Organic codes

Poorly organized spaghetti code, filled with convoluted pathways that jump back and forth within the code stream, make continued support difficult and create an environment in which future changes are likely to cause unanticipated problems. Alternately, well-organized code allows efficient maintenance with appropriate tracing and variable tracking. 

Stam NJ, Van Huizen F, Van Alebeek C, et al. Genomic organization, coding sequence and functional expression of human 5-HT2 and 5-HT1A receptor genes. Eur J Pharmacol 1992 227 153-162. 

The Memory Reconstruction Method, in conclusion, gives us two general principles that must be valid for all systems which increase their own complexity, and embryos are such systems. The MRM model predicts therefore the existence of biological structures which are equivalent to reconstruction codes and to memory matrices. More precisely, the model leads to the conclusion that in embryos there must be codes and memories which are made of organic molecules, i.e. organic codes and organic memories. At this point, therefore, we can go back to biology and look for the existence of such structures in real life. 

The genetic code is the only organic code which is officially recognised in the textbooks of modern biology, but it is also a model where we find characteristics that must belong to all organic codes. To start... 

The function of an organic code, in conclusion, is to give specificity to a liaison between two organic worlds, and this necessarily requires molecular structures - the adaptors - that perform two independent recognition processes. In the case of the genetic code the adaptors are tRNAs, but any other correspondence between two independent molecular worlds needs a set of adaptors and a set of correspondence rules. The adaptors are required because the two worlds would no longer be independent if there was a necessary link between their units and a code is required to guarantee the specificity of the link. 

The adaptors were theoretically predicted by Francis Crick in order to explain the mechanics of protein synthesis, but they are necessary structures in all organic codes. They are the molecular fingerprints of the organic codes, and their presence in a biological process is a sure sign that that process is based on a code. 

Figure 4.10 The first messengers of cell signalling can be processed in a variety of ways. Different signals can have the same effect and equal signals can lead to different results, thus showing that signal transduction is based on organic codes.

The experimental results, in brief, have proved beyond doubt that outside signals do not have instructive effects. Cells use them to interpret the world, not to yield to it. Such a conclusion amounts to saying that signal transduction is based on organic codes, and this is in fact the only plausible explanation of the data, but of course we would also like a direct proof. As we have seen, the signature of an organic code is the presence of adaptors, and the molecules of signal transduction have indeed the typical characteristics of adaptors. 

In signal transduction, in short, we find the three characteristics of the organic codes ... 

Figure 4.11 Signal transduction is implemented by a system of three molecules (a receptor, a mediator and an amplifier) that collectively function as the adaptor of an organic code.

Neural embryonic development, in conclusion, appears to be understandable only if we admit that its mechanism is based on organic codes and organic memories. Without these structures, an explanation becomes virtually impossible, and one can only hope that future research will be able to prove conclusively the reality of their existence. 

It is important to notice that this is very different from the mechanism of chemical evolution. Kauffman and Dyson, it will be remembered, have shown that the probability of a spontaneous transition from chaos to order increases with the complexity of the system, but in this case the order (or antichaos) is not a result of natural conventions and has nothing to do with organic codes. 

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