Tuesday, October 20, 2015

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


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

are made for the purposes of further illustrating the definition or apparent definitions, of “chemical selection”. This is informative of what “chemical selection” is “understood” to be by current biochemistry, but elaborates more on what chemical selection is at least meant to be. One can find helpful diagrams of RNA and DNA as well as proteins and how, it is currently theorized, these basic molecules might have self-catalyzed or replicated. However, we can find nothing about these definitions that would allow us to test the version of "chemical selection" in Biochemistry. 5th ed as I explain in part I. link HERE http://causaldistinctions.blogspot.com/2015/08/i-use-of-natural-selection-to-explain.html. A key argument against their theory is the lack of testability of its propositions as I explained in Part I... 
'If “chemical selection” is indeed a real testable theory or mechanism, as it is cited many times in peer reviewed literature, such as these, then can it be falsified? In other words, what is it about ANY chemical reaction that one can envision, that would proceed differently, WITH or WIHOUT so called the mechanisms described as natural “chemical selection?” I say that if you cannot answer that question, it does not pass muster for science.'
 

My two relevant lead theories discussed previously are:
"Does Life Violate The Second Law Of Thermodynamics? Implications Of Virtual Closed Systems" MKK http://causaldistinctions.blogspot.com/2015/05/does-life-violate-second-law-of_14.html
"I Propose A Challenge To Maximal Flow Theories By A New Theory: Indifferent Time" MKK
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 ‘5th Edition.’ 

 

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

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

 

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

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

 

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

 

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

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

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

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

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

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

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

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

 

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

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

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

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

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

 

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

 

Notes:

1. Biochemistry 5th Edition (2002)