The Selection and Evolution of Oscillations
It is proposed that certain oscillations in the prebiotic soup are evolutionarily fit because their component chemicals have physical properties that cause them to accumulate in environments where they are protected from high energy events. Protected and unprotected oscillations are described. Selection of protected oscillations and optimal protection. It is proposed that specific oscillations will become favoured and that oascillations will evolve toward biochemical pathways. The evolution of pathways, specificity and catalysis is discussed. It is noted that the bounding of catalysed oscillations will require a three dimensional object, such as an oil droplet. Possible mechanisms for the evolution of self-oscillating biochemical pathways, allostery, biochemical homeostasis and cyclic biochemical pathways are presented.
Evolution of Oscillations
Selection of Oscillations, Adaptation into Biochemical Pathways
4.1 Selection of Prebiotic Oscillations
Protected Oscillations; Specificity; Fast reactions; Catalysis;
4.2 Selection of Actively Oscillating Reaction Pathways
Self-Oscillating Reactions; Biochemical Pathways; Allostery; Homeostasis; Cyclic Pathways.
Copyright Statement
4.1 Selection of Prebiotic Oscillations
The primordial soup is thought to have formed in an environment that was, by today's standards, physically hostile and chemically aggressive. The early earth was warm and will have produced many storms and attendant lightning, its high volcanic activity will have created emissions of acidic chemicals, meteorite impacts will have been common and, with no ozone layer to protect it, the earth's surface will have endured high fluxes of ultra violet light emanating from the sun. In such an environment, organic chemicals will have been subject to many high-energy, irreversible chemical reactions that could change the material content of any oscillation exposed to them. However, some environments would have been such as to protect chemicals from the randomizing effects of these conditions. Likely examples of such sheltered environments will have been rocky surfaces or submarine sediment etc.
4.1.1 Selection of Protected Oscillations
Organic compounds have a range of physicochemical properties and, by chance, some will have had properties causing them to accumulate in protected environments. A compound with such properties would have been "protected" from randomization. The extent of its protection would have depended on its chemical stability, its partition equilibrium constant between protected and unprotected environments and on the rates at which it enters and leaves protection.
An oscillation dA < > nA will be fully protected from randomization if all the compounds on both sides of the oscillation are protected at all times. The material content of a fully protected oscillation will tend to increase because randomizing, high energy reactions in the exposed soup will, by chance, synthesize some of its chemical components which will then enter protected environments.
An oscillation dA < > nA will be partially unprotected if any of the compounds on either side of that oscillation are unprotected. The extent of the unprotection will depend on the number of unprotected compounds in the oscillation and on the relevant partition equilibria and their equilibrium constants. The material content of unprotected oscillations will tend to decline as randomizing chemical reactions in the soup irreversibly convert their content to other compounds. In other words, oscillations are subject to selection and protected oscillations will be selected in preference to unprotected oscillations.
4.1.2 Optimally Protected Environments
The rate at which oscillation are selected will be influenced by a variety of factors. An oscillation will be favoured if its components accumulate in protected environments but an environment may be too sheltered. It may be so protected as to receive little warmth from the sun, producing a slow equilibrium. It may be so sheltered that it never exchanges material with the exposed, randomizing primordial soup, so that chemicals newly formed within the prebiotic soup, and which might otherwise enter the protected environment, fail to do so and are lost to further high energy reactions.
In such cases, the rate of selection of oscillation will be low, even though the equilibrium degree of protection is high. Hence, there will exist some optimal degree of protection, one in which the combination of temperature fluctuation, rate of reaction and rate of exchange with the soup are such as to optimize the rate of selection. The exact nature of this optimally protected environment is hard to define, will depend on many variables and will vary from oscillation to oscillation; it is even likely to vary from night to day, so that the day night rhythm will impact onto the nature of selection. It would be infeasible to analyze a system with so many undefined variables to the point where one could predict optimal protection and it has not been attempted here.
Nonetheless, because of their physicochemical properties, it does seem clear that certain chemicals will be protected from high-energy, randomizing processes. Because of this protection, those oscillations that contain a preponderance of protected chemicals will be selected over time. By contrast, those oscillations whose component chemicals are more exposed to randomization will tend to be deselected.
4.1.3 Selection will favour some Specific Oscillations in Optimal Environments
By definition, only a minority of chemicals will be optimally protected and, purely as a matter of chance, high multiplicity oscillations will not normally be optimally protected; that is to say, if an oscillation contains many compounds, one or more of those compounds is likely to be unprotected and so expose the entire oscillation. If an oscillation is highly specific then, purely as a matter of statistics, there is a better chance that its component chemicals will be well highly protected. (Of course, there is also a higher probability that both the compounds of a specific oscillation will be unprotected but those oscillations will be deselected and do not alter the central argument.)
Selection will thus favour those, specific oscillations whose chemical components reside in optimally protected environments. The result is that, over time, a selective process should occur that causes these chemical mixtures to predominantly involve those organic compounds that are subject to specific interconversions and oscillations. In other words, evolutionary processes acting on a random mixture of organic chemicals will select specific, protected, chemical oscillations at the expense of those that are non-specific and unprotected. (This aspect of the theory suggests an origin for biochemical specificity.)
4.1.4 Fast Reactions and Highly Specific Catalysts
When a new compound is formed in the prebiotic soup it needs to enter a protected environment as rapidly as possible where it will be "safer." That rate will depend upon the rate at which it partitions into a protected environment.
Also, if two oscillations contain compounds that compete for the same, vacant protected space, selection will favour that which occupies the space first, the oscillation whose reaction is fastest. Many variables determine the rate of a reaction but one of the most important is the presence or absence of a catalyst. An oscillation will be fastest and be selected if it is aided by the presence of a catalyst. Combining this requirement with the need for specificity means that the catalyst should catalyze just one reaction or, at most, a narrow range of reactions. Further, we believe that the earth cooled very slowly. During that cooling, an oscillation may have been selected at a higher temperature but then become unfavorably slow at a lower temperature. In these circumstances, the previously selected oscillation may have come to depend upon catalyst for its continued existence. As time passed, and the earth cooled further, the catalyst's activity would need to increase further, implying that the catalyst, itself, would become subject to evolution in order to maintain an oscillation. (This form of selection suggests an origin for enzyme catalysis.)
Once catalysts are involved in maintaining oscillations, bounding in chemical space becomes insufficient. Some means is needed to keep the reagents and catalyst close to one another. Hence, the question of boundary formation must be revisited in order to identify a mechanism of bounding in normal space and the reasons why an oscillation should co-evolve with its catalyst. These considerations lead to the suggestion, discussed later, that the selected, catalyzed oscillations occurred in, or on the surface of, emulsive phases, such as oil droplets.
4.1.5 Catalytic Selection may lead to Selection of Specific Reaction Pathways
The possibility of selecting oscillations using highly specific, active catalysts raises the possibility of another type of oscillation, one which involved one or more intermediates. Thus, one might conceive of the following oscillation dA < > iA < > jA < > nA, in which neither iA nor jA need be present for an extended time but in which each step would require a separate catalyst. The selective advantage of such a pathway might be that, since iA and jA are transient, they need not be as protected as the terminal compounds, dA and nA. (Selection for catalyzed oscillatory pathways suggests an origin for enzyme-catalyzed biochemical pathways.)
4.2 Selection of Actively Oscillating Reaction Pathways
The previous discussions took little account of the day night cycle and some of its arguments could be applied to an earth with neither day nor night. In this section, the importance of the sun as a data source will becomes more clear and its rhythm will come to dominate the chemistry of prebiotic oscillations. We will conclude that self-oscillating reactions with a period of one day will be selected in preference to the passive, solar driven oscillations we have discussed so far. This section is important for the theory being proposed but the reasons for making these steps may need clarification and certainly need linking to the biochemistry and the thermodynamics of living systems. Here, something resembling biology will begin to emerge from the primordial soup.
4.2.1 Preamble
Many of the biochemical pathways in modern organisms are arranged so that the pathway's first enzyme is subject to "allosteric" control by the last product of that pathway. This arrangement is selectively valuable because it means that, if the concentration of the product metabolite is low, the allosteric enzyme and hence the biochemical pathway, can become switched on, so synthesizing the necessary product. Such control mechanisms make metabolic sense and are firmly established aspects of biochemistry and biochemical explanation. This is one of the ways in which organisms maintain their internal environments and textbook discussions of it may be found under the heading of "homeostasis".
The evolutionary question is, "How could such control mechanisms have evolved?" The present argument about prebiotic oscillations offers a plausible, but far from obvious, answer to that question. As it happens, the feedback and control loops implied by the allosteric control of biochemical pathways are very similar to the control loops needed to create self-oscillatory behaviour in any chemical reaction. It is well established that biochemical pathways often become self-oscillatory (for examples see Berridge et al., 1979) and that these feedback loops explain these observations. Therefore, the question, "How did allosteric control evolve?" may reasonably be replaced with the question, "How did self-oscillatory biochemical pathways evolve?" It is this rephrasing that allows the problem of the evolutionary origin of allosteric control to be addressed.
Note also that it is not simply biochemical pathways that have this property of self-oscillation - theoreticians point out that all living systems seem to exist in a thermodynamic zone that poises them on the edge of oscillatory behaviour. (See, for example, Winfree, 1980). The present theory of prebiotic evolution offers some explanation for this general property.
Oscillatory reactions in simple chemistry are known and well understood; an example is the Belousov-Zhabotinsky reaction. Although they are known, and their biochemical implications widely discussed, (for example, see Boerlijst and Hogeweg, 1991) self-oscillating chemical reactions are very rare and are sensitive to conditions and contamination. Thus, self-oscillating chemical reactions require controlled chemistry. Chemists can set them up in the laboratory but self-oscillating chemical reactions will not emerge by chance in random mixtures. Not only do such reactions require controlled chemistry, as will shortly be mentioned, they also need a separate power supply – an energy releasing reaction that becomes coupled to the oscillating reaction. Oscillatory biochemical pathways could not have emerged and been sustained unless they were selected for. Giving a mechanism for the emergence of such pathways shows how adaptive design, operating on prebiotic oscillations, could provide the evolutionary history needed for lifelike entities to emerge.
4.2.2 Selection of Self-Oscillating Pathways
So far, this discussion has concerned the selection of passive oscillations, oscillations driven by the energy flux from the sun's daily rhythm. However, that discussion leads to the possibility of adaptation, of new pathways emerging that do not just oscillate passively but are actually self-oscillating. This, in its turn, creates new possibilities for selecting chemical oscillations during prebiotic evolution.
If a chemical oscillation were to be self-oscillating, with a natural period of one day, then it could have a selective advantage over passive oscillations. Consider a specific oscillation dA1 < > iA1
< > jA1 < > nA1 in which the day component first dA1 is optimally protected during the day and the nighttime component nA1 is optimally protected during the night. This oscillation would enjoy a selective advantage if, instead of responding passively to the daily change in temperature, it were to anticipate the forthcoming evening or morning and begin reacting before the inevitable temperature change. It would win a selective competition with a similar but passively oscillating pathway because it would, so to speak, be primed to occupy protected environments as they became available. Another way to say this is that, if a self-oscillating pathway, dA < > iA < > jA < > nA, has a time period with the same frequency as the externally imposed driver, then its amplitude might be expected to rise due to effects analogous to resonance. Such selection would favour enhancing the self-oscillations until a point of maximum amplitude is reached; the limit being just prior to the point where its oscillations become chaotic. This is exactly the domain that thermodynamicists identify as occupied by living things.
All self-sustaining oscillations, including self-oscillating chemical reactions, have one, thermodynamically unavoidable property - they need an energy input from some linked, energy releasing process, in this case an energy releasing chemical reaction. In other words, self-oscillating reactions are not passive reactions. They do not derive their energy from the sun but from some linked, energy releasing chemical reaction. Hence, selection of a self-oscillating pathway implies selection for an oscillation linked to some chemical energy source. The energy needed to maintain the oscillation is then drawn from the energy released by this other chemical reaction. In other words, selection for self-oscillating chemical reactions implies selection for oscillations that feed.
The oscillation has also become a data processing chemical reaction that functions by replicating its input to produce a data output and which draws the necessary power from a parallel energy releasing chemical reaction, a driver reaction. The oscillating pathway has become simple, evolving data system that has a data input, and a separate power input, a data process that will interpret its input data, it is subject to selection and it has a data output that will drive the next cycle of the oscillation.
(This aspect of the theory suggests an origin for
1. The self-oscillatory behaviour of many biochemical pathways,
2. The allosteric control mechanisms found in biochemical pathways
3. The fact that biological systems need chemical energy inputs.)
4.2.3 Selection of Cyclic Pathways
The existence of self-oscillating metabolic pathways suggests a mechanism for the origin of cyclic biochemical pathways, such as the tricarboxylic acid cycle, which are of central importance in metabolism. The evolutionary mechanism would be as follows. Consider two self oscillating pathways, dA < > iA < > jA < > nA and dA < > kA < > lA < > nA, which have the same terminal cmpounds but different intermediates. Joining these two oscillations together would produce a closed loop with material moving back and forth along two different pathways. Suppose, further, that these two pathways do not oscillate in perfect symmetry - that is, one reaction is relatively fast going forward and the other rleatively fast going backward. (Note - this situation is not thermodynamically prohibited since these oscillations are not equilibrium reactions, they are coupled to chemical driver reactions.)
Fig. 4.1 A diagram to show how two self-
oscillatory pathways that each begin and
end with the same compound, can merge
to form a cyclic pathway.
Thus, one can describe the kinetics of such a chemical loop as the sum of two components, a chemical oscillation plus a chemical cycle. Evolution would optimize such a system in a way that would depend upon its properties. It the loop generated material of value to the protocell as a whole, evolution can be expected to have optimized the loop by eliminating the oscillatory component. Thus chemical oscillations offer a mechanism whereby a chemical cycle can evolve. Emergence of such a cycle requires further selective steps beyond the emergence of oscillations but it does not seem intrinsically improbable.
(This aspect of the theory suggests an origin for metabolic cycles.)
Copyright Statement
© John A Hewitt MA PhD (Cantab.)
The work described here was performed as an independent investigation by John A Hewitt who asserts the right to be recognized as its author and as the originator of the novel ideas presented here. The topics to which this claim applies include, but are not limited to, the application of bioepistemic evolution to the prebiotic situation, the discussion of the sun as a data and power source for prebiotic evolving systems, the recognition of sun-induced chemical oscillations as information carriers subject to evolutionary selection and to the theories for the origin of biochemical pathways and self-oscillatory, allosteric and cyclic biochemistry that result.
This study is a greatly extended version of a poster originally presented at the Royal Society meeting on conditions for the emergence of life on the early earth, London, 13 & 14 February, 2006. This internet version was made available on 6 September, 2006. Comments and criticism are solicited - see the "contact & copyright" link for contact details.