March 13, 2019 | David F. Coppedge

Codes Cannot Create Themselves

To make a code, you have to start with a mind. Then you need to design a sender and a receiver that know the code.

In the previous entry, we saw scientists acknowledging that biological codes are real and ubiquitous. From the simplest microbe in Archaea to the most complex mammal, biology is suffused with coded information passing between senders and receivers. The late Dr. A.E. Wilder-Smith emphasized the point that a code means nothing in and of itself. It only becomes meaningful when both sender and receiver understand the language convention.

Continuing our look at papers in a special issue of Biosystems, “Code Biology,” we examine how materialistic evolutionists attempt to explain the origin of codes before life began. Remember, “natural selection” is of no value before accurate replication in a genetic system, because natural selection doesn’t work (even if it could) unless it can pass on benefits to the offspring. As with natural selection, belief that codes will write themselves amounts to faith that miraculous “stuff happens.”

Insuperable problems of the genetic code initially emerging in an RNA world (Wills & Carter, Biosystems). This is perhaps the ultimate show-stopper for the most popular theory for the origin of life: what is the origin of biological information. Wills and Carter know that error catastrophe will ruin any bottom-up theory, such as the RNA World. They realize that principles must be invoked that transcend Darwinian natural selection. Therefore, God—that would be the logical conclusion. But instead, they take a leap of faith that somehow “self-organization” can perform a robust, rapid, concerted coding system.  This amounts to a miracle.

Differential equations for error-prone information transfer (template replication, transcription or translation) are developed in order to consider, within the theory of autocatalysis, the advent of coded protein synthesis. Variations of these equations furnish a basis for comparing the plausibility of contrasting scenarios for the emergence of specific tRNA aminoacylation, ultimately by enzymes, and the relationship of this process with the origin of the universal system of molecular biological information processing embodied in the Central Dogma. The hypothetical RNA World does not furnish an adequate basis for explaining how this system came into being, but principles of self-organisation that transcend Darwinian natural selection furnish an unexpectedly robust basis for a rapid, concerted transition to genetic coding from a peptide·RNA world.

Causation, constructors and codes (Hofmeyr, Biosystems). Note: a “formal cause” is the blueprint or plan for something. An “efficient cause” is what brings it about. A “universal constructor” was Von Neumann’s theoretical entity that could reproduce itself endlessly, calling attention to the requirements for such a machine.

Relational biology relies heavily on the enriched understanding of causal entailment that Robert Rosen’s formalisation of Aristotle’s four causes has made possible, although to date efficient causes and the rehabilitation of final cause have been its main focus. Formal cause has been paid rather scant attention, but, as this paper demonstrates, is crucial to our understanding of many types of processes, not necessarily biological. The graph-theoretic relational diagram of a mapping has played a key role in relational biology, and the first part of the paper is devoted to developing an explicit representation of formal cause in the diagram and how it acts in combination with efficient cause to form a mapping. I then use these representations to show how Von Neumann’s universal constructor can be cast into a relational diagram in a way that avoids the logical paradox that Rosen detected in his own representation of the constructor in terms of sets and mappings. One aspect that was absent from both Von Neumann’s and Rosen’s treatments was the necessity of a code to translate the description (the formal cause) of the automaton to be constructed into the construction process itself. A formal definition of codes in general, and organic codes in particular, allows the relational diagram to be extended so as to capture this translation of formal cause into process. The extended relational diagram is used to exemplify causal entailment in a diverse range of processes, such as enzyme action, construction of automata, communication through the Morse code, and ribosomal polypeptide synthesis through the genetic code.

The evolutionary dynamics of language (Luc Steels, Eörs Szathmáry, Biosystems). This paper is self-refuting. Unless there is a connection to truth, language is meaningless.

The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits. (i) It makes a bridge to neurobiological models of the brain that have also adopted an evolutionary dynamics point of view, thus opening a new horizon for studying how human brains achieve the remarkably complex competence for language. And (ii) it suggests a new foundation for studying cultural language change as an evolutionary dynamics process. The paper sketches this novel perspective, provides references to empirical data and computational experiments, and points to open problems.

Carrying pieces of information in organocatalytic bytes: Semiopoiesis—A new theory of life and its origins (Dos Santos, Biosystems). This scientist compares information in codes to information in molecules—a category mistake. In molecules, the sequence carries properties but not information. In genetics, the sequence is the crucial aspect. It conveys semiotic (symbol-based) information. Dos Santos tries to make “organocatalysts” his bridge from molecules to information-carrying genetic biopolymers. It won’t work, any more than random collections of letters attracted by magnets will form meaningful sentences. Dos Santos also confuses life with systems that “can evolve by natural selection.” Life is much more meaningful than “stuff happens”!

Living beings have been classically described as autopoietic machines: chemical systems, which maintain a reproducible steady state by producing their components and boundaries. On the other hand, very simple autopoietic micelles have been produced in laboratory. They consist in micelles able to catalyse the production of their own surfactants. However is very clear that these autopoietic systems are unable to evolve. In this way, these autopoietic micelles cannot be associated to living organisms, which are always linked by evolutionary relationships. Here I claim that living beings are a class of autopoietic systems able to conserve molecular information, a feature denoted by the term semiopoiesis. By defining the molecular information of their products, semiopoietic systems control their interaction with the medium and, by being able to convey molecular information beneficial to the maintenance of the organization to their offspring, semiopoietic systems can evolve by natural selection. Information can be described as a specific state or order assumed among a set of other possible states or orders. Thus, molecular information is the specific order by which the molecular components are ordered, such as the sequence of nucleotides in nucleic acids or of amino acids in proteins. However, molecular information is not limited to copolymers. The atoms in small organic compounds may also present diverse orders, giving rise to isomers. Different isomers can present very distinct chemical and physical properties such that the biophysical-chemical properties of an organic compound are determined by its composition and molecular information i.e. the specific positions in which their atoms are posited. This molecular information can be conserved during reactions catalysed by selective organocatalysts. In this way, organocatalysts appear as plausible candidates to primitive hosts for the genetic information, before the emergence of systems based in biopolymers. The bases of a putative organocatalysts-based evolution are discussed. Finally, I argue that organocatalytic micelles can be designed to produce programmable materials, artificial photosynthesis, self-building materials and artificial life with relevant industrial impact.

Materialists, you cannot get here from there. Mindless molecules do not make codes. It takes programming: someone with intelligence and a goal to make molecules and organisms understand one another. Symbols are meaningless without minds. A creator can select an arbitrary symbol and endow it with meaning, and build machines that can respond when they see the symbol. The symbol itself, or a set of symbols, will do nothing. You could bounce the nucleotides “ATG” against another molecule all day but it will not go fetch methionine and snap it to itself, much less a left-handed one, then call up another molecule with the precise anticodon to match, and then send it to a precision machine to assemble it to a growing chain of precisely-sequenced amino acids.

The ridiculous lengths to which PhDs go to assume life will build itself up without a mind shows you that there is no answer, except intelligent design, to explain the origin of life. We saw in the previous entry that life is suffused with coded information. We’re glad this special issue of Biosystems looked at the problem, but frustrated that all the scientists ignored the obvious implications of what they observe in living systems.

 

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