Tuesday, October 20, 2015

Important Follow Up To: "II. Is Theoretical Biology HIding A Critical Flaw In Selection..." (More depth into 'Chemical Selection' as per 'Biochemistry 5Th Edition')

I'm posting this as a supplemental post to my previous "II. Is Theoretical Biology Hiding A Critical Flaw In Selection Theory Proper: Molecular Selection is A Crack in The Foundation" http://causaldistinctions.blogspot.com/2015/10/ii-is-theoretical-biology-hiding.html. The following sections from Biochemistry. 5th ed. Berg JM, Tymoczko JL, Stryer L. (2002) http://www.ncbi.nlm.nih.gov/books/NBK22508/

are made for the purposes of further illustrating the definition or apparent definitions, of “chemical selection”. This is informative of what “chemical selection” is “understood” to be by current biochemistry, but elaborates more on what chemical selection is at least meant to be. One can find helpful diagrams of RNA and DNA as well as proteins and how, it is currently theorized, these basic molecules might have self-catalyzed or replicated. However, we can find nothing about these definitions that would allow us to test the version of "chemical selection" in Biochemistry. 5th ed as I explain in part I. link HERE http://causaldistinctions.blogspot.com/2015/08/i-use-of-natural-selection-to-explain.html. A key argument against their theory is the lack of testability of its propositions as I explained in Part I... 
'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.'

My two relevant lead theories discussed previously are:
"Does Life Violate The Second Law Of Thermodynamics? Implications Of Virtual Closed Systems" MKK http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html
"I Propose A Challenge To Maximal Flow Theories By A New Theory: Indifferent Time" MKK
In addition to making an argument for my lead theories, VCS and Indifferent Time, which are independent of the chemistries and are instead related to forces or energies of the components, I have replied with essentially a basic experiment, well actually two. They reference complex data in Biochemistry. 5th ed to defend their arguments, and I employ the use of household items, one with food color, and the other using a carrot, to illustrate the problems with these arguments. Here is an excerpt from the TEXT which I refer to as ‘5th Edition.’ 


“Once the necessary building blocks were available, how did a living system arise and evolve? Before the appearance of life, simple molecular systems must have existed that subsequently evolved into the complex chemical systems that are characteristic of organisms. To address how this evolution occurred, we need to consider the process of evolution. There are several basic principles common to evolving systems, whether they are simple collections of molecules or competing populations of organisms.

This is a dense paragraph with many arguments and leading assumptions that are hidden within it which must be elucidated at a more basic level. Let’s examine what these might be. It presumes that “simple molecular systems must have existed that evolved into…chemical systems…that are characteristic of organisms.” It still is not clear what "evolved into..." means chemically to basic molecules, but if one is familiar with even the basic “characteristics of organisms” even in a vague sense, this logic should strike us as intuitively suspicious. Do organisms really act like molecules? That would be a basic question that comes to mind. However we note that the key word “characteristics” is not defined, and that's likely not accidental. What characteristics might these be, and why aren't these 'characteristics' stated in basic chemical terms? Again, it is nothing but nebulous talk even in a so-called reference text on the subject of "chemical evolution."


Furthermore, what is neglected in the biochemistry here in this text, but also in de Duve (2005), are the physicality of the organisms. Organisms’ characteristics are to oppose the tendencies of their environment, of the tendencies of molecules to passively move or transfer. Such tendencies” are called diffusion, or random motion. One does not have to know anything about chemistry to understand the theory I propose in VCS and also Indifferent Time, where we consider the “chemistry” whatever it may be as a black box, and instead consider its outputs. In short, the experimental results, the outputs cannot be understood if we view the system as the collection of molecules proposed here. It is applicable to ANY collection of molecules, as we see in how VCS is applied even to inanimate machines.

Nonetheless, we might wonder why such chemistry cannot produce the results of so called “self organization” or “evolution” as claimed in texts like these. Why can’t chemistry do this? It has to do with an understanding of basic forces, but also the tendencies of matter to disorganize and reach lower energy, and lower organization.


Consider a very basic experiment one can do in their kitchen.  If you drip food color into a glass of water, you will see diffusion. The droplet of color will slowly fade into the water. That is the tendency of molecules to find their lowest concentration in a given volume, but also to disorganize, like steel balls cast on a floor spread randomly. Molecules oppose each other by electronegative forces of repulsion. They are colliding and bouncing off one another in solution. (And this is true even when they react and combine, their products diffuse into their surroundings by random collisions.) So this property is just an example of other properties that are key” properties of lifeless matter and molecules, like food color, RNA or proteins, and are independent of the type of molecules we are discussing.


How is this related to living things? All higher organisms, eukaryotes, (plants and animals which reproduce by sex, have sexes, and are multicellular) are composed of cells. When cells die, their internal salts, Na and K disperse and reach equilibrium with their surroundings. This is related to osmotic potential, but what is known is that this potential is a force exerted by the cell, and constantly requires energy of the cell to maintain. Examples are turgor pressure in a carrot sitting on your counter top. Place a carrot in salt water, and it will go limp. However, if the limp carrot is placed in normal tap water, it will resume its turgor pressure, and become crisp.

The interesting question about the carrot is the following. If the carrot is cooked in the microwave, or hot water, it no longer has this property of maintaining turgor pressure. Why? Before we ask this question, we should ask, would it be possible for a system of molecules in or near a deep sea vent, to arrange themselves such that they oppose their own diffusion. Would we expect that some molecules, perhaps some very unique molecules that we obtained from a chemistry shoppe, would be able to self arrange in a glass of water and oppose their random motion? Yes it might be possible. However, this trick would be because of energy of the molecules themselves, interacting with the water, or with another molecule by what is known as a chemical transformation. In other words, we know that in order for the molecules to oppose the force which is trying to make them spread out to infinity, (again by self collisions) it will “cost” energy to keep them together. We know this because the molecules would have to exert a force to oppose this tendency of dispersion, i.e their own collisions. And the reversal of this tendency is always one of the first signs that a cell is dying. For the purposes of preventing diffusion, would it help if they were attractive molecules? Yes. We could use a non-water interacting solid, like metal, or sand (SiO2). Or maybe a molecular complex based on charge attractions, PEI /DNA, some random examples coming to mind. However, none of these examples would be fair to illustrate what living organisms do with their chemistry. Because in living organisms, none of these, metal, sand or PEI/DNA are useful to organisms. And in fact, cause their termination. Why? That’s another question, discussed elsewhere. However, what we do know is that organisms use many molecules, water, salts and proteins, that by their nature, must be soluble in water and MUST be diffusible. So we are left with a non-answer. We have not answered why certain molecules in biochemistry of cells, will not diffuse, since they actually have a FORCE of diffusion, or repulsion upon them that is constant in the cell. (we note again, the turgor pressure of the carrot). The carrot, maintains its pressure, not because such maintenance or any such chemical reaction in the organism are spontaneous, as the text mistakenly claims, but because energy is consumed by the living cells of the carrot, via storage molecules, starch is converted to energy which drives the cellular pumps which actively intake water through the carrot’s skin. This example illustrates energy balance and the physicality of how living organisms interact with inanimate molecules like water. This is why the assumption that Indifferent Time and also VCS are very important to the lead theories I have discussed elsewhere HERE and HERE. The carrot is merely an example of what cells do, and in our bodies, obviously cells are pumping water (or nutrients) constantly, and none of these processes can be said to be SPONTANEOUS, meaning they would occur passively, without the input of energy, OR SPONTANEOUS in the sense that chemical reactions are known to be spontaneous. The response of a carrot to salty or unsalty water, is not a chemical phenomenon, as such a phenomenon would assume that the carrot is dead, and non-living matter. This is not a “trick” of words. The statement is true if we say it is not a biochemical phenomenon. Biochemistry is defined as chemistry which involves biological relevant molecules, the definition required for this discussion. It is not necessary for such chemistry to be “living”. We could quite literally take that statement I just made, and equate that with the theory I have discussed at a more theoretical level in VCS.

The confusion about the terminology is the blame of the author(s) of the book I discuss here, and is no doubt deliberate. For example their use of the term “species” is deliberately confusing in order to equate “chemistry” and “molecules” with organisms even with behavior of organisms, i.e. “competing” and “evolving”. Molecules, obviously do not have sex. Nor do precursor molecules, those which existed before RNA or proteins, have DNA, so there is no genetic inheritance in H2, CO2 and other basic molecules. The notion of “evolution” is very suspicious in its use here, and is used casually as though we don’t understand these distinctions. We are to assume that molecules, given enough time, can simply self order.

See the quote from 5th Edition below: “Without this ability of reproduction, each “species” of molecule that might appear is doomed to extinction.’ Chemical species are not the same as organism “species” but 5th Edition, makes such statements I believe to infer that there may be some support here that they can be casually equated or assumed to be the same. But that is the methodology by which this text makes its arguments. We do not make such assumptions and these are careless, and as we’ve seen in the example of diffusion and other elementary examples, they do not account for observations we might see in our home kitchens, without any formal training in biology.

Next 5th Edition , discusses what chemically evolving systems might be:

..First, the most fundamental property of evolving systems is their ability to replicate or reproduce. Without this ability of reproduction, each “species” of molecule that might appear is doomed to extinction as soon as all its individual molecules degrade. For example, individual molecules of biological polymers such as ribonucleic acid are degraded by hydrolysis reactions and other processes. However, molecules that can replicate will continue to be represented in the population even if the lifetime of each individual molecule remains short.

A second principle fundamental to evolution is variation. The replicating systems must undergo changes. After all, if a system always replicates perfectly, the replicated molecule will always be the same as the parent molecule. Evolution cannot occur. The nature of these variations in living systems are considered in Section 2.2.5.

A third basic principle of evolution is competition. Replicating molecules compete with one another for available resources such as chemical precursors, and the competition allows the process of evolution by natural selection to occur.”


These next assumptions, which are the basis of “chemical selection”assume many other unusual if not known, properties of molecules, which are not supported by any chemical terminologies that I’m aware of. The reason they are not known is because of the Second Law and the copious experimental evidence which negates these models (evidence not discussed in5th Edition) .

The reader should be confused by terms such as “competition” without knowing advanced chemistry, as it implies that molecules, i.e. the food color, somehow are animated and perhaps “compete with one another” for “available resources.” Food color, will actually behave identically to other molecules, in terms of yielding to the laws of diffusion. DNA and RNA though complex molecules, are merely polymers composed of sub units, called nucleotides, A,C,G, and T’s. But a nucleotide is a much simpler molecule than Red #4 food color. And Red #4 is simpler than H2, or CO2, which are the source of H and carbon in DNA. Can any of these defining “qualities” of “evolving molecules” be seen in either our food color example or in the carrot? i.e. in the carrot’s ability to regulate the flow of water in and out of the cells that compose it? How would the properties of the food color/water be similar to those of the carrot? The food color experimeint illustrates what should happen in the carrot, which can be viewed as a collection of molecules, not different, we might presume than any other collection of molecules. But what we also find is that the example of diffusion, the repulsion of molecules against each other, is a property of chemistry, applicable to any system of molecules.

It is though the 5th Edition wishes the student to understand that chemical “evolution” can entirely circumvent the laws of chemistry or that chemical knowledge (i.e chemical reactions) is irrelevant to premises which in fact are chemical.

5th Edition, just like other proponents of “chemical selection” provide no defining qualities that make one kind of molecule unique from another, again, we are concerned with forces. How do molecules oppose their own forces which repel them apart? Or, make them combine in stable arrangments, i.e chemical reactions, that oppose the formation into RNA? But these are the kinds of questions we ask in the VCS theory.

So what if any, are the examples of this “evolution” of molecules? The text further provides “examples” of self-replicating or organizing RNA, which I will address next*.


What the text does not go into are the key principals, of why random molecular behavior might at all be expected to yield evolving molecules. A key point I raise in the prior post and discussion of de Duve’s (2005) paper and others that are referenced by Lane, Herschy and others in support of “chemical selection.”



1. Biochemistry 5th Edition (2002)


Tuesday, October 13, 2015

II. Is Theoretical Biology Hiding A Critical Flaw In Selection Theory Proper? “Molecular Selection” Is A Crack In The Foundation. Is Molecular Selection just pseudo-science?

This discussion is follow-up to a prior post, and is pertinent to my lead theories ‘Virtual Closed Systems’ (Does Life Violate The Second Law? Implications of Virtual Closed Systems, and ‘Indifferent Time’, as well as other discussions that I have initiated on my blog site. I note for reference my discussion of R. Pascall’s paper (2013) on Kinetic Stability Theory, as further relevant to basic questions about the validity of “molecular selection” as chemistry, and as meeting qualifications of scientific research, i.e. basic feasibility at a theoretical or experimental level. It begs the question, as to why this kind of “research” is valid for publication in so called “peer reviewed” magazines. I have already presented evidence, both theoretical and experimental, that such nonsensical science is no better than “perpetual energy”.  These are not perpetual energy devices, but are claims of self-organizing, self-ordering matter, matter which they allege oppose laws of diffusion and heat-dissipation (fundamental to chemistry), and are equally dubious, and forbidden by the second law, as well as the first- as they are made without a single positive experiment or without any definition of what such a theory is in terms of how it would be disproven or negated. There are the absence of any test criteria or even a defined hypothesis. Yet these “molecular selection” and “maximal flow” theories, apparently, continue to be flogged in peer reviewed magazines. Ironically, unlike bogus perpetual energy claims, these theories as “molecular selection” get a free ride in the magazines, openly, with no resistance whatsoever from the scientific community. That does a great disservice to science, to those who adhere to scientific principals, and to the fair, pursuit of science now, and in the future.  In other words, such pseudoscience promoted as “peer reviewed” does great harm which cannot be quantified. The reason I bring up these points is that they conflict with my lead theories, and that is the purpose of this discussion, and the reason I shall continue to bring up the errors shown in current papers relevant to Virtual Closed Systems theory and Indifferent Time.

*If the reader does not have the time to read this entire article I would strongly suggest you skip to the section “NOTES” at the bottom. This where I dissect the supposed supportive references of molecular selection in detail.

The article I reference here appeared in Transactions A of the Royal Society Phil. Trans. R. Soc. A (2011) 369, 620–623 doi:10.1098/rsta.2010.0312 http://rsta.royalsocietypublishing.org/content/369/1936/620

I explore further into the enigma surrounding the so called “molecular selection” and find only more ‘nothingness’, a critical void of actual evidence to support it. Just more references from its proponents who claim to have observed it, or rather that someone else observed it and reported on it. And many of these cited in recent papers, “some of the first observations of (molecular selection)” like Mills (1968) or Spiegelman (1967) are almost 50 years ago. It is a term or at least the concept that it embodies, that I’ve recently encountered in a number of locations, and heard it utilized first hand as an explanation for molecular behavior. Molecular selection has a number of aliases, self-organization, molecular evolution, and the like, but is also now a foundation of so called ‘molecular paleobiology,’ Fournier G. et al. (2015) http://www.ncbi.nlm.nih.gov/pubmed/25791872.

To start off, perhaps it should be noted that in the article itself, de Duve references his previous work of virtually the same title but almost two decades earlier: “Vital Dust: Life As Cosmic Imperative” (Vital Books, NY 1995). de Duve also cites three of his other works in his short review article, these are:

de Duve C. (1991) Blueprint for a cell: the nature and origin of life (Neil Patterson Publishers, Burlington, NC).

de Duve C. (2002) Life evolving: molecules, mind, and meaning (Oxford University Press, New York, NY).

de Duve C. 2005 Singularities: landmarks on the pathways of life. New York, NY Cambridge University Press doi:10.1017/CBO9780511614736 (doi:10.1017/CBO9780511614736)CrossRef

On first “blush” it would almost appear as though de Duve has simply re-published a scientific article here from his book, published almost two decades prior. Does this qualify as new research for a published scientific article? Apparently it does qualify , and de Duve explains:

“The title of this essay appeared, but without the question mark, as the subtitle of my book Vital Dust [1]. In that book and in others [2–4], I defended the view that life is an obligatory manifestation of matter, written into the fabric of the universe, and that there must be many sites of life, perhaps even intelligent life sometimes, in many parts of our galaxy and in others..”

Biologists like de Duve are clearly aware that their theory involving a chemical first or “bottom up” approach to the origins of life would likely involve a great number of chemical optimization steps:

“The conclusion emerging from this summary analysis is that the origin of Earth life, being dependent on deterministic chemical reactions and on frequently optimizing selection processes, must have been close to obligatory under the physical–chemical conditions that obtained at the site of its birth. This contention is further supported by the fact that a very large number of steps must have been involved.”

By “very large number of steps must have been involved” we can presume that de Sousa and other proponents, are essentially claiming that the chemical development of life, the precursor reactions, must have been numerous, i.e. involving numerous reaction steps. And so their theory asserts that life is a chemical reaction product, albeit a product that had an extremely low probability of occurance.

Furthermore, the next part of the same paragraph strongly suggests that de Duve, like other biologists, is fully aware of the argument that a series of low probability events would, (S1…S2…S3…) if required to occur in succession of each other, lead to a very unlikely probability of the final event, as per normal probabilistic calculations would provide:

“For the final outcome to have a reasonable chance of taking place, most of those steps must have had a ‘reasonably high probability’ ([12], p. 1034) of occurring. Otherwise, the probability of the entire succession ever coming to fruition tends to become vanishingly small [1,12].”

So, returning to the theoretical issues: what would be the probability of a series of theoretical chemical steps, which lead up to a complex molecule such as the first RNA? If some steps (1-3) leading to a molecule were to occur only by chance alone, this would roughly be calculated as the p(molecule occurring) = p(step 1) * p(step 2) * p(step 3) and so on, but with each probability the frequency, or probability of its occurrence decreases. The probability multiplies again, when we attempt to envision getting three of those molecules, all by chance. This raises the fraction by a power of 3, making it even less likely an event, particularly if the fraction of molecules ever achieving unlikely conformations, let alone remaining stable in solution, becomes very remote if not theoretically prohibitive. And so the claim that RNA or some precursor molecule came about exclusively by chance “roll of the dice” is highly problematic since it may involve many possible reactions or side reactions, but moreover, these are more theoretical equilibriums, reactions that one can’t show normally in chemistry because they are energetically disfavored. So it may be surprising, to some, that this doesn’t sound at all like chemistry. But given the vanishingly low probability, and the lack of steps with “reasonable high probability” it should be surprising that this chemical pathway is considered feasible at all? No reasonable, high probability steps are ever described. The purely probabilistic “mechanism” we have just outlined here, has nothing to do with chemistry proper, it is not relevant to mechanism; and in fact, assumes no mechanism as such an assumption would mean that probability itself , chance, was not the factor. (the probability of obtaining “heads” five times in a row, by simple probability, isn’t calculable if there is higher probability of heads due to some mechanical aberration.) The argument that chemistry involves species reacting in more probable situations with more probable reactive species, is not the same argument. [It is in fact, the “propagating chemistry” I discuss HERE that I discuss as an alternative description of the pre-life or pre-RNA chemistry they propose to self-assemble. The reason is that the theoretical products they propose, to propagate and by chance, interact in one reaction after another, again by chance, defies the second law, as solutions do not behave in this way. Each microstate is reacting and reaching a lower energy state simultaneously.] Furthermore, in my view, the central assumption of their argument that there is a finite probability of a reaction should be in question, as we find no physical examples of this in nature. None on the bench. Their entire model of chemistry does not hold true even in the most elementary bench chemical model. Their model of using chance or probability is misrepresentative, since chemical reactions are actually highly probable, not improbable. Otherwise chemistry would not be such a precise science. The certainty by which these microstates reach their products, precludes the notion that it is not certain, or has opened the door to “other chemistry” they imply, i.e. the self-propagating chemistry of their model.

Nature does not advance by “mistake.” The idea that a flood or storm occurred randomly is not the same as the mechanics behind the storm, which did not impart a force by chance. And simply because molecules may end up with other molecules in solution by chance, does not mean that the reaction itself is driven by chance, by probability. So one has to consider thermodynamics of what is driving the chemical reaction itself. It has to be a chemical reaction. And yet a chemical reaction would involve certain reaction pathways, i.e. S1…S2…S3 and so on, as well as the loss of useful energy, but this obviates a purely chance scenario. The chance” dictated by the 2nd law of thermodynamics preempts their model of self-propagating chemistry in this case. Chemistry is mechanism driven, in theory. It is the model of the hypothesis in question here, the framework, (not the specifics of what those reactions actually are) since we should have doubts (based on their lack of providing any chemical examples) that it’s even clear what it should be. We realize that the question of “a chance of RNA” forming from n molecules, is a distinct question from “what are the species or precursor reactions leading up to RNA?” those are independent issues of one another. And I would argue, there is no substantive basis to claim a reaction will occur if you cannot name what those individual reaction components are. Otherwise, we could make all kinds of ridiculous predictions, Pb could turn to Au for example, “by chance, even despite it’s highly astronomically low frequency” and that claim is not permitted.

There is also a chance, the bio-physicists will tell us that entropy (an event N) may proceed in the opposite direction that it is favored, though extremely slight, and I explore HERE. That’s the thinking of statistical mechanics with respect to this problem. But the biologists and bio-physicists are likely keenly aware that there’s a bigger problem, and that’s the thermodynamic barrier. RNA is much more organized, and is a unique molecule, never found on asteroids or meteors. It isn’t lying around, and that’s because it has been manufactured by an intelligent organism, already containing DNA. To get around this dilemma, I believe that’s why they argue so vehemently for the ability of matter to self-organize, and for some kind of alleged “natural molecular selection” to be this force which can bridge the thermodynamic divide, and help physics run in a direction it isn’t meant to, if only for a short time. If you’re reasonably going to pursue that theory, you have to weigh probability of many theoretical events, and it gets very remote when these are stacked together, so selection is supposed to operate here. Which brings us back to our discussion…about improbability of those steps S1,S2,S3…n occurring! It has seemed relatively “easy” for biologists to say “an organism will outcompete or eat a lesser organism, and thus a more “evolved” complex organism will survive, but it’s not at all easy to envision that with inanimate chemistry, with molecules. So this is, in my opinion a theater in which the self-selection theory can be looked at very carefully, and if looked at too closely, it is found to be grossly lacking in substance or evidence to support its basic feasibility, that would be a single chemical experiment. Let us not raise the bar too high. A single step from S1 to S2 showing a reversal in the tendency of the second law would suffice to demonstrate this. Recall the statement that by de Sousa and others, that there is “chemistry before selection”. Yes where, how and when? I and other practitioners would be more than interested to see such evidence of self-selecting molecules, but the fact that such chemistry would have many useful implications to drug research also has a flip side- such claims in this arena would need to be shown as distinct from the myriad other chemistries already known. The obvious question that I raise here and elsewhere (see comment I made in Quanta https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/ is that it is theory, a theory of chemistry, and yet there is no chemical reaction for us to examine, not even in theory. But let us return again to the probabilistic argument i.e for dissipative theory, the basis of their theory, an example with links here https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/.

What de Sousa must also realize is that this same argument , i.e. the increasing improbability of a final event, gained by a series of highly unlikely events, applies to selection theory- not only for its alleged implications for bio-chemistry, but for selection theory in general. However, what is very different about this reference of de Sousa’s, or rather the context in which natural selection is discussed, is that it is specifically regarding hypothetical environments, chemical steps, which are not known. I don’t believe that it fully resolves this issue. de Sousa means for the context of chemical natural selection to be not that different from so called Darwinian Natural Selection, and in fact teaches that molecules may be selected for in much the same way as Darwinian Natural selection  implies as he states in the same paper:

“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. This process is inseparable from replication itself and must have appeared at the same time as the first replicating molecules in the development of life. “

The notion that life might be driven by what is “most stable” shows a very striking misunderstanding of the chemistry underlying biological systems. Many drugs cause their toxicities on bioorganisms for this very reason, because they are the most stable binding to a specific site, or energetically stable configuration, i.e with organism’s DNA, or an enzyme , which is more stabily binding to the natural molecule. Furthermore, many examples of more stable formations are highly toxic to life, precipitation of water (ice) is a lower energy form of water, but also the binding of metals to organism’enzymes, Pb, Hg, and other toxic metals are only toxic because they bind more strongly, than the more biologically desirable Ca or Mg ions.  These thought experiments verify to us that the arrangments of living chemistries are not the most stable that are possible, but the stability is resisted. How? By infusion of energy by the organism. Consumption of energy prevents water from freezing inside the cells, or tissues, it keeps chemical gradients from reaching stable states. It is absurd to believe that it is a function of a mere chemical reaction, even in theory, since the energy component, is missing from their description. (These are factors I address in my theory of VCS and elsewhere, in “indifferent time”.) They have omitted the energy argument completely in “chemical selection”, and have ignored the opposing forces , diffusion, exothermic drivers, and unavailability of free energy, that oppose the very chemistry they propose.

Many are aware that similar arguments have been made against natural selection theory, for a number of years at a theoretical if not mathematical level.  (For example, those regarding the mathematical improbability of successive improbable events i.e mutations in some tens of thousands of genes leading to positive forward progress), BUT it is also well known these arguments have been rejected vehemently by the core of evolutionary biology.

That it is not rejected here, but is in fact embraced as a feasible mechanism, makes this admonition somewhat more surprising. If de Sousa had made such an indictment of natural selection theory, in the non-chemical sense and in the normal contexts of Darwinian Evolution or New Synthesis, i.e. that natural selection of organisms allegedly operates by similar if not analogous mechanisms that de Sousa himself discusses here and elsewhere, it would be outright rejected as blasphemy against New Synthesis. In fact such views likely would not see the light of day” in terms of peer-reviewed publications. But the important aspect of this reference is that it clearly shows that evolutionary biologists are fully aware that natural selection theory has the same basic weaknesses as chemical natural selection.

Why the willingness to openly discuss the mathematical improbabilities here in the case of chemical selection?” The clear articulation of the theoretical issue of natural selection from a mathematical perspective, the multiplication of probabilities” shows a keen awareness that this SHOULD be a very critical issue in natural selection theory proper. Here, a biologist clearly illustrates the very mathematical probability issue that is denied as being irrelevant elsewhere. Does this show that evo biologists are avoiding the discussion of contrary theoretical evidence? Barring molecular sex, that is, the hypothetical sexual selection of one “attractive” molecule for another sexy molecule, what are we to make of this in terms of the selection theory? Let us review the quote: “…Otherwise, the probability of the entire succession ever coming to fruition tends to become vanishingly small” Would de Sousa agree that the probability that a theoretical series of chance mutations (which are indifferent) also leads to events in organisms i.e. forward “progress” would be viewed as “vanishingly small?”  

What still remains to be understood, are highly ambiguous (if not pseudoscientific) statements such as: 
“Additional evidence for [molecular selection] is provided by the growing number of instances of evolutionary convergence ….There are reasons to believe that molecular selection may similarly come close to optimization under sufficiently stringent constraints…”
in the article that are statements allegedly, about physical phenomenon, completely without supporting chemical evidence or citation. Again, it is impossible for us to determine what chemically, “evolutionary convergence” might mean, let alone “evolution” in terms of chemistry. Does water evolve? How about NaCl? If we are to believe for even a moment that this “chemical selection” is based in science, these chemical distinctions must be made clear by de Sousa and others of the “chemical evolution.” They must provide clear examples of what reactions are chemical evolution and which are not. That is the problem with evaluating any of their examples, such as nucleic acid chemistry. They fail to realize that nucleic acids are merely polymers, no different than the chemistry governing their monomers, these are the ubiquitous rules governing chemistry. The formation of DNA complex, though much more complex than simple atoms, is in principal energetically following the same rules as any other chemical process in inanimate systems). Such terms as “molecular selection”, “optimization” and “sufficiently stringent constraints” have no physical meaning in chemistry or are not defined by the authors of these kinds of claims, (i.e. where is a reaction NOT optimized?) but yet are cited repeatedly and with emphasis by their peers in other publications as fact. And as I have demonstrated here, the “optimization” of chemical processes, at least non-manipulated, natural ones, tend towards disorder and lower energy, but not with less available free energy than they had before, but essentially, the same unavailable energy they had before. So they purport to discuss chemical theoretical processes that are entirely imbalanced in their energy. And as I’ve commented elsewhere in another essay, the molecular selectionists purport to describe a kind of “perpetual energy mechanics”, alleged processes that generate more freely available energy than they consume. The claims of “molecular selection” are as vacuous and shaky in their evidence as they are in their definitions. What reasons are there specifically, to believe that “molecular selection” is a bona fide physical phenomenon, meaning one that is actually different than any other chemistry involving molecular species? Or, that there is anything resembling “optimization” in natural chemistry? They must realize that “optimizing” could imply that their chemistry they propose, in theory whatever it may be, will not ever occur as it is more “optimal” for it not to. It is tiresome that they continue to wave their hands with nucleic acid experiments, which are known to behave within the laws sof chemistry that are applicable to all other molecules, and make certain claims without specifying why a particular nucleic acid is unique, i.e. “evolving”. The term “optimize” imbues the inanimate chemistry with properties it does not have. What we do know, but what molecular selection proponents fail to acknowledge, is that the optimization of all inanimate chemical reactions favors products with less energy and energy of a form that is less available to do work, not the opposite. de Sousa’s argument in this paper to equate molecular selection principals with natural selection theory in general, i.e., Darwinian selection, I believe raises new and important theoretical questions about selection theory in general. But more importantly, it fails to address the problem of “chemistry before natural selection” as it cannot account for imbalance in available energy, a problem that my new theory of VCS, specifically addresses.

Addendum: (September 25,15) When I present my case to reviewers for a new molecular species, say one that is releasing high nitric oxide levels, I must present a reaction that involves two species A and B and give justification for why those species will combine. These are fundamental to chemistry. Furthermore, I must typically provide evidence of a product of A and B, and not just A-B but presumably one that will release another by-product, NO. That means that I now have presented both theoretical and empirical evidence. The proponents of “molecular selection” intend for us to believe that they have evidence of propogative reactions leading to simple nucleic acids. Nucleic acids are far too complex a product , to be used as “evidence” for their chemical arugment, and they have not examples of this in nature (outside of those made my organisms). So, their burden instead, should be to provide evidence of a much more simpler reaction, which gives a product that then drives another. The question that I ask of this theoretical reaction they provide, is thus: does this reaction oppose forces in solution? Does it oppose diffusion, or of its own dissipation of energy, terminating in a few steps? If they insist on maintaining their exemplary reaction is some kind of nucleic acid I pose the same problem(s) for that reaction as well. It is identical. There is no evidence that they provide here and yet it is published by various peer reviewed publiications as though it is factual based chemistry. These publications have not been held accountable fairly, to the same rules that are applicable to other scientists working in chemistry.




(*The so called molecular seletion or “molecular evolution’ is chemistry that is proposed without doing experimental controls or basic verification done in chemistry

Regarding the primary reference de Sousa quotes, recall one of de Sousa’s central arguments: “Originally formulated by Darwin….natural selection also affects replicating molecules such as RNA, as first shown by Spiegelman [7]”

I looked specifically at the citation, the key one, that is apparently cited by de Sousa as evidentiary for “molecular selection”. If you look at a similar Spiegelman and Mills paper, of the exact same year, which deals with in vitro RNA, and RNA viruses, you will find that these are neither self-replicative molecules, nor are they replicating in natural environments, that is, without assistance of RNA enzymes extracted from an organism. There is absolutely no evidence to conclude that reaction of these inanimate molecules will improve their odds of reacting further in “successive” steps as proposed by molecular selection proponents. This is a better reference to Spiegelman’s key work, and others (see below), investigating, “natural selection” and also so called environmental selection of the molecules of interest, which are RNA and also enzymes which process RNA in vitro.






It is interesting that de Sousa and others have chosen these references for support of molecular selection, as there are much better examples of the exact experiment Spiegelman and Mills performed, and these are well known in a process called PCR invented by Kary Mullis. Spiegelman states in his paper:


The availability of a molecule which has discarded large and unnecessary segments provides an object with obvious experimental advantages for the analysis of many aspects of the replicative process.”


That might have been inspiring to Spiegelman and Mills back in 1967, but it is not in any way showing how RNA is “discarding large and unnecessary segments”. Unnecessary to whom? Furthermore, it is hardly showing Darwinian natural selection” as de Sousa claims it to be, and further, it is a gross misinterpretation or at worse, a reading into, artificial non-real desires or wants of molecules which don’t exist. And simply because it is in print, in a cited reference ( citation=^170) doesn’t change these facts. It is well known that small products of DNA are faster replicating than larger kb sized strands, owing to the processing speed of the thermal stable polymerase, typically TAQ polymerase. In fact it is well known that smaller lengths consume nucleotides far better than longer DNA segments, an effect known as “noise” or non-specific binding and one that DNA researchers attempt to avoid. I could say much more about this, but what is relevant is that the reference is not what de Sousa and others claim it to be. That is a fact. And simply because Spiegelman invoked the words “natural selection” and believed with certainty that he’d found evidence” for RNA segments, “discarding” unnecessary segments, he was obviously reading into molecules, artificial wants or desires that do not physically exist. If de Sousa really meant this to be a reference supporting the “first demonstration” of self-replication, he’s truly traversing himself here. The main gist of Speigelman appears to be taken out of context by de Sousa, an investigation into how RNA virus operate, not to show self-replication, AND critically, it is with RNA and enzymes which process RNA. So it is yet another primary reference which does not support or define “molecular selection” experimentally, at least not in a non-teleological sense. The evidence we have for replicating RNA would give no support for de Sousa’s statement that molecules “desire optimization” or that some non-chemical phenomenon as chemical selection is occurring in molecular broths in the sea, or hydrothermal vents or anywhere else..(see the paragraph where de Sousa states “additional evidence…” above). What you will find however, if de Sousa is willing to cite these references, is that RNA and the enzymes that process RNA, do not exist or function outside the test tube for long. Why is that? Let us do a thought experiment. Let us put large quantities of highly active DNA or RNA along with enzymes, into a large vat of chemical amino acids and salts. After a time t (sufficient), will we find the DNA or enzyme to be HIGHER in order? That is, more reactive than it was at t=0? Consider that molecules in free communication with adjacent molecules react with these, and reduce their energy with a variety of irreversible chemical processes. What we expect to find is that the molecules did select other species, but these are lower energy species, to effectively dissipate stored energy or potential energy. In fact, there is no evidence to lead us to believe that any other chemistry is expected. This basic experiment would directly refute their claim of self-order would it not? It’s merely an example of the kind of experiment that they should run as a control, and explain why and how, their chemisty is or would be any different. And it’s the exact question I would suspect that de Sousa and others who support the delusion and pervasive myth surrounding “molecular selection”, would not want to answer.



  1. http://www.weizmann.ac.il/complex/tlusty/courses/landmark/Speigelman1967.pdf
  2. In Vitro Analysis of Self Replicating Molecule, S Spiegelman 1967 http://www.jstor.org/stable/27836918?seq=1#page_scan_tab_contents


  1. Fournier GP1, Alm EJ. (2015) Ancestral Reconstruction of a Pre-LUCA Aminoacyl-tRNA Synthetase Ancestor Supports the Late Addition of Trp to the Genetic Code. J Mol Evol. pr;80(3-4):171-85. doi: 10.1007/s00239-015-9672-1. Epub 2015 Mar 20.

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.

Saturday, July 11, 2015

II. An Unexpected Application of Virtual Closed Systems: Self Sustaining Machines

Opportunity Rover, NASA

Firstly, before we examine the implications of Virtual Closed Systems (VCS) to the interesting problem of self-sustaining machines, I want to identify some of these misconceptions. Although I’ve already discussed them they are important to identify since when they are accepted as true, then they directly interfere with understanding physical concepts here or in the grander scheme of things, make the correct evaluation of any new scientific theory irrelevant. *The latter argument is more severe, but it is accurate, as the rather blind acceptance of any current assumption without a physical basis n essence justifies the acceptance of other assumptions without physical basis.

1.       “Dissipative processes in nature are actively doing work to cause change” (we discuss this specifically. This teleology is largely taking the form of Constructive Law but also other postulates.

2.       Molecules can evolve and even select themselves. (see links)

3.       Salt gradients can remove “waste” molecules from a system. Again, this is an assumption that nature is actively doing work in an ‘open system’. As with the continuous cooling coffee mug” we see that entropy is ‘maximized’ continuously in natural systems, as any VCS is in continuous physical contact with any other region at all times, hence the notion of continuity.

4.       A surprising result gained from testing VCS theory is that such natural “engines” even if they exist, would not fully account for how life currently obtains energy and removes entropy. What has not been recognized is that the force of entropy can be at a maximum within a cell, and still must be opposed by the cellular system. That opposition (to the tendency toward S in requires an impetus or opposing force FN or FL.

[One of the real burdens of describing my theories is to attempt to overcome the stereotypes that have been created en masse. The evolutionary scientists (or perhaps we should say ‘those who utilize the selection model, in chemistry or in biology) have already created preconceived notions in people's heads that alert them to theories which offer alternative perspectives, (i.e. to ‘selection theory’) and to automatically ignore them. It is rather brilliant psychology on their part. (Little wonder there's an outpost on the fringe of this empire known as evolutionary psychology). They even have some of the physicists whom I greatly respect, such as Hawking, essentially going along with this way of thinking. But one of the effective tools they use is to engage and foment creationist sentiments, thus creating a villianous anti science meme that they can invoke at will, against anyone they perceive as a threat to their ideas. They have gone to the press to create this strawman so large and well known that it is very difficult for many not to step into it and avoid their use of that label. [To get some appreciation for just how far these "tendrils" have expanded, look no further than the current debate about "free will." Press this button as I have just possibly done here, and you will be automatically relegated to that of a non-scientist, "a believer".] The villainous anti-science meme is not isolated to evolutionary scientists, but is used against their own, including physicists, who often raise their hands and say “…I’m not saying evolution is wrong”) and one need not look very far in the science commentary sections of major papers for recent examples. But it is hoped that if we state that invoking "selection" is not a recognized or valid chemical term, force, or impetus, it should not give valid cause to immediately stop reading this article.

The other stereotypes they play to great effect is the "intitutionalization" or “credibility” card. They have created an institution around their scientific ideas, but not only that, many of the basic tennets that I am proposing to overturn, to challenge, are essentially the sacred cow theories that are taught in higher education, i.e. “life agrees with the second law” or mis-education about what a force actually is, or entropy, or basic causality, so the education problem is significant hurdle to any new thinking outside that requires new operators or paradigms outside that perimeter, and frankly I'm not sure students in this day and age are even given the right tools and open background in which to objectively evaluate in a truly evidence based approach, what the best theory is, or what precisely should be the criteria of a theory. This is in my opinion a STEM problem. As I noted in an earlier post on “Constr…Law” a Physics Educational Board has adopted Constructal Law into their curriculum. In my opinion thermodynamics will need to change in order to come to terms with the problems that it cannot currently solve, and with new rules of causality, it is stuck in the days of Boltzmann and Carnot.

In other respects, I have mapped to some extent the reactions to my theory, (which manifests or is embodied as a critique of cyrrent theories) and the main one I encounter is a complete lack of understanding of its basic principals. They grasp part of it, but it is usually only that crucial aspect that apparently disagrees with other theory. These are apparently, scientifically educated people. I've heard them say "the forces in nature are not balanced as you say, but are continuously out of balance." That is entirely the wrong meaning, and a hostile reading of what I stated. I was speaking of normal forces as it relates mathematically, to a larger principal. Have they not actually read or studied Newton's laws of motion, the essence of what a force is?

Some are unable to even consider it, because I can detect that they have attached some extraneous meaning a false premise, which is used to reject it out of hand. I bring these issue to light because I engage other theories only for the purpose of testing their predictions in the context of the unexplained phenomena I have described here, i.e. that "self-evolving" molecules, a favorite go-to of evo theorists, do not explain chemistry in any way and misguide it.]


Now, I want to turn to the issue of how machines can self-maintain themselves, an issue we discussed previously.

One of the other aspects of this problem is in definitions and observations. I would ask of a reader of my theory, the following. Do you believe that a mechanical device can sustain itself without human intervention?
No? Or, Yes?

[And by “sustain itself" we are asking theoretically speaking, because to do so it will encounter Q number of events thwarting it, and it will have to have R number of responses. However the response or maintenance we realize will have to come from systems which are themselves subject to degradation, and so these too will have to be maintained. The clock starts we realize, the moment after these systems are manufactured by humans, both on their energy source but also materials. We note further, that the clock begins on the systems that make new systems, in other words "without intervention" means it is isolated and so the machine making new machines, say on Mars, would be subject to the same law of degradation, what makes the new factory parts..etc? And so those who believe that machines will "take over" the earth are largely engaged in a kind of fantasy world or at least they have no basis to resolve the paradox just described here. But we turn away from this momentarily to ask the more pressing question:] 

If biological and mechanical devices are equivalent as many have said, does this mean that biological devices should not be sustainable?

See also my definition, or basic principal I wrote yesterday, Friday..(June 3'15

That question goes to the heart of the issue I've raised in the virtual closed system model. And I'm not sure the argument is entirely understood. Let's assume the answer is yes, a machine will require human intervention to continue operation. [Such a question is highly relevant to autonomous machines, for example machines like the Curiosity rover on Mars, and the problem of how to make them more self-sustaining, or even independent.] I've postulated this to be reflective or resultant of an underlying principal of a system that not only behaves, as it is closed, but also can be seen to be deficient in a certain form of useful energy, the kind that can do work. We answer yes, because we see that not only does the machine run out of reserve, potential energy, it also exhausts its supply of another form of energy, energy capable of doing useful work, so that its potential entropy decreases. What can be seen is that in this situation it is deficient of this, which I believe I've called "relative entropy" and we've defined it as total energy required in Eo to include all of imputed energy flowing into the system. I've kept it very general as its obvious that even at the most basic level, I'm not going to be agrreed with on this entropy. Most will assert that the robot or machine, only requires human intervention because it is not advanced enough yet, not because of a basic thermodynanic barrier.

I'll return to that point, but I want to discuss the other implication that is derived from this answer "yes". Because we also made the correlation between inanimate and animate machines here, under this postulate as a test , and many probably will see its a test if the second law as it relates to living things. Once equated, which I justified by invoking one of Newton's rules of philosophy, (though we can just equate it anyway for argument, we don't need his permission!) Then we can ask, do living machines also have the same dilemma? In the system that they are contained in, a virtual system with energy entering and leaving, will they undergo a senessence identical to any other organized machine? Why , or why not? As I said in my paper, the answer is 'not' , and the reason is because living machines" acquire energy from the outside , from the sun. And these are plants. Plants ARE moving, highly structured, elborate "machines". We don't have to think of mobile creatures to get sophisticated- plants are incredibly sophisticated, and derive their energy directly from sunlight. No middleman required.

[*So in this sense this theory is actually quite useful. It predicts that for machines to be self sufficient, they would need to extract energy just like plants. But it raises an interesting question, is the solar energy they extract really the total energy needed for self-maintenance, i.e. to avoid the dilemma facing the Martian robot all on its own? In other words, does this theory correctly predict that another kind of energy is necessary, this relative entropy" and is extracted by plants since they are essentially mechanical and do work on their environment, and are independent. So we would be talking about a completely new kind of energy extraction required, one that is somehow extracting relative entropy from sunlight to be used by the isolated factory and machines to sustain themselves, it must be sufficient in extraction efficiency, to overcome the positive entropy accumulating in that system.]


I want to go back to the equilibrium statement, [where I discussed equilibrium in terms of Condition I or II] I mention the minor condition of 3 b.y. (billion years) that's a critical point. We have already this experimental case of plants, a 'machine' that sustains itself by using energy from sunlight, as a test case of the virtual closed system that is for all intents, perpetual. Those who claim it is not, even theoretically perpetual, I believe should provide evidence to the contrary (as we have not "theoretical" case in which they are not). I say 3 billion years may as well be perpetual. That to me is a dilemma worth considering, because of, and in light of, the barrier encountered by the complex robot in the previous example. In light of the answer "yes" complex machines will always require human intervention, as they CANNOT operate continuously in a closed system. Critically, nor can they operate in virtual closed systems, which I propose can exist within open systems.

That brings us to the other issues of energy inputs and equilibriums, particularly entropy equilibrium , of the system with the outside.

Why can't a machine like curiosity, run perpetually? The key realization here is that it lacks the input of a critical energy, relative entropy, and I posit further, that there is no way physically for it to gain this back. Yes it is an ingenious device, it will run for a long time, but its lifetime is limited by availability not of potential energy of solar or nuclear power, which is indefinite, but by depletion of this "relative entropy", another form of entropy.

So the question is, how do living machines exist, and how do they sustain themsleves as perpetual "machines?"

With this theory, of VCS, we can see that the problem of understanding the origin of life is  surprisingly, and intricately, related to the practical problem of how to make machines that are capable of exploring the vast reaches of our solar system and beyond. It predicts that although these machines may be built to extract energy from their surroundings, solar or other, this form of energy may not be sufficient, as such an isolated machine is located in a system in which it is being depleted of relative entropy to maintain itself. We are speaking hypothetically, as there is no current means to extract this relative entropy from a source such as sunlight. Based on the VCS theory, we can conclude that living things, which are bio mechanical and self-sufficient even in a virtual closed system, are able to extract this form of energy to offset their own increase in entropy.

The other implication that may be apparent is that in conventional machines there is no FL, that is FL =0, despite the input of energy. Why is that? This is a rather surprising finding. particularly since it appears to be obvious that machines do a great deal of work. If I throw a ball down a mountain, the ball will do new work, that is work not on average produced by the mountain's natural erosion. I will effect a change in doing so. Likewise if I build a contraption that lodges itself in a river, and diverts the course of the stream in any way, this also does some net work in addition to the level normally expected in the system. Such manipulations are measurable and real. The machine does oppose certain forces and does work, but this work, in terms of its net average against the system, does not exceed FsubL. The work it does is identical to the work my heavy ball does in rolling down the hillside. The critical notion is to realize the continuum principal at work and the Normalized forces surrounding the system. the consequence of the net forces "exerted" by the machine predicts that such a machine cannot be self-sustaining. It does work in one respect, but fails to do work, to oppose the tendency the net force vectors which are tearing its structure apart. The machine, we realize in a VCS model, does not oppose any of the surrounding forces, but instead, diverts these to a lower form of energy. But there is no difference between the energy I am "winding up" in the ball, which then converts to kinetic energy as it collides, and the energy stored in the gas tank of a machine. This relates again to "relative entropy" the inability to extract this form of energy from the rather abundant solar energy flowing through the VCS, which comprises the total energy, Eo, incident on the system. FL is opposed by FN the normal force opposing it, as we've described elsewhere.