The Origin of Life and Chemical Chirality
This essay extends "the evolution of prebiotic oscillations," to suggest mechanisms for the emergence of chiral specificity in biochemistry. The first suggested mechanism is that, when the molecules of a racemic mixture of a chiral amphiphile form a monolayer, the L and D forms tend to the separate into separate zones or rafts that become separate loci for competing, evolving oscillations. One of the two isomeric oscillations will prevail and lead to the subsequently observed isomeric specificity.
The second suggested mechanism is that chirality arises because L and D evolving oscillations, which become metabolic pathways, can form the two arms of a metabolic bistable, analogous to the bistable circuits widely used in electronic devices. This mechanism is discussed for the amino acids and its requirements discussed in the context of known enzymes of amino acid metabolism. Implications of this mechanism are discussed.Chemical Chirality and the Origin of Life
Abstract
1 Introduction
2 Chirality
3 Chirality as a Problem in Understanding the Origin of Life
4 Resolving Racemic Mixtures into their Separate Isomers
5 Amphiphilic Rafting Theory of Chemical Chirality
6 The Bistable Metabolism Theory of Chemical Chirality
7 Other Theories for the Origin of Chirality
8 Discussion and Conclusion
References
Abstract
This essay concerns the origin of the chiral specificity found in biochemical compounds, for example the left handedness of most amino acids. The author previously suggested a theory for the origin of life by "The Evolution of Prebiotic Oscillations," which is accessible on this web site. This essay will extend that study by suggesting two compatible but non-exclusive mechanisms for the emergence of chiral specificity during this prebiotic evolution.
The first suggested mechanism is the chiral rafting theory which suggests that, when a racemic mixture of an amphiphile forms a monolayer, the L and D forms tend to separate into separate zones or rafts. These separate zones then become separate loci for evolving oscillations that compete with one another. Later, one of the two isomeric oscillations prevails and leads to the subsequently observed isomeric specificity.
1 Introduction
Scientists do not yet understand how life on earth arose but, over the past two to three decades, this "origin of life" problem has become a growing topic of scientific debate and the subject matter of an increasing number of scholarly articles. Thus the "Origin of Life" (OOL) is increasingly seen as a field of science in its own right with its own cadre of specialist researchers. The aim of the OOL field is to convincingly describe the process that created life as we know it. That aim is very easy to state but very hard to achieve and the origin of life remains a major unsolved problem in science.
The great difficulty in developing theories for the origin of life is that there is no way to make observations or carry out experiments that can test the proposed theories. The result is a large corpus of theorizing that tends to be undisciplined by factual data. In other words, a distinct tendency to speculative ideas and "evidence free science," as one observer has described it.
In part, this unconstrained theorizing arises from the nature of the field, factual data is scarce. However, speculation need not be completely evidence free and there are three important constraints that limit the range of reasonable OOL theories.
The first constraint is the belief that some process of evolution must have occurred during the period prior to the emergence of life as we now know it.
The theory of evolution is not, strictly speaking, a theory for the origin of life, it is a theory for the origin of species, that is to say, a theory for how, over many generations, one species changes to one or several other species. The theory of evolution is not a fact, it is a theory. However, it is supported by such a wide array of observations that few scientists seriously dispute it. On the other hand, there is some debate and dispute about whether the theory of evolution should also be treated as a theory for the origin of life. In the opinion of this author, the theory of evolution should also be so treated as an origin of life theory. Even if it were not so treated, evolution is so influential that it still constrains such theories because the life that emerges must be adapted to its environment and be capable of evolving. Hence, scientifically acceptable origin of life theories must either be evolutionary theories in their own right or be coherent with evolution by natural selection.
The second constraint on origin of life theories is its starting point, the growing evidence we now have about the chemical nature of the early earth and the conditions that prevailed there. This evidence comes from studies of the earth itself and, increasingly, from the knowledge of the solar system that has emerged from the US and other space programs. The earth is believed to have formed from a swirling mass of dust surrounding our newly formed sun and to have been lifeless at the time of its emergence. Most scientists believe that life formed from non-life on that early earth, that life is somehow a product of the conditions that once existed there but how and why those conditions should have led to life is a mystery. Although life changed the earth, it left the other planets untouched and the solar system reveals much about the earth as it would have been before life began. How could life emerge from the kind of chemical environment we now believe to have existed on the early earth and what series of natural events and processes were involved? This starting point informs our ideas about the processes that would be expected to have occurred on the early earth.
The third constraint on the origin of life field is its end point, the chemical insights we now have into biology, through biochemistry, molecular biology and the other biological sciences. Many volumes have been written about biological chemistry and how the chemistry of life operates. These facts are the end point of whatever processes eventually led to life.
These two sets of available data, the starting and end points of the origin of life, circumscribe the OOL field; they leave that field with the worthy aim of filling the gap by suggesting processes and events that might have led to life as we now know it.
Still, the OOL field remains unlike most other fields of science; it is a field where direct observation is impossible and in which laboratory experimentation often bears a very doubtful relationship to the subject. Put simply, we cannot find an environment in which we can observe life as it emerges, or do experiments to create life in the test tube; we can neither observe new living cells as they materialize from some inorganic slime on the ocean floor nor, for experimental purposes, incubate a test tube for a million years.
In fact, there are some experimental studies that aim to provide support for one or other OOL theory but the results invariably leave one unconvinced about the correctness of the original idea. Indeed, the assumptions underlying experimental work in this field often seem so improbable that, by normal scientific standards, they would be seen as worthless. In other words, for all practical purposes, the OOL field is a scientific debate that aims to address well-defined questions but is conducted in the virtual absence of direct evidence.
So, the origin of life field operates in an observational cavity, with too little data to really probe the earliest processes that led to life so that most of our hypotheses remain untestable ideas. The boundaries of the cavity are marked with increasingly good, factual knowledge but no data directly illuminates its central questions and it is against this backdrop that theories for the emergence of life must be judged.
Nonetheless, while it is true that debate in this field is conducted without real observational evidence, the fact remains that an answer must exist. Life did emerge; an OOL process did exist - otherwise we would not be here. Further, we do have this evidence about start and end points and theory of evolution to discipline our thoughts. Thus, although the field has a problem with lack of evidence, the charge of "evidence free science" is not completely true. Sensible theories, disciplined by boundaries of evolutionary grand theory and observational fact, can be constructed.
In sum, a good origin of life theory should be constrained by the evidence about the starting and end points of life on earth and by the theory of evolution by natural selection. Ideally, it should :-
- Merge with evolutionary theory as conventionally applied to biology. This can be most simply achieved by a theory that is, itself, an evolutionary theory.
- Describe an origin of life process that is consistent with current ideas about conditions on the early earth and make starting assumptions that stray as little as possible beyond the evidence about those conditions.
- Interpret outcomes that are as consistent as possible with the current properties of life as we now know it the end point of the origin of life process we are seeking to understand.
Different names can be given to the process that led to the emergence of life, for example abiogenesis or prebiosis. Several origin of life hypotheses have been proposed and the author has already reviewed the major proposals except where directly relevant, they will not be further reviewed here.
The author has also proposed his own theory for the origin of life, "the theory of prebiotic oscillations," which is the most the most parsimonious origin of life theory yet advanced. It described how
- How sun induced daily or yearly temperature cycles, acting on chemical equilibria in the primordial soup, will produce chemical oscillations
- How those oscillations will be subject to a prebiotic chemical evolution.
- How that evolution could have led to chemical specificity, to biochemical pathways, to protocells and to the various classes of macromolecule found in life.
2 Chirality
Chemical chirality was discovered in 1815 by Jean-Baptiste Biot, a French physicist. He noted that when plane polarized light was passed through certain chemicals, prepared from biological sources, the plane of the light's polarization was seen to rotate, either clockwise or anticlockwise. By contrast, the same chemicals, when made in the laboratory from simple compounds, proved not to rotate the plane of light in either direction. The puzzle was twofold. First, why should this rotation occur in any chemical, whether or not made from living things? Second, even more puzzling, why should the same chemicals, made in the laboratory fail to rotate the plane of light?
These puzzles were solved thirty years later by Biot's compatriot, the great chemist, Louis Pasteur. Pasteur explained, chirality arises from the same asymmetry, left or right-handedness, that human hands display. We all know that our hands are both "the same" and yet, in a certain way our left hand is different from our right hand. Our hands are actually "asymmetric" and are related to one another in the same way that any object is related to its mirror image. The molecules of many organic compounds exhibit this same mirror asymmetry. Biot had discovered a manifestation of this left or right asymmetry expressed at a chemical level. This essay is concerned with the evolutionary origins of biochemical asymmetry but biological asymmetry is a much larger topic. Interested readers will find a popular, recent review in McManus (2002).
In organic chemistry, atoms of carbon will often form four bonds, each pointing to the four corners of a tetrahedron as shown in fig 2.1. If all four of these bonds are connected to different groups, the resulting molecules are asymmetric in the same way as are left and right hands. A carbon atom bonded to four different groups in this way is called a "chiral centre" and compounds with a chiral centre in their molecules exist in left and right-handed forms. Such compounds are said to exhibit "optical isomerism," while the left and right-handed forms are "optical isomers." The left-handed form (the L isomer or "L enantiomer") would rotate the plane of polarized light in one direction, perhaps anticlockwise, and the right-handed form (the D isomer) would rotate the plane of light in the other direction, which would be clockwise. Compounds made in the laboratory are normally equal mixtures of the two or isomers and such mixtures are called "racemic mixtures." In racemic mixtures the optical rotations caused by the two components cancel one another so that the mixture does not rotate the plane of polarized light at all. This result is expected since, as a matter of symmetry, the L and D forms of a compound will have equal free energies and therefore be synthesized in equal amounts. Compounds with more than one chiral centre will normally have 2n isomers, where n is the number of chiral centres. Hence, complex compounds can have a great many optical isomers since they may have many chiral centres.
Living things are made from organic compounds that exhibit chiral "specificity." That is to say, the organic compounds from living things normally contain only one of the possible optical isomers; when living things synthesize organic compounds, they normally make only one of the possible optical isomers and when organic compounds are used as foodstuffs, the consuming organism is normally able to utilize only one of the optical isomers.
Taking a very well known example - all proteins are made from amino acids arranged in a specific sequence. Twenty amino acids are normally found in proteins, including alanine, (2-aminopropanoic acid) whose formula is shown in the diagram. (Note, that alanine is an α-amino acid because the amino group (-NH2) is attached the α-carbon of the organic acid which, in modern, nomenclature is the "2" carbon atom, the first carbon after the –COOH group of an organic acid. All the amino acids found in proteins are α-amino acids.) The α-carbon of alanine does have four different groups (H, CH3, NH2 and COOH) attached and alanine therefore has two optical isomers. Only one of those isomers, the L-isomer, is found in proteins and the same is true for all the amino acids found in proteins. In addition, when this biological alanine is synthesized by the cell, only the L-isomer is produced. By contrast, alanine made in the laboratory is normally a racemic mixture.
3 Chirality as a Problem in Understanding the Origin of Life
In general, any chemical compound made in the laboratory is expected to be produced as a racemic mixture and that, in a nutshell, is the problem that chirality presents to any chemical theory for the origin of life. So far as we can tell, the earth and the universe are, as near as makes no difference, uniform, symmetric environments and there can have been no sophisticated chemistry proceeding during the early stages of evolution. And yet life is asymmetric.
The process we are seeking to understand must take a symmetric world and from it create asymmetric life. Somehow, the earth's initial symmetry must be broken to create asymmetric life forms. How that might have happened is the problem that has bedeviled this field. As mentioned earlier, this author has already suggested a theory for the origin of life, "the theory of prebiotic oscillations." If that theory is correct, then it must be consistent with the emergence of asymmetry.
This essay will now aim to incorporate chiral specificity into the evolution of prebiotic oscillations. The original work did not mention chirality per se but, to some extent, the theory of prebiotic oscillations did address the origin of chiral specificity by offering a theory for the origin of chemical specificity in general. What remains is to directly address the problem of chirality itself. Thus, this essay follows on from the earlier study and aims to fill this gap, to add further detail to the theory of prebiotic oscillations by incorporating a reasonable, hypothetical, pathway for the origin of chirality. This essay will not further consider competing theories for the origin of life except insofar as they bear on this problem of chirality.
4 Resolving Racemic Mixtures into their Separate Isomers
Chemists can separate racemic mixtures and prepare pure samples of the separate optical isomers. The process of separating of optical isomers is called "resolution" or enantiomer separation. Many organic chemistry texts will include a discussion of the techniques available to achieve and a specialist work on such methods is Toda (2004). There are four techniques commonly described for resolving optical isomers. How these techniques work is significant for the present discussion, so they will be described here.
4.1 Crystal Picking
The first successful resolution of optical isomers was achieved by Louis Pasteur. He worked with salts of tartaric acid, an organic acid with two chiral centres. A compound with two optical centres would normally have four optical isomers but tartaric acid has only three due to its internal symmetry and one isomer, mesotartaric acid, does not rotate the plane of polarized light at all - the two optical centres cancel one another out. For simplicity, we will ignore this third isomer and mention only the D and L forms.
Pasteur prepared a series of salts of the acid and allowed them to form crystals from solution. As chance would have it, the L and D isomers of a racemic mixture of these salts separate into distinct crystals. Pasteur took such crystalline samples and examined the individual crystals with a magnifying glass. He found that the crystals themselves exhibited an asymmetric form, so that there were left handed crystals and right handed crystals. He prepared separate samples of L and D crystals by examining each crystal in turn and accumulating samples of the two forms. He then dissolved the two in water and examined the rotation of plane polarized light for these two samples. He found that one sample rotated the plane of polarized light to the left and the other rotated it to the right. It was also clear that the left and right handed crystals contained the left and right handed enantiomers of tartaric acid.
Pasteur had thus succeeded in resolving a racemic mixture and his results led him to the modern interpretation of optical isomerism. However, for the most part, crystal picking is not a good method of resolving isomers. Very few compounds crystallize to yield large crystals with suitably distinguishable forms, so in many instances, this method of isomer resolution would fail. Even in those rare cases where the method would succeed it is very laborious. Nonetheless, Pasteur's result has a take home message that is important for the present study, namely that when racemic mixtures crystallize, the two isomers tend to crystallize separately. In due course, we will refer to that result.4.2 Reaction with Optically Active Reagents
Optically isomers can be separated from one another by either reaction or chemical complex formation with some other optically active compound. For example, a racemic mixture of carboxylic acids (RCOOH and LCOOH) might be reacted with an optically active alcohol (R'OH) to form the corresponding esters. The result would be a mixture of esters (RCOOR' and LCOOR'.) The two esters formed in this way are chemically distinct from one another and could be separated by conventional methods, such as distillation. The original reaction can then be reversed to generate the pure isomers of the organic acids.
4.3 Chromatography on Optically Active Media
Simple chromatography techniques are widely known and need only a minimal explanation here - schools often teach colourful experiments in paper chromatography to quite young children. Samples do not need to be coloured but this makes the results visible. Chromatographic techniques usually involve a mobile phase and a fixed phase. In the simplest studies, the fixed phase is a piece of filter paper or blotting paper. A sample which, during demonstrations, might be a mixture of differently coloured vegetable dyes, is spotted onto the paper and dried. The mobile phase is a liquid, perhaps water, but many other liquid solvents are used. The solvent is allowed to soak up the paper and carry the sample with it. The different dyes are observed travel up the paper at different rates, depending upon how tightly they adhere to the paper.
In professional laboratories paper is used as a fixed phase but other support media, especially silica, are more common. On a silica support chromatography would not normally separate optical isomers but, at least in theory, some separation might occur on paper supports. The reason for the difference lies in the support material. Silica, itself, is not an optically active material whereas paper, being cellulose and a natural product, is optically active. In general, optically active support media may resolve optical isomers whereas optically inactive supports cannot do so. Although paper chromatography might achieve some separation of optical isomers, paper does not turn out to be good at such separations and laboratory suppliers offer much better materials for chirally specific chromatography (see for example http://www.chromtech.se/). Chiral separation are technically important in many fields - for example because many, medically important drugs are optically active and therapeutic effectiveness may depend upon using the correct isomer or excluding an isomer associated with undesirable side effects.
The principle behind the way in which optically active, chromatographic media resolve racemic mixtures is illustrated in fig 4.1. The fixed chromatographic medium is represented by the plane surface. Since the support matrix is optical active, it will contain groups that may be represented as asymmetric with a specific rotation, as shown. When racemic mixtures are presented to this surface, the two isomers bind to it to in quite different ways. One isomer may be a very good fit while the other is a poor fit. To describe this situation another way, the optically active surface has binding site that have either an L or D configuration, let us say, the L form. The L and D isomers of a racemic mixture associate differently with that surface, will produce different degrees of chemical interaction, different partition equilibrium constants between the surface and the bulk solvent and different rates of movement in chromatography. As a result, the two isomers can be separate by chromatography on an optically active surface.4.4 Enzyme Action
The same principle becomes even more striking when we consider enzyme action. Enzymes work by a lock and key mechanism. The enzyme has a binding site, somewhere on its surface, illustrated by the dark L that can be seen on the enzyme. The normal substrate fits exactly into that binding site but, as the figure illustrates, this mechanism demands stereospecificity. A left handed key will not fit a right handed lock. Hence, enzymes can work on only one isomeric form of a compound.
5 Amphiphilic Rafting Theory
This essay will describe two chemically reasonable mechanisms for the emergence of chiral specificity in biology. These are :-
- The "amphiphilic rafting" theory and
- The "bistable metabolism theory."
The second theory is the author's preference and is described in section 6. The chiral rafting theory, described in this section, uses ideas inherent in the laboratory resolution techniques described in the previous section. The essence of this mechanism was described by Wachtershauser (2006) but, since the theory of prebiotic oscillations suggested that amphiphiles played an important role in early prebiotic evolution, it will also be discussed here.
According to the theory of prebiotic oscillations, amphiphiles such as primordial lipids and some protein-like molecules, will have been located on the surface of oil droplets during the earliest stages of evolution. The droplet is covered in amphiphilic molecules so as to form a layer, a single molecule thick. These layers have the properties of "liquid crystals," which means that they are fluids along the plane of the surface of the layer but are fixed in the vertical axis. In other words, the molecules can move laterally in the surface but cannot leave it. Later, as protocells were appearing, amphiphiles will have formed the inner and outer surfaces of vesicles which surfaces also have this liquid crystal property.
Many amphiphilic molecules are chiral and exist in L and D forms. If a racemic mixture of an amphiphilic compound forms a liquid crystal layer at an oil water interface, it is to be expected that the amphiphile molecules will form these liquid crystals in a way that is two dimensionally analogous to the three dimensional chiral separation described in Pasteur's work on crystal picking. In analogy to Pasteur's observations, it is to be expected that some regions of the surface will be coated in the L isomeric liquid crystal while other regions are coated in the D isomer. We expect to see the emergence of L and D regions of the amphiphile on the surface and some sort of boundary lines between the L and D regions must exist, comprising non-crystalline fault lines.
The term used for such separate regions in a two dimensional liquid crystal is "raft." This expected separation into rafts of the L and D forms of amphiphiles in an oily surface seems, in principle, to be experimentally testable and there are many studies of the behaviour of optically active liquid crystals, including racemic mixtures. Unfortunately those studies mostly concern the technically important, multilayer arrays of amphiphile molecules, rather than monolayers and, at the time of writing, the author has found no study describing monolayers of L and D amphiphiles or lipids separating as rafts. However, the formation of rafts for chemically different amphiphiles is well established. (See, for example, Niemala et al. (2007)).
So, applying Pasteur's result in the two dimensional context, one expects that amphiphiles on the surface of droplets will distribute themselves into rafts in which some regions are predominantly L and others are predominantly D. It is likely that some racemic amphiphiles, acting as emulsifiers, would distribute themselves onto the surface of micelles or droplets so that the separate droplets became predominantly L and D, some being bounded by a fringe of predominantly L amphiphile molecules and others by a fringe of predominantly D molecules. Hence an emulsion of a racemic amphiphile and oil droplets might be expected to produce L droplets and D droplets. These droplets would then produce chirally separate but competitive protocells that would be subject to selection. Our presently observed chiral specificity stems from those selections.
For a time, the L and D oscillations would have evolved alongside one another in their separate but competing branches of the primitive phylogenetic tree but something would have happened to unbalance their symmetry. Something would create this imbalance and, sooner or later, the twofold symmetry would be broken. For example, some beneficial new catalyst might have emerged that would coevolve with an existing oscillation. Rare events would not normally occurr simultaneously in both L and D branches of the prebiotic "phylogenetic" tree – some random occurrence would break the symmetry. Once such an event occurred, the processes of reproduction and extinction would take over to leave one winner and one loser. Once the evolving L oscillation had taken the lead, its concentrations would grow at the expense of its competitor and so increase the chance of further advantageous mutations occurring in the leading branch. Thus, the leader will draw still further ahead, while the disadvantaged laggard would face eventual extinction.
Predicting the winner in the evolutionary race between L and D oscillations is thus like predicting the outcome of balancing a pencil on its point. The pencil will fall one way or the other but one cannot say in advance which way it will fall. Some slight initial imbalance or imperfection in the surface may guide it one way but even if pencil and surface were both completely uniform and balanced, still it will fall. In the same way, evolution would ultimately select either L or D isomers, but not both.
Thus the theory of chiral rafting becomes, in principle, very similar to the bistable metabolism theory, to be discussed shortly; both predict an outcome of either L or D isomers but make no prediction as to which isomer will emerge preeminent.
6 The Bistable Metabolism Theory of Chemical Chirality
The chiral rafting mechanism is chemically plausible but remains open to criticism as a theory of chirality. For example, it leaves unclear why the unfavoured isomer should have died out quite as completely as seems to be the case and it does not directly explain why other metabolites, besides the chiral amphiphiles, would have become chiral. Extensions to the theory are needed to include other metabolites.
A last criticism is that the theory of amphiphilic rafting makes no direct use of the principles of bioepistemic evolution, the idea that evolution is primarily concerned with data. Bioepistemic evolution is this author's primary concern and one wants to place chirality in the same, bioepistemic context and see chiral separation in bioepistemic terms - that is, consider chiral separation as a data process.
The theory of prebiotic oscillations proposed that sun-induced, prebiotic, chemical oscillations were identified as evolvable objects on the prebiotic earth. That theory noted how such oscillations are defined in "chemical space" and showed how their evolutionary adaptation might lead to the emergence of metabolic pathways. Hence, the present discussion can assume the prior existence of chemical oscillations and it can also perceive metabolic pathway as connections in chemical space – a perception that draws a rough analogy between metabolic pathways in chemical space and the wires an electric circuit draws in three-dimensional space.
Combining these ideas, we can consider the data processing properties of mirror image metabolic pathways much as we might consider the properties of mirror image electrical circuits. There is a well known electrical circuit, a "bistable circuit," that can have mirror symmetry but nonetheless exhibits achiral properties in operation. In other words, when switched on, a bistable circuit undergoes chiral separation and it is this separation that may teach us about chiral separation during chemical evolution.
Many biochemists will not have come across bistable circuits but they are not exotic rarities; they are often used in electronic systems and are widely and cheaply available for purchase. This section will first describe the properties of bistable electronic circuits and then propose and discuss the "bistable metabolism theory of chemical chirality," a theory that draws on those properties.
6.1 The Bistable Circuit
Fig 6.1 shows a simple bistable circuit that uses several resistors and two transistors – visible as the circular components. A transistor is a solid state device with no moving parts. For many purposes a transistor may beconsidered a simple, voltage controlled switch, or as a resistor whose resistance can change from a high value to a low value in response to a controlling voltage. A transistor has three terminals which are visible in the diagram. The top and bottom terminals are marked C and E and act as the transistor input and output. It is the resistance between C and E that varies. The third, controlling terminal of the transistor is the base, b. Very little current is drawn when a voltage is applied to the base but that voltage is the controlling voltage. The base voltage determines the electrical resistance between C and E. Typically, if the base voltage is high, the resistance will be low. (Though note that some transistors work the other way round.)
The bistable circuit shown has two output terminals labeled A and B and connected to the two transistor E outputs. As seen in the diagram, the output from each transistor is linked to the base of the other transistor. These are the crucial connections that produce the crossover inhibition of the output voltages. If one of the transistors has a high voltage output, say output voltage A, then that voltage will be fed into the base of the opposite transistor and will ensure that output voltage B is low. This low output will be fed into the base of transistor A and ensure that its output remains high. Thus the circuit is stable with output corresponding to {A "on" and B "off") and, since the circuit is symmetrical, the alternative output of {A "off" and B "on"} is also stable. On the other hand, it can be readily seen that symmetrical output states such {A "on" and B "on"} or {A "off" and B "off"} are not stable.
Hence a bistable circuit can only produce one of two output states –
{A "on" and B "off"} or {A "off" and B "on"}. In other words, a bistable circuit is an electrical circuit which, when unpowered, has complete chiral symmetry but, when power is applied to the circuit, the resulting pattern of electrical power flow is always chirally asymmetric.
6.2 Bistable Metabolism
Thus far, we have described the bistable as an electrical circuit that can have physical mirror symmetry but which, when switched on, is subject to asymmetric electrical flows and voltages, with one side of the mirror plane being switched on and the other side switched off. In principle, a device with bistable properties can be built to use other power sources than electricity; for example, one could construct a fluidic or light powered bistable device, it would simply be a matter of connecting the necessary valves and other components.
Importantly for our present purposes, one could build a bistable device that uses chemical power and an arrangement of metabolic pathways. Such a bistable metabolic arrangement would arise if the crossover inhibitions acted on one or more of the enzymes in a component of the mirror opposite pathway. Metabolic bistables are not just a theoretical possibility - examples are known in the metabolic pathways of real organisms. Metabolic networks are widely studied (see, for example, Guimera and Amaral (2005)); in addition, bistable behaviour is known is such networks (for example, Aon et al. (1989)) and is of great interest as it may underlie the metabolic "decision making" that determines how cells develop or act in response to the environment.
Although, current, bistable metabolisms are interesting and suggestive, they are not the immediate point here. The modern biosphere is built from L amino acids, it is already chiral and modern metabolic bistables cannot have exactly mirror image pathways. However, for theoretical purposes, we can conceive of a prebiotic, metabolic network that includes a symmetrical bistable, with its two arms composed of mirror image L and D compounds. The "bistable metabolism theory" takes this conception and proposes it as the origin of chemical chirality in amino acids and living things in general.
6.3 Assumptions of the Theory of Bistable Metabolism
Since the present work draws on the theory of prebiotic oscillations it takes the assumptions and conclusions of that theory as its own assumptions. Thus the theory of bistable metabolism takes a "metabolism first" approach to prebiotic evolution and assumes that metabolic processes are already in place prior to the emergence of chiral specificity. It also adopts all the other assumptions of the "theory of prebiotic oscillations" and the other ideas of bioepistemic evolution from which it is derived.
It is easiest to describe the bistable metabolism theory in terms of amino acids, since they are the basis of the chirally specific enzyme actions that are involved throughout the metabolic pathways. Also, since enzymes process all other metabolites, an understanding of amino acid chirality can make chiral specificity immediately understandable in other groups of compounds.
Accordingly, the theory of bistable metabolism will consider chiral specificity among the amino acids and state the following further presumptions about the prebiotic world. These are as follows :-
- It will be assumed that a prebiotic chemical evolution led to life and occurred from within a completely random mixture of organic chemicals, the primordial soup. Among many other components, this early, primordial soup is taken to contain racemic amino acids, with both L and D isomers being present in equal amounts for each compound. In part, these assumptions are not necessary for the bistable mechanism to be valid - it would work with non-racemic mixtures as starting materials and non-random mixture of chemicals. Nonetheless, the most parsimonious assumption is the one stated and is worth stating because the bistable mechanism can work from such a starting point.
- It is assumed that L and D amino acids were initially subject to the same chemical reactions as one another, leading to analogous chemical equilibria and the same prebiotic pathways, as described in the "theory of prebiotic oscillations."
- It is assumed that any and all protoenzyme activities arising from the evolution of prebiotic oscillations were initially present in mirror symmetric sets. In other words, that all protoenzyme activities operating on amino acids operated with equal activity on both the L and D forms.
- Finally, it is assumed that, amongst those protoenzyme activities, there existed activities that could chemically convert the oppositely chiral, D and L amino acids to some chiral inactive compound. This is a crucial assumption as these activities would provide the crossover inhibitions needed to produce the bistable behaviour.
6.4 The Bistable Theory of Homochirality
The theory then asserts that this pattern of metabolic processes, powered by an energy metabolism, will form an evolving system that acts as a metabolic bistable. Selection will drive it to adopt one out of the two possible chiral pathways and, importantly, it will inactivate and deselect the isomeric pathway and drive it into extinction. In short, evolution will be required to make a choice between the two alternate but chirally equivalent pathways, a choice that is analogous to that made by a bistable electronic circuit.
The electronic bistable is an example of asymmetry emerging from symmetry when power is applied. The mechanism of this conversion is fully understood and the aim now is to match the workings of the bistable circuit with the hypothetical workings of possible primordial amino acid metabolism.
In this new context, the transistors of the bistable electrical circuit are replaced by the L and D branches of a primordial amino acid metabolism. The proposed situation is depicted in Fig. 6.2 with L and D metabolic branches marked in circles. Note that in the diagram the term etc. means chiral compounds that metabolically related to the amino acids. Arrows on the diagram show the direction of biochemical influence, with the solid lines indicating organic chemical material flowing through a pathway, and the dashed line shows the point where an inhibitory enzyme activity is created leading to the point on the opposite pathway that it inhibits by catalyzing the conversion of organic material back to an achiral form.
The enzymes of both pathways must exhibit the catalytic activities needed to create chiral specificity, or that retain the chiral specificity should it already exist. (In the latter case, for example, the same enzyme may be part of both left and right pathways, active on both L and D precursors, so long as the chemical activity retains the preexisting chirality and does not racemize it.) From this diagram, it can be seen that at least one, possibly two, pairs of chirally specific enzymes are needed. The chirally specific enzymes that are definitely needed are the crossover inhibition enzymes. The L pathway must produce an enzyme, composed mainly of L-amino acids, whose activity degrades D-amino acids to an achiral form or to L-amino acids. The most likely candidate enzymes are the amino acid dehydrogenases and, by way of evidence, it is notable that enzymes with D-amino acid dehydrogenase activity are known and found in many prokaryotic cells. (Other possible enzyme activities might include a stereospecific racemase or even an enzyme to directly convert D-amino acids to the corresponding L-enantiomer but such enzymes do not seem so well known.) In the bistable model, such crossover activity formed by the L pathway would have been matched a similar activity in the D pathway that would have preferentially degraded L-amino acids. These two crossover inhibition activities are shown as dashed lines in the figure. Their presence in primordial L and D-amino acid metabolism would produce a pattern of pathways closely resembling an electronic bistable. This, in its turn, should lead to one branch of the bistable, either L or D-amino acid metabolism, being switched on, or being selected at the expense of the other. In other words, the final, operating, metabolic network should end up with either L or D-amino acid metabolism, but not both. Either the L pathway or the D pathway will be switched off, while the other will remain switched on and lead to all subsequent life forms as is now observed. One can now ask, "If prebiotic evolution produced a bistable, biochemical circuit leading to a selection of L rather than D amino acids, do any remnants of the necessary activities still exist in modern metabolic pathways?"
6.5 Some Observations Relevant to the Bistable Theory
As previously noted, metabolic pathways can produce bistable behaviour, so there seems no fundamental reason for not examining the problem of chirality in the manner described in this essay.
The crucial pathways are the crossover inhibition reactions and the best evidence would be enzyme with the necessary spectrum of activities. The most likely enzyme activities would be an amino acid dehydrogenase that would convert any D amino acid to the corresponding but achiral 2-oxo-carboxylic acid. (For example, pyruvic acid (2-oxo-propanoic acid) is a non-chiral compound produced by oxidative deamination (dehydrogenation combined with deamination) of either L or D alanine.) It is notable that the dehydrogenase enzyme is active against all the D-amino acids, so one does not need to seek separate enzymes for each amino acid.
Also note that an L-amino acid dehydrogenase is found in modern cells but, of course, it is made from L-amino acids. As the bistable model would predict, the D-amino acid dehydrogenase is much more active than is the L-amino acid dehydrogenase.
In a sense, the enzyme activity directed against D-amino acids in modern cells is surprising, since most cells contain very little D-amino acid. However, D-amino acids do exist. They are found, for example, in the peptido-glycan cell walls of many bacteria but it should be noted that the peptide linkages formed there are not formed on a ribosome. D-amino acids are associated with many antibiotics. For example, the D-alanine-D-alanine linkage is found in the bacterial cell wall and penicillin is an analogue of that linkage. Penicillin's activity as an antibiotic depends on its inhibition of an enzyme, D-alanyl-D-alanine carboxypeptidase, that is involved in forming these links.
There are other groups of antibiotics that consist of small, often cyclic, peptide molecule that are, again, not made on ribosomes. It is notable that many of these antibiotics include D-amino acids in their sequence.7 Other Theories for the Origin of Chirality
Though few observers feel that any firm conclusion can be given, there is an extensive literature discussing possible reasons for symmetry breakage in biology. A complete literature review will not be given here and readers seeking more detail are referred to Johnson (2005), the most recent formal review consulted by this author.
Existing theories may be grouped into certain categories (here largely borrowed from Rajan (2006)) – first, physical and environmental theories, second, statistical or chance theories, all of which require a subsequent amplification, and, third, biological theories.
7.1 Physical and Environmental Theories
Chiral specificity may, according to some workers, arise from a violation of symmetry inherent in nuclear physics that causes the L and D forms of compounds to have slightly different energies. Such asymmetry would create minutely different values for equilibrium constants and shift the selection of equilibrium oscillations to favour the slightly more abundant isomer. This kind nuclear symmetry violation undoubtedly exists but its chemical effect is expected to be miniscule, much too small to overcome racemization. Accordingly, this author rejects such theories.
Other theories posit that the chirality of biological chemistry arose prior to the emergence of life, either in outer space or on the earth. Supporters of space as an origin for chirality point to meteorite observations, noticeably the "Murchison" meteorite, which has been report to contain small amounts of organic compounds, including amino acids, reportedly including a small (2 or 3 %) excess of the L isomer. (These reports may be incorrect since some workers have failed to find this excess and attribute the observations to earthly contamination.) Assuming that the observations are real, the origin of this isomeric excess is proposed to be either differential ionization due to circular polarization of light from stars or the sun. Such mechanisms might produce some enantiomeric excess but the observed and expected departures from a racemic mixture are small and not capable of explaining the 100% selection for L amino acids found in life.
Some observers look for an earthly explanation for asymmetry; for example, the earth's spin and magnetic field together create an asymmetric system that might produce chiral chemical effects. However, experiments indicate that such effects would be minimal. They also note that some rocks are asymmetric. If those rocks were involved in catalysis, they might favour one optical isomer over the other. Hence, it is argued, the organic chemistry seen on the prebiotic earth may have arisen from reactions catalyzed on rocky surfaces. It is true that some minerals do have chirally specific surface properties and any catalysis they produce may be chirally specific but, again, the theories are unsatisfactory. Such chiral rocky surfaces are not common and nobody has yet proposed a chemistry that could achieve much resolution, even within a local environment. Such a mechanism could not achieve a chiral resolution of the entire prebiotic earth.
Nonetheless, some theoreticians think that the competition between L and D isomers may be imperceptibly biased, making it inevitable that we would end up with L amino acids rather than D amino acids. (See, for example, Hazen, Filley and Goodfriend (2001)).
7.2 Statistical Chance Theories
The idea behind theories of this type is that of chance. If you toss a coin once, you are bound to one head or one tail from one trial, 100% one way or the other. Any statistical study that involves only a small number of trials will have a wide scatter. There is a good example of this occurring during chiral resolution in chemistry. Some compounds (sodium perchlorate, for example) are not, themselves, chiral but produce crystal forms that may be either left or right handed. If one crystallizes such a compound, with stirring, one possible outcome is that either left hand or right hand crystals will be prepared, with equal probability, but that one does not necessarily obtain a mixture of the two forms. The crystallization process effectively selects one or the other by chance. This selection is understandable in terms of chemistry, the formation of the first crystal, either L or D, is a chance event which directs the further growth of that crystal. Fragments break off the primary crystal and act as nuclei for the further growth of crystals of the original form and the sample eventually crystallizes in just one form.
Observations like this have inspired the idea that biological chirality emerged by an analogous mechanism but the theory is strained and the analogy invalid. The crystallization process depends upon the simplicity of the underlying compounds and the energy released when the crystal forms its internal order. Living structures do not normally crystallize, they are too complex for that, and they must absorb energy for their formation. In the circumstances, this sort of theorizing is hard to support.
7.3 Biological Theories and Origin of Life by Chance
Biological theories can be divided into two groups. First, those that propose an origin based on a prebiotic chemical evolution and, second, those that propose an origin based upon some improbable chance event.
Chemical evolution theories present chiral specificity as necessary aspect of biological function that emerges from evolution. From an origin of life perspective, such theories imply that chirality emerged from or alongside life as it evolved. The present author agrees with chemical evolution view and "the evolution of prebiotic oscillations" specified a chemical mechanism. Unfortunately, most other studies do not specify the mechanisms proposed but it can be generally argued that some prebiotic process of chemical evolution led to the emergence of life. One can only add that such perspectives need elaborating with chemical mechanisms and indications of how such process might lead to chiral specificity. The present essay provides that specification with the theories of chiral rafting and "bistable metabolism."
The second group of biological theories involves chance events, essentially the idea that complex living things emerged in a single bound. The idea is that some single but highly improbable event that created a living entity ab initio and that this living entity became the ancestor of all life on earth. This author finds such ideas profoundly unsatisfactory. They seem to imply whatever chiral specificity was characteristic of this earliest life form led the chirality we now see. In other words, presently observed chirality arose from the biological proliferation and adaptation that followed this random but chirally specific emergence.
The idea that a living thing emerged as a single chance event is very implausible for many reasons, not least that the resulting life form would be ill-adapted to its environment and would be expected to go promptly extinct.
8 Discussion and Conclusion
This essay began with quite limited objectives – to discuss how the theory of prebiotic oscillations could lead to the chiral specificity observed in living things. To this end, the nature of chemical chirality has been reviewed and the laboratory methods used to separate (separate) L and D enantiomers discussed. A number of previous approaches to this problem published in the scientific literature have been summarized. All such approaches can be categorized into two groups. The first and currently most popular group of theories tend to imply that chiral specificity arose prior to the emergence of life but it has been here argued that such ideas are unworkable. The second group of theories suggest that chirality arose alongside and as part of the emergence of life, an approach that seems more reasonable. Thus, it is argued that chiral specificity is a product of the evolutionary emergence of life and that understanding the emergence of chirality should be seen as part of the greater problem of understanding the origin of life.
Theories for the origin of life are often grouped into two headings, "replicator first" theories and "metabolism first" theories. The author's prior work "the theory of prebiotic oscillations" is a metabolism first mechanism and both the "chiral rafting" theory and the "bistable metabolism" theory fit into the metabolism first approach. These two theories and do not seem competitive with one another, they both seem chemically reasonable and do not contradict one another's assumptions. Hence, both may be perceived as valid but this author prefers the theory of bistable metabolism since it makes the near complete elimination of one isomeric pathway more easily understandable. Further, since it applies to the amino acids, it speaks to enzyme synthesis and so makes it easy to see why clearly chiral specificity would apply to most metabolites.
In any event, it seems that the metabolism first approach can interpret the emergence of chiral specificity. By contrast, no "replicator first" theory seems able to explain the origin of chirality, rather existing theories tend to assume that chirality has already emerged by some purely physico-chemical process before the chance emergence of their replicator molecules. It may be that some replicator first approach will be devised that can interpret the later emergence of chirality but this author is unable to see how that would work. In any event, the bistable metabolism theory is plainly a metabolism first theory and does not fit into the replicator first approach at all.
In summary then, the bistable metabolism theory proposed here has the great merit of being a simple, workable and conceptually elegant approach to a problem that has perplexed many observers for decades. The mechanism for the origin of chirality is plausible and seems to work at a data level, at a chemical level and at the level of evolutionary adaptation. The bistable metabolism theory could well have led to the chiral specificity now seen in living systems. However, as with all discussions of the origin of life, one cannot say that selection did occur in this fashion, or that this mechanism is the only possible origin of chiral specificity. The alternative, chiral rafting mechanism is also a chemically reasonable, metabolism first, approach. Neither description can be proven, nor does one seem to exclude the other. The greatest claim one can make in a field of this type is that the bistable metabolism theory offers a mechanism that seems chemically and evolutionarily reasonable and fits with our present understanding of amino acid metabolism. Limited as that claim may be, it is as much as can be claimed.
One might attempt to develop the bistable metabolism theory in a number of ways, of which three will be mentioned. First, we recall the existence of metabolic pathways that involve D-amino acids and their association with antibiotics. The fact that these compounds and pathways exist suggests the primordial existence of a wider biochemistry involving D-amino acids. It is expected that such a primordial biochemistry would have produced cross-over inhibition against and L-amino acid activities. Since current day antibiotics inhibit or kill cells with an L-amino acid metabolism, one may argue that some of these antibiotic producing pathways once had a crossover inhibition role that was subsequently co-opted into an L-amino acid cell. In other words, that some of these D-amino acid, antibotic pathways are remnants from an earlier D-amino acid metabolism. These metabolisms would have survived because their crossover, inhibition role remained competitively useful to those L-amino acid cells that could produce the antibiotic but resist its activity.
A second topic of interest would be to consider metabolic analogues to other, simple, digital, electronic circuits. One circuit that comes immediately to mind is the "astable circuit," a device that is very similar to a bistable and sometimes confused with it. An astable incorporates capacitors in the crossover inhibition connections that create a time delay in that connection. The result is that such circuits can be made to switch at a steady rate between their two stable states – the rate depending upon the value of the capacitance and resistance. Some reflection upon the properties of astables might enhance our understanding of the oscillatory behaviour of metabolic pathways. Perhaps the most interesting metabolic, digital circuits would be data storage circuits, the metabolic equivalents of which would include DNA, the genetic material, as a long term data store, and RNA as a shorter term, metabolic, data storage circuit.
The third and last point to be made about the bistable theory concerns a quite disparate branch of science, namely the neurobiology of the brain. Physically, at least, the human brain seems to be a symmetrical organ, with two, apparently identical, hemispheres. However, when in use, our brains exhibit a widely described asymmetry of operation, exemplified by the way we usually prefer to work with our right hand, which we control with the left hemisphere of the brain. Language, logic and analytical skills also reside in the left hemisphere but, by contrast, our right brain does not seem to be logical or analytical, rather it is synthetic and emotional, with a strong sense of aesthetics. We can only speculate about how this brain asymmetry came about but the brain and the bistable do share some small degree of similarity. Both seem to be physically symmetric and to become asymmetric in use and when powered up. Also, there the two hemispheres of the brain are connected and it is possible that those connections may have similarities with the crossover connections in bistable circuits. Could it be that those crossover connections are, in part, inhibitory, so that the brain operates as a multiply cross-connected bistable? If so, one is left to wonder about which hemisphere of the brain is switched on and which is switched off or, more probably, switched into another state. Perhaps one could consider bistables in which neither half is switched off but are switched into different states - where the crossover connections switch the opposite hemisphere into a different pattern of functional roles. This line of thought is interesting but it leads well off topic and is best left for readers to ponder.
References
Aon M. A., Cortassa S., Hervagault J. S. & Thomas D. (1989) pH induced bistable dynamic behaviour in the reaction catalysed by glucose-6-phosphate dehydrogenase and conformational hysteresis of the enzyme Biochem J. 262 795-800
Bonner W. A. (1999) Enantioselective Autocatalysis. V. The Spontaneous Resolution of the Tri-O-Thymotide Origins of Life and Evolution of the Biosphere 29 317-328
Earl D. J., Osipov M. A., Takezoe H., Takanishi Y. and Wilson M. R. (2005) Induced and spontaneous deracemization in bent-core liquid crystal phases and in other phases doped with bent-core molecules Physical Review (E) 71; Num 2; Part 1, pages 021706
Guimera R. & Amaral L. A. N. (2005) Functional Cartography of Complex Metabolic Networks Nature 433 895-900
Hazen R. M., Filley T. R. and Goodfriend G. A. (2001) Selective adsorption of L- and D-amino acids on calcite: Implications for biochemical homochirality PNAS 98 5487-5490
Johnson Louise (2005) Asymmetry at the Molecular Level in Biology European Review 13 (Supp. Number 2) 77-95
McManus C. (2002) Right Hand, Left Hand The Origins of Asymmetry in Brains, Bodies, Atoms and Cultures BCA, London
Niemela P. S., Ollila S., Hyvonen M. T., Karttunen M. & Vattulainen I. (2007) Assessing the Nature of Lipid Raft Membranes PLoS Computational Biology 3 306-312
Pereto J. (2005) Controversies on the Origin of Life International Microbiology 8 23-31
Rajan A (2006) How did protein amino-acids get left handed while sugars got right-handed? Term Paper for Physics 569, Univ. of Illinois, Urbana-Champaign (This student paper is a good, straightforward review and accessible on the internet.)
Toda F. (2004) Enantiomer Separation: Fundamentals and Practical methods Kluwer, Dordrecht
Wachtershauser G. (2006) From volcanic origins of chemoautotrophic life to Bacteria, Archaea and Eukarya Phil. Trans. Royal Society B 361 1787-1808