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Genetic Information, Physical Interpreters and Thermodynamics; The Material-Informatic Basis of Biosemiosis

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Abstract

The sequence of nucleotide bases occurring in an organism’s DNA is often regarded as a codescript for its construction. However, information in a DNA sequence can only be regarded as a codescript relative to an operational biochemical machine, which the information constrains in such a way as to direct the process of construction. In reality, any biochemical machine for which a DNA codescript is efficacious is itself produced through the mechanical interpretation of an identical or very similar codescript. In these terms the origin of life can be described as a bootstrap process involving the simultaneous accumulation of genetic information and the generation of a machine that interprets it as instructions for its own construction. This problem is discussed within the theoretical frameworks of thermodynamics, informatics and self-reproducing automata, paying special attention to the physico-chemical origin of genetic coding and the conditions, both thermodynamic and informatic, that a system must fulfil in order for it to sustain semiosis. The origin of life is equated with biosemiosis.

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Notes

  1. The definition is easily extended to continuous probability distributions.

  2. Energy has had the status of the formless Urstoff of the cosmos since Einstein derived his celebrated relation, E = mc 2, in which he demonstrated the quantitative equivalence of energy and mass. Mass, identified with weight in pre-Newtonian physics, is the classical measure of the amount of substance, whether divisible (compound) or indivisible (atomic), comprising anything in the physical universe.

  3. There are alternatives to this probabilistic definition of Shannon information (Muller 2007), most importantly the algorithmic definition which measures the minimum number of bits needed to specify a procedure for generating a given string of letters.

  4. The integrity of the code part of the algorithm is not maintained directly by the ribosomal mechanism, but by an independent suite of enzymes known as aminoacyl-tRNA synthetases (AARSs).

  5. The dependence of the origin of Beethoven’s Ninth on the pre-existence of the human genome (the fact of Beethoven’s humanity) obfuscates the main question and arises only because the symphony is a human artifact and not some other complex object.

  6. This fallacy is expounded by Dawkins (1986, p73).

  7. As discussed elsewhere (Wills 2009), when supplied with information within a certain range of compatibility, a cellular interpreter executes the extraordinary feat of transforming itself into a new self-constructing interpretation of the supplied information.

  8. An audio CD player is a general interpreter for the transfer of information from spatial patterns of information on an optically readable disc to corresponding audio “objects”, commonly comprised of temporal patterns of voltages and currents in the solenoids of electromagnetically driven speakers.

  9. The XOR encryption system described here would be ineffective against attempts (code-breaking) to circumvent it. However, all of the same arguments apply to much more sophisticated systems of encryption. The XOR system has been chosen only for illustrative purposes.

  10. Reverse-order complementary sequences for T 1 and T 2 (and therefore E 1 and E 2) have been chosen in recognition of the possibility discussed by Chandrasekaran et al. (2013).

  11. The information-function relationship of coding reflexivity is not always unproblematic. It can only be unambiguously established for classes of polymers whose structure-function relationship (mapping from polymer sequence to catalytic properties) is sufficiently asymmetric (Nieselt-Struwe and Wills 1997).

  12. This is accomplished by symbolically “back-translating” the sequences of E 1 and E 2 to determine the sequences of T 1 and T 2. A similar procedure must be followed to produce self-reproducing automata (Von Neumann 1949). The “description” tape must be devised and specified by the programmer.

  13. Gánti did not consider that a von Neumann-type “description” was necessary for biological inheritance and epigenetic effects prove him correct. However, it is hard to envisage how the extraordinarily detailed control of processes in biological systems could be achieved without the logarithmic reduction in the complexity of the system’s specification that an information-based mapping from cause to effect makes available (Schrödinger 1944; Eigen 1971, 2013).

  14. The expectation that errors in the production of protein components of the translation apparatus will be self-amplifying was framed by Orgel (1963; 1970) as an “error catastrophe” problem.

  15. The endpoint of coding evolution may not have been reached before different threads separated into the first semi-autonomous organisms.

  16. The bifurcation of the sets of codons and amino acids into functionally distinct subsets did not necessarily require the emergence of two structures as distinct as those portrayed in Figure 1, but that is what appears to have happened and become locked into all subsequent molecular biological evolution.

  17. There is increasing evidence that the Class I and II core structures were encoded in the complementary strands of a single nucleic acid gene (Chandrasekaran et al. 2013).

  18. Darwin’s principle of natural selection has been applied successfully to the understanding of autocatalytic macromolecules (Eigen 1971) and somewhat less successfully to single genes (Dawkins 1976; Hubbard 2013; Newman 2013).

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Acknowledgments

I am grateful to Kay Nieselt for her hospitality and to the Carl Zeiss Foundation for financial support. I thank William R. Buckley for his helpful comments.

Since this paper went to press, new evidence has been presented to support the view that the cores of the Class I and II AARS enzymes played a fundamental role in the origin of life. [Li, L., Francklyn C., & Carter, C. W. (2013) Aminoacylating urzymes challenge the RNA World hypothesis. J. Biol. Chem., 288, 26856–26863].

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  1. Integrative Transkriptomik, Zentrum für Bioinformatik Tübingen, Wilhelm-Schickard-Institut für Informatik, Universität Tübingen, Sand 14, Tübingen, 72076, Germany

    Peter R. Wills

  2. Department of Physics, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand

    Peter R. Wills

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Wills, P.R. Genetic Information, Physical Interpreters and Thermodynamics; The Material-Informatic Basis of Biosemiosis. Biosemiotics 7, 141–165 (2014). https://doi.org/10.1007/s12304-013-9196-2

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