This is a preview of Chapter Three from forthcoming book on Evolution by Other Means…?
Alexander Graham Cairns-Smith
THE POSSIBLE ORIGINS OF NATURE’S FIRST CRYSTALINE (QUANTUM) COMPUTERS
Cairns-Smith is a Scottish molecular biologist and organic chemist and his crystalline origins theory leads on naturally from the previous chapters, as it corresponds to the fundamental and inherent properties of patterns of scale, self-organisation, replication: ‘remembered’ patterning and modification according to environmental factors, that can be essentially, scaled up to possibly account for the evolution of the cells and the complex molecules of life – its code.
Smith-Cairns’ concept is not an alternative to the Darwinian model, as are many of the others presented in this book, but rather, it deals with the origins aspect of cellular life along with the code of life, that our current model has never fully addressed. Below is a short excerpt that should give an insight into his main hypothesis.
Life’s Crystal Code
To Alexander Graham Cairns-Smith, that glimmer may owe something to the sparkle of a crystal.
Cairns-Smith, an organic chemist at the University of Glasgow, sees a significant relationship between the structure of DNA molecules and the structure of certain kinds of mineral crystals. He says that while patterned structures that replicate themselves are common in the inorganic world of crystals, it is a rare quality in the organic world — DNA and RNA are the only organic molecules we know of that strongly exhibit this characteristic.?
Mullen (2009, ‘Astrobiology Magazine’ 19th March)
Essentially, Cairns-Smith’s novel proposal can be seen from the 1960s onwards via his many books and numerous articles on the topic of the self-replication of clay crystals in solution as a precursor to molecular life and its ability to replicate itself. Some of the main publications are listed as follows: The life puzzle: on crystals and organisms and on the possibility of a crystal as an ancestor, 1971, by A.G., Cairns-Smith, Toronto University Press ; Genetic takeover – and the mineral origins of life, 1982, by A.G., Cairns-Smith, Cambridge University Press ; Clay minerals and the origin of life, 1986, by A. G. Cairns-Smith and Hartman, H., (eds.,), Cambridge University Press. UK  and, Seven Clues to the Origin of Life – a scientific detective story, 1990, by A.G. Cairns-Smith, Cambridge University Press .
Essentially, Cairns-Smith’s concept, as it specifically applies to the clay crystalline matrix origin of coding complexity, not only proposes a useful model to account for rather humble beginnings of life from non-life, but he takes this one step further and suggests we may be looking at an actual ancestor when we observe the complex growth processes of such crystalline forms as stated in Origin of Life, (ed.,) C. H. Waddington, Transaction Publishers, 2009 in the chapter entitled:
An approach to a blueprint for a primitive organism
We might think of the replication of the unit cell of a crystal, or better the replication of a pattern of dislocations, during the growth of a crystal…Rather than consider theoretical models of replication processes that closely mirror those of modern organisms we should perhaps look very hard at the simple processes of replication which already exist in profusion in the physico-chemical world, and to consider these not simply as models, but as potential ancestors.
Cairns-Smith (2009, 58)
Now, I would propose an ancestrally shared condition or system, rather than a literal ancestor, as discussed previously where evolution appears to be a process of simpler and more primitive systems that tend towards complexity and organisation on every possible scale, but Cairn-Smith’s model is certainly more than a simple model, and does, indeed appear to have a very real and tangible link to organic life as you will see further on in this chapter.
Peeling back the Crystal-Coded Onion
… Life’s First Barcode?
…, clay mineral layers not only attracted certain chemicals from the environment to their surfaces, the mineral layers also acted as the first genetic information carriers, much as the base pairs in DNA do today.
“The objects that I’m particularly interested in are mixed-layered crystals, in which the crystal structure consists of beautifully formed layers packed on top of each other, but with an arbitrary sequence,” says Cairns-Smith. “In that respect, they’re like a DNA molecule, which has base pairs, little platelets inside it which are stacked on top of each other. It is the sequence of this stacking which creates the information.”
Cairns-Smith doesn’t think the clay mineral crystals were “alive” anymore than a DNA sample is thought to be alive. Instead, by acting as the first genetic materials for early life, clay mineral crystals created a link between the worlds of inorganic and organic chemistry.
At some point, life launched free of its inorganic genetic origins — the organic substances that evolved from chemical interactions on the mineral layers became stable enough to live apart from their birthplace, and complex enough to replicate themselves into the future.
Some mineral layer combinations probably worked better than others when it came to marshalling the organic molecules that were to eventually become genetic materials.
Mullen (2009, ‘Astrobiology Magazine’ 19th March)
Basically, I have outlined the main characteristics of crystal growth below, and emphasised, what I think are the most interesting facts regarding crystals as they correspond to Smith-Cairn’s hypothesis. This should help to get a broad feel for his concept. For instance, for anyone that doesn’t already know the fascinating properties of crystal growth (but I’m sure you do), this is just a brief overview reminder. I will start with the snow-crystal or snowflake structures as they, like biological life, need a starter seed, a trigger to trigger growth (some inorganic material, just as a snowflake has to be first seeded from a speck of dust in the clouds). Then their growth pattern follows a very clear and predictable molecular (molecule bonding etc) pathway via hydrogen bonds in the case of snow-crystals.
A snowflake starts out as a basic geometric prism (always six-sided in the case of snowflakes or cubes as in salt crystals) and this informs the underlying pattern in every direction along the main axes in proportion to itself. Each level of growth is a complete scale of growth and this pattern will be repeated over and over again on all the finer scales until the crystal has reached the full capacity of its sustainable system. And all of this is in direct relation to its environment, temperature and surface conditions, water molecules and float rate etc.
Then of course, they melt and the whole process can start over if the conditions are right. Their final shape and form (even though they all follow the same fundamental principles of growth) there are modifications made according to the fluctuations in the growing conditions and hence: the expression no two snowflakes look the same comes to mind.
However, the type of crystal growth and form that Cairns-Smith uses such as rock crystals in a clay solution as outlined in the quote above, does highlight the rather amazing properties of memorised and replicated patterning, where, if a small part of the whole crystalline structure becomes dislodged as it forms; the parent matrix/lattice from which it came directs the growth and development matrix pattern of the daughter crystalline structure, this will vary slightly if its growing conditions/surface is different or changed in some way – modified.
Recall the concept emerging within the nested scales of complexity model, where a small change at the beginning can ultimately have quite a large effect further down the line, well, clay-crystal growth in solution is fundamentally similar and ultimately, conditioned in its overall shape and form by rules that are seemingly applicable and universal to almost all living structures as far as we can tell; just as much as to crystalline ones as well.
I should also point out that Nature does not grow one snow-crystal arm at a time, any more than a snowdrop puts on one petal at a time. Each stage of fractal-like growth is a whole phase or stage and completes this stage before taking the self-similar repeating pattern to another more elaborate and complex (and typically larger) scale. In combination then, crystal growth gives us all the essential processes and principles embedded within life itself.
Crystal growth for instance, has the properties of fractal-like growth at different complete scales, patterned memory and its modifications according to environmental factors during growth that can be ‘remembered’, via imprinting that can be replicated ‘inherited’ allowing further divergent growth and has fundamental properties of predictable, measurable, fractal-like (self-similar patterns repeated at all scales) shape and form.
In other words, crystal growth also mirrors at its most fundamental level, all the main characteristics embedded within the genetic code, epigenetic modification processes, cellular memory and adaptation according to environmental conditions discussed in the previous chapters, only on a much more primitive scale of complexity.
Once again, it seems that we may be looking at building upon the same principles of earlier systems to evolve much more complex systems: nested scales of complexity. Therefore, in order to explore this concept fully, particularly with regard to the genetic code itself, we need to rewind the possible evolutionary scenario for the evolution of the gene code within the context of the cells and as complex organisms are made up of lots of interacting cells – this should begin to reveal the nested scales of complexity embedded within the evolutionary development process which is clearly in evidence from the very small and primitive to the very complex and large.
We will therefore start with a brief overview of what we can establish as the essence of how the current DNA and the genetic code operates (bearing in mind the fact that the epigenome operates above this code and is also inherited with continuous finer modifications and the fact that these modifications may have been much more dramatic, rapid and profound during earlier evolutionary development as strongly indicated from the scientific literature which will become clearer as we proceed).
By peeling back the coded onion and working our way down to the level (scale) of the crystal code itself, and maybe even go a little deeper than this, this will help us to identify and assess the entire spectrum of scaled complexity operating. So beginning with our first and most complex level, when we think of DNA, it boggles the mind how such a system could itself have evolved.
However, if we try to not get distracted by all the details of complexity and look for simpler versions of forms of the DNA molecules, then we can begin to see the underlying principles that are common to more primitive (less specialised and presumably earlier scales of complexity) versions of the system.
The following excerpt just scratches the surface of the outer layers of genetic scales of complexity. It is taken from a science paper on ancestral pre-cursers to DNA is highlighted in the slightly different chemical composition of a more primitive version of DNA molecule known as TNA.
The TNA world that came before the RNA one
Once it was recognised that DNA is key to the molecular self-replication that underpins life, chemists have sought to understand the origins of this double-helical molecule in that primordial age. It was quickly assumed that RNA, a single-stranded nucleic acid, may have been the precursor genetic material to DNA, and the RNA world hypothesis was born. But what gave rise to RNA? Chemists in the US are starting to home in on another nucleic acid, TNA: threose nucleic acid. ..
Bradley (2012, 8th January)
Another article exploring this recent discovery of the TNA molecule expands a little upon the interesting properties of this molecule in terms of an ancestral (more primitive) form of DNA and its key features of self-organisation, (self-assembly – fold into meaningful shapes via molecular bonding) and replication is given below:
Did an Earlier Genetic Molecule Predate DNA and RNA?
One approach to identifying molecules that may have acted as genetic precursors to RNA and DNA is to examine other nucleic acids that differ slightly in their chemical composition, yet still possess critical properties of self-assembly and replication as well as the ability to fold into shapes useful for biological function…
According to Chaput, one interesting contender for the role of early genetic carrier is a molecule known as TNA, whose arrival on the primordial scene may have predated its more familiar kin. A nucleic acid similar in form to both DNA and RNA, TNA differs in the sugar component of its structure, using threose rather than deoxyribose (as in DNA) or ribose (as in RNA) to compose its backbone.
The TNA world that came before the RNA one…
Threose, which has one fewer carbon atoms than ribose, is simpler than RNA not because it has fewer atoms, but rather because it can be synthesised from a single starting material,’ explains Chaput. . The researchers have now demonstrated that these selected TNA molecules can fold into complex shapes with discrete ligand-binding properties.2 Fundamentally, the work demonstrates a property of TNA that was not clear before the team began but was known, of course, in RNA and DNA. ‘This provides evidence that TNA could have served as an ancestral genetic system during an early stage of life,’ Chaput tells Chemistry World.
Astrobiology (2012, 13th January)
Now, this begins to reveal at least three scales of genetic complexity that are all built upon the previous system, starting with TNA, a more complex molecule: RNA and finally our more familiar DNA: the most complex of them all. The other important point within the above article excerpts relating to the TNA as a DNA precursor is that it works from simpler systems and builds upon these whole systems operating at a more primitive level to essentially do the same thing in more complex and later systems. And this is exemplified in the fact that TNA, apart from having lesser carbon atoms than ribose (RNA constituent), but it could be synthesised from a single starting material to get going.
This clearly demonstrates how Nature tends to start with simpler processes and then elaborates upon these recipes according to the ingredients available such as the molecular complexity of sugars used. In other words, Nature seems to have evolved systems (that are ancestral to all) building upon the principle of earlier versions on increasing scales of complexity. But in order to begin understanding this level of complexity, even at the TNA scale, we need to go a little deeper still and see some of the systems that may have led to the coding complexity of life that brought it to the TNA level in the first place. I will, therefore, briefly introduce you to some of the main players of the whole genetic system, if you are not already familiar with the whole system, via the review below:
How Do Genes Work
… each gene is really just a recipe for making a certain protein. And why are proteins important? Well, for starters, you are made of proteins. 50% of the dry weight of a cell is protein of one form or another. Meanwhile, proteins also do all of the heavy lifting in your body: digestion, circulation, immunity, communication between cells, motion-all are made possible by one or more of the estimated 100,000 different proteins that your body makes.
But the genes in your DNA don’t make protein directly. Instead, special proteins called enzymes read and copy (or “transcribe”) the DNA code. The segment of DNA to be transcribed gets “unzipped” by an enzyme, which uses the DNA as a template to build a single-stranded molecule of RNA. Like DNA, RNA is a long strand of nucleotides.
The Tech Museum of Innovation (2013)
We may, therefore, be looking at different recipes and increasingly elaborate processes involving several players that have specialised functions in the present form of the genetic system. And as you can see, proteins and special proteins (enzymes) do the lion’s share of the work, once the DNA code (recipe) is unzipped, transcribed/translated. Therefore, if RNA existed as a precursor to DNA and even RNA may have had a precursor and more primitive and direct interpretative system in relation to proteins, it might be useful to investigate proteins a little further within the context of the cell.
Proteins are the end products of the decoding process that starts with the information in cellular DNA. As workhorses of the cell, proteins compose structural and motor elements in the cell, and they serve as the catalysts for virtually every biochemical reaction that occurs in living things. This incredible array of functions derives from a startlingly simple code that specifies a hugely diverse set of structures.
In fact, each gene in cellular DNA contains the code for a unique protein structure. Not only are these proteins assembled with different amino acid sequences, but they also are held together by different bonds and folded into a variety of three-dimensional structures. The folded shape, or conformation, depends directly on the linear amino acid sequence of the protein.
… Within a protein, multiple amino acids are linked together by peptide bonds, thereby forming a long chain. Peptide bonds are formed by a biochemical reaction that extracts a water molecule as it joins the amino group of one amino acid to the carboxyl group of a neighboring amino acid. The linear sequence of amino acids within a protein is considered the primary structure of the protein.Proteins are built from a set of only twenty amino acids, each of which has a unique side chain. The side chains of amino acids have different chemistries…
Nature Education (2014)
What is particularly interesting about the above excerpt, as it might apply to the nested scales of complexity model, is that proteins would appear to have their own direct, primary code (even though the modern genetic system now triggers and codes for these protein templates) that gives them their unique identity and function. It is also interesting that at one stage in evolutionary terms, DNA didn’t exist, and RNA did, while at another level, RNA may not have existed and only the simpler system of TNA existed and something similar in terms of coding must have existed before that. The only clear candidate is the amino-acids with their ability to chemically bond (memorise these bonds re the Turing’s Model of the chemical basis of Morphogenesis and cellular differentiation) and it may, therefore, be simply a matter of scale.
As noted above, it is amino-acids which give proteins their primary structure and seems to point to an evolutionary preserved condition and therefore suggests a more primitive coding system (an amino-acid code perhaps) for shape, form, organisation and function of the protein system that emerged from environmental factors triggering chemical bonding sequences that remembered, a bit like memory foam?
It is this potentially more primitive and direct coding system of amino-acids that, in its most direct and primitive form, provided the primary information of ‘How to Build a Protein’ where, the DNA now does this in a fairly indirect way and on several levels, seemingly, using all of the elements of amino-acids, enzymes, proteins, cellular functions, biochemical and molecular sequences, DNA code, epigenetic processes adapted to run the fully optimised and efficient genetic system we recognise today.
Visual account of protein investment in cellular functions
Proteins and, by extension, genes perform numerous biological functions ranging from the catalysis of chemical reactions to the formation of physical cell structures and the processing of environmental signals.
Liebermeiste et al (2014, 8488)
If we excluded the reference to genes from the above excerpt and substituted it with a sequence of bio-chemical bonds, and taking into account the biochemical and context-dependent epigenetic system that also operates above and beyond this essential coding, we could say that the system of producing differentiated proteins, each with their own little string of amino-acid code, expressing the underlying amino-acid code according to environmentally-triggered and adaptive responses, is a self-contained environmentally sensitive primitive genetic/epigenetic coding that co-evolved within the context of the cells and itself is a precursor to the TNA/epigenetic-type coding system.
For instance, the key point of the excerpt below is that proteins possess the same fundamental properties of self-organisation as does DNA, RNA or TNA.
Protein Self-Organization: Lessons from the Min System
One of the most fundamental features of biological systems is probably their ability to self-organize in space and time on different scales. Despite many elaborate theoretical models of how molecular self-organization can come about, only a few experimental systems of biological origin have so far been rigorously described, due mostly to their inherent complexity. The most promising strategy of modern biophysics is thus to identify minimal biological systems showing self-organized emergent behavior.
Loose et al (2011, Abstract)
This article goes on to describe the best and least complex examples that they thought useful to experimentally assess, being a particular type of protein (noted in the title) which self-organises according to its environment. To reiterate this fundamental property of proteins to self-organise according to their environment and to memorise their state (not essentially requiring DNA code to form themselves into meaningful shapes), the excerpt below highlights these differential behaviours of enzyme/proteins below in an article entitled: Scale-free flow of life: on the biology, economics, and physics of the cell
Ambiguity in protein localization, interactions, structure, and function
Taking into account the fact that a protein’s conformational landscape depends on environmental context and on the protein’s own state (e.g., posttranslational modifications), one can envisage that different environments and different protein states may elicit different “behavioral routines” in the same protein. In other words, it is very likely that any given enzyme/protein possesses, in fact, a whole repertoire of context- and state-dependent behavioral routines rather than a single routine, the repertoire that has been “hard-wired” into protein structural dynamics as a set of useful sequences of coupled conformational transitions selected and “remembered” in the course of the co-evolution of a given enzyme/protein and its host.
If proteins can seemingly arrange and shape themselves and make connections in space and time depending upon the context and interactions as they begin to assemble themselves, just as the cells themselves appear to do via their own biochemical switching program and remember their state, then, it could be suggested that proteins within the context of the cells are forerunners or a more primitive systems of genetic memory conservation and the interface between the outside and inside biochemical world, pattern sequence formation and epigenetic imprinting.
It is also of interest that proteins form families or networks of their own kind as you will see in the next article excerpt and this is perhaps akin to the cellular families that can be triggered into becoming differentiated neurons, bone, and the soft-tissue cells in direct response to environmental factors via chemical diffusion/fusion systems discussed in the previous chapter. Are we looking at differentiated proteins just like their differentiated cellular kin? Is this another scale of the primitive genetic whole system? Recall that the differentiation of cellular families is epigenetic in nature (it operates above and beyond the coded sequence of genes and expresses them differentially).
What Are Protein Families?
All proteins bind to other molecules in order to complete their tasks, and the precise function of a protein depends on the way its exposed surfaces interact with those molecules. Proteins with related shapes tend to interact with certain molecules in similar ways, and these proteins are therefore considered a protein family. The proteins within a particular family tend to perform similar functions within the cell.
Proteins from the same family also often have long stretches of similar amino acid sequences within their primary structure. These stretches have been conserved through evolution and are vital to the catalytic function of the protein. For example, cell receptor proteins contain different amino acid sequences at their binding sites, which receive chemical signals from outside the cell, but they are more similar in amino acid sequences that interact with common intracellular signaling proteins. Protein families may have many members…
Proteins are built as chains of amino acids, which then fold into unique three-dimensional shapes. Bonding within protein molecules helps stabilize their structure, and the final folded forms of proteins are well-adapted for their functions.
Nature Education (2014)
This system (amino-acid chains and molecular bonding to form unique families of proteins), could have easily been the precursor system of the cellular differentiation according to biochemical processes described in the previous chapter. In many ways, the protein/amino-acid system provides a genetic precursor to even TNA as although it may have a different chemical composition: essentially it possesses the crucial properties of self-assembly with its ability to fold into useful shapes for biological function and these states are triggered environmentally, are context-dependent and can be memorised and these critical properties seemingly operate at all scales as indicated below.
Self-Assembly at All Scales
Self-assembly is the autonomous organization of components into patterns or structures without human intervention. Self-assembling processes are common throughout nature and technology. They involve components from the molecular (crystals) to the planetary (weather systems) scale and many different kinds of interactions. The concept of self-assembly is used increasingly in many disciplines, with a different flavor and emphasis in each… In dynamic self-assembly […] the interactions responsible for the formation of structures or patterns between components only occur if the system is dissipating energy.
The patterns formed by competition between reaction and diffusion in oscillating chemical reactions […] are simple examples; biological cells are much more complex ones. The study of dynamic self-assembly is in its infancy. We define two further variants of self-assembly. In templated self-assembly […] interactions between the components and regular features in their environment determine the structures that form. Crystallization on surfaces that determine the morphology of the crystal is one example […]; crystallization of colloids in three-dimensional optical fields is another […]. The characteristic of Biological self-assembly […] is the variety and complexity of the functions that it produces.
Whitesides and Grzybowski (2002, p. 2418, ‘Science Magazine’ 29th March)
Apart from the obvious reference to the self-organising ability (and memory imprinting) of crystalline structures (which we will return to in relation to Cairns-Smith’s model further on) and the reference to the diffusion system well-known in chemistry and applied in Turing’s model for cellular differentiation as outlined previously, the information within the article referenced above, goes into the many different means by which natural systems can self-organise. To simplify this, I suppose the best way perhaps of describing how natural non-living systems can self-assemble, is that we could say there is a polarity between ‘N’ and ‘S’ of a magnet and certain particles would be attracted, or not attracted and orientated and arranged accordingly (iron filings in the presence of a moving magnet would be self-assembled).
Now to apply this to biological self-organisation using one example, we could equate this to biological cells as we know that cells have little polar-type attractors and non-attractors which relate to water-loving molecules and water-hating molecules (hydrophilic and hydrophobic respectively). Because of this property, cells do amazing things. It is a little like oil and water, where the oil in water will form whole droplets to avoid getting wet; so obviously, the oil is full of hydrophobic molecules which are more like the oily lipid membrane that protects the inner watery cellular environment that has seemingly been conducting chemical catalyst – bonding and chain building as well as molecular synthesis experiments for a very long time to get as sophisticated as cells are today.
As for coding, we could say that this can be understood, even at its most primitive and simple scale as akin to our modern use of the binary code system for computer languages. Binary code is simply ‘0s’ and ‘1s’ but, look at how much code can be written from the arrangements and the ordering of this code. It is either on or off/activated or not. For instance, in the biological or magnetic system, every negative is a non-bond ‘0’ and every positive polarity is a positive bond ‘1’ or ‘on’ or ‘off’, which would be a foundational and simple code. However, if we bring the ability to memorise these ‘on’, ‘off’ coded sequences, into the equation, eventually, molecules will find each other a lot quicker and these chemical reactions and diffusions will get very efficient at firing together if they are triggered into doing so, akin to Turing’s biochemical ‘On’, ‘Off’ switching.
The article excerpt above: Self Assembly at All Scales, demonstrates that self-assembly is observable within many natural systems at a molecule level, so it is not surprising that chemical bonds of attraction or non-attraction can eventually form chains of bonds that in turn, build proteins or become special proteins (macro-molecules) that self-assemble (or self-fold three-dimensionally according to temperature, negative or positive polarity etc) as you will see below, proteins have very similar characteristics to cells and their building blocks: the amino-acid chains have their own code. The article excerpt below is rather technical and long, but I thought it was worth highlighting so that you get an idea of the protein/amino-acid system and its code.
Introduction to protein structure and structural bioinformatics
The 20 Amino Acids and Their Role in Protein Structures
The amino acids are put together into a polypeptide chain on the ribosome during protein synthesis. In this process the peptide bond, the covalent bond between two amino acid residues, is formed. There are 20 different amino acids most commonly occurring in nature. Each of them has its specific characteristics defined by the side chain, which provides it with its unique role in a protein structure. Based on the propensity of the side chain to be in contact with polar solvent like water, it may be classified as hydrophobic (low propensity to be in contact with water), polar or charged (energetically favorable contact with water).
The charged amino acid residues include lysine (+), arginine (+), aspartate (-) and glutamate (-). Polar amino acids include serine, threonine, asparagine, glutamine, histidine and tyrosine. The hydrophobic amino acids include alanine, valine, leucine, isoleucine, proline, phenylalanine, tryptophane, cysteine and methionine. The amino acid glycine does not have a side chain and is hard to assign to one of the above classes.
However, glycine is often found at the surface of proteins, often within loops, providing high flexibility to these regions. Proline has the opposite effect, providing rigidity to the protein structure by imposing certain torsion angles on the segment of the polypeptide chain. The reason for these effects is discussed in the section on torsion angles. These two residues are often highly conserved in protein families since they are essential for preserving a particular protein three-dimensional fold…
…Most protein molecules have a hydrophobic core, which is not accessible to solvent and a polar surface in contact with the environment (although membrane proteins follow a different pattern). While hydrophobic amino acid residues build up the core, polar and charged amino acids preferentially cover the surface of the molecule and are in contact with solvent due to their ability to form hydrogen bonds (by donating or accepting a proton from an electronegative atom).
Very often they also interact with each other: positively and negatively charged amino acids form so called salt bridges, while polar amino acid side chains may form side chain-side chain or side chains-main chain hydrogen bonds (with polar amide carbonyl groups). It has been observed that all polar groups capable of forming hydrogen bonds in proteins do form such bonds. And since these interactions are often crucial for the stabilization of the protein three-dimensional structure, they are normally conserved.
What is of particular interest here, I believe, is that when we look for the precursor system of protein/cellular and amino-acid/TNA/RNA/DNA coding system, this brings us right down to the level/scale of Cairns-Smith’s clay crystals in solution hypothesis and the inherent self-organising properties embedded within it. We have looked at self-organisation principles, self-patterning/folding and chemical/molecular bonds in response to environmental factors and interactions and ability to memorise (akin to memory foam) patterns, bonds and connections and how these might equate with the crystalline coding with modification pattern of growth and development, but we haven’t yet looked at another key feature of the crystal code within cellular structures which is clearly inherent in biological cellular systems and that is self-replication.
It is actually quite difficult to pin-point this characteristic within biological life, but we can infer that as crystalline formations can replicate, with slight modification, from their parent matrix/lattice, a daughter formation that can grow and break off, thus cloning itself, that this method may underpin a more complex and more sophisticated means of reproduction seen within living systems today. So it may be useful to go back as far as possible on the borderlands of life itself and see what we can deduce about replication beyond (and on a more complex scale) the inert crystalline patterns that may have given their cue to first life.
All viruses contain nucleic acid, either DNA or RNA (but not both), and a protein coat, which encases the nucleic acid. Some viruses are also enclosed by an envelope of fat and protein molecules. In its infective form, outside the cell, a virus particle is called a virion. Each virion contains at least one unique protein synthesized by specific genes in its nucleic acid. Viroids (meaning “viruslike”) are disease-causing organisms that contain only nucleic acid and have no structural proteins. Other viruslike particles called prions are composed primarily of a protein tightly integrated with a small nucleic acid molecule.
As indicated above, in many ways, proteins are actually akin, albeit seemingly a much more primitive and potential precursor to the modern type cell, and have become a major part and function of the cell itself. Well, in the context of viruses, this primordial code-carrier dressed in a protein sheet, may be significant. The key characteristic of viruses is that they are the great replicators and are not that dissimilar in function to computer viruses, as they don’t have the ability to replicate and make lots and lots of copies of their own code and little programs to spread virally outside the context of your computer any more than biological viruses being effective outside the context of the modern cell.
But I have to say that Nature’s viruses are actually not all bad and indeed, viruses are seemingly essential to life and life itself would not have evolved much further if viruses hadn’t have developed such a cosy (symbiotic) relationship with cells. Or, it could be suggested that viruses being made of essentially the same stuff as primitive cells (chain of code and a protein sleeve for protection) are a more mobile version of the cells themselves.
For instance, some researchers prefer a cellular metabolism first hypothesis and have come up with ingenious means of how this could have occurred under natural conditions. Others have suggested the virus first hypothesis, but based upon the model used here, I would be inclined to see the viral coded critters protected by a protein sheet as a whole system which later became another scaled-up level of complexity of the whole system and some versions of that cellular/metabolic and amino-acid coding and primitive protein system became mobile (what we would call a free-living virus, which thankfully doesn’t seem to exist any longer, but this may not have always been the case – see below.
Could Giant Viruses Be the Origin of Life on Earth?
The ancestors of modern viruses may have laid the groundwork for cellular life as we know it
In the world of microbes, viruses are small—notoriously small. Pithovirus is not. The largest virus ever discovered, pithovirus is more massive than even some bacteria. Most viruses copy themselves by hijacking their host’s molecular machinery. But pithovirus is much more independent, possessing some replication machinery of its own.
Pithovirus’s relatively large number of genes also differentiated it from other viruses, which are often genetically simple—the smallest have a mere four genes. Pithovirus has around 500 genes, and some are used for complex tasks such as making proteins and repairing and replicating DNA.
“It was so different from what we were taught about viruses,” Abergel said
Arnold (2014, ‘Quanta Magazine’ 17th July)
However, present-day viruses seem to be fairly restricted and only effective in the context of cells and this seems to be therefore a fairly fixed symbiotic relationship. And as you will see in the final chapter of this book, viral-like mobile remodelers of the genome in times of stress, means that viruses may have been major players in the fact that we are here at all.
We can begin to see how Nature may have used the systems and materials to produce scaled-up variations on the same fundamental theme and to form these as whole systems from the ground up. Mobile non-cellular viruses (but made of the same stuff) and cellular colonies co-evolving in a symbiotic relationship perhaps? Take, for example, the scaling from amino-acids, to more complex molecules such as TNA, RNA and finally DNA, protected by flexible and environmentally sensitive protein rings (segments) and we can begin to see how and perhaps why, the code cannot operate outside the context of the cell and vice-versa. This co-dependent, environmentally-driven system leading to the modification of the code itself, becomes even more intriguing when we explore another key feature of viruses, namely the fact that they are assembled from a two-dimensional crystalline structure as outlined in the excerpt below.
Two-dimensional crystalline structure assembled from outer shells of a virus
In a paper published in Soft Matter, September 2013, scientists announced their discovery of a two-dimensional crystalline structure assembled from the outer shells of a virus. A virus consists of a protein shell protecting an interior consisting of either DNA or RNA.
“We are excited about the potential of virus-like particles as building blocks for creating new nanostructures,” said the paper’s lead author, Masafumi Fukuto, a physicist in the Condensed Matter Physics and Materials Science Department at Brookhaven National Laboratory. “For the particular virus that we studied, we discovered two new forms of 2D crystals that are distinct from previously observed hexagonal and square crystals.”
Rowe (2012,’Physics.Org’ 21st February)
As seemingly, amino-acids are the primary (primordial) code and assembled (chemically-bonded by natural organising properties of these molecular systems at all scales) and their outer protective coat of the proteins with their own organisational properties according to polarities etc, we now have a further clue to the sophistication of this holistic and symbiotic system in terms of the crystalline nature of the protein/coding system itself. The underlying crystalline nature of this system is further supported in the next section where just about everything in the body, from the proteins in your eye lens to whole protein systems, and from DNA and the formation of the double helix is crystalline.
We could be seeing the emergence of the software and the hardware required to carry out fundamental coding (chemical bonding, chemical ‘on’, ‘off’ switching, which have all the hallmarks of the more developed coding and cellular system allowing for macro-molecular synthesis via special proteins – enzymes etc); and we now have the basis of an environmentally sensitive and controlled system for the reproduction/replication of the primary coding format in the form as a crystalline organism itself – as seen in the virus-type entity.
The gives us an insight into how the crystalline hypothesis can be taken to a completely distinct new, but related level, as you will see in the following section. This is where the whole system would appear to take an unexpected quantum leap in crystalline complexity and perhaps it is this level of sophistication that makes it alive as you will see below.
Quantum Liquid Crystalline Life
From the most fundamental properties embedded within clay-crystal in solution, we can begin to see how Cairns-Smith’s theory may work, particularly, if we understand it as a more primitive, scaled-down version of the whole cellular/genetic/epigenetic coding system. For instance, at a highly evolved level and on a larger scale of the whole system, proteins and their crystalline structure are no better exemplified by those found in your eyes. See below:
Soon, sight-saving treatment to protect eyes from cataract
It has long been known that human eyes have a powerful ability to focus because of three kinds of crystalline proteins in their lenses, maintaining transparency via a delicate balance of both repelling and attracting light.
ANI (2013, ‘Zee Health News’ 6th December)
Furthermore, the powerful efficiency of liquid crystals as a highly responsive information system and the source of coordinating a whole organism with its patterning and structural properties is strongly indicated in the following excerpt and points to the ability of these crystalline properties of, and within cells. Note that LCLCs stand for lyotropic chromonic liquid crystals.
Scientists to Advance Biology-Liquid Crystal Research
Liquid crystals represent the fourth phase of matter…
Certain organic materials exhibit the liquid crystalline state as they transition between the solid and the liquid states, known as mesophases. Though liquid crystals are best known for their application in displays, they also are an essential part of all life. Liquid crystals in organisms include the amphiphilic lipids of cellular membranes, the DNA in chromosomes, all proteins, especially cytoskeletal proteins, muscle proteins, collagens and proteoglycans of connective tissues. These adopt a multiplicity of mesophases that may be crucial for biological structure and function at all levels of organization, from processing metabolites in the cell to pattern determination in development, as well as the coordinated locomotion of whole organisms.
Kent State University (2005, ‘Physics.org’ 11th October)
As noted above, the liquid crystal phase is also important to DNA in the chromosomes which, is elaborated upon in a little more detail in another science excerpt below:
Liquid crystalline phases of ultra-short DNA and RNA sequences
The ability of long, hydrated, double-stranded DNA to form liquid crystal phases has been known for more than 50 years and played a key role in the initial deciphering of its structure…Recent collaborative work between the Boulder group and the Complex Fluids and Molecular Biophysics group of the University of Milan has shown that self-pairing, or complementary, DNA oligomers as short as six base pairs can exhibit chiral nematic and columnar LC phases …
Zanchetta and Nakata (n.d)
The chiral pairs they are talking about referring to right or left-handedness, meaning the orientation of how structures line up. So, therefore, the more recent data is pointing to very powerful memory systems and ordering of molecular sequences – not to forget the ability of these molecules to fold in meaningful ways and self-organise and perhaps this begins to give us an insight into the shape and form of the double helix structure of the DNA code itself. This is described below.
Polymers and Liquid Crystals
A molecule that is not identical to its mirror image. This gives a chiral substance its characteristic twisted shape, due to the fact that its molecules do not line up when combined.
cholesteric liquid crystals
Also known as Chiral Nematic. Similar to the nematic phase, however, in the cholesteric phase, molecules in the different layers orient at a slight angle relative to each other (rather than parallel as in the nematic). Each consecutive molecule is rotated slightly relative to the one before it. Therefore, instead of the constant director of the nematic, the cholesteric director rotates helically throughout the sample. Many cholesterol esters exhibit this phase, hence the name cholesteric…
Nematic liquid crystals with chiral centers form in two dimensional nematic-like layers with directors in each layer twisted with respect to those above and below so that the directors form a continuous helix about the layer normal.
Case Western Reserve University (2004).
This suggests an explanation for how the distinct double helix structure with its meaningfully arranged molecules may have bonded. This twisted ladder effect as a property of certain liquid crystalline behaviour in solution is indicated in the excerpt below. It also begins to give you an insight into the more dynamic properties of self-organising, shaping/forming and patterning within the solution with different polarities (context-dependent) when observed within certain liquid crystals.
Liquid Crystal Droplets gemstones
In a study published in the Proceedings of the National Academy of Sciences, researchers from the University of Pennsylvania and Swarthmore College describe new research into a type of liquid crystal that dissolves in water rather than avoids it as do the oily liquid crystals found in displays. This property means that these liquid crystals hold potential for biomedical applications, where their changing internal patterns could signal the presence of specific proteins or other biological macromolecules.
The researchers placed these liquid crystals into water droplets, which in turn were placed in oil, producing an emulsion. At high enough concentrations within the droplets, the liquid crystals exhibit a twisting pattern visible under an optical microscope.
Lerner (2014, ‘Phys.Org’ 21st January 21)
In other words, this information above regarding the polarity of cellular/protein and their crystalline properties in particular liquid solutions and at specific quantities, under certain conditions, can be extrapolated to infer that the metaphase transition (of liquid crystals) allowed for a high level of fluidity and structure to propel the whole genetic system within the context of the cell to coordinate itself into living organisms.
And the main driver may have been informational were, the cellular system – the flexible hardware was itself a little organelle (miniature functional part of a cell) and responsive enough to adapt to varying environmental conditions and in turn, update the software accordingly. Basically, the cells and code working together (not forgetting the epigenetic code), in a feedback loop between organism and environment with the ability to remember, replicate and adapt and pass on the new information.
The information aspect of liquid crystal systems is seemingly the key to understanding this process and must be understood in the context of the crystalline properties and behaviour of proteins and cells in general. The crystalline coding system is exemplified in the short excerpt below, even though it is discussing a technological application of liquid crystal information storage systems, it may be relevant to our discussion of Nature’s crystalline information system.
Liquid crystals light way to better data storage
As cell phones and computers continue to shrink, many companies are seeking better ways to store hundreds of gigabytes of data in small, low-power devices.
A special type of liquid crystal, similar to those used in computer displays and televisions, offers a solution. Unlike CDs and DVDs, which store information only on their surface, lasers can encode data throughout a liquid crystal. Known as holographic storage, the technique makes it possible to pack much more information in a tiny space.
American Institute of Physics (2010, ‘ScienceDaily’24th June)
Nature doesn’t have lasers as far as we know, but light can be focussed differentially from natural light frequencies in different spectrums and this we are all familiar with in the form of photosynthesis used by plants. We could suggest from all of the above that as exemplified in the proteins in the cells of the eye and their liquid crystalline properties, that this is a good clue to how Nature may have focussed light in a similar way to arrange molecules as information storage systems, presumably prior to cellular colonies becoming whole coordinated cellular organisms.
As suggested all along and indicated above and as you will see below, with regard to protein liquid crystalline behaviour, the genetic code cannot be seen in isolation to the protein and/or cellular system. Therefore, if we now look at the cell itself with its self-similar properties of ordering and meaningful structuring in direct relation to its interactions and biochemical/molecular environment, polarities in solution and temperature, we can gain an insight into the fundamentals of the whole interactive system.
Lipids and Membrane Structure
Membrane fluidity: The interior of a lipid bilayer is normally highly fluid (…). In the liquid crystal state, hydrocarbon chains of phospholipids are disordered and in constant motion.
At lower temperature, a membrane containing a single phospholipid type undergoes transition to a crystalline state in which fatty acid tails are fully extended, packing is highly ordered, and van der Waals interactions between adjacent chains are maximal.Kinks in fatty acid chains, due to cis double bonds, interfere with packing of lipids in the crystalline state, and lower the phase transition temperature. Cholesterol, an important constituent of cell membranes, has a rigid ring system and a short branched hydrocarbon tail. Cholesterol is largely hydrophobic. But it has one polar group, a hydroxyl, making it amphipathic is the ability…
Rensselaer Polytechnic Institute (2015)
Now when you hear about taking care of your cholesterol levels and taking your fatty-acids, you might think differently about what this actually means. This excerpt also brings to mind the discussion of the oil and water type attraction and repulsion system (polarity and charge) or the water-loving molecules and those trying to avoid water, working much like a magnetic field, akin to the Morphogenetic field well known by its effects to anyone studying cellular and embryological development? As the excerpt above outlines, liquid crystalline behaviour is very much context-dependent.
The all-important behaviour of certain proteins is further explored in the excerpt below in terms of the liquid crystalline properties and the fundamentally similar behaviour and equally context-dependent nature of cells and the fundamental properties of the code itself. However, when this next article talks about mutants, they mean a change occurring from a different solution (environment). Although quite a difficult science paper to follow, it does highlight a few key points about proteins and their underlying self-organised amino-acids (there are only 20 combinations and these are ubiquitous on the planet and beyond – apparently).
The self assembly of proteins; probing patchy protein interactions
This work suggests a mechanism by which protein …interactions can be probed in a systematic manner. This type of data is critical if good molecular models to predict protein behavior are to be developed. .., we created a protein, which forms two different crystal types, one that melts when the solution is heated and one that melts when the solution is cooled, with co-existence of the two crystal forms at 303 K, the point at which the individual liquidus lines for the single mutant variants overlap.
This observation is unprecedented. On a broader level, this work is a starting point which will require a combination of further experiments and complementary simulations to more clearly understand the interplay between the complex, competing forces controlling protein self-assembly and crystallization. However, it is clear that the surface characteristics of the protein, defined by the surface amino acids, can lead to a variety of condensed phases for the same protein. A change in the external environment, e.g. temperature, results in some amino acids contributing more to the protein self-assembly behaviour than others, leading to the variety of structures that we observe.
James et al (2015, 5419)
What I believe is most significant from the point of view of the nested scales of complexity model as it is employed throughout this present book, is that the article excerpt above states that it is clear “that the surface characteristics of the protein, defined by the surface amino acids, can lead to a variety of condensed phases for the same protein” which directly reflects the nested doll principle, where the surface features of the more primitive amino-acid system informs the main characteristics of the next level up: proteins. It is the spaces in between the nested dolls that give us the most information, rather than getting distracted by all the detail of variations from these interactions that lead us in the wrong direction when trying to peel back the scaled layers of this genetic onion.
Our more modern molecular science now tells us that cells, particularly pluripotent cells (unprogrammed), are highly sensitive to their environment/temperature/chemical landscapes and that this can cause a chemical chain reaction that programs the cells to become differentiated. Therefore, looking at evolution in terms of levels and scales of complexity, it is perhaps not that surprising that, proteins and at another scale: enzymes are similarly sensitive to their environments and interactions with each other and this can inform their shape and form and ultimately function. On another scale, this mirrors the crystalline growth system and with the added phase transition and dynamically responsive and fluid system of liquid crystalline growth and development, we now have the foundation for speciation (the differentiation of the pluripotent) organisms themselves.
The self-assembly properties are, therefore, seemingly, a complex interplay of molecular interactions in solution and at different temperatures, proteins surface interactions and differential polarities and tensions and memory bond via natural attractors or polarity factors than bind particular chemicals/molecules leading to self-assembly at an atomic level and later (on another scale), a chemical and then molecular and macro-molecule scale. This complex interplay between the interactions of whole systems such as the liquid crystalline condensed phase and a very dynamic complex system leads us back to D’Arcy Thompson’s application of whole complex system dynamics (derived from the branch of physics he unbeknownst to himself helped to develop – Systems Theory as indicated in the introduction).
This, of course, brings us to the scaled-up version of cellular systems and its interplay with the coding system and the organisms themselves. As we have been going from the bottom up and scaling each of these systems all the way, it is natural to see if the dynamic fourth phase of matter of the crystalline system: liquid crystal phase, is actually in evidence during the latter stages of embryological development or indeed, after the cellular differentiation stage. Indeed, as seen below, there is evidence to support the important role of liquid crystal phase during an organism’s development.
The study below is by MengMeng Xu and Xuehong Xu (Affiliations: Duke University School of Medicine, Department of Physiology Centre for Biomedical Engineering Technology, Centre for Stem Cell Biology and Regenerative Medicine, University of Maryland Medical School and Shaanxi Normal University School of Life Science, USA/China).
The patchy history of this much-neglected area of this type of fascinating research is outlined below in the introduction, followed by the more recent conclusions based upon a number of studies. There is a little bit of scientific terminology which may not make a great deal of sense, but the main idea from this article is that there is very good support for the presence of the liquid crystal stage (dynamic phase transition) during early development (embryogenesis) and I have presented it here to reiterate the fact that all of these interacting systems appear to have co-evolved in relation to environmental factors and interactions, that it is reflected at every scale of life and this has implications for how the species itself came into being in the first place.
Liquid-Crystal in Embryogenesis and Pathogenesis of Human Diseases
In 1979, a systematic publication summarizing the state of research on liquid-crystals in biological organisms was published [Brown GH et al 1979]. After this historic publication on liquid-crystals and biology, the field remained largely dormant for more than two decades. However in 1978 and 1979, Haiping He and Xizai Wu, who had continued pursuing this field despite international disinterest, reported their findings on liquid-crystal involvement during chicken development. For the first time, they revealed that massive quantities of liquid-crystals in the liver, yolk sac, blood, and many other developing tissues and organs of chicken during embryogenesis. Their later studies also reported similar liquid-crystalline structures during fish development.
In 1988, another group reported the existence of vaterite CaCO3 within the liquid-crystals found in yolk fluid, identifying the spherical calcified structures first reported in 1979 as one of three iso-forms of calcium carbonate [Feher G 1979, Li M et al 1988]. Subsequent studies have identified liquid-crystalline structures to be omnipresent in the liver during avian development [Xu XH et al 1995a, 1995b, 1997]. Recent studies have revealed that liquid-crystals play a critical role in the preservation of calcium and other trace elements required for embryo development [Xu MM et al 2009, 2010, 2011; Xu XH et al 2009, 2011a]…
General characteristics of embryonic liquid-crystal
During embryogenesis, liquid crystals are widely distributed in the tissues of vertebrates and invertebrates, including Apis cerana chrysalis, fish, reptile, avian and mammal early embryo in vitro [X XH et al 1993, 2009, 2011a, Xu MM et al 2009 2011]. In chicken development, more than twenty different organs and tissues exhibit liquid crystal droplets including liver, meso and metanephros, lungs, blood in heart, and brain. The presence of liquid crystal normally appears at different developmental stages depending on the tissue type, and lasts until early postnatal stages. The earliest liquid crystal droplets appear on the inner embryonic disc during the second day of development [He H et al 1978]. Regardless of their distribution, however, the liquid crystal droplets eventually vanish within three to four weeks into the postnatal period, also depending on tissue type maturation [X XH et al 2009, 2011a]…
Based on current discoveries obtained via XRD, SAXS, confocol microscope, and polarization microscopy in combination with cryo-section, push-release procedure for fluidity measurement, and thermal stage for phase transition progress has been made in the field of liquid crystal function in embryogenesis and pathogenesis of human diseases. With this methodology, the research has proved that, during the embryo development, liquid crystals are readily identifiable in the embryo through their Maltese Crosse birefringence texture. Liquid crystals with this configuration display strong fluidity accompanied with shape-changing properties under direct pressure conditions.
Xu and Xu Xu and Xu (2012, 637, 643 and 649)
This much-neglected field of study became a focus for the research of Mae-Wan Ho who began to take a multi-disciplinary approach as you will see below and discusses the process of Morphogenesis and pattern formation (recall Turing’s model of the Chemical Basis of Morphogenesis). According to the excerpt above, and the following excerpt, Ho and her collaborators certainly do seem to have discovered the most interesting phenomenon at the interface between different fields of science (just as D’Arcy Thompson being a Polymath also discovered in an era when such tools were not yet available to support his deep insights).
The science paper is entitled: Organisms as Polyphasic Liquid Crystals, in Bioelectrochemistry and Bioenergetics 41, 81-91, 1996  and its authors are: Mae-Wan Ho, Julian Haffegee, Richard Newton, Yu-ming Zhou, John S. Bolton and Stephen Ross and reflects the collaboration between the fields of biology, bio-electrodynamics and physics and the sub-field of quantum mechanics to name but a few.
Liquid crystals and pattern determination
One of the first generalizations to emerge from developmental biology is that early embryos and isolated parts of early embryos show a strong tendency to form whole organisms. This gave rise to the notion of a morphogenetic field – a spatiotemporal domain of activities organized globally to form the whole organism…
At the start of embryogenesis, the morphogenetic field exhibits ‘pleuripotency’ or ‘totipotency’, where all parts has the potential to develop into any structure. In the course of early embryogenesis, however, determination occurs in which the different parts of the embryo become more and more restricted in their developmental potential. The determined state can be demonstrated by transplantation and grafting experiments. If a piece is removed from an embryo before determination and transplanted to a different location, or grafted to another embryo, then the piece will develop in harmony with its surroundings. If the same experiment is carried out after determination, the graft will develop into the structure it was determined to be, irrespective of its surroundings. Thus, the graft may develop into a limb on the back of the host, for example. The process of determination was discovered a century ago, but its basis remains largely unknown despite impressive advances in the molecular genetics of morphogenesis in recent years.
The significant feature of pattern determination is that the determinative influences not only possess dynamic field-like characteristics, but are material and transplantable. …
A vital clue to the basis of determination may have been provided by Totafurno and Trainor (…) who successfully interpreted classical experiments on transplanting and grafting limb-buds in salamander, in which supernumery limbs were often induced, in terms of a non-linear vector field. This vector-field is precisely the sort that is embodied in liquid crystal phase alignments. … liquid crystals go through in transitions from the liquid to the solid state, which are comparable to the successive stages of determination of the limb-buds in amphibians…
There is indeed a wide range of liquid crystalline mesophases from the most dynamic and liquid – possessing orientation order in one dimension without any translationnal order – to the most solid – with orientation order in 3-dimensions and also a large measure of translational order. It is conceivable that in the course of development, the relevant liquid crystalline mesophases do undergo transitions from the dynamic and fluid to the relatively more (meta)stable, patterned regimes…
Ho et al (1996, Liquid Crystals and Pattern Formation)
More of this research can be found in the book, noted above and entitled: The Rainbow and the Worm: The Physics of Organisms (2008, extended 3rd edition) by Mae Wan Ho . Essentially, Mae-Wan Ho, from her deep research and experimental work and observations, led her to propose that the liquid crystalline phase and its high precision and holistic resonant molecular ordering during Morphogenesis, could be explained in terms of quantum coherence, a well-known phenomenon within the tiny atomic world describable by quantum mechanics and its intrinsic link to another branch of physics which studies the dynamic properties of the liquid crystalline complexity as seen in her talk below. Her observations also dovetail with and are pertinent to the study outlined earlier by Xu and Xu (2012) .
What it means to be Quantum Coherent
Quantum coherence and the liquid crystalline “rainbow worm”
The “rainbow worm” is this little fruit fly larva I first encountered in 1992 as it was hatching from its egg. We placed a batch of eggs in a continuously irrigated chamber on a microscope slide under the polarizing microscope and waited. The microscope was set up so we can see the organism developing and getting energized, right through to the arrays of molecules that make up its tissues and cells. …But what do the colours mean?
Geologists use the polarising microscope to identify rock crystals. We have slightly modified the setting, but the principle is the same. The rainbow colours are generated by crystals with orderly arrangements of atoms and molecules. We were puzzled at first. In rock crystals or liquid crystals outside the organism, molecules and atoms certainly have an orderly arrangement that stays ordered because there is no movement. But in the living organism nothing is static, the molecules and atoms are moving all the time. So how can they maintain the molecular order required to generate the brilliant crystal colours? …
The only explanation is that the molecules are moving coherently together, so much so that they appear as ordered as a static crystal. To cut a long story short, the molecules, especially the big ones, macromolecules like proteins and nucleic acids, thoroughly infiltrated with water, are in a dynamic liquid crystalline state. To begin with, they are completely aligned with their electrical polarities to form a continuum that links up the whole body, permeating throughout the connective tissues, the extra-cellular matrix, and into the interior of every single cell. More importantly, all the molecules, including the water, are dancing together as a whole, and the more active they are, the more coherent, hence the brighter the colour…
So, these beautiful images of living organisms are direct evidence of their high degree of coherence. And this high degree of coherence itself depends on the liquid crystalline matrix that enables every single molecule to intercommunicate, synchronize and syncopate with every other. The water, making up some 70 percent by weight of the organism, is the most important part of the living liquid crystalline matrix, without which it cannot form. Many molecules, DNA and proteins, would not be stable; and would not function without water; water is also crucial for the intercommunication that enables the organism to work as a coherent, perfectly coordinated whole […] …Mainstream biology has steadfastly ignored the liquid crystalline organism and all its implications.
Ho (2008, ‘Institute of Science and Society’ 1st October)
Mae-Wan Ho’s theory becomes even more compelling when we understand that Nature, apparently, has been using quantum coherence – a well-known phenomenon described by quantum mechanics – for a very long time. This quantum aspect of cellular life has apparently been sitting under our noses all this time. For instance, it is positively “jaw-dropping” says Johnjoe Mc Fadden (working on the quantum nature of Nature) in a recent article seen in Discover Magazine entitled: Solving Biology’s Mysteries Using Quantum Mechanics.
“Physicists had been battling for years to build a quantum computer — and now it seemed that all that time they may have been eating quantum computers for lunch, in the leaves in their salad!”
Merali (2014, ‘Discover Magazine’, 2th December)
One key principle of the quantum world is that the word quantum itself basically means a discrete packet with irreducible parts – i.e. it is all about whole systems and it is a tiny world as otherwise, things get too noisy and busy for the quantum effects to operate. This is elaborated upon and echoes some of Mae-Wan Ho’s conclusions in a science paper in the Journal of Physics conference papers (2011) by Seth Lloyd in the following:
Quantum Coherence in Biological Systems
Nature is the great nano-technologist. The chemical machinery that powers biological systems consists of complicated molecules structured at the nanoscale and sub-nanoscale. At these small scales, the dynamics of the chemical machinery is governed by the laws of quantum mechanics. Quantum mechanics is well known to exhibit strange and counterintuitive effects. Accordingly, it makes sense to investigate the extent to which peculiarly quantum effects such as coherence and entanglement play an important role in living systems. Quantum mechanics and quantum coherence play a central role in chemistry. Quantum coherence and entanglement determine the valence structure of atoms and the form of covalent bonds. Quantum mechanics fixes the set of allowed chemical compounds and sets the parameters of chemical reactions. Indeed, the very fact that there are only a countable, discrete set of possible chemical compounds arises from the fundamentally discrete nature of quantum mechanics. Chemistry, in turn, lays down the rules for what biological structures are possible and for how they function. Biomolecules can contain many atoms (billions in the case of DNA). As molecules become larger and more complex, quantum coherence becomes harder to maintain. Vibrational modes and interactions with the environment tend to decohere quantum superpositions. Consequently, most biomolecular mechanisms have traditionally been modeled as essentially classical processes…
Lloyd (2011, 1)
Therefore, once you start to become a quantum computer in Nature’s scheme of things: it seems that you will become the best quantum computer possible, as you are not just one giant complex cell, driven slavishly and randomly by your genetic code. You are made up of a whole fractal network of trillions of interacting and cooperative, communicating nano-scale liquid crystalline quantum cellular system. Using this ingenious system of making miniature copies of the original system of patterning and being able to continually modify the program, update it according to adaptive needs and in direct relation to the environment, is the ultimate quantum computer, and it is biological, seemingly. This brings us to Mae-Wan Ho’s discussion on quantum liquid crystalline organisms compared to our most recent attempts to develop quantum computing as outlined in the article excerpt below.
The quantum coherent organism and quantum computation
…Quantum superposition and quantum entanglement are the signatures of quantum coherence, and they have been attracting a lot of attention with regard to the possibility of a quantum computer, as opposed to the conventional classical computer now in use.
A quantum computer operates on the quantum bit or ‘qubit’ instead of the ordinary bit in a classical computer. While the ordinary bit is a simple binary 1 or 0, the qubit can hold 1, 0, or crucially, a quantum superposition of 1 and 0. In fact, it can hold anything up to an infinite number of values in superposition […] .A quantum computer can in theory do computations that are intractable with a classical computer or achieve exponential speedup in solving certain problems. And building an actual quantum computer has become the holy grail of a new breed of quantum information technologists…
To my mind, the perfect quantum computer already exists: it is the quantum coherent living organism…
Consider the elementary process of a protein folding into shape, a difficult problem even for the fastest classical computer. It takes about 300 years for a classical computer to simulate a small peptide of 23 amino-acid residues (with associated water molecules) to fold into shape. By running simulations simultaneously on some 140 000 individual computers around the world, researchers took over three weeks […]. Real proteins, however, fold to perfection in several microseconds […].
It is very important for proteins to fold correctly. Incorrect folding makes proteins aggregate into insoluble, inflexible clumps associated with wasting diseases such as mad cow disease, Alzheimer’s Diesease, Huntington’s and Parkinson’s Disease…The model of the quantum coherent organism depends on reciprocity and cooperation, rather than relentless Darwinian competition as in the mainstream model …
Hopefully, this is a new paradigm that will support a new world order that’s much closer to how nature is, that will enable us to live sustainably within her…
Ho (2008, ‘Institute of Science and Society’ 1st October)
Using this system, it is therefore perhaps not that surprising that life got so complex, but it is quite astounding that we may now be looking at quantum evolution that is a polar opposite and several billion light-years from our current Darwinian model. Furthermore, now having used the Matryoshka principle to look at the coding system at every possible scale, maybe we should begin taking a salad leaf out of Nature’s recipe book and use this to build our future technology in accordance with hers. At least the nano-technologists are beginning to recognise this, perhaps the biologists will begin to catch up – but I’m afraid they will have to let go of their pet theory first or they will completely miss the point.
For instance, I came across an excerpt which seems to be at least looking in the right direction. It is a bit technical, but hopefully, you’ll get the idea. The solution would appear to be those liquid crystals again and I like their idea of scalability:
Nuclear magnetic resonance quantum computing using liquid crystal solvents
Liquid crystals offer several advantages as solvents for molecules used for nuclear magnetic resonance quantum computing (NMRQC). The dipolar coupling between nuclear spins manifest in the NMRspectra of molecules oriented by a liquid crystal permits a significant increase in clock frequency, while short spin-lattice relaxation times permit fast recycling of algorithms, and save time in calibration and signal-enhancement experiments.
Furthermore, the use of liquid crystalsolvents offers scalability in the form of an expanded library of spin-bearing molecules suitable for NMRQC. These ideas are demonstrated with the successful execution of a two-qubit Grover search using a molecule (13C?1HCl3) oriented in a liquid crystal and a clock speed eight times greater than in an isotropic solvent. Perhaps more importantly, five times as many logic operations can be executed within the coherence time using the liquid crystalsolvent.
Yabbibu (1999, Abstract)
Final Thoughts on the Evolution of Computer Technology and its Nature’s Bio-Chemical/Crystalline System
Just as another little thought experiment, picture how the abacus was once, and indeed, still is useable as a self-contained counting system for tens of centuries before Babbage’s first computation machine or, the punch-card system used to code for the first IBM computers and the same principle of coding that allowed the great textile mills to pattern their linens and clothes, where the same design could be repeatedly produced from the same underlying pattern of a series of holes in a card, even in different factories. If one card got damaged; you could always make copies from the original or modified copies.
The telegraph system used another type of code, producing information that could be passed between vast distances; then came the telephone and we now have mobile phones. The typewriter was used mechanically and eventually we got the electric one, once we had electricity of course, but it was still a typewriter. And from the camera to moving photographs to film and eventually sound, we all ended up with viewable boxes in our homes that we call televisions. And of course, the internet once the typewriter technology merged with the television to become your keyboard and monitor; the coded punch-cards were put on floppy discs and the computing machine became a supercomputing device and when the phone came into the equation and merged with the computing system, well, we know that the whole system became greater than the sum of its parts, in fact, it is going quantum, yet each part was once a whole system, and you can still see whole functional systems within the greater whole. All the systems, irrespective of how primitive it may seem to us today, were once fully functioning technologies in their own right.
The main difference between this analogy and Nature is that Nature would appear to be highly efficient at using all the available resources and is the great recycler and adapter. At every level of life, even the microbial world, still have critical jobs to do. From the bottom feeders up: to ourselves and everything in between which is essentially made of stardust anyway, are part of one whole sustainable natural system. And perhaps instead of thinking of literal ancestors, i.e. the computer keyboard descended directly from the old Imperial Typewriters, and trying to find the missing link for what gave rise directly to the mouse and its imminent demise (nearing extinction apparently) and it has become an endangered species due to the superior advances of the touch-screen, we should perhaps see that the systems behind these innovations are fundamentally the same at every scale and it is this that is ancestral to them all.