From Matter to Self-Organizing Life

[Pythagorean]

The title is the name of a Science book review on the following book:

From Strange Simplicity to Complex Familiarity, by Manfred Eigen, published back in April.

The review was published in the current issue of Science, but it's behind a paywall. It's interesting though, if you're at a university you might be able to access it through the library.

http://www.sciencemag.org/content/342/6154/39.summary

Has anyone here read the book? An excerpt from the review:

The book offers a joyful but not shallow route through the complications that arise on the way from elementary particles to complex forms of life. However, Eigen only touches on some additional complications: If evolving entities can interact, then the fitness landscape (which provides the basis for evolution) may itself be a dynamic product of the interactions (5). In this way, evolutionary dynamics can lead to eternal cycles (6), which would only be halted by effects not covered by basic mathematical models of evolution.

(5) M. A. Nowak, K. Sigmund, Science 303, 793 (2004)
(6) B. Sinervo, C. M. Lively, http://www.tb.ethz.ch/education/model/RPS/sinervo.pdf (1996)

The five chapters of the book are:

1) Matter and Energy
2) Energy and Entropy
3) Entropy and Information
4) Information and Complexity
5) Complexity and Self-Organisation

 

[Pythagorean]

The abstract of the first paper (5) is interesting:

Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

 

[atyy]

Why is it interesting? It just says one has to pay attention to dynamics, and not just optimize blindly.

 

[Pythagorean]

I think it says not to optimize at all, really, and it doesn't just say what not to do, it suggests that game-theoretic perspective is a more appropriate conceptual toolbag. This is interesting to me, in particular, because I use genetic algorithms to realize unknown physiological parameters and I've been struggling with the contradiction of searching for a single optimum in a diverse landscape.

 

[atyy]

More appropriate than what? Isn't "evolutionary game theory" the new name for the same old thing - dynamics. In a particular form of evolutionary dynamics - eg. frequency dependent fitness - it is conceptually analogous to game theory. But it is basic and not new.

http://www.life.umd.edu/classroom/zool360/L18-ESS/ess.html
http://www.biology.arizona.edu/biomath/tutorials/polynomial/applications/fds.html
http://www.sparknotes.com/biology/animalbehavior/behavioralecology/terms.html

More generally, what is the "environment"? In thermodynamics we know the division is arbitrary. So in evolution the "environment" of an organism includes other species. If the environment changes - including the frequency of other species - the fitness of the organism can change.

 

[atyy]

Here, for example, is a discussion of related concepts - "Nash equilibrium" and "Evolutionarily stable strategy" - from two different fields.

http://en.wikipedia.org/wiki/Evolutionarily_stable_strategy

What's new then? If you look at what's taught in undergraduate biology http://www.life.umd.edu/classroom/zool360/L18-ESS/ess.html, there are the assumptions of infinite populations and interactions between all pairs (dynamics on a fully connected graph). The recent work, including that by Nowak who co-authored the review, is the extension to finite N and graphs that are not fully connected. There are effects that are not obvious even if one knows the result for large N and full connectivity.

 

[Pythagorean]

More appropriate than what?

Optimization algorithms. Finding a single minimum. Regardless of whether your system is dynamic or not. It's not just about not blindly optimizing, it's about the fundamental conceptual conflict of looking for an optimum in a system with degeneracy and variability. Yet many (in my department) still do use optimization.

Isn't "evolutionary game theory" the new name for the same old thing - dynamics

I don't know any game theory beyond the prisoner's dilemma, but that's not apparent to me. I think Lotka-Volterra might be an example of something that is dynamics but not game theory, and prisoner's dilemma, there is no state so I don't conceptualize it as dynamical. So, maybe you use a lose definition of dynamical, but I don't see anything close to 1-to-1 there, just some overlap.

 

[Pythagorean]

What's new then?

I'm not claiming anything is new. It seems like you have a bone to pick with your aggressive questions. What's the problem?

 

[atyy]

I'm not claiming anything is new. It seems like you have a bone to pick with your aggressive questions. What's the problem?

Just making sure that basic things are not being propagated as novel. I edited my post #6 to indicate what's new about recent work - the study of the dynamics on finite, structured graphs.

There is a state in all of this, it's truly (stochastic) dynamics. Most of the mathematics is Markov chains.

Here's Taylor, Fudenberg, Sasaki and Nowak's review http://www.ped.fas.harvard.edu/people/faculty/publications_nowak/BMB04.pdf , where the derivation from dynamics is clear. They review the classic results, then go on to the finite N results which are new.

I've never read (too dense) http://ptp.oxfordjournals.org/content/88/6/1035.full.pdf+html , but it is a quite famous article about (I think) the statistical lattice version of the Lotka-Volterra equations you mention.

BTW, if you think I'm aggressive, sorry, but here's my confession: what on Earth is an experimental neurobiologist like me doing with this? It showed up in a model of the neuromuscular junction http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1001352 (see Fig 7).

 

[Pythagorean]

I don't have a great idea of the of the atmosphere to judge the global novelty of literature. I know that optimization approaches are commonplace in physiological modelling and I go a different route and this was something that articulated my feelings on estimating parameters to make model match observation.

I've heard that when a spine makes transcription requests from the soma (like via TIPS after microtubial invasion or other BDNF pathways) that the contents of the package ( presumably things like psd95 carried by motor proteins) can be hijacked by spines closer to the soma as they pass by. I guess that the paper you mention contributes to the same idea of neural darwinism with respect to synapses. I can imagine a high level experimentalist (like a neuropsychologist or someone looking at systems development) might use this to explain system behavior in networks.

 

[atyy]

I don't have a great idea of the of the atmosphere to judge the global novelty of literature. I know that optimization approaches are commonplace in physiological modelling and I go a different route and this was something that articulated my feelings on estimating parameters to make model match observation.

I've heard that when a spine makes transcription requests from the soma (like via TIPS after microtubial invasion or other BDNF pathways) that the contents of the package ( presumably things like psd95 carried by motor proteins) can be hijacked by spines closer to the soma as they pass by. I guess that the paper you mention contributes to the same idea of neural darwinism with respect to synapses. I can imagine a high level experimentalist (like a neuropsychologist or someone looking at systems development) might use this to explain system behavior in networks.

Perhaps it's novel with respect to your application. In those papers they are simply exploring the space of dynamical system models. But you want to use it to fit your model to data?

As far as I know, if the model landscape has many local minima, which is usually the case with nonlinear systems of high dimension, there is no "general solution". The field of "deep neural nets" was stuck for many years for that reason, but around 2006 Hinton and Salakhutdinov found a trick to initialise the parameters so that the final optimzation could be done in decent time and without getting stuck. For models with few parameters and which are analytically tractable or for which you have enough computer power to cover space by brute force, the general hope is to solve for qualitative differences is different parts of parameters space, so that one can get a prediction at least about the general region one is in - when possible, this is the best since it does not assume that only one set of parameters are consistent with the data. I've seen http://www.ncbi.nlm.nih.gov/pubmed/23864375 and http://www.ncbi.nlm.nih.gov/pubmed/23629582 , but IIRC, your models involve voltage-dependent conductances etc, which I'm least familiar with how to fit, and which are usually considered difficult.

 

[Pythagorean]

Probably not even truly novel in my application; I read the suggestion of using genetic algorithms in a paper written by Wulfram Gerstner reporting on the results of an INCF modelling competition and of course, multiple models comes from Eve Marder's "Multiple Models..." paper (though I couldn't even tell you if her paper was "novel", it's not even really the kind of judgment I care about, I guess; I learned something from it).

Yes, conductance models have a lot of degeneracy, probably because of all the hyperbolic tangent functions (or Boltzmann functions if you like). "Fitting them" is not enough, it's not unique. You also have to see how, for a particular fit, different qualitative/emergent changes arise from small changes in the parameters. So probably some application from perturbation theory will become an important part of analyzing the dynamic "traits" of a particular parameter distribution.