Saturday, September 22, 2012

46. Emergence of Autocatalytic Sets of Molecules

Life depends on molecules of RNA, DNA, proteins, polysaccharides, etc. How did such large molecules ('polymers') get synthesized spontaneously from their building blocks, namely nucleic acids, amino acids, sugars, etc.?

A polymer is a long molecule, the backbone of which usually comprises of a chain of covalently-bonded repeat units (monomers). There can be variations, either in that the bonding is not covalent everywhere, or in that not all subunits are identical. Examples of polymers and polymer solutions include plastics such as polystyrene and polyethylene, glues, fibres, resins, proteins, and polysaccharides like starch.

Short polymers can form spontaneously in Nature? Recall the lock-and-key mechanism I described in Part 44. Suppose a monomer has a shape and charge distribution such that another monomer can fit snugly into some part of it. There are random collisions among the monomers in a fluid medium, and usually they do not stick together, and simply bounce off after a collision. But once in a while the collision may be such that the two monomers have just the right orientation for a lock-and-key fitting. Then the chances of the two sticking together and forming a stable dimer are much larger.

Dimers can lead to trimers, and so on, resulting in polymers. But this can at best be a rather low-probability, and therefore very slow, process, and only short polymers can possibly form spontaneously in reasonable time.

Then how did very long polymers like RNA, DNA get formed? There had to be a mechanism for speeding up the rates of polymerization. The answer came from the emergence of autocatalytic sets of molecules.

Catalysis is a process that facilitates or speeds up a chemical reaction. Often a chemical process involves two or more intermediate reactions. A catalyst is a molecule that speeds up the production of an end product of the chemical process by participating in the intermediate reactions, but separating at the end of the chain of reactions, thus becoming available all over again for further catalysis. Often, a chemical reaction may almost never occur if no catalyst is present. Enzymes are examples of proteins that assist (i.e. catalyse) chemical reactions in biological systems.

Photosynthesis carried out by green plants in the presence of sunlight is another familiar example involving catalysis. Chlorophyll is the catalyst here. Through a number of intermediate reactions, the net reaction is as follows:

CO2 + H2  C6H12O6 + O2

That is, carbon dioxide combines with water to produce glucose and oxygen. This is the oxygen we breathe.

Autocatalytic sets of molecules are those which can catalyse the synthesis of themselves. Autocatalysis requires that a given 'factor' (say A) should be able to convert a substrate or precursor B into a new factor of the same type: A + B 2A + C. The idea of autocatalysis was introduced by Calvin (1969) as a mechanism for 'molecular selection', with implications for how life emerged on Earth.

Stuart Kauffman carried Calvin’s idea much further for explaining how long polymers like RNA could form spontaneously during the course of chemical evolution on our Earth. In the so-called primordial soup, namely a fluid in contact with rocks of various types, there existed small molecules of amino acids, nucleic acids, etc. Given enough time, some of them must have undergone random polymerization reactions of various types; i.e., short polymers got formed. It is entirely possible that at least some of these short polymers, with side chains and branches hanging around, acted as catalysts for facilitating the production of other molecules which may also be catalysts for another chemical reaction. Thus: A facilitates the production of B, and B does the same job for C, and so on. Given enough time, and a large enough pool containing all sorts of molecules, it is quite probable that at some stage a molecule, say Z, will get formed (aided by catalytic reactions of various types), which is a catalyst for the formation of the catalyst molecule A we started with.

Once such a loop closes on itself, it would head towards what we now call 'self-organized criticality' (SOC). There will be more production of A, which will lead to more production of B, and so on, finally reaching a 'critically stable' configuration.

The plausibility advantage of this scenario visualized by Kauffman is that there is no need to wait for random reactions. And once a threshold has been crossed, the system inches towards the edge of chaos and acquires robustness against destabilizing agencies.

Kauffman argued that this order, emerging out of molecular chaos, was akin to life: The system could consume (metabolize) raw materials, and grow into more and more complex molecules. It progressed into a situation where the forebears of DNA started appearing:

Once a set of autocatalytic reactions had established itself, it went on incrementally evolving into still more complex sets of molecules. Chance events and/or new external conditions resulted in the emergence of a slightly more complex version of, say, one of the molecules in the autocatalytic set. A further round of chemical Darwinism and evolution of a new set of autocatalytic set of molecules followed. And so on, till molecules as complex as RNA, DNA and proteins emerged on the scene, which have life-sustaining and life-propagating properties.

The question of the emergence of order and complexity in open systems was investigated in the 1970s by the Nobel Laureate Prigogine. An important feature of his work on open systems was that self-reinforcement or positive feedback is also needed for self-organization or pattern formation to occur. Only then can small chance events become magnified, sometimes taking the system to new valleys in phase space (basins of attraction). This ‘law of increasing returns’ or positive feedback, illustrated above by autocatalytic sets of reactions, can often lead to a multiplicity of qualitatively new outcomes. The actual outcome may depend on chance initial conditions, a feature characteristic of highly nonlinear systems.