Code biology and the problem of emergence
Introduction
Recognition of the nature and role of codes in life is clearly a major advance in biology. The neo-Darwinian synthesis incorporated the notion of the genetic code. However, as originally characterized by Crick and Watson, the reproduction of DNA and RNA was understood, as Erwin Schrödinger had suggested in his influential work, What is Life? as analogous to the reproduction of arrangements of molecules with the growth of a crystal. A few years later when it was found that the sequence of nucleotides in DNA determines the sequence of amino acids in proteins, the same analogy was utilized. As originally formulated, DNA produces RNA which produces proteins, and what kinds of proteins are produced are simply the effect of the order of nucleotide bases in the DNA and then the RNA with the kinds of proteins produced being determined by stereochemistry. DNA, identified with Mendelian genes, insulated from influences of the rest of the organism by the Weismann Barrier, could then explain the characteristics of phenotypes. Proteins, produced by DNA and RNA, form three dimensional structures which form living organisms. This was seen as a triumph of the bottom up, reductionist form of explanation, reducing life to nothing but arrangements of chemicals and their interactions organized in such a way that organisms have the attributes that enable them to survive and reproduce themselves more successfully than other arrangements of chemicals. Characterizing such arrangements of nucleotide bases as encoding information, incorporating information science based on the work of Claude Shannon and Norbert Weiner into biology, was not a significant challenge to this reductionism. We were left with a characterization of organisms as gene machines, or machines for reproducing DNA (or occasionally, RNA by itself).
The code biology of Marcello Barbieri shows why this neo-Darwinian synthesis has to be rejected. Proteins are not determined by stereochemistry, even in the most primitive forms of life. The bridge between genes and proteins is provided by transfer RNA that have one recognition site for a group of three nucleotides, a codon, and another for an amino acid. The two recognition sites are spatially separated and chemically independent and there is no necessary, chemically determined relationship between codons and amino acids. The production of proteins involves ‘conventions’ in the sense that which proteins are produced by RNA could be otherwise with different conventions. These are codes in the sense that there is encoding of information which is then decoded according to these conventions. This is a complex process involving a carrier of genetic information, a messenger RNA, a peptide bondmaker consisting of a piece of ribosomal RNA, and transfer RNAs that can carry both nucleotides and amino acids. This means that protein making in the most primitive life forms involves three different types of molecules: messenger, ribosomal and transfer RNAs. So, in each cell there is a ‘ribonucleoprotein system’ translating the genotype into proteins. Along with the genotype, the particular type of DNA which produces RNA, there also has to be a ‘ribotype’ (a term introduced by Barbieri), the code which is essential to determining which proteins will be produced (Barbieri, 1981). The relation between information and proteins is not dyadic but triadic. Life is in the process of translating RNA to produce proteins, not in the information encoded in the RNA (or DNA) or the proteins. Dawkins referred to genes as replicators, but this confuses the object, the genes, with the ‘agent’ of replication. Furthermore, there are two activities, copying and coding, with the agent being the codemaker operating between the genes and the proteins. In fact, genes do nothing. The agency is replicating and coding by the codemaker. Using the analogy of a city, such encoded information is like blueprints, and the houses are what is produced on the basis of these blueprints, with the life of the city being the process of coding and replication involved in the production of proteins (Barbieri, 2003, 158f.).
Barbieri (2014, p.168) characterized a code as always involving ‘a set of rules that establishes a correspondence between two independent worlds.’ After the discovery of the genetic code, biologists discovered a whole range of codes, which although defined differently, had this feature in common. Understanding the role of codes and coding in this way introduces semantics into the most basic processes of biology, Barbieri argued. Proteins are the ‘meaning’ of genes for the ribonucleoprotein system of the cell, and it is by virtue of this meaning that cells reproduce themselves. The prokaryotic cell code was the first great invention that began life. Since then, there have been a series of such inventions of codes with the emergence of more complex forms of life, although each of these has not replaced the previous forms, and each new form of life presupposes and is built on the codes of earlier forms of life (Barbieri, 2008, p.31). Eukaryotic cells involved a new code, as did the development of multi-celled organisms, then animals, vertebrates, amniotes, mammals, primates and homo sapiens with the codes of language and the codes of cultures. Recognition of these diverse levels with their codes involves recognizing that each level has its own epigenesis, and this requires recognition of far greater complexity to evolution than acknowledged in the neo-Darwinian synthesis.
The biggest problem is accounting for the emergence of these codes. The first challenge is to explain the emergence of the genetic code in the most elementary forms of life, after which explaining other codes associated with the emergence of more complex organisms and living processes should be relatively easy. Trying to explain life as the product of RNA molecules reproducing themselves or catalysing the replication of other RNA molecules has been shown to be impossible because of the instability of the processes involved (Barbieri 2003, p.140f.). With qualifications, Barbieri (2003, p.131ff.) aligned himself with a different tradition going back to Alexander Oparin, arguing that metabolism came first, and examined efforts of those following Oparin such as Tibor Gánti, Stuart Kauffman and Freeman Dyson to fill out the details of how such metabolic processes could have begun and developed. Dyson showed that such metabolisms did not have to replicate exactly and could have supported inert or parasitic molecules, including RNA molecules. It is in the context of such metabolism that RNA, initially produced as a waste with the potential to be dangerous to this metabolic process, could have taken over the metabolism to reproduce itself, as does a virus, in the process, stabilizing the process of replication of the metabolism. Barbieri rejected this for failing to acknowledge the complexity of coding and offered an alternative theory of how coding could have emerged under these conditions. His proposal (1981; 2003, p.145; 2019a) involved still accepting the metabolism first hypothesis but recognizing that primitive RNA able to catalyse peptide bonding, that is, polymerising ribosoids, could have been operative within this metabolism, creating a ribotype world. Primitive ribosoids could become protoribosomes. While far more promising than the alternatives, accounting for the emergence of the complex ordering involved in coding and replication is still a huge problem, as Barbieri has acknowledged. The code that appears to have emerged with the beginning of life, although ‘conventional’, is universal and has not changed during the history of life. How could this complex and highly successful code have originated? To add plausibility to his theory, Barbieri (2019b) has recently conjectured that such codes could have developed by a process of ‘ambiguity reduction’, allowing that the first codes were poorly defined. Even allowing this, it is still a challenge to show how the first code even in its ambiguous form could have originated.
Section snippets
The reality of emergence: against reductionism
In addressing this challenge, it is first necessary to consider what emergence could mean. The idea of emergence as a major feature of evolution had been developed and strongly defended in the first decades of the Twentieth Century, most importantly, by Henri Bergson, Samuel Alexander, Conwy Lloyd Morgan and C.D. Broad (Blitz, 1992). These philosophers influenced Alfred North Whitehead (Gare, 2002), who in turn was a major influence on the theoretical biology movement, particularly the work of
Thermodynamics, hierarchy, Heterarchy and life
This leaves the problem of accounting for why new constraints should have been interpolated, including those associated with life. To explain this, Salthe (2005; 2018) invoked thermodynamics and the universal drive to eliminate energy gradients to achieve equilibrium, transforming ‘useful’ energy (negentropy or exergy) into entropy. He aligned himself with the work of Ilya Prigogine (1988; 1996) who speculated on how the universe began not from a singularity but from the instability of the
Beyond the Newtonian model of science
This raises the further problem of considering what is the relationship between functions and fractionated components, most importantly, the mechanisms that play a role in its functioning, and how could such complex relations ever have emerged. To address this problem it is necessary to question the identification of science with the mathematical modelling of entailments, leaving no place for explanations of what is not entailed. In arguing this, Rosen was not breaking sufficiently with the
The emergence of codes
All this provides a very different perspective for comprehending the emergence of codes. The way of thinking being opposed here is exemplified by Richard Dawkins who always started with clearly identified components of living processes and examined how they could have come together to function as a machine, and then tried to show how this machine can be explained purely through chemistry and ‘natural selection’. With this approach, context is ignored except insofar as it provides a source for
Conclusion
What I have tried to show in this paper is that while code biology invalidates the reductionism of orthodox biology, there is still a problem of accounting for the emergence of codes. Contributions to solving this problem provided by Pattee, Salthe, Juarrero, Rosen, Kauffman, Noble and others are important, but do not sufficiently interrogate the deepest assumptions on which modern science is based. It is necessary to draw on the more radical thinking of Simondon utilizing his notions of
Declaration of competing interest
This paper was unfunded and there is no conflict of interest.
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