomes

This looks a lot like Schrödinger’s equation, but since there’s no factor of and is real-valued, it’s more like the heat equation or the ‘master equation’, the basic equation of stochastic mechanics.

For an explanation of Schrödinger’s equation and the master equation, try Part 12 of the network theory series. In that post I didn’t include a minus sign in front of the That’s no big deal: it’s just a different convention than the one I want today. A more serious issue is that in stochastic mechanics, stands for a *probability distribution*. This suggests that we should get probabilities into the game somehow.

### The replicator equation in terms of probabilities

Luckily, that’s exactly what people usually do! Instead of talking about the population of the th species, they talk about the *probability* that one of our organisms will belong to the th species. This amounts to normalizing our populations:

Don’t you love it when notations work out well? Our big **P**opulation has gotten normalized to give little **p**robability

How do these probabilities change with time? Now is the moment for that least loved rule of elementary calculus to come out and take a bow: the quotient rule for derivatives!

Using our earlier version of the replicator equation, this gives:

Using the definition of this simplifies to:

The stuff in parentheses actually has a nice meaning: it’s just the **mean fitness**. In other words, it’s the average, or expected, fitness of an organism chosen at random from the whole population. Let’s write it like this:

So, we get the **replicator equation** in its classic form:

This has a nice meaning: for the fraction of organisms of the th type to increase, their fitness must exceed the mean fitness. If you’re trying to increase market share, what matters is not how good you are, but how much *better than average* you are. If everyone else is lousy, you’re in luck.

### Entropy

Now for something a bit new. Once we’ve gotten a probability distribution into the game, its entropy is sure to follow:

This says how ‘smeared-out’ the overall population is among the various different species. Alternatively, it says how much *information* it takes, on average, to say which species a randomly chosen organism belongs to. For example, if there are species, all with equal populations, the entropy works out to So in this case, it takes bits of information to say which species a randomly chosen organism belongs to.

In biology, entropy is one of many ways people measure biodiversity. For a quick intro to some of the issues involved, try:

• Tom Leinster, Measuring biodiversity, *Azimuth*, 7 November 2011.

• Lou Jost, Entropy and diversity, *Oikos* **113** (2006), 363–375.

But we don’t need to understand this stuff to see how entropy is connected to the replicator equation. Marc Harper’s paper explains this in detail:

• Marc Harper, The replicator equation as an inference dynamic.

and I hope to go through quite a bit of it here. But not today! Today I just want to look at a pathetically simple, yet still interesting, example.

### Exponential growth

Suppose the fitness of each species is independent of the populations of all the species. In other words, suppose each fitness is actually a constant, say Then the replicator equation reduces to

so it’s easy to solve:

You don’t need a detailed calculation to see what’s going to happen to the probabilities

The most fit species present will eventually take over! If one species, say the th one, has a fitness greater than the rest, then the population of this species will eventually grow faster than all the rest, at least if its population starts out greater than zero. So as we’ll have

and

Thus the probability distribution will become more sharply peaked, and *its entropy will eventually approach zero*.

With a bit more thought you can see that even if more than one species shares the maximum possible fitness, the entropy will eventually decrease, though not approach zero.

In other words, *the biodiversity will eventually drop* as all but the most fit species are overwhelmed. Of course, this is only true in our simple idealization. In reality, biodiversity behaves in more complex ways—in part because species interact, and in part because mutation tends to smear out the probability distribution We’re not looking at these effects yet. They’re extremely important… in ways we can only fully understand if we start by looking at what happens when they’re not present.

In still other words, *the population will absorb information from its environment*. This should make intuitive sense: the process of natural selection resembles ‘learning’. As fitter organisms become more common and less fit ones die out, the environment puts its stamp on the probability distribution So, this probability distribution should gain information.

While intuitively clear, this last claim also follows more rigorously from thinking of entropy as negative information. Admittedly, it’s always easy to get confused by minus signs when relating entropy and information. A while back I said the entropy

was the average information required to say which species a randomly chosen organism belongs to. If this entropy is going down, isn’t the population *losing* information?

No, this is a classic sign error. It’s like the concept of ‘work’ in physics. We can talk about the work some system does on its environment, or the work done by the environment on the system, and these are almost the same… *except one is minus the other!*

When you are very ignorant about some system—say, some rolled dice—your estimated probabilities for its various possible states are very smeared-out, so the entropy is large. As you gain information, you revise your probabilities and they typically become more sharply peaked, so goes down. When you know as much as you possibly can, equals zero.

So, the entropy is the amount of information you have left to learn: the amount of information you *lack*, not the amount you *have*. As you gain information, this goes down. There’s no paradox here.

It works the same way with our population of replicators—at least in the special case where the fitness of each species is independent of its population. The probability distribution is like a ‘hypothesis’ assigning to each species the probability that it’s the best at self-replicating. As some replicators die off while others prosper, they gather information their environment, and this hypothesis gets refined. So, the entropy drops.

### Next time

Of course, to make closer contact to reality, we need to go beyond the special case where the fitness of each species is a constant! Marc Harper does this, and I want to talk about his work someday, but first I have a few more remarks to make about the pathetically simple special case I’ve been focusing on. I’ll save these for next time, since I’ve probably strained your patience already.

“This should make intuitive sense: the process of natural selection resembles ‘learning’.”

Nature is one tough teacher.

Yes: only students who pass every test get to live.

Amazing how fast even microbes ‘learn’ with such a strict teacher.

The sum in the denominator of should probably be indexed by j.

Okay, I’ll do something like that.

Replicators with dispersion in rates and adaptation times could probably explain the huge dynamic range in relative abundance distributions. This was touched on in Part 8.

I’ll have to think about that!

I think the use of phrases like “absorb information from the environment” are a little too passive. I’d say a more informative analogy is that processes “acquire information from the environment”, with the process of acquisition being limited to asking questions of the form “I think x is a good answer, am I right?” (i.e., not just yes-no questions but yes-no questions about very specific things). Of course, the diff eqn framework you’re looking at doesn’t use the notion of the fitness of offspring being some function (either stochastic or some other type) of the parents fitness, so there’s no analogue of this effect in what you’re directly looking at.

But in looking for links between information theory and biology, particularly biodiversity, I’d be inclined to look at how information theory looks at the “question strategy” issues. (E.g., if you really want to maximise your probability of getting

someright answer, you’re best served by testing “answers” at widely spaced parts of the configuration space, but biological evolution seems to churn out individuals who are only slightly different from their parents. Why is that? One quick possibility is that “evolutionary inference” thinks the parents are already quite close to the answer, so small modifications are called for. Or maybe it’s one or multiple other reasons…)David wrote:

Evolutionary biologists are trained to avoid ‘teleological’ or ‘purposive’ accounts:

This is important for avoiding some mistakes. But I think it’ll be very interesting for evolutionary biology to collide with machine learning, where people with goals are designing systems

in order toachieve those goals. Deen Abiola’s comments below show what I mean.Here you’re talking about what evolutionary inference “thinks”, which would give you a rap on the knuckles in those biology courses.

More seriously, but relatedly, biologists are really interested in to what extent we can think of evolution itself as having been optimized for something… instead of just being a fixed method whereby other things get optimized. The buzzword for this puzzle is the evolution of evolvability:

If you allow me to display my ignorance here: doesn’t this depend on what you assume as possible for ? (for example, the constant )

Suppose we take two species and who have some symbiotic relationship, but have to share a finite area. E.g. suppose that ( is a positive coefficient):

and similar for , but with and exchanged.

Then for large and will both go to 1/2. Also in this case I would say that the replicators gathered information about their environment (even though this example may not be very realistic) however it appears to me that the entropy becomes maximal. Am I doing something wrong?

Frederik wrote:

Yes! My remarks in the section “Exponential growth” only apply to the pathetically simple special case where is actually independent of , so the population of each species grows or declines exponentially. This is a very boring case, and it would be almost silly to even mention it except that

for short times, we can approximate the solution of any equationby a solution of the linear equation

This is my ultimate reason for introducing the pathetically simple special case. However, you’ll note that in this section, I only analyze the behavior of this case

as .So, the lessons here won’t apply to more general cases—at least, not without tons of qualifications. Next time I’ll look at the short-time behavior of the same pathetically simple special case, and get some more lessons.I should have made this more clear. I’m not explaining things very well since I’m learning it and/or making it up as I go.

Your example is a nice one, since it illustrates the importance of inter-species interactions, which are completely absent in the pathetically simple special case I discussed. I’ll talk more about those later!

There’s a lot of interesting stuff to say about how information flows in situations where species are competing or cooperating with each other, but it’s more complicated than “so, the entropy drops”. Very often it rises.

For now, try this:

• Marc Harper, The replicator equation as an inference dynamic.

Last time I began explaining the tight relation between three concepts: entropy, information and biodiversity […]

Hi John!

I’m happy to see that you are still interested in the topics. I want to recognize some other researchers that have had similar ideas (and that I based some of my work on). In particular, Cosma Shalizi independently discovered the analogy between the discrete replicator dynamic and Bayesian inference; I.M. Bomze was the first (as far as I can tell) to use relative entropy / cross entropy to analyze the replicator dynamic and proved many important results; and Shun-ichi Amari and his many collaborators wrote briefly about the connection between information geometry and the replicator equation circa 1995 and in subsequent works.

Unfortunately I found out about much of these researchers’ work after I had finished my graduate thesis — some of it would have been much easier to figure out! In any case, there’s credit where credit is due!

Over on G+, Deen Abiola wrote:

John Baez wrote:

Deen Abiola wrote:

Deen Abiola wrote:

Marc Harper wrote:

Deen Abiola wrote:

In Part 9, I told you about the ‘replicator equation’, which says how these fractions change with time […]

This would be a version of the replicator equation, which I explained recently in Information Geometry (Part 9). […]

I have been intrigued by the similarity of the definition of entropy to the formula for the n’th prime number;

p(n) = n*ln(n) + …

Is this similarity only accidental or does it have a meaning?

This is my talk for the workshop Biological Complexity: Can It Be Quantified?

• Biology as information dynamics.