`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms

We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation

Wieler solenoids, Cuntz-Pimsner algebras and K-theory

We study irreducible Smale spaces with totally disconnected stable sets and their associated $K$-theoretic invariants. Such Smale spaces arise as Wieler solenoids, and we restrict to those arising from open surjections. The paper follows three converging tracks: one dynamical, one operator algebraic and one $K$-theoretic. Using Wieler's Theorem, we characterize the unstable set of a finite set of periodic points as a locally trivial fibre bundle with discrete fibres over a compact space. This characterization gives us the tools to analyze an explicit groupoid Morita equivalence between the groupoids of Deaconu-Renault and Putnam-Spielberg, extending results of Thomsen. The Deaconu-Renault groupoid and the explicit Morita equivalence leads to a Cuntz-Pimsner model for the stable Ruelle algebra. The $K$-theoretic invariants of Cuntz-Pimsner algebras are then studied using the Cuntz-Pimsner extension, for which we construct an unbounded representative. To elucidate the power of these constructions we characterize the KMS weights on the stable Ruelle algebra of a Wieler solenoid. We conclude with several examples of Wieler solenoids, their associated algebras and spectral triples

A Survey of Quandle Ideas

This article surveys many aspects of the theory of quandles which algebraically encode the Reidemeister moves. In addition to knot theory, quandles have found applications in other areas which are only mentioned in passing here. The main purpose is to give a short introduction to the subject and a guide to the applications that have been found thus far for quandle cocycle invariants.Comment: Submitted to conference proceedings; embarrassing misspellings of various names corrected. Many apologies and thanks to readers who pointed out correction

Asymptotically rigid mapping class groups and Thompson's groups

We consider Thompson's groups from the perspective of mapping class groups of surfaces of infinite type. This point of view leads us to the braided Thompson groups, which are extensions of Thompson's groups by infinite (spherical) braid groups. We will outline the main features of these groups and some applications to the quantization of Teichm\"uller spaces. The chapter provides an introduction to the subject with an emphasis on some of the authors results.Comment: survey 77