Biology subjects

Rodrick Wallace

Publications and source records attributed to Rodrick Wallace.

4 recordsLinked to original sources

bioRxiv2014

Metabolic free energy and deterministic-but-for-error biological codes: a ‘Data Rate Theorem’ aging model

The living state is cognitive at every scale and level of organization. Since it is possible to associate a broad class of cognitive processes with dual information sources, many pathologies can be addressed using statistical models based on the Shannon Coding, the Shannon-McMillan Source Coding, the Rate Distortion, and the Data Rate Theorems, as these impose powerful necessary condition constraints on information generation and exchange, and on system control. Deterministic-but-for-error biological codes do not directly invoke cognition, although they may be essential subcomponents within larger cognitive processes. A formal argument, however, places such codes within a similar framework, with metabolic free energy serving as a control signal stabilizing biochemical code-and-translator dynamics in the presence of noise. Demand beyond available energy supply then expresses itself in punctuated destabilization of the coding channel, affecting a spectrum of essential biological functions. Aging, normal or prematurely driven by psychosocial or environmental stressors, must eventually interfere with the routine operation of such mechanisms, triggering chronic diseases associated with senescence. Amyloid fibril formation, intrinsically disordered protein logic gates, and cell surface glycan/lectin kelp bed logic gates are reviewed from this perspective. The results, however, generalize beyond coding systems having easily recognizable symmetry modes.

Systems Biology↗

bioRxiv2014

Does ‘information control the living state’?

We generalize the recently-uncovered Data Rate Theorem in the context of cognitive systems having a dual information source, including those of the living state that is particularly characterized by cognition at every scale and level of organization. The unification of information theory and control theory via the Data Rate Theorem is not additive, but synergistic, generating new statistical tools that greatly constrain the possible dynamics of that state. Thus, in addition to providing novel conceptual approaches, this emerging body of theory permits construction of models that, like those of regression analysis, can provide benchmarks against which to compare experimental or observational data.

Biophysics↗

bioRxiv2014

Biochemical ‘Cambrian’ explosion-implosions: the generation and pruning of genetic codes

Tlusty's topological analysis of the genetic code suggests ecosystem changes in available metabolic free energy that predated the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. These coevolved via a `Cambrian explosion' until, very early on, the ancestor of the present narrow spectrum of protein machineries became evolutionarily locked in at a modest level of fitness reflecting a modest embedding metabolic free energy ecology. Similar biochemical `Cambrian singularities' must have occurred at different scales and levels of organization on Earth, with competition or chance-selected outcomes frozen at a far earlier period than the physical bauplan Cambrian explosion. Other examples might include explosive variations in mechanisms of photosynthesis and subsequent oxygen metabolisms. Intermediate between Cambrian bauplan and genetic code, variants of both remain today, even after evolutionary pruning, often protected in specialized ecological niches. This suggests that, under less energetic astrobiological ecologies, a spectrum of less complicated reproductive codes may also survive in specialized niches.

Evolutionary Biology↗

bioRxiv2013

Embodied cognition, embodied regulation, and the Data Rate Theorem

The Data Rate Theorem carries deep implications for theories of embodied cognition, extensions providing a spectrum of necessary conditions dynamic statistical models useful in empirical studies. A large deviations argument, however, implies that the regulation and stabilization of such systems is itself an interpenetrating phenomenon necessarily convoluted with embodied cognition. For humans, the central regulatory role of culture has long been known. Although a ground-state collapse analogous to generalized anxiety appears ubiquitous to such systems, lack of cultural modulation in real-time automatons or distributed cognition man-machine cockpits makes them subject to a pathology under which all possible targets are enemies.

Neuroscience↗