Typogenetics: An Artificial Genetic System

Varetto, Louis

doi:10.1006/jtbi.1993.1013

Cited by 19 publications

(13 citation statements)

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“…It can be regarded as one of the rst arti cial chemistries and has been further investigated by Morris, Varetto, and others [98,137,138]. The molecules of the system are character sequences (called strands) over the alphabet A, C, G, T. The reaction rules are "typographic" manipulations based on a set of prede ned basic operations such as cutting, insertion, or deletion of characters.…”

Section: Typogeneticsmentioning

confidence: 99%

Artificial Chemistries—A Review

2001

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This article reviews the growing body of scientific work in artificial chemistry. First, common motivations and fundamental concepts are introduced. Second, current research activities are discussed along three application dimensions: modeling, information processing, and optimization. Finally, common phenomena among the different systems are summarized. It is argued here that artificial chemistries are "the right stuff" for the study of prebiotic and biochemical evolution, and they provide a productive framework for questions regarding the origin and evolution of organizations in general. Furthermore, artificial chemistries have a broad application range of practical problems, as shown in this review.

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Section: Typogeneticsmentioning

confidence: 99%

Artificial Chemistries—A Review

2001

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“…In computational terms, this idea is most transparently represented in the E-calculus, a formulation developed by Church [3] and equivalent to Turing's machine-tape system, in which objects encode functions that act on other objects to produce new objects. A number of systems of this general kind, broadly falling under the heading of artificial chemistries [7], have been implemented as computer simulations [9,33,60]. Fontana notes in defense of this abstraction that ''The molecular level seems to be the first level in physics where a combinatorial variety of structures can 'manipulate' each other in a way that is strikingly similar to 'symbolic manipulation.'…”

Section: Objects and Rolesmentioning

confidence: 99%

“…Its relation to the paradigm summarized above lies in its strict association of information with matter, inviting an obvious parallel between the biological protein + DNA/RNA system and the computational/constructional machine+tape system. The underlying connection it draws between a sequential string of data (tape) and a sequential string of genes (DNA/RNA) recurs implicitly and explicitly in various forms as a pervasive computational metaphor for genetic information [17,18,28,30,38,60]. …”

Section: The Machine-tape Paradigmmentioning

confidence: 99%

From Machine and Tape to Structure and Function: Formulation of a Reflexively Computing System

Salzberg

2006

Artificial Life

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The relationship between structure and function is explored via a system of labeled directed graph structures upon which a single elementary read/write rule is applied locally. Boundaries between static (information-carrying) and active (information-processing) objects, imposed by mandate of the rules or physics in earlier models, emerge instead as a result of a structure-function dynamic that is reflexive: objects may operate directly on their own structure. A representation of an arbitrary Turing machine is reproduced in terms of structural constraints by means of a simple mapping from tape squares and machine states to a uniform medium of nodes and links, establishing computation universality. Exploiting flexibility of the formulation, examples of other unconventional "self-computing" structures are demonstrated. A straightforward representation of a kinematic machine system based on the model devised by Laing is also reproduced in detail. Implications of the findings are discussed in terms of their relation to other formal models of computation and construction. It is argued that reflexivity of the structure-function relationship is a critical informational dynamic in biochemical systems, overlooked in previous models but well captured by the proposed formulation.

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“…In that model, they result from a map of interactions between genes. It appears indeed difficult to realize a realistic functional representation, but several works have been done in that direction within the domain of typogenetics [43] or based on auto-catalytic sets of instructions and autopoietic automata such as Tierra [44], where the elements of a “digital reactive soup” are sets of functional instructions (in pseudo-code). Those sets are small programs that represent biochemical elementary actions such as “cut” or “copy” or “destroy”, coupled with probabilistic interactions [45,46].…”

Section: Co-evolutionmentioning

confidence: 99%

“…Here we stress that not only stereochemical direct interactions between amino-acids and their respective current codons can constitute a primordial genetic code, but also that if some amino-acids have polymerized, they could in return help to confine nucleic bases so that their probability to polymerize into an XNA strand is increased. In addition to the coupled stereochemical and structural encoding [54], this process constitutes a good molecular basis for supporting theoretical works of artificial genetics such as typogenetics [43] that lead to the emergence and preservation of auto-catalytic loops from a dual system composed of XNA sequences (initially random sequences) and after translation (hypothesized) the corresponding set of peptides, some of which could have had a certain catalytic activity.…”

Section: Ancestral Processes Inherited From the Origins Of Lifementioning

confidence: 99%

RNA Relics and Origin of Life

Demongeot

Glade

Moreira

et al. 2009

IJMS

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A number of small RNA sequences, located in different non-coding sequences and highly preserved across the tree of life, have been suggested to be molecular fossils, of ancient (and possibly primordial) origin. On the other hand, recent years have revealed the existence of ubiquitous roles for small RNA sequences in modern organisms, in functions ranging from cell regulation to antiviral activity. We propose that a single thread can be followed from the beginning of life in RNA structures selected only for stability reasons through the RNA relics and up to the current coevolution of RNA sequences; such an understanding would shed light both on the history and on the present development of the RNA machinery and interactions. After presenting the evidence (by comparing their sequences) that points toward a common thread, we discuss a scenario of genome coevolution (with emphasis on viral infectious processes) and finally propose a plan for the reevaluation of the stereochemical theory of the genetic code; we claim that it may still be relevant, and not only for understanding the origin of life, but also for a comprehensive picture of regulation in present-day cells.

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Typogenetics: An Artificial Genetic System

Cited by 19 publications

References 0 publications

Artificial Chemistries—A Review

Artificial Chemistries—A Review

From Machine and Tape to Structure and Function: Formulation of a Reflexively Computing System

RNA Relics and Origin of Life

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