MAKING SENSE OF EVOLUTION

Last night I finished reading yet another book on evolution, which makes over thirty or so I have read. Admittedly, this is just a miniscule number of those available. There seems to be a common theme found in those that deal with abiogenesis, the beginning of life. This book, like most books on the subject, was not sensible. Inevitable, the authors of these books treat life as something extremely exotic. The oldest theme of many of these books on evolution, which I do not bother to read, takes by far the most extreme treatment; those who gave up trying to explain it; thus, eschew science and succumbed to the lazy religious driven; God did it; end of the story. Interestingly enough, Charles Darwin pretty much limited himself to a very through and methodical description of forms and behavior of life presumably to avoided the wrath of religious critics—clever avoidance used to get the massage across but required in 1859.

Life Ascending: Ten Great Inventions of Revolution by chemist +Nick Lane is, in my opinion, an especially good book in may ways but takes the usual approach for books on this subject. One of the first things the author does is reveal his attitude toward life as a mysterious phenomenon by invoking exotic environments in respect to where life began. He speaks at length about hot thermal vents in the deepest part of the oceans belching hydrogen sulfide and carbon dioxide at over 400 or 500 degrees centigrade. He uses the intriguing name “black smokers” and then moves to hydrogen emitting “white smokers” with an entirely different chemical environment in respect to hydrogen ion concentrations, among other things: both as exotic as his perception of life. He even mentions the finding of carbon compounds in certain meteors to suggest that life might have “started” from this source in outer space.

All of this is in violation of my contention that life is not exotic; it cannot “exist” in extreme environments let alone “evolve” in such environments. We must have a relatively narrow range of pH (hydrogen concentrations, and temperatures to exist. We cannot have life without proteins; proteins denature at high temperatures, and pH values out of a very narrow range alter the chemical characteristics of amino acids hence alter their function. In addition, the molecules that duplicate themselves, such as DNA and RNA have melting points, really the temperature at which double stands of nucleotide base pairs separate and are no longer able to carry out their vital function, which suggest an even narrower temperature range. It is a difficult figure to be exacting  about but DNA strands start separating at about 143 or so degrees Fahrenheit so the evolution temperature must be below this. In addition live cannot exist in pH environments that deviate from 7.2. 

Life is sustained by the slow accumulation and release of the suns energy. Scientists have worked out how this happens chemically. Almost every schoolchild learns very early in life about how chemicals can store and release energy and almost every child learns about photosynthesis and elementary cell metabolism as well—use oxygen, release carbon dioxide and need a supply of carbohydrate. They may even learn about organisms they need methane, and not oxygen, for example.

What they do not seem to learn is the concept of thermodynamic equilibrium of biological systems. The reason for this is obvious; the details of this concept are overwhelming and often not appreciated even by scientists; anything with the word thermodynamics in it is chilling. The truth is that is what we are, plants are, bacteria are. We, like all of the earths’ biota, are the results of three billion years accumulation of interrelated metabolic reactions. The much heralded concept of “natural selection” is based on the principle that a reaction would not take place if it did not contribute to the thermodynamic equilibrium of that metabolism, not all metabolisms, but that metabolism even in the remotes of ways. This is not simple; it is the top of the ladder of the three billion years of physicochemical events. If the reaction did harm it obviously would not be reproduced but if it did no harm or contributed even in this minor way to the overall metabolism, it would be reproduced.

The concept of an actual “chemical bottom rung” of the evolutionary ladder is a concept I have never seen addressed. Perhaps, the experiments of Stanly Miller and Urey come the closest but are terrible incomplete. Given that a chemical reaction must be physically possible before it can happen, then a “protein” catalysts or enzyme could not evolve if the chemical reaction did not preexist, which sounds like a benign statement on face value but will be a very disturbing statement for some. Every reaction that is now enzyme mediated somehow must takes place without a protein enzyme—there are something like 2,709 enzymes involved in human metabolism alone according to an article in the journal Genome Biology; Computational prediction of human metabolic pathways from the complete human genome. I have seen estimates of 250,000 enzymes in the worlds’ biota; who know how accurate these numbers might be are, any bodies guess. The number exceeds the number of genes in any genome. None of them could have evolved if the reaction they catalyze did not preexist; shocking but true.

Given that, enzymes are families of proteins—not just a single molecule but many, many molecules reproduced by a well worked out mechanism—and the realization that protein families are the product of some sort of memory results in the implication that random DNA and or RNA polymers or both existed before protein enzymes existed. There can be no memory of amino acid sequences without some way to remember them: this mechanism has been worked out in detail as well. It also means some mechanism for creating the formation found in proteins or at least peptides (short chains of amino acid) existed before natural selection could take place—there has to be something from which to select, which is speculation. In addition, there are myriad coenzymes that contribute or alter enzyme activity. “Natural selection” is the choice of proteins with even primitive enzyme activity that promote reactions that contribute to thermodynamic equilibrium, which has to be selection of DNA and RNA that code for that protein. It seems overwhelming but is not a dog chasing its tail kind of story, peptide bond formation its self, the hooking together of amino acids, is one of the reactions enhanced by enzymes.

Amino acid sequences; found in families of enzyme proteins, the heart of enzyme activity; cannot be reproduced (remembered) without some kind of coding; something to remember. Coding can only develop out of random sequences of nucleic acid bases because obviously RNA or DNA could not have formed randomly with such codes. Equally as obvious, codes could not develop without positive feed back information from reactions that positively contribute to the thermodynamic metabolism of an organism’s metabolism. The point here is that each organism, Archaea, bacteria, plant, animal, what ever, has an overlapping “intermediary” metabolism natural selection has shaped. The earths biota evolved out of a compatible environment and not out of some hot vent in the bottom of the ocean or a meteorite.             

URL: firetreepub.blogspot.com Comments Invited and not moderated