Premises of the Theory of Prebiotic Oscillations

The theory begins with the premise that chemical equilibria within the prebiotic soup shift backwards and forward as a result of temperature changes from day to night. This results in the prebiotic soup containing a large number of regular daily oscillations. The sun is the energy and data source that induces these chemical oscillations, which will be selected by high energy reactions in the soup and thus be subject to evolution. Criteria will be given to describe their selective fitness and their bounding in chemical space.

The Theory of Prebiotic Oscillations

The Theory of Prebiotic Oscillations

3.1  Description and Premises
3.2  Power and Data in Prebiotic Evolution
3.3  The Boundaries of Prebiotic Oscillations in Chemical Space
Copyright Statement

3.1  Premises and Description

The theory of prebiotic oscillations takes two sets of premises, that standard physics and chemistry applied on the primordial earth and that the principles of bioepistemic evolution applied within that environment.

Elaborating from those premises, it is taken that the earth's early chemical composition included a complex mixture of organic chemicals, the prebiotic or primordial soup, and that life evolved on earth through normal chemical processes which operated on that soup to produce an evolutionary process.

More precisely, it is suggested that the primordial soup contained some components that took part in equilibrium reactions whose equilibrium constant, K_c, varied with temperature. This assumption implies that the soup's composition varied from day to night - in other words, that its the composition would oscillate with a day night rhythm. These oscillations in chemical composition are taken to interpret the data input arising from the sun's daily variation and to be the starting point for the evolution of life.

The principles of bioepistemic evolution are then applied to those oscillations.

It is argued that, even during its earliest stages, prebiotic evolution and the evolutionary origin of life can be treated in terms of evolving systems. An evolving system needs power for its operation, must have at least one data input and must produce a data output that is the input for the next generation. Also, evolving systems, including prebiotic evolving systems, must contain data processes - these being that data is replicated with variation, interpreted to produce information which is selected from to produce knowledge. The product, knowledge, is encoded as input data for the next generation of evolution.

That the organic chemicals of the soup can be randomized by high energy events occurring in exposed regions of the early earth.

Such high energy events might include lightning bolts, UV exposure arising from the sun due to the absence of an ozone layer during that period, meteoritic impact or extremes of temperature arising from volcanic activity. All such events are estimated to have been much more common on the prebiotic earth than they are today. The theory of prebiotic oscillations considers how such high energy events might select from these organo-chemical oscillations and how those selections, occurring together, might come to alter the composition of the prebiotic soup itself.

That the organic environment of early earth included emulsions of oil in water.

Bioepistemic evolution requires that evolving systems are self-bounding. The premise, that oil emulsions are involved in prebiotic evolution, is included because such droplets interact with amphiphiles in such a way as to create a natural bounding that satisfies the self-bounding requirement. It will be proposed the boundary formation of prebiotic evolution from oscillations occurring within the medium of oil-water droplets, especially the oil-water interface. It will further be proposed that many early, selected oscillations would have involved amphiphilic compounds as these compounds are often emulsifiers and do tend to create and stabilise oil droplets, thus putting the "self" into the self-bounding properties of such oscillations.

3.2  Power and Data in Prebiotic Evolution

Any computer or other commercial data processing system has at least two important inputs, one for data and one for power. Despite its name, a data source is actually a power source but the data source delivers a very weak energy flux that is modulated in such a way as to encode the required data input. The energy flow from this data input is normally too low to drive the operations of commercial data processing systems and this role is filled by the separate power source. Often, the power source drives an amplifier whose job is to increase the signal strength from the data source and so enable the data processing operations of the system. This arrangement applies to most commercial computer systems and also to living things.

3.2.1 Adaptive Design and the Convergence of Power and Data in Prebiotic Evolution

All modern living things have respiratory systems that provide the power needed to operate their data processing devices. In other words, all modern living things, no matter how primitive, have a power input that is separate from their data input and which provides energy for their data processing devices. Biological data processing systems incorporate DNA replication, transcription and translation processes, sense organs and nervous systems and finally actuators, such as muscles or other motile apparatus that can act on selected information. In each case, a data signal controls and can be amplified by a power input.

The sun is the ultimate power source for all these biological data processing devices, either directly, in photosynthesizing plants, or from food that the animals eat. The inner, molecular workings of many of these biological data processing devices are well understood and exhibit many of the characteristics of machines – though to a lesser extent than do the electronic circuits of commercial systems. For example, a ribosome has a clearly defined structure that enables input chemical energy to drive the synthesis of proteins whose amino acid sequence is governed by RNA triplet sequence. Thus, the low free energy content of an RNA base sequence controls the high energy input of an energetically activated, aminoacyl tRNA intermediate. It is this machine-like character of biological data processing devices that enables a low power data input to control the high energy fluxes coming from the power input - as the saying goes, "power is nothing without control."

Biological data processing devices are very fit for their purpose. Their power inputs are often very efficiently controlled by their data inputs which can easily appear to have been designed for the role. However, scientists argue that biological data processing devices were not "intelligently designed" but that they arose by another, very different, design mechanism, "adaptive design." The idea of adaptive design is that, over time, "fit" organisms will be those that perform their biological functions successfully, which means, in terms of natural selection, that they replicate their data and transmit copies of it to further generations. Successful, selected organisms will be those that perform the necessary data processing operations optimally, which will be those whose data processing devices become steadily more "machine-like" in their design and operation.

Adaptive design by evolution is a conceptually more parsimonious mechanism than the alternative - that some intelligent agency intervened to initiate life processes - and most scientists therefore argue that all biological data processing devices arose by adaptive design. However, this concept implies that there can have been no adaptive design prior to the early stages of prebiotic evolution. Hence, evolutionary theories of prebiosis cannot invoke a "designed" data processing device and, since such devices are necessary if a low energy data input is to control any high energy power input, prebiotic evolving systems cannot have used low-powered data inputs. It follows that the data inputs for prebiotic evolving systems must have been high-powered.

The simplest suggestion is that there was only one input into the evolving systems of prebiosis and that this single input delivered its high powered energy in a form that was modulated to deliver data as well as power. (In principle, one might consider two or more separate, high powered inputs, one of which was modulated to deliver data. This situation may have actually applied with, for example, the sun as a data source and volcanism as a power source, but this possibility will not be further considered since it does not seem to conceptually change the resulting discussion. The simple situation has prebiotic evolution being driven by a single energy input, operating at high power and delivering its input in a form modulated to carry data as well as energy.)

The sun seems the best candidate for this role, providing a very high energy input modulated by the earth's rotation to deliver a repeating data input in the form of a day-night rhythm. The solar data signal is very boring, on-off, on-off …0,1,0,1 …day-night, day-night etc. However, this data signal was detectable across the entire surface of the earth, and was delivered with such power that even simple, chemical responses could be expected to detect it and, perhaps, to interpret its presence.

Therefore, the sun is a likely candidate to be simultaneously the source of power and data for prebiotic evolution. This essay will assume that the sun does perform this dual role in prebiotic evolution and that the prebiotic soup responds to the sun according to the known rules of chemistry.

3.2.2 Dynamic Responses in an Organo-Chemical Soup

The earth's power input from the sun is modulated according to a day night cycle so that much of its surface becomes alternately warm and cold. This heating and cooling is a passive response to a data signal but rocks, river and seas are too static in their response to warming and cooling to become the loci for evolution. Evolution is a theory of change, and change can emerge more easily from the dynamic responses to be found in organic chemistry.

The primordial soup is thought to have contained a complex mixture of organic chemicals and it is to be expected that, within this soup, there will have existed a great many, equilibrium reactions of the form

Chemists characterize such reactions by their "equilibrium constants." Equilibrium reactions involve dynamic equilibria because the underlying reactions never stop. Rather an equilibrium chemical composition is achieved where the rate of the forward reaction becomes equal to the rate of the back reaction. Equilibrium reactions are low energy reactions, which is to say that they have a low "activation energy" which is why they continue at low temperatures. Most equilibrium reactions are temperature sensitive – meaning that the position of the equilibrium will shift left or right as the temperature changes. It is to be expected that, as the earth goes through its daily cycle of warm days and cool nights, the positions of many such equilibria will shift from left and right and back again on a daily basis.

Therefore the overall chemical composition of the prebiotic soup can be expected to undergo a daily oscillation (or fluctuation) between two extreme compositions D and N, corresponding to day and night. The overall, day-night oscillation can be symbolized as D < > N and could be described as the sum of many individual oscillations, all involving different chemical compounds and arising from different chemical equilibria. Nonetheless, both the overall oscillation and each of the individual component oscillations involve standard, equilibrium chemistry. All these oscillations are "driven oscillations," which exist only because of the external input of driving energy from the sun and its day-night rhythm.

3.2.3 Chemical Oscillations in a Complex Mixture can be Subject to Evolution

The bioepistemic point of this essay is that, from an IT systems viewpoint, these solar induced chemical oscillations meet the requirements for being evolving systems, which is to say that

1. Prebiotic oscillations receive and respond to a repeating data input.
2. They interpret that input into periodic variations in chemical composition.
3. Prebiotic oscillations are sustained by an external free energy supply.
4. Oscillations are subject to selective competition.
5. As will be discussed, prebiotic oscillations are self-bounding and thus are distinct from one another.

This essay will suggest that prebiotic oscillations are, indeed, subject to evolution and that their evolution is the origin of life on earth. Note, it will not be suggested that any chemicals evolve. Evolution is always about data and data sets and it is the oscillatory patterns within the concentration profile of the primordial soup that reflect their data input and become subject to evolution.

Each component oscillation can be seen as a separate evolving system, separately interpreting the data input from the sun's day-night rhythm. The data input itself is always replicated and "transmitted" to the next generation because it comes from the spin of the earth which repeats reliably. Hence, the input data is replicated each day, which is a "generation." For each swing of this daily, day night oscillation, a certain amount of the sun's free energy is converted and this will power the evolving prebiotic oscillations which were the evolving systems of prebiotic evolution.
While these separate oscillations seem to have the potential to compete with one another, to prove selectively fit or unfit and to evolve, bioepistemic evolution and the systems viewpoint raise three issues that need consideration. The first issue is boundaries. If the different oscillations are to compete with one another they must, in some way be separate from one another. The oscillations must bound themselves in such a way as to divide each of the different oscillations from their competitors. The nature of these boundaries needs to be identified and this will be looked at in the next section. The second issue is that of the selective processes that might lead one oscillation to grow, to prove fit, when compared with competing oscillations. This consideration will occupy the succeeding sections. The third issue is the variation that must occur so that new, fitter oscillations can emerge over time. This issue will not be considered separately but will be allowed to emerge during the course of the discussion - as chemical compositions vary, so do the available oscillations.

3.3 The Boundaries of Prebiotic Oscillations in "Chemical Space"

Competitive evolutionary selection requires that the competing evolving systems must have a boundary that separates one from another in order that fit systems can be selected. Prebiotic oscillations are no exception, if oscillations are to be selected they must, in some way, be self-bounding so that they can become distinct from one another. It seems unlikely that prebiotic oscillations could be bounded in three-dimensional space but chemical oscillations are bounded in "chemical space."

3.3.1 The Boundaries Around Oscillations

The earth's prebiotic environment would not have been uniform; it would have included the sea, from the ocean depths to the surface oceans, shallow seas, coastal regions and tidal estuaries, liquid mixtures, coastal ponds and emulsions, rocky surfaces on land, with different latitudes, elevations and chemical compositions and there would have been volcanic outlets, more than can be found today, both beneath the sea and on the land. This variety of environments is important for an understanding of evolution but none of them suggest an environment where chemical oscillations could become spatially bounded and compete with one another. After all, the prebiotic soup was a random mixture of chemicals that would spread around all environments. There will have been local concentrations of chemicals but it is unlikely that the boundaries of evolving prebiotic oscillations could have been drawn in three-dimensional space.

However, such boundaries might have been drawn in another kind of space. By shifting our thoughts away from three dimensions and to organic chemistry we can define the dimensions of a "chemical space," in which the boundaries of chemical oscillations can be identified.

The chemistry of carbon is very complex with more than ten million different organic compounds already identified, far more than all the compounds known for every other element except carbon. There seems to be no limit to the number of possible different carbon compounds, their amount seems as limitless as the quantity of integer numbers. One could attach a separate number to every possible organic compound. (As an aside, chemists do maintain databases of such numbers, Beilstein numbers or CAS registry numbers, which are used to unambiguously identify compounds and avoid problems with identification.) These numbers could be arranged along axes to create chemical dimensions, much like the axes of Euclidean space. All possible organic compounds could then be represented as points in this chemical space.

Within chemical space, prebiotic oscillations would be bounded and would compete with one another. An oscillation would involve compounds connected to one another via low activation energy reactions. They would be connected to other oscillations only via the high energy reactions and those high energies bound the oscillation.

3.3.2 Describing Oscillations

Equilibrium organic reactions must involve a minimum of two compounds, a reagent and a product, one on the left and one on the right. However, organic reactions often produce more than one product from any given reagents and, since these reactions are reversible, more than one compound could usually appear on the left side to produce each product on the right side. Hence, any given prebiotic oscillation may involve more than two compounds and may involve several.

It follows that oscillations will not usually be specific oscillations involving just two compounds. A few oscillations will be specific in this way but others will be complex and will involve several compounds on either side of the equilibrium sign. Some will involve many compounds but, no matter how many such compounds may be involved, in "low energy" organic chemistry the number of compounds in an oscillation will always be finite.

Individual oscillation can be labeled as _dA < > _nA etc, where _dA and _nA denote the sets of organic compounds that interconvert during this day-night oscillation.

The different compounds that are elements (in a mathematical sense) of those sets would be denoted as _dA₁, _dA₂ etc. A compound is part of the oscillation _dA < > _nA if it is contained in either or both of these sets _dA and _nA.

Any compound that is not a member of these two sets is not part of that oscillation but may be part of another oscillation _dB < > _nB. One can allocate a multiplicity to any particular oscillation that will be the total number of compounds on both side of the oscillation. Thus, for example, a totally specific oscillation would have a multiplicity of 2, with both _dA and _nA containing one compound each interconverted by a specific reaction. Non-specific oscillations are those that have a large number of different compounds on one or both sides of the oscillation or, which is the same, are subject to side reactions that lead to other chemicals being included in the oscillation.

The number of compounds in an oscillation will be finite because many organic reactions are impossible at low energies; high energy barriers must be overcome if the rules of standard organic chemistry are to be broken - if carbon backbones are to be rearranged or functional groups interconverted. In chemical space, each compound in an oscillation is connected to other compounds in that oscillation by low energy chemical pathways but any starting compound can take part in only a finite number oflow energy reactions. Thus, in chemical space, an oscillation is a finite group of compounds set in an energy valley, surrounded on all sides by the high energy barriers that define non-equilibrium, high activation energy reaction pathways. These high energy barriers effectively define boundaries in chemical space between different oscillations. Provided only low energy reactions are involved, an oscillation will never exchange its material content, its carbon atoms, with other oscillations. To put this point another way, the carbon atoms of one oscillation can never enter another oscillation unless they pass over the barrier of a high activation-energy, irreversible reaction. Only high energy reactions are capable of rearranging the carbon backbones of organic compounds or interconverting disparate functional groups.

In this way, organic oscillations are self-bounding and one can think of different oscillations as separate entities. The organic chemistry of each oscillation delimits its own boundary in chemical space and each oscillation contains a certain amount of organic material, a certain quantity of carbon. The material content of each oscillation will remain stable, neither gaining nor losing material unless high energy events intervene. Thus oscillations can compete for carbon material only through the agency of high energy reactions. However, on the prebiotic earth as we now conceive it, many high-energy events will occur. An oscillation will gain material whenever high energy processes synthesize its constituent compounds and, conversely, will lose material whenever its constituent compounds suffer irreversible reactions that transform its carbon content into the component compounds of other oscillations.

Thus, an oscillation will prove "fit" if, on balance, it is accreting material as a result of high energy processes and "unfit" if it is losing material. Evolutionary selection of oscillations will, therefore, be a function of the extent to which an oscillation is exposed to, or protected from, high energy events in the prebiotic earth and this essay can move on to discuss the selection of oscillations.

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.