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This is a schematic representation (with a high degree ofabstraction) of the mechanism of protein synthesis, which can beinstantiated with details of DNA base sequence, complementary RNAsequence, and the corresponding order of amino acids in the proteinproduced by the more specific mechanism. Molecular biology textbooksare replete with diagrams of mechanism schemas. A mechanism schema canbe instantiated to yield a description of a particular mechanism. Incontrast, a mechanism sketch cannot (yet) be instantiated; componentsare (as yet) unknown. Sketches have black boxes for missing componentsor grey boxes whose function is known but whose entities andactivities that carry out that function are not yet elucidated. Suchsketches guide new research to fill in the details (Craver and Darden2013).

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This stage is practically a reverse process of the protein synthesis on a ribosome.

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Molecular biologists discover and explain by identifying andelucidating mechanisms, such as DNA replication, protein synthesis,and the myriad mechanisms of gene expression. The phrase “theoryof molecular biology” was not used above and for good reason;general knowledge in the field is represented by diagrams ofmechanisms. Discovering the mechanism that produces a phenomenon is animportant accomplishment for several reasons. First, knowledge of amechanism shows how something works: elucidated mechanisms provideunderstanding. Second, knowing how a mechanism works allowspredictions to be made based upon the regularity in mechanisms. Forexample, knowing how the mechanism of DNA base pairing works in onespecies allows one to make predictions about how it works in otherspecies, even if conditions or inputs are changed. Third, knowledge ofmechanisms potentially allows one to intervene to change what themechanism produces, to manipulate its parts to construct experimentaltools, or to repair a broken, diseased mechanism. In short, knowledgeof elucidated mechanisms provides understanding, prediction, andcontrol. Given the general importance of mechanisms and the fact thatmechanisms play such a central role in the field of molecular biology,it is not surprising that philosophers of biology pioneered analyzingthe concept of mechanism (see the entry on mechanisms in science).

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To understand, what kind of mechanism resolves this typically linguistic problem of removing homonym indefiniteness, it is necessary firstly to postulate a mechanism for the context-wave orientations of ribosomes in order to resolve the problem of a precise selection of amino acid during protein synthesis [Maslow, Gariaev 1994].

When they are involved in protein synthesis, the number of base pairs in the ribosome A-site exceeds 3 [45].

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This, the wave-biocomputer model asserts, only begins to explain the apparatus of protein biosynthesis of living organisms, providing an important interpretation for the initial stages within this new proposed composite hierarchic chain of material and field, sign, holographic, semiotic-semantic and, in the general case, of figurative encoding and deciphering chromosome functions.

The basic statements of this proposed preliminary model of matter-wave sign processes in protein biosynthesis are as follows:

as the site of protein synthesis

In this sense, the code is the first stage in a chromosome’s plan of building a biosystem, since the genome language is multidimensional and pluralistic and is capable of setting up more than just a protein synthesis task.

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This is a remote influence, connected with the protein synthesis continuum; it’s also an example of the genetic apparatus’ non-local functions, whereby the protein-synthesizing apparatus recognizes mRNA not only in parts (by nucleotides, locally), but in one piece (non-locally) as well.

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that serves as the “start” codon for protein synthesis.

Here, the translation context effect is clearly seen as a strategic influence of distant mRNA codons on the inclusion (or non-inclusion) of certain amino acids in the composition of a protein being synthesized.