Information and Entropy in Biological Systems (Part 6)

1 June, 2015

The resounding lack of comment to this series of posts confirms my theory that a blog post that says “go somewhere else and read something” will never be popular. Even if it’s “go somewhere else and watch a video”, this is too much like saying

Hi! Want to talk? Okay, go into that other room and watch TV, then come back when you’re done and we’ll talk about it.

But no matter: our workshop on Information and Entropy in Biological Systems was really exciting! I want to make it available to the world as much as possible. I’m running around too much to create lovingly hand-crafted summaries of each talk—and I know you’re punishing me for that, with your silence. But I’ll keep on going, just to get the material out there.

Marc Harper spoke about information in evolutionary game theory, and we have a nice video of that. I’ve been excited about his work for quite a while, because it shows that the analogy between ‘evolution’ and ‘learning’ can be made mathematically precise. I summarized some of his ideas in my information geometry series, and I’ve also gotten him to write two articles for this blog:

• Marc Harper, Relative entropy in evolutionary dynamics, Azimuth, 22 January 2014.

• Marc Harper, Stationary stability in finite populations, Azimuth, 24 March 2015.

Here are the slides and video of his talk:

• Marc Harper, Information transport and evolutionary dynamics.


Information and Entropy in Biological Systems (Part 5)

30 May, 2015

John Harte of U. C. Berkeley spoke about the maximum entropy method as a method of predicting patterns in ecology. Annette Ostling of the University of Michigan spoke about some competing theories, such as the ‘neutral model’ of biodiversity—a theory that sounds much too simple to be right, yet fits the data surprisingly well!

We managed to get a video of Ostling’s talk, but not Harte’s. Luckily, you can see the slides of both. You can also see a summary of Harte’s book Maximum Entropy and Ecology:

• John Baez, Maximum entropy and ecology, Azimuth, 21 February 2013.

Here are his talk slides and abstract:

• John Harte, Maximum entropy as a foundation for theory building in ecology.

Abstract. Constrained maximization of information entropy (MaxEnt) yields least-biased probability distributions. In statistical physics, this powerful inference method yields classical statistical mechanics/thermodynamics under the constraints imposed by conservation laws. I apply MaxEnt to macroecology, the study of the distribution, abundance, and energetics of species in ecosystems. With constraints derived from ratios of ecological state variables, I show that MaxEnt yields realistic abundance distributions, species-area relationships, spatial aggregation patterns, and body-size distributions over a wide range of taxonomic groups, habitats and spatial scales. I conclude with a brief summary of some of the major opportunities at the frontier of MaxEnt-based macroecological theory.

Here is a video of Ostling’s talk, as well as her slides and some papers she recommended:

• Annette Ostling, The neutral theory of biodiversity and other competitors to maximum entropy.

Abstract: I am a bit of the odd man out in that I will not talk that much about information and entropy, but instead about neutral theory and niche theory in ecology. My interest in coming to this workshop is in part out of an interest in what greater insights we can get into neutral models and stochastic population dynamics in general using entropy and information theory.

I will present the niche and neutral theories of the maintenance of diversity of competing species in ecology, and explain the dynamics included in neutral models in ecology. I will also briefly explain how one can derive a species abundance distribution from neutral models. I will present the view that neutral models have the potential to serve as more process-based null models than previously used in ecology for detecting the signature of niches and habitat filtering. However, tests of neutral theory in ecology have not as of yet been as useful as tests of neutral theory in evolutionary biology, because they leave open the possibility that pattern is influenced by “demographic complexity” rather than niches. I will mention briefly some of the work I’ve been doing to try to construct better tests of neutral theory.

Finally I’ll mention some connections that have been made so far between predictions of entropy theory and predictions of neutral theory in ecology and evolution.

These papers present interesting relations between ecology and statistical mechanics. Check out the nice ‘analogy chart’ in the second one!

• M. G. Bowler, Species abundance distributions, statistical mechanics and the priors of MaxEnt, Theoretical Population Biology 92 (2014), 69–77.

Abstract. The methods of Maximum Entropy have been deployed for some years to address the problem of species abundance distributions. In this approach, it is important to identify the correct weighting factors, or priors, to be applied before maximising the entropy function subject to constraints. The forms of such priors depend not only on the exact problem but can also depend on the way it is set up; priors are determined by the underlying dynamics of the complex system under consideration. The problem is one of statistical mechanics and it is the properties of the system that yield the correct MaxEnt priors, appropriate to the way the problem is framed. Here I calculate, in several different ways, the species abundance distribution resulting when individuals in a community are born and die independently. In
the usual formulation the prior distribution for the number of species over the number of individuals is 1/n; the problem can be reformulated in terms of the distribution of individuals over species classes, with a uniform prior. Results are obtained using master equations for the dynamics and separately through the combinatoric methods of elementary statistical mechanics; the MaxEnt priors then emerge a posteriori. The first object is to establish the log series species abundance distribution as the outcome of per capita guild dynamics. The second is to clarify the true nature and origin of priors in the language of MaxEnt. Finally, I consider how it may come about that the distribution is similar to log series in the event that filled niches dominate species abundance. For the general ecologist, there are two messages. First, that species abundance distributions are determined largely by population sorting through fractional processes (resulting in the 1/n factor) and secondly that useful information is likely to be found only in departures from the log series. For the MaxEnt practitioner, the message is that the prior with respect to which the entropy is to be maximised is determined by the nature of the problem and the way in which it is formulated.

• Guy Sella and Aaron E. Hirsh, The application of statistical physics to evolutionary biology, Proc. Nat. Acad. Sci. 102 (2005), 9541–9546.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations. The analogy with statistical physics also reveals that, contrary to a basic tenet of the nearly neutral theory of molecular evolution, the frequencies of adaptive and deleterious substitutions at steady state are equal. Finally, just as the free energy function quantitatively characterizes the balance between energy and entropy, a free fitness function provides an analytical expression for the balance between natural selection and stochastic drift.


Network Theory in Turin

23 May, 2015

Here are the slides of the talk I’m giving on Monday to kick off the Categorical Foundations of Network Theory workshop in Turin:

Network theory.

This is a long talk, starting with the reasons I care about this subject, and working into the details of one particular project: the categorical foundations of networks as applied to electrical engineering and control theory. There are lots of links in blue; click on them for more details!


Information and Entropy in Biological Systems (Part 4)

21 May, 2015

I kicked off the workshop on Information and Entropy in Biological Systems with a broad overview of the many ways information theory and entropy get used in biology:

• John Baez, Information and entropy in biological systems.

Abstract. Information and entropy are being used in biology in many different ways: for example, to study biological communication systems, the ‘action-perception loop’, the thermodynamic foundations of biology, the structure of ecosystems, measures of biodiversity, and evolution. Can we unify these? To do this, we must learn to talk to each other. This will be easier if we share some basic concepts which I’ll sketch here.

The talk is full of links, in blue. If you click on these you can get more details. You can also watch a video of my talk:


Information and Entropy in Biological Systems (Part 3)

20 May, 2015

We had a great workshop on information and entropy in biological systems, and now you can see what it was like. I think I’ll post these talks one a time, or maybe a few at a time, because they’d be overwhelming taken all at once.

So, let’s dive into Chris Lee’s exciting ideas about organisms as ‘information evolving machines’ that may provide ‘disinformation’ to their competitors. Near the end of his talk, he discusses some new results on an ever-popular topic: the Prisoner’s Dilemma. You may know about this classic book:

• Robert Axelrod, The Evolution of Cooperation, Basic Books, New York, 1984. Some passages available free online.

If you don’t, read it now! He showed that the simple ‘tit for tat’ strategy did very well in some experiments where the game was played repeatedly and strategies who did well got to ‘reproduce’ themselves. This result was very exciting, so a lot of people have done research on it. More recently a paper on this subject by William Press and Freeman Dyson received a lot of hype. I think this is a good place to learn about that:

• Mike Shulman, Zero determinant strategies in the iterated Prisoner’s Dilemma, The n-Category Café, 19 July 2012.

Chris Lee’s new work on the Prisoner’s Dilemma is here, cowritten with two other people who attended the workshop:

The art of war: beyond memory-one strategies in population games, PLOS One, 24 March 2015.

Abstract. We show that the history of play in a population game contains exploitable information that can be successfully used by sophisticated strategies to defeat memory-one opponents, including zero determinant strategies. The history allows a player to label opponents by their strategies, enabling a player to determine the population distribution and to act differentially based on the opponent’s strategy in each pairwise interaction. For the Prisoner’s Dilemma, these advantages lead to the natural formation of cooperative coalitions among similarly behaving players and eventually to unilateral defection against opposing player types. We show analytically and empirically that optimal play in population games depends strongly on the population distribution. For example, the optimal strategy for a minority player type against a resident tit-for-tat (TFT) population is ‘always cooperate’ (ALLC), while for a majority player type the optimal strategy versus TFT players is ‘always defect’ (ALLD). Such behaviors are not accessible to memory-one strategies. Drawing inspiration from Sun Tzu’s the Art of War, we implemented a non-memory-one strategy for population games based on techniques from machine learning and statistical inference that can exploit the history of play in this manner. Via simulation we find that this strategy is essentially uninvadable and can successfully invade (significantly more likely than a neutral mutant) essentially all known memory-one strategies for the Prisoner’s Dilemma, including ALLC (always cooperate), ALLD (always defect), tit-for-tat (TFT), win-stay-lose-shift (WSLS), and zero determinant (ZD) strategies, including extortionate and generous strategies.

And now for the talk! Click on the talk title here for Chris Lee’s slides, or go down and watch the video:

• Chris Lee, Empirical information, potential information and disinformation as signatures of distinct classes of information evolving machines.

Abstract. Information theory is an intuitively attractive way of thinking about biological evolution, because it seems to capture a core aspect of biology—life as a solution to “information problems”—in a fundamental way. However, there are non-trivial questions about how to apply that idea, and whether it has actual predictive value. For example, should we think of biological systems as being actually driven by an information metric? One idea that can draw useful links between information theory, evolution and statistical inference is the definition of an information evolving machine (IEM) as a system whose elements represent distinct predictions, and whose weights represent an information (prediction power) metric, typically as a function of sampling some iterative observation process. I first show how this idea provides useful results for describing a statistical inference process, including its maximum entropy bound for optimal inference, and how its sampling-based metrics (“empirical information”, Ie, for prediction power; and “potential information”, Ip, for latent prediction power) relate to classical definitions such as mutual information and relative entropy. These results suggest classification of IEMs into several distinct types:

1. Ie machine: e.g. a population of competing genotypes evolving under selection and mutation is an IEM that computes an Ie equivalent to fitness, and whose gradient (Ip) acts strictly locally, on mutations that it actually samples. Its transition rates between steady states will decrease exponentially as a function of evolutionary distance.

2. “Ip tunneling” machine: a statistical inference process summing over a population of models to compute both Ie, Ip can directly detect “latent” information in the observations (not captured by its model), which it can follow to “tunnel” rapidly to a new steady state.

3. disinformation machine (multiscale IEM): an ecosystem of species is an IEM whose elements (species) are themselves IEMs that can interact. When an attacker IEM can reduce a target IEM’s prediction power (Ie) by sending it a misleading signal, this “disinformation dynamic” can alter the evolutionary landscape in interesting ways, by opening up paths for rapid co-evolution to distant steady-states. This is especially true when the disinformation attack targets a feature of high fitness value, yielding a combination of strong negative selection for retention of the target feature, plus strong positive selection for escaping the disinformation attack. I will illustrate with examples from statistical inference and evolutionary game theory. These concepts, though basic, may provide useful connections between diverse themes in the workshop.


PROPs for Linear Systems

18 May, 2015

Eric Drexler likes to say: engineering is dual to science, because science tries to understand what the world does, while engineering is about getting the world to do what you want. I think we need a slightly less ‘coercive’, more ‘cooperative’ approach to the world in order to develop ‘ecotechnology’, but it’s still a useful distinction.

For example, classical mechanics is the study of what things do when they follow Newton’s laws. Control theory is the study of what you can get them to do.

Say you have an upside-down pendulum on a cart. Classical mechanics says what it will do. But control theory says: if you watch the pendulum and use what you see to move the cart back and forth correctly, you can make sure the pendulum doesn’t fall over!

Control theorists do their work with the help of ‘signal-flow diagrams’. For example, here is the signal-flow diagram for an inverted pendulum on a cart:

When I take a look at a diagram like this, I say to myself: that’s a string diagram for a morphism in a monoidal category! And it’s true. Jason Erbele wrote a paper explaining this. Independently, Bonchi, Sobociński and Zanasi did some closely related work:

• John Baez and Jason Erbele, Categories in control.

• Filippo Bonchi, Paweł Sobociński and Fabio Zanasi, Interacting Hopf algebras.

• Filippo Bonchi, Paweł Sobociński and Fabio Zanasi, A categorical semantics of signal flow graphs.

I’ll explain some of the ideas at the Turin meeting on the categorical foundations of network theory. But I also want to talk about this new paper that Simon Wadsley of Cambridge University wrote with my student Nick Woods:

• Simon Wadsley and Nick Woods, PROPs for linear systems.

This makes the picture neater and more general!

You see, Jason and I used signal flow diagrams to give a new description of the category of finite-dimensional vector spaces and linear maps. This category plays a big role in the control theory of linear systems. Bonchi, Sobociński and Zanasi gave a closely related description of an equivalent category, \mathrm{Mat}(k), where:

• objects are natural numbers, and

• a morphism f : m \to n is an n \times m matrix with entries in the field k,

and composition is given by matrix multiplication.

But Wadsley and Woods generalized all this work to cover \mathrm{Mat}(R) whenever R is a commutative rig. A rig is a ‘ring without negatives’—like the natural numbers. We can multiply matrices valued in any rig, and this includes some very useful examples… as I’ll explain later.

Wadsley and Woods proved:

Theorem. Whenever R is a commutative rig, \mathrm{Mat}(R) is the PROP for bicommutative bimonoids over R.

This result is quick to state, but it takes a bit of explaining! So, let me start by bringing in some definitions.

Bicommutative bimonoids

We will work in any symmetric monoidal category, and draw morphisms as string diagrams.

A commutative monoid is an object equipped with a multiplication:

and a unit:

obeying these laws:

For example, suppose \mathrm{FinVect}_k is the symmetric monoidal category of finite-dimensional vector spaces over a field k, with direct sum as its tensor product. Then any object V \in \mathrm{FinVect}_k is a commutative monoid where the multiplication is addition:

(x,y) \mapsto x + y

and the unit is zero: that is, the unique map from the zero-dimensional vector space to V.

Turning all this upside down, cocommutative comonoid has a comultiplication:

and a counit:

obeying these laws:

For example, consider our vector space V \in \mathrm{FinVect}_k again. It’s a commutative comonoid where the comultiplication is duplication:

x \mapsto (x,x)

and the counit is deletion: that is, the unique map from V to the zero-dimensional vector space.

Given an object that’s both a commutative monoid and a cocommutative comonoid, we say it’s a bicommutative bimonoid if these extra axioms hold:

You can check that these are true for our running example of a finite-dimensional vector space V. The most exciting one is the top one, which says that adding two vectors and then duplicating the result is the same as duplicating each one, then adding them appropriately.

Our example has some other properties, too! Each element c \in k defines a morphism from V to itself, namely scalar multiplication by c:

x \mapsto c x

We draw this as follows:

These morphisms are compatible with the ones so far:

Moreover, all the ‘rig operations’ in k—that is, addition, multiplication, 0 and 1, but not subtraction or division—can be recovered from what we have so far:

We summarize this by saying our vector space V is a bicommutative bimonoid ‘over k‘.

More generally, suppose we have a bicommutative bimonoid A in a symmetric monoidal category. Let \mathrm{End}(A) be the set of bicommutative bimonoid homomorphisms from A to itself. This is actually a rig: there’s a way to add these homomorphisms, and also a way to ‘multiply’ them (namely, compose them).

Suppose R is any commutative rig. Then we say A is a bicommutative bimonoid over R if it’s equipped with a rig homomorphism

\Phi : R \to \mathrm{End}(A)

This is a way of summarizing the diagrams I just showed you! You see, each c \in R gives a morphism from A to itself, which we write as

The fact that this is a bicommutative bimonoid endomorphism says precisely this:

And the fact that \Phi is a rig homomorphism says precisely this:

So sometimes the right word is worth a dozen pictures!

What Jason and I showed is that for any field k, the \mathrm{FinVect}_k is the free symmetric monoidal category on a bicommutative bimonoid over k. This means that the above rules, which are rules for manipulating signal flow diagrams, completely characterize the world of linear algebra!

Bonchi, Sobociński and Zanasi used ‘PROPs’ to prove a similar result where the field is replaced by a sufficiently nice commutative ring. And Wadlsey and Woods used PROPS to generalize even further to the case of an arbitrary commutative rig!

But what are PROPs?

PROPs

A PROP is a particularly tractable sort of symmetric monoidal category: a strict symmetric monoidal category where the objects are natural numbers and the tensor product of objects is given by ordinary addition. The symmetric monoidal category \mathrm{FinVect}_k is equivalent to the PROP \mathrm{Mat}(k), where a morphism f : m \to n is an n \times m matrix with entries in k, composition of morphisms is given by matrix multiplication, and the tensor product of morphisms is the direct sum of matrices.

We can define a similar PROP \mathrm{Mat}(R) whenever R is a commutative rig, and Wadsley and Woods gave an elegant description of the ‘algebras’ of \mathrm{Mat}(R). Suppose C is a PROP and D is a strict symmetric monoidal category. Then the category of algebras of C in D is the category of strict symmetric monoidal functors F : C \to D and natural transformations between these.

If for every choice of D the category of algebras of C in D is equivalent to the category of algebraic structures of some kind in D, we say C is the PROP for structures of that kind. This explains the theorem Wadsley and Woods proved:

Theorem. Whenever R is a commutative rig, \mathrm{Mat}(R) is the PROP for bicommutative bimonoids over R.

The fact that an algebra of \mathrm{Mat}(R) is a bicommutative bimonoid is equivalent to all this stuff:

The fact that \Phi(c) is a bimonoid homomorphism for all c \in R is equivalent to this stuff:

And the fact that \Phi is a rig homomorphism is equivalent to this stuff:

This is a great result because it includes some nice new examples.

First, the commutative rig of natural numbers gives a PROP \mathrm{Mat}. This is equivalent to the symmetric monoidal category \mathrm{FinSpan}, where morphisms are isomorphism classes of spans of finite sets, with disjoint union as the tensor product. Steve Lack had already shown that \mathrm{FinSpan} is the PROP for bicommutative bimonoids. But this also follows from the result of Wadsley and Woods, since every bicommutative bimonoid V is automatically equipped with a unique rig homomorphism

\Phi : \mathbb{N} \to \mathrm{End}(V)

Second, the commutative rig of booleans

\mathbb{B} = \{F,T\}

with ‘or’ as addition and ‘and’ as multiplication gives a PROP \mathrm{Mat}(\mathbb{B}). This is equivalent to the symmetric monoidal category \mathrm{FinRel} where morphisms are relations between finite sets, with disjoint union as the tensor product. Samuel Mimram had already shown that this is the PROP for special bicommutative bimonoids, meaning those where comultiplication followed by multiplication is the identity:

But again, this follows from the general result of Wadsley and Woods!

Finally, taking the commutative ring of integers \mathbb{Z}, Wadsley and Woods showed that \mathrm{Mat}(\mathbb{Z}) is the PROP for bicommutative Hopf monoids. The key here is that scalar multiplication by -1 obeys the axioms for an antipode—the extra morphism that makes a bimonoid into a Hopf monoid. Here are those axioms:

More generally, whenever R is a commutative ring, the presence of -1 \in R guarantees that a bimonoid over R is automatically a Hopf monoid over R. So, when R is a commutative ring, Wadsley and Woods’ result implies that \mathrm{Mat}(R) is the PROP for Hopf monoids over R.

Earlier, in their paper on ‘interacting Hopf algebras’, Bonchi, Sobociński and Zanasi had given an elegant and very different proof that \mathrm{Mat}(R) is the PROP for Hopf monoids over R whenever R is a principal ideal domain. The advantage of their argument is that they build up the PROP for Hopf monoids over R from smaller pieces, using some ideas developed by Steve Lack. But the new argument by Wadsley and Woods has its own charm.

In short, we’re getting the diagrammatics of linear algebra worked out very nicely, providing a solid mathematical foundation for signal flow diagrams in control theory!


Carbon Emissions Stopped Growing?

15 May, 2015

In 2014, global carbon dioxide emissions from energy production stopped growing!

At least, that’s what preliminary data from the International Energy Agency say. It seems the big difference is China. The Chinese made more electricity from renewable sources, such as hydropower, solar and wind, and burned less coal.

In fact, a report by Greenpeace says that from April 2014 to April 2015, China’s carbon emissions dropped by an amount equal to the entire carbon emissions of the United Kingdom!

I want to check this, because it would be wonderful if true: a 5% drop. They say that if this trend continues, China will close out 2015 with the biggest reduction in CO2 emissions every recorded by a single country.

The International Energy Agency also credits Europe’s improved attempts to cut carbon emissions for the turnaround. In the US, carbon emissions has basically been dropping since 2006—with a big drop in 2009 due to the economic collapse, a partial bounce-back in 2010, but a general downward trend.

In the last 40 years, there have only been 3 times in which emissions stood still or fell compared to the previous year, all during global economic crises: the early 1980’s, 1992, and 2009. In 2014, however, the global economy expanded by 3%.

So, the tide may be turning! But please remember: while carbon emissions may start dropping, they’re still huge. The amount of the CO2 in the air shot above 400 parts per million in March this year. As Erika Podest of NASA put it:

CO2 concentrations haven’t been this high in millions of years. Even more alarming is the rate of increase in the last five decades and the fact that CO2 stays in the atmosphere for hundreds or thousands of years. This milestone is a wake up call that our actions in response to climate change need to match the persistent rise in CO2. Climate change is a threat to life on Earth and we can no longer afford to be spectators.

Here is the announcement by the International Energy Agency:

Global energy-related emissions of carbon dioxide stalled in 2014, IEA, 13 March 2015.

Their full report on this subject will come out on 15 June 2015. Here is the report by Greenpeace EnergyDesk:

China coal use falls: CO2 reduction this year could equal UK total emissions over same period, Greenpeace EnergyDesk.

I trust them less than the IEA when it comes to using statistics correctly, but someone should be able to verify their claims if true.


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