Dichotomy in the definition of prescriptive information suggests both prescribed data and prescribed algorithms: biosemiotics applications in genomic systems

"Assembly Theory" in life-origin models: A critical review

Any homeostatic protometabolism would have required orchestration of disparate biochemical pathways into integrated circuits. Extraordinarily specific molecular assemblies were also required at the right time and place. Assembly Theory conflated with its cousins-Complexity Theory, Chaos theory, Quantum Mechanics, Irreversible Nonequilibrium Thermodynamics and Molecular Evolution theory- collectively have great naturalistic appeal in hopes of their providing the needed exquisite steering and controls. They collectively offer the best hope of circumventing the need for active selection required to formally orchestrate bona fide formal organization (as opposed to the mere self-ordering of chaos theory) (Abel and Trevors, 2006b). This paper focuses specifically on AT's contribution to naturalistic life-origin models.

Selection in molecular evolution

Evolution requires selection. Molecular/chemical/preDarwinian evolution is no exception. One molecule must be selected over another for molecular evolution to occur and advance. Evolution, however, has no goal. The laws of physics have no utilitarian desire, intent or proficiency. Laws and constraints are blind to "usefulness." How then were potential multi-step processes anticipated, valued and pursued by inanimate nature? Can orchestration of formal systems be physico-chemically spontaneous? The purely physico-dynamic self-ordering of Chaos Theory and irreversible non-equilibrium thermodynamic "engines of disequilibria conversion" achieve neither orchestration nor formal organization. Natural selection is a passive and after-the-fact-of-life selection. Darwinian selection reduces to the differential survival and reproduction of the fittest already-living organisms. In the case of abiogenesis, selection had to be 1) Active, 2) Pre-Function, and 3) Efficacious. Selection had to take place at the molecular level prior to the existence of non-trivial functional processes. It could not have been passive or secondary. What naturalistic mechanisms might have been at play?

Information prescriptions, 1930-2013: an international history and comprehensive review

OBJECTIVES

Recently, government agencies in several countries have promoted information prescription programs to increase patients' understanding of their conditions. The practice has a long history and many publications, but no comprehensive literature reviews such as this.

METHODS

Using a variety of high-precision and high-recall strategies, the researcher searched two dozen online bibliographic databases, citation databases, and repositories, as well as many print sources, to identify and retrieve documents for review. Of these documents, ninety relevant English-language case reports, research reports, and reviews published from 1930-2013 met the study criteria.

RESULTS

Early to mid-twentieth century reports covered long-standing practices and used no rigorous research methods. The literature since the mid-1990s reports on short-term trial projects, especially of government-sponsored programs in the United States and United Kingdom. Although the concept of information prescription has been in the literature and practiced for decades, no long-term research studies were found.

CONCLUSIONS

Most of the literature is anecdotal concerning small pilot projects. The reports investigate physician, patient, and librarian satisfaction but not changes in patient knowledge or behavior. Many twenty-first century projects emphasize materials and projects from specific government agencies and commercial enterprises.

IMPLICATIONS

While the practice is commonly believed to be a good idea and there are many publications on the subject, few studies provide any evidence of the efficacy of information prescriptions for increased patient knowledge. Well-designed and executed large or long-term studies might produce needed evidence for professional practice.

Redundancy of the genetic code enables translational pausing

The codon redundancy (“degeneracy”) found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PI_o) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.

A symmetry model for genetic coding via a wallpaper group composed of the traditional four bases and an imaginary base E: towards category theory-like systematization of molecular/genetic biology

Background

Previously, we suggested prototypal models that describe some clinical states based on group postulates. Here, we demonstrate a group/category theory-like model for molecular/genetic biology as an alternative application of our previous model. Specifically, we focus on deoxyribonucleic acid (DNA) base sequences.

Results

We construct a wallpaper pattern based on a five-letter cruciform motif with letters C, A, T, G, and E. Whereas the first four letters represent the standard DNA bases, the fifth is introduced for ease in formulating group operations that reproduce insertions and deletions of DNA base sequences. A basic group Z₅ = {r, u, d, l, n} of operations is defined for the wallpaper pattern, with which a sequence of points can be generated corresponding to changes of a base in a DNA sequence by following the orbit of a point of the pattern under operations in group Z₅. Other manipulations of DNA sequence can be treated using a vector-like notation ‘D_j’ corresponding to a DNA sequence but based on the five-letter base set; also, ‘D_j’s are expressed graphically. Insertions and deletions of a series of letters ‘E’ are admitted to assist in describing DNA recombination. Likewise, a vector-like notation R_j can be constructed for sequences of ribonucleic acid (RNA). The wallpaper group B = {Z₅^×∞, ●} (an ∞-fold Cartesian product of Z₅) acts on D_j (or R_j) yielding changes to D_j (or R_j) denoted by ‘D_j◦B_(j→k) = D_k’ (or ‘R_j◦B_(j→k) = R_k’). Based on the operations of this group, two types of groups—a modulo 5 linear group and a rotational group over the Gaussian plane, acting on the five bases—are linked as parts of the wallpaper group for broader applications. As a result, changes, insertions/deletions and DNA (RNA) recombination (partial/total conversion) are described. As an exploratory study, a notation for the canonical “central dogma” via a category theory-like way is presented for future developments.

Conclusions

Despite the large incompleteness of our methodology, there is fertile ground to consider a symmetry model for genetic coding based on our specific wallpaper group. A more integrated formulation containing “central dogma” for future molecular/genetic biology remains to be explored.