What can information-asymmetric games tell us about the context of Crick's ‘frozen accident’?

Jee, Justin; Sundstrom, Andrew; Massey, Steven E.; Mishra, Bud

doi:10.1098/rsif.2013.0614

Cited by 13 publications

(16 citation statements)

References 40 publications

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“…The idea of “freezing” implies that if P reduces in size then the code can be “unfrozen” and therefore malleable. This relationship between P and genetic code malleability can be shown via simulation, with codon reassignments occurring more frequently when P is smaller [ 126 ]. Consistent with these considerations, when the relationship between P and numbers of codon reassignments in mitochondria was examined [ 37 ], it was found that the number of mitochondrial codon reassignments is positively correlated with mitochondrial proteome size.…”

Section: Proteome Size As a Constraint On The Genetic Codementioning

confidence: 99%

Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint

Massey

2015

Life

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The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of “neutral emergence”. The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these “pseudaptations”, and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an “unfreezing” of the codon – amino acid mapping that defines the genetic code, consistent with Crick’s Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a selective pressure in the evolution of sexual reproduction, and differences in translational fidelity. Lastly, the utility of the concept of an informational constraint to other diverse fields of research is explored.

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Section: Proteome Size As a Constraint On The Genetic Codementioning

confidence: 99%

Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint

Massey

2015

Life

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Section: Resultsmentioning

confidence: 99%

“…In contrast, Batesian molecular mimicry involves a conflict of interest between sender and receiver genes. Batesian molecular mimics of mRNAs and tRNAs may be termed 'deceiver' mRNAs [33] and 'deceiver' tRNAs [14], respectively. Virus mRNAs are all effectively deceiver mRNAs, tricking the host translational apparatus into translating them regardless.…”

Section: Resultsmentioning

confidence: 99%

“…This model of a bio-molecular signaling game implies that the first signaling games were played between bio-molecules in the earliest life forms, once the bio-molecules were large enough to exert specificity [ 33 ] [ 14 ] [ 34 ]. This in turn implies that ‘meaning’ first arose from the primordial soup, as the first signal was strategically sent, between a pair of replicating macro-molecules.…”

Section: Resultsmentioning

confidence: 99%

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How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology

Casey¹,

Massey²,

Mishra³

2020

Preprint

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Mimicry is exhibited in multiple scales, ranging from molecular, to organismal, and then to human society. ‘Batesian’ type mimicry entails a conflict of interest between sender and receiver, reflected in a deceptive mimic signal. ‘Mullerian’ type mimicry occurs when there is perfect common interest between sender and receiver, manifested by an honest co-mimic signal. Using a signaling games approach, simulations show that invasion by Batesian mimics will make Mullerian mimicry unstable, in a coevolutionary chase. We use these results to better understand the deceptive strategies of SARS-CoV-2 and their key role in the COVID-19 pandemic. At the biomolecular level, we explain how cellularization promotes Mullerian molecular mimicry, and discourages Batesian molecular mimicry. A wide range of processes analogous to cellularization are presented; these might represent a manner of reducing oscillatory instabilities. Lastly, we identify examples of mimicry in human society, that might be addressed using a signaling game approach.

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“…It has been postulated that the game's origin might have been in the primordial RNA world taking place among mRNA and tRNA precursors in response to invasion by prebiotic amino acids; they might have created codon -anticodon signalling conventions to string the amino acids in a way that avoids toxic forms such as homopolymers or random concatenation. The resulting action of the receiver is the production of a peptide, and the utility of the signal lies in its benefit to fitness of the whole organism, to both sender and receiver [75].…”

Section: The Genetic Code Is a Signalling Conventionmentioning

confidence: 99%

Origin of biomolecular games: deception and molecular evolution

Massey

Mishra

2018

J. R. Soc. Interface.

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Biological macromolecules encode information: some of it to endow the molecule with structural flexibility, some of it to enable molecular actions as a catalyst or a substrate, but a residual part can be used to communicate with other macromolecules. Thus, macromolecules do not need to possess information only to survive in an environment, but also to strategically interact with others by sending signals to a receiving macromolecule that can properly interpret the signal and act suitably. These sender–receiver signalling games are sustained by the information asymmetry that exists among the macromolecules. In both biochemistry and molecular evolution, the important role of information asymmetry remains largely unaddressed. Here, we provide a new unifying perspective on the impact of information symmetry between macromolecules on molecular evolutionary processes, while focusing on molecular deception. Biomolecular games arise from the ability of biological macromolecules to exert precise recognition, and their role as units of selection, meaning that they are subject to competition and cooperation with other macromolecules. Thus, signalling game theory can be used to better understand fundamental features of living systems such as molecular recognition, molecular mimicry, selfish elements and ‘junk’ DNA. We show how deceptive behaviour at the molecular level indicates a conflict of interest, and so provides evidence of genetic conflict. This model proposes that molecular deception is diagnostic of selfish behaviour, helping to explain the evasive behaviour of transposable elements in ‘junk’ DNA, for example. Additionally, in this broad review, a range of major evolutionary transitions are shown to be associated with the establishment of signalling conventions, many of which are susceptible to molecular deception. These perspectives allow us to assign rudimentary behaviour to macromolecules, and show how participation in signalling games differentiates biochemistry from abiotic chemistry.

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What can information-asymmetric games tell us about the context of Crick's ‘frozen accident’?

Cited by 13 publications

References 40 publications

Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint

Genetic Code Evolution Reveals the Neutral Emergence of Mutational Robustness, and Information as an Evolutionary Constraint

How Signaling Games Explain Mimicry at Many Levels: From Viral Epidemiology to Human Sociology

Origin of biomolecular games: deception and molecular evolution

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