Tuesday, August 18, 2015

I. The Use of Natural Selection to explain Chemical Behavior Raises New Questions About Natural Selection’s Actual Meaning

Purpose: This is a review of a review paper by C. de Sousa, Life As Cosmic Imperative? Phil. Trans. R. Soc. A (2011) 369, 620–623 doi:10.1098/rsta.2010.0312, and more generally, a concept known as “chemical selection.”

What is critical and central in the review paper (but more importantly to the field of chemical-origin-of-life science) is the use of “natural selection” as an underlying methodology, and if we assume that the “selection” invoked in this paper is the same interpretation of natural selection used in Cristian de Sousa’s and others, then I believe it raises new questions about what selection theory actually is. In the contexts that de Sousa and many other references (Lehninger 1980) have used it, selection is a theoretical and as yet, unproven chemical concept. It is invoked as a physical concept which in de Sousa’s words is the following:

“Selection is different. Originally formulated by Darwin as the mechanism of

evolution of reproducing living organisms, natural selection also affects replicating

molecules such as RNA, as first shown by Spiegelman [7] and since repeated

in a variety of ways by many investigators. In both cases, the essence of the

process lies in the imperfections of reproduction. For all sorts of reasons, whenever

entities are replicated, variants of the original model are inevitably produced.

Selection acts on those variants to automatically bring out those that are most

stable and, especially, most capable of producing progeny, under the prevailing

conditions. AND…” Natural selection acts blindly on the products of chance. It has no foresight.”

And what is interesting is that “natural selection” in de Sousa’s meaning would somehow presume to rewrite the laws of chemical behavior. It is already known that chemical reactivity is governed by chance, chance collisions of species in solution etc. and distributions of energy. But what is important from de Sousa and many other references that build on de Sousa’s “natural chemical selection model” is that it is not at all clear, what the chemical definition of natural selection actually means.  De Sousa defines natural chemical selection as a process occurring “after chemistry” in stage II.

“The first stage depended exclusively on chemistry. The second stage likewise involved chemistry, but with the additional participation of selection, a necessary concomitant of inevitable replication accidents.”

Stage II? What kind of chemical physics is this meant to be? De Sousa has no evidence for any chemical species copying themselves in nature, that is, outside of molecules derived from already extant life. A key differentiation, since his hypothesis asserts that it Stage I, “it was all chemistry”. This does not occur outside of cells, and has only been shown artificially in laboratories (i.e. PCR, rtPCR), but when these tests are done correctly they produce a negative. Should we also expect that since natural selection is falsifiable chemically it cannot be reproduced in nature, that the model of this paper also based on the same “natural selection” should meet the same burden and has been falsified by contrary laboratory results, again those actually simulating natural conditions?

If “chemical selection” is indeed a real testable theory or mechanism, as it is cited many times in peer reviewed literature, such as these, then can it be falsified? In other words, what is it about ANY chemical reaction that one can envision, that would proceed differently, WITH or WIHOUT so called the mechanisms described as natural “chemical selection?” I say that if you cannot answer that question, it does not pass muster for science. We may apply this simple test to those cases where it is claimed that “self-replication” has been confirmed in vitro, asking how the confirmed case differs from the non-confirmed case and the chemical difference(s) expected in each.

De Sousa states: “Up to this event, only chemical reactions were involved”. ..and “After

it occurred, selection was added to chemistry.” We are then to understand that something, was “added to chemistry.” And we wish to know what that something might be. If so, if one claims that this additional property exists in some cases, but not in others, how would you show that it is falsifiable? Would we expect…X…behavior of chemistry? Whatever X might be, a new reaction which selects itself towards, products? Let us write A+C-à D+E and demonstrate one example, only one, in which the chemical species proceed toward products D and E by this alleged process called “natural chemical selection.” Is there one example in all of the literature that answers this question? Again, whereby there is as he claims, a stage I and stage II. And again, de Sousa is echoing in a review, the generalized belief that this is a real phenomena. As with any real phenomena there must be falsifiable conditions, theoretical or actual, proposed in order to verify its existence. This is only one of the aspects of my objections to this paper, the other is outlined below and is more theoretical.

Saturday, August 15, 2015

III. Why The Failures Of Nano-Pump-Hydrothermal Vent Models Are Predicted By My New Theory: VCS

I'm discussing what I'll refer to as Nano-Pump Hydrothermal Vent Models (the leading origin of life model) within the context of my new theory VCS "Does Life Violate The Second Law of Thermodynamics". The preface to this discussion, I've omitted, but will appear shortly in a separate post.

The micro pores of deep sea vents have been compared to “micro pumps” or even to power sources (see refs, Mitchel 1959, Lane et al 2010, Russell et al 2014, ). “This would be a routine source of power for life, not random like a lightening strike” …“It works something like a battery..” (see Live Science, Nick Lane Jan 10, 2013)

Alright, so if we can imagine that there are these nano-sized batteries all along the surface of these deep hydrothermal vents e.g. the ones in “lost city” then we can also imagine that to have something theoretically analogous to a battery the battery must be driving some process?** It must power something, as all batteries, even ones that are passively discharging, drive at the very least, the generation of heat, and by “generation of heat” we mean that we can detect some elevation in temperature relative to the environment surrounding the “battery.” Likewise, if these are tiny “pumps” then they, the nano-sized pumps are creating a gradient by their “action” against their surroundings. It’s a good workable analogy because it very precisely illustrates the difference between what my theory is and what is currently believed. We’ve talked about the ‘continuity principal’ and what it predicts is that these “batteries” or “pumps” that are apparently lining the vent surfaces, are not actively doing anything against their surrounding medium. Are we really to believe that nature is spontaneously driving these tiny nano-sized batteries or pumps on the vent surface? And if so, why? How does a natural thermal heat vent, brimming with hot, hydronium ions generate tiny batteries or pumps that then allegedly operate to OPPOSE the very force, then nano-environment of ions, that is surrounding them? Would we expect that a vortices in a stream might somehow build up or develop a force which opposes the forces which create the vortex? For a force to exist, such as FN it would necessarily have to be a Force that is applied against the system. Clearly they wish to have perpetual energy device spontaneously self-generating to oppose these forces, such that they can claim that this would exemplify a natural engine that “life,” some form that has never been seen, will “learn” to adapt. Experimentally, we can test the notion of these nano-batteries or pumps using the VCS theory. The virtual closed system can be viewed as the microstate surrounding each proposed “battery” or pump lodged within the pore structure of the hydrothermal vent column. What we can see is that this proposed theory of “water world” has difficulty in demonstrating how the energy Eo that is flowing through such a VCS will change its vector and generate a force opposing itself. Eo, which can be represented as the heat from the vent, OR the differential ion concentration driving a proton gradient, i.e. a pH gradient, is obviously in great supply,  that is Eo. But in this Eo fluxing through our VCS, we can see that it lacks a particular form of energy “relative entropy” which is available energy to do work on its surroundings. This is an active form of energy, in motion, which we would observe as actual reversal of flow or ion gradient at the interface of the VCS the “entropic barrier” and we would measurably detect such nano-forces.  We have also theorized that the reason such a nano-force is not observed is because of a lack of an impetus or opposing normal force which I’ve described as FN but also FL . FN  would be the force “experienced” by an application of FL but in principal either FN , FL designates the other’s presence in the solution. Without such a force, there can be no work done as the flow of Eo (the super heated basified water) proceeds unopposed from its source to its destination, i.e. through the VCS micro state and into the surrounding seawater. My theory predicts that we should not observe an FL, nor should we observe a nano-battery as they describe, which causes some effect on its surroundings. Such nano-pumps or batteries would need to do some unit of work on their surroundings. But as we predict, the entropic potential is equivalent on both sides of the entropic barrier, inside and outside the VCS, thus we find no greater potential to do work towards the VCS or away from it. In other words delta S is the same across any given VCS we measure at the surface of the vent, and we expect to find no VCS’s that are spontaneously generating entropic potentials greater or lesser than average. We futher would find that Fsub(thermal vent) exerts a force equal and opposite to its surroundings , which we can describe as – FTHERM. The consequence of this principal is that we do not find vector such that this vector would be FN +FTHERM> FTHERM over time. This would not be the case for an Archea found near the vent. We would find that it, or any other living organism, generates a force FN on its environment.

The test of this new theory is of course to detect and measure some effect of these proposed nano-batteries or pumps on their environment. This type of measurement is technically feasible, at least in bench type models (which could in fact, take porous sections and measure ex vivo, if such pH or heat differenitals promote nano-engines that “pump” or do work to cause change. Concentration gradient could be observed by microscopy or by fluorescence, or by a variety of other means available. A positive would confirm the “water world” hypothesis. A negative would I believe give evidence for VCS theory. The control is a living cell. We can measure such concentration gradients in for example, drug studies which I can perform in living cells and quantitatively measure. It is proposed by such researchers, that micro or nano compartment or cells are present in the thermal vent tubes. Such compartments could be simulated by a porous material infused with basic water. So we might infuse such an artificial vent with a small detectable molecule, like MTN, and examine microspopically if this tracer does in fact concentrate in regions or not.

[**I want to emphasize that the notion of the battery itself can introduce some degree of confusion. The battery in the strict sense of my theory I’ve proposed, actually is an inanimate system which does not exert a FL or FN. In fact, a true battery, though “charged” will behave if we consider it in terms of entropy, exactly like the systems around it. The illusion that it is “doing” something other than in fact, decaying or reaching a lower energy level, is one that is projected on the device by the intelligent being that manufactured it. A battery is no more capable of doing work than a hammer or a rock [which might be elevated at some potential, i.e. perched on a shelf or located on a mountain, but the same notion applies to molecules or atoms.] This is an important physical distinction that further delineates what VCS theory is, from the current perspective, i.e. that there are “tiny batteries” in vent tubes which may power nano-chemistries. 8.8.15]

It has been proposed by researchers supporting the Hydrothermal –Origin of life- vent theory that cellular membrane pumps are found in deep sea vent systems:

“Autotrophic cells, including phototrophs and chemolithotrophs, also use proton gradients to power carbon fixation directly. The universality of chemiosmotic coupling suggests that it arose very early in evolution, but its origins are obscure. Alkaline hydrothermal systems sustain natural proton gradients across the thin inorganic barriers of interconnected micropores within deep-sea vents” see Herschy, …Lane..et al (2014) “An Origin of Life Reactor To Simulate Alkaline Hydrothermal Vents” http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247476/

From the same reference:

“…We discuss the construction and testing of the reactor, describing the precipitation of thin-walled, inorganic structures containing nickel-doped mackinawite, a catalytic Fe(Ni)S mineral, under prebiotic ocean conditions. These simulated vent structures appear to generate low yields of simple organics. Synthetic microporous matrices can concentrate organics by thermophoresis over several orders of magnitude under continuous open-flow vent conditions.”

It is not necessary, chemically to reproduce this experiment in exact detail as there is no basis to assume that such an experiment is in fact positive. Any more than we should expect that a new chemical configuration will demonstrate a reaction that generates more free energy than it consumes, any chemical experiment will suffice to negate that premise and re-affirm the first law of thermodynamics. It is claimed here, (Herschy 2014) that some chemicals are concentrated within the pores at “orders of magnitude” levels [higher than what] they otherwise might be. Are we to understand that this is not the simple effect of deposition, due to, for example, the same effect of virtually any heated surface in contact with brine, the heated surface causing drop out and precipitation due to a real surface gradient and superheating and concentrating? (“scaling” is one example.) When super heated salt water turns to steam the solubility coefficient of the salts previously dissolved in that water decreases (it’s a supercritical fluid), and the salts deposit on the heated surface. The surface in this case is the ocean floor where the mineral column builds. However, such heated surfaces are not in fact “causing” micro environs to operate autonomously, such as what I propose a VCS would do. The pores are not causing concentration of organics themselves, but are the product again, of a net surface behavior, driven by an energy source. The problem is to show that the individual pores are themselves, acting, just as we know cells to act, individually on their environs (exerting the control) to concentrate molecules, but at a more basic physical level than obviously cells do. The fact that the tight research community advocating these theories cannot provide any physical scenario i.e. analogous example or model, to bridge chemistry with animate processes they presume to explain, except by invoking the terms “selection” or “learning” lends more support to my thesis that a real alternative theory is needed in this problem space and debate.

de Duve comes very close to actually stating what he means by chemical “selection” but never quite reaches it. He indicates that in the current theory of origins of life, chemical processes must exhibit “selection” after there is chemistry.

“Selection is different. Originally formulated by Darwin as the mechanism of evolution of reproducing living organisms, natural selection also affects replicating molecules such as RNA, as first shown by Spiegelman [7] and since repeated in a variety of ways by many investigators. In both cases, the essence of the process lies in the imperfections of reproduction. For all sorts of reasons, whenever entities are replicated, variants of the original model are inevitably produced. Selection acts on those variants to automatically bring out those that are most stable and, especially, most capable of producing progeny, under the prevailing conditions. AND…” Natural selection acts blindly on the products of chance. It has no foresight.”

What this explanation lacks specifically is, as I’ve discussed here, a model for the thermodynamics. The “natural selection” de Duve invokes has no means of overcoming the natural tendencies, the opposing forces, which are driving the dissipation of reactants toward lower concentrations not higher. The apparent proton-pumping “force” that Duve and others invoke as that which driving chemistry in useful ways, (presumably useful to pre-biotic forms in terms of supplying higher energy chemical feed stocks), is imaginary, as there is nothing actively selecting molecules to move against entropy; for example, Fick’s law of diffusion and Fourier’s heat dissipation law. The same occurs in the heated vents under the sea, but they have failed to realize that the concentration effects due to thermophoresis, are only a minor aspect and are in fact, operating in normal directions in favor of dissipation. This can be envisioned by considering an example of a cascading waterfall. [I’m thinking of systems of natural pools I’ve encountered while hiking in local mountains.] We can see in the water fall the collection of smaller smooth stones in the bottoms of the deeper pools, and fewer stones aggregating towards the edges. The system is energetically analogous (despite being much larger in scale) to what is occurring in so called concentrating “vesicles”, (in which molecular particles are aggregated by flow within nano-compartments) but here, we simply replace the molecules with the pebbles. The molecules, like the pebbles are deposited for a moment, but then are pushed through, randomly. We do not find movement of the smooth pebbles of the stream which on average oppose the motion of the stream. The movement of these pebbles, the vast majority are in line with the forces of the moving water. That is because of the vectorial direction of force taking the shortest pathway, the lowest height, (and least resistance to gravity) towards the waterfall’s lip. What is interesting from the standpoint of chemical “natural selection” however is the realization of its invisibility (meaning its physical absence) in terms of describing actual chemical behavior. What is chemical “natural selection” aside from some imaginary term invoked to fill the gaping hole, the chasm that must be traversed between inanimate chemistry, i.e. the failures of Haldane and many others, and the replication chemistry of nucleic acids, which ONLY occurs inside a cell or with the aid of a living thing (such as a virus). We don’t know of any replication occurring outside cells, even in the case of ocean virus, I believe they must utilize bacteria or some living cellular host. Moreover, so called chemical “natural selection” invoked by de Duve and others, has no structure, or formula, or even a model, for traversing the thermodynamic issues that face molecules as they purportedly “trudge” across that divide.

A radical new approach is needed to this intractable problem.

So we’re speaking here not specifically to any type of chemistry itself, but to a difference in fundamental approach to the problem. The authors have continued largely from work that was started back in the 1950’s with Mitchel, where Mitchel “equates” the interface between living cells and the environment surrounding them. The authors have made the case that various disequilibrium processes, are actively operating as engines to drive self-assembly and phosphorylation chemistries, among others, in a kind of natural factory or even a bio-nursery, in which primordial living forms were assembled. They are misled in the belief, however, that there is a single vector of force that can be found that points in the right direction supporting that premise. And what they have neglected is that for every motion of a virtual or actual “motor” or engine that they envision, there are more vectors in that very same turbulence or pH gradient, or temperature gradient that are directly opposing these motions. Hence my comment that not a single vector of force is operating in their favor of such a theory as “pumps” or of what amount to be entropic systems which are running in reverse, that is, they have excess energy to do useful work, that is the essence of negative entropy which I’ve discussed elsewhere (also see Schrodinger’s “What is Life?”). That thermodynamic indictment of “constructive” theories, and the like, is the unexpected result of my analysis with VCS. For example they claim that the earth’s mantle system has been operating for “200-300 million years” as “effectively an engine” to move lower mantle to the surface and drive geochemical processes in the earth, which are purported as sources of primordial drivers. They are surprisingly oblivious of the vectors of force in these cases, and my earlier comment that they apparently wish to invoke a kind of “perpetual energy” mechanics is of concern.  Where exactly does that excess energy come from to drive a potentially biologically useful reaction, to pump electrons in the way chemistry has been understood for over 100 years, (nothing new there) again in a natural, dissipative system? Their theory of natural pumps which evolve from natural dissipative processes, reduces to an entropy generator which is running in reverse. Which I would define as simply the claim that a system will oppose itself, which is not possible, but is only feasible in principal if energy is supplied from the outside. For example, if someone were to claim that they have a “motor” which requires no structural input or design, and can do some amount of work on its natural surroundings, that would be a rather surprising if not dubious claim. But the other implication of “perpetual energy” mechanics is that they are obviously coming up with useful work energy that isn’t present in the system.
Again, (regarding their “perpetual energy like claims…” this is the same fault that is found in perpetual devices, (see the patent office for a history of such pseudo science) they do not account for the actual loss of energy of their device (or experimental apparatus), just as these authors do not account for the total loss of available energy (in their experiments) or concomitantly, the source of such useful energy. Though they present no equations, chemical or otherwise, they infer them, by their claim that phosphorylation and other chemistries that would be critical to theoretical early life, are “driven” by these entropic systems. That is patently false. None of the chemistries that these authors have described, absolutely none, will be driven oppositively, by the inanimate chemical pumping “systems” they purport to occur readily or preferentially, in the opposite way of their actual natural tendencies, i.e. toward less energetic lower energy products, products which deter and oppose life. This is well known since living things must add energy to such systems by the extraction from Eo [total initial or incident energy entering the system] from the sun’s energy or from other readily available chemical energy.
In contrast, the predictions of the VCS theory are independent of what form of energy one begins with, it is irrelevant if it is chemical or mechanical. So if we are to actually imagine that a thermal sea vent can in fact drive concentration gradients AWAY from their natural tendencies, we should be very surprised at that claim. The very forces that are identified in these papers I’ve cited here, are forces which actively oppose living structures in every respect. Concentrated brine, thermal disequilibrium, diffusion and natural “pumps” or “engines” are falsely described as working towards life, when in fact these are environmental forces which the living creatures which live around these vents must constantly oppose. Prigogine’s far from equilibrium systems are disruptive not constructive, they are merely dissipative of energy, and cooling diffusion and disequilibrium are all synonymous and congruent with higher entropy, not lower.