Category: The Steps of Creation

#9 Spontaneous Order

by clarevmerry, posted in The Steps of Creation

“Since Darwin, we turn to a single, singular force, Natural Selection, which we might as well capitalize as though it were the new deity.” (Kauffman 1995, page 8).

Stuart Kauffman tackled the question of the origin of life and mounted a major challenge to the accepted belief that Natural Selection is the only source of complexity in biology in 1995 in his book, At Home in the Universe: the Search for the Laws of Complexity.  His research into mathematical models and computer programs showed that in serial computer programs almost any random change produces garbage.  Almost all small changes in structure lead to catastrophic changes in behaviour, and only redundancy allows some changes to be tolerated.  Taking the lessons learned in computer programming to understand the emergence of life, Kauffman concluded that the NeoDarwinist concept concerning the role of Natural Selection in this area is almost certainly wrong. 

Kauffman states that there are two fundamental limits to selection: firstly, in some complex systems, any minor change causes catastrophic changes in the behaviour of the system; in these cases gradualism does not help and selection cannot assemble complex systems.  Secondly, “Selection runs headlong into an ‘error catastrophe’ where all accumulated useful traits melt away.” (Kauffman 1995, page 183).  Thus, Darwin’s thesis concerning gradualism is wrong – that minor useful variations can be accumulated bit by bit over time to construct organisms that are able to adapt by mutation and selection (Kauffman 1995, page 152).

Natural Selection occurs, but it has always had a ‘handmaid’ that Kauffman believes is spontaneous order.  Thus, Kauffman ’s solution is self-organization as a precondition to evolvability.  There are limits to what selection can achieve.

“Were cells and organisms not inherently the kinds of entities such that selection could work, how could selection gain a foothold?  After all, how could evolution itself bring evolvability into existence, pulling itself up by its own bootstraps?”  (Kauffman 1995, page 188).

“Most biologists have believed for over a century that selection is the sole source of order in biology, that selection alone is the “tinkerer” that crafts the forms.  But if the forms selection chooses among were generated by laws of complexity, then selection has always had a handmaiden.  It is not, after all, the sole source of order, and organisms are not just tinkered-together contraptions, but expressions of deeper natural laws.” (Kauffman 1995, page 8).

So what is this natural law?

Kauffman introduces the concept of Emergent Properties; if you keep adding ingredients, at a certain threshold, a new level of complexity emerges.  The origin of life is a collective emergent property of “complex systems of chemicals” he states (page 19).  He believes that Emergent Order underlies not only the origin of life, but also much of the order seen in organisms.

Thus, for Kauffman the concept of Emergent Properties:

  • Is really the recognition that Natural Selection cannot explain the coming into being of everything concerning life.
  • Recognizes discontinuities in levels of complexity that demand a different explanation.
  • Is a rejection of Reductionism in biology i.e. the idea that the living organism as a whole can be explained by a description of the parts of which it is composed; the ‘nothing but’ explanations.

Concerning the origin of life, Kauffman believes that as the molecular diversity of a prebiotic chemical system increases beyond a certain threshold of complexity, an autocatalytic set of chemicals will arise that sustains itself and reproduces.  This would be a living metabolism.  Life is the collective property of systems of interacting molecules.  Whenever a collection of chemicals contains enough different kinds of molecules, a metabolism will crystallize from the broth. 

“If this argument is correct, metabolic networks need not be built one component at a time; they can spring full-grown from a primordial soup.  Order for free, I call it.”  (Kauffman 1995, page 45).

Kauffman, in his upbeat style, expected life to be synthesized within one or two decades.  He describes a model consisting of buttons and threads to illustrate the idea of connections between elements (buttons or dots) and a phase transition in which the whole becomes interconnected.

Kauffman proposes, concerning the origin of life, that as the diversity of molecules in our system increases, the ratio of reactions to chemicals becomes higher.  When the number of catalysed reactions is about equal to the number of chemical dots, a giant catalysed reaction web forms, and a collectively autocatalytic system snaps into existence.  A living metabolism crystallizes.  Life emerges as a phase transition (Kauffman 1995, page 62).

These autocatalytic sets apparently did not have DNA or RNA, and no genetic code (Kauffman 1995, pages 72-73, 275).  Kauffman attempts a scenario explaining how they can evolve without a genome. 

He writes, if we are to believe that life began when molecules spontaneously joined to form autocatalytic metabolisms, we will have to find a source of molecular order, a source of the fundamental internal homeostasis that buffers cells against perturbations, a compromise that would allow the protocell networks to undergo slight fluctuations without collapsing.  He concludes that it must be another case of order for free.

Kauffman rightly observes that one way to get such a network to behave in an orderly manner would be to design it.  But he proposes that autocatalytic metabolisms arose in primeval waters spontaneously, built from a random conglomeration of whatever happened to be around (Kauffman 1995, page 75).  Thus, a natural law must be found.

He investigates the behaviour of a dynamical system using light bulbs wired together randomly and blinking on and off.  The range of possible behaviours is the state space in which the system is free to roam.  When the system is supplied with an attractor, no matter what initial state it starts from, the system will run through a sequence of states, and settle into a same state cycle producing a repeating pattern of blinking lights.

In a large dynamical system, tiny attractors will trap the system into tiny subregions of its state space.  Among the vast range of possible behaviours, the system settles into an orderly few.  The attractors, if small, create order.  He states that tiny attractors are a prerequisite for the Order for Free that we are seeking (page 79).

According to the laws for orderly dynamics, a sparsely connected network K = 2 in which each light bulb receives two inputs and is assigned a Boolean function, will settle down into 317 states.  On the other hand, K = 4 or K = 5 networks exhibit chaotic behaviour.  Kauffman proclaims that this is Order for Free; such systems do not show sensitivity to initial conditions and they are not chaotic.  Once such a network is on an attractor, it will return to the same attractor with very high probability if it is perturbed.  This, he claims, is homeostasis (page 83).

In searching for a universal law of self-organization, Kauffman defines dynamical order as springing from a phase transition between stability and chaos; the most complex behaviours occurring at the edge of chaos.  Spontaneous order happens when a system “squeezes” itself onto tiny attractors (page 92).

Subcritical (orderliness) and supracritical (explosive diversity) regimes, and a phase transition drive the creation of molecular diversity in the biosphere, he concludes.  Kauffman proclaims that cells evolve to the subcritical-supracritical boundary. There is a supracritical biosphere and subcritical cells – and this is a new universal biological law!  (Kauffman 1995, pages 128-129). 

Kauffman suggests that most of the order of ontogeny[1] is spontaneous, a natural expression of self-organization that abounds in very complex regulatory networks.  Thus, biological evolution would not be the result of selection alone.

The real examples cited by Kauffman of “Order for Free” as opposed to the mathematical models he uses are as follows:

  • Crystals – a crystalline seed chooses and orientates the molecules that spontaneously link themselves to it causing the crystal to grow in a defined manner.
  • Snowflakes exhibit six-fold symmetry.
  • An oil droplet in water forms a sphere.  Lipids spontaneously form a bilipid vesicle in water. 
  • After viruses have been liquidized (broken up), they will self-assemble again as viruses because this gives them a lower energy state.
  • The patterns in pinecones and other plants known as phyllotaxis are generated by growth processes in the growing tips (the Fibonacci series).  (See footnote[2]).

Comment

I entirely agree with Kauffman that Natural Selection cannot put together organisms as the starting point for evolution.  Order is the condition for the occurrence of evolution; it cannot be imposed by evolution in terms of the origins of biological systems.

Kauffman writes that the living world is graced with a bounty of order.  I agree, but I do not believe it is ‘order for free’.

Kauffman combines poetry with science, he writes: the life around us must somehow be the natural consequence of the coupling of free energy in the universe to forms of matter.  How?  No one knows.  ………. Here is a mystical longing, a sacred core……..  “If we are, in ways we do not yet see, natural expressions of matter and energy coupled together in nonequilibrium systems, if life in its abundance were bound to arise, not as an incalculably improbable accident, but as an expected fulfilment of the natural order, then we truly are at home in the universe.”  (Kauffman 1995, page 20).  – I can see how this would have appeal for some people.

Kauffman puts forward the view of holism – that life emerged whole.  This is not mysticism he says, as if answering a critic.  However, it seems to me that this so-called universal law of self-organization goes with a type of new age belief in the earth as god: a type of pantheistic view.  I have gone into Spontaneous Order in depth because of the current popularity of this idea. 

John Maynard Smith[3] has accused Kauffman of practicing “fact-free science”.  Kauffman’s mathematical theories have a total lack of chemical details.

My opinion is that when Kauffman writes about order in the context of systems treated mathematically, order means featurelessness.  Its opposite is total randomness or chaos.  The use of Boolean canalizing functions produces pattern with order.  For example, an F = 2 system with Boolean functions applied as attractors will cycle through 317 states.  In my opinion this is not interesting order, it is sclerotic order characterized by simple repeating patterns.  It does not carry meaning.

The examples Kauffman gives of ‘Order for Free’ are simple, repeating patterns found in nature.  They all have an explanation.  They are due to the different types of bonds that may be formed between the elements that compose the molecules.  The last example of the pattern found in pinecones may be due to homochirality (left or right symmetry) in the carbon-based organic molecules of life.

Patterns have their own fascination, but these are simple patterns, not complex patterns.  I do not deny that patterns can be generated spontaneously, but they are only a relatively simple facet of reality; they do not carry complex meaning.  On the contrary, life is complex and carries meaning.

[1] Ontogeny is the development of an organism from the fertilized egg to its mature form.  Developmental biology studies ontogeny.

[2] One of the first people to recognize the patterns in nature was Alan Turing.  He presented the Turing Hypothesis of Pattern Formation, an example of which is Fibonacci phyllotaxis in a paper in 1952.  The paper consists of a decoding of nature in mathematical equations.  During the Second World War Turing worked as a code-breaker at Bletchley Park for the Allies.

Turing, Alan (1952) The Chemical Basis of Morphogenesis  Philosophical Transactions of the Royal Society of London  Series B 237 (641): 37-72.

[3] Smith J. M. (1995)  Life at the edge of chaos?  New York ReviewMarch 2, pages 28-30.

#8 Ribozymes?

by clarevmerry, posted in The Steps of Creation

Let us look in detail at the catalytic properties of RNA.  The single intron of the large ribosomal RNA of Tetrahymena thermophila (a ciliated protozoan) has self-splicing activity in vitro.  This RNA was named a ribozyme because it is an RNA that acts like an enzyme.   However, most, if not all other RNA-based catalytic reactions are thought to take place in conjunction with proteins.  Spliceosome and ribosomal RNAs have the ability to catalyse peptide bond formation, but they are better described as catalytic ribonucleoproteins than ribozymes since they do not make the role of proteins unnecessary.

Large ribozymes mostly include members of the group I and group II intron family found in algae, fungi and plants.  These are self-splicing introns.  Group I ribozymes use an external guanosine (G) nucleotide as a cofactor and group II ribozymes require an active site containing Mg2+ ions for catalysis.  Group I and group II introns self-splice under certain conditions in vitro, but require proteins to fold the intron RNA into the catalytically active structure in vivo.  The proteins are either encoded by the introns themselves or encoded by other genes (Allison 2007, pages 69-73 and 455-457).

Small ribozymes found in viruses and viroids act as riboswitches involved in gene regulation.  The other small ribozymes are involved in self-replication of the circular RNA of viruses (Allison 2007, page 75).

From this detailed account it can be seen that ribozymes represent a limited case found in a few organisms.  Intron-splicing by a ribozyme is catalytic and leads to modification of the RNA itself.  This characteristic contradicts the classic definition of an enzyme as being a substance that increases the rate of a chemical reaction, but is not itself changed in the process.  Therefore, a ribozyme does not simply act as an enzyme made of RNA rather than protein.

The autocatalytic nature of RNAs cited as ribozymes is highly questionable when one pays attention to detail.  It emerges that in vivo none of these RNAs act alone – their catalytic properties are dependent on proteins to initiate folding that makes the RNA structure catalytically active.  Therefore, RNA ribozymes do not act alone, but in conjunction with proteins.  It looks like proteins won’t go away.

I have not used the word hypothesis in connection with RNA World because it is untestable.  It is a speculation upheld by an almost mystical view of Natural Selection in which Natural Selection acts in a world of personified molecules that ‘want’ to replicate.  Shapiro accuses the adherents of these origin of life theories as creating a mythology whose truth cannot be challenged even in the face of adverse evidence (Shapiro, 1986, page 32).

“In the origin-of-life field, a particular theory or point of view is frequently elevated to the status of a myth.  It is then treated only as a doctrine to be validated, and not one to be challenged.”  (Shapiro 1986, page 33).

#7 RNA World

by clarevmerry, posted in The Steps of Creation

Watson and Crick published on the double helix structure of DNA in 1953.  By then it was known that the cell was not just a collection of molecules in cytoplasm bounded by a membrane, but a miniature world of metabolic pathways precisely regulated by an information-carrier: the DNA molecule.

Over the next decades, DNA replication was found to be facilitated by complementary base-pairing; the transcription of gene sequences was found to involve RNA and protein transcription factors; and the role of genes in regulatory feedback networks was investigated.  The composition of transfer RNA was determined by R. W. Holley in 1965.

It became apparent that the probability that the genetic system evolved by chance, even given the age of the Earth counted in thousands of millions of years, or even given the expanse and duration of the entire universe, is virtually nil.

Calculations showed that if mutation is truly random and unguided, any way of trying to derive a functional genetic system from it, ends in massive error catastrophe (Eigen and Schuster).  Probability became a favourite subject of Creationists and NeoDarwinists tried every possible way of getting round it.

There was also the chicken and egg problem under a new guise; DNA is transcribed, edited and translated by RNA, protein transcription factors and enzymes that are themselves DNA products.  Which came first, DNA or RNA and proteins?  In the genetic system of all known free-living organisms, no one component could have arisen without the other components.  Calculation of the probability that all the different components of the system arose by chance at once shows that this would be nothing short of a miracle.  Monod writes that the origin of the genetic code is a veritable enigma: 

“The code is meaningless unless translated.  The modern cell’s translating machinery consists of at least fifty macro-molecular components which are themselves coded in DNA: the code cannot be translated except by products of translation.  It is the modern expression of omne vivum ex ovo.  When and how did this circle become closed?”  (Monod 1970, page 135).

Thus, it was proposed that there once lived a form of life that was simpler than anything known.  The hypothetical first cell, the ‘progenote’, had a genome composed only of RNA.  RNA carried the genetic information and catalysed its own replication.  This proposition is called RNA World. 

The idea that there could have existed a form of life run by RNA was first voiced by Carl Woese in a book entitled The Genetic Code in 1967[1], and further elaborated in 1977.  The idea was again expressed in an article by Francis Crick in 1968[2].  However, the idea of RNA World was really put together by Walter Gilbert in 1986[3] after the discovery of ribozymes.  The hypothesis has had mixed fortunes, but it has now become very popular with its supporters speculating that at a hypothetical stage in the evolution of life some 4000 million years ago, life would have been represented by autocatalytic, self-replicating RNA molecules.

The central dogma of molecular biology – ‘DNA makes RNA makes protein’ – is therefore reversed by origin of life theorists, with DNA appearing last.

Investigations to support RNA World have included experiments to get single-stranded RNA to copy itself in a test-tube.  These attempts have ended in tangles of RNA and persistent failure.  Replication and single-strandedness appear to be incompatible.  The idea that RNA might have had a catalytic function in the place of protein enzymes has been encouraged, however, by the discovery that some RNAs catalyse chemical reactions in the cell.

[1] Carl Richard Woese (1967) The Genetic Code: The Molecular Basis for Genetic Expression  Harper & Row

[2] Francis Crick (1968) The Origin of the Genetic Code.  Journal of Molecular Biology Vol. 38 (3), pages 367-379.

[3] Gilbert, W. (1986)  The RNA World.  Nature Vol. 319, page 618.

#6 Miller-Urey Experiment

by clarevmerry, posted in The Steps of Creation

Great excitement was generated by an experiment performed in 1953 by Stanley Miller and Harold Urey.  They set up an apparatus containing methane, ammonia and hydrogen gases with water vapour to represent the hypothetical early Earth atmosphere and passed electric sparks through it to simulate lightning strikes.  In this reducing atmosphere, the heavy energy input breaks bonds in the gases, and upon cooling bonds reform giving new carbon products.  The broken bonds reassociate in a random way such that many different molecules are produced.  The most abundant product was tar, but there were also two simple amino acids, glycine and alanine in small quantities.  (The amino acid alanine has the formula: CH3CH(NH2)COOH).

Robert Shapiro alludes to his own experiments in which he heated various combinations of organic chemicals together as resulting in a dark, sticky tar.  He had hoped to produce the chemistry of life, but ended up with what he describes as a “gunky mess” (Shapiro 1986, page 206).  Tar is an organic material with excessive bonding.  It is a dead organic material that may originate from life, but it is not helpful to a living organism or as a starting point for life.

Shapiro gives a very good account of the experiments to discover the origin of life that have been conducted over 50 years of the 20th century.  However, he concludes that;

“The very best Miller-Urey chemistry, as we have seen, does not take us very far along the path to a living organism.  A mixture of simple chemicals, even one enriched in a few amino acids, no more resembles a bacterium than a small pile of real and nonsense words, each written on an individual scrap of paper, resembles the complete works of Shakespeare.”  (Shapiro 1986, page 116).

#5 Metabolism without Enzymes and Cell Membranes?

by clarevmerry, posted in The Steps of Creation

Clay Catalysts

Metabolic processes within cells are catalysed by protein enzymes.  It was realized that the formation of macromolecules had to be catalysed by something, and unless life pulled itself up by its own bootstraps these catalysts could not be enzymes.  So, it was proposed by A.G. Caines-Smith in 1985 that clay composed of silicates was the catalyst of protometabolism (see footnote[1]). 

Proto-cell Membranes

It was soon realized that since the entire sea could not function as a metabolism, it had to be compartmentalized.  It was observed that cell membranes are composed of phospholipids that naturally form spheres when placed in water.  So, it was proposed that the protocell was bounded by a very simple lipid membrane that formed spontaneously.  The problem with this simple model is that the protocell would be isolated from its environment.  The phospholipid membrane of the hypothetical protocell would not allow molecules that fuel metabolism to enter the protocell, nor would it allow toxic waste products out.  Isolation from the environment spells non-viability for cells.

The cells we know have a phospholipid bilayer plasma membrane with both embedded and peripheral proteins that regulate the entry and exit of substances into and out of the cytoplasm.  The selectively permeable cell membrane maintains a steady internal environment within the cell.  Water and some small molecules can cross the phospholipid membrane and follow their concentration gradient, but larger molecules such as glucose and amino acids, and also ions are assisted across the membrane by carrier proteins that are specific to each molecule or ion.  Transmembrane proteins include channel proteins, carrier proteins, cell recognition proteins, receptor proteins and enzymatic proteins and transport may be active requiring the expenditure of energy donated by ATP.

The conclusion to this short section is that simple membranes would isolate a cell, making it unable to function as a cell, and complex membranes containing channels and carrier proteins that allow the cell to interact with its environment are complex.

[1] Cairns-Smith A.G.  (1985)  Seven Clues to the Origin of Life  Cambridge University Press; Cairns-Smith A.G. (1993) Genetic Takeover: And the Mineral Origins of Life Cambridge University Press

#4 Primeval Soup Theory

by clarevmerry, posted in The Steps of Creation

The Primeval Soup Theory for the origin of life on Earth was first proposed by J. B. S. Haldane (1892-1964), a British Marxist biologist who lived in the USA and Britain, and Alexander Oparin (1894-1980) of the USSR.  It is the idea that life arose from inorganic matter under conditions proposed as having existed on the early Earth, but not existing now.

There are various versions of the Primeval Soup Theory differing in some details.  All must include a reducing atmosphere since organic macromolecules will not form naturally without it.  Hence it is proposed that the atmosphere of the early Earth was composed of methane, ammonia and hydrogen.  There was a sea of water formed from condensed water vapour.  The energy which would trigger the emergence of life came from flashes of lightning, ultraviolet radiation or even meteorite impact.  The effect of the light or heat energy on the atmosphere of strange gases would be the formation of organic, carbon-based molecules that would accumulate in the water which thus became a prebiotic soup.

It is now known that if the early atmosphere was so reducing that it did not contain any carbon dioxide, then the Earth would have been covered with ice.  The discovery of the exotic world of hydrothermal vents then led to the hypothesis that life emerged in one of the places on Earth that had reducing conditions in a limited location.

The primeval soup would contain carbohydrates the components of sugars; amino acids the components of proteins; and nucleotides the components of DNA and RNA.  Thus, it is proposed in the Primeval Soup Theory that all the ingredients of life were present as building blocks on early Earth.  It has been observed that the building blocks of life do combine with each other in predictable ways.  At this point the Natural Selection argument is used to explain that little organic molecules (monomers) have an advantage if they become big organic molecules (polymers) and if they learn to self-replicate.  The survival of the fittest idea is applied to molecules, which form themselves into a protometabolism whose function is to form new types of molecules.  The idea of the evolution of macromolecules was proposed by Francis Crick and Leslie E. Orgel in 1973.

Robert Shapiro points out that the proposed compositions of the atmosphere of early Earth and the ‘soup’ are hypothetical, and may never have existed at all.  He also points out that the water of this ocean would prevent the formation of biological macromolecules since water prises nucleotides apart from each other by breaking sugar-phosphate bonds and severing bases from sugars (Shapiro 1986, pages 173-174).  Thus, DNA and RNA macromolecules in water become nucleotide small molecules.  Also, in the presence of water peptide polymers and proteins slowly break down into their amino acid components.

It seems that, whereas in the world of speculation, ‘Natural Selection’ as the driver builds up complex molecules, in the real world thermodynamics breaks down complex molecules into simpler ones.

#3 Origin of Life: Theory and Politics

by clarevmerry, posted in The Steps of Creation

As far as the history of ideas is concerned, the notion that life can arise from non-life was linked to the rise of Communism during the 20th century and its atheistic underpinning.  It was a necessary corollary to belief in Dialectical Materialism that Soviet scientists find an origin to life that did not involve God.  Thus, origin of life theories of the 20th century stepped forward hand in hand with the political ideals of the day.

Soviet scientists claimed that just as Marxism shows that history must drive itself forward towards the triumph of Communism, the beginnings of life drove itself forward towards the colonization of Earth by an imperative logic.  Soviet scientists believed that the cytoplasm of the cell contained the means of running the metabolism of the cell (just as the worker’s collectives supposedly ran the Soviet Union).  They hotly denied that the genetic material found in the nucleus of the cell contained the program for running the cell.  They claimed that the idea that the nucleus runs the cell was part of elitist ideology.  DNA had been discovered by scientists in Western Europe and was therefore denounced as a capitalist hypothesis. 

It seems that history had the last word, since genes did not go away and Communism fell.  However, the idea that life arose by chance or by some natural means that did not involve God remained in circulation and became part of the official dogma of NeoDarwinism.