Sunday, May 31, 2015

'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, Eo (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. Eo<< 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 Eo 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

Monday, May 25, 2015

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-



 **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. , , , , , , , , , , , , , , , ,






Thursday, May 21, 2015

Are We Meant To Explore Beyond Our Solar System?



Jupiter with Europa (NASA)



I had a dream the other night about siphoning hydrogen off the surface of Jupiter and piping it across our solar system. Why? To power a space colony of course, or better yet, a new kind of space craft capable of many-orders-of-magnitude faster travel than current vehicles. Of course, these would need vast quantities of energy. Hydrogen would seem to be the logical solution. Hydrogen powers stars, after all. But in space, being large is not really a problem, there is after all, space.

In the background of such ideas were some other thoughts, given our very preliminary information about our "local" place in our galaxy, the Milky Way, and our vague (but rapidly growing) understanding of how much of the physics works of star formation and "baby" proto planetary disks, it seems plausible that we are perhaps "meant" to know or to discover regions beyond our solar system. These are hints in the cosmic "wind" perhaps from distant places we must someday explore, yet these are not on the forefront of consciousness. But, the recent findings about planetary atmospheres, comet geology, lunar oceans, and proto-earths continue to pour in. Do we have the technology, to go at fast enough speeds to explore our local galaxy? I believe we can, it is physically possible. And the latest results of what are essentially "ion drives" maybe only at the "steam engine" level now, but only improving, show that we can in theory go 10X faster than what vehicles do currently.
Protoplanetary disk in Taurus (Hubble/NASA)



But I would add something else here. We are also making breakthroughs in robotics and AI as well as genetics. It may be feasible or it  might even become prudent for us as a species to explore our galaxy in terms of using these advancements that can extend what is possible for exploration. Robots don't age. But neither do genomes.

And I believe the first real milestone would need to be a colony, not necessarily on a local planet, but in an artificial structure, a satellite. It seems this is the only way to induce artificial gravity, what is currently necessary to offset those <g effects. It seems moon habitation wouldn't solve this issue. But this also would be a step towards actually inhabiting space and proving travel is possible. A self sustaining orbiting colony would prove more than even Martian colonization, as it would demonstrate a key point. That independent colonization and artificial gravity are feasible.

Will we have the ability to move forward? When the time comes? This would seem to require a 'critical mass' of knowledge. At a cultural level. And in that respect, the test of our technology to advance beyond what is even imaginable now, may be a higher priority than simply one of aesthetics or a popular "preference." Much like we observe the past, already written in the stars, the future will be our judge, and it is definable by our actions. Did we delay our "race" forward, precious time ticking away by needless concern about the local trivialities, the battles that did not matter? (When we should have moved much faster to overcome our biological and technological limits?) It is difficult to imagine that we could still be a culture of war, for too much longer, wasting precious years in self destruction. An industrial shift would be required, to make propulsion, exo-energy sources (hydrogen mining), artificial gravity, AI, and biotechnology for the next great exodus. The galaxy calls like the distant shores of an unexplored continent...











Other Applications of Virtual Closed Systems: Machines

Virtual Closed Systems do apply to machines and this has a surprising implications. A machine must have some entropy in itself, that is lower than outside the boundary. We are defining them differently, as having some minimal level of potential energy, the kind that can do some useful work. So this energy unlike Eo has to have a relative entropy associated physically with its form, such that it is useful (in the way we define the term here).
Machines are inanimate structures containing some level of "potential energy", which is a unit that has a density lower than S (ex) external to the boundary.
We note that its potential can be defined by its capacity to re-achieve equilibrium with its exterior, we also see consequentially, that it is also closed.

But such machines have been in existence long before man made the first "smart phone."
Organisms make these machines, structures which "assist" in keeping and maintaining system's boundaries and opposing entropy.
Examples would be the structures of diatoms and toroidal molusc shells. They built their homes, which served as protection from ancient seas.

But we are simply attempting to understand these structures much like one would see the shell's capacity to oppose the force of surf crashing on top of it. Except that the physics here is relating to the potential of these structures to cause change in their environments.
Other forms of these machines would be energy storage "devices' of very small scales, even molecular scales.

Tuesday, May 19, 2015

A Second Look At Quanta's "How Structure Arose In The Primordial Soup": What are evolving proteins?


I took a second look at an article in Quanta, "How structure arose in the primordial soup". I realized that they had ignored completely my questions, two of them, and never bothered to clarify what they meant by "evolving proteins" or for that matter "learning proteins?". Though the author, Emily Singer, who strikes me as somewhat technical, did answer three (3) OTHER commentators' technical questions. Perhaps I'm still reeling from getting blocked and then 'unblocked' from Quanta.
I'm sorry, is science now something that you can mold to your liking? Tailor it, so as to avoid obvious, relevant information or contradictory evidence at your leisure? Just because you're a writer of an article? They bother to mention some sort of triumvirate" of genomics and proteomics and something else, but fail completely to include the glaring fact that no one has ever made molecules "evolve." How will such a story differentiate itself from "bat-shit crazy" ideas? The stuff more appropriate to fiction. And I have nothing against fiction, mind you, but standards are standards and science is not a genre. In avoiding and cherry picking the science, they only open the door to such nonsense as "lightening bolts", why not? Anyone can go to the Quanta article and see that neither of my querries, are somehow deemed relevant to their strange, baffling chemistry of "evolving proteins." Who are we fooling? At the very least such "science" does a disservice to those who actually work with proteins in applied settings. But where is this 'evolution? so that others may duplicate such experiments.

"Most researchers believe that the code began simply with basic proteins made from a limited alphabet of amino acids. It then grew in complexity over time, as these proteins learned to make more sophisticated molecules."

 And again, I believe it is grossly distorting what science currently "knows" even theoretically, are the barriers to understanding the primordial life problem. Some red flags are the self-leaning title, which presumes to answer "how" the soup arose, not "if", as if to imply that we are now on to the finer details of that story. Furthermore, no one has demonstrated polymers that self-replicate, so to imply that's already a hurdle that's been passed is obviously wrong. And "evolution" is not a chemical process, these are proteins, they do not "learn". It would be akin to a title like "researchers are now delving into finer details of how perpetual energy works..." Stop the press?!
Is rationality, yet another victim of the instantaneous gratification demanded by such articles? There is significant if not overwhelming evidence that this pathway, which they all-out assume molecules can violate, is not feasible, which they have apparently ignored, but I discuss in my paper. One sign of a strong theory is its ability to discuss available evidence and findings. Signs of non-supportive theories are unfortunately, just the opposite, the avoidance of contradictory evidence.

 There are many researchers who assume certain paradigms, and thus commence with research, but I'm frankly dumbfounded by the unblinking assumptions of this article, and also its technical backing. References are cited as though again, the focus we're to understand, is not "if" but on "how" this is purported to work. Where's the feasibility? (I reference a 2013 Cambridge study indicating only "progress" towards a soup model, whatever that might mean).

It assumes that the informed public is largely ignorant, but slanting your article to imply that they are now examining finer details of an intractable problem, instead of the big picture questions, i.e. do we really know, even remotely, what the composition was? Does a disservice to scientific reporting. It also completely misleads the informed public about the basic problems of the theory, or theories, which I noted, are never even mentioned. Just because Haldane in 1929, worked diligently on primordial soup, doesn't mean that the chemical basis is worked out any more now, than it was then. And there were alternate theories of Boltzmann's atom model, i.e. a non-atom model, which were just as wrong then as they would be now. The "issue" about amino acid ratio is absurdly detailed, as are the so called "ancestral molecules", (again this points an arrow to a chemical theory) and it's not clear if the contributors to these theories, like Greg Fournier, and many others in this field, really understands that the proof of concept of his model is non-existent. I propose that no such proof exists, and give reasons why here (it has nothing to do with WHAT kinds of molecules you are starting with):

Thanks to a large degree on the misapprehension of laws such as constructal laws, it is currently a widely held belief that the earth acts as a kind of heat regulator, like a refrigerator or a heater, depending on what is apparently 'needed.'
Although I querried the scientists, who authored the paper about the issues relating to their self- selecting and evolving polymers, I did not get a response to these valid questions. Here is what I wrote to the authors, (below).. and I've since incorporated it into my new theory, which I'm giving folks a peek at here:

Though constructal law itself has been criticized, the concensus is that inanimate is a phenomena connected with the animate, or vice versa .. so this incorrect view is not only owing to "Constructal law", but also to MEP , so called maximum entropy production, among others.
Why else would the scientists use such fuzzy, non defined terms like "evolving" or selecting molecules,
I asked them to define what evolving might mean in terms of a molecule, in terms of chemistry, but there was no reply from the researchers themselves. Again it appears that researchers are going along with the flow, several theories combined to give the illusion of something real. Molecules select themselves based on some preference, and systems export entropy much like a refrigerator does. Look no further than the "work" of MEP theory, (Kleidon but also RC Dewar, 2005 ..) constructal law, or the combined *dissipation-natural selection theory recently from MIT. *Which has been advocated in different forms.
The earth is viewed as an engine, regulating the temperature of the atmosphere. Whereas it is true that our atmosphere does obviously cycle, these dissipations are in continuity , a "continuity principal" I'm introducing ("see Fig 2. Condition 1, B") but also here (#13), such that their normal forces are not opposed, these movements are in line with the packets of energy received from the sun. This means that the system will progress towards a least resistive path. I also propose in the paper, that only a normalized force, 
In reality, in the "Virtual Closed System" theory, there is no means for groups of molecules to export entropy. Despite their insistence that the earth's cycle can do so. Again thanks to the "myth" promulgated by these other theories. Discussion turns into 'they said it was so.."  in what amounts to a kind of conventional bait and switch routine, where only part of the story is known and knowledge of its greater workings of the theory, is deferred. Based on continuity of the forces involved, inanimate molecules are subject to the same dissipative phenomenon, as their surroundings. That principal is a thermodynamic Coda on their so called self redirecting or self improving primordial broths.
 
Again they simply refuse to reply to my big questions about feasibility of "self-assembly", the elephant in the room.. and it seems this kind of "research approach" in which smaller irrelevant questions are taken in stride, but big ticket items ignored, ones that obviously contradict the "findings" and befuddled "learned proteins" might help sell it in an article, but only muddy the very definition of science.

Monday, May 18, 2015

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.






Thursday, May 14, 2015

Sci Blogging By Following Nature Pub Rules: My Blog Is an 'Archive'


I'm following accepted archival publication "rules", non-commercial use, pre-publishing and internet sharing guidelines on this site. (See Elsevier's web publishing guide). My intent is also to comply with the Nature Pub Group "embargo" rules for blogging and pre-pub sharing to archival sites (see below). As many are probably aware, there are a number of archival sites, like arXiv.org where one can find pre-publications of articles. The intent of that sharing on an archive, as I understand it, is to give non-commercial availability and non-formalized peer-review.
 

Notice regarding blog 'copy' here:

The article(s)/ work, was originally published in a blog published by
Matthew Kosak, and the attached copy is provided by Matthew Kosak for the
author’s benefit and for the benefit of the author’s institution/blog, and is for
non-commercial research and educational use including without
limitation use in instruction at your institution, sending it to specific
colleagues that you know, and providing a copy to your institution’s
administrator.
All other uses, reproduction and distribution, including without
limitation commercial reprints, selling or licensing copies or access,
or posting on open internet sites, such as personal or institution’s
website or repository, are prohibited. For exceptions, permission
may be sought for such use through contacting the author.

 

 

Also see the following relevant guidelines for pre-publication policies on archival sites and especially scientific blogging:

 

¨       "When blogs make sense" discusses the use of the archival arXiv.org
 site
http://www.nature.com/nature/journal/v466/n7302/full/466008a.html

 

¨       "It's good to blog" Nature 457, 1058 (26 February 2009) | doi:10.1038/4571058a; Published online 25 February 2009

 

¨       "More researchers should engage with the blogosphere, including authors of papers in press." http://www.nature.com/nature/journal/v457/n7233/full/4571058a.html



The following appears on the Nature.com site under "Editorial Rules"
http://www.nature.com/authors/policies/embargo.html


What should be most "eye catching" are the Nature Publishing Group rules of pre-publication (see below)
I am  posting these on my blog specifically, as I am making every effort to comply with these rules of pre-publication.

"Material submitted to Nature/ Nature journals must not be discussed with the media, except in the case of accepted contributions, which can be discussed with the media only once the publication date has been confirmed and no more than a week before the publication date under our embargo conditions…
…The benefits of peer review as a means of giving journalists confidence in new work published in journals are self-evident. Premature release to the media denies journalists that confidence. It also removes journalists' ability to obtain informed reactions about the work from independent researchers in the field.
For all these reasons, Nature journals have refused to publish papers prematurely released to the media. Journalists who break our embargoes have been removed from the press-release circulation list, and we shall continue to use this sanction when appropriate.

 

Some relevant links on pre-publication for scientific blogs (from the NPG site):

 

  • “Nature Methods: Deja vu? (what constitutes prepublication and how to avoid it). “..Our policy is also to allow posting of data on recognized preprint servers before submission. Although these servers are more common in the physics and mathematics communities, some established preprint servers such as arXiv, have biological categories. Preprint servers can be considered as 'online meetings', where content is posted for immediate discussion and feedback among a wider audience..”

 

Does Life Violate The Second Law of Thermodynamics? Implications of 'Virtual Closed Systems'


[Update 5.19.15:
I am giving people a peek here at a new theory I've developed.  
This is a new theory involving what I refer to as "Virtual Closed Systems" .  This theory is meant, hopefully, to address the rather well known problem of open or closed systems, (the thermo depictions of earth) in which life forms, (and was basically a chemical product) , essentially due to what is known as extreme non-equilibrium behavior of matter, of basically systems of molecules that are disturbed from normal motion by dissipation of energy. First and foremost it needs to be acknowledged that the existing idea, of far or extreme disequilibrium makes certain , basic assumptions that I'm challenging here. The most basic, that energy entering the system, i.e. sunlight, can have sufficient useful energy within it, to yield, molecules, or products that are capable of doing more work on the system, than less. One might assume that is 'negative entropy', but I'm introducing another idea there. Other assumptions, upon which the greater disequilibrium theory also rest, are already in dispute, because they have not been experimentally proven. The negative results are also important. This discussion does tie in with another partial theory I introduced in another blog I wrote earlier. But at any rate, I am making hypotheses that are hopefully testable, and in fact can be shown by experiments here. The more I think about closed virtual systems and the implication for either mechanical robots, or of living machines, the more I'm convinced this new concept is useful for evaluating this problem. Is life really related to disequilibrium of ordinary matter? Is it a dissipation process? Those are some of the interesting questions.]


The second law is defined specifically for closed systems. In a closed system the amount of available energy to do work will decrease over time. This mirrors the definition of entropy, also defined for closed systems, as "the quantitative measure of the amount of energy not available to do work." (1), [1b] ) (American Heritage Dictionary, Schrodinger 1944).

The classic argument actually is that life does not violate the second law of thermodynamics because it (life) is NOT in a closed system (2). We live in an open system, with our sun providing ample energy to power life on planet earth. (but also, to drive the earth’s systems of dissipation)

Consider also, that in a closed system, a perpetual energy machine is not possible, as it will continuously generate a small quantity of entropy in each iteration, regardless of its efficiency. The generation of lower forms of energy means that it will eventually exhaust the available supply and cease to operate. (3)

But here is a very interesting question: Is a perpetual energy machine possible in an open system? (4) If it is not possible, which we can assume is experimentally verifiable, then does this actually infer that the so called "open" system is not really open? (I use a proposition or rule that if the experimental results or effects or identical, their causes must be equivalent. (5) [see Newton's Rules of Philosophy, Principia (2nd Edition 1713)].

There are two primary assumptions based on apparent experimental results or observational experience, to support the assertion that life does not violate the second law: 1) life avoids so-called "heat death" by constantly absorbing energy from the sun. If this energy inputted into the system were to cease, then obviously life would cease, and 2) the earth is always viewed as an open system (6).

My point regarding the perpetual energy machine, is that it is possible that despite the fact that it might not be possible to formally show that we exist in a closed system, [based on (6.1)] the experimental observations of non-perpetual energy machines, and passive heat transfer, strongly imply that it BEHAVES as though it is a closed system. What then would be the difference? [So I invoke here the principal of equivalence. If two systems have identical effects, their causes must be equivalent. (5)]

If life is in essentially the same kind of system as the perpetual energy machine, which (we can assume for the purpose of this argument), then we would therefore have the same kind of problem for both (7). (By this rule, a “living machine” doesn't get a pass any more than any other machine). By the implication of this rule, or postulate we have now justified a new hypothetical space, in which a “closed system” may in fact exist within an open system, and we can consider the consequences of such a “virtual” system in Fig 1.
 
Fig 1.  The Virtual Closed System Showing the Energy horizon (dotted) and Eo << required for useful work) t= 4 b.y.

 
 
Fig 2.

 

  1. Condition I* The system’s Entropy (actual) is the same inside and outside

Sinside = Soutside And we assume it has already reached equilibrium after >4 B.Y.

Energy available to do work (inside) = Energy available to do work (outside

In Condition I, in which it started with Eo << below the threshold w/o life.

 

  1. We can however, imagine another condition, “Condition II”** in which the system theoretically began with some organized matter. However, since we postulate (based on equivalence principal) the model applies to machines, inanimate matter as well as Living Machines”.  And postulate that this is now a Virtual Closed system, with an entropy boundary, so any initial organized matter present at t=0 would undergo “heat death” or decay (inside that space enclosed by the entropy boundary).

[*In condition I we have essentially defined an equilibrium state, established over an assumed, very long time period, (i.e. 4 b.y. billion years) relevant to what is the available energy to do work, inside and outside the virtual sphere. This is not a maximum entropy state, but is meant to delineate an “indifferent entropic state” in which the available work energy has reached equivalence. The unexpected consequence, is perhaps, that this condition also would apply to other time states, much more recent, and could be envisioned in principal, as continuous. It is the basis of what is proposed here, as a ‘continuity principal’ of how useful energy is flowing from its source and is explored further in a later section. But this is further elaborated upon and supported by the "Indifferent Time” principal invoked in my other paper which examines micro states in balance (See indifferent time theory and my comment  below regarding “solar packets” [4] ).
**Condition II would follow from the stipulation of Condition I but we’ve added the additional test condition of adding some initial quantity of order at some arbitrary time.]



In any closed system, the available energy for doing useful work, decreases over time (8). This rule applies equally to our virtual closed system with its entropic horizon. According to this law, a machine would eventually accumulate entropy and cease to operate. Given these results, we may ask the following: Why does this, our modified law applicable now to virtual closed systems, not apply to "living machines". [The answer, is that it does not apply differently to one or the other. Entropy applies equally to all processes inside the system.] We then have the question, how does life avoid disorder?, and its inevitable decline? (9)


In consideration of the foregoing principals, we can also state (or propose) that the mere input of solar energy, of heat, does not at least in any experimental sense, ever demonstrate that this input of energy will do useful work on the system of molecules on planet earth (10). [This may seem to be a rather bold statement, but it bears scrutinizing further (below).] I have also elaborated with a comment in quanta see my reply [23]

So this is yet another strong, experimentally verifiable result, (also furthering our aforementioned propositions) which supports the notion of a system that BEHAVES as though it were closed. (And that such interaction(s) of a hypothetical ordered state (or non-ordered state at equilibrium) with its environment can be duly considered physically with this new virtual model and various possible implications tested.)
Thus, if we take the definition of the second law to mean that a system will eventually accumulate entropy, that is, quantitative non-useful energy, then any system including a living one, should cease. (11)
Thus, we have obtained a new result, based on a virtual closed system, its properties of being closed*, verified by our principal of equivalence (above). That is, it does not comply with (6.1), (6.2), nor with (2) as it has no physical means of drawing order into itself, or of increasing the useful work energy contained within, to lower its equilibrium entropy density relative to the outside (12) The fact that it has no intrinsic ability to lower its entropy also is critical to its “closed” nature). We would expect such a system to effectively demonstrate a similar measurable potential energy density inside such a (virtual closed) space and outside, after equilibrium S
inside = Soutside at sufficient time, or ≥4 b.y..This essentially defines the closed behavior of such a space. (13)


In this regard, and in consideration of the principal of virtual closed systems, we have experimental evidence, that perpetual energy machines also are impossible in so called "open systems" [again on earth no perpetual machine is possible, not even one that runs on solar energy (14)*. [*a proposition based on a virtual entropy system proposed here, in which the machine therefore has no means of reducing its own entropy] as well as evidence, chemically, that energy from the sun does no useful work on the system. (14)  ..And we are again, also defining “open systems” such that these are composed of smaller closed systems, in which energy flows in and out through an entropic horizon (15). This can account for why an “open system” still works to pose a theoretical limit on the possibility that a machine can self-regulate its interior entropy- (16)]

Thus, based on this new theory, it appears that living systems composed of molecules, do violate the Second Law of Thermodynamics (17) based on condition I and II either the system was never at disequilibrium S(inside)=S(outside) or it would decay rapidly, to reach this state), and further, this is based on the preponderance of experimental evidence, e.g the failures in laboratories to show otherwise (see
Zeravcic 2014, Attwater 2013, Weissbuch 2009, C Huber 1998, Haldane 1929)). Though this is not strictly true. Living systems (which are natural, self-replicating systems) composed of molecules also appear to violate a number of other laws, including Fick's law of diffusions and Fourier's law of passive heat flow. Living cells have systems for removing entropy, and they have existed for a very long time, for all intents and purposes, in perpetuity.(18) With this new model it can hopefully be better understood why that is.
 
*Sub-Conclusions: We can see that the virtual closed system" model diagramed here allows us to resolve the original question we asked previously: "is a perpetual energy machine possible in an open system?" The answer is that one must consider the system differently, and if this is the case, if it is considered as a bounded virtual space, we can surmise that the net energy capable of doing work will decrease inside this volume...even in so-called open systems (19).

Discussion:

The position that life does not violate the second law is one of the most ubiquitous statements one will find in virtually any text (web sites and also technical papers) relating to the subjects of life and physics. (19.1)

Here is an example:

http://chemwiki.ucdavis.edu/Physical_Chemistry/Thermodynamics/Laws_of_Thermodynamics/Second_Law_of_Thermodynamics “Some critics claim that evolution violates the Second Law of Thermodynamics, because organization and complexity increases in evolution. However, this law is referring to isolated systems only, and the earth is not an isolated system or closed system. This is evident for constant energy increases on earth due to the heat coming from the sun. So, order may be becoming more organized, the universe as a whole becomes more disorganized for the sun releases energy and becomes disordered. This connects to how the second law and cosmology are related, which is explained well in the video below.” (19.2)

The statement above is generalized and is not new but represents the dogma currently. [A position that has been only strengthened over the years by various pioneers in the field of thermodynamics and living systems (see Schrodinger’s “What is Life” 1944) Schrodinger virtually invented the principal of explaining living things by his concept of “negative entropy” in which organisms extract (or attract) lower entropy to themselves from their surroundings, but he clearly recognized the problem confronted by the cell of lowering its internal entropy] (Boltzman, 1866 also recognized it [2] as critical to life). One will find only slight variations on this statement if he searches the technical literature. Let us examine what this argument is saying. The sun is generating vast quantities of entropy in its conversion of its hydrogen fuel reserves to heat and also light energy. According to this model, we can imagine that the earth is receiving some form of useful energy, Eo , capable of doing work, and the COST of that in accordance with the second law, is that the net system, the sun and earth taken as a whole, create more entropy than they gain, in terms of ordering. The order in this case would obviously represent living organisms, but could apply to any ordered system, including inanimate machines. What this argument fails to account for, and what I am attempting.. in pointing out here, is that when it is portrayed in this way, we must assume that the light energy coming from the sun is capable of doing work, it is a form of energy that is higher than the system it is shining on, the earth, (or other planets and objects, let’s not forget those.) This problem I am addressing can be better seen with my virtual system diagram. We also note, that the boundary does not have to be spherical and is only shown (this way) for convenience. It could in fact represent the boundary of the machine, its organizational interface (with its exterior environment), thus the “entropy horizon” would not be spherical it would be 3D and conforming to the machine’s interface.(20) Machine = ordered systems required for its existence/operation.(20.1) And the outer boundary is defined as everything else. I drew the spherical shape which also, best represents organized life’s basic unit, the cell.

(We note: The “order” in a system might actually increase, e.g. in the formation of crystalline substances and ordered lattices. However the capacity of that system to have energy that has a capacity to do work is diminishing. (And that is how we are defining entropy here as well as it’s implications to the second law.) We can simply state for these purposes that the earth, if left alone at some theoretical instant in time, would progress towards equilibrium, owing to the fact that the earth is continually “attempting” to reach equilibrium and shed heat it is gaining from the sun. So it is valid to assume that for the next unfathomable period of time- external energy, capable of doing work will always be higher outside, as it is ENTERING the system of the earth, externally. We can neglect, the entropy produced by the sun, or that ΔS is always positive for the system outside in space. (21) Our question is: Does life violate the second law? And so for these purposes these definitions should suffice. We have not stated anything special yet about the heat energy coming from the sun except to say that this is and must be at a higher level on the outside and is assumed to be continuous.)

Heat is work and work is heat, but heat only does work when the moving molecules… recall these are vibrating, are withheld at some pressure, in other words the molecules must be restrained from their normal motions, otherwise we simply have waste heat, doing no work. Unfortunately, this is precisely what occurs in nature. We do not find in nature, barriers which restrain moving molecules laden with heat, to do work on the system. More simply put, nature imposes no normal force against heat, quite the contrary, it passively allows heat to escape, and it does so with high probability. So the dogmatists are merely presenting a story which has no mechanism to function. The problem is not so subtle, and it is the problem essentially that nature imposes no barrier, no normal force against heat. Recall that in the very definition of work, WORK , W, is defined as an application of force per unit time. Or force applied through a distance. The key to that statement is “force”. Where do we see such a resistive force in nature? But more precisely, and this is critical, the probability of such a force existing is prohibitively small or non-existent. So this is in a sense, another way of stating the second law of thermodynamics. (22)

It does not matter if we are talking about vibrating molecules or molecules cascading down a slope, resisted and guided in their path, by the normal forces of a stream bed. We see in this case that the molecules ARE being resisted by normal forces. Wala! Says the dogmatist, or Eureka! What we stated was that the probability of such a normal force barrier, appearing spontaneously to do work is virtually zero, for all intents it is zero, particularly if we are increasing the magnitude of W. (22.1) So in the case of a stream flowing down hill, it has great potential to do work, but in nature, no one is there to impose a dam, unfortunately, and in fact what the second law means is that there is no force, no physics that will make a dam possible. The system is “rigged” against such resistance. Thus we can see that the great potential energy of a moving stream is wasted.

The point of this argument is to take this knowledge and apply it to the statement “life does not violate the second law.” Since we now know based on this new argument I have presented here, that this is not correct. [the second law is intact as is the general assumption of entropy increasing outside the system]. We again consider the “micro state” , “micro” relative to the earth’s surface. Whereas it is true that the vibrating molecules (instigated by heat from the sun) that enter the sphere have the capacity or potential energy, we find just as the case above, that there is no resistive force to slow their motion. There must be a resistive normal force in order for any work to be extracted from this potential. We also see that the probability of such a normal, resistive force being imposed on these molecules is virtually zero i.e. the P <<<< 1 and is given by the equation. The notion that life does not violate the second law thus has a 99.99999..+% probability of being false. (23)

 

As I have already stated, this argument can be falsifiable, if the probability is determined and is at some level that is significant. There is significant physical evidence to support my case, however. The evidence that the energy incident on the entropy horizon, is capable of doing work, is negative. In view of the postulate here, the normalized force problem, we would not expect that this energy from the sun is capable of doing work on the system of the earth’s molecules. But there is another issue from this model. 2) we would also not assume that the entropy in the system, and this is again defined within or at the interface of the entropy horizon of the machine, would not continue to accumulate. Both cases I or case II, (in addition to the normalization force problem) would predict that under the known understood laws, any organized or ordered system would undergo heat death. (24)

Rule: heat exchanging or passing through an arbitrary region cannot do useful work unless it encounters a normal force (opposing its motion.) (25)

 

Other discussion/references: In a recent review of the physics of far from equilibrium biology and physics, Axel Kleidon considers Earth’s systems that are pushed far from thermodynamic equilibrium by living things: convective cycles, weather patterns, mantle subduction, tides, etc. This would be in essence, condition II that we treat in this paper, however, Kleidon is not concerning his paper with earth’s system from the perspective of condition I, in which we attempt to answer if theoretically, the solar energy is itself capable of doing useful work. The solar heat driving convection, is not an isolated force. But according to the theory I propose here, such a force would not be possible to do work against the other surrounding forces or its own contribution. (26) It is claimed (by one reviewer) that earth is in disequilbrium”, witness hurricanes, tidal forces, and other forces. What is it specifically at disequilbrium with? Is an asteroid on approach towards our solar system, at disequilibrium? No it simply has momentum, mass times its velocity. The heating and cooling drive the convective processes of the earth’s oceans, however, none of these winds or tides actually move against the impetus that drives them towards dissipation. As we have already pointed out, the stream flows downslope, unimpeded, and can therefore do no work against the force of gravity. (It is itself, subject to this force.) The movement of a stream would not be observed, if the earth were not in the path of the solar radiation, absorbing the energy. So it can’t really be seen as the “purpose” of the earth to dissipate this energy. Some tremendous percentage of solar energy simply radiates off into space, missing the planets (ref.) we will not, according to these principals, be able to find “natural machines” that in fact do work, as the sun’s energy, exerting a force, does not work against itself. [It is not possible for a force to have two simultaneous actions.] Which can be demonstrated microscopically. (26b) It might be supposed that turbulence builds clouds blocking the sun or cooling, much like Brownian motion might interfere with heating or cooling. There is no “interference.” These are taking the least path of resistance towards dissipation. And it is truly very difficult to imagine how one can make the claim that there is some “engine” within a natural system, speeding energy and wasting it in the least path of resistance. No engines that I know of, operate by offering least resistance and least work possible to effect their surroundings. That is precisely what occurs without a resistive force, and one cannot be found in these natural systems in the context of doing work. (26C) [note: (see my argument#16-17 from “Indifferent time” http://causaldistinctions.blogspot.com/2015/04/i-propose-challenge-to-maximal-flow.html specific to the arbitrary introduction of forces into diagrams “artificially assuming a force entering the microstate” which “in reality these are not ‘entering’ but are part of the system” and the assumption causes problems for causality.. (26D)

Also, a planet is not doing ‘work’ any more than an asteroid is ‘doing work’ by deflecting the solar wind (from deeper space) and moving in its orbit. So the question itself, that we ask here, cannot be properly defined under conditions where these terms are not differentiated. The process by which heat is dissipated or released also is not strictly a case where such heat is being ‘generated.’ As much as occurring, again continuously. As we note in the ‘*continuity principal’ in Fig 2]

Many of the maximum entropy production (MEP) advocates seem to be extremely confident in their physical results, they obviously believe that they are correct and that such models are experimentally subtantiable. However, can these scientists describe how MEP would apply to the problem of improving drug function in a cell? Perhaps we are to believe that a cell model is less complex than turbulence in a solution? If this theory of MEP truly is so widely cross-applicable to physics, why is it not directly applicable to solving chemical problems in drug activity? What principal of MEP is not already fully encompassed by other theories of chemical behavior and structure? When we examine a theory like MEP at the molecular level, we can find that there isn’t a behavior that it claims that is verifiable, MEP is no different than passive heat flow or passive diffusion, which have been known for 500 years. On the other hand, the theory I propose here can be tested. We can physically measure the amount of work that the system may do at different times, say at arbitrary states of I, II, and III and show that the available work diminishes, in agreement with observation. I have adapted these basic principals to a much broader application. (27) [see ref # (Lucia et al 2014) in my other archival paper “Can constructal theory be proven…? http://causaldistinctions.blogspot.com/2015/03/is-constructal-theory-by-adrien-bejan.html as some are apparently applying constructal theory to cancer models and treatments, and constructal theory is a ‘preferred dissipation’ model like MEP see my note [17] below]

Viewing a planet as a system such as a “Giai system”, seems reasonable for the life infused earth, but it wilts rapidly, when such a thesis is applied to the moon. In fact, far from equilibrium dynamics does not seem to encompass radiation from lunar soil in the same way as it does convection of an ocean. Nor it appears would the Giai hypothesis seemingly have any bearing on an asteroid floating between Mars and Jupiter. And yet a body such as the moon or a smaller asteroid, reflects heat and dissipates heat from its surface, in the same fundamental, physical manner as the earth. It would not seem unreasonable to require that a theory must apply to all objects as these all exhibit similar fundamental behaviors of energy exchange. These examples point out the risks of over anthropomorphing theory to meet pre-conceived notions, particularly ones that seem appealing to the mind or socio-poliitical or cultural aspects. Hence the necessity to reduce the problem to elemental units, and my reference to the passage of energy through open space. What is the purpose of open space flux of energy through a surface? None. No Gaia hypothesis applies to such space,  nor it seems a “Maximum Entropy Generator” to the moon or our system’s asteroids. These are the objective elements of vectoral forces. But that is the objectivity that is demanded of the physics. No doubt, the theories advocating some aesthetic balance or drive will still have more appeal, but the cost of that appeal is the murkiness that masks reality and ethereal elegance.

 

Conclusion:

In conclusion, I believe this theory is substantiated by empirical experience and evidence, including many of the experiments I myself have conducted (here and elsewhere) that shown convincing evidence that chemical processes in general, starting with order as in the condition II described previously, lead to products which are then successive end points leading towards products of increased entropy and a lower capacity to do work. Most importantly, these experiments show the lack of any resistive force, chemically resisting that path that is intrinsic in these in vitro chemical systems.
What is that resistive force? Where does it come from? that resistive force F (sub R) =F sub L, (28) necessary to do work, would be Critically present to ANY equation that relates thermo to how life evades thermo currently and in the past.

 

As Schrodinger remarked “ in his work, it has already been supposed that life somehow opposes second law, that is, unlike the inanimate system, it avoids decay. It was already known that the sun supplied a critical energy needed by life to avoid this decay, also pointed out in the same work by Schrodinger and known to others [1]. This however, is not quiet what is at issue here. Because it was assumed by Schrodinger that the basic physics of the second law were intact, it was only really a matter for genetics and biology to work out the details as Schrodinger in fact, remarks at the start of Chapter 6, “Delbruck's molecular model, in its complete generality, seems to contain no hint as to how the hereditary substance works, Indeed, I do not expect that any detailed information on this question is likely to come from physics in the near may future.” So that echoes the modern view rather precisely, minus of course the progress that’s been accomplished in modern biology since 1944. [*5.5.15 It has been supposed that life must operate against the second laws’ prediction for a closed system, but it is a generally believed principal if not dogma, that it is not violating the second law. Though what we find here, is that has depended on both how life was defined, i.e. as a bio-machine, or how the system has been defined.] The real question is, is life violating thermodynamics, a much different meaning than “opposing” or “overcoming” the law, (e.g. much as organisms resist gravity, they don’t actually violate gravity). What is not realized by other skeptics of the second law’s applicability, but IS recognized here, is that the system model ‘open or close’ problem, really only works for animate systems. Only in factories (exemplified in the manufacture of highly ordered systems like computers) do we have the proper meaning of “the exterior system increases entropy much more than the system in which entropy is negative. The same holds true for cells and living things. So this model is somehow projected upon inanimate ones, to be equivalent. Add the fact that animate is equated with inanimate, (in so many sources, Prigogine 1973, Schrodinger 1944, as an underlying assumption of physics..) and one can see the (foundation of this largely unwavering) support for this belief. Furthermore, (and to that point) I also believe that what is at issue here is the problem of the lack of definition between animate and inanimate.

 

 

Notes and References

  1. The second law is stated more formally as “the change in entropy of the system will always increase, OR it is always positive. δS=δQ/T≥0. (Schrodinger, “What is Life” 1944) “(Chapter 6 LIVING MATTER EVADES THE DECAY TO EQUILIBRIUM) When a system that is not alive is isolated or placed in a uniform environment, all motion usually comes to a standstill very soon as a result of various kinds of friction; differences of electric or chemical potential are equalized, substances which tend to form a chemical compound do so, temperature becomes uniform by heat conduction. After that the whole system fades away into a dead, inert lump of matter. A permanent state is reached, in which no observable events occur. The physicist calls this the state of thermodynamical equilibrium, or of ‘maximum entropy.'” So we can see that the ME or MEP was already clearly stated in 1944 by Schrodinger.

1b. {5.9.15 We will further define this entropy more universally as the system will tend towards a state in which a quantity of energy is no longer contained such that it will spontaneously do work on the system around it, though this is specifically in Case II, where some order exists, technically speaking, the classical definition of entropy does not apply based on Case I, that is a surprising implication of this virtual space and that condition. The notion that useful work declines in a closed system is itself a man-made imposed condition which is not apparent, or known to be apparent, in natural systems.}

  1. “The general struggle for existence of animate beings is not a struggle for raw materials – these, for organisms, are air, water and soil, all abundantly available – nor for energy, which exists in plenty in any body in the form of heat Q, but of a struggle for entropy, which becomes available through the transition of energy from the hot sun to the cold earth.” Boltzmann, L. (1886). The second law of thermodynamics. Populare Schriften, Essay 3, address to a formal meeting of the Imperial Academy of Science, 29 May 1886, reprinted in Ludwig Boltzmann, Theoretical physics and philosophical problem, S. G. Brush (Trans.). Boston: Reidel.
  2.  “Newton’s Rules of Reasoning in Philosophy” (from Principia, editions 2nd (1713) and 3rd (1726) tans. A Motte 1729:http://en.wikipedia.org/wiki/Philosophi%C3%A6_Naturalis_Principia_Mathematica Rule 2: “Therefore to the same natural effects we must, as far as possible, assign the same causes.”

 

  1. One can, based on the “time equivalence” principal, (I show elsewhere) conclude that everything (in true isolated, inanimate systems..ie natural systems), is at thermodynamic equilibrium, the only constraints would be the amount of time and perhaps the scale of the system in question. This means that in essence, there is no such thing as “thermodynamic equilibrium” in an absolute sense or a physical sense, it cannot be observed or defined. It is an artificially imposed, relativistic statement, unlike the law of gravity or even of heat dispersion itself (Claudius), or diffusion (Fick’s law). Equilibrium is not a dynamic itself, it is not a tendency, unlike other physical laws. Actually, entropy states just the opposite, natural systems tend toward non-equilibrium. Equilibrium is simpliy an observed state, a “shelf” or “paused state” in dis-equilibrium, which is principally why I don’t believe it is experimentally or observationally justifiable to claim that any system finds a state of maximum dissipation or equilibrium, that is adding or imposing artificial conditions. We can imagine, that it is physically analogous to a similarly absurd claim that a body at rest, a ball lying on a table for example, is a new physical or preferred state. There is no such law nor does this information make any predictions, and equilibrium of moving molecules in a coffee cup are analogous to any other motion. And further still, where does one find these equilibria? Find these in nature do you? There are no “coffee cups” with their molecules at equilibrium which is an exasperating point, when such an experiment is then used to correlate to systems in nature, it is simply “begging the question” further. This is yet another experiment to show the fallacious logic that is currently used to support the use of current equations and models, these apply IF one can assume such an equilibrium can exist (one arbitrarily established by an imposed force or introduced force), these apply (conditionally) IF some level of organization, of order exists in order to replicate once, as many sources have presumed in their underlying hypothesis for the origin of life based on thermodynamic principals. There is no evidence to make this assumption, and that assumption (hopefully) is not made here in this paper presently.

 

  1. Jeremy L. England, (2013) "Statistical physics of self-replication" doi:10.1063/1.4818538, v 139 J. Chem. Phys.
  2. England, 2013 ,”New Physics Theory Of Life”, Natalie Wolchover, Quanta Magazine ( Jan 22, 2014) https://www.quantamagazine.org/20140122-a-new-physics-theory-of-life/ “Although entropy must increase over time in an isolated or “closed” system, an “open” system can keep its entropy low — that is, divide energy unevenly among its atoms — by greatly increasing the entropy of its surroundings.”… “Life does not violate the second law of thermodynamics. ”
  3. My comment relating to how energy from the sun effects force balance on earth, thermodynamically. In Quantum Magazine, May 5, 2015 at 4:08 pm “To C.H. (commentator), May 2, 2015. It is not that I'm saying things are in balance in so much as I say that the force applied is in balance (in the cases mentioned). There is an oppositive force of equal magnitude , I'm making that claim for specific reasons discussed. I should probably state that it applies to the equilibrium condition, though it's implied when I state 'normal force' N-bank. As I diagrammed a bit more clearly: http://causaldistinctions.blogspot.com/2015/04/i-propose-challenge-to-maximal-flow.html In such a force diagram, we're not talking about conditions for "all of time" or even 1 billion years, but it is assumed for example, that a book resting on a table is in equilibrium, in an interval (of virtual time), and thus experiences an equal and opposite force pushing back. However, we also know that the third law applies in non equilibrium, the net force does not have to be equal magnitude since it is only proportional to the mass , ball 'A' can impose a force, 'ma' but ball "B", a smaller 'ma' so the net force might be highly scewed in the other direction, and b will go backwards, hence non equilibrium. But if you notice I am also making the case" for molecular based theory of a macro state, which you'll notice is being negated by constructal Law and Bejan basically states "it isn't necessary to consider molecular theory to obtain macro behaviour", which I paraphrase, but he's dispensing with particles and I'm showing why that's wrong.But returning to equilibrium condition, let's assume the river bank is more or less in equilibrium, in this state the force opposing the water is equal and opposite. The interesting notion is the causality of how that equilibrium was achieved. If you consider that the greater source of non equilibrium is the sun, and if we imagine there are packets" of this energy incident on our planet, which translate to the motions of storms and.. rivers then any non equilibrium from that equilibrium state, is thus some unit of that packet, it is not ridiculous to say it is molecular scale, as you're aware of planetary scale weather theories based on molecular theory, ie how well CO2 absorbs sunlight, or how water dipole effects its heat absorption more than say, co2 (no dipole) or any other gas really. But the big point of my derivation, its implication, is only to state that the non equilibrium is due to these packets- the non equilibrium of the river is caused by Fluxes in these energies, NOT by the river itself, nor by the change in the river bank. There is no such thing as constructal law governing a river as we have just defined the rivers motion as the sum of these "pushes" from the sun, (being counterbalanced by normal forces of the bank and river bottom) so these are as much relevant to the rivers (acting) force than what we observe (on earth),..a river is not a discreet, defined thing in terms of this physics.(I should also say that this kind of "being a stickler for precision", in causality is relevant to the thermo issues here, but also to the problem of equating animate and the inanimate..which you'll note is assumed in the article above, and by maximal flow laws).

 

  1. G. Sewell, A Second Look at the Second Law, Appl. Math Lett. (2011) “Anyone who has made such an argument is familiar with the standard reply: the Earth is an open system, it receives energy from the sun, and entropy can decrease in an open system, as long as it is “compensated’’ somehow by a comparable or greater increase outside the system…”Of course the whole idea of compensation, whether by distant or nearby events, makes no sense logically: an extremely improbable event is not rendered less improbable simply by the occurrence of ‘‘compensating’’ events elsewhere.”

 

Paul Peter Urone, College Physics, Brooks/Cole, 2001 (via Sewell paper). “It is true that the evolution of life from inert matter to its present forms represents a large decrease in entropy for living systems. But it is always possible for the entropy of one part of the universe to decrease, provided the total change in entropy of the universe increases.”

Angrist, L. Hepler, Order and Chaos, Basic Books, 1967 (via Sewell paper). “In a certain sense the development of civilization may appear contradictory to the second law. . . . Even though society can effect local reductions in entropy, the general and universal trend of entropy increase easily swamps the anomalous but important efforts of civilized man. Each localized, man-made or machine-made entropy decrease is accompanied by a greater increase in entropy of the surroundings, thereby maintaining the required increase in total entropy.”

Problems: Sewell correctly points to the problem which is being largely ignored, that of the apparent non-probabilistic tendency of life. However, he leaves the question open as to what might be entering the system. He also does not apparently address the expected and obvious counter argument that is present in a discipline outside of physics, e.g. modern Darwinism or modern synthesis-MKK

  1. Brig Klyce, (updated 2015), http://www.panspermia.org/seconlaw.htm“Sometimes people say life violates the second law. This is not the case..we know of nothing in the universe that violates that law.”
  2. Nick Lane “New Research Rejects 80-year Theory of ‘Primordial Soup’ as the Origin of Life” http://www.wiley.com/WileyCDA/PressRelease/pressReleaseId-67977.html “Textbooks have it that life arose from organic soup and that the first cells grew by fermenting these organics to generate energy in the form of ATP. We provide a new perspective on why that old and familiar view won't work at all,” said team leader Dr Nick lane from University College London. “We present the alternative that life arose from gases (H2, CO2, N2, and H2S) and that the energy for first life came from harnessing geochemical gradients created by mother Earth at a special kind of deep-sea hydrothermal vent – one that is riddled with tiny interconnected compartments or pores.”
  3. JBS Haldane (1929) Primordial Soup theory. http://en.wikipedia.org/wiki/J._B._S._Haldane
  4. Avshalom C. Elitzur (1994) Let There Be Life: Thermodynamic Reflections on Biogenesis and Evolution.” “…The evolution of any type of self-replicating systems, even the simplest ones, is shown to be highly efficient in extracting, recording and processing information about the environment. A variety of related issues yield some surprising conclusions when discussed in the thermodynamic context.
  5. Claudia Huber and Gunter Wachtersha“Peptides by Activation of Amino Acids with CO on(Ni,Fe)S Surfaces: Implications for the Origin of Life” 31 JULY 1998 VOL 281 SCIENCE
  6. S. W. Fox and K. Dose, 1977 “Molecular Evolution and the Origin of Life” Dekker, New York.

 

  1. See Kleidon’s “ Life, hierarchy, and the thermodynamic machinery of planet Earth” Axel Kleidon doi:10.1016/j.plrev.2010.10.002
  2. John Whitfield, Complex systems: Order out of chaos Nature 436(7053):905--907 (August 2005) “Can the behaviour of complex systems from cells to planetary climates be explained by the idea that they're driven to produce the maximum amount of disorder?”
  3. See Kleidon’s et al, (page 4) “The following two papers deal with hydrological processes on land. Zehe et al. (2010) evaluate the effect of preferential flow associated with biogenic soil structures on hydrological fluxes using nonequilibrium thermodynamics. They show that these structures act to maximize dissipation of chemical potential gradients within the soil.” (Axel Kleidon et al. Maximum entropy production in environmental and ecological systems Phil. Trans. R. Soc. B (2010) 365, 1297–1302)

I have already commented on theories such as these, Kleidon et al. The premise is that one might obtain data in this case, on “hydrological fluxes” such that there is some base line state. Then, presumably, over some period of time there would be another state, one in which there is a shift towards some other stable state. But one can see that in this experiment, the assumption has to be made that the system will progress from where it was in an initial condition to some other state, presumably a measurable rate of flux, etc in another condition. That presumes that there is some other physical reason for this change in state to occur, which further assumes, as I’ve already argued, that it is some OTHER condition or state that the system is not already in.* In other words, why is the MEP not already realized in condtion I or the initial state? as a function of it set up as a physical system, BEFORE it was set up to be measured? These are the experimental questions for the theory of MEP and other so called optimization theory.

We also see in the quote I have provided, the rather disturbing realization that it resembles very much maximal flow theory, with its ‘preferential flow’ maximizing energy dissipation in ‘biogenic soils’. [We further note that in fact “figure 1a” of this paper (Kleidon’s 2010 ‘MEP..’) apparently deals with a phenomenon described as “temporal evolution into steady state” which depicts a change in a system (not specified). What is also interesting, is the use of figure 1b, which depicts two resistors in a circuit. Are we to imagine that the resistors are now looked at chemically? Since the actual resistance of the wires is a function of their chemical composition, the type of metal etc. and we might also see such a system simply as a chemical one, subject to rust and degradation, but we can see also, that there is no preferred view of such systems. What is it physically that makes the circuit a physically distinct system from its molecular parts? Entropy could, in theory, be considered for just the wires, or just the chemical composition of the atoms in those wires, there is no justification here for any particular view.]

 

Kleidon et al, in the paper, (see page 1) also offer this working definition of the second law but also what they mean by an example of the maximum entropy principal (MEP): “The second law states that for isolated systems that do not exchange energy or mass with their surroundings, the entropy of that system can only increase. Over time, this law translates into an evolutionary direction by which a system evolves to a state of thermodynamic equilibrium, which is characterized by the absence of gradients in temperature or chemical species.” It would appear that they are simply stating, or restating that the “entropy of the system can only increase” thus reach a maximum. Again, whereas I don't disagree that a system of molecules will diffuse until that diffusion stops, this doesn’t appear to really be a “maximum”. Can we not now examine THIS system, the one in equilibrium? In reality there are no examples of systems in perfect equilibrium on this planet. Every known mechanical contraption, every system we invent, must degrade, none are safe. So the so called equilbirum of molecules in a container, are not really in an equilibrium if one simply changes the time frame, in that context such a theory simply doesn’t add up to finer scrutiny. And the same causal analysis I apply to the non-equilibrium of a container, also applies to natural systems, since after all, that is really the main purpose of MEP, to discuss natural systems of the earth, convection, winds, storms, and others. It would be highly untenable to examine a river or vortex, and state that such a system is now in some sort of equilibrium. Based on what observation? Or law? We could just as easily state, as Clausius did, that heat is lost from a system over time until it reaches equilibrium with the surroundings. But we can also see such a view is relative. What are the surroundings? The kettle cools to the termperature of the room, but the room is still maintained at a higher termperature than the outdoors. It is a relative concept and we would not really state that the temperature of the kettle has reached some sort of minimum, not in a generalized sense as this simply wouldn’t be verifiable. Without any relative specifications we don’t have a system to speculate upon. As I’ve already stated, there is no difference between the arbitrary states of I,II and III.. But this statement is not physically differentiable from “the ball has now come to rest on the table.” That is just as true as the beaker has reached equilibrium. But neither of these facts by themselves, provides a theory that predicts a future state. We find that such relative states, though possibly useful in applied situations, are not useful in our causal analysis of virtual closed systems and implications to the Second Law.

 

  1. Pascal R, Pross A: The nature and mathematical basis for material stability in the chemical and biological worlds, J Syst Chem 2014, 5:3
  2. Isabelle Weissbuch et al., “Racemic β-Sheets as Templates of Relevance to the Origin of Homochirality of Peptides: Lessons from Crystal Chemistry”Acc. Chem. Res., 2009, 42 (8), pp 1128–1140 DOI: 10.1021/ar900033k
  3. James Attwater “In-ice evolution of RNA polymerase ribozyme activity” Nature Chemistry, 2013. DOI: 10.1038/NCHEM.1781 Note: Their conclusion regarding RNA replication (2013) in an associated press release of the paper 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."
  4. Strother, 2007, “Lectures” Boston College site: https://www2.bc.edu/~strother/GE_146/lectures/14.html “The second law, therefore seems to violate what we see happening with in biological systems that appear to create more ordered systems over time. And the chemistry of the evolutionary process involves the exchange of energy in a system, so it is subject to the second law. We get around this problem by defining the "system" that is subject to the second law as including the Sun and Earth - thus, the energy arriving from the sun and its interaction with Earth's (biological) surface results in an overall entropy increase, even though, locally, on the Earth's surface, biology causes an apparent decrease in entropy.”
  5. Regarding the whole Sun-Earth system and “getting around the problem by defining the ‘system’ that is subject to the second law..”, I’m reminded of this very issue today (in a comment section I participated in, (see link to “Quanta” below) It goes like this. I stated: “a system of molecules lacks the capacity to remove entropy” The answer (an actual one I received): “MK, Think of a refrigerator, the refrigerator operates between two reservoirs, and its waste heat is pumped out.” 

Undiswayed, the commentator then described how molecules in sea water, e.g. salt gradients are examples, of how massive groups “pump entropy” into space during their heating and cooling cycles, (this presumably would lower entropy by creating crystals, which as I’ve described above, is not actually reducing ‘entropy’ the way we have defined it here, in a better form.) but I went on to explain this in more detail see below (I respond on Quanta May 5,2015

  1. I respond (5.5.15) on Quanta see Emily Singer “How Structure Evolved in The Primordial Soup” April 146, 2015 https://www.quantamagazine.org/20150416-how-structure-evolved-in-the-primordial-soup/


May 5, 2015 at 4:57 pm Jon, it is not so much the details of “how” in the model you discuss, but the relative differences in entropy or disorder that I’m referring to. The earth is in a state of shedding order, and heat, it is “trying” to reach equilibrium, and if we imagine that the sun is not inputting energy, then the earth’s conveyors and salt density gradients would progress towards equilibrium. That, on a global scale is what is occurring in a simple bench top beaker system with a collection of molecules. But that relative disorder is key because you’re assuming that clusters of molecules in one region, will have “advantage” over others, when in fact each cluster is “trying’ to rob energy, i.e. increase entropy of the other cluster, as in a salt density gradient trying to diffuse towards another region around it. In such unbounded states you have a real theoretical problem of showing feasibility of advantaged or stable gradients of molecules, especially ever achieving useful polymers, as we know that useful polymers in beakers are degraded. Storms and ocean density gradients encourage mass scale mixing and molecular diffusion, working against order. What evidence might there be to say these natural forces/processes you mention do not increase disorder? It is a fascinating question.

  1. This paper makes testable assertions, a primary one being that the construction of constructs, i.e. in nature, via absorption of external energy, the sun or geothermal, might result in products but these products are not of the sufficient entropy to lead to other products. As the model shows, the entropy is always higher outside the horizon, than inside, which is measurable [entropy must drop externally, (the net entropy i.e. the sun or of space) before molecules can propagate outwardly or heat can flow]. The difference is that this “Virtual Closed System” Fig 1 is occurring within an OPEN system, with copious energy (sunlight) entering from the outside. [No one ever observes that the chemicals on their shelves “improve” with age. Nor do the products they generate. The downhill tendencies, the entropy of these bench chemistries are already well known and not surprising to most chemists. One would expect even more accelerated entropy production in nature.] They have excessive entropy contained within these systems, and the reason for this it is hypothesized, is the lack of a normal force, Fn. Regarding the self-assembly from inanimate, there have already been attempts made over 100 years ago by Traube in “La biologie Synthetique” (1912) in bizarre experiments with manganese. So other researchers have been attempting and failing in this for over 100 years.

 

  1. The consequence of the presence of this normalization force is that the passive flow of heat would then do work, and further, that it would generate a different form of heat, heat which has even less capacity (a net capacity) to do less work on the system than before, or perhaps none at all. The passive flow of heat from the sun, and the earth’s convective belts, should in principal do no useful work, against the surrounding system. Thus it would generate no quantity of this ‘heat’ a lower capacity for work. This ‘normalizing force’, FL would also have with it a proportional unit of heat, QL, generated at a specific rate of heat production ΔQL per unit change in time. We might view the “test subject” or test matter or structure inside the entropy horizon (either conforming to its outer surface, or surrounding it as the sphere diagramed) as a hypothetical ‘structure’ composed of essentially force vectors in motion presumably from the convective forces set in motion by the sun’s energy. If we then imagine that the convective forces are essentially Brownian à macroscopic turbulence and massive vortex, and that some small quantity of this can be envisioned that is moving through a space, then we might imagine any one of these as having a potential to form order but also a potential to decrease it. The probability would be equal for both states. We also note that the ‘test subject’ does no work against its surroundings, since the Fn this vector, is a resultant of surrounding vectors, much like a stream of energy flowing. The appearance of order of  crystallization in such a conveyor system, can be calculated to be of higher order but this is an imaginary, non relevant value (as we’ve defined earlier), as its reference is virtual (to a hypothetical system in which it is not formed). In reality, the crystal formation is simply lower order, ‘in flow’ or ‘in stream’ vectorally, with its surroundings. Based on this diagrammatic experiment, we would not expect that such massive crystalline formations would in any way generate F subL against its surroundings. Rather, we’d expect that any quantity of order set up by these vectors, or artificially added to the system and placed within the entropy horizozn, to exhibit some loss of order, irreversibly over time, such that the energy it radiates is of lower capacity to do work on the surroundings. But we note also, that in th is case, no FL is present.

Addendum:

It can be imagined that the particles in motion (see radiative diagram in Fig. 3, below) are given some momentum from the sun, that is, they have some energy available EA or ES (EA=ES) meaning that this is the source of the heat or paritlce motion (and labeling differently from waste heat which is of a lower form), which does in fact exert a pressure for example, in the atmosphere as it energizes and translates motion to molecules there. What is not shown but can be envisioned, is the same EA net from the sun, say some quantity of this heat, being instead incident upon a floating dust cloud. In this case we see some of the EA being only slightly diminished and continuing onward as it is deflected, whereas some is absorbed by the particles (by direct collision of the energetic particles with atoms in the dust) and is translated into motion of the dust and radiated heat QN loss. So the net energy is always, in the case of the earth or the dust cloud, essentially QN+ EA2 (net ('final'))+kinetic motion = EA1 (net) 'starting' from sun. But in the case of the earth, there appears to be a normalized force FL that is imposed and this imposition has some probability that is >>0, where the probability of a FN in this case is virtually 0. What I show earlier in the case of “indifferent time” is that these incidents of normalized force, be they a normal force of a river bank, the water resisting pressure of the particle in momentum ( a packet of solar energized particles exerting a force) or the land, these forces do not appear to anything but passive, and thus only help move the energy EA in the least resistive pathway available. (Much as we’d expect of the particles in a nebular dust cloud) they simply excite and then relax as energy is reemitted back into space.) What then is the difference? This is a key issue.
*The available energy to do work, must be proportional to some average number of particles N with some average energy E. But if we trace such a “packet” after incidence upon the atmosphere, or on the magnetic field, it (the net EA) will be diminished in each drop of the “energy ladder”. The massive quantity of heat radiated from the earth cannot be completely waste heat, it must have some fraction of ES + a lower form of heat QN).
 
Fig. 3 The earth is constantly attempting to shed its heat energy absorbed from the sun and reach a thermal equilibrium or maximum entropy. The constant absorption of Available Energy, EA from the sun prevents this (yellow) by driving essentially the disequilibrium in the conveyor which I depict as an energy ladder. I have not shown the “entropy horizon” diagram here (for simplicity). Normally, the available energy of the sun cascades along a series of steps, ejecting waste heat (that can’t do work) QN in each step, and the remaining available heat proceeds along until it eventually radiates to space. Not shown are the numerous steps, but clearly, each step is robbing the available energy, the active heat (ES = EA) of its capacity to do work on the system. I show also with the wiggly line across a step” a normalization force or FL, which also exhibits a unique QL at some special rate of loss. What should be diagramed is essentially the partilces bunching up against a wall, forming a gradient or pressure’ experienced by the FL normalization force, which also extracts some proportional amount of work WL not shown.

 
Regarding the Eo, in which I define it as having energy (sun light energy), but such energy is << than that required to do useful work on the system, I do not intend for this definition to be unnecessarily obtuse. I’m actually referring to a concept that I believe is reasonably testable. Though (for reasons of the argument I make here), there are no known cases of self replicating inanimate systems that we know of in nature (nor on the bench top). Rather, in every case where there are self replicating systems that we encounter in nature, these require some input, not only of energy, but also of order, at some minimum threshold level. I don’t believe this is well understood but the concept seems rather straight forward. Obviously, the ‘seed’ order cannot be below what is required and intuitively we recognize that living things required not only DNA, but also a cell body. My point here is that we can envision these “virtual closed systems” as actual systems present in nature, and I believe they are, that is in fact at least one of the testable constructs of this paper. Such ‘virtual closed systems” would be isolated in a significant way from the environment around them, likely by a semi-permeable barrier. Such a barrier would of course, allow energy to enter. This energy might be in the form of potential energy, such as that from chemicals in for example a heat vent, or it might be in the form of kinetic energy or both. There are certainly many potential regions we can envision on earth, and lakes would be one example. Water is entering the lake, bringing organized molecules, and they might congregate in this region as there is a barrier to the movement of molecules out of the lake by the structure. Sunlight enters, as does some geothermal heat, so this would be Eo, and my statement , Eo << work required” is that this is not at a sufficient level to do work on the molecules in the lake. A similar case might be found in isolated regions of tide pools, or caves. The mere fact that there are molecules present in these locations, that have some gradient, either in concentration or in their energy state, does not indicate that self replication is possible. This does not show in my mind, evidence that the sufficient energy level can be met. We already have for example, a massive virtual closed system, and that is the earth, with its sunlight providing a massive gradient in terms of potential energy. We can imagine many different syntheses in which molecules are ‘made’ spontaneously and yet we also know that this thermodynamic model is fundamentally flawed. Even if it was possible that advanced organic molecules were being made en masse, in some isolated primordial lake, the supposition of this model would require that the driver of the process is the energy of the surrounding system.
However, this situation lacks an energy model, and the complex molecules being made are going to be made, that is true, but it is a process that resembles normal synthesis on the bench, not self replication. And that it is still not shown how such a system of molecules will pump out other molecules, to form a gradient. That is the problem that all of the articles regarding elaborate self replication computerized models seem to lack, no thermodynamic model. Never mind the actual molecules themselves, how are groups of replicating DNA or RNA and proteins going to be shown to actively oppose their surroundings? [*in bench models we have roughly Condition II, but not exactly. It is experimental fact that these systems still run down hill” even from their energy inputs, the external supply, (which themselves run downhill think of the power plant), and they proceed more TOWARDS equilibrium of total work potential S inside= S outside than AWAY from it. For example, what happens when the pelltier driven thermal cycler is turned off?] So we have instead the case of Condition I, in which the equilibrium is established after some time. and S inside =S outside. And that can occur even in cases where vast quantities of energetic molecules are being made naturally. They are simply part of a more elaborate energy exchange process in which energy is being dissipated, they are NOT in fact showing an exception to the Virtual Closed System,” but demonstrate that the available energy (density) capable of doing work is equivalent inside the entropic horizon and outside it.
If living things including ourselves, were in fact, a form of “energy dissipation system” much like other systems, in what fundamental way would we , living things, be different than other systems? But what is also clear is that in such a system, in which life is a dissipation system, albeit a much supposedly better dissipation system (see Prigogine 1977 et al..) then we simply have the problem of such a system be determined from the external energy sources that it dissipates. In other words it is a fundamental issue of causality.