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Category Archives: Evolution

Abiogenesis enigma: Protein’s origin

Proteins

As you might know, proteins are one of the major “building blocks” of cells; there’s up to 10.000 different types of proteins, all manufactured inside each cell. Abiogenesis theorists  obviously supports the view that these molecules have arisen “by chance”, in a prebiotic world, billion years ago, however, to date, they have absolutely no clue about it, as we can read from this article:

“Proteins are the most complex chemicals synthesized in nature and must fold into complicated three-dimensional structures to become active. This poses a particular challenge in explaining their evolution from non-living matter. So far, efforts to understand protein evolution have focused on domains, independently folding units from which modern proteins are formed. Domains however are themselves too complex to have evolved de novo in an abiotic environment. We think that domains arose from the fusion of shorter, non-folding peptides, which evolved as cofactors supporting a primitive, RNA-based life form (the ‘RNA world’).” 1

So, why is it so complicated to explain its origin? Despite the often repeated innuendo that life and all of its components has “assuredly” originated through natural means, the clear failure of scientists to solve this puzzle can be easily explained by some truths about proteins, its synthesis, structure and so on. After that, no one can reasonably take its abiogenetic origin as logically granted. These truths also explain without shadow of doubt the intriguing fact that absolutely no single protein (even the lesser one, composed of only 8 amino acids) has ever been observed to appear anywhere in the world, outside the cells and high-tech labs, of course!

What’s a protein?

“Proteins are large biological molecules consisting of one or more chains of amino acids. Proteins perform a vast array of functions within living organisms, including catalyzing metabolic reactionsreplicating DNAresponding to stimuli, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in folding of the protein into a specific three-dimensional structure that determines its activity.

A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids;” 2

Talking about amino acids, we’d like to recall another crucial problem for abiogenesis: The absence of self-occurring homochiral mixtures. As it has been told in a previous article, the laws of thermodynamics obliges the occurrence of racemic mixtures, ever:

“The left and right handed forms have identical free energy (G), so the free energy difference (ΔG) is zero. The equilibrium constant for any reaction (K) is the equilibrium ratio of the concentration of products to reactants. The relationship between these quantities at any Kelvin temperature (T) is given by the standard equation:

K = exp (–ΔG/RT)

where R is the universal gas constant (= Avogadro’s number x Boltzmann’s constant k) = 8.314 J/K.mol.

For the reaction of changing left-handed to right-handed amino acids (L → R), or the reverse (R → L), ΔG = 0, so K = 1. That is, the reaction reaches equilibrium when the concentrations of R and L are equal; that is, a racemate is produced.”

Therefore, any abiogenetic theorist has this astounding problem to deal with from the very beginning; without homochiral monomers, we can have zero possibility of a ‘magic’ protein self-assembling…

 

Protein synthesis

 

It’s quite uncanny that intelligent people with advanced knowledge on the subject might attempt to conceive hypothesis of such molecules originating spontaneously, in the wild and morbid inorganic environment, because for cells to build proteins, an intricate, complex and laborious process must take place!

 

 

First, genetic information is needed:

“Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid (for example AUG (adenineuracilguanine) is the code for methionine).”

 

Many proteins use more that one of the 64 possible codons to be built. Moreover, that specific genetic code must be first translated, transcribed:

“Genes encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (also known as a primary transcript) using various forms of Post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome.”

Oh great, a bit complicated, isn’t it? Please, read the Wikipedia article referring to the messenger RNA, for further comprehension of what it is, its manufacturing, composition, etc; all of which adds up more complexity for the protein origin’s explanation.

 

 

The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase “charges” the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus.[6]

The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa). Yeast proteins are on average 466 amino acids long and 53 kDa in mass.[5] The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.[8]

 

Phew! How complicated! You may ask now: are we finally done? And I reply you: Huh, nope! Now that the ribosome, together with the rRNA and more than 50 other proteins, has finally finished the process, a protein is formed. However, it is always found in a  random coil shape. So what? This shape is mostly useless for its usage on organism, as we can read:

Each protein exists as an unfolded polypeptide or random coil when translated from a sequence of mRNA to a linear chain of amino acids. This polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the neighbouring figure). 3

In that randomly coiled shape, the protein is highly unstable, breakable, useless for cell building, so, for proper biological use and better stability, the protein folding process must take place. This 3D-shape is known as the native state.

The correct three-dimensional structure is essential to function, although some parts of functional proteins may remain unfolded.[4] Failure to fold into native structure generally produces inactive proteins, but in some instances misfolded proteins have modified or toxic functionality. Several neurodegenerative and other diseases are believed to result from the accumulation of amyloid fibrils formed by misfolded proteins.[5] Many allergies are caused by incorrect folding of some proteins, for the immune system does not produce antibodies for certain protein structures.[6]

Another importance of the protein folding is:

 

Minimizing the number of hydrophobic side-chains exposed to water is an important driving force behind the folding process.[9] Formation of intramolecular hydrogen bonds provides another important contribution to protein stability.[10] 

 

And how does the folding occurs?

 

 

The amino-acid sequence of a protein determines its native conformation.[7] A protein molecule folds spontaneously during or after biosynthesis. While these macromolecules may be regarded as “folding themselves“, the process also depends on the solvent (water or lipid bilayer),[8] the concentration of salts, the pH, the temperature, the possible presence of cofactors and of molecular chaperones.

The process of folding often begins co-translationally, so that the N-terminus of the protein begins to fold while the C-terminal portion of the protein is still beingsynthesized by the ribosome. Specialized proteins called chaperones assist in the folding of other proteins.

Although most globular proteins are able to assume their native state unassisted, chaperone-assisted folding is often necessary in the crowded intracellular environment to prevent aggregation; chaperones are also used to prevent misfolding and aggregation that may occur as a consequence of exposure to heat or other changes in the cellular environment.

There are two models of protein folding that are currently being confirmed: The first: The diffusion collision model, in which a nucleus is formed, then the secondary structure is formed, and finally these secondary structures are collided together and pack tightly together. The second: The nucleation-condensation model, in which the secondary and tertiary structures of the protein are made at the same time. Recent studies have shown that some proteins show characteristics of both of these folding models.

The essential fact of folding, however, remains that the amino acid sequence of each protein contains the information that specifies both the native structure and the pathway to attain that state. Folding is a spontaneous process independent of energy inputs from nucleoside triphosphates. The passage of the folded state is mainly guided by hydrophobic interactions, formation of intramolecular hydrogen bonds, and van der Waals forces, and it is opposed by conformational entropy.

Only after the folding process, we have an useful, stable protein, with a properly designed shape with its up to four layers, so that the molecule can perform its biological function.

But, remember, many conditions and external factors can destroy proteins, such as hydrolysis (it’s a slow, but ceaseless process, because proteins are metastable, hydrophobic) and others:

Under some conditions proteins will not fold into their biochemically functional forms. Temperatures above or below the range that cells tend to live in will cause thermally unstableproteins to unfold or “denature” (this is why boiling makes an egg white turn opaque). High concentrations of solutes, extremes of pH, mechanical forces, and the presence of chemical denaturants can do the same.

A fully denatured protein lacks both tertiary and secondary structurel. Under certain conditions some proteins can refold; however, in many cases, denaturation is irreversible.[15] Cells sometimes protect their proteins against the denaturing influence of heat with enzymes known as chaperones or heat shock proteins, which assist other proteins both in folding and in remaining folded. Some proteins never fold in cells at all except with the assistance of chaperone molecules, which either isolate individual proteins so that their folding is not interrupted by interactions with other proteins or help to unfold misfolded proteins, giving them a second chance to refold properly. This function is crucial to prevent the risk of precipitation into insoluble amorphous aggregates.

 

For a further an in-depth study about different factors capable of disrupting proteins, read the following articles:

https://en.wikipedia.org/wiki/Protein_biosynthesis

http://creation.com/native-folds-in-polypeptide-chains-1 (a series of 6 parts)

 

To conclude our observation, it’s impossible not to be sceptic of any theoretic proposition that claims self-caused origin of proteins, because it turns out that science unveiled tons of facts that easily prevent any possibility of such proposed scenario:

 

-Absence of homochiral monomers forming in the environment;

-Necessity of genetic specific information;

-Need for an highly controlled ambient, with proper Ph level, temperature, absence of mechanical forces that may easily damage, disrupt the protein, toxins, etc; 

-Need for specific methods to protect the protein against hydrolysis, oxidation;

-Necessity of having 50 other types of protein already manufactured to help on the protein synthesis;

 

The question raises: how in the world could such a specific set of conditions be found in a prebiotic Earth? Such condition can only be barely found in a first-class laboratory, driven by qualified and experienced scientists!

You might as well enjoy watching this short video talking about protein synthesis:

 

References

1. <http://www.eb.tuebingen.mpg.de/research/departments/protein-evolution/protein-evolution.html>

2. <https://en.wikipedia.org/wiki/Protein>

3. <https://en.wikipedia.org/wiki/Protein_folding>

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J. G. Mendel: Why his discoveries were ignored for 35 (72) years?

From: http://www.weloennig.de/mendel02.htm

Some critical comments about the effects of Darwinism on Biological Research by Pioneers of Genetics as well as further Biologists and Historians of Biology.

Especially in the decade after the publication of Darwin’s ORIGIN (1859) the scientific world was eagerly awaiting the discovery of the laws of heredity by some experimental or other scientist(s). After two lectures in 1865, Mendel published his famous Pisum-treatise VERSUCHE ÜBER PFLANZEN-HYBRIDEN in 1866. His work was quoted at least 14 times before 1900, the year of its ‘rediscovery’. There were references in such widely distributed works as Focke’s DIE PFLANZEN-MISCHLINGE (1881), THE ENCYCLOPAEDIA BRITANNICA (1881) and the CATALOGUE OF SCIENTIFIC PAPERS OF THE ROYAL SOCIETY (1879).The treatise had been sent to the libraries of some 120 institutions including the Royal and Linnean Society of Great Britain. Moreover Mendel had 40 additional reprints at his disposal, many of which he sent to leading biologists of Europe. In fact, professor Niessl (1903 and 1906) emphasized that Mendel’s work was “well known” at his time. So in the face of the expectations just mentioned, – why was the discovery of the laws of heredity ignored by most scientists for more than 35 years, until 1900, and by the “true Darwinians” (Mayr) for another 37 years? That is 72 years in all!

The reasons have been hinted at or clearly stated by several pioneers of genetics as de Vries (1901), Bateson (1904, 1909, 1924), Johannsen (1909, 1926) as well as several historians of biology and/or biologists as Niessl (1903, 1906), Richter (1941, 1943), Stern (1962), Lönnig (1982, 1986, 1995), Callender (1988) and Bishop (1996):

All the evidence points to the main reason as follows: Mendel’s ideas on heredity and evolution were diametrically opposed to those of Darwin and his followers. Darwin believed in the inheritance of acquired characters (and tried to back up his ideas with his pangenesis hypothesis, which even Stebbins called an “unfortunate anomaly”) and, most important of course, continuous evolution. Mendel, in contrast, rejected both, the inheritance of acquired characters as well as evolution. The laws discovered by him were understood to be the laws of constant elements for a great but finite variation, not only for culture varieties but also for species in the wild (Mendel 1866, pp. 36, 46, 47). In his short treatise EXPERIMENTS IN PLANT HYBRIDIZATION mentioned above Mendel incessantly speaks of “constant characters”, “constant offspring”, “constant combinations”, “constant forms”, “constant law”, “a constant species” etc. (in such combinations the adjective “constant” occurs altogether 67 times in the German original paper). He was convinced that the laws of heredity he had discovered corroborated Gärtner’s conclusion “that species are fixed with limits beyond which they cannot change”. And as Dobzhansky aptly put it: “It is…not a paradox to say that if some one should succeed in inventing a universally applicable, static definition of species, he would cast serious doubts on the validity of the theory of evolution”.

As the Darwinians won the battle for the minds in the 19th century, there was no space left in the next decades for the acceptance of the true scientific laws of heredity discovered by Mendel and further genetical work was continued mainly by Darwin’s critics among the scientists. In agreement with de Vries, Tschermak-Seysenegg, Johannsen, Nilsson, et al., Bateson stated (1909, pp. 2/3):

“With the triumph of the evolutionary idea, curiosity as to the significance of specific differences was satisfied. The Origin was published in 1859. During the following decade, while the new views were on trial, the experimental breeders continued their work, but before 1870 the field was practically abandoned.

In all that concerns the species the next thirty years are marked by the apathy characteristic of an age of faith. Evolution became the exercising-ground of essayists. The number indeed of naturalists increased tenfold, but their activities were directed elsewhere. Darwin’s achievement so far exceeded anything that was thought possible before, that what should have been hailed as a long-expected beginning was taken for the completed work. I well remember receiving from one of the most earnest of my seniors the friendly warning that it was waste of time to study variation, for “Darwin had swept the field“” (emphasis added).

The general acceptance of Darwin’s theory of evolution and his ideas regarding variation and the inheritance of acquired characters are, in fact, the main reasons for the neglect of Mendel’s work, which – in clear opposition to Darwin – pointed to an entirely different understanding of the questions involved (see above).

However, the idea of Bishop (1996) and Di Trocchio (1991) as to Mendel that “most of the experiments described in Versuche are to be considered fictitious” or “…we are today forced by a series of anomalies and incongruities to admit that Mendel’s account of his experiments is neither truthful nor scientifically likely, and that the strategy he really followed must have been completely different” (Di Trocchio 1991, p.487 and p. 491, emphasis added) is in my opinion for several reasons untenable. (1) It does not match Mendel’s character which is distinguished by humility, extreme modesty and accuracy in handling things. (2) Too much is known about his life, work and correspondence to simply deny the existence of the work he has described (see the publications of Orel, Stern, Weiling and many others). (3) Fisher’s claims of fraud in Mendel’s data have already been disproved by several geneticists and historians of biology (Lamprecht 1968, Pilgrim 1986, Weiling 1995, Vollmann and Ruckenbauer 1997, and many other authors, see below). Working with Pisum for 7 years, I myself have found very similar data for several characters as Mendel had. In an answer to Edward, Ira Pilgrim commented (1986, p. 138): “…one had better have a good deal more evidence (such as a set of loaded dice or perhaps the information that the man is a known cheat) before accusing someone of cheating, which is what Fisher did to Mendel, and those who cite Fisher are doing now.”

On the other hand, if not only the accusations of Fisher but also those of Di Trocchio and Bishop were true, they would make Mendel’s work one of the greatest hoaxes in the whole history of science (“he counted 19,959 individuals” etc., Zirkle) – and at the same time the most ingenious fiction ever produced: an invention hitting directly upon the truth of the laws of heredity with many basic repercussions on nearly all biological and medical areas and our understanding of the living world. However, as long as there are no real foundations for these suspicions and as long as no convincing proofs can be advanced, – proofs which could stand the test of any honest court trial, the accusations fall back on those who produce them: fiction, invention and/or lies in the minds of the inventors (according to A. Kohn, Mendel belongs to the “false prophets”, M. Gardner states that “even Brother Mendel lied” (emphasis added) and V. Orel (1996, p. 207) lists further such examples).

The more I ponder and test the accusations regarding Mendel’s works, the more improbable and absurd the accusations appear to me, and the question comes to my mind: Could it be that now – after the creation position of a scientific giant like Mendel has become clear to so many observers – these accusations are the last resort of a more or less unconscious method of evolutionary philosophy to discredit Mendel and his work after all? 

Hubert Markl comments on the accusations of dishonesty against some renowned scientists (1998, p. VII): “Even if Galilei, Newton or Mendel had cheated when presenting the reasons and evidence for the natural laws they had discovered, that which they had recognized as being true, is nevertheless true, because it was found to be right in multiple tests” (see the original German sentence in the next chapter).

Although this is in principle correct, – being deeply impressed by another study of Mendel’s VERSUCHE ÜBER PFLANZEN-HYBRIDEN (1866), – concerning Mendel I think that this comment is unnecessary (as for Galilei and Newton, I do not want to give an opinion here). I presume the proof for the authenticity and precision of Mendel’s work is to be found in – among other things – the paragraph concerning the seventh of the characters studied by Mendel. He writes (p. 11) [English Version according to http://netspace.org/MendelWeb/Mendel.html]:

“With regard to this last character it must be stated that the longer of the two parental stems is usually exceeded by the hybrid, a fact which is possibly only attributable to the greater luxuriance which appears in all parts of plants when stems of very different lengths are crossed. Thus, for instance, in repeated experiments, stems of 1 ft. and 6 ft. in length yielded without exception hybrids which varied in length between 6 ft. and 7 [and] 1/2 ft.”

Thus, in this paragraph Mendel clearly describes a case of heterosis, hybrid vigour, over- or superdominance (as the phenomenon was later named from 1914 [heterosis] onward) (as for the history of the term, the genetical basis of the phenomenon and further examples, see Lönnig 1980:Heterosis bei Pisum sativumL.). Moreover, Mendel describes a second case of heterosis when continuing (pp. 11/12):

“T h e    h y b r i d    s e e d s    in the experiments with seed-coat are often more spotted, and the spots sometimes coalesce into small bluish-violet patches. The spotting also frequently appears even when it is absent as a parental character” (spaced by Mendel).

Without a theoretical basis (which is still controversial for many cases of heterosis even in our age of molecular biology) and in the absence of any experiments, it is not possible to simply ‘invent’ such unexpected phenomena of science. Rather one must “stumble over” such totally unaccustomed and unpredictable curiosities of nature to report them to an amazed audience. Dominance in all of the characters Mendel described was already astonishing enough, but the two cases of overdominance (heterosis, superdominance) represent strong evidence that Mendel had exactly done what he described. (Mendel’s explanation of the superdominant plant length found, “which is possibly only attributable to the greater luxuriance which appears in all parts of plants when stems of very different lengths are crossed” is hardly more than a tautology [here a more inclusive restatement of the phenomenon to be explained: it does not answer the question why the greater luxuriance occurs in all plant parts, of which the unusual plant length is an ingredient]. Mendel’s statement shows that he was really at a loss for any theoretical/genetical answer for the heterosis-phenomenon he had encountered and precisely described.)

One could, perhaps, object that the phenomenon of hybrid vigour had been mentioned before Mendel. However, to describe heterosis for definite characters and organs in definite sizes and quantities in definite species and culture varieties (and all that without any knowledge of the genetical and/or molecular basis of the phenomena reported), so that the experiments not only appear unlikely (in fact, unlikely!), but also prove to be entirely reproducible and true – without really having made them at all – is so improbable that we can confidently forget this objection.

Concerning Mendel’s paper, I agree on the scientific level with Mayr and Stern. Curt Stern stated (1966, p. v): “Gregor Mendel’s short treatise, ‘Experiments on Plant Hybrids’ is one of the triumphs of the human mind. It does not simply announce the discovery of important facts by new methods of observation. Rather, in an act of highest creativity, it presents these facts in a conceptual scheme which gives them general meaning. Mendel’s paper is not solely a historical document. It remains alive as a supreme example of scientific experimentation and profound penetration of data” (Stern and Sherwood 1966). Mayr concurs (1982, p. 726) that by this comment Stern has “so well” characterized Mendel’s achievement.

Glycolysis and Alcoholic Fermentation

Glycolysis (from glycose, an older term for glucose + -lysis degradation) is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+. The free energy released in this process is used to form the high-energy compounds ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).Yeast cells obtain energy under anaerobic conditions using a very similar process called alcoholic fermentation,  also referred to as ethanol fermentation, is a biological process in which sugars such as glucose, fructose, and sucrose are converted into cellular energy and thereby produce ethanol and carbon dioxide as metabolic waste products.

Glycolysis requires 11 enzymes which degrade glucose to lactic acid (Fig. 2). Alcoholic fermentation follows the same enzymatic pathway for the first 10 steps. The last enzyme of glycolysis, lactate dehydrogenase, is replaced by two enzymes in alcoholic fermentation. These two enzymes, pyruvate decarboxylase and alcoholic dehydrogenase, convert pyruvic acid into carbon dioxide and ethanol in alcoholic fermentation.

The most commonly accepted evolutionary scenario states that organisms first arose in an atmosphere lacking oxygen.1,2 Anaerobic fermentation is supposed to have evolved first and is considered the most ancient pathway for obtaining energy. However, there are several scientific odds against that.

First of all, it takes ATP energy to start the process that will only later generate a net gain in ATP. Two ATPs are put into the glycolytic pathway for priming the reactions, the expenditure of energy by conversion of ATP to ADP being required in the first and third steps of the pathway (Fig. 2). A total of four ATPs are obtained only later in the sequence, making a net gain of two ATPs for each molecule of glucose degraded. The net gain of two ATPs is not realized until the tenth enzyme in the series catalyzes phosphoenolpyruvate to ATP and pyruvic acid (pyruvate). This means that neither glycolysis nor alcoholic fermentation realizes any gain in energy (ATP) until the tenth enzymatic breakdown.

Enzymes are proteins consisting of amino acids united in polypeptide chains. Their complexity may be illustrated by the enzyme glyceraldehyde 3-phosphate dehydrogenase, which is the enzyme that catalyzes the oxidation of phosphoglyceraldehyde in glycolysis and alcoholic fermentation. Glyceraldehyde phosphate dehydrogenase consists of four identical chains, each having 330 amino acid residues. The possible number of different combinations of these amino acid chains is infinite.

 

Glyceraldehyde-3-phosphate dehydrogenase

 

To illustrate, let us consider a simple protein containing only 100 aim acids. There are 20 different kinds of L-amino acids in proteins, and each can be used repeatedly in chains of 100. Therefore, they could be arranged in 20^100 or 10^130 different ways. Even if a hundred million billion of these (10^17) combinations could function for a given purpose, there is only one chance in 10^113 of getting one of these required amino acid sequences in a small protein consisting of 100 amino acids. By comparison, Sir Arthur Eddington has estimated there are no more than 10^80 (or 3,145 x 10^79) particles in the universe! Consider the 10 enzymes of the glycolytic pathway. If each of these were a small protein having 100 amino acid residues with some flexibility and a probability of 1 in 10^113 or 10^-113, the probability for arranging the amino acids for the 10 enzymes would be: P = 10^-1,130 or 1 in 10^1,130, and this result is only the odds against producing the 10 glycoytic enzymes by chance. It is estimated that the human body contains 25,000 enzymes. If each of these were only a small enzyme consisting of 100 amino acids with a probability of 1 in 10^-113, the probability of getting all 25,000 would be (10^-113)^25,000, which is 1 chance in 10^2,825,000…

Figure 2

 

 

There are still other problems with that theory. There are numerous complex regulatory mechanisms which control these chemical pathways. For example, phosphofructokinase is a regulatory enzyme which limits the rate of glycolysis. Glycogen phosphorylase is also a regulatory enzyme; it converts glycogen to glucose-1-phosphate and thus makes glycogen available for glycolytic breakdown. In complex organisms there are several hormones such as somatotropin, insulin, glucagon, glucocorticoids, adrenaline thyroxin and a host of others which control utilization of glucose.

In addition, complex cofactors are absolutely essential for glycolysis. One of the two key ATP energy harvesting steps in glycolysis requires a dehydrogenase enzyme acting in concert with the “hydrogen shuttle” redox reactant, nicotinamide adenine dinucleotide (NAD+). To keep the reaction sequence going, the reduced cofactor (NADH + H +) must be continuously regenerated by steps later in the sequence (Fig. 2), which requires one enzyme in glycolysis (lactic dehydrogenase) and another (alcohol dehydrogenase) in alcoholic fermentation.

Further, at one point, an intermediate in the glycolytic pathway is “stuck” with a phosphate group (needed to make ATP) in the low energy third carbon position. A remarkable enzyme, a “mutase” (Step 8), shifts the phosphate group to the second carbon position—but only in the presence of pre-existent primer amounts of an extraordinary molecule, 2,3-diphosphoglyceric acid. Actually, the shift of the phosphate from the third to the second position using the “mutase” and these “primer” molecules accomplishes nothing notable directly, but it “sets up” the ATP energy-harvesting reaction which occurs two steps later!

 

by Jean Sloat Morton, Ph.D.

 

References

1 A.I. Oparin, Origin of Life, New York: Dover Pub., lnc., 1965, pp. 225-26.
2 (Jark and Synge (eds.), The Origin of Life on the Earth, New York: Pergamon Press, 1959, p. 52.
3 Ernil Borel, Probabilities and Life, New York: Dover Pub., Inc., 1962, p. 28.

 

Cite this article: Morton, J. S. 1980. Glycolysis and Alcoholic Fermentation. Acts & Facts. 9 (12).

From: http://www.icr.org/article/glycolysis-alcoholic-fermentation/

 

Water and origin of life

 

Although water is portrayed by many as the solution to, or star player in how life came to be, the fact is that water spontaneously breaks down complex molecules that living organisms need to exist: such as DNA,* RNA, proteins and their components.**   For example, an article on Molecular Cloning says that  “Proteins are usually soluble in water solutions because they have hydrophilic amino acids on their surfaces.”1

 

Amino acids have been called the building blocks of life, and when two or more are joined together they are called a peptide and the bond that holds them together is called a peptide bond.  When ten or more are linked together they may be called a polypeptide, and if they are ordered and folded correctly, they become a protein.  And in a wikipedia article on peptide bonds we are told that a peptide bond can be broken by … hydrolysis” ***  (just by) … “adding … water” … (and that the) “… bonds in proteins are metastable, meaning that in the presence of water they will break spontaneously.” 2

 

A simple video explain dehydratation and hydrolysis:

 

Another article on this topic 3  says that hydrolysis is:

 

“A chemical reaction in which water is used to break the bonds of certain substances. In biotechnology and living organisms, these substances are often polymers … such as that … (exist) between two amino acids in a protein … “

 

Dr. A. E. Wilder-Smith, (Ph.D. organic chemistry) also brought this out in a book he wrote on life’s complexity and origin.4

 

“Amino acids and other building blocks present in the macromolecules of living matter aggregate to form larger units … by … (a reaction) called condensation.****  The combinations usually involve the elimination of one molecule of  water between two combining molecules.  It is the removal of this molecule of water which presents the major difficulty  …  For, the removal of this water molecule from between two combining molecules requires energy which must … be supplied in some fashion.

“A further difficulty arises in this question of the elimination of water.  For, in the prebiotic world, it is assumed that the condensation reaction took place in the presence of a large … (supply) of water which would tend, according to the law of mass action, to hinder the condensation process and … (promote)decomposition (or breakdown of peptides and polypeptides). … The more water, the less condensation.”

 

“If the reaction is to proceed in the direction of the dipeptide, (or two amino acids that are joined together) … the water molecule … (that results) must be removed from the reaction system since the reaction is reversible.  If it is not removed … (it will) hydrolyze (or separate) the dipeptide back again to the constituent amino acids …”

 

This means the “primordial soup,” or “warm little pond”  where Darwin speculated that life began could not have been simply water, since it would “hydrolyze” or break down complex molecules back into their basic original amino acid as soon as they formed.  Dr. Charles McCombs explains the problem as follows in an article he wrote on the subject of why life by chance  is virtually, if not utterly and completely impossible.  

 

“Every time one component reacts with a second component forming the polymer, the chemical reaction also forms water as a byproduct …  There is a rule of chemical reactions … called the Law of Mass Action that says all reactions proceed in a direction from highest to lowest concentration. This means that any reaction that produces water cannot be performed in the presence of water. This Law of Mass Action provides a total hindrance to protein, DNA/RNA, and polysaccharide formation because even if the condensation took place, the water from a supposed primordial soup would immediately hydrolyze them. Thus, if they are formed according to evolutionary theory, the water would have to be removed … which is impossible in a “watery” soup.5

 

But because the “watery soup” in living cells is surrounded by a membrane, the “water” inside the cell “behaves very differently” 6  than ordinary water.  In fact, the “water” in a cell is not water but a blend of water, amino acids, proteins, and many other chemicals called cytosol. This mixture is the result of the DNA’s ability to regulate what goes in and out of the cell — via  numerous channels that control and regulate what is allowed to pass through the cell membrane, and thus to create and maintain a favorable environment and PH for DNA, RNA and protein synthesis, and life itself to exist. 

If the concentration of amino acids is high enough, some of them will link up with others to form dipeptides and tripeptides.  An article on this subject states that:

“is important to recognize that by whatever reactions polymerization (or the joining of amino acids)occurred, they had to be reactions that would occur in an essentially aqueous environment. This presents difficulties because condensation of amino acids to form peptides, or of nucleotides to form RNA or DNA, is not thermodynamically favorable in aqueous solution.”{6}

The explanation for this is partly that the concentration of amino acids decreases as amino acids form pairs (called dipeptides) in a solution. This decreased concentration causes the velocity of the peptide synthesis reaction to slow down, and some dipeptides begin breaking up, again becoming single amino acids. The solution reaches equilibrium when just as many dipeptides dissociate as associate. A very tiny fraction of the dipeptides add another amino acid to form a tripeptide. … Oligopeptides (Oligo=few) and polypeptides (poly=many) will form only very rarely. Tripeptides dissociate faster than dipeptides in the same solution. 7

In this regard, a tripeptide has only three amino acids, while the simplest protein ever found has at least eight: connected in a specific order.

Jeffrey P. Tomkins makes the following statement in a book on the design and complexity of the cell:

 

“… plasma membranes are … quite complex and … (function) as more than just a barrier … Some key functions  of the membrane involve the import and export of chemical compounds through specialized transmembrane channels, sensory and signaling processes via specialized receptor proteins imbedded in the membrane, and osmotic (water) regulation … through special portals.” 8

“Within the … membrane is the internal cell matrix … called cytosol or cytoplasm, which is a semi-fluid substance.  …  Like the … membrane, the complexity of … cytoplasm seems to grow with every new discovery in cell biology.” 8

 

Tomkins also tells us that water must be regulated and controlled outside the cell as well in what is called the “extra cellular matrix.”  

This means that the water of yesteryear, or the distant past, almost certainly performed just like the water of today, and that water, dirt and chemicals, could not have created life anymore than fuel, dirt, and metallic ore, — by themselves — could create a car, motorcycle, or an  airplane: even in millions, billions, or trillions of years.  

 

 

A typical human cell would undergo 2,000 to 10,000 spontaneous DNA hydrolysis damage events every day just because it is an aqueous environment.(The only reason that DNA functions as well as it does is that cells come equipped with an amazing array of cooperative DNA repair mechanisms. For example, polymerase replication during cell division might produce 6 million errors per cell, but then proofreading machinery can reduce this to 10,000 and then mis-match repair machinery could reduce this to 100. It appears to be impossible, however, to replicate the 6 billion nucleotides in a human cell in a completely error-free manner.

A way to remove water is with certain high-energy chemicals that absorb water, called condensing agents. If the reaction between condensing agent C and water is:

C + H2O → D (2)

and if ΔG2 of reaction (2) is negative and large enough, it can couple with reaction (1):

H2NCHRCOOH + H2NCHR′COOH + C → H2NCHRCONHCHR′COOH + D (3)

ΔG3 = ΔG1 + ΔG2. If ΔG3 is large and negative, the equilibrium constant for reaction 3, K3, will be large, and this could conceivably produce reasonable quantities of polymers.

Some researchers used the condensing agent dicyanamide (N=CNHC=N) to produce some peptides from glycine, even claiming, ‘dicyanamide mediated polypeptide synthesis may have been a key process by which polypeptides were produced in the primitive hydrosphere.’

However, the biggest problem is that condensing agents would readily react with any water available. Therefore it is a chemical impossibility for the primordial soup to accumulate large quantities of condensing agents, especially if there were millions of years for water to react with them. Yet the Sydney Fox experiment used a 30-fold excess of dicyanamide. And even with these unrealistic conditions, 95% of the glycine remained unreacted, and the highest polymer formed was a tetrapeptide.

 

 

*   Although chemists can make DNA in their laboratories, they can only do so under highly controlled conditions that simulate cytosol. They achieve this by using a pre-existing DNA or gene (template), using the right amount of water, magnesium chloride, and salt buffersand by using a pre-existing microscopic / molecular copy machine called DNA polymerase.  Such would not be the case in nature, since genes are not known to form by themselves, nor even simple proteins that consist of only 8 amino acids: much less complex ones that consist of 900–1000 of them, such as DNA polymerase — along with a motor protein called helicase: that actually spins like a motor (at 1800 rpms) and that unwinds the DNA.

 

**   When two amino acids come together they are called a peptide, and the reaction is called condensation or a condensation reaction **** or dehydration synthesis.  A nucleic acid is a synonym for a nucleotide, and when two or more nucleotides join together they are called an oligonucleotide.

 

***  According to the American Heritage Dictionary of Science, hydrolysis is “a process of decomposition in which a compound is broken down and changed into other compounds by … (absorbing, or being diluted with) water.  For example, in food digestion, the food absorbs water and is broken down by hydrolysis.  The same dictionary says that to hydrolyze means “to decompose by hydrolysis …”  and that organic molecules such as “Nucleic acids, proteins, and polysaccharides contain many bonds that hydrolyze …  In this regard, the combining word hydro- simply means “of or having to do with water.”

 

****  Think of a Condensed can of Campbell’s Soup.  The fact that it is “condensed” simply means that water has been removed.

 

References

1.   http://opus.bibliothek.uni-wuerzburg.de/volltexte/2003/554/pdf/Thesis-complete-2-library.pdf


2.   Peptide Bond at http://en.wikipedia.org/wiki/peptide_bond.


3.   http://biotech.about.com/od/glossary/g/hydrolysis.htm

 

4.   The Creation of Life: a cybernetic approach to evolution, 1970, pp.25-26. Available online through various book sellers. 


5.   
Chemistry by Chance: a formula for non-life, Charles McCombs: Acts & Fact, 2/09, pp. 30-31:www.icr.org/article/4348/  


6    http://en.wikipedia.org/wiki/Cytosol#Water


7.   
Chemistry Refutes Chance Origin of LifePart III, by Jon Covey, B.A.,  and Anita Millen, M.D., M.P.H.,  www.creationinthecrossfire.com/Articles/ChemistryRefutes3.html 


8.   
The Design and Complexity of the Cell,  Jeffrey Tomkins, Ph. D., 2012, pp. 24-25;http://www.icr.org/design-cell/  


9.   Ref. 7 above by Tomkins, p. 79.


10. 
Life, DNA, and Proteins: Why raw materials on earth cannot produce life, at http://in6days.tripod.com/id6.html

 

See more in: EarthAge.com ; CMI

 

 

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