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The Mystery of the Left-Handed Molecules in Proteins: Is it solved by The Matrix?

Monday, December 29th, 2008

Origins of Left-Handed (UP) Molecules of Proteins - SoftwareA Big Puzzle asking for Matrix’s solution.

(This Article: Actual State = Under Construction - Translated to: nothing yet) 

 From:          http://creationsafaris.com/epoi_c03.htm#epoi60 at Creationsafari.com which is about the book “Evolution: Possible or Impossible”, by JAMES F. COPPEDGE, Ph.D. 
PUBLISHED BY
PROBABILITY RESEARCH IN MOLECULAR BIOLOGY
Northridge, California 91321
          I will keep working this issue because it is very important and I am asking to people for looking the Matrix’s models and help me to improve the solution that I am seeing from the Matrix’s Models. 






                                        Page 55          
Chapter 3 The Mystery of the Left-Handed Molecules in  Proteins                                                                

 There are here mysteries which prepare immense labors for the future,
 and from this time invite  the most serious meditations of science... Louis Pasteur
 

OVER A HUNDRED years have passed since Pasteur wrote those words in 1860.  He was referring to one of the strangest puzzles in biology, that proteins are made exclusively of “left-handed” molecules.2  Although immense labors have been done as he suggested, the mystery remains without adequate solution to this day. ——————————————————————————————————————————————————————————————————————————————————–                           COMENTARY FROM A STUDENT OF THE  MATRIX:                                                         ——————————-xxxxxxxxxx—————————                  Looking to the picture of our last non-biological ancestral, the solution seems evident. It pops up abruptly to our eyes, our sixty sense. The logic is irrefutable! It is an issue concerning to the difference between opened systems and closed systems. Between the growing flow of energy/information and the entropic flow. Observe the Matrix’s  software of the ancestral from who living beings received the genetic code: the left side is energy/information/evolution growing; the right side is the reverse of the flow, so, it can not be expressed by opened systems like biological systems.      But, when we try to explain it logically or to communicate it, several problems arises. So, we will need working this issue. What is the solution? Protein is – I think – the biological counterpart of the circuit’s channel carrying the flow of information in shape of energy, it is the biological tool that reproduces the dynamics produced by the dimension time. Look to the picture of the closed software. The rounded circuit can be broken in parts, infinitely. Then, each protein is a biological counterpart of a bit of the circuit. The software flow has only one direction: from left to right. It is clockwise. Left to right… We have the irresistible tentation for to see just here the solution to the big mistery! Each protein is a channel made by several aligned amino-acids. Amino-acids, as we can see in my book, are the biological fractals from the Matrix’s software in shape of the last ancestral. and they are different among themselves due each one being the tool for each universal sistemic function. Protein - anyway - must be a structure by which runs a flow of energy, and the flow must be from left to right…      Another detail we can not forget: biological systems have suffered a severe, drastic mutation, turning on an opened system.  Then, only left-handed molecules are selected for to become part of any biological system, organic matter and protein. But, a detailed observation shows that things are not so easy. For instance: if the universal software is for both – electro-magnetic, mechanical, biological systems – why Nature produces de right handed structures? Look to the following picture below: why and for what Nature produces the D-alanine, the mirror’s image? Ok we know that Nature produces everything in pairs, since the quantum balloons left and right spinned ( see my models of “The Yukawa Quantum Baloons”). We know that the opposite material particles makes anti-matter. But… we don’t know any opposite biological systems made with right handed molecules. So… this issue needs an extra and indispensable effort from Matrix’s students. I feel that this study will be driving us towards a new big discovery.)

 Ok, let’s go back to the book:

        


The Mystery of the Left-Handed Molecules in Proteins                 57 

          To preface the left-handed mystery, it may be of value to those in other fields if we first review what proteins are like. They are, of course, a major class of the complex molecules of which all living things are made.  Since all molecules consist of atoms bonded together, we can get an idea of the size of a molecule by the number of atoms it contains.  Water, for example, has three atoms.  Nitric acid has five.  Now, by comparison, the smallest of proteins contains around a thousand atoms, and the largest has close to a million!  Proteins, then, are enormous compared to most molecules.
    In primary structure, proteins are long, slender filaments or threads.  Even giant molecules, like proteins, are unbelievably small from our viewpoint.  In fact, Max Perutz of Cambridge University notes that a protein fiber is 500 times thinner than the thinnest object a good optical microscope could reveal.
4  This miniature long filament is often precisely folded into a somewhat globular shape which differs for each type of protein.
Proteins Are Chains of Amino Acid Molecules     It seems to be a universal rule in biology that complex things are built from simple components.  This is a source of amazement to scientists.  It also makes it much easier for us to understand things like proteins and DNA. —————-

(Comentary from the Matrix: “Why they don’t go ahead asking to Nature: Why? They considers atoms as simple components. Once time, the whole Universe was constituted only by atoms. The atoms did not have a material environment for to developing something more complex than they were. So, they had created the complexity from nothing? The answer maybe is: hierarchy of natural systems.  Every natural system, like atoms, are situated between to other systems, one below and other above. The superior system, which have more complexity than atoms systems, at the time of life’s origins was the astronomical system. It is not impossible that the informations coming from that system, in shape of photons from stellar radiation, or cosmic radiation, has driven the simple atoms at Earth’s surface, for to reproduce the astronomical complexity (see the Matrix’s chapter about “Yne non-living genes and DNA”). ——————————


    Proteins are simply long chains of smaller molecules called amino acids. There are twenty varieties of these that are commonly used in proteins.  These will be listed in chapter 6.  There are indications that all of the twenty kinds occur in proteins of all organisms. 
    The number of these building blocks in a single protein ranges roughly from 100 to 50,000, since there is great variety in the size of different proteins.  The hormone insulin is usually called a protein although it is smaller than this range, having only 51 amino acids.  It is not, however, a completely typical protein. The average number of amino acids in proteins of the smallest known living thing is 400, at the very least.
 


58               Evolution: Possible or Impossible?

    There are many thousands of kinds of proteins, and they form numerous different jobs in living things.  Many are digestive enzymes, others are structural molecules, and some perform their specialized tasks as hormones or as hemoglobin in blood cells. All of this complexity comes from those twenty amino acids and the particular order in which they are arranged in the chain. A different sequence may make an entirely different type of protein.
    Commenting on this, one scientist noted: “Thus, from about twenty different amino acids, the colossal array of different proteins required by different forms of life is constructed.”
7 Amino Acids Also Are Built on a Simple Plan
    It is fortunate for our understanding that even the amino acids possess a degree of uniformity.  All are made of four kinds of atoms: carbon, hydrogen, nitrogen, and oxygen.  Two of the amino acids also have a sulfur atom each.
    Besides this, all of the amino acids are exactly alike in the main section or “backbone” which consists of three atoms, two of which are carbon and the other nitrogen.  The center one of those three, which is a carbon atom, is called the alpha carbon.  (“Alpha,” being the first letter of the Greek alphabet, is usually written in Greek in scientific writings, thus: α.  To avoid complexity, we will spell out in English any such Greek letters.)
    Having noted some of the similarities, we now come to the difference between the amino acids.  To the central carbon atom, the alpha carbon, there is attached a side group, often called the R group.  The sole difference between the various types of amino acids is that each has a different side group. 
    In the various amino acids, the distinguishing side group contains from one to eighteen atoms.  The considerable diversity in these side groups makes possible many of the things proteins do.  They have different electrical and chemical properties which affect other molecules.  Other amino acids at various distances in the same protein chain may be attracted in this way, with the following result:
    When the units of the protein chain are in any particular

The Mystery of the Left-Handed Molecules in Proteins                 59

sequence, the resulting chain will coil or spiral and fold in a specific way.9  This final shape makes the protein able to do its unique job in the cell.
    When two amino acids are united, a “peptide bond” is formed between them, and a molecule of water is released.
10  It takes energy to get the amino acids to bond together.  It is difficult to bring this about outside of living things.  In the laboratory it can be done by special techniques.11 
    In living organisms, on the other hand, protein chains are linked up or polymerized rapidly.  This system for making proteins is very complex and efficient, employing special enzymes and several other unique molecules.  It is an extremely interesting process that takes place under direction from the DNA code, the hereditary “language of life.”  It will be described in chapter 9.
How Can a Molecule Be Left-Handed?     Amino acids can exist in both right-handed and left-handed forms.  A person’s two hands show how this can be.  They have the same components – fingers and thumbs – yet they are different. The thumb of one is on the left and the thumb of the other on



60               Evolution: Possible or Impossible?the right.  They are “mirror images” of each other.  Some molecules are like that.
    Let’s imagine that we are able to look at an amino acid molecule.  Remember that each is built on the same simple plan. The three atoms of the backbone are in the direct line of the protein chain when the amino acid is united with others.  In the center is the alpha carbon atom.  On one end of it there is a nitrogen atom, and on the other end another carbon.12  If we look at it from the carbon end, it will be possible to tell whether it is left- or right-handed (see Figure 2).
 FIGURE 2

Left-handed Right-handed

A Pair of Molecules             Left- and right-handed amino acid residues.  The molecules shown are L-alanine and D-alanine (L = levo, or left- handed; D = dextro, or right-handed).  Alanine is the simplest of the amino acids which are isomeric or handed.
    The bonds in the figure are not drawn to scale, but are lengthened so that the left- and right-handedness is more easily seen.  In real molecules, the bonds are shorter so that the “surfaces” overlap, making the molecules more compact.  The initials on the atoms indicate carbon, nitrogen, oxygen, and hydrogen.  Note that the only difference between the two is the position of the side group, on either the left or right side.


The Mystery of the Left-Handed Molecules in Proteins                 61         Notice the center carbon atom of the backbone.  It appears to be elevated a bit compared to the other two atoms of the main part.  That alpha carbon is asymmetric, that is, different on every side.  This difference is not in the atom itself, but it results from the fact that the four items bonded to it all are different.
    As we view it from our vantage point at the carbon “end” of the amino acid
13  (considering the lower carbon atom in Figure 2 as the carbon end), we note that the central or alpha carbon has two side projections that angle outward to the right and to the left.  On one side, this extension is simply a hydrogen atom.  Opposite it is the side group mentioned earlier, the group which differs for each of the twenty amino acid types.
    If that identifying side group is on the left, the molecule is “left-handed.”  If instead it protrudes to the right, the amino acid is said to be “right-handed.”
    These two forms of the same chemical contain the exact same components and are called isomers or stereoisomers of that chemical.  Their side groups are just positioned oppositely in space. Each form is the antipode of the other.  They are enantiomorphs or enantiomers of each other.
    We may note in passing that this difference was discovered in an accidental way.  A French physicist named D. F. Arago in 1811 shined a beam of plane-polarized light through a quartz crystal.  He discovered to his surprise that the plane of the light was twisted or rotated as it passed through the crystal.  Later it was found that some chemicals dissolved in water would also cause this twisting of the beam of light.  Whether the light was rotated to the right or to the left depended on the substance used.  Solutions which rotate polarized light in this manner are said to be optically active, since they deflect the path of light.
    Pasteur, while investigating this strange phenomenon in 1848, found that the optically active substance he was studying was made of one-handed molecules.
14  To his surprise, he found that optically active materials from living things were different from


62               Evolution: Possible or Impossible?optically active crystals of inorganic substances like quartz. Crystals of the latter come in both left- and right-handed configuration, whereas the individual molecules are neither left- nor right-handed.Only Left-Handed Amino Acids in Proteins     Francis Crick, codiscoverer of the DNA structure, describes this strange characteristic of the molecules of living organisms: It has been well known for many years that for any particular molecule only one hand occurs in nature.  For example the amino acids one finds in proteins are always what are called the “L” or “levo” amino acids, and never the “D” or “dextro” amino acids.  Only one of the two mirror possibilities occurs in proteins.15      That is the mystery.  English biologist John Maddox called it “an intellectual thunderbolt that natural proteins should contain only the left-handed forms of the amino acids.”16 
    This is a special difficulty for those who believe that life originated from nonliving matter by natural processes.  A. I. Oparin, Russian biochemist, has perhaps had more to do with current evolutionary thought than any man since Darwin because of his pioneering attempts to explain the origin of life through natural chemical processes.  He brought up this mystery in a recent book thus: “It is necessary to touch briefly on a problem which has been discussed in the literature for a long time.”
17 
    In an earlier book he went more into detail.  The atoms involved in the different positions (right and left) are subject to the same forces.  When amino acids are formed, that varying side group could just as easily be on the right as on the left.  Says Oparin:
    The probability of the formation of one antipode or the other is therefore the same.  As the law of averages applies to chemical reactions the appearance of an excess of one antipode is very improbable, and, in fact, we never encounter it under the conditions of non-living nature and in laboratory syntheses . . . .
    In living organisms, on the contrary, the amino acids of


The Mystery of the Left-Handed Molecules in Proteins                 63which naturally occurring proteins are made always have the left-handed configuration. . . . This ability of protoplasm selectively to synthesize and accumulate one antipode alone is called the asymmetry of living material.  It is a characteristic feature of all organisms without exception but is absent from inanimate nature.
    Pasteur pointed out this fact as follows: “This great character is, perhaps, the only sharp dividing line which we can draw at present between the chemistry of dead and living nature.”18 
    In modern times, many others have expressed the same surprise as Pasteur.  For example, Linus Pauling, Nobel laureate in chemistry:     This is a very puzzling fact . . . . All the proteins that have been investigated, obtained from animals and from plants, from higher organisms and from very simple organisms–bacteria, molds, even viruses – are found to have been made of L-amino acids.19    He concludes, “Nobody knows why it is that we are built of L-amino acid molecules, rather than of D-amino acid molecules.”20 
    Dr. Larry Butler, who teaches biochemistry at Purdue University, has said, “In all respects chemically and physically (except for physical properties associated with asymmetry . . . ) D- and L-amino acids are not only equivalent but indistinguishable.” 21 
    Professor Dennis Englin calls attention to an amusing experiment.  Scientists now can hook up proteinlike chains which contain both the L- and D-amino acids, and put such chains into a living organism, e.g., a bacterium.  The organism immediately takes them apart, and in some cases rebuilds the amino acids in the left-handed form! 22 


64               Evolution: Possible or Impossible?          Professor William Stokes of the University of Utah sums up the situation on this baffling question of the two forms as far as normal proteins are concerned:     They are as identical in all other respects as a pair of gloves. When amino acids are prepared artificially, both L- and D- varieties occur in statistically equal amounts.  But living things can use and construct only the left-handed type, probably for hereditary reasons going back to the first ancestor of all life on earth.23      Looking at it from the naturalistic standpoint for the moment, we may ask: How could living things have gotten started which use only left-handed amino acids in proteins?
    The first problem is to discover how any amino acids could originate by natural means.  For this, the current explanation is to postulate a primitive atmosphere that was totally different from ours today.  Then it is claimed that amino acids might have been formed from that prescribed atmosphere by the action of ultraviolet rays, lightning, and perhaps heat.
24 



The Mystery of the Left-Handed Molecules in Proteins                 65    In experiments with this presumed primeval atmosphere, whenever any amino acids have been obtained in elaborate laboratory tests, they have consisted of both L- and D- varieties.
    So we still have the problem.  Even if the amino acids had occurred in that atmosphere naturally, these experiments indicate that the supply would have been “racemic” or mixed, instead of all L- or all D-.
25  Efforts to Account for the Left-Handed Phenomenon
    Scientists have let their imaginations range far and wide in quest of a solution.  Without exception, each avenue has proved considerably less than satisfying.  Materialists, for lack of anything better, have had to sound confident and to depend on one or another of the ideas put forward.  One gets the impression that many just have a vague hope that maybe some one of these explanations may be valid, without specifying which specific one.
    A summary of these attempts is given in Appendix 1, page 243, following the final chapter.  The reader is encouraged to turn to it if he desires the details on this subject.
    For a century, these efforts to find the answers have continued.  Long and imaginative labors using many laboratory approaches have managed only to get “unequal amounts of enantiomers to form,” by using reagents, catalysts, crystals, solvents, etc.26  This is sometimes hailed as if it indicated success, and is credited to the “entirely expected effect of the atomic neighborhood, biasing, say, the ease of approach of the various reacting molecules to one of the possible sites of action.”  One such “success,” we may note, yielded “an excess of 6 percent,” the amount of one hand as compared to the other.27 
    All well and good, but getting “unequal amounts” is a far cry from explaining nature’s success in producing 100 percent (all L-) products.  Even if a way is found, the question will persist:



66               Evolution: Possible or Impossible?Why is it so difficult for our most intelligent scientists to solve in modern laboratories what nature has done without apparent effort?No Satisfactory Answer Has Been Found     After considering all the attempts, it is clear that unless chance could do it, there is at present no adequate answer from a naturalistic standpoint to explain how this left-handed condition began.  As a result, there is little evidence of any agreement or consensus among scientists regarding its source.  Oparin must presume that this stereoselectivity started without prior design. Any other belief would be inconsistent with his communist philosophy.  (Interestingly, that viewpoint – dialectical materialism – is not atheistic after all.  Professor Claude Tresmontant of the University of Paris has pointed out with unanswerable logic that communists are actually pantheists, worshiping matter-in-motion.)28 
    Dr. Oparin never does make clear which of all the various ideas he prefers, to account for the origin of the exclusive use of left-handed amino acids in proteins, but he assumes it happened naturally, nevertheless.  He is admirably straightforward in realizing the difficulty:
    Even when we know how the asymmetry arose, though, we still cannot answer the question of why one antipode, rather than the other, should occupy such a monopolistic position in the life of all the organisms inhabiting the Earth.  This question is important for an understanding of the essential nature of life but it remains for future investigators to supply the answer.29      On that subject, Pauling made this imaginative comment:     The earth might just as well be populated with living organisms made of D-amino acids as with those made of L-amino acids.  A man who was suddenly converted into an exact mirror image of himself would not at first know that anything had changed about him. . . . He could drink water, inhale air and use the oxygen in it for combustion, exhale carbon dioxide, and carry on other bodily functions just as well as ever – so long as he did not eat any ordinary food.  If he were to eat ordinary plant or animal food, he would find that he could not digest it.30 



The Mystery of the Left-Handed Molecules in Proteins                 67    He then noted a strange coincidence.  As long ago as 1872, Lewis Carroll’s Through the Looking Glass was published.  In it, Alice (in a land of mirror images) said, “Perhaps looking-glass milk isn’t good to drink.”31  It is possible that Lewis Carroll was aware of Pasteur’s work in this field.
    In attempting to account for the one-handed phenomenon, Oparin and others have depended upon natural selection.  As we will see in chapter 5, there is no way that natural selection could have operated at all until there was a way to duplicate all the essential parts accurately.  There is no method known whereby this could take place except the intricate DNA-RNA-enzymes-ribosome process which we will examine in later chapters.  Therefore, natural selection is of no help whatever in the effort to find the way that left-handed amino acids obtained their complete monopoly in naturally occurring proteins.
No Natural Solution Unless Chance Could Produce This Effect     Since natural selection was unable to operate before accurate duplication, and since no way has been found to account for the exclusive use of left-handed components in proteins, chance is all that is left, from the materialistic standpoint.  Some evolutionists have recognized this explicitly.  For example, S. E. Bresler, a top biochemist in the U.S.S.R. Academy of Science, wrote,     How and why the complete separation of stereo isomers in living tissue was started remains an enigma. . . . We can only speculate that this remarkable phenomenon originally occurred as the result of very rare large-scale fluctuations associated with the origin of life.32      By this he plainly means chance fluctuations.  Before applying the rules of probability, there are two questions we need to resolve: (1) Can each of the amino acids be linked with any other, regardless of hand? (2) Will they link with equal ease whether of the same or the opposite hand?33 



68               Evolution: Possible or Impossible?Left- and Right-Handed Amino Acids Can Be Linked     Are the two forms of the amino acids shaped so that any of them can unite, whether they are L- or D- in type?  The answer is yes.  Whether left- or right-handed, any amino acid can be linked with any other of either hand.  There seem to be no exceptions.34 
    Pauling wrote (1964) : “We have no strong reason to believe that molecules resembling proteins could not be built up of equal numbers of right-handed and left-handed amino acid molecules.”
35    Since that was written, this has actually been done on numerous occasions in many laboratories, resulting in a voluminous literature in the scientific journals.
    While it is true that opposites can be linked in the laboratory, what about that question if we consider the conditions that evolution assumes to have been existing before life began?  Dr. Sidney W. Fox, of the University of Miami has done experiments which involve this.  Some years back, Dr. Fox heated all the common amino acids at 200o C temperature under certain conditions and obtained chains containing all the amino acids.36  When asked if both left- and right-handed amino acids were included in the same chain, he replied that he was almost 100 percent certain that they were, but that there was no way to tell absolutely at the time.37  Temperatures of 170o C and above were typically used in such experiments. 














The Mystery of the Left-Handed Molecules in Proteins                 69Will Opposites Join With Equal Ease?     Although there is a degree of uncertainty on this subject at the present stage of scientific knowledge, it appears that the answer lies in one or the other of the following extremes, or somewhere between: (1) There may be equal ease of linking opposite hands, on the average.  This seems most likely, when considering all the factors.  The individual amino acids are different in ease of fit.  Some work better with the same hand, and some with the opposite.  The shape of the chain, when it begins to form a spiral, also may be involved.
    (2) The other possibility is indicated in a few reports of preference for the same hand in some particular instances.
38  In some other instances there is preference for the opposite hand.39  The extreme limit seems to be a possible preference of 6/7 for the same hand.  It is quite unlikely that this is the case on any general basis, but we will use it as one limit to consider.
    Since this subject gets quite technical, we will include the details in Appendix 2, page 249, leading to the conclusions which have just been stated briefly.  The reader can experiment with models of the amino acids in order to satisfy himself on the comparative equal ease of fit, whether of the same or opposite hand.  Numerous opposite hand linkups are routinely made in various laboratories with no notice of any more hindrance than with the same hand,40 except in the occasional instances mentioned.
    In the next chapter, probability reasoning will be applied to these two outside limits – equal ease of linkup, or 6/7 preference for the same hand.
                                                           END