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

D'Onofrio, David J; Abel, David; Johnson, Donald E.

doi:10.1186/1742-4682-9-8

Cited by 8 publications

(16 citation statements)

References 47 publications

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“…As mentioned before, a number of approaches have been proposed exploit group-theoretic methods. These cover the rules for composition of triplet of bases ‘XXX’, the ways of reading codons, and models to compose geometric solids such as the tetrahedron and hexahedron, [ 12 , 18 - 21 , 33 , 34 , 50 ]. The rules for treating this aspect (transcription and translation of DNA bases’ information) are not established in the present article.…”

Section: Discussionmentioning

confidence: 99%

“…However, as for further processing of the triplets of bases e.g., ‘ACG’ and ‘AUG’, a considerable number of models have been reported e.g., [12,18-21,33,34,50]. We refrain from pursuing this issue at present.…”

Section: §8 Further Applications Of the Composition Category-like Promentioning

confidence: 98%

“…In the transcription of RNA bases, the ‘RNA splicing’ process is well-known, whereby ‘intron sequences’ are excised, and ‘exon sequences’ are combined to condense effectual information for further interpretation in protein synthesis. However, as for further processing of the triplets of bases e.g., ‘ACG’ and ‘AUG’, a considerable number of models have been reported e.g., [ 12 , 18 - 21 , 33 , 34 , 50 ]. We refrain from pursuing this issue at present.…”

Section: §8 Further Applications Of the Composition Category-like Promentioning

confidence: 99%

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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

Sawamura

Morishita

Ishigooka

2014

Theor Biol Med Model

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BackgroundPreviously, 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.ResultsWe 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 ‘Dj’ corresponding to a DNA sequence but based on the five-letter base set; also, ‘Dj’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 Rj can be constructed for sequences of ribonucleic acid (RNA). The wallpaper group B = {Z5×∞, ●} (an ∞-fold Cartesian product of Z5) acts on Dj (or Rj) yielding changes to Dj (or Rj) denoted by ‘Dj◦B(j→k) = Dk’ (or ‘Rj◦B(j→k) = Rk’). 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.ConclusionsDespite 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.

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Section: Discussionmentioning

confidence: 99%

Section: §8 Further Applications Of the Composition Category-like Promentioning

confidence: 98%

Section: §8 Further Applications Of the Composition Category-like Promentioning

confidence: 99%

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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

Sawamura

Morishita

Ishigooka

2014

Theor Biol Med Model

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“…Information aspects of evolution were also discussed by other authors (see, e.g., Yokey, 2000, 2002, Trevors and Abel, 2004, D'Onofrio et al, 2012, Wills et al, 2015. Wilson (2010) considered the problem of multi-level selection that is actively discussed now (Allen et al, 2013, Nowak andAllen, 2015).…”

Section: Mechanisms Of Speciation and Evolutionary Innovationsmentioning

confidence: 97%

Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution

Melkikh

Khrennikov

2017

Progress in Biophysics and Molecular Biology

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A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown that these mechanisms, at the molecular level, cannot work steadily in terms of classical mechanics. Quantum mechanisms of changes in the genome, based on the long-range interaction potential between biologically important molecules, are proposed as one of possible explanation. Different variants of interactions of the organism and environment based on molecular recognition and leading to new species origins are considered. Experiments to verify the model are proposed. This bio-physical study is completed by the general operational model of based on quantum information theory. The latter is applied to model of epigenetic evolution. We briefly present the basics of the quantum-like approach to modeling of bio-informational processes. This approach is illustrated by the quantum-like model of epigenetic evolution.

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“…Articles about "prescriptive informa tion" and "prescribed information" as used in cellular genomics were excluded [42], Although important for further study, reports of nursing and other allied health information prescriptions were also excluded.…”

Section: Literature Retrieval and Inclusion Criteriamentioning

confidence: 99%

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

McKnight

2014

J Med Libr Assoc

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

Cited by 8 publications

References 47 publications

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

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

Molecular recognition of the environment and mechanisms of the origin of species in quantum-like modeling of evolution

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

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