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 F_N 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 E^o that is flowing through such a VCS will change its vector and generate a force opposing itself. E^o, 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 E^o. But in this E^o 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 F_N but also F_L . F_N  would be the force “experienced” by an application of F_L but in principal either F_N , F_L designates the other’s presence in the solution. Without such a force, there can be no work done as the flow of E^o (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 F_L, 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 – F_THERM. The consequence of this principal is that we do not find vector such that this vector would be F_N +F_THERM> F_THERM 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 F_N 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 F_L or F_N. 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.

'Self Replicating Molecules': Why This Theory Should Be Rejected

One paper on Self Replicating Molecules [1] begins thus…“The ability to invent new materials that replicate themselves would lead to a paradigm shift in materials discovery.”  I do not doubt that. But so would the ability to invent new machines that produce more energy than they consume. That too, would revolutionize a few things as well. Sadly, neither one of these is based on solid physics, and largely this is due to the similar problems of thermodynamics.

We note that in the abstract of this paper, it is proposed to “test” virtual colloidal particles in computer simulations. And it concludes that it makes (with such computer models) such virtual colloidal particles replicate successfully. When one considers the fact that these are computer algorithms making simulated molecules, such claims are rather dubious, as to their correlation to actual physics. We note that these “molecules” themselves, are nothing but algorithms, which they’ve assigned certain rules, not unlike any other programming system, they of course must have logical rules of how the program responds. But unlike nature, how does a program “behave” differently than the experimentor expects? In theory, aren’t these results precisely what the program dictated them to be? Another very important question to ask, in my opinion is to the relevance of such models in showing anything useful, particularly since “self replicating molecules” would be expected to be real chemistry. This is after all an applied division of science, and though I’m quite familiar with computer models in chemistry, there is a very large difference here. In chemistry, one is not attempting to prove necessarily that thermodynamics might be violated. The models are based largely, on pre-existing empirically validated assumptions. These assumptions are not unlike more simplistic mathematical models of chemistry that are ubiquitous, i.e. stoichiometric laws, rate constants, and so on, that current computer models must account for.

On the other hand, there is no existing demonstrable model for self-replication of molecules. Nor are there or would there be under such circumstances, any parameters for doing so. In other words given the problem area and the circumstances facing such experimentation, are computer models not doing more to convince researchers of a possibility that doesn’t exist? For one thing, how precisely, does one “test” an output in a virtual system in an independent fashion?

I’m going to summarize and conclude the disagreements of my theory with self-replicating systems here:

http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html

Firstly, the self-replicating model presumes that the potential entropy can arbitrarily be maintained by the molecular system. In other words, it assumes that entropy can be passively removed by the system of molecules, in direct contradiction to what I propose HERE. (i.e. in a virtual closed system where the potential of S(inside) is equivalent to the potential of S(outside) in a natural system as posited by Condition I.

Secondly, they are in fact assuming a non-self replicating system in performing a computer simulation. One cannot “model” such a system by using a computer to demonstrate the production of self replicating molecules as this violates the entropic boundary. We can state that in this case, they are adding external work energy, and artificially lowering the entropy potential of the system. As I discuss in the case of machines, either perpetual energy or perpetual motion machines are forbidden in the virtual closed system of Condition I or Condition II. These results are not what would be expected. The amount of useful work energy, E^o (We have made no distinction between total potential energy here, it is net energy) that is presumably entering the system is not sufficient, i.e. E^o<< than the useful work energy required to maintain the machine against its intrinsic increase in entropy. I have defined potential entropy as the actual difference in entropy between itself and its surroundings. And though we can imagine that potential energy is being added to the system from an outside source, capable of doing work, thereby creating the impression that the entropy is being lowered) what is discovered in this model is that in the closed virtual system no work is being performed and there are specific conditions that are discussed for why this does not occur. As I further discuss in (27) HERE, we discover that there is a critical lack of any imposed resistance. Diffusion and heat loss occur passively from the energetic molecules until they reach the classic maximum entropy permitted. The problem in understanding this new theorem is defining entropy differently. Boltzmann, Schrodinger and others have defined this I believe, classically, without making exceptions to animate vs inanimate systems. We are defining this in a special case of the virtual closed system, which is a natural system without sufficient input of E^o to do useful work on the system. As we’ve said, in this case we should not expect to find a potential difference in entropy between the inside and outside of such a system, i.e. across the “entropic barrier”, as there is no means to increase or decrease the absolute entropy of a system of molecules, nor can the actively transport lower entropy into and across the barrier to reduce entropy. This is rather surprising and disagrees or contradicts with the conventional entropy definition.

 

The dictates of such a system are not the natural model, if they were, then obviously they would already know what the algorithm was for the Second Law. Obviously these are not known to  anyone. They are obviously not taking into account the entropy that is built up in their system. If they did, they would realize that it conforms to the Virtual Closed System model I’ve described recently. Regarding replication that is demonstrated, again, in computer simulations, there is perhaps, more “real” replication in a SIMS game. The “respawn” that occurs in many games is one example of perhaps “self-replication” that follows rigid programming rules and algorithms of the program, but of course no one seriously believes this has any bearing to reality. The offices that the programmers of SIMS use, likely don’t look like the Harvard physics, nor do their algorithms say they’re following some arbitrary “chemical rules”, but the way in which “Mr Sim” and “Ms Dor”,  “get together” and “replicate” is presumably based on algorithms with similar hard and logical assumptions, just like a simulator at a physics lab. Enter the variability of inputs of a player, and you have perhaps many different “unexpected” outcomes. These are no more “chemical” than the SIMS buildings are physical structures obeying the laws of engineering.

One of the presumptions of my thesis is in fact that it is not possible for such manipulations to be conducted on a system, as these directly interfere by the disruption of the input of useful energy into the system. Self replacing systems violate the “entropic barrier” of a virtual closed system, of which an inanimate system of molecules is contained, if it is truly self-contained and isolated as is assumed.

Under such conditions, they would have more chance in waiting for the spontaneous evolution of prokaryotes than of witnessing the self replication of a group of molecules. And if my theory is correct, the unexpected result is that it may be much much harder in fact, to observe a system of molecules self-replicate than the former situation, with the proviso that there is space for the evolution of higher life forms, (i.e. the virtual closed system is large enough). So allow another 3 billion years,…thus one would have to wait essentially, for an infinite amount of time. Also, if my theory is correct, we find that it might be easier to make energy and violate the first law, than to do what the proponents of self-replicating molecules propose to attempt. Where is the energy diagram, the pathway? If this theory is correct, such energy barriers might be of much greater difficulty for self replication of small groups of molecules, than for entire organisms [2].



1. Zeravcic, Z and Brenner, M Self Replicating Colloidal Structures (2013)http://www.pnas.org/content/111/5/1748.full.pdf+html
NOTE: The paper might not in fact assume a strictly closed system, however it is cited as support for theory of Self Replicating Molecules more generally, and specifically to those references I've already discussed in other blogs.
2. (see argument 5 *http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html)
3. Saccana et al (2010) http://www.physics.nyu.edu/pine/reprints/SacannaPineCOCIS2011.pdf

Of Beer, Sailing, alien life, And Some Practical 'Every Day' Implications Of a New Theory

Don’t take my word for it. It’s a proven fact of science. Self-replication has never been demonstrated in the laboratory. That is, I suspect, why the authors in the Cambridge study, one of the references I site HERE, are deliberately "hedgy" with such statements as “It's great progress…but we’re still far short of a molecule that replicates itself.*” Progress. What does it mean? The word doesn’t mean that you’ve arrived, in fact it doesn’t (necessarily) mean you’ve even gotten close. You might have just started, or just thought about starting a journey. It's actually rather ambiguous. If you stand outside on a dark night and jump away from the earth as hard as you can, does this mean you’re making "progress" in getting to the moon? It’s a good analogy I believe closer to the physical reality of the problem than it might portend, and not such a ridiculous analogy as I'll explain in a moment.

I’ll give you one more that's relevant to encapsulating the true meaning of such "progress" and that’s the mathematical paradox of always getting “halfway there..”explained to me some time ago by an algebra teacher who was a bit of a comedian. It goes like this: If the distance you traverse is always defined as half way between the point you start at and the point at which you finish, you are correct in saying that you are "making progress" but do you ever get to your destination? The corollary I remembered was: You can’t get anywhere by half-assing it. Both are excellent analogies if not metaphors, for depicting the so-called “progress” that so many peer reviewed articles seem to convey  or believe they are making, despite the fact that there is no known agreed to theoretical basis for believing it is possible.** The first statement is factual, but the subtle take-home point im attempting is that there's no such thing as achieving the "partially" impossible.

There is a good reason for all of this, and I’m providing a new theory to explain why that is HERE "Does Life Violate The Second Law of Thermodynamics? Implications of Virtual Closed Systems". The problem of life’s origins is steeped heavily in a messy intimidating science called thermodynamics. But thermodynamics is not actually so intimidating or messy or even theoretical. It is exactly the kind of science that you may have discussed, unknowingly with friends while you were taking a trip in your car and you debated about the most ‘economical’  route to take from here to there. However, I think a very good practical example of this sort of science of energy accounting is in sailing. The confounding problem I have had many interesting debates about is “is it possible to make a sail craft move directly upwind, even slowly?” One of my favorite sail contraptions to test the idea, is not a sail, but involves a kind of spinning wheel with cupped sails on it, that rotates in the wind because the "cups" pick up more wind on one side (going with) than on the other (going against), and so it drives a propeller. It should be easy to steer such a craft into the wind, just ease the tiller. After one realizes all the various contraptions that might do the job, the gut feeling is that you’re breaking some kind of law of nature. And you are. Well that in essence, is in layman’s terms what the theory I’m describing is about, it is applicable to those same more tangible and conversable issues as “sailing into the wind”. But a talk about how life might spontaneously emerge from a mucky film of organics on a rock or in a pond, is also what I would classify as “beer conversation” which can be had on a boat or at a barbecue. It’s that practical. But unfortunately in my paper, there are no beers. Just the same,this article is labeled appropriately, “beers sold separately.”

Briefly, I’ll diagram according to the specifics of my paper, why the exhibitioners at the booth, the ones you may or may not have the luxury of seeing at the “Royal Society” exhibit in London town, have it completely wrong in terms of trying to sail “straight into the wind” and defy the laws of nature. (and don’t take my word for it, only. that’s what they meant by “we’re making progress”. You can make progress too, in going straight into the wind, the only problem is, it’s really no progress at all in terms of NET result. The only way you get to go a bit straight up into the wind, is because you already went off in a direction AWAY from the wind, so your NET progress reveals that you actually lost distance, not gained. That is why NET is so important in my paper and anyone else’s, (especially when a few beers might be involved).
And what these researchers are claiming, in papers like these, is precisely that they making progress in making self-replicating molecules, but the problem is that they are not showing you what the NET result is. They do not include the fact that they are adding work and energy to set up such experiments, that would be the DOWNWIND requirement, as we just explained, we have to go downwind a lot in order to then steer back up wind. These researchers don't include that bit in their equation, and that is the point I make in my paper, though it's indirectly implied by the formula. The other derivation of my paper would take it a bit further, however. And I believe if one truly understands what it is I'm theorizing, my analogy I make between spontaneous self-replication and jumping hard to get to the moon will make sense. Perhaps these are more examples" than analogies!

My belief is that if a theory of science is actually real, if it has certain operational aspects to it, it should be applicable to many different scenarios, because it is interconnected. In other words, you CAN get anywhere from here, if you’re willing to use the not so ridiculous metaphor (more analogous) that we can "walk" via the thermodynamics of energy flow from any point to another point. Energy is always accounted for, it is never lost, just altered. The point is, you can follow energy around, just like matter, and see where it goes and what it’s doing. When we truly "follow" what these researchers are claiming, we can see that they do not include a very critical picture in terms of where the energy came from to make their molecules do things on the bench. That also, is in layman's terms another principal I discuss in another blog.

I said I’ll be brief and already I’m heading towards 2-3 pages! So I better wrap it up. Let’s go back to the conept of NET gains, and specifrically if we can to what it is they claiming over at the exhibit in London. They say:

"Reactions between water, CO₂ and the rock mineral olivine in these oceanic melting pots can give rise to the organic building blocks needed from life, from amino acids needed for proteins to the lipids found in cell membranes. These organics can be concentrated by convection within these vents, theoretically giving rise to protocells and complex organic molecules including DNA."

Which isn’t at all different from what’s already been done and said many times before, it’s just a new fangled variation. This represents in thermodynamic terms, a "contraption" or scheme for how to sail into the wind. The fact that it's chemical makes no difference in thermo science. Which isn't frankly much different than what everyone else is doing, or has been attempting for over a hundred years.

In a “nut shell” they’re talking about self-assembly and stating that if you have some random molecules, say rich organics just like Haldane’s (of 1929), [or some rich organic molecules I've made in the lab] if we shine light on it and give it heat, long enough, it will generate more complex molecules, which may then organize to form even “protcells” and DNA, but at that point we can assume that they mean a proto-form. That’s a bit more complex that saying you can “sail directly into the wind.” But not much. That is the simplicity of mathematics and physics. Well we can apply the diagram from my paper to show this won’t work. Wee can put the theoretical ocean with its broth (think something like vegemite only more diluted, AND supernova gamma irradiated, or perhaps like comet residues or the dredgings from a Europan lake) in that bubble and expose it to heat energy from a source, say the sun. The ‘bubble’ or virtual closed system, is really just a convenient way to calculate NET gains of energy or loss. We have energy going in and energy leaving, it’s very simple. What we want to see is if we’re making progress over time. (let me say one more thing, this isn’t about THEM specifically, the well meaning siceintist manning the booth, it’s about this one idea in question, and we’re trying to see if it’s really practical or not). So heat and energy have been flowing into the bubble, into the virtual closed system, and have we made progress? Well, hardly anyone, including myself can just look at molecules and tell you if they’ve improved or not, howeer, fortunately we don’t require the normal sophisticated tests for measuring if S is more negative or not, another intimidating word Entropy. We can in fact, simply take the molecules and see if we can do any work with them, in other words if we put them in a machine, one that is VERY efficient and doing the least possible effort (possible), can we measure any work energy? This can be measured in simple calories the same calories used everywhere. The answer is or should be, if my model is correct, and theirs is wrong, no. After we allow the system to cool for a few minutes to room temp” i.e. the surroundings, we should not be able to extract any work from those molecules. But the other thing I haven’t specified is how long we let it go. Keep in mind that we are taking the organic molecules as is, from the broth, and exposing them to heat energy of the sun for a period of time. We measure different time point, say after 1 day, and 5 days, and a month, and then plot our progress.

How are we measuring a NET gain? That is automatically “calculated in” with our experiment. This is because we are taking ground state materials, from the sea water, and then measuring if these molecules can do work. The difference in work will be the NET gain in work, relative to the environment. One can criticize this experiment by saying “well, all of the molecules received sunlight!” how can there be a difference? That would be a good question to ask of their theory. We can repeat the experiment and illuminate different parts for different times, let them sit for a few hours to equilibrate, (assume the sun sets) and then measure them. We should not have differences in work. And again, we have not even attempted to form a form of life, just more complex molecules capable of doing useful work. How does it relate to sailing? The “wind” in this experiment was the sunlight, the energy supplied by it. And our “sailboats” were…?

The reason my paper is worth a read, is because I am dealing for the first time ever, with WHY this result is possibly expected. That it is expected is more or less highly probable. Frankly I find it rather absurd that they continue to get mileage out of this approach, for example, of claiming "progress" and I've criticized it as doing something akin to perpetual energy, (which I believe it is virtually doing just that, and one can see why that is with a Virtual Closed System). 

And the other criticism I've leveled at them is the fact that they refuse to describe the chemistry, it is instead usually just "smoke and mirrors" and hand waving. If we truly HAD such chemical systems, in which we simply put a random mixture of organics into a vial and added heat or light to make them “evolve” and "select themselves" we would already have these types of chemistries everywhere. But we don’t. So that’s a question to ask the booth exhibitors, why aren’t there spontaneous generators? Because most chemists know that putting a random broth of chemicals in a bottle outside in the sun doesn’t make new useful polymers. There is a good reason that these experiments have failed since Leduc and others in the 1890’s (P Leduc 1911 "Mech of Life). The fact is that thermodynamics is not well understood, and the territory has been opened up greatly by the unspecified nature of this arena. Though it has been stated in different forms, that nothing can violate the second law, it does not put boundaries on how much entropy can be made. Living things are considered as variations of dis-equilibrium phenomenon, the current position. It has never been shown, theoretically, or in a practical sense, why it won’t work- not until now. It is perhaps hard to believe how a theory can have implications to sailing, how life might arise on other planets, and even beer, but that is the fascinating aspect of this basic theory.


 

 *(Note that they [physicists] did believe that the Higg's boson was real, in theory, and then were successful in proving it physically)

 

 

1.  Regarding "self-replicating" molecules here's a good article-

http://arstechnica.com/science/2013/10/25/quest-for-self-replicating-rna-edges-closer-to-origin-of-life/Nature Chemistry, 2013. DOI: 10.1038/NCHEM.1781

 **Their conclusion regarding RNA replication (2013) was the following: "It's great progress, but the result still comes far short of a molecule that can copy itself. For one thing, the ribozyme tended to stop short of the end of the molecule it was copying, mostly because the two fell out of contact."

2. P. Leduc 1911, "Mechanism of life" https://archive.org/details/mechanismoflife029804mbp

 

 

 

Authors Should Explain Why bcl2 and P53 Genes Are Not Important To Skin Lightening in Neandertals? A Problem in The Methodology of Harvard Paper http://dx.doi.org/10.1101/016477

[What is the purpose of this thread? In actuality, this thread shares commonality with the other theories I have proposed in these blogs, relating to causality, and is therefore relevant to the other theories I have discussed here. Part of science is testing alternative, new, if not existing hypotheses, and so this discussion is also relevant to that issue in a broader sense. This relates to the existing causality in organisms, the selection model and its "effects" on the presence of traits and/or genes, and so this discussion is highly relevant to the causality of that model. In my opinion, the bcl-2/p53 gene issue" is a good test of their central hypothesis. But a far better theory which at least may encompass such complex phenomenon would be one grounded in thermodynamics, and that begins with the correct view of thermodynamics relative to machines, and living things, in a new theory, Virtual Closed Systems]


I do enjoy a lively science discussion. Especially fending off nasty troll attacks whilst attempting to engage the author(s) in the errors of their papers. That is why I'm still waiting for the source authors of the Disqus article I posted about earlier, over here, to reply to a relatively straightforward scientific question regarding a significant issue with their methodology. I don't care much for "we've done it this way all along" reply, that sort of mind set, though of great befit to dogmatists, would have us believing in pre-Copernican astronomy and all other sort of 'weird shit', also known more technically, as non-science.
But there is also I believe good reason to criticize this paper if only because of its rushed sense of delving into a subject with minimal data, (It's far more complex than identifying just a couple of genes) and bespeaks an agenda that goes beyond science, and so another aim here is to simply point out that other than having done the sequencing, I don't believe they are even close to making any case for what they're concluding. Isn't the subject far too complex for the limited information available?, why the necessity to rush to sketchy unfounded conclusions? Here's the paper: http://biorxiv.org/content/early/2015/03/13/016477

According to the article: "The paper doesn’t specify why these genes (SLC24A5 and SLC45A2) might have been under such strong selection. But the likely explanation for the pigmentation genes is to maximize vitamin D synthesis, said paleoanthropologist Nina Jablonski of Pennsylvania State University...or, evolving pale skin that absorbs UV more efficiently or favoring lactose tolerance to be able to digest the sugars and vitamin D naturally found in milk. [2]"

I also note that a well meaning scientist, a geneticist, attempted to answer the question, but unfortunately tried to lead us away from the issue by invoking an argument that disqualified the question (certainly a good attempt, well done!). He wanted to assume that it wasn't an issue because, he didn't believe it was an issue. "These genes" he said, couldn't possibly be changing, because if they did, it would be fatal, meaning non-inheritable. A fine bit of logic if it was correct. But here's at least one reason that fails. There are many subtle mutations of these genes I brought up, and that is precisely why they are important to causing so many variations in how people, today, respond to cancer. Look no further than the extensive work done on bcl-2 mediation and up-regulation of cancer resistance to drugs among others. And we know some are at risk for cancer under all sorts of conditions, while others might not be, and  the gene P53 is one that essentially "turns on" cancer. I heard nothing further. One can argue that P53 and bcl-2 don't mutate under any circumstance, but that contradicts the other evidence outside of evo-biology, in cancer research, that these are important genes in mediating cancer. So then we are simply talking about the specific regulating genes, why aren't these factored in? The problem of their methodology has not gone away by naming some other genes, which they fail to mention. I could just as easily argue that Vitamin D genes are also regulated by other genes, which are also not mentioned in their paper.

So we can see that the claim here in their paper and elsewhere, that skin lightened to yield more Vitamin D production, is offset by the potential increase in skin cancer risk to the individual. At the very least if one claims one variable changed, i.e. a gene for Vitamin D production, they need to show why these other variables, genes for brcl-2 or P53 stayed the same. That's a basic methodology of science. These genes absolutely were present in Neanderthals, as they are very important basic genes. So where's the genomic sequencing that might support this?


Disqus authors, and that includes source authors benefiting from the publicity of their papers, do in fact, respond to comments on their blogs, and this comment I posted there was virtually the same day it was posted onto the site, so it was plenty "fresh". And though the atmosphere on their particular press-release is "dog eat dog" that's no excuse for not replying and they should enter the fray they created and permitted, just like all the rest. I posted essentially the same question on their archive site bioRxiv, but have had no response. One would think that out of seventeen or so authors on the paper, one might have the time...

If we imagine skin lightening, in ancient Neanderthals and Homosapiens, early humans who migrated to Europe, thus de-protecting itself from the sun's harmful rays, it would be logical to ask how this might increase skin cancer rates and if this would not outweigh the apparent "benefits" of more Vitamin D? But even if both had to change, how do we know, from a theoretical standpoint, which of these was the most important? A true believer in his ability to discern Vitamin D production in skin as the single most important reason for ascendance should also be able to reasonably explain why the 19,997 other genes were NOT so significant in that same alleged outcome, just as one is forced to do in any other science. As the two other genes I brought but by way of example, are directly involved in the body's response to skin cancer as well as other cancers, that is really the other question here, the methodology used to discern one gene's influence over another.

We are to somehow ignore the direct biochemical contributions of these genes or at least regulating genes for P53 and bcl-2 effects in cancer survival in ancient peoples, while we pretend that a gene for Vitamin D, is the important factor. It's been argued that evolution needs to eventually be more quantitative like the other sciences (see R. Highfield 2013, Edge "What Theory Needs To Be Retired?). But that isn't really at issue here, methodology, the basis of causal analysis of the problem, should not be at a different standard for one science field or another. Chemists and physicists do not have a magic eraser that can be used to wipe out causative factors that are important to the general thesis, that may obviously be contradictory, why then should these scientific authors not be held to the same standards?




Notes:
1. The question I posted to the author's on the bioRxiv site:
My question is regarding the methodology behind the paper, an "upstream" issue as to why the authors chose to select only certain genes such as the SLC...A5 and SLC...A2 as opposed to looking at many other genes that may have been available in the samples. A central working hypothesis is that these genes in question gave some advantage, that led to skin lightening and possibly greater Vitamin D production. The question is, how can other genes like bcl-2 and P53 genes be excluded as being extremely important, to "Eight thousand years of Nat Selection..." since these are critical to modulating cancer susceptibility (see Genta studies etc on cancer) and would be it seems, more activated when skin lost pigmentation? Would the risk of higher cancer rates not offset advantage of Vitamin D production? It is not a mutually exclusive issue, it is a matter of why as I ask above, the methodology does not require looking at these other critical genes in the skin, and their impact. So how can they be excluded from the study?

2. Iain Mathieson, Iosif Lazaridis, Nadin Rohland, Swapan Mallick, Bastien Llamas, Joseph Pickrell, Harald Meller, Manuel A. Rojo Guerra, Johannes Krause, David Anthony, Dorcas Brown, Carles Lalueza Fox, Alan Cooper, Kurt W. Alt, Wolfgang Haak, Nick Patterson, David Reich "Eight thousand years of natural selection in Europe"

doi: http://dx.doi.org/10.1101/016477

 

3. http://news.sciencemag.org/archaeology/2015/04/how-europeans-evolved-white-skin

Summer Science Exhibition of Self Healing Polymers Of Case Western and Oxford University Smack of 'Pipe Dreams'

Can a structural, material really self-repair? And can molecules, or polymers, really snap into action" to fill holes and restructure a panel? The exhibitors of "Self-Mending Polymers" at the Royal Society apparently believe so:

"New plastics could enable car and aircraft components to fix themselves when broken.
Biological materials, such as bone and skin, can regenerate after damage. But until recently such self-repair was almost unknown in man-made materials. Our exhibit shows how materials, called polymers, can be designed to contain complementary molecular surfaces that will reconnect to repair damage. Self-healing polymers could vastly improve the durability and safety of critical components in cars and aircraft."

This physics I see here, is remarkably similar to the self-replicating polymers that are claimed in other peer reviewed articles, at least one of which I reference in my new paper. Self-replicating polymers, are a close cousin techno-kin to these self healing auto-body materials and also "self healing concrete".

It is not that I oppose technological progress in any sense, but one can hardly call progress in the unachievable "progress." And I define unachievable as a theory or mechanism of action, which apparently violates physical laws, namely, the Second Law of Thermodynamics. But we are speaking of inanimate polymers, not living ones, and in the case I examine, of "virtual closed systems" there is no allowed artificial addition of useful energy from the outside, it is assuming a natural system. So how do such polymers deal with weathering and cracking? The same as any other substance, we'd expect, and such changes are irreversible.

What immediately set off my radar however, was the sentence "Our exhibit shows how materials, called polymers..." Really? It truly gives the impression that they believe they've invented "polymers", and is a poor choice of words, if not concept, smacking of over-hype.

The whole point of a structure is that it has achieved a lower form of energy, of stability, such that it takes input of heat, and work, to unravel that structure. This is why it's much harder to cut steel than to cut through plastic. Hardness is related to the bond energies, and to internal structure. But that's not precisely what's relevant here. We're talking about after the fact restructuring, self healing materials. Where does the energy come from? Unless this is some form of "green slime" which really does no work, it simply flows passively into a hole, (which btw is not strictly true as the air pressure is in fact doing work to close it), you're not going to have both structure and hole repair built into one, they oppose each other. It's not physically possible, unless of course their material has an unreacted or uncured component, which then ADD additional energy. But that's not a polymer. That's a device of some kind.
But my new theory which I am letting people take a peek at here, does in fact relate to self-replication systems and similar problems, via a new theory "Virtual Closed Systems".
At a theoretical level, this is a virtual closed system, and we can evaluate it in a similar way to the other examples I discuss here. They draw parallels to their polymers with natural repair, such as bone and others. However, we do not find in nature, for example, inorganic materials, inanimate materials that repair themselves after damage. And I address a new physical theory for why that result is more likely observed, if not exclusively observed.

Polymers and molecules essentially "do as they like", and they should not be able in principal to violate the second law of thermodynamics any more than any other polymer or molecule. So my paper appears to have some growing applications, but might be useful to actually addressing this problem.