Its been difficult trying to work out a transitory phase from a bunch of concentrated amino acids and nucleic acids and simple biomolecules related to various early metabolic pathways, particularly iron sulphide and hydrogen, and then going from such an early, plausible humble 'soup' in a bubble, to the complex and smartly self regulating structures found in living cells, using complex transcription by proteins from embedded data (DNA) to RNA which then heads out of the chromosome, towards primarily the nucleolus where the RNA to transcribed to manufacture Ribosomes, which in turn our shipped out where they then take more mRNA which comes from the intelligent exposure and active copying by complex proteins on the DNA scaffold, and then finally transcribe the mRNA into proteins. Some RNA exists in a number of unknown forms and structures, some of which are very large molecules, and which have unknown functions. The RNA and the nucleic acid is in turn found in many complexes some large and some simple, like the 'energy' molecule, ATP. It seems likely that early biochemistry originates at vent sites and involves the chemistry of iron and sulphur to prooduce a proto-cell bubble that helps create the necessary conditions to concentrate hydrothermally generated organic molecules - namely amino acids, and nucleic acids, along with molceules like acetyl and methyl groups.

Why do amino's and and nucleic acids gather into larger molecules or polymers? Because they are more stable in more complex forms, and thats the observation of what happens to basic broths of these ingredients heated and pressurised in lab models of vent sites - the naturally formed amino's string up to form what are the basic components of proteins. The same seems to happen with nucleic acids, the building blocks of RNA.

So, the issue is the transition from primitive proto-RNA and protein, to a system where certain complex molecules survive due to beneficial interactions conducive to life, by an early mechanism essentially that of Natural Selection of surviving molecules.

Here we are conceiving not only of the proteins of living systems, but the dynamic RNA based world. The two are fused together. In my view, this 'ribo-proteome' runs the cell and predates the DNA system. DNA in my view is a result of the gathering complexity which must be being selected for in this early soup, leading towards a 'rebooting' system for reconstructing the ribo-proteome only when it decays beyond a certain point, as complex systems should do, leading towards a state of equilibrium, that whilst can seem rather diverse and complex, is not living. From this RNA model, we need a more complex DNA supersystem to act as a memory to help select and rebuild the functioning ribo-proteome.

It seems that the ribo-proteome emerges through a 'metabolic' process - an 'autocatalytic' decay that becomes fitter and fitter at interacting with chemical energy that normally decays the complex system, but gradually the complex system is induced to convert this mechanism into a self-selecting mechanism that pulls out and protects the more beneficial higher complex orders and structures in the cell.

We initially conceive of a concept in which bilogical, metabolic processes start to naturally emerge and are systems of stray entropy agents - AKA 'free radicals' that naturally try to arise in a topography, reflecting cell structure based on a bubble- the sort naturally found to form at vent sites and which have a number of curious properties that resemble life in those extreme systems. This may work by controlling which molexcules accumulate inside the bubble, and what passes through the membrane. The membrane structure is an electro-magnetic one as well, effecting forces inside the proto-cell and which have a selective and organising effect on what accumulates where (i.e. the iron-sulphur(?) membrane filters passing molecules or protons that are present in the hydrothermal system, and which attack the most vulnerable accumulating biomolecules (nitrogen conrtaining organics). The result however needs to drive a parallel selection of more complex structures, or even build nucleic acids and amino acids in vitro, that are selected for based on their capacity to inturn congregate with other molecules, and through increased structure, are both more stable and potentially 'fitter' in some overall capacity critical to further selection later on, as the system evolves. That further selection has to be based on survival of the emerging order. That in turn introduces a system of natural selection on evolving bubbles.

So what is envisaged is a heirachy of complexity, shaped like a pyramid, in which at the bottom, 'primitive end' we have the simple chemistry of metabolic pathways which are designed to capture stray 'free radicals' and convert them into a less destructive and potentially harnessable standardised set of by-products (i.e. electrons and protons), then a higher level of organisation in the ribo-proteome, which is like an inner wall in a 'city' in which all the structures represent levels of order and complexity. The entropy therefore occurs most towards the outside of the heirachy, and the organisation naturally selects, somehow, towards 'pushing' entropy out towards the simpler molecules, and leaving those of the ribo-proteome less vulnerable generally, This as we go through the lines of city defenses, we have less enemies marauding about able to cause damage(entropy) as we head up into the city (towards higher complexity) In practice this I think was loosely arranged in superstructure like this, with complexity naturally increasing towards the cell centre. If stray radicals make it past this inner line of defense, they can make it past to the castle ramparts - the DNA. In practice the DNA is not only made like a 'castle', but the analogy is that it is well defended by other systems that function like metaphorical 'antioxidants' soaking up free radicals. So it tends to survive whilst other systems, by being less stable, are thereby as a natural virtue of instability, more likely to interact and be altered / suffer entropy. The battle for order is a battle against that. The key is to think of DNA as a way for structure to 'hide' from most forces of entropy, and when entropy does come knocking on the door, DNA may actively 'rebuild' the structures in the rest of the cell that is more effective at intercepting 'free radicals', thereby automatically protecting itelf. So radicals move up the heirachy - when 'outer' lower order systems have decayed, higher order 'avoidant' systems then become the next line of defense, and as they decay, activate the highest line of defense, that is forced to interact, and thereby induce effects (i.e. in our sophisticated form, this is cell stress inducing DNA transcription). The question is, how does RNA interact to select for mirror copies of its own complexity (i.e. DNA), which selects out RNA complexity that happens to be effective in terms of controlling entropy in the desired way?

And before this even, in an RNA first-life model, how did RNA-protein interactions select for RNA sequences that selected the best proteins?

How did the complexity select the complexity?

What I think must be a general rule is that, in a complex system, interacting components that survive the longest, naturally select for this end result. The selection process is for molecule forms that interact with other molecules to create structures that get rid of 'radicals'. In so doing the survival qualities are that the molecule avoids interaction with the undersirable - something large molecules I think naturally do in these circumstances.

Those that both interact the most, and survive the longest, are in side some natural physics that would produce a selective pressure through entropy. The selection of organisation I believe boils down to the particular physical laws inside the proto-cell - that is, that they are not classical and are naturally the result of quantum phenomena, and that the earliest selection of complexity is based on the capacity of longer lived and more interactive molecules to 'tune out' of radical {i.e. proton) interactions that are destructive to it, or pass them through other complex systems, which as they decay, allow the rebuilding and stability of the complex system that runs the show, as a function of their very interactivity and stability, thus it is self breeding somehow, and is selective towards greater quantum interactivity through molecular structure and forces that this structure and entropy (metabolism, eventually) together help to create - creating also a physical natural selection in the i.e. magnetic fields set up at the molecular scale by cell structures and form with electron/proton movements, which supports these quantumly selected molecules.

The purpose of complexity in living energy systems, is to 'hide' from the effects of entropy, by displacing it to more unstable systems. The entropic forces, when they do arise in the complex system, tend instead to power interactions only of the selected form - the form converts the entropy into 'compatible' radicals and mechanisms, by forcing it through a 'filter' of more reactive, less stable structures, which the complexity actively rebuilds.

As entropy regenerates the free molecules for constructing larger complexity, a natural tendency towards self replication of certain 'fit' structures that naturally combine randomly, is needed to explain this, and still the missing component. This can be partly explained by the fact that replication results in more of a defensive molecule, protecting that complexity, as well as urvival of complex forms, which helps them to be more numerous than entropy should allow.



Check out the nucleosome, for an example of the packaging and organisation of DNA:

http://en.wikipedia.org/wiki/Nucleosome

"Several enzymes (for example, RSC, SWI/SNF) have been observed to change the position of nucleosomes in vitro.[12] Their purpose is to expose genetic information held within the nucleosome core particle when it is required by the cell. It has been suggested that remodeled nucleosomes not only have altered positions on the DNA template but have stable or semi-stable altered structures as well. These altered states may be necessary for transcription to occur."

WOOOSH. Right over my head.

Complex systems should decay. In life they dont, because life selects for complexity, due to the fact that those systems can reproduce, thus increase there effects on the cells, and a selective pressure in the cell weeds out those that aren't good for it as a whole, including its intitial structure and chemistry, which we think naturally accumulates biomolecules and makes them link up to form the first complex structures.

What these systems do, is divert forces of entropy (things which cause decay, 'free radicals' as people mean them) and divert them down paths of entropy, that take unstable, decayed (already reacted) parts of the system, and allows the complex system to replicate on it rebuilding the complexity in one system by imprinting it on another.

Selective forces have tended to create better complexities at doing this, but I also think its a natural physical property in the extreme circumstances of early life, for complex systems that can reproduuce, to be more productive to the stability and survivival of the others that are also naturally fittest at doing so, as well as themselves*, whereby an internal selection works very quickly and continuously, at the level of what entropies, and what becomes more complex and survives against normal entropic expectations (decay).

*so we've introduced an economics concept as well


What weve also said, is that this selection works through the local quantum interaction properties, and that those that are more 'fit' are natural prodducts of such weird physics, in some way, primarily, it effects the way identical molecules interact, and alters them such that they can effect, through their interactional wualities, the survival of themselves as well as those structures forming naturally in the soup, which also interact in their special way. Thus an 'energy club' has formed that is more stable and insulates itself with some of the molecules it interacts and combines with. These carry off the chemical sources of entropy or refine it into more useful, less destructive forms, that can be readily harnessed (i.e. as it became, proton and electrons in structured movements).

the larger molecules interact only in safer, more controlled ways, and those ways evolve to help themselves, as structures, and the group, through there particular ability to interact, and interact selectively (which assists stability and then forces entropic sources of selection, to being within the complex layer only (from complex molecules to other similatr complex molecules, and i thin this broadly trends towards survivability of larger complex forms and particular complex forms, which in turn, to survive, cannot be destructive to proto-cell structure, or else it will disolve. creating an external selective pressure. Coupling the early metabolic channeling of entropy to this cell survival (as chemical gradients and membranes) is an end result of this improving selection, conducive to the emergence of more powerful biological material and further selection of higher complex forms to be capable of then reproduction as they are coupled to the product of this.

We haven't really solved how at all, just examined the possibility of a co-selective pressure, an evolution of form, between the environment made by the cell and the components with in it, that allows for more complex forms to survive and influence in this way, subsequent forms (molecules, complexities). We are hypothesising that a selective pressure exists under the conditions within the proto-cell, to create the quantum conditions that allow for greter complexity through survival (and selection) of complex forms that emerge, and that there are feedbacks and co-evolutions of form as well, as the system ptogresses, build on early versions of decay that became metabolic processes.

So there is a quantumly influenced decay of complexity, that makes it a preferred form that can develop in the cell, because it displaces potential harmful interactions (that are entropic to that structure) to other systems. If this was naturally selected for in a particular, molecularly noisy, physical environment, then it creates the first glimpse of an explanation for how the universe was pre-configured to allow life and living systems, like those in the first post of this page, to emerge. I think McFadden at the University of Surrey may have proposed something along these lines for DNA, and so I must credit him with some inspiration if this turns out to be right.

Ther must be a better way of saying what I tried to say here - fortunately some of the basic ideas are well chewed on and McFadden does a wicked job of explaining them;



One really cool idea emerging is that the proto cell structure (maybe a bubble at vent sites) creates magnertic fields that make warm quantum mechanical interactions much more plausible - if so, I think what would bea result, is that the natural selection on these forms, is altered and that quantum mechanical properties of molecules in this scenario select for increasing complexity.

So there is a combining of natural selection of some 'fitter' structures, where 'fit' is based on their interaction with sources of entropy, with quantum mechanical properties of certain structures, and through QM interactions, an evolution of the order around increasing network fitness at converting forces of entropy into more active selection of complexity occurs.

This naturally leads to life, and the result is that life would be written as a natural outcome of the laws of physics where certain elements and conditions co-arise.

Quantum-selection of order, by the emergent order, in specialised scenarios, may explain these deep mysteries.

As the cell structure is selected for, its meatbolic and structural fitness increases - i.e. it generates stronger and stronger electro-magnetic fields - therefore, the special entropy that emerges in this system increases the environmental mechanism that helps the quantum mechanisms that lead to more selection and order. This means that the controlling systems in a cell are dependent on the setting up of a physical environment that allows for these magical interactions.

Don't really have anything to add, but wanted to say thanks for all the posts of this type, ATB. They're always an interesting read.

thanks, I'm amazed anyone can get through them, when I reread them I am frustrated that no matter how hard I tried, they have come across ambiguously and confusingly.

One of the specific predictions based on these arguments, is that in complex systems, the more complex parts have to be selected for an ability to 'avoid' harmful interactions with 'radicals' in their environment, which would be accomplished specefically through a tendency to select for interactions with similar as well as particular companion molecules - that is, as we go up the complexity scale, molecules tend to interact specifically with their 'own kind', because if they didn't, they would be subject to entropy so much that this level of complexity could not persist, and thereby accumulate via molecular interactions driven by general entropy.

This prediction was implied particularly to DNA....

Well, check this out, just discovered;




-the principle suggested could apply to even particular sequences of DNA as above. That is not very surprising, as we thought that such mechanisms that enable molecules to 'find each other', which are quantum mechanical, would work right down to the specific molecules that tag sections of DNA for replication and various specific sequences of RNA and individual mated molecules. The uses of moving tags and the DNA sequence itself is 'seeking out' certain molecules to interact with it, at the exclusion of others.

What I think is happening here in the above finding, although it is not a strong chemical reaction but rather electro-magentic interactions, is that an un-identical DNA sequence allows for unpaired regions to interact with other surrounding molecules - this in turn would increase the chances of electron transfer that could cause chemical/electromagnetic reaction of that DNA leading to its entropy. Since it is a storage medium, it must be designed to avoid such interactions. It does not appear to be a trial and error association, but rather molecules attached to the DNA have to compute together what bonds they can make as a group to other molecules, thus it pairs up with best matches rather than weak matches. When the pairings decay, this results from entropic forces but the design would facilitate the sacrifice of some order to protect the rest, and survives by channeling it elsewhere - higher systems survive by their relationships with other systems and their ability through these repeating interactions, to then exclude interactions that are harmful to that higher order structure.

So I think that the above DNA macro-molecules would naturally 'mate up' with the most similar molecules bercause such interactions become effective channels for them to receive potentially entropic energy, and pass this through increased numbers of bonds and thereby, it is fitter at survival as a union. This fitness is related to the number of bonds its more reactive areas can make to other long lived complex forms. These bonds manifest as an attractive force, and attractive forces work by allowing attracted components to have more channels to remove energy interactions that would drive the movement and decay of that component, thereby acting as a repulsive rather than attractive force. By working together, more complex systems set up particular reklationships which can act as conduits to pass entropic forces to other less stable sacrificial 'lambs' to which they may be connected. This acts as an energy pathway. When components receive an increase in energy, this manifests as an effective increase in the field of forces around in, generating change in order, entropy and repulsion. Attractive processes between components in any complex system I view as 'teams' that work to channel away sources of energy that would normally cause their order to change and degenerate, and that at the various scales, and at all scales in my view, local entanglement of the sub-atomic particles of their respective fields, result in these attractive processes. In this way, all universes in which objects condense and attract, will manifest quantum behaviors and via selective pressures, somewhere, the mechanism will eventually lead towards life.

Thus, the repeated interactions generate quantum interactions that enhance this avoidant property of more complex molecules (i.e. large DNA). The selection of selective behaviors is a result of evolution of any complex system like that in life (takes entropy to generate more order), and essential for it. That selectivity is manifest through quantum relationships.

Quantum mechanical behaviors are always enhanced and regenerated by isolation and repetition of particular interactions.

Biological molecules harness energy / vibrations (from electromagetic waves and electron motions from other molecules and particularly water) and convert it by channeling it through mutually exclusive networks until it 'reappears' in the normal entropic machinery found in the less complex, more reactive lower end molecular world, which is a sacrificial shield by virtue of its greater reactivity (inter-activity with ions and radiation).

I wonder if that latest finding on pairing DNA would suggest how DNA identifies regions to repair - damage to one would reduce local interactions and allow energy to leak out to similar molecules on 'receiver' molecules around the DNA. allowing damaged sections to be tagged for repair.



To go back to the complexity theories I'm trying to descrivbe, what we suggest is that in complex systems, longer lived, higher complexity hasd a tendency to interact selectively with only other, more complex systems, which in turn are selective. Thus selective systems tend to seek each other out, and as you go up the complexity ladder, and more long lived systems, yopu get more of this selectivity prejudice, thus forming a kind of higher-information network that seeks out the most similar discriminating order - a bit like a molecular aristocracy!