"A Man's a Man for all that!" - Rabbie Burns

"Religion? No thanks. I prefer not to outsource my brainwashing." - Bunc
Trying to get your average Joe creationist to understand the phrase scientific theory is as hard as getting a fish to enjoy mountaineering. Its an unimagined world for them - it requires a complete reversal of their normal modes of thinking and being. The fact that humans could explain the complexities of this world without a creating God is a world view they cannot grasp. It's like asking a tuna if it appreciates the view from the top of Mount Everest. Bunc

Mar 2, 2008

Complexity, Self organisation and evolution

In previous posts on the subject of the Evolution/ Creation debate I have as an aside made some remarks to the effect that I suspected that evolution through natural selection might be connected to some more fundamental properties of the Universe - in particular thermodynamics and entropy. I claim no great knowledge about these things but it has always struck me that life as a process has some interesting connections to these issues.

I wasn't aware at that time that there has actually been some studies and speculation in this field. I came across an interesting article which highlighted some research in the field of computational evolution.

The second law of Thermodynamics suggests that in a closed system the system will move to Thermodynamic equilibrium ( move towards maximum Entropy) and will be in its maximum state of disorder. However the real world at the local scale often does not function locally as though it is a closed system and we often see order emerging from disorder - crystallisation, snowflakes etc etc.

An article in wiredscience discusses some interesting work by Guy Hoelzer which involved computational modeling of population genetics. In his own words his approach;


..involves a different approach from traditional mathematical modeling: it allows us to spread a population across a large [and uniform] space in the computer model. One thing I find is that as mutation occurs in the system, it drives genetic divergences in a spatially localized way. I get spacial self-organization. One sub-species dominates in one place; a different sub-species in another place. If I allow genetic incompatibilities to evolve through mutation, we get speciation. Speciation is a process of self-organisation of the gene pool; in this case, it's not driven by adaptation to environmental conditions.


In other words he sees evidence of the "computational organism" beginning to show evidence of speciation even without selective pressures from the environment or from interaction with other species. This begins to sound more like an emergent self organising feature of a complex system rather than the traditional Darwinian process of natural selection.

It is interesting to speculate if life may have at it's core some fundamental self-organising and diversifying principles of this nature which are then magnified by natural selective processes. Another paper at wired science makes a broader case for a further revision of current evolutionary thinking using concepts of complexity theory.

( Note to readers - you will be disappointed if you think that any of this lends weight to Intelligent Design)

Update: Here's another article about the issues of complexity

9 comments:

Looney said...

Just regarding the second law and closed systems, and, well, mechanics being my specialty ...

The classical form of the second law is formulated with respect to a closed system. The more generalized and practical one used in engineering is for open systems, and includes a surface flux term to take into account the effects of a system not being closed to the surroundings. If the surface flux term is zero, than it reduces to the classical closed system form.

If we take are control volume to be a sphere centered about the solar system, and then increase the radius and look at what happens to the terms, then the surface flux tends to become negligible compared to everything else and the effect is nearly identical as for a closed system. Thus, the argument against the second law - that it is only valid for a closed system - is basically a technicality.

Bunc said...

I make no claims to understand all the theoretical background in respect of the different uses of the concept of Entropy and the Second Law. ( I gather there is some debate also over whether Entropy is fundamental or derived)

However given the little that I know it interests me because at first sight Life seems to run "against the grain" in the sense that it constructs order from disorder by harnessing external energy.

Clearly no real life system can be truly closed because, trivially one could always take a larger scale frame of reference and then consider this to provide the external environment to the system under consideration.

I think when we are considering life on this planet it is clear that the system operates, at this scale and on the timescales within which living things operate, as an open system.

The Earth is an open system in respect of the energy received from the Sun - from which ultimately life takes energy in order to produce complexity. (Ignoring chemotropes - life that uses purely chemical sources of energy.)

What interests me is that we see other examples of local systems producing order from disorder ( snowflakes etc) although to do so there clearly has to be an increase in disorder elsewhere in the system. These examples of "spontaneous" organisation interest me because it shows that given basic physical laws and chemical interactions localised complexity can arise.

This gets me wondering if this same process somehow underlies life and that natural selection then acts to further refine that complexity in terms of it's fitness to reproduce in that system.

I saw a recent documentary of a mine ,in the Swiss Alps I think it was, where they had uncovered a chamber filled with gypsum crsytals metres long and wide.

Clearly such conditions would only probably have just been right to produce such an event perhaps once or twice in the Earths history. The conditions clearly had to be just right to allow such localised complexity to develop.

I suspect that Biogenesis is like that - the localised conditions must be just right but that if they are then some self-organising process allows complexity to develop.

I must read up on all this.

By the way I am currently reading "The Road to Reality - a Complete guide to the laws of the Universe" by Roger Penrose. My Maths is rusty but I am gradually ploughing my way through it. ( Its over 1,000 pages so not a one night read!) Have you read it?

I read one of his previous books "The Emperors new Mind" which essentially, if I recall correctly, culminated in him developing an argument that Quantum effects in certain cell structures may be responsible for "free will".

Looney said...

Wow, 1,000 pages on the laws of the universe! Good luck on completing it. I have a few thousand pages awaiting me already, so it probably won't end up on the reading list soon.

We have bifurcation theory in mechanics which is related to the formation of different species in the form that the article seems to be using. The mathematics comes in useful for constructing buildings, but also explains why you can't crush a beer can the same way twice in a row! Some of the properties can be quite fascinating.

Bunc said...

Reading some stuff on fractals and Chaos theory a long time ago I think I recall something that was related to bifurcation theory - is that so?

Looney said...

It seems to me that there is a relationship between fractals and Chaos theory on the one hand and bifurcation on the other, but I must admit that I haven't really gotten too serious about the mathematics. It doesn't directly impact my job, so I try to know just enough in case I run across a situation where it might be useful and I need to dig further.

LoneRubberDragon said...

The statements that the earth makes an open system under the sun is quite true. Light energizes biochemistry, allowing new chemical species to form. Biological chemicals most easily form diverse species of "digital" chemical bonds in DNA, RNA, and protien, forming "quantum code" polymers, allowing, expecially among protiens with polar charge, fatty, hydrophobic and hydrophylic reaction centers, for numerous low energy reactions, catalysis, and chemical species. My blog, LoneRubberDragon.blogspot.com, section 3 Evolutionary design schematically outlines numerous examples of orders arising from simplicities, quite naturally, in locally energy open system processing.

LoneRubberDragon said...

I can add a post on the general theory of combinatorial chemistry:

ABIOGENESIS CHEMICAL EVOLUTION

BACKGROUND
A combinatorial chemistry feedback in an open system, with hypercycle catalytic reactions, alone, can suffice to create an increasing complexity inorganic chemistry that eventually intersects biochemistry, in naturally inherent reactions contained in a natural combinatorial chemistry in feedback.

COMBINATORIAL CHEMISTRY 1
[1a.0] Now combinatorial chemistry can be generalized to chemistry that combinatorially explores all possible interactions of all chemical species available in a chemical environment, like an early earth ocean bay, with tides, hydrothermal vents, sunlight with or without UV, dark areas deep in the water or under rocks, for protection from UV and sunlight, lightning, pH variation, evaporative concentration, and currents to mix a natural initially inorganic chemical soup with hundreds of minearls, metal ions, etc. in a preorganic molecule soup.

HYPERCYCLE CATALYTIC CHEMISTRY
[2.0] Hypercycle catalytic reactions are subsets of the combinatorial chemistry, where, A helps catalyze B helps catalyze C helps catalyze A, from other present chemical species, as an example of a short hypercycle loop of three nodes. [2.1] Hypercycle catalytic reactions can be loops, and networks, embedded within a normal combinatorial chemistry.

COMBINATORIAL CHEMISTRY 2
[1b.0] Going back to combinatorial chemistry, let's say in the ocean there's to begin with, 1000 Species of chemicals and chemical inducing factors, S, such as hydrogen ions as acid, water molecules, methane, dissolved minerals, metal ions, photons of light from infrared to UV, radioactive particles in early half life rich early earth materials from its recent supernova formation, different energy free electrons from lightning, lipids, amino acids from lightning, heating and cooling around hydrothermal vents, simple sugars, etc.. [1b.1] There is an approximate top level pseudocode (which can be glossed over to reach final math characteristics after the pseudocode) of a differential equation that shows the equilibrium balance of reactions, is:

[1b.2]
InitialSpecies = S;
InitialAverageConcentration = 0;
for(s = 1 to S)
{
InitialAverageConcentration += Concentration{s} / S;
}
for(s = 1 to S) //how many species in a reaction
{
__Reaction = array{s elements};
__for(s1 = 1 to s)
__{
____for(s2 = s1+1 to s)
____{
______for(s3 = s2+1 to s)
______{
... //nest to depth of s
______________for(ss = ss-1 to s)
______________{
________________if( all sx < sx+1, and all sx != sy) //no repeats
________________{
__________________//calculate net chem species present change
__________________//for this specie reaction set for a unit of differential time
__________________NewSpecies{S' set} = F1(Reaction{s1,s2...ss});
__________________NewConcentration{S + S' set} = F2(Reaction{s1,s2...ss});
________________}
______________}
... //nest to depth of s
______}
____}
__}
__FinalSpecies = S + S';
__FinalAverageConcentration = 0;
__for(s = 1 to S + S')
__{
____FinalAverageConcentration += Concentration{s} / (S + S');
__}
}

[1b.2] Linguistically, this can be interpreted as, taking 1 to S chemicals at a time, in every combination, to observe reaction rates of current S chemical species, s at a time, to see the effect on all S and possible new S' chemical species generated that were previously not existing before. [1b.3] For example, for two species taken from a given 1000 species, S, we see there is (1/2)*(S^2 - S), or 499,500 Reaction{s1,s2} nodes, with positive or negative reaction rates for existing species S, or new species of S'. [1b.4] That is, say, S1 + S2 might breakdown S1, catalytically by S2, into S3 and S4, and S2 remains untouched. [1b.5] S1 has a negative reaction rate as it breaks down into trace amounts of S1, while S3 and S4 have positive reaction rates, as S1 is turned into S3 and S4, in the presence of S2. [1b.6] On the other hand, say, S1 + S2 helps produce a totally new chemical outside of S, of S'1, by S1 and S2 combining to form S'1. [1b.6] S1 and S2 have negative reaction rates being consumed, as the new S'1 has positive reaction rates. [1b.7] These reaction rates also change in time, as the concentrations used by F1(Reaction{s set}) and F2(Reaction{s set}) calculations, increase or decrease accordingly. [1b.8] At the same time, there are more reactions to analyze, continuing with three chemicals in a Reaction{s1,s2,s3} analysis, where there is (1/2)(1/3)*(S^3 - S) or about 167 million reaction nodes. [1b.9] So of these millions of Reaction{s1,s2,s3}, many will have no effects, some will break down or build up products already existing, and others will make new chemical species that never existed before, from the species that exist in the ocean to begin with, S. [1b.10] Mathematically analyzing combinations from s = 1 for single molecule auto-reactions, to s = S, for S species of initial chemicals, in total, there are:

ReactionNodes = SUM( s=1 to S: of: Factorial(S) / (Factorial(s)Factorial(S-s)) ), or

ReactionNodes = 2^S - 1 = 2^1000 - 1 = 10^301 reaction nodes for 1000 chemical species S, where,

(1) the majority of non-reactions change nothing, (2) some break down species, (3) some build up species, and (4) some generate new chemical species. [1b.11] So starting with 1000 chemical species, with an S' formed out of 10^301 of, say, 1000 new chemical species S' (a conservative rate of 1 in 10^298 being effective stable new chemical species), such that in a year, there can be 2000 species of flourishing chemicals, leading to 10^602 reaction nodes to analyze for all potential reactions at each node, generating, say, 2000 new species of chemicals (at an even more conservative rate of new chemical specie formation). [1b.12] So then after another year there's 4000 chemical species at some concentration, with 10^1204 reaction nodes, generating, say, 4000 new species (even more conservative to the combinations available), added into next year's variation. [1b.13] So one can see an exponential feedback of chemical species, some more robust than others, in numbers, durability, variation, reaction rate selection forces, hypercycle catalytic reproduction, and reactivity, from 1000 to 2000 to 4000 and so on, until there is a low but signifigant saturation of millions of reactive catalytic various chemical species in a gallon of ocean, all competing for the ocean's limited chemical resouces, and giving rise to potential natural metabolic pathways absorbing glucose and photons of light, in complex reaction sets, paths, cycles, and netowrks, that support reproducing hypercycle networks of catalytic chemicals, all inherent and naturally contained, in the combinatorial chemistry feedback matrix growing in time.

[1b.11] A Cretionist claim would have to show that of the 10^301 reaction nodes, in a 1000 chemical specie example ocean, would permit no (zero) new chemical species to form and thus remain in static chemical equilibrium. But given the massiveness of potential in 10^301 reaction combinations in a mixing ocean of a combinatorial chemistry in feedback, if it shows even a very minor positive rate of new chemical species formation, such a non-zero feedback would provide a numerical backbone to natural blind chemical evolution turning into life, as chemical species reach continually higher levels of complexity and variety, with competition and selection forces, in the combinatorial chemistry in feedback, from the very beginning of chemistry, in robust reactive new molecules, contained in chained catalytic reactions, and with a form of digital chemistry, contained in the discrete chemical species, and in the discrete codes of polymer proteins, RNA, and DNA nucleotide chains, that are eventually intersected by combinatorial chemistry, with a proven positive dS/dt.

Even just 100 chemicals in an ocean, would allow 2^100 or 10^30 possible reactions, so even small chemical soups start with an inherent potential for new chemical specie feedback growth of complexity, without external guidance being absolute necessity.

REFERNCE MATERIAL
Clay catalyzation of RNA polymerization, and adsorbtion release characteristics, and protocell theory:
http://www.rpi.edu/dept/chem/chem_faculty/profiles/pdfs/ferris/ELEM_V1n3_145-150.pdf
http://www.ncbi.nlm.nih.gov/pubmed/11539614
http://exploringorigins.org/protocells.html

Hypercycle chemistry:
http://en.wikipedia.org/wiki/Manfred_Eigen

Combinatorial chemistry:
http://en.wikipedia.org/wiki/Combinatorial_chemistry
http://en.wikipedia.org/wiki/Oparin
http://en.wikipedia.org/wiki/Abiogenesis

Miscellaneous:
http://en.wikipedia.org/wiki/Miller_urey
http://en.wikipedia.org/wiki/Abiogenesis
http://en.wikipedia.org/wiki/Astrochemistry

Bunc said...

Hi Loneruibberduck,
Thats a hell of a name you got there by the way.

Your detailed comments about combinatorial chemistry and the complexity of the reactions that emerge is very interesting and exactly the kind of thing I have in mind when talking about the emergent properties of complex systems.

One of the things that I didnt see referrred to specifically in your comment was the evidence that certain relatively simple biochemical chemicals apparently have the ability to self catayse their own production. Its not hard to envisage then that an early chemical soup can products emerge from reactions which then begin to ratchet up the ladder of complexity on the way to life.

LoneRubberDragon said...

Well, in a subtle way, sentence [1b.10] refers to just such autocatalytic autoreproducing properties, when analyzing single molecule self reactions. But a hypercycle catalytic chain of A+b1+b2->A+B, B+c1+c2->B+C, and C+a1+a2->A+C, is also self reproducing, in the sense that all three example nodes inherently cooperatively help each other reproduce, and all it takes is to naturally have a Reaction[s1,s2...s8,s9] that achieves this feat, inherently embedded within all of the combinations of (2^ChemicalSpecie) of full combinatorial matrix reaction nodes.

Likewise, one can explain the arrival of a "complex" photosynthesis, by a chain of reactions that capture a photon, and form a glucose through even a complex route of reactions that can be circuitous through the larger 2^S matrix, and the glucose can help in other networks build the same molecules that perform the photosynthesis in the first place. So here, a large network of hypercycle catalytic reactions supports itself, of great complexity, as a mathematical reaction object contained in 10^301 reactions super set. For that matter, metabolism and protein, RNA, and DNA hypercycle catalytic and reaction networks of the most symbiotic feedback digital polymer codes, for the whole system, can be developped the same way, where their efficacy makes them numerous in forward reactions and mutual-reactions.

And it is actually a simple experiment to make, and surprising that it isn't known 60 years after Miller-Urey, because now it just takes adding 100 to 1000 presumed natural chamicals to a giant box with circulation, simulated deep sea vent, lightning, and fake sunlight with UV, and shady spots simulating rocks, and then pull out a tiny soup sample every day, and run it through a mass spectrometer, to see the weights of various molecules, and see if the numbers of chemical species grows in complexity, and at what rate complexity feeds back on itself in the CombChem matrix, or prove the Creationists claim, that it reaches a finite, and sub-living, steady state chemistry after some time, for example where the feedback specie rate of dF(10^301 [reaction nodes])/dt <= 0.00000....00000. Why it hasn't been performed as an experiment, yet, given the tools of today, is somewhat suspect, but it is easy. It would clarify the coefficient of feedback for different size populations of chemical soups.

LoneRubberDuck!? *blushes* Yeah, it *is* a name, definitely *grins*. I like that, reminds me of the Duckie character in the great little 80's movie, "Dream a Little Dream" ... which always gets me a little misty at the end.

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