A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost

Molecular codes translate information written in one type of molecules into another molecular language. We introduce a simple model that treats molecular codes as noisy information channels. An optimal code is a channel that conveys information accurately and efficiently while keeping down the impact of errors. The equipoise of the three conflicting needs, for minimal error-load, minimal cost of resources and maximal diversity of vocabulary, defines the fitness of the code. The model suggests a mechanism for the emergence of a code when evolution varies the parameters that control this equipoise and the mapping between the two molecular languages becomes non-random. This mechanism is demonstrated by a simple toy model that is formally equivalent to a mean-field Ising magnet.Comment: Keywords: molecular codes, rate-distortion theory, biological information channels, stochastic maps, genetic code, genetic network

The Value of Information for Populations in Varying Environments

The notion of information pervades informal descriptions of biological systems, but formal treatments face the problem of defining a quantitative measure of information rooted in a concept of fitness, which is itself an elusive notion. Here, we present a model of population dynamics where this problem is amenable to a mathematical analysis. In the limit where any information about future environmental variations is common to the members of the population, our model is equivalent to known models of financial investment. In this case, the population can be interpreted as a portfolio of financial assets and previous analyses have shown that a key quantity of Shannon's communication theory, the mutual information, sets a fundamental limit on the value of information. We show that this bound can be violated when accounting for features that are irrelevant in finance but inherent to biological systems, such as the stochasticity present at the individual level. This leads us to generalize the measures of uncertainty and information usually encountered in information theory

Structure or Noise?

We show how rate-distortion theory provides a mechanism for automated theory building by naturally distinguishing between regularity and randomness. We start from the simple principle that model variables should, as much as possible, render the future and past conditionally independent. From this, we construct an objective function for model making whose extrema embody the trade-off between a model's structural complexity and its predictive power. The solutions correspond to a hierarchy of models that, at each level of complexity, achieve optimal predictive power at minimal cost. In the limit of maximal prediction the resulting optimal model identifies a process's intrinsic organization by extracting the underlying causal states. In this limit, the model's complexity is given by the statistical complexity, which is known to be minimal for achieving maximum prediction. Examples show how theory building can profit from analyzing a process's causal compressibility, which is reflected in the optimal models' rate-distortion curve--the process's characteristic for optimally balancing structure and noise at different levels of representation.Comment: 6 pages, 2 figures; http://cse.ucdavis.edu/~cmg/compmech/pubs/son.htm

Predictability, complexity and learning

We define {\em predictive information} $I_{\rm pred} (T)$ as the mutual information between the past and the future of a time series. Three qualitatively different behaviors are found in the limit of large observation times $T$: $I_{\rm pred} (T)$ can remain finite, grow logarithmically, or grow as a fractional power law. If the time series allows us to learn a model with a finite number of parameters, then $I_{\rm pred} (T)$ grows logarithmically with a coefficient that counts the dimensionality of the model space. In contrast, power--law growth is associated, for example, with the learning of infinite parameter (or nonparametric) models such as continuous functions with smoothness constraints. There are connections between the predictive information and measures of complexity that have been defined both in learning theory and in the analysis of physical systems through statistical mechanics and dynamical systems theory. Further, in the same way that entropy provides the unique measure of available information consistent with some simple and plausible conditions, we argue that the divergent part of $I_{\rm pred} (T)$ provides the unique measure for the complexity of dynamics underlying a time series. Finally, we discuss how these ideas may be useful in different problems in physics, statistics, and biology.Comment: 53 pages, 3 figures, 98 references, LaTeX2

Occam's Quantum Strop: Synchronizing and Compressing Classical Cryptic Processes via a Quantum Channel

A stochastic process's statistical complexity stands out as a fundamental property: the minimum information required to synchronize one process generator to another. How much information is required, though, when synchronizing over a quantum channel? Recent work demonstrated that representing causal similarity as quantum state-indistinguishability provides a quantum advantage. We generalize this to synchronization and offer a sequence of constructions that exploit extended causal structures, finding substantial increase of the quantum advantage. We demonstrate that maximum compression is determined by the process's cryptic order---a classical, topological property closely allied to Markov order, itself a measure of historical dependence. We introduce an efficient algorithm that computes the quantum advantage and close noting that the advantage comes at a cost---one trades off prediction for generation complexity.Comment: 10 pages, 6 figures; http://csc.ucdavis.edu/~cmg/compmech/pubs/oqs.ht