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

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

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

'If “chemical selection” is indeed a real testable theory or mechanism, as it is cited many times in peer reviewed literature, such as these, then can it be falsified? In other words, what is it about ANY chemical reaction that one can envision, that would proceed differently, WITH or WIHOUT so called the mechanisms described as natural “chemical selection?” I say that if you cannot answer that question, it does not pass muster for science.'

 

My two relevant lead theories discussed previously are:

"Does Life Violate The Second Law Of Thermodynamics? Implications Of Virtual Closed Systems" MKK http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html

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

 

In addition to making an argument for my lead theories, VCS and Indifferent Time, which are independent of the chemistries and are instead related to forces or energies of the components, I have replied with essentially a basic experiment, well actually two. They reference complex data in Biochemistry. 5th ed to defend their arguments, and I employ the use of household items, one with food color, and the other using a carrot, to illustrate the problems with these arguments. Here is an excerpt from the TEXT which I refer to as ‘5^th Edition.’ 

 

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

 

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

 

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

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

 

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

 

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

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

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

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

 

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

 

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

 

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

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

 

These next assumptions, which are the basis of “chemical selection”assume many other unusual if not known, properties of molecules, which are not supported by any chemical terminologies that I’m aware of. The reason they are not known is because of the Second Law and the copious experimental evidence which negates these models (evidence not discussed in5^th Edition) .

 

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

 

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

 

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

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

 

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

 

Notes:

1. Biochemistry 5^th Edition (2002)

http://www.ncbi.nlm.nih.gov/books/NBK22508/

 

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

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

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

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

evolution of reproducing living organisms, natural selection also affects replicating

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

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

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

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

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

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

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

 

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

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

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

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

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

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

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

Opportunity Rover, NASA

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

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

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

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

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

 

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

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

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

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

 

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

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

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

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

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

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

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

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

 

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

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

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

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

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

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

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". DOI: 10.1098/rsob.130156 http://rsob.royalsocietypublishing.org/content/3/11/130156
 

 

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 4^th 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 F_L.

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?

 

 

 

 

 

 

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

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

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

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

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

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

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

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

 

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

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

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



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

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

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


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

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

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

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


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

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

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




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

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

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

 

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