‘DARWIN VS. D’ARCY’, a scientific alternative to Darwinism… Preview for Beta Readers… Available NOW!

Darwin vs, D’Arcy, Evolution by non-Darwinian Means … Beta Preview Available to view here

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Darcy vs Darwin new book cover

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Mariabrigit

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Everything is Scale-Dependent: “Something Universal is Going on…”(G. West – physics applied to biology)

nested-dolls-principle-of-evolution

”Everything around us is scale dependent…

It’s woven into the fabric of the universe…

It is truly amazing because life is easily the most complex of complex systems,…

‘But in spite of this, it has this absurdly simple scaling law. Something universal is going on …”

Johnson (1999, ‘New York Times’ 12th January, excerpts taken from an interview with G. West – physicist working on biological systems)

Link

Whether it be: the growth rate of any organism from a gnat to an iguana, and from algae to great oak forests: everything seems to be governed by universal laws of fractal-like nested scales of complexity. The  Sigmoidal growth & development ‘S’ Curve is one of those laws that Nature appears to abide by. See info graphic above for the Sigmoidal Growth Curve.

Growth models based on first principles or phenomenology?

…growth curves are almost universally sigmoidal…

West et al (2004, Introduction)

Link

As Physics begins to reunite with biology…for instance, as a result of his research, Geoffrey West (Physicist who collaborates with biologists) has come to the realisation that Nature is full of universal patterning that is predictable. As these identifiable scales of magnitude and fractal-like patterning are measurable, this is therefore a very powerful scientific tool which, can begin to reveal the previously unknowable aspect of growth and development: EVOLUTIONARY Species development.

GROWTH & FORM

There is something, an essential and indispensable something, which is common to them all, something which is the subject of all our transformations, and remains invariant (as the mathematicians say) under them all.

D’Arcy Thompson (1945, 1085)

Link]

The identification of the universal patterning embedded at every scale is not such a new concept. Indeed, there is a growing body of support for D’Arcy Thompson’s profound observations (see above quote) of the underlying nature of Nature. I have attempted to apply these universal scaling concepts (invariants) in an effort to discover a form of development we cannot so readily observe in real-time: the rate and patterning of evolutionary development of the species on every scale.

The initial investigation started with D’Arcy Wentworth Thompson’s (1860 – 1948) alternative evolutionary scenario (non-Darwinian) which could be best summarised as: SCALING LAWS EMBEDDED IN ALL LIFE & APPLIED TO THE DEVELOPMENT OF LIFE itself.

All in all, I believe that the above info graphic is the best summary that I can think to make regarding the essential essence of the discoveries made whilst researching the deep historical record of alternative evolutionary theories; naturalistic theories (and very much testable and empirically supported ideas of the past) which, I have come to believe, from simply following the evidence: has the potential to completely topple the entire Darwinian tree (roots and all).

The Search for the Laws of Self-Organization and Complexity

…A few deep and beautiful laws may govern the emergence of life and the population of the biosphere…

Kauffman (1996, 23)

Link

If you are interested in finding out more about the Matryoshka (nested scaling laws) and how this model applies directly to evolutionary complexity, it is detailed with clickable links to all the scientific literature in Chapter One of a newly published e-book. It is available for Free as I believe that the information is so important that it should be shared widely and with as much ease as possible. So all I ask, if you go for the free copy, is to SHARE WIDELY so that others can find this information and access it for themselves.
EVOLUTION BY OTHER MEANS..?

evolution by other means book one cover resized for smashwords.pngTHIS IS THE FREE KINDLE E-BOOK VERSION

Click on Cover above for your free Kindle copy (you don’t need a Kindle to read it – you can just download the free app for your mobile device/computer etc from Amazon’s online store).

When you click on the link, you will find out more information about the book and its contents and you also have the option to pay something for the book by simply putting in an amount – it has a secure paypal transation attached, but you don’t have to use paypal if you don’t want. Otherwise, just download it for free: $0.00 and you will have your own copy delivered straight to your mailbox and/or to read there and then.

For Other Version: E-Pub etc click here

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You can go on to Amazon where you usually shop and simply do a search for “evolution by other means..?” I could not sell it on Amazon for Free, so it is a cheap as I could possibly make it (99c excluding VAT).

Enjoy

MariaBrigit

NATURE’S 1st LIQUID CRYSTAL (QUANTUM) COMPUTERS?

This is a preview of Chapter Three from forthcoming book on Evolution by Other Means…?

DNA nebula molecule compared

CHAPTER THREE

Alexander Graham Cairns-Smith

(Born 1931)

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)

[54]

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 [55]; Genetic takeover – and the mineral origins of life, 1982, by A.G.,  Cairns-Smith, Cambridge University Press [56]; Clay minerals and the origin of life, 1986, by A. G. Cairns-Smith and Hartman, H., (eds.,), Cambridge University Press. UK [57] and, Seven Clues to the Origin of Life – a scientific detective story, 1990, by A.G. Cairns-Smith, Cambridge University Press [58].

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)

[59]

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)

[60]

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 snow flake 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 snow drop 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)

[61]

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)

[62]

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 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 coded 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)

[63]

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.

Protein Structure

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)

[64]

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 – recall the previous discussion in chapter two and 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)

[65]

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 bio-chemical 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)

[68]

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.

Kurakin (2009)

[66]

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…

Conclusion

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)

[67]

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)

[69]

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 how much code can be written from the arrangements and 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.

Karadaghi (2015)

[70]

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.

Virus Structure

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.

Davidson (2015)

 [71]

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 cozy (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)

[72]

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 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)

[73]

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 is 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)

[74]

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)

[75]

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)

[76]

The chiral pairs they are talking about refer 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

chiral molecule

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…

cholesteric mesophase

    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).

[77]

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 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)

[78]

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 where, 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)

[79]

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)

[80]

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, the liquid crystalline behaviour is very much context depend. .

The all-important behavior of certain proteins is further explored in the excerpt below in terms of the liquid crystalline properties and the fundamentally similar behavior 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

Conclusions

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)

[81]

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.

As discussed in Chapter Two (see preview of 1st five chapters), we know 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 such as the liquid crystalline condensed phase and a very dynamic system indeed as you will see below, leads us back to the idea that D’Arcy Thompson proposed that the most interesting discoveries are to be made on the borderlands of disciplines, where one science meets another as discussed in Chapter One. Similarly, the excerpt article above indicates that it is the interplay of the different forces on the borderlands of amino-acid and protein surfaces in the context of their environment that creates dynamic and very interesting results.

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]…

Conclusion

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)

[82]

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 on the borderlines or the interface between different fields of science (just where D’Arcy Thompson said we would find the most interesting answers). The science paper is entitled: Organisms as Polyphasic Liquid Crystals, in Bioelectrochemistry and Bioenergetics 41, 81-91, 1996 [83] 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)

[83]

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 [84]. 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) [85].

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)

[86]

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)

[87]

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)

[88]

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)

[89]

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)

[90]

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 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 super computing 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.

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The Scaled Fractal nature of Nature

William Blake

(1757 – 1827)

To see a World in

a Grain of Sand

And a Heaven in a Wild Flower

Hold Infinity in the palm of your hand

And Eternity in an hour…

-‘Auguries of Innocence’

My Fractal Journey

It all started, I suppose  now when I look back, when I was about seven years of age and standing in-line with the rest of my class (funny word to use – we don’t do grades in Ireland). It was the height of the ‘troubles’ and it was a convent school for girls right in the centre of it all. (I have given away my age and background here; perhaps a little too much). Anyway, what has this to do with my first fractal revelation?

Well, the setting is quite relevant, but the time may not be so. The room that we were all standing in was filled with lines of girls according to their age and class, and this room had a special name – ‘The Red-Room’  on account of it having a checkered patterned floor of red and pale coloured tiles. This room  should however, have been called the mirrored room as the two main opposing walls were adorned with massive gilded framed mirrors and of course, there was the expected statuette and other religious paraphernalia, along with obligatory singing high-pitched Nun vamping on the slightly discordant ivory keys (she was one of those rare fun-loving Nuns and her name was Sister Anne).

Some of you may have already guessed from the set-up, what I suddenly and profoundly came to understand – in what could only be described as a silent eureka moment;  remember, I’m only seven – so I don’t know any of this intellectually, nor do I have a language for it – at least not  until I was a very mature adult – my early education was really woefully poor – but you could say that all that I learned in that moment was good enough for anyone’s life-time and I was in school at the time.

Suddenly, everything came into sharp focus. The long sequential rows, on every scale, reflected in the opposing panes, ran to what seemed to be infinity in ever-decreasing lines of green-clad girls. Anyone who has ever studied fractals knows that self-similar patterns are reflected at scales within scales and the more you zoom into the deeper and smaller levels, you find the same type of pattern  reflected repeatedly. It’s just a matter of scale.

 

Mandelbrot_Set-Zoom_in
Mandelbrot Set Zoom CC. licence Wikimedia

I cannot put into words how profound this deep understanding of things, the world (before the usual indoctrination of how the world works according to the cultural dictates of our time) that came like an instant download in that moment. But it probably did guide me at some deeper level (after several years of research) towards an understanding of the inherent fractal nature of Nature. This brings us to one of the main players in a very distinct (non-Darwinian) but, dynamically  much more explicable model of evolutionary thinking (click on the title below for a short bio and a summary of his ideas along with some other forgotten theories of evolution in a related article on this site and/or read on for the summary of a more universal scaling fractal explanation of his concepts and how they relate to an over-arching alternative evolutionary model, which dovetails (fractally at every scale) with several other alternatives:

D’Arcy Wentworth Thompson

(1860 – 1948)

EVOLUTIONARY FRACTAL SCALING LAWS OF LIFE

 

D’Arcy Thompson was born the year after Darwin published his famous book On the Origin of Species. And in 1917 D’Arcy published his own quite famous book: On the Growth and Form and much extended and updated version in the 1940s (See Thompson 1917 [link] and Thompson 1945 [Link]). In his major treatise, he uses the known processes and principles of the physical sciences of chemistry, physics etc in conjunction with biology and by applying the language and tools of mathematics, he essentially quantified and established inherent patterns of growth and form that Nature appeared to consistently use in the production of even the most complex organisms.

He essentially, came to a distinctively different way of understanding evolutionary development and ultimate complexity by applying the main principles of the processes known to operate within non-biological complex systems, to biological systems and discovering that there was something universal underpinning them all, as indicated in his 1945 edition On Growth and Form.

There is something, an essential and indispensable something, which is common to them all, something which is the subject of all our transformations, and remains invariant (as the mathematicians say) under them all.

D’Arcy Thompson (1945, 1085)
http://archive.org/stream/ongrowthform00thom/ongrowthform00thom_djvu.txt

About D’Arcy
… the dynamic influence of starting conditions lies in the morphology of shells and horns. These are the permanent, non-living, three-dimensional record of a temporary, two-dimensional living state – the base of the horn, or the mantle of the shellfish. D’Arcy Thompson showed that all horn and shell morphologies could be described in simple mathematical terms readily derived from the incremental nature of growth… For instance, geometrical rules of packing determine cell arrangements. These need not be specified, but can arise spontaneously. Yet the packing arrangement may be “useful” in minimising the space occupied by the cells, by maximizing cell-cell contacts, by establishing different categories of cells (“inside” versus “outside”), and so on…

― University of Dundee and the University of St Andrews (2010)
Link

In other words, D’Arcy Thompson’s general alternative views on evolutionary processes were in principle based upon scaling laws of fractal patterning and these universals embedded in Nature,  led him to propose and apply a very different kind of descent with modification: as summarised in the excerpts given below taken from his epilogue of the 1945 edition On Growth and Form.

Note that protozoa refer to the entire kingdom of animals, and are four-limbed animals and that this is a later edition of D’Arcy’s book (1945).

On Growth & Form
…for eighty years’ study of Darwinian evolution has not taught us how birds descend from reptiles, mammals from earlier quadrupeds, quadrupeds from fishes, nor vertebrates from the invertebrate stock…
… Our geometrical analogies weigh heavily against Darwin’s conception of endless small continuous variations: they help to show that discontinuous variations are a natural thing, that “mutations” -or sudden changes, greater or less-are bound to have taken place, and new “types” to have arisen, now and then. Our argument indicates, if it does not prove, that such mutations, occurring on a comparatively few definite lines, or plain alternatives, of physico-mathematical possibility, are likely to repeat themselves: that the “higher” protozoa, for instance, may have sprung not from or through one another, but severally from the simpler forms; or that the worm-type, to take another example, may have come into being again and again.

Thompson (1945, 1093-95, Epilogue)

Link

In summary, D’Arcy Thompson seems to propose throughout all his chapters in relation to the main topics addressed, that biological life has followed the same fundamental processes inherent in other complex and naturally organising phenomenon and he believed that by tracing the intrinsic patterning and scale employed by Nature, we can begin to see the methods of producing continuous novel and increasingly diverse formations of shape and form that could be implicated in the great variety of species; and yet may be commonly connected by sharing underlying patterns of fundamentally similar properties and employing the same means of development to reach their own particular level of intrinsic complexity. How he arrived at his conclusions are best summarised below:

Transformations: The Visual Influence of D’Arcy Thompson
D’Arcy passionately believed in giving students as great a breadth of knowledge as possible, telling them if you dream, as some of you, I doubt not, have a right to dream, of future discoveries and inventions, let me tell you that the fertile field of discovery lies for the most part on those borderlands where one science meets another. There is a cry in the land for specialization. . . but depend upon it, that the specialist who is not reinforced by a breadth of knowledge beyond his own specialty is apt very soon to find himself only the highly trained assistant to some other man. . .
Try also to understand that though the sciences are defined from one another in books, there runs through them all what philosophers used to call the commune vinculum, a golden interweaving link, to their mutual support and interpretation.

Jarron (2013, 83-4).
Google books

For instance, as a result of more recent collaborations between physicists and biologists attempting to identify the obvious universals embedded in life (in the spirit of what D’Arcy Thompson had proposed as the most productive way to pursue scientific investigations), Geoffrey West and others have been led to discover consistent power laws, universals and invariants in Nature, along with fractal networks common at all scales and all of this phenomenon having predictable properties, led West to declare the following in the excerpts from an interview in the New York Times below:

”Everything around us is scale dependent…
It’s woven into the fabric of the universe…

It is truly amazing because life is easily the most complex of complex systems,’ …. ‘But in spite of this, it has this absurdly simple scaling law. Something universal is going on …”

Johnson (1999, ‘New York Times’ 12th January)
Link

The video below should give you a general insight into the type of research and the findings which point to the fact that underlying all of biological complexity are, surprisingly simple universal scaling laws governing fractal-like networks.

Perhaps, I should point out at this stage, that the more recent collaborations between physicists and biologists have led to the re-evaluation and acknowledgment of D’Arcy Thompson’s work and contributions to revealing the deeper complexity of biology, but they seem to take the cautionary approach to stating these laws and invariants of scale and form in more general and less emphatic terms than D’Arcy Thompson did as indicated below. They also do not go as far as re-assessing our current model of evolutionary complexity in the light of these findings as D’Arcy Thompson was prompted to do (but perhaps they don’t know about the fundamental flaws in our existing paradigm in the first place). If you are in any doubt, I would suggest reading the link to the readable quote book here , it’s a flip book and reads just like the real thing and see what an increasing number of well-respected scientists thing about the science behind the Darwinian form of evolution, particularly our modern synthesis):

Life’s Universal Scaling Laws
Although few today would articulate Thompson’s position so provocatively, the spirit of his characterization remains to a large extent valid, despite the extraordinary progress during the intervening century. The basic question implicit in his discussion remains unanswered: Do biological phenomena obey underlying universal laws of life that can be mathematized so that biology can be formulated as a predictive, quantitative science?
Most would regard it as unlikely that scientists will ever discover “Newton’s laws of biology” that could lead to precise calculations of detailed biological phenomena. Indeed, one could convincingly argue that the extraordinary complexity of most biological systems precludes such a possibility. Nevertheless, it is reasonable to conjecture that the coarse-grained behavior of living systems might obey quantifiable universal laws that capture the systems’ essential features. This more modest view presumes that, at every organizational level, one can construct idealized biological systems whose average properties are calculable.

West and Brown (2004, 36)
Link

Therefore, we could go one of two ways here and either acknowledge that even in the light of our more modern approaches to trying to understand biological complexity, D’Arcy Thompson’s model is still highly relevant; albeit as an idealised concept and useful for grasping the essence of biological systems and how they appear to work. On the other hand, we could take the position that D’Arcy Thompson took, based upon a much broader approach to the most up-to-date evidence from many fields of study and apply them to biological systems and restate his universal patterning of life in terms of biological laws that hold at every level in Nature – This is the underlying principle – The fractal Nature of Nature; the apparent driver and the underpinnings of the non-random directional change and the principle that makes meaningful and highly efficient forms, shapes and patterns in nature. See first five chapters of forthcoming book (needs final edit) to get an idea of how all this fractal scaling applies to biological complexity and by inference evolution.

final backcover info for evolution book one

In the aforementioned book, the scientific evidence has led to me taking the latter approach and as you will see: his dream of placing biology en par with the mathematical descriptions afforded physics and chemistry really do appear to hold across the entire spectrum and at every scale of life. They are quantifiable and predictable, not just descriptions of life, but a key to unlocking many of its mysteries embedded in the evolutionary process itself. In my mind, this is good science, as these laws and equations of scale can be tested and applied to find out things we could not otherwise directly measure.

For instance, by looking to fundamental properties within naturally developing non-biological complex systems, where, under certain conditions, rapid and profound changes can be brought about via catalysing the whole system in a single leap, D’Arcy Thompson applied this principle to evolutionary development and suggested that whole functional cellular life and its highly organised organisms could have come into being likewise a number of times under broadly similar catalytic conditions. He also understood that a very small change (initial starting conditions) at the beginning; can make a huge difference further down the line, reflecting yet another fundamental characteristic of natural complex systems. This led him to suggest that primitive life could have been triggered into taking fundamentally divergent paths by simply having different starting conditions.

D’Arcy Thompson suggested that as several distinct groups were discernible, based upon his study and observations of quite distinct body-plans and internal systems of a broad range of species, that these may represent the resultant divergent forms alluded to above. He referred to these distinct groupings of organisms as “discontinuous types”, meaning that Nature drew upon their underlying form and inherent systems to produce many scaled-up and increasingly complex versions of the same fundamental forms “Types” with degrees of modification according to the group’s intrinsic evolutionary potential.

Who Wrote The Book of Life?
Picking Up Where D’Arcy Thompson Left Off
NASA scientists are using Thompson’s biomathematical studies of life forms on Earth to postulate about life forms throughout the universe. There are certain universal conditions that will always affect the shape of a life form, wherever that life may be.”Everywhere Nature works true to scale, and everything has a proper size accordingly,” wrote Thompson. “Cell and tissue, shell and bone, leaf and flower are so many portions of matter, and it is in obedience to the laws of physics that their particles have been moved, moulded and conformed.” … Gravity, for instance, acts on all particles and affects matter cohesion, chemical affinity and body volume. Other influences that are consistent throughout the universe are temperature, pressure, electrical charge and chemistry.

NASA (1999, May 28th)

  Is the nature of Nature, simply a matter of fractal scales…?

DNA nebula molecule compared

What do you think?

Please comment, share and otherwise join me in this conversation if you are as fascinated,  as I am, by our Natural world and seek some serious answers, email me at: diggingupthefuture@gmail.com

 

Cheers Maria Brigit

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Epigenetic Antidote to the Selfish Gene

Find out why we need an antidote in the first place & why  Charles Darwin wasn’t to blame & how Mr. Richard Dawkins has a lot to answer for in readable flip book (just like the real thing): ‘Old Mr. Darwin Wasn’t to Blame: The Little Book of Evolutionary “Quotes”‘ You will discover what an increasing number of  scientists really think about our current theory of evolution…& get an idea of what might be replacing it.

3D old mr darwin book

and/ or watch the short video below.

Why we are living with Darwinism and why it matters…

This is part of a series which will review the history of why and how we are presently living with Darwinism and it will address why it matters. It is a historical overview and assessed in the light of to-day’s scientific understanding of the deeper complexities of life…

Darwin photo 1855

Darwin wrote in a 27 May 1855 letter:
“if I really have as bad an expression, as my photograph gives me, how I can have one single friend is surprising.”

John van Wyhe, ed. 2002-. The Complete Work of Charles Darwin Online (http://darwin-online.org.uk/)

CAMBRIDGE –ENGLAND – 1909
Darwin Celebrations
50 years since the publication of
‘On the Origin of Species’ & 100 years from his birth

Below is an excerpt taken from *Ronald Fisher’s notebook as quoted directly in AWF Edwards ‘Mathematizing Darwin’. (A. W. F. [Anthony] Edwards is one of Britain’s most distinguished geneticists. He studied genetics at Cambridge as one of the last students of R. A. Fisher, and like Fisher he has contributed actively to both genetics and statistics)

*Ronald Fisher along with JBS Haldane, & Sewall Wright- Founders of the Modern Synthesis

“I first came to Cambridge in 1909, the year in which the centenary of Darwin’s birth and the jubilee of the publication of The Origin of Species were being celebrated. The new school of geneticists using Mendel’ s laws of inheritance was full of activity and confidence, and the shops were full of books good and bad from which one could see how completely many writers of this movement believed that Darwin’s position had been discredited”

Edwards (2011, 422).

http://link.springer.com/article/10.1007/s00265-010-1122-x

cambridge-alt-lrg

Source: postcard View of Sydney Street: Circa 1910; Photographer: Unknown; Publisher: W H Smith Kingsway series.http://www.keytothecity.co.uk/postcard.php?Id=57&CityId=15&From=Students

RonaldFisher1912
R. A. Fisher born 1890 – died 1962 age 72

Fisher is known as one of the three principal founders of population genetics, establishing a mathematical and statistical basis for biology and uniting natural selection with Mendelian genetics, and as one of the chief architects of the modern evolutionary synthesis.

A W F Edwards argues that Fisher’s close links to Darwin’s sons, meant that he had the means to Mathematize Darwin’s theory:

Abstract
Ernst Mayr called the first part of the evolutionary synthesis the ‘Fisherian synthesis’ on account of the dominant role played by R.A. Fisher in forging a mathematical theory of natural selection together with J.B.S. Haldane and Sewall Wright in the decade 1922–1932. It is here argued that Fisher’s contribution relied on a close reading of Darwin’s work to a much greater extent than did the contributions of Haldane and Wright, that it was synthetic in contrast to their analytic approach and that it was greatly influenced by his friendship with the Darwin family, particularly with Charles’s son Leonard….

http://link.springer.com/article/10.1007/s00265-010-1122-x

In another paper by AWF Edwards he states:

Richard Dawkins named him “the greatest biologist since Darwin. Not only was he the most original and constructive of the architects of the neo-Darwinian synthesis. Fisher also was the father of modern statistics and experimental design. He therefore could be said to have provided researchers in biology and medicine with their most important research tools, as well as with the modern version of biology’s central theorem.”

http://www.genetics.org/content/154/4/1419.full

Regarding the founders of the population genetics, Berkeley Education website state the following:[they]
“… showed how natural selection could operate in a Mendelian world. They carried out breeding experiments like previous geneticists, but they also did something new: they built sophisticated mathematical models of evolution.”
http://evolution.berkeley.edu/evolibrary/article/history_19

Who was Mendel and how was he so important in the modern synthesis?

Gregor Mendel wasn’t the only one with an interest in heredity, and he wasn’t the first to work with plants. So why were his results almost unknown until 1900 and the rediscovery of the laws of inheritance?
The common assumption is that Mendel was a monk working alone in a scientifically isolated atmosphere. His work was ignored because it was not widely distributed, and he didn’t make an effort to promote himself. In actual fact, the reasons are more complex.
Mendel was part of the social and scientific circle of the time. He attended the University of Vienna, and came into contact with many prominent scientists. He had opportunities to travel to and attend scientific conferences. His paper, when published in 1865 in The Proceedings of the …Natural Science Society, was exchanged with the publications of at least 120 other associations and societies, and was available in many libraries and scientific institutes. In addition, Mendel sent out 40 reprints to some of the most famous botanists at the time.
https://www.dnalc.org/view/16189-Biography-4-Gregor-Mendel-1822-1884-.html

In ‘The Genetical Theory of Natural Selection’  A. W. F. Edwards (2000) states:

The Eclipse of Darwinism: It is difficult for us, as the century turns, to imagine the scepticism that surrounded Darwin’s theory of evolution by natural selection 70 years ago and astonishing for us to recall that Mendelism itself was regarded in some quarters as antithetical to it.
http://www.genetics.org/content/154/4/1419.full

It is really not that astonishing if you review the history and even the views of more modern scientists regarding the very real issues embedded in not only Darwin’s origial theory, but its genetically modified form. For instance, In 1914 Hugo De-Vries in  ‘THE PRINCIPLES OF THE THEORY OF MUTATION’:

…the basis, which the practice of artificial selection seemed to afford to the theory of natural selection, is a fallacious one, and that the idea of evolution by means of slow and imperceptible steps must therefore be abandoned.
— DeVries (1914, 80)
http://www.jstor.org/stable/1640345

The following excerpt below explains how de Vries and others were fully aware of Mendelian inheritence:

Hugo de Vries was born in Haarlem, Netherlands. He was a Professor of Botany at the University of Amsterdam when he began his genetic experiments with plants in 1880. He completed most of his hybridization experiments without knowing about Mendel’s work. Based on his own results, de Vries drew the same conclusions as Mendel. De Vries published his work in 1900, first in French then in German. In the French report there was no mention of Mendel, but this was amended by de Vries in the German paper. It is possible that de Vries read Mendel’s paper before he published his own, and included Mendel’s name in the later printing when he realized that other people also knew about Mendel’s work. De Vries may have thought that his own conclusions were superior to Mendel’s.
… He observed that the original plant would occasionally have offspring with significant phenotypic differences such as leaf shape and plant sizes. Some of the offspring would pass the new “sport” (mutation) to their progeny; these de Vries designated as new species.

It is now known that de Vries had the right idea, but for the wrong reasons. Most of the variants that de Vries isolated from Oenothera lamarckiana were due to aberrant chromosomal segregations, and not to mutations associated with specific genes.
https://www.dnalc.org/view/16222-Biography-6-Hugo-de-Vries-1848-1935-.html

In other words, bringing Mendel’s inheritance laws into the picture did not automatically mean that the Neo-Darwinian version of genetic mutations (which are very different to the leaping evolutionary speciation observed by De vries) give it any validity. Nor did the natural selection problem ever go away even if it was dressed up in fancy population models and statistically mathematised to fit with Darwin’s theory and Mendel’s inheritance.

In a nut shell: De Vries’ theory and several other distinctly different theories, rejected gradualism and the idea of selection. For De Vries, gradualism was certainly not the way nature produced speces, as borne out by his years of studies and experiments. Furthermore, he argued that natural selection did not have the power to produce new and novel variations and in some cases was actually detrimental to evolving a new species. This is clearly documented in the review of De Vries’ Mutation Theory in the journal SCIENCE dating back to 1910:

It has long been recognized that natural selection really explains, not the origin of species, nor even the origin of adaptations, but the elimination of the unfit, and the persistence of adaptations; the fact that characters, both adaptive and non-adaptive, specific or not specific, must exist before they can be selected was previously well nigh lost sight of. The mutation-theory, then, seeks to account for “the origin of specific characters” (p. 211). In the second place, “Spontaneous variations are the facts on which this explanation is based” (p. 45), or, “We may express the essence of the mutation theory in the words: ‘Species have arisen after the manner of so-called spontaneous variations’” (p. 165). This marks the fundamental distinction between Darwinism and de Vriesism. … from the standpoint of the theory of mutation it is clear that the role played by natural selection in the origin of species is a destructive, and not a constructive one.” … Mutations are characterized first, by being entirely new features, “In contradistinction to fluctuating variations which are merely of a plus or minus character (p. 213); second, by the abruptness with which they appear, and third, by being transmitted by inheritance’ without selection. They arise suddenly and’ without any obvious cause; they increase and multiply because the new characters are inherited”

——   ‘Science’, (May 13th 1910, p. 741)

http://www.jstor.org/stable/pdf/1634773.pdf?acceptTC=true

To find out just how right he was check out the following article:
https://diggingupthefuture.com/2015/08/10/part-two-if-it-didnt-happen-by-neo-darwinian-means-how-did-evolution-occur/

Our modern synthesis has consistently rejected leaps in complexity as a real fact of the fossil record. And Darwin’s species problem (how one species changes into another), remains unresolved as noted in ‘Resynthesizing Evolutionary and Developmental Biology’:

“The origin of species — Darwin’s problem — remains unsolved”

–  Gilbert, Opitz, and Raff (1996, 361)

http://www.evolbiol.ru/large_files/gilbert.pdf

See ‘Lamarck and the Sad Tale of the Blind Cave-Fish’ for more backgroud. https://www.smashwords.com/books/view/524805

(paperback version link) http://www.amazon.com/Lamarck-And-Tale-Blind-Cave-Fish/dp/178280465XI

Returning to De Vries, genetic mutations came to mean something entirely different to what De Vries had originally proposed. The modern synthesis now had a problem. If they had excluded any other means of changing a species, how was a species supposed to change? They did some experiments of genetic reshuffling of existing gene-pools of the same species and proposed that the only way to create genetic novelty (not employing De Vries’ ideas or any others who had demonstrate real, rapid and profound emergence of a new species) was to mathematically model the assumed rate of genetic mutations (mistakes in the copying process as genes are passed along the ancestral line) passed between populations, particularly those isolated and recombined gene-pools later down the line, and even though nobody ever seen a species change or become anything other than it was before (apart from some superficial type colour or variegated changes), they extrapolated this to all of evolution and based upon the assumption of direct ancestral relationships via linear descent from a common ancestor, attempted to demonstrate when one species gave rise to another (branching lineages and ancestral missing links were feverishly searched for) and calculated the timing of such assumed splits based upon the rate of genetic mutation (the molecular clock assumed to tick at the same rate for all species throughout evolution). Unfortunately, our ancestors may not be as common or related, at least not in the way we think and the genetic mutation (molecular) clock doesn’t appear to work that well:

DNA mutation clock proves tough to set

Geneticists meet to work out why the rate of change in the genome is so hard to pin down.

 In the past six years, more-direct measurements using ‘next-generation’ DNA sequencing have come up with quite different estimates. A number of studies have compared entire genomes of parents and their children — and calculated a mutation rate that consistently comes to about half that of the last-common-ancestor method.

A slower molecular clock worked well to harmonize genetic and archaeological estimates for dates of key events in human evolution, such as migrations out of Africa and around the rest of the world1. But calculations using the slow clock gave nonsensical results when extended further back in time — positing, for example, that the most recent common ancestor of apes and monkeys could have encountered dinosaurs. Reluctant to abandon the older numbers completely, many researchers have started hedging their bets in papers, presenting multiple dates for evolutionary events depending on whether mutation is assumed to be fast, slow or somewhere in between. (Callaway in Nature 10th March 2015)

http://www.nature.com/news/dna-mutation-clock-proves-tough-to-set-1.17079

 Furthermore, mutations don’t appear to bring about a new species, just deformed or dead things and population modelling used by the Neo-Darwinists has been described as numerology as seen in the following quotes by  LYNN MARGULIS

Neo-Darwinists say that new species emerge when mutations occur and modify an organism. I was taught over and over again that the accumulation of random mutations led to evolutionary change [which] led to new species. I believed it until I looked for evidence.-

— (Teresi 2011, 68) ‘Discover Magazine’ April edition

http://discovermagazine.com/2011/apr/16-interview-lynn-margulis-not-controversial-right

Mutations, in summary, tend to induce sickness, death, or deficiencies. No evidence in the vast literature of heredity changes shows unambiguous evidence that random mutation itself, even with geographical isolation of populations, leads to speciation.

 Margulis & Sagan (2008, 29) Acquiring Genomes: A Theory of the Origins of the Species

http://books.google.ie/books?id=DS-VehE00ncC&q=Mutations%2C+in+summary%2C+tend+to+induce+sickness%2C+death#v=snippet&q=Mutations%2C%20in%20summary%2C%20tend%20to%20induce%20sickness%2C%20death&f=false

When evolutionary biologists use computer modeling to find out how many mutations you need to get from one species to another, it’s not mathematics—it’s numerology.

Teresi (2011, 71) ‘Discover Magazine’ April edition

http://discovermagazine.com/2011/apr/16-interview-lynn-margulis-not-controversial-right

… Then how did one species evolve into another? This profound research question is assiduously undermined by the hegemony who flaunt their correct solution. Especially dogmatic are those molecular modelers of the tree of life who, ignorant of alternative topologies (such as webs), don’t study ancestors.., they correlate computer code with names given by authorities to organisms they never see! Our zealous research, ever faithful to the god who dwells in the details, openly challenges such dogmatic certainty.

— Margulis (2006, 1) ‘The Phylogenetic Tree Topples’
https://www.americanscientist.org/issues/pub/2006/3/the-phylogenetic-tree-topples

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Lamarck! Who mentioned the ‘L’ word?

all along...
all along…

In a recent paper entitled: Transgenerational Epigenetics: Current Controversies and Debates by David Crews and Andrea C. Gore, they outline the following under the heading: History of Epigenetics (2014):

Investigators in the field of epigenetics come from one of two distinct lineages, one derived from classic genetics and the other from evolutionary biology.[…] Preformationists believed that adult features were present fully formed in the egg and simply unfolded during growth; August Weissman belonged to this group and asserted that the eggs contained all of the elements (later known as genes) to determine the phenotype that would develop. Those believing in epigenesis held that traits emerge as a consequence of the progressive interaction of the constituent parts of the zygote with the environment in which it develops. Although others such as Jean-Baptiste Lamarck and Charles Darwin were believers in epigenesis, the pivotal role of the environment in the developmental process was first demonstrated empirically by Oscar Hertwig (1894) and subsequently by Richard Woltereck (1909). p. 372

http://www.utexas.edu/research/crewslab/pdfs/Crews_Gore_Chapter_Final.pdf

And Professor Denis Noble’s statement regarding his endorsement of an important collection of papers in book form entitled: Transformations of Lamarckism From Subtle Fluids to Molecular Biology, relating to Lamarckian principles of evolution and the epigenetic inheritance of non-genetic modifications (environmentally-driven adaptations) phenomenon clearly highlights the link to Lamarck and our current understanding of molecular processes in the following:


“This book is long overdue. Lamarck and Lamarckian ideas were not only ignored but actively ridiculed during the second half of the 20th century. As the subtitle of this book indicates, some of the most cogent reasons for reassessing those ideas come from within the citadel of molecular biology itself. A great strength of the book is that it does not seek to reintroduce Lamarckian ideas as they were originally formulated; rather, the Lamarckian perspective is used to assess where the modern synthesis needs extending or even replacing […}”(Noble 2011)

http://mitpress.mit.edu/books/transformations-lamarckism


Below is an excerpt from an article on Science Daily entitled:

Non-genetic inheritance and changing environments

Date:
November 1, 2013
Source:
De Gruyter

“Until recently, biological information was thought to be transmitted across generations by DNA sequencing alone. Furthermore, adaptation to the environment was thought to only occur with Darwin’s mechanism of rare mutations of the DNA that are selected for the reproductive advantage that they provide. However, scientists are now paying increased attention to non-DNA factors that are inherited and can actually help offspring adapt to their environment. An article published last week in Non-Genetic Inheritance — an open access journal by Versita, brings attention to this new mode of inheritance. The authors refer to a process called Transgenerational plasticity (TGP). Plasticity is a term used to describe how an organism changes its phenotype (e.g. morphology, physiology or behaviour) to adapt to its environment. For example, some animals become more hairy when bred in cold conditions. Transgenerational plasticity refers to offspring developing the adaptations, when the parents experience the environment.”

See link for full article http://www.sciencedaily.com/releases/2013/11/131101091739.htm

Now you might notice from reading the above quote from the science article, that if you know anything about epigenetics and Lamarckian acquired characteristics – as documented many times on this blog and the fact that Lamarckian evolutionary principles in more modern parlance – EPIGENETICS is synonymous with a radical new synthesis emerging within evolutionary biology, not once do they mention the ‘L’ (Lamarckian word) or even the ‘E’ word (epigenetics) for that matter. Yet Transgenerational plasticity which is non-genetic inheritance (epigenetic markers that change the expression of the genes without changing the DNA sequence itself) which is a highly adaptive (flexible plasticity) that all organisms have in-built and acts in response to their environments, is exactly what the article is talking about. Indeed, the article on ScienceDaily website quoted above goes on to quote Eva Jablonka – a scientist who has written extensively on EPIGENETIC inheritance and species adaptability according to environment by non-genetic means. Here is what she says in the article, but note the ‘E’ word is never mentioned, probably because many scientists are now concurring that it is essentially Lamarckian evolution in action.

“Commenting on the surveys, Eva Jablonka from The Cohn Institute for the History and Philosophy of Science and Ideas, at Tel Aviv University, says: “This excellent review raises pertinent questions about the adaptability of organisms and opens up important research questions. It is a vital contribution to our understanding on how organisms adapt to changing conditions, and I agree with the authors that trans-generational plasticity has to be considered if we are to predict the response of organisms to such conditions, an issue that seems to be of particular significance today.”

Please watch the short video where Eva talks explicity about the profound implications of epigenetics

Please, please, mainstream science promoters of the Neo-Darwinian genetic mutation driven evolutionary so-called synthesis, please stop this nonsense now and get with the wonderful new and diametrically opposite epigenetic (Lamarckian) synthesis instead. Darwin himself was certainly not opposed to Lamarckian type evolution (as documented in my blogs and books – see epigenetic caterpillar free e-book on site for example), so why have the Neo-Darwinists been so unjust in their suppression and ridicule of Lamarck? Well, that is another story, and again in some of my books and forthcoming works. Suffice to say, it is well documented and there is absolutely no reason why Lamarckian principles should have ever been subjected to the ridicule they have historically been exposed to. Furthermore, Lamarckian principles were updated and brought in-line with the deeper understanding of genetics (inheritance) around the turn of the 20th century and were gaining much popularity as the Saltationist/Mutationist (meaning large global changes seen in the development of cells and embryos could be extrapolated to understanding rather radical and profound changes in an evolving species in conjunction with its environment). I have written extensively on these alternative scientific and empirically testable ideas and experiments before the evangelising Neo-Darwinian movement began to take hold in the first part of the 20th century.

Cheers

Maria Brigit

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