Protein Folding Structures

The simplistic physical models of attraction and repulsion are inadequate for complex systems. A biomolecule is such a complex system. Attempts to model the folding patterns of biomolecules have been ongoing for at least three decades now and there is no predictive solution available at present. Heuristic models of prediction based on AI are being tried at present. We will wait to see if any of that works. But even if it does work, it still doesn't explain how biomolecules fold. Heurisitics of AI is certainly not the way biomolecules are folding. Then how are they folding? This problem requires us to rethink how structures are formed by drawing upon ordinary notions of societal, organizational, and ecological structures.

The study of chemistry today rests on the idea that two opposite charges attract, and similar charges repel. Let’s call that idea “opposites attract” for simplicity. But is this the only way that complex structures are produced in the world around us?

We can think of several alternative mechanisms by which complex structures arise if we consider organizations, ecosystems, and societies. For example, we know that “complements attract” to form organizations and teams. Likewise, “commonality attracts” as people with similar goals come together for a common purpose. Then, “neutrality attracts” as we are drawn toward societies where there is equality, justice, meritoriousness. Then “individuality attracts” because qualities like knowledge, beauty, wealth, power, fame, and detachment that are inherently attractive. All these descriptions are based on types or qualities, which can be organized into a hierarchy.

  • At the highest level, a person becomes inherently attractive by the acquisition of qualities like knowledge and beauty, and by that attraction, new relationships with other individuals are formed. This is the principle of individuality attracts.
  • Then, at a slightly lower level, qualities like justice, morality, equality, and freedom make a society attractive, and that brings people within the society, to practice and propagate these qualities. This is the principle of neutrality attracts.
  • Then, at an even lower level, the commonality of goals—within the broader individual pursuits, which are also free—brings people together to form organizations and teams. This is the principle of commonality attracts that creates groups.
  • Then, at an even lower level, the individuals in a group take on complementary roles or functions based on their strengths and weaknesses. This is the principle of complementarity that leads to the formation of organizational structures.
  • Then, at the lowest level, there are attractions between opposites like genders, although they create a structure when there are also complementary roles, similar goals, sufficient freedom, and each individual has inherently respectable qualities.

Modern scientific theories of molecular structures are based entirely on the attraction of opposites (defined as positive and negative charges). But if we were to treat the atoms as qualities, then the principle of structure formation would be primarily based on the commonality of purpose and the complementarity of roles. To perform these roles, individual atoms would be selected based on their capabilities. Since all capabilities may not be utilized within a structure, role, and purpose, therefore, the stability of the structure would also depend on the movement of abilities from one role to another, within or across different purposes, and the enrichment of abilities within a role and purpose with passing time. Finally, since every change brings adjustments, therefore, the potential for enrichment would be traded-off with stability based on how well-adjusted an individual is within a given role, goal, and structure.

If matter is devoid of meaning and purpose, then we can rely only on attraction between opposites. But if matter has collective purpose, then structures emerge due to complementary functions performed by individuals. If matter has indiviudal purpose (i.e., each atom is modeled as a person), then structures change to enrich each individual with greater potentials. However, since enrichment requires readjustment, therefore, structures remain stable due to the contradictory purpose of stability.

A far more sophisticated idea of structure emerges when we treat nature as persons and qualities. A far more robust, versatile, and intuitive idea of structural change appears along with it. This kind of sophistication, intuitiveness, robustness, and versatility is required to demystify the evolution of complex molecular structures.

Of course, protein folding structures are just one example of such complexity. The principles can be generalized across other kinds of structures involving organizations, societies, and ecosystems. Change vs. stability can also be driven by different causes noted above, which means that even if the effect is the same, the cause may not be the same. The science of structure cannot be understood if we limit ourselves to one type of causality. A more sophisticated and versatile model of change is needed for it.