Saturday, June 27, 2015

POEM: "Nothing As Far As The Eye Can See"


The semiphores all red, we go anyway
Nothing as far as the eye can see
No friends beyond this place, not even a hut or a lean to
Or maybe a cave. Just miles of toil yet, no... months

An old wooden house, as this would be a mirage
I regard the martini in my hand, fill it with skepticism
Where were you crafted?
Was your spirit obtained by hook or crook
Craft or pleasure
Were you reborn, distilled of the same grains as Hannibal gulped as he sleigh an army, letting their blood?

You are the molecular Pearl shell
Of a hundred days and nights
Ripped away discarded, sifted, purified ..
The history is dizzying
And the night tips sideways
Slipping again..
Barely keeping its stars in place
They'll fall into the trees if not done with care
Where exactly were we supposed to go?

Nothing as far as the eye can see
Yet we go anyway.

Tuesday, June 23, 2015

Problems Of A Paper Advocating 'Dynamic Kinetic Stability' Theory In Light Of A New Virtual Closed System 'VCS' Theory


I discuss the problems of another theory called "Dynamic Kinetic Stability” or DKS, which is described in a paper by R. Pascal, (see below) as “..a stability kind specific to persistent replicating systems and derived from the dynamic persistence associated with exponentially driven self-replication.” I mention the paper in the context of my Virtual Closed System theory (VCS) and  "Indifferent Time" (links below) that refute not only 'maximal flow' but also so-called chemical selection, and natural selection coupled energy dissipation theory.
 
"Does Life Violate The Second Law Of Thermodynamics? Implications Of Virtual Closed Systems" MKK
http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html

"I Propose A Challenge To Maximal Flow Theories By A New Theory: Indifferent Time" MKK
http://causaldistinctions.blogspot.com/2015/04/i-propose-challenge-to-maximal-flow.html



This appears to be one of the first papers I’ve encountered that attempts to somewhat boldly account for the chemistry i.e. with a kinetic stability theory, in addition to the thermodynamic problem relating to life’s origins. It is one of the few papers that appears to be rather honest about the fact that the problem at hand is immense, and that self organizing processes resembling pre-transitional states of life would likely not resemble life in terms of thermodynamics and the normal processes by which free energy is lost. It does not rely on far from equilibrium “smoke” to fill in the gaps. A general comment regarding the impetus for many of these papers: I have to wonder if it is not so much a driver of life that is sought but a new mechanism for creating a grander illusion that the problem is near fixing. Fool the reader into believing that your equations are formidable enough to be “possible” and plug enough references, and one can make at least a case, so in this sense it is true evolution if not of the theories themselves. At least there were several cases where this paper described the holes.

But returning to the problem at hand. The paper itself is not without major issues. Most of the diagrams in my view; for example the catalytic chains contrasting traditional enzymatic pathways or cycles vs theoretical kinetic cycles that might drive molecules forward, are essentially depicting a theoretical chemistry that must be occurring in nature. It does not realistically account for what that might entail, as there are not simply chemical competition occurring, as physical draining of energy, dissipation and other random processes found in any natural setting. These are omitted. The conclusion from these diagrams is that nature must be doing chemistry, useful chemistry, and making useful molecules with higher free energy, (in thermodynamic terms) just as one would expect from a chemical factory. Can nature do this? And where is the proof of concept at the most basic molecular level?

The other major weakness of the paper is that it fails to answer many of the other theories that are in existence, namely that self-organization is possible in lightening bolts, eddies, concentration gradients and so on. The emphasis on Lotka and other references, which have purported to show stability of critical molecular species like triplet RNA, coupled with so-called energetic expressions for fitness, is to me a non-starter. It at least admits that if you had in theory, A, B, and C groups of evolving molecules like RNA’s and others, how would one in theory show that any of these would not circumvent the process by reacting counterproductively to lower free energy rapidly and bring the system to thermodynamic equilibrium? That would be the problem of “persistence.” The amount of time required for some of the more organized species allegedly, to remain unreacted for a time to allow a different process to commence.

“On the other hand, indications from previous reports [16–22] and supported by our present analyses (Scheme 1) have shown that a form of stability that is different from thermodynamic stability is needed to understand how far-from-equilibrium chemical states may have gained a form of persistence, thereby opening the possibility of self-organization toward life.”

The paper concludes that essentially: “Irreversibility and the kinetic power of reproduction seem to be, at least in principle, sufficient to allow the emergence of life and there is no need to seek out some hitherto unknown physical law to explain the origin of the specific behaviour associated with living organisms.”

It concludes that the catalytic and kinetic aspects should not be overlooked, but are important in addition to thermodynamic (self-organization) and even 'chemical selective processes'. It further concludes that vaguely all of these must be considered simultaneously. It then gives a reasonably good summary of two basic problems facing the study, understanding abiotic formation of feed stocks or organic building blocks present in abiotic processes, but then the more difficult issue of how these would be driven to self assemble. A final distinction is made between Boltzmann’s chemical based theories the chemical world that is known, and its own theory of DKS dynamic chemical stability (“..a stability kind specific to persistent replicating systems and derived from the dynamic persistence associated with exponentially driven self-replication”), as though these are separate entities and yet there is no physical evidence in the paper or any other sources, for DKS occurring. In the sense that it defines it (DKS) as unique from Boltzmann’s physical chemical processes, it is probably more accurate to correct the intro statement “DKS- a process that is ‘usually” not observed in regular chemistry..” to “DKS is a process“never” observed in regular chemistry." I believe it gives support to the notion that current thermodynamics is critically lacking, though it fails to address the issues with thermodynamics itself, hence its advocation of DKS though it's not clear at all how it would be co-joined with thermodynamics, and instead, this paper shows the need for a basic new approach to the problem.



[*The intro to this article was updated on 10/13/201]

1. Pascal R (2013) "Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics". http://rsob.royalsocietypublishing.org/content/3/11/130156
 

 

Saturday, June 20, 2015

Why The Other Planets?




Saturn Nightside


There is much debate these days about the role of science and faith, (two diametrically opposed worldviews), in the nature of our existence and purpose. And despite over four centuries of astronomy and numerous unmanned and manned explorations of the moon and surrounding planets, almost all of the debate focuses on the origin of life on earth and of the origin of earth itself. And it is not just 'creationists' and religious scholars, but also to some extent, scientists who are to blame. Why is that? We, in the twenty first century know that we are not alone, and never were. We have companions that are very close to us, which are in fact alien. They are alien worlds, millions of miles separate from earth, and world's to themselves. It is such a simple question. And seemingly obvious. What are they for? Asked from a religious-historical standpoint, what purpose do the planets serve? "Purpose" is a question that would seemingly have ramifications religiously, just as the recent genome data sparks controversy and more questions for our existence and purpose. Are they for our entertainment? To invoke wonder? Or do they serve as some kind of example, perhaps to value our own world even more? Maybe we should ask simply because no one else is?

In one of my favorite films "The Great Race" Peter Faulk the wise fool, asks the "Professor" constantly for advice, I take artistic liberty in imagining him asking such a question now: "Hey, professor, uhh I know they orbit the sun, they have orbital periods, ya ya sure, but what are they FOR? The earth is for us, right?" Is the earth really only for us? Does not the evidence of our relatedness to the code shared by all life on the planet, say something of our collective purpose and even, stewardship? The anachronism serves to illustrate a general viewpoint of TV shows and classrooms in the subject. The question of what the planets are for, is equally troubling if asked from a religious or scientific perspective. It challenges the comfort gained by precise data, facts and figures, as these seem to only shroud the problem further, they do not answer why the giant planets are here. This is not a shortcoming of more persuasive oratorio or speech, but defines I believe, the real gap between where we are now and where we need to be. Learning of the climates and conditions of other planets may not only improve ones local understanding of their own planet, it may de-vilify the very technology and knowhow that is needed to address the problems.

In the days of Galileo, the mere knowledge that other moons circled Jupiter threatened the Vatican's position that the earth was the center of the universe..The geocentric view in which all objects the 'stars' the moon, the sun, were placed in spheres, orbiting the earth. It marked the great rift between science and religion based worldviews. But how far have we really come from that time? Some leading scientists attempting to meld science with religion, such as Dr. Francis Collins, the former head of the Genome project speculate broadly on the nature of creation and of the modern synthesis theory, that is modern science's account of life's origins. They discuss the big bang and the possible role of God in the Big Bang, but also in the possible directing of "God's instruction manual" as he refers to the genome. In such a view, the earth is the sole focus of our origin, just as it is in the Bible (see Collins' book, "The Language of God" 2006). Another leading scientist, for example, the paleontologist Andrew Parker, has recently come out with a book ("The Genesis Enigma..") touting the hypothesis that Genesis is in fact very consistent with scientific theory of the Big Bang and origin of earth and life on our planet. What is interesting though is that Genesis only mentions the earth and "the heavens", it never mentions the other planets. They are not important? How so? How do you misplace an object that is 317 earths? (see Jupiter's mass http://nssdc.gsfc.nasa.gov/planetary/factsheet/jupiterfact.html) Or Saturn, which is 95 times the mass of earth. Both planets orbit the sun just as earth does, though they take considerably longer, about 13 earth years for Jupiter for example. The focus we are to understand, is to again backwards accommodate ancient texts with science, even modern science. It appears that even today, four hundred years since the discovery of the moons of Jupter by Galileo, science confronts the modern equivalent of geocentrism with such eye opening wonders as close planetary flyby's and comet landings, as real as gravity. And these are largely ignored. It is interesting that now, just like in the days of Vatican Inquisition, when Jesuits weighed the biblical implications of "infinitesimals" and forbid their teaching, science is still encountering issues of compatibility. Is it really incompatibility? Is science not, at its most serene, not simply exploring what is already there? It seems time for some of these scientists to open their eyes, and see for themselves, the light of saturn reflecting off its rings, not as some "sign" of philosophical alarm, or harm to their own personal beliefs, but of simple wonder of our existence shared by all peoples. If we again return to Collins' thoughtful reasoning for how science or Design, might explain or might not explain our origins based on how DNA of our genes is constructed, but also the big bang model, can we also consider the issue of the missing planets from the book of Genesis and their purpose or purposelessness in Collins' literal view of Creation? Collins asks frequently such questions as, "why would God put 'junk' DNA in our genome, what purpose would this serve?" Yet, Collins and intelligent designers would likely never ask "why would God put large gaseous planets in our solar system? Such unquestioning puts earth as a central focal point of the discussions about what should be the greater solar system and denies the obvious and very large bodies orbiting across our skies at night, which might ask if they could: "why were we not included in your book?" The scientists who look for scientific truth to support their beliefs seem to want to focus only here, only on earth. How are they any different from Jesuit mathematicians or astronomers who refused to consider the moon's of Jupiter four hundred years ago? Why would God create other planets which serve no purpose to earth? I have heard plenty of the science-religion melding or accommodating arguments from some scientists, for how God might have steered evolution, or God might have balanced physics in such a way that the Universe is more favorable to intelligent beings as ourselves, moving this constant or that constant ever so slightly, and this is the anthropocentric view. But we are talking about giant planets, Jupiter and Saturn, and Uranus and Neptune. Why would God miscalculate and create at least eight other planets which serve no purpose? The sweeping masses that can be seen moving silently through our night sky, in their orbits of our sun, should be worth their weight in evidence against what is essentially a modernistic, geocentric view of the universe. A scientific compatabilism that serves only itself, has no legitimate claim to science, and is irrelevant to belief, except as I've said by deliberately fomenting its apparent incompatibility with religion (the fault of some scientists who make it so). If such accommodationist views still are considered relevant, it is extremely myopic, and scientifically and culturally narrow minded, of our species, to neglect the purpose of entire worlds, some of which might harbor life in their orbiting moons (consider Europa for example).

There is much energy invested in the search for other life in the solar system, and for earth like planets. The mathematics- the odds, favor finding an earthlike world. It seems odd to concentrate so heavily on the search for extraterrestrial life outside the solar system, when we in fact have extraterrestrial systems, nearby. The creation of these worlds, and of our solar system..are unknown histories that really should be a pressing question for our species. Because wherever they came from, their source must be magnificent and beyond scales of comprehension. Could such a source be reachable? Could it be visible to us if we decided to build an instrument to scan for it? Consider that even now, the mysteries of the universe are deepening. It is possible that 75% of the matter, meaning what is out there in the heavens, is dark or invisible, OR that some other force is working upon it besides gravity.

 As of the date that I first drafted this article, a new and significant discovery has been made about the "outer" solar system. Amateur astronomer's discovered a previously unknown planet, VP113 or unofficially "Biden's" planet. It is a frozen, pinkish world covered in ice. But this finding suggests that there may be other planets orbiting well past Pluto, even other giant planets which might explain why smaller objects like Biden's planet have irregular orbits. It extends the limits on the size of our solar system and if there are so many potential undiscovered planets orbiting, what else might be there?

 We have opened the discussion to some extent to the purpose of the planets, at least as a more open question that is or should be of equal relevance as the 'purpose' of our genetic relatedness. At the same time, however, the true nature of the other planet's existence should invoke wonder of a deeper kind, that is not limited merely to our own world. I believe the other planets ask us to question even beyond what we currently know or are prepared to ask, perhaps limited to ask, currently about biological science and where we originated. The issues of our origins are most assuredly related to the birth of the other planets around us, and their history, a history that is virtually unknown to us. One might say "these are merely interpretations, different views of the same evidence before us." But is it really such a subjective 'interpretation' if we as a species are falling short in our technology that ensures our survival? Perhaps the cutting of funds for basic technological research is not so "subjective" but has real impacts on our race to the next frontier. Given the consequences of not being prepared for a wayward asteroid, I don't believe we could really have "too much technology" to deal with such a challenge, the real concern would be to not have enough.

Civilizations five hundred years ago could not fathom jet airplanes or supersonic trains because the fastest transportation system was still the horse. It was not because of a lack of brain power. It was simply a lack of knowledge of what was possible. Could we be in similar circumstances? Believing that we cannot even approach light speed travel, because the ____ engine has not been discovered? Ancient mariners did not look at the sea as being a gateway to other rich continents, because they didn't know these even existed. The average citizen in 17th century London, had no idea he could make a fortune in gold in a place now known as "California." The New World was not only a waste of time, it was a place to die, and very quickly.

To date, we have spent a great deal on the discussion of earth-creation here on earth. But in doing so, we neglect our neighboring planets. We neglect our place essentially in the system we live in. The nature of our existence is a mystery that extends to places far beyond earth itself, and is tied with the other planets around us, these are fields of astrophysics and astrobiology. Like civilizations before us, we need to educate ourselves on these other worlds, the secrets they harbor, and just like ancient mariners, learn about new ways of navigating across them.





NOTES:
1. Saturn (NASA/Flickr www.flickr.com/photos/ugordan/719346540
2. Francis Collins (2006) "The Language of God."
3. New planet, Eris is heavier than Pluto by 27%http://www.nature.com/news/2007/070611/full/news070611-10.html
4. New planet VP113 discovered outside solar system. http://rt.com/news/dwarf-planet-biden-unlikely-region-505/ and Trujillo, C. A. & Sheppard, S. S. Nature 507, 471–474 (2014).
5. http://www.nature.com/news/private-asteroid-hunt-lacks-cash-to-spy-threats-in-orbit-1.17810
6. Amir Alexander (2014) "Infinitesimal: How a Dangerous Mathematical Theory Shaped the Modern World".http://www.barnesandnoble.com/w/infinitesimal-amir-alexander/1115382359?ean=9781429953924

Thursday, June 11, 2015

POEM: "In The Puff Of Its Exhaler"


Marjoram and bits of tempest
A spinning glowing disk twirls, in a corner, on a string
The candle blows itself out, in the wind of a thought.
I wanted to count the days, lazy, like smoke
Intertwining, meshing like those layers of the levitated dust
Coming to life.
They've nearly reached the critical
The mass of doubt, so perfunctory
That assembles in the dark corners of a universe
Where no one pretends
I've left them, the switches, the to's and fros, which stretch and reach like glassy waves
That's the place, when no one's looking, for it to rise out of the glowing, ..
Of course no one's looking, there's no one there to look.
That's in the sadness, again, of the ''puff'' ..that is missing an exhaler, its source..
In the plain and simple destruction

Saturday, June 6, 2015

Editorial on 'A Second Look At "How Structure Arose In The Primordial Soup" V2: Thoughts On 'Continuity Principal'


Author Note: 6.7.15 This is my original draft of an article I'd posted earlier. Why another look? Because this blog, happens to be the only format I'm aware of in which to address the scientific errors of an article, the very one in question. My other version contains more detailed links. You might expect that the source author who's worked in the field for a decade, would provide a reference, perhaps to a researcher who has pioneered 'self-evolving molecules,' But none are obviously available. How does one venture into a new field, I.e. the study of self replication, when the basic feasibility of such an enterprise has no scientific reference to support it? The comment sections beneath their articles "are not the place for technical discussions", but then neither are the actual publications, there isn't an editorial section, so where is this venue for scientific dialogue and appropriate discussion of the material reported in the article? I can only tag the authors, Greg Fournier, and co-authors, re-post, and "hope" that they may feel compelled by their own nagging desire for scientific accuracy? Is this after all, not the central driver of science? Is it really too much to ask, for even the most basic questions as these: 1) "What are "evolving molecules" and where is this self evolving "chemistry" described in detail? 2) When was feasibility of this sub-field of "molecular ancestory" established and by whom, i.e. reference? I believe that the authors should kindly either explain what these concepts are, or retract and provide an apology for posting such an article they're not willing to discuss, as though its science is based on some established principals (several of which I highlight), principals of which they, and they alone are apparently privy to.  In the mean time, we shall forge ahead with Virtual Closed Systems theory, some of what I'm exhibiting here in my blogs.



I took a second look,  at an article in Quanta, "How structure arose in the primordial soup" and again, I believe it is grossly distorting if not factually misleading, about what science "knows" even theoretically about primordial life. Some red flags are the leaning title, which answers "how" mind you, not "If" as to imply that we are now on to the finer details of that story. Is rationality, yet another victim of the instantaneous gratification demanded by such articles?

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. It assumes that the informed public is largely ignorant, but slanting your article to imply that they are now examining finer details instead of the big picture questions, i.e. do we really know, even remotely, what the composition was? It also completely misleads the informed public about the basic problems of the source author's theory, which of course, are never even mentioned. Just because Haldane in 1929, (who is apparently credited with the term) worked diligently on primordial soup, or Leduc in the 19th century, doesn't mean that the chemical basis is worked out any more now than it was then. The "issue" about amino acid ratio is absurdly detailed, as are the so called "ancestoral" molecules, giving the misleading impression that it is only the minutia now, of the primordial soup that is being analyzed, its actual "code" whatever that would be, and it's not clear if the contributor of the article, Greg Fournier, as well as 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. In fact I've proposed that such claims of self-organization are really "perpetuating chemistry" which I believe more aptly encapsulates the working of their theory. Most apparently believe that such perpetual chemistry is feasible, thanks to articles like these that give them a bully pulpit or megaphone, take your pick.

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 'needed.'
Although I queried 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 the inanimate is a phenomena connected with the animate, or vica 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 work of MEP theory, (Kleidon 2013 but also 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 principal I'm introducing (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, FL will be capable of doing work.

In reality, in the Virtual Closed System theory, there is no means for groups of molecules to export entropy. Despite their insistence that the earths cycle can do so. Again thanks to the "myth" promulgated by these other theories. Discussion turns into 'they said it was so.."  in what is a conventional bait and switch routine, where only part of the story is known and knowledge of its greater workings of the pseudo 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 the big questions about feasibility, the elephant in the room.. and it seems this kind of research approach in which a path is discussed as though the theory is accepted, and contrary theory ignored (i.e. what is "chemical evolution?") is not or at least should not, be conventional in science.

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


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

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

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

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

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

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

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

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