Tuesday, June 23, 2015

Problems Of A Paper Advocating 'Dynamic Kinetic Stability' Theory In Light Of A New Virtual Closed System 'VCS' Theory

I discuss the problems of another theory called "Dynamic Kinetic Stability” or DKS, which is described in a paper by R. Pascal, (see below) as “..a stability kind specific to persistent replicating systems and derived from the dynamic persistence associated with exponentially driven self-replication.” I mention the paper in the context of my Virtual Closed System theory (VCS) and  "Indifferent Time" (links below) that refute not only 'maximal flow' but also so-called chemical selection, and natural selection coupled energy dissipation theory.
"Does Life Violate The Second Law Of Thermodynamics? Implications Of Virtual Closed Systems" MKK

"I Propose A Challenge To Maximal Flow Theories By A New Theory: Indifferent Time" MKK

This appears to be one of the first papers I’ve encountered that attempts to somewhat boldly account for the chemistry i.e. with a kinetic stability theory, in addition to the thermodynamic problem relating to life’s origins. It is one of the few papers that appears to be rather honest about the fact that the problem at hand is immense, and that self organizing processes resembling pre-transitional states of life would likely not resemble life in terms of thermodynamics and the normal processes by which free energy is lost. It does not rely on far from equilibrium “smoke” to fill in the gaps. A general comment regarding the impetus for many of these papers: I have to wonder if it is not so much a driver of life that is sought but a new mechanism for creating a grander illusion that the problem is near fixing. Fool the reader into believing that your equations are formidable enough to be “possible” and plug enough references, and one can make at least a case, so in this sense it is true evolution if not of the theories themselves. At least there were several cases where this paper described the holes.

But returning to the problem at hand. The paper itself is not without major issues. Most of the diagrams in my view; for example the catalytic chains contrasting traditional enzymatic pathways or cycles vs theoretical kinetic cycles that might drive molecules forward, are essentially depicting a theoretical chemistry that must be occurring in nature. It does not realistically account for what that might entail, as there are not simply chemical competition occurring, as physical draining of energy, dissipation and other random processes found in any natural setting. These are omitted. The conclusion from these diagrams is that nature must be doing chemistry, useful chemistry, and making useful molecules with higher free energy, (in thermodynamic terms) just as one would expect from a chemical factory. Can nature do this? And where is the proof of concept at the most basic molecular level?

The other major weakness of the paper is that it fails to answer many of the other theories that are in existence, namely that self-organization is possible in lightening bolts, eddies, concentration gradients and so on. The emphasis on Lotka and other references, which have purported to show stability of critical molecular species like triplet RNA, coupled with so-called energetic expressions for fitness, is to me a non-starter. It at least admits that if you had in theory, A, B, and C groups of evolving molecules like RNA’s and others, how would one in theory show that any of these would not circumvent the process by reacting counterproductively to lower free energy rapidly and bring the system to thermodynamic equilibrium? That would be the problem of “persistence.” The amount of time required for some of the more organized species allegedly, to remain unreacted for a time to allow a different process to commence.

“On the other hand, indications from previous reports [16–22] and supported by our present analyses (Scheme 1) have shown that a form of stability that is different from thermodynamic stability is needed to understand how far-from-equilibrium chemical states may have gained a form of persistence, thereby opening the possibility of self-organization toward life.”

The paper concludes that essentially: “Irreversibility and the kinetic power of reproduction seem to be, at least in principle, sufficient to allow the emergence of life and there is no need to seek out some hitherto unknown physical law to explain the origin of the specific behaviour associated with living organisms.”

It concludes that the catalytic and kinetic aspects should not be overlooked, but are important in addition to thermodynamic (self-organization) and even 'chemical selective processes'. It further concludes that vaguely all of these must be considered simultaneously. It then gives a reasonably good summary of two basic problems facing the study, understanding abiotic formation of feed stocks or organic building blocks present in abiotic processes, but then the more difficult issue of how these would be driven to self assemble. A final distinction is made between Boltzmann’s chemical based theories the chemical world that is known, and its own theory of DKS dynamic chemical stability (“..a stability kind specific to persistent replicating systems and derived from the dynamic persistence associated with exponentially driven self-replication”), as though these are separate entities and yet there is no physical evidence in the paper or any other sources, for DKS occurring. In the sense that it defines it (DKS) as unique from Boltzmann’s physical chemical processes, it is probably more accurate to correct the intro statement “DKS- a process that is ‘usually” not observed in regular chemistry..” to “DKS is a process“never” observed in regular chemistry." I believe it gives support to the notion that current thermodynamics is critically lacking, though it fails to address the issues with thermodynamics itself, hence its advocation of DKS though it's not clear at all how it would be co-joined with thermodynamics, and instead, this paper shows the need for a basic new approach to the problem.

[*The intro to this article was updated on 10/13/201]

1. Pascal R (2013) "Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics". http://rsob.royalsocietypublishing.org/content/3/11/130156


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