Systems of correspondences - Systems of ideas in circuit

At the present stage of evolution we have to deal with coevolutionary systems which present emergent properties. What is evolving today (and since a long time ago now) are not single entities but entire complexes of sophisticated networks at all levels, from genomes to phenotypes, from prokaryotes to Internet.

What is informed by the genome are integrated systems of functional domains, which constitute elemental units for a great diversity of emergent codes. All these codes share the principles of specificity modulated by digital-analogical consensus working within a triadic logic in the process of emergence of complex phenotypes.

The different functional domains in a single protein allow its interaction in and with different directions of the network and with different actors of the system. Each functional domain represents a correspondence with other domains distributed in the products that are coded in the genome, as well as correspondences with products coded in or by the environment, including organisms of the same or different species³.

For example, a homologous phosphorylisable sequence (i.e.: a sequence which is susceptible to being phosphorilated in a particular residue) can be encountered in different proteins combined with a variety of other domains that give its particularity to the protein. In this way, the code of phosphorylation is distributed in the whole system. These correspondences at the level of functional domains is what is actually coded in the genome i.e.: networks of correspondences which are used to constitute metabolic codes; not complete complex phenotypes. What is coded in the genome are

3This is related to the “principle of correspondences” as discussed in Uexküll et. al. (1993: 12) which states that “in the sphere of living things each affordance presupposes a counteraffordance - that is, it can be realized only through an interaction”.

the elemental units of specificity which are used and arranged modularly in the

distributed network, as well as the “recipes” for successful structural elements. Part of the arrangement is implicit in the complex architecture of the genome. But the model for integrating circuits is an analogue implicit in the embryonic signalome (see section 3.1.2). The analogical “know-how” to ensemble and differentiate systems of

correspondences must be inhereted in the embryonic signalome. Once cells start dividing, the new cells get the library and the whole system of interpretation. During differentiation the library remains the same, therefore differentiation starts by changes in the signalome (see section 3.1.1).

The combinatorial possibilities of domains constitute complex codes with different infrastructural organisation and mechanisms but which share common logical principles. In this view, DNA is a library of distributed architectures of

integrated systems of corresponding (specific) sequences: the emergent digital units of the DNA code. The sequences or domains - be that binding sites, integrating repetitive motifs, protein domains, regulatory sequences, etc. - are used modularly within

systems of correspondences and specificities that reach beyond the organism into its niche.

Let’s take for example the following evolutionary consideration about a family of signal-transduction components:

“Both Gsα and Ras are members of a family of intracellular GTP-binding switch proteins collectively referred to as the GTPase superfamily ... The many similarities between the structure and function of Ras and alpha Gs-alfa and the identification of both proteins in all eukaryotic cells, indicate that a single type of signal-transducing GTPase originated very early in evolution. The gene encoding this protein subsequently duplicated and evolved to the extent that cells today contain a superfamily of such GTPases, comprising perhaps a hundred different intracellular switch proteins. These related proteins control many aspects of cellular growth and metabolisms” (Lodish et. al., 2000: 905).

It is not that these proteins control these many aspects by themselves. They are a part of a sophisticated network that in its complex relations regulates the coordination of many simultaneous processes. Whereas it is said that a single type of protein

originated very early in evolution and from there came all its variants, it has to be emphasised that the function of the protein has to be seen in coevolution with the integrated network in which it functions. The protein cannot pop up being already potentially “useful” (functional) to something (within a system) and then “jump” into a circuit where that “usefulness” has a value. It is not plausible, to me, that a

functional signalling molecule emerges, then it diversifies into 100 different variants and then each variant jumps into a slightly different but homologous mechanism within 100 different networks. Somehow the components and/or the networks must coevolve.

Be that as it may, convergence should not be considered as something uncommon. The same idea can be achieved with similar, or even with totally

different, infrastructure. Convergence may occur at different levels. It can be that two different signals act through totally different infrastructural arrangements in eliciting the same genetic response. It can also be the case that the pathway is very similar but some steps are in some ways different. There can also be an instance in which some identical steps or mechanisms are used in pathways that lead to different “final”

responses. In other words, there is convergence in the use of modular components.

Pathways can be modularly arranged (by using existing ideas) to produce answers to similar and new kinds of challenges. The evolution of hierarchical specificities requires a different evolutionary mechanism, not so much based on single genes, but on modular components. Certain forms in the context pose a question, so to speak, of which the emergent component is an answer, a “functional” idea or a sign. This can be appreciated in the evolution and development of many specificities, like for example antibody and antigen in mammalians, or avirulence factors and response-determinants in plants.

At ecosystem level, biodiversity is the library for the ecological systems of correspondences which are involved in the development and organisation of

ecosystems. If we destroy the information, i.e.: if we interrupt networks, we destroy the regeneration capacity of the ecosystem. Conversely, if we disable ecosystem-function, the information loses its sense, there will be no context for its interpretation.

These two metasystems of correspondences, the genome and biodiversity, are in correspondence with each other. So besides a taxonomy of species, we are now developing a taxonomy of circuits.

What evolves and develops are systems of correspondences.

What survives are “systems of ideas in circuit”.