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


Saturday, June 6, 2015

Of Perpetually Cooling Coffee Mugs and How It Relates To Life In The Universe

My coffee mug full of my favorite morning brew will not re-heat itself, much to my annoyance. After being filled with hot coffee, it will gradually cool in the air hovering around my desk until it reaches the same temperature as the room. The reason it cools is the resultant of the “Second Law”, and the mysterious physics surrounding that law, a physics which is still not entirely understood, as this is also related to “time’s arrow” why things tend to proceed in a certain direction but not in another. What is also fact. There are no molecules that I can add to that cup that will assist in performing a reversal of that process. Yes there are molecules I can add that add heat. But this heat, once released will also dissipate. (think of the “icy” hot pack cooling). The molecules in the cup “wish” to relieve themselves of their excessive excited energy, transferring it to other’s they encounter at the wall, then returning inwardly to “pick up” more energy from other encounters inside the cup of coffee. They will do so until things have reached equilibrium. I placed some terms in quotations deliberately so as to not imply there is anything actively occurring in the molecules actions, but these ideas are important I believe to illustrating the point.

What of the problem of “self-replicating molecules? How does coffee relate? Coffee relates to everything, as everyone knows. It's said to fuel entire cities. The problem is related thus. If we imagine adding these special molecules, that can re-heat the coffee as it sits on my desk, how would they work? Perhaps there is some very clever way to make molecules do this. After all scientists are doing some rather ingenious things. Well, they would have to in some way, reverse their normal tendency to “grab” energy from higher energy or faster moving molecules, and instead collide with the slower ones on average more often than not. In other words, to go against their natural tendencies. (in other words they’ would have to be self-directional. Are these possible? Maxwell proposed such a molecule, a ‘demon’. Which came to be known not surprisingly as "Maxwell's demon," but that should give some indication of their physical possibility.
[On that note, we can now tie in the problem of life on other planets, as this issue is also related to specially functioning molecules. actually molecules which do a whole lot more than "simply" reverse the flow of heat in a system. these are self replicators. In addition to increasing their local energy supply, they make copies of themselves.]

Self replicating molecules on the other hand, would need to operate in a similar way as self heating molecules in my coffee mug, but with a special caveat. They also must copy themselves. Like a cooling coffee mug, a chemical process of any kind also will proceed forward until it reaches equilibrium, as anyone who’s lit fireworks on the 4th has found out, fireworks after they're burnt, don’t re-light. They're expended. (And by the way, any process molecules is "chemistry". Self replicating molecules can only replicate by chemistry, by "reactions" with other species.) So returning to self replicating molecules, those claimed by various scientists, what this really means is "self reacting" or continuously reacting. And we’ve replaced the fancy jargon with a more accurate depiction of what is occurring. They would need to perform a reaction, say some conversion, but then instead of completing their task and sitting in continuous equilibrium they would recruit more energy from their surroundings AND more molecules in order to do more reactions. Imagine fireworks that instead of going out, sit for a moment while they collect energy from their surroundings and perhaps organics from the grass or wherever, and then continue to burn. Sound too good to be true? We’ve just described the very process by which these self replicating molecules would need to operate. And we see that there isn’t just a problem of heat being driven back inwardly, from the surroundings, there is also the issue of recruiting molecules from the surroundings that are already spent, reacted, and are known as “waste”. Biological systems have these same issues. But so would so-called "primordial" molecules on other planets ones on which life hasn't yet started (the proto-disk in Taurus for example we showed earlier).

A chemical process using very special molecules is going to have the same thermodynamic issues as the molecules in my coffee mug, heat will be actively removed (active in the sense that to reverse this, it takes work to oppose it), hence the reason I have to continuously put the mug back on the burner. Where are these self-heating molecules?

In order for (our self replicant) molecules to replicate they need to shuffle energy, (recruit it to do work) but where will this energy be supplied? We can imagine that heat is being supplied, ambiently and perpetually to the system itself, which is containing the molecules. Will they heat up? We have a closed system problem, what I have described as a "virtual closed system" in which the system does not appear to be closed, as it is being bathed in potential energy, and yet it still undergoes thermodynamic equilibrium. It is not reversed. So perhaps that is a definition, such systems (virtual closed systems) can be immersed in potential energy but still not “see” a reversal. If you notice, also, we’ve biased the system. We’ve assumed a potential and therein lies the problem that is revealed by such a system. Lets place the mug on our balcony in full sunlight. It is now exposed to the energy of the sun and the surroundings. There is in fact considerable energy in these surroundings, relatively speaking, if we consider the alternative, the vacuum of space near earth , which is extremely cold, sufficient to freeze our cup-of-joe solid in minutes. The mug is surrounded in heat, sunlight and heat from the earth, will it under these conditions, heat up? The answer is that it will sometimes, say in broad daylight, but it will also cool at night, so your answer might then depend on the time of day. The correct answer, however, is that it does not heat, as it is merely reaching equilibrium, a continuity status with its surroundings. The technical reason for proving this fact, is to simply measure the temperature of the liquid. One reason it seems to be warmer is because we’ve placed it in an organized structure, but also because we are not measuring surrounding walls etc. You’d have to be very convincing science to convince anyone that this is a means of heating our coffee (leaving it out on the balcony.) and yet it IS receiving considerable heat from its surroundings? Why doesn’t it concentrate this heat in our mug?, and perhaps there are molecules that can do this, or at least help to do this, as they have claimed. And that is what is claimed, as we just noted self-perpetuating chemistry must recruit heat towards itself actively opposing the Second law. That is false, of course, as even well known "heating molecules" (hot packs) expire and give up energy, just like energetic hot water molecules do.

The point of “being warmer”, of having a warmer cup of joe as opposed to luke warm” is regarding the issue of traversing the "entropic horizon." A boundary , we can think of as roughly the mug itself, through which cooler molecules pass, but hotter molecules do not go back through the entropic horizon in the reverse. We're already aware that hotter molecules do not pull themselves out of the air and find our cooler mug like fireflies, at least not in this universe. We also note. Nothing is being done in the case of the mug on the balcony, to reverse the Second Law process. Thus the cup is the same average temperature as the air, the walls and floors of the balcony. Not much of an improvement, and technically, this action we've taken seems less and less like “heating” the mug. Not in the special sense that we’re using in this new theory (which is to OPPOSE the Second Law in some way). Considering the above issues, is leaving the mug out on the balcony opposing the Second Law, even if it is being warmed, is the law being opposed at any time? Are the molecules recruiting higher energy molecules and building up heat or are they passively dissipating to their surroundings? It's a good question to ask those who quickly answered that it must be in the process of being heated by the sun. (Again we must act as though we are imagining the mug as though we are not physically in the room, because we CAN influence its likelihood of heating or cooling but that is a distinct problem, not relevant here. Our initial question or subject you will recall, was "life on other planets.." if life already existed there, such questions as self heating coffee mugs are irrelevant). The other issue however, is to consider probability of that mug heating, next to say, its surroundings. If we take the temperature of the back side, not exposed to the sun, and average this, we will get a temperature roughly equivalent to the temperature of the water inside the mug. It turns out that heating the water in the mug is not achieving a temperature much different if any, from the air temperature. Would special molecules assist in changing this situation? How would these molecules aggregate in nature, what force would help them to coalesce into a region like a “virtual mug” somewhere in the ocean or a pond or anywhere else, to alter this outcome of temperature differential? So what we've done is to imagine that the mug, is simply a volume of liquid, roughly 8 oz, and could be a puddle that we'd "walk by" in virtual space. Does one walk around in nature and imagine one puddle getting warmer than another by sunlight? The same reasoning applies to the mug of coffee.

It is easy to be tricked by the context of the problem, the mug appears to be heated by the sun, as we are observing it and interpret these results differently than what they physically are. Self reacting or continuously reacting molecules, are the more correct physically accurate name of such a technology, a “technology” we can test in our virtual  mug example, but any other example will do. We also realize now, that to do reactions continuously, molecules need to move themselves in ways that oppose natural physical forces, they must recruit new, reactive molecules from their surroundings, AND also more heat from their surroundings (to do work), they must do at least what is IMPOSSIBLE for my coffee mug to do on my desk, self heat. In reality, this process of heating a mug is 1) not a process for heating the mug, 2) not more likely to heat the mug than any other solid object nearby, or to raise it above the temperature of the surrounding air. The mug we realize is a virtual closed system, but allows us to catch a glimpse of how this problem is so universal, even to much more profound issues as self-replicating molecules.

We have also seen the problem of virtual closed system in which a system is bathed in a potential energy stream. Despite the mug being bathed in external heat from the sun and from the earth, it does not heat up, not in the sense that is critical to perpetual reactions or self-heating mugs, (that’s an illusion of our observation, we measure only the heat from the sun warmed side, not the average of the water) instead it achieves the ambient temperature of its surroundings. We cannot realistically say we’ve heated our mug, when it required heating the entire cosmopolitan area to that temperature. Conclusion: putting your mug out to “heat” in the sun simply doesn’t work. Let’s use on other example. The untidy room. The untidy room is littered with shoes, some loose papers, and odd items that don't belong. But we can use this as a good example of how the Second Law applies even here but also to self-ordered molecules. If we expose the room to constant heat does this “un-mess” the room? Why not? Shouldn’t there be some probability that adding heat will reverse SOME process here in the room? In reality, adding heat to the room can in fact do nothing to restore order, in fact, it only degrades or reduces order, (as ambient heat energy degrades any material) and I discuss this Condition I and II, but that runs contrary to the predictions of disequilibrium thermo of the papers I’ve sited. These examples of its failures show that the virtual closed system is correctly predicting what is required for actual self-replication, but also segues into the concept of imposed resistance force that is FL.
In conclusion: Thermodynamics is universal across the universe. If it is so impossible to find self-perpetuating chemistries here on this planet, or self heating molecules to heat our coffee mugs, why should we expect, based on current physics, that these molecules would originate elsewhere?