The Origin of Life

The Sweet Crystal Hypothesis

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Sweet crystal Break Unzip

  1. Introduction
  2. Catalytic activity
  3. Mutation
  4. Insulation
  5. Polymers
  6. Polysaccharides
  7. Clays and polymers
  8. Sweet crystals
  9. Breaking up
  10. Unzipped
  11. New genes
  12. Marriage
  13. Friction
  14. Divorce
  15. Death
  16. In closing
  17. References

  1. Introduction
  2. The Sweet Crystal hypothesis is an attempt to account for the origin of an organic genetic substrate.

    When Cairns-Smith formulated his theory of crystalline ancestry - which accounts for the main mechanism by which life can form from inorganic precursors - he was percieved as not having provided a very detailed scenario for the introduction of organic material. Rather he showed how life can form, demonstrated that genetic takeovers were possible, illustrated that there would be selection pressure for carbon-based systems once they arose, and then suggested that the rest of the story was simply a matter for natural selection.

    This state of affairs apparently left some of those who had not read Genetic Takeover [1] unsatisfied. They felt as though the origin of their sort of life had not really been explained at all. They did not see where nucleic acid came from - and the origin of cell walls was still a mystery.

    While some of the details have no-doubt been lost to history, it seems that some of the subsequent paths in the early evolution of organisms can be identified with a reasonable level of confidence. Even where this is not the case, it may prove helpful to identify in some detail at least one plausible scenario by which evolution can lead away from crystalline organisms, towards ones more easily recognisable as our ancestors.

    We'll try to be more specific - at least in some areas - than Cairns-Smith was in chapter 9 of Genetic Takeover [1].

  3. Catalytic activity
  4. Crystalline organisms would need to undergo selection in order to maintain their morms in the face of mutational pressures - just as modern ones do.

    Richard Dawkins once presented an interesting definition of the term "gene":

    any hereditary information for which there is favorable or unfavorable selection bias equal to several times or many times its rate of endogenous change.

    - The Extended Phenotype [2] - p. 287.

    By such a definition in order for crystal genes to qualify as such, the are likely to need to be under strong selection - simply because crystal organisms are likely to have experienced some of the worst mutation rates ever experienced by organisms anywhere.

    Unfortunately, crystal genes appear likely to have rather weak phenotypic properties. This focusses attention on those types of crystal where their genome can have the most effect on its environment in a manner that has an immediate impact on their rate of reproduction.

    I believe this focusses information away from those crystals that grow in two dimensions and store information in one.

    The problems with such crystals when considered as organisms include:

    • that these crystals effectively shield their genes from the environment - by enclosing them inside themselves;

    • the region where the genes might most easily be expressed is the same area where they are engaged in growth;

    • There is no real equivalent to programmable catalytic surfaces. Polytype repeat patterns can only really encode a one dimensional catalytic "hand" - and a one- dimensional hand is not ideal for manipulating things with.

    There are other problems: Type 1 genetic crystals seem likely to grow more slowly, be less likely to break and reproduce, and store less information than their Type 2 counterparts.

    On the positive side they may have better transmission fidelity - and be less likely to lose what information they already hold.

    I think that on balance, such considerations focus attention on the other types of crystal organism - those with programmable catalytic surfaces with which they can interact with the environment.

  5. Mutation
  6. In "Mendel's Demon" Mark Ridley makes the case that a lack of error correction technology was historically one of the forces that kept organisms simple for so much of the duration of the evolution of life on Earth:

    Life can only be as complex as its rate of copying error permits. Life has to stay on the right side of the mutational meltdown. If the rate at which mutation introduces error exceed the rate at which natural selection removes it, the life form will mutate itself into oblivion.

    - Mendel's Demon [3] - p.79.

    All modern organisms make an effort to lower their mutation rates - with error correction, sex - and so on.

    There are a number of mutational effects that act on crystalline organisms. Here we will consider two of them - which we will argue are common - and ask how organisms might go about reducing them.

    • Lateral growth

      • Most crystals have some tendency to grow in all directions. Often certain directions are preferred - but usually there is some chance of growth perpendicular to the favored direction(s). A crystal organism that grows using a screw dislocation can arrange itself so that growth only occurs in one direction - and growth in other directions requires surface-nucleation to happen - thus reducing the chances of it happening to small values. However preventing such growth completely seems likely to prove difficult.

    • Mechanical damage

      • When crystals break, their crystalline structure can be stressed at the point of the break, causing defects. Hopefully these defects will get repaired by dissolution and re-crystallization - the standard crystal error correction mechanism - but sometimes they will persist - and be replicated. Much the same can happen when a crystal falls, is grown into by another crystal or is broken by collision with a moving object. Practically any mechanical stress can produce mutations.

  7. Insulation
  8. We argue that crystals will attempt to deal with these effects by employing other molecules from their environment.

    Nearby molecules tend to attach themselves to the edges of growing clays anyway, due to electrostatic forces at the edges of the material.

    However crystal organisms will attempt to bond with such molecules in such a manner that results in their sides being covered up while their growing ends remain exposed.

    How can a growing crystal selectively control on which surfaces nearby molecules attach themselves?

    One crude method which could be employed to this end would be to have charged edges, but neutral faces. This would mean that charged or polarized molecules from the environment would attach themselves to the sides of the crystal - but not to its growing ends.

    However more effective solutions seem likely to involve the catalytic grooves along the sides of the growing crystals. A crystal organism could use the to grab molecules and hold them there. This would allow more discrimination to be applied in choosing the types of molecules that were involved.

  9. Polymers
  10. That polymers might be used as a means of reducing sideways growth has long been recognized:

    Were polyphosphates among the first biochemicals? A third point is that phosphates, and particularly polyphosphates, might have been useful for an early clay-based life - as a means of preventing sideways growth of genetic crystals, or as metal complexing agents or as strings to hold clay platelets together.

    - Genetic Takeover [1], p. 344.

    Besides reducing errors there are other reasons why clays might be interested in getting involved with organic molecules. Small volumes of organic compounds can result in large differences in the physical properties of the clay minerals, and their immediate environment.

    For example organic compounds act as peptizing agents (acting to disperse the clay particles) or as flocculating agents (causing them to stick together). They can act as an pathway to interactions heavy metal ions, and affect the tensile strength of the materials they are bonded to - and so on.

    In a number of respects the most interesting materials from this point of view are organic polymers. Polymers are so called because they consist of long chains of simpler organic structures known as "monomers".

  11. Polysaccharides
  12. Carbohydrates are organic compounds that usually contain carbon, hydrogen and oxygen in a 1:2:1 ratio.

    They are (mainly) divided into monosaccharides, disaccharides, oligosaccharides, Polysaccarides (corresponding to "1", "2", "few" and "many" sugar units).

    Polysaccharides consist of that subset of carbohydrates with "many" repeating monosaccharide units in a chain - where "many" should be interpreted as meaning "more than ten or so".

    They are ubiquitous in the modern world. Cellulose, starch, chitin, xanthan gum, carrageenan, gum arabic and gum tragacanth are among the more well-known polysaccharides.

  13. Clays and polymers
  14. There has been a significant volume of research into the association of clays with certain types of organic polymer. The interest seems to come from two main directions: the oil industry is interested in manipulating and dispersing clays during the drilling process - and ecologists want to understand how bacteria influence and control the consistency of soils.

    Both areas of research involve polysaccharides:

    • Oil

        The oil industry uses a wide range of organic compounds to control the materials it has to deal with. It uses emulsifiers, surfactants, detergents, lubricants, and so on.

        Polysaccharide functions in the industry include cooling the drill bit, preventing fluid loss through the borehole, and preserving the properties of the materials which are being drilled through. The drilled materials often include clay minerals.

    • Earth

        Polysaccharides in soils are of interest mainly due to their roles of cementing and stabilizing aggregates. They typically originate from bacteria in the soil.

        While they are generally incapable of reaching between individual grains they play an important structural role by combining with clay particles - and bridging the gaps in this way.

    As a result of these sorts of studies, we now know much about the properties of clays in conjunction with polysaccharides, in the context of adding polysaccharide material to clays in order to modify their properties.

    In addition, there has been some recent research relating to interactions between RNA and montmorillonite - with the origin of life in mind. The idea appears to have been for the clay to take on the role of catalyst - freeing RNA from the role of making enzymes that catalyse its own formation.

    Dr. James P. Ferris has led much of this research [5][6][7][8][9][10][11][12].

    The theory presented here builds on these results - showing how the polymers may be systematically lined up next to one another, providing a source of mechanical force which separates them at regular intervals, shows how catalytic grooves designed specifically for this purpose might come to exist and relieving the RNA of the responsibility of initially forming an evolving system.

  15. Sweet crystals
  16. We propose here that clay organisms came to contain grooves designed to act as catalytic surfaces synthesizing and retaining polysaccharide chains.

    They did this mainly for protection against physical disturbance - and to avoid the mutational force represented by sideways growth - which otherwise threatens to obliterate them.

    Initially coverage would have been thin - and the protection offered slight.

    Short polysaccharides synthesized by a crystalline organism

    However some protection is generally better than no protection at all - and even irregular coverage by monomer units would act to inhibit sideways growth, and cushion against physical blows.

    Over time, better coverage would be selected for.

    There is no shortage of other possible applications which such bonded chains might have.

    The polysaccharide chains lengthen

    As time passes, specific catalytic grooves could come to form - designed to select specific types of monomer units. Linear grooves in clays can form asymetrically - so the solution to many problems of orientation would have been available.

    Crystals can be naturally chiral

    Not all of the effects of the polysaccharide chains will be positive.

    For example, it seems likely that the addition of polysaccharide material will increase the tensile strength of the crystal. This might sound positive - but in an environment where splitting equates to reproduction, it is rather unlikely to be beneficial. However, growing more slowly is certainly preferable to suffering a genetic error catastrophe - for that represents the end of life.

    As with all theories of the origin of long polymer chains the question of the origin of the monomer units arises. Although the theory presented here is no more vulnerable to criticisms in this area than any other, we would like to briefly draw attention to a novel solution involving multiple species.

    One species might synthesize sugar bases - perhaps in order to make its local environment more sticky. Another species can then utilise this material in constructing polymers for protection against mutations. Complexity need not be concentrated in any single individual. Instead it can come from a combination of several species in the same environment.

  17. Breaking up
  18. No consider how a polysaccharide-coated crystalline rod is likely to break up.

    The whole rod

    There are several main possibilities:

    • A clean break

      A clean break

      Here the two crystals part company as they would "normally" do, and continue growing separately.

    • Attachment


      Here the two crystals remain joined at a "hinge" - perhaps eventually coming to join along their entire length. The chances of this sort of thing happening depend on the relative sizes of various forces - and it is probably not a very likely outcome.

    • Single unzip

      Single unzip

      More likely is an "unzipping" process. Here the bond between the polysaccharide and the clay is weaker than the bonds between individual monosaccharide units - and as a consequence when force is applied at either end the polysaccharide comes "unzipped" from one of the crystals.

    • Double unzip

      Double unzip

      Another sort of "unzipping" is theoretically possible: the "double unzip".

      This works because the force applied at the crystal-polymer junction depends on the angle between them. The more obtuse the angle, the greater the force. The result is that the two sides of the zip keep approximately in step with one another.

      A true double zip is not very likely to happen in practice. It only arises in a relatively narrow range of conditions.

    The event depends to some extent on whether the unzipping occurs in a single process, or in a series of jerks.

    If the event is more-or-less continuous, the "single unzip" seems the most likely outcome.

    On the other hand, if the crystal is jerked around a bit, an approximate symmetry between the ends (while the unzipping has paused) suggests that unzipping is equally likely to start again at either end. Several factors can break the symmetry:

    • the end attached to the smaller crystal has a more variable angle between the polymer and the crystal;

    • One end is likely to have "given" most recently. The chances are that the angles have been preserved somewhat since then - and it is most likely to give again;

    • One end of the crystal is likely to be anchored down.

    You can get some idea of the likely outcomes of this type of event by performing simple experiments involving joining two rods together with sticky tape.

  19. Unzipped
  20. We will first consider something like the "single zip" - one of the most likely outcomes - given that the breaking strength of the polysaccharide is not too low.

    When the unzipping is complete, two crystals remain:

    The survivors

    The one on the left has an attached polysaccharide bundle. We will refer to this as the "mother" crystal.

    The one on the right has empty grooves where polysaccharides once lay. That one will be referred to as the "daughter" crystal.

    The daughter's empty grooves can be expected to slowly fill up again, creating a new polysaccharide adjacent to the existing ones.

    The mother's fate is less certain. There are several possibilities. One is that the trailing polysaccharides will attach itself to some other physical object, and eventually get unzipped - resulting in a situation similar to that of the daughter.

    Another possibility is that the polysaccharide will wrap over the the growth face of the crystal and get caught on the other side - effectively preventing growth.

    Tangle prevents growth

    Lastly there's the possibility that crystal growth will continue - and offer the possibility that the polysaccharides will gradually lie down in new grooves that are constructed beneath them.

    Resting down again

  21. New genes
  22. No doubt by this stage the reason for the interest in the different type of break-up patterns has become obvious.

    This model overcomes a number of difficulties in conventional models of the origin of carbon-based genetic systems.

    In particular:

    • It provides a mechanism whereby the formation of polysaccharide material might be catalyzed - in what would otherwise be thermodynamically unlikely volumes;

    • It suggests that these might be systematically laid down next to one another in parallel grooves designed to hold them there;

    • It provides a source of mechanical force necessary to tear them apart - in the absence of specialized machinery to perform this task;

    • It removes any obligation to act as a high-fidelity transmitter of information. Genetic functions can form slowly - and it does not matter how pathetic and feeble the results are initially, since they do not need to act as the sole support for an evolving system.

    The last point may be the most significant one.

    The selective force responsible for the use of the polysaccharide material is reducing mutational load - through providing insulation from the environment and inhibiting sideways growth.

    It plays a structural role - and the role of a mutation damper - before any genetic functions are involved.

    The origin of genetic functions will lie in some sort of self-perpetuating influence between adjacent polysaccharide chains.

    If molecules are more likely to take on the forms of their neighbours, then that can act as the origin of an inheritance mechanism transmitting information through the polymers - largely independently of the crystal substrate.

    It does not take much imagination to see that genetic functions would be useful. For example, the ability to influence the form of the coiled-up polysaccharide is likely to be an aspect of the organism's phenotype of some interest to selection.

    The crystals can co-operate in facilitating relationships between adjacent polymers - should it prove advantageous for them to do so:

    Friendly neighbours

    Here the catalytic grooves are shaped in such a way that adjacent polymers are placed in close contact with one another.

    Without mechanical force being applied to the polymers by the growing (and thus breaking) crystals, it seems likely that the polymers would remain attached to the crystal surface - where they are likely to be rather stable [13][14].

  23. Marriage
  24. We expect that the resulting symbiotic relationship will persist for an extended period.

    The clay genes find the organic ones useful, and the organic genes can't reproduce without the clay ones at all - at least not until they can produce a whole family of fancy enzyme-like structures to catalyse their own replication.

  25. Friction
  26. The organic genes need not reproduce at the same speed as the mineral ones. Each division of a crystal may provide opportunities for several organic genes to copy themselves - and all or none of them may succeed.

    Also, if existing "floating" disaccharides, ogliosaccharides and polysaccharides can join to existing crystals, then the "death" of an existing polysaccharide-coated crystal (e.g. through heating) may liberate the attached polysaccharides - who can then go on to attach to other crystals.

    Differences in reproductive opportunities between the crystal organisms and the organic ones seem likely to result in conflicts of interest between them.

    Symbiotic organisms exist most harmoniously together when their reproductive systems are tied together - and neither can reproduce in the absnce of the other.

    For the polysaccharide/crystal alliance, this condition will not ever have held - the reproduction opportunities of the organic genes may be correlated with those of their crystal forbearers - but the correlation will never have been perfect.

  27. Divorce
  28. While initially the organic genes are completely dependent on the crystal ones to catalyse their formation, the arrangement was only ever a temporary one.

    Crystal genes were necessary in order to form the first organisms - for reasons A. G. Cairns-Smith explained eloquently. Organic polymers naturally form sticky tars - not self-organising structures. About as near as they come to spontaneous self-organisation is in creating forms - but foams are next to useless from the point of view of reliably transmitting heritable information.

    However - once they come into existence - organic genes can perform all the other functions performed by clay genes much more efficiently.

    Ultimately, the ease of self-assembly of the crystalline genes was also their undoing:

    Organic molecules are better for "high tech" machinery. This is mainly because the atoms in them are held together more securely. These atoms do not self- assemble at all well: it is much more difficult to make coherent orderly multi- atom structures conatining carbon than to make, say, such silicon-oxygen structures: but, once made, carbon-based structures can retain their individual complexity indefinitely. By contrast a crystalline structure formed from water solutions is always in danger of dissolving away again in water; and very small crystals, or small pieces of crystal are particularly liable to fall apart or re-arrange. It is the other side of the same coin: if you can self-assemble easily, you can self-disassemble easily too. This is alright for "low-tech", perhaps, but it is limited. You need more than sticks and string for serious engineering.

    - Seven Clues to the Origin of Life [4], p. 112-113.

  29. Death
  30. Eventually the organic polymers found a way to dispense with the primitive crystal genes.

    They arranged for the existence of better catalysts of their precursors than the clays could manage to build - and found a way to copy themselves using them.

    It might have seemed like a small step to have introduced those first crudely-replicating polymers, but it was fatal to the whole clay system. In any competition between organic and inorganic control systems, the organic ones would be almost bound to win in the end - because metastable structures can be engineered more finely with the use of organic molecules. Anything clay could do organic molecules would eventually come to do better.

    - Genetic Takeover [1], p. 386-387.

  31. In closing
  32. We believe we have identified the mechanism by which genetic systems composed of organic polymers are most likely to have formed.

    Of course there are many remaining puzzle pieces in the story of life's origin. For example, we have not looked at the origin of cell walls.

    The plausibility of the hypothesis discussed here can be evaluated by examining the details of the underlying chemistry involved.

    Ultimately, we see synthesis of living organisms from inorganic precursors as the acid test of origin of life theories.

  33. References
    1. Genetic takeover - and the mineral origins of life, A. G. Cairns-Smith, Cambridge University Press, 1982;
    2. Mendel's Demon - Gene Justice and the complexity of life, Mark Ridley, Oxford University Press, 1999;
    3. The Extended Phenotype, Richard Dawkins, Oxford University Press, 1982;
    4. Seven Clues to the Origin of Life - a scientific detective story, A. G. Cairns-Smith, Cambridge University Press, 1985;
    5. Synthesis of Long Prebiotic Oligomers on Mineral Surfaces, James P. Ferris, Aubrey R. Hill Jr., R. Liu, and Leslie E. Orgel, Nature 381, 59-61, 1996;
    6. Formation of RNA Oligomers on Montmorillonite: Site of Catalysis, G. Ertem and James P. Ferris, Origins of Life and Evolution of the Biosphere, 28, 485-499, 1998;
    7. Montmorillonite Catalysis of RNA Oligomer Formation in Aqueous Solution. A Model for the Prebiotic Formation of RNA., Dr. James P. Ferris, Journal of the American Chemical Society, 155, 12270- 12275, 1993;
    8. Prebiotic Synthesis on Minerals: Bridging the Prebiotic and RNA Worlds., Dr. James P. Ferris, Biol. Bull, 196, 311- 314, 1999;
    9. Prebiotic Synthesis on Minerals: RNA Oligomer Formation,, Dr. James P. Ferris, in "The Chemistry of Life's Origins," (J. M. Greenberg, C. X. Mendoza-Gomez and V. Pirronello, eds.) Kluwer, Dordrecht, Netherlands, 301-320, 1993;
    10. Oligomerization of Uridine Phosphorimidazolides on Montmorillonite: A Model for the Prebiotic Synthesis of RNA on Minerals,, Dr. James P. Ferris, P.Z. Ding and K. Kawamura, Origins of Life and Evolution of the Biosphere, 26, 151-171, 1996;
    11. Clay catalysis of oligonucleotide formation: Kinetics of the Reactionof the 5'-Phosphorimidazolides of Nucleotides with the Non-Basic Heterocycles Uracil and Hypoxanthine, Dr. James P. Ferris and K. Kawamura, Origins Life Evol. Biosphere, 29, 563-591, 1999;
    12. Kinetics and Mechanistic Investigation for the Oligonucleotide formation from 5'-Phosphoimidazolide of Adenosine, Uridine and Inosine on Na+-Montmorillonite, Dr. James P. Ferris and K. Kawamura, 11th International Conference on the Origin of Life, Orleans, France, 1996;
    13. Clay-Nucleic Acid Complexes: Characteristics and Implications for the Preservation of Genetic Materials in Primeval Habitats,, Marco Franchi, Emilia Bramanti, Laura Morassi Bonzi, Pier Luigi Orioli, Cristina Vettori and Enzo Gallori, Origins of Life and Evolution of the Biosphere, 29: 297, 1999 ;
    14. Clay mineral as a resting-place of genetic material in primeval habitats, Marco Franchi and Enzo Gallori, Origins of Life and Evolution of the Biosphere, 30: 322, 2000; |