Front-loading and Self-Organization

In 2007, Michael Denton (and JB Edelmann) published a paper entitled “The uniqueness of biological self-organization: challenging the Darwinian paradigm (in Biology & Philosophy 22:579-601). I hope to review this paper in more detail in the future. But while I am not too keen on the “challenge the Darwinian paradigm” angle, it is definitely worthy considering how the phenomenon of self-organization might relate to front-loading evolution.

Denton introduces self-organization as follows:

In their book Biological Self-organization Camazine et al. (2001) define selforganization:

‘‘As a process in which pattern at the global level of a system emerges solely from numerous interactions among the lower level components of the system. Moreover the rules specifying interactions among the system’s components are executed using only local information, without reference to the global pattern. In short pattern is an emergent property of the system rather than being imposed on the system by an external ordering influence.’’

In the article, Denton and Edelmann cite protein-folding as one example. If you’ll remember, I have encouraged people to think more deeply about the role of proteins in evolution, wondering to what extent evolutionary success is itself a protein-dependent phenomena.

Denton and Edelmann do not directly address this issue, but their discussion is relevant:

The complex 3D forms of proteins are not specified in a genetic program but arise epigenetically via self-organization (Monod 1972: 89–97). The process of folding is basically a phase transition (Florey 1969) between the initial disordered chain and the tightly packed 3D crystal like form of the native conformation. Each of the approximately 1,000 folds represents a primary natural self-organizing form (like an atom or crystal) and adaptations are clearly secondary modifications of a primary form given by physics (Denton and Marshall 2001; Denton et al. 2002).

This is an intriguing point. The folds are not the products of selection; the folds are the products of natural law that in turn work to facilitate selection, thus front-loading. And as we have seen, this toolkit of protein folds has provided natural selection with an abundant pool of possible functions to help life persist and adapt. And there is a distinct brilliance in using this design material:

Consider the advantages that accrue to the cell from the self-formative robustness of proteins. Firstly, the cell is relieved of the enormous burden of having to specify and organize the fabrication and assembly of 1,000 complex 3D atomic architectures—a process that would be costly in energetic and informational terms. In effect the cell gets 1,000 immensely complex atomic forms that unerringly assemble into their proper native conformations billions of times each second. Secondly, as self-organizing forms, each fold is able to maintain and regain its native conformation in the turbulent chaos of the cell’s interior, which may involve anything from the movement of a few atoms to the unfolding of sections of the amino acid chain (Brandon and Tooze 1999). Thus the cell has no need of any complex repair algorithms involving sensors, feed back control and special ‘‘repair machines’’ to reassemble them into the ‘‘proper configuration’’ after deformation. To get its tool kit of protein forms the cell needs only to specify linear amino acid sequences and the environmental conditions for their folding—the right pH, ionic strength etc. Moreover, because the folding is a process of energy minimization, the cell needs to expend no energy on the actual folding process. Once the linear sequences of amino acid and nucleotide residues have been chemically linked, nature provides both the three-dimensional complexity of the forms and the thermodynamic energy for their assembly. Unlike virtual automata, ‘‘nano assemblers,’’ (Drexler 1986) or macroscale machines such as Lipson and Pollack’s (2000) robotic life forms, the programs specifying the protein folds (the linear nucleotide sequences of the genes) are vastly less complex than their 3D structures.

The natural robustness of proteins has another consequence. The authors of a recent paper comment (Przytycka et al. 1999): ‘‘A protein’s function is due to a comparatively small number of residues, suitably interspersed throughout the sequence. This process of embedding functional residues in a robust framework constitutes a versatile mechanism to confer multiple functions upon a given fold.’’ The folds are thus able to maintain their core architectures in the face of considerable amino acid sequence variation, and this contributes another important element of fitness. It makes possible adaptive substitutions that do not disrupt the underlying fold architecture and this facilitates functional molecular evolution. It is the generic robustness of the basic fold frameworks that permit such sequential ‘‘tampering’’ and consequent functional variation.

Self-organization thus helps a designer maximize the impact of a minimal investment. The vast array of functions carried about by proteins is within the reach of life because life need only string together amino acids to tap into the toolkit of protein folds. And that multiple functions can be derived from a given fold simply enhances the ability to bury designs and make them accessible for purposes of front-loading.

Another puzzle piece may be falling into place: Front-loading and self-organization are two phenomena that can co-exist in a synergistic fashion. Self-organization may be part of front-loading and front-loading can build on or exploit self-organization.

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