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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/

 

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Oh, homochirality…

Naturalistic theories have many insurmountable problems, dilemmas, if not for their anti-theistic commitment, many brilliant, renowned persons would never bother to conceive such a stupid wishful thinking, because the odds for a mere protein to form itself without intelligent influence are astronomical, in fact, impossible! Read now some scientific facts against the homochirality to happen by chance.

An organism is composed of countless molecules, the “building blocks” of life. Nearly all biological polymers must be homochiral (all its component monomers having the same handedness. Another term used is optically pure or 100 % optically active) to function. All amino acids in proteins are ‘left-handed’, while all sugars in DNA and RNA, and in the metabolic pathways, are ‘right-handed’. Whether or not a molecule or crystal is chiral is determined by its symmetry. A molecule is achiral (non-chiral) if and only if it has an axis of improper rotation, that is, an n-fold rotation (rotation by 360°/n) followed by a reflection in the plane perpendicular to this axis maps the molecule on to itself. Thus a molecule is chiral if and only if it lacks such an axis.

A 50/50 mixture of left- and right-handed forms is called a racemate or racemic mixture. Racemic polypeptides could not form the specific shapes required for enzymes, because they would have the side chains sticking out randomly. Also, a wrong-handed amino acid disrupts the stabilizing α-helix in proteins. DNA could not be stabilised in a helix if even a single wrong-handed monomer were present, so it could not form long chains. This means it could not store much information, so it could not support life.

To begin with, it’s a well known FACT that homochiral molecules are never found outside a cell (except, of course, in labs, under the human, therefore intelligent,  manipulation). Why? Laws of physics, dear!

consequence of the Laws of Thermodynamics. 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. A famous textbook correctly stated:

‘Synthesis of chiral compounds from achiral reagents always yields the racemic modification.’ and ‘Optically inactive reagents yield optically inactive products.’ (Morrison, R.T. and Boyd, R.N., 1987. Organic Chemistry, 5th ed. Allyn & Bacon Inc. p.150)

It also states:

‘We eat optically active bread & meat, live in houses, wear clothes, and read books made of optically active cellulose. The proteins that make up our muscles, the glycogen in our liver and blood, the enzymes and hormones … are all optically active. Naturally occurring substances are optically active because the enzymes which bring about their formation … are optically active. As to the origin of the optically active enzymes, we can only speculate’

Nonetheless, they (the naturalists) are “sure” of the casual origin of everything… They just can’t explain HOW could it happen, nor can they show the farthest, slightest evidence of the nothingness creating things that violate its laws, such as homochirality! English biologist John Maddox called it “an intellectual thunderbolt that natural proteins should contain only the left-handed forms of the amino acids.”. But it was not for the lack of efforts and guesswork. The famous Oparin once went on to say:

“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 which 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.”” (A. I. Oparin, Life, Its Nature, Origin and Development (New York: Academic Press, 1961), pp. 59, 60)

Ever since, many theories were proposed, in an effort to solve this unbelievable puzzle, but they have all failed, as we’re going to see some now.

How can we separate the left from the right?

It’s not that simple! First of all, you need of intelligence behind the process… To resolve a racemate, another homochiral substance must be introduced. The procedure is explained in any organic chemistry textbook. The idea is that right-handed and left-handed substances have identical properties, except when interacting with other chiral phenomena. The analogy is that our left and right hands grip an achiral (non-chiral) object like a baseball bat equally, but they fit differently into a chiral object like a left-handed glove. Thus to resolve a racemate, an organic chemist will usually use a ready-made homochiral substance from a living organism.

However, this does not solve the mystery of where the optical activity in living organisms came from in the first place. An world conference on ‘The Origin of Homochirality and Life’ made it clear that the origin of this handedness is a complete mystery to evolutionists (Cohen, J., 1995. Science, 267:1265–1266). The probability of forming one homochiral polymer of N monomers by chance = 2–N. For a small protein of 100 amino acids, this probability = 2–100 = 10–30. Note, this is the probability of any homochiral polypeptide. The probability of forming a functional homochiral polymer is much lower, since a precise amino acid sequence is required in many places.

A further problem is that homochiral biological substances racemize in time. This is the basis of the amino acid racemization dating method. Its main proponent is Jeffrey Bada of the Scripps Institution of Oceanography in La Jolla, California(Bada, J.L., Luyendyk, B.P. and Maynard, J.B., 1970. Science, 170:730–732). As a dating method, it is not very reliable, since the racemization rate is strongly dependent on temperature and pH, and depends on the particular amino acid (Gish, D.T., 1975.  Impact series #23, ICR). Racemization is also a big problem during peptide synthesis and hydrolysis. It shows that the tendency of undirected chemistry is towards death, not life.

Beta decay and the weak force

β-decay is one form of radioactive decay, and it is governed by one of the four fundamental forces of nature, the weak force. This force has a slight handedness, called parity violation, so some theorists thought β-decay could account for the chirality in living organisms. However, the weak force is aptly named—the effect is minuscule—a long way from producing the required 100 % homochirality. One specialist in the chirality problem, organic chemist William Bonner, professor emeritus at Stanford University, said, ‘none of this work has yielded convincing conclusions’. Another researcher concluded:

‘the exceptional prebiotic conditions required do not favour asymmetric β-radiolysis as the selector of the exclusive signature of optical activity in living nature.’

Another aspect of parity violation is that the L-amino acids and D-sugars have a theoretically slightly lower energy than their enantiomers so are slightly more stable. But the energy difference is immeasurable—only about 10–17 kT, meaning that there would be only one excess L-enantiomer for every 6×1017 molecules of a racemic mixture of amino acids.

Homochiral template

Some have proposed that a homochiral polymer arose by chance and acted as a template. However, this ran into severe problems. A template of 100 % right-handed poly-C (RNA containing only cytosine monomers) was made (by intelligent chemists!). This could direct the oligomerisation (formation of small chains) of (activated) G (guanine) nucleotides. Indeed, pure right-handed G was oligomerised much more efficiently than pure left-handed G. But racemic G did not oligomerise, because:

‘monomers of opposite handedness to the template are incorporated as chain terminators … This inhibition raises an important problem for many theories of the origin of life.’ (Joyce, G.F., Visser, G.M., van Boeckel, C.A.A., van Boom, J.H., Orgel, L.E. and van Westrenen, J., 1984. Nature, 310:602–4)

Do you like probabilities? Let’s see what Dr. Harold J. Morowitz of Yale University has found on his extensive research for discovering the theoretical limits for the simplest free-living thing which could duplicate itself.

“He took into consideration the minimum operating equipment needed and the space it would require. Also, attention was given to electrical properties and to the hazards of thermal motion. From these important studies, the conclusion is that the smallest such theoretical entity would require 239 or more individual protein molecules.
This is not very much simpler than the smallest actually known autonomous living organism, which is the minuscule, bacteria-like Mycoplasma hominis H39. It has around 600 different kinds of proteins. From present scientific knowledge, there is no reason to believe that anything smaller ever existed. We will, however, use the lesser total of 239 protein molecules from Morowitz’ theoretical minimal cell, which comprise 124 different kinds. 
It was noted earlier that there obviously can be no natural selection if there is no way to duplicate all of the necessary parts. In order to account for the left-handed phenomenon, chance alone, unaided by natural selection, would have to arrange at least one complete set of 239 proteins with all-left-handed amino acids of the universal 20 kinds. There is reason to believe that all 20 of these were in use from the time of life’s origin.
Using figures that were furnished by Morowitz, it can be calculated that the average protein molecule in the theoretical minimal living thing would contain around 445 amino acid units of the usual 20 kinds. One of the 20 types of amino acids, glycine, cannot be left- or right-handed, because its “side chain” is not really a chain, but merely a hydrogen atom like the one opposite it. It can be presumed that this minimal theoretical cell would in many ways resemble bacteria in its make-up. In some bacteria, glycine accounts for just over 8 percent of the total amino acid molecules, so we will estimate that in the average protein of the minimal cell, there will be 35 glycine units in the chain. That will leave 410 of the total 445 which could be either left- or right-handed.

If amino acids had been formed naturally in the “primitive” atmosphere, they would have occurred in statistically equal amounts of the left- and right-handed isomers. This became clear from experiments described in the preceding chapter. That means, then, that if a protein chain is to form by random linkups, all 410 of the nonglycine sites could be occupied with equal ease by either L- or D-type amino acids.
The first one has a 1 out of 2 chance of being left-handed. The same is true for each of the other 409. Since we are now figuring this at equal probability for either hand, the probability at anyone site is not affected by the amino acid before that one in the chain.
To calculate the probability in such a case, the formula to use is the multiplication rule, the heart of probability theory. Mathematician Darrell Huff said it thus: “To find the probability of getting all of several different things, multiply together the chances of getting each one.”
To get the probability of all 410 of the isomeric or handed amino acids of just one protein chain, we must multiply the 1/2 probability which is the case for each position in the chain. It is like flipping a coin 410 times, hoping to get all heads. For each step, there is 1 chance in 2, so we must multiply the 2 by itself (2 x 2 x 2 x . . . x 2). using the figure 410 times. That is 1 chance in 2410. (The exponent means: Multiply together 410 two’s.)
It will be easier to work with this figure if we translate it
to powers of 10 instead of powers of 2. As you know, multiplying 10 by itself is just adding another zero. The equivalent of 2410 is roughly 10123.

The probability that an average-size protein molecule of the smallest theoretically possible living thing would happen to contain only left-handed amino acids is, therefore, 1 in 10123, on the average.
That is a rather discouraging chance. To get the feel of that number, let’s look at it with all the 123 zeros: There is, on the average, 1 chance in –
1,000,000,000,000,000,000,000,000,000,000,000,000,000,
000,000,000,000,000,000,000,000,000,000,000,000,000,000,
000,000,000,000,000,000,000,000,000,000,000,000,000,000
that all of the amino acids of a particular protein molecule would be left-handed!” (creationsafaris)

Well, it’s a bit annoying when atheists, materialistic people claim to live completely exempt of faith, after seeing these frightening numbers against them!

“Life on Earth is made of “left-handed amino acids (L-amino acids)”. The question of why organisms on Earth consist of L-amino acids instead of D-amino acids or consist of D-sugar instead of L-sugar is still an unresolved riddle. In other words, a major mystery of life on Earth is that organisms are exclusively made up of left-handed amino acids. Therefore, the effort to solve this problem is one of the biggest in research into the origins of life, a subject that remains enveloped in mystery. “ (PhysOrg)

Sources: 

CMI;

Crev.info

God bless you all!

Building blocks very instable

From: http://creation.com/origin-of-life-instability-of-building-blocks

 

by 

Evolutionary propaganda often understates the difficulty of a naturalistic origin of life. Production of traces of ‘building blocks’ is commonly equated with proving that they could have built up the required complicated molecules under natural conditions. The instability of ‘building blocks’ in non-biotic environments is usually glossed over.

The RNA/DNA base cytosine is not produced in spark discharge experiments. The proposed prebiotic productions are chemically unrealistic because the alleged precursors are unlikely to be concentrated enough, and they would undergo side reactions with other organic compounds, or hydrolyse. Cytosine itself is too unstable to accumulate over alleged geological ‘deep time’, as its half life for deamination is 340 years at 25°C.


Populist RNA-world propaganda

A pro-evolution booklet called Science and Creationism, recently released on the Internet by the National Academy of Sciences (NAS),1 summarized the origin of life section as follows:

‘For those who are studying the origin of life, the question is no longer whether life could have originated by chemical processes involving nonbiological components. The question instead has become which of many pathways might have been followed to produce the first cells.’ 2

No one disputes the existence of living organisms on earth, and that cells indeed are capable of using simple building blocks to generate the required complex biochemicals at the necessary time, location and concentration. The question is whether the massive co-ordination of the metabolic processes which perform such feats could have arisen without intelligent guidance and driven by only statistical and thermodynamic constraints.

The NAS book glosses over the enormous chemical and informational hurdles which must be jumped to go from non-living matter to even the simplest living cells (see also Q&A: Origin of Life).3,4,5 It’s not too surprising, considering the heavy atheistic bias of the NAS, which was documented in the journal Nature,6 and which was probably partly responsible for their demonstrable scientific unreliability in the area of origins.7 It is even less excusable to ignore the difficulties documented in their own journal—Proceedings of the National Academy of Sciences (PNAS), USA, as will be shown here.

Production of ‘building blocks of life’

Science and Creationism argued:

‘Experiments conducted under conditions intended to resemble those present on primitive Earth have resulted in the production of some of the chemical components of proteins, DNA, and RNA. Some of these molecules also have been detected in meteorites from outer space and in interstellar space by astronomers using radiotelescopes. Scientists have concluded that the “building blocks of life” could have been available early in Earth’s history.’2

Even if we granted that the ‘building blocks’ were available, it does not follow that they could actually build anything. For example, under plausible prebiotic conditions, the tendency is for biological macromolecules to break apart into the ‘building blocks’, not the other way round.8 Also, the ‘building blocks’ are likely to react in the wrong ways with other ‘building blocks’, for example, sugars and other carbonyl (>C=O) compounds react destructively with amino acids and other amino (–NH2) compounds, to form imines (>C=N), a common cause of browning in foods.9

Furthermore, some of the building blocks are very unstable. A good example is ribose, which is obviously essential for RNA, and hence for the RNA-world hypothesis of the origin of life.10 A team including the famous evolutionary origin-of-life pioneer Stanley Miller, in PNAS, found that the half life (t½) of ribose is only 44 years at pH 7.0 (neutral) and 0°C. It’s even worse at high temperatures—73 minutes at pH 7.0 and 100°C.11 This is a major hurdle for hydrothermal theories of the origin of life. Miller, in another PNAS paper, has also pointed out that the RNA bases are destroyed very quickly in water at 100°C—adenine and guanine have half lives of about a year, uracil about 12 years, and cytosine only 19 days.12

Most researchers avoid such hurdles with the following methodology: find a trace of compound X in a spark discharge experiment, claim ‘see, X can be produced under realistic primitive-earth conditions’. Then they obtain pure, homochiral, concentrated X from an industrial synthetic chemicals company, react it to form traces of the more complex compound Y. Typically, the process is repeated to form traces of Z from purified Y, and so on.13 In short, the evolutionists’ simulations have an unacceptable level of intelligent interference.14

Much of the populist evolutionary propaganda resembles the following hypothetical theory for the origin of a car:

‘Design is an unscientific explanation, so we must find a naturalistic explanation instead. Now, experiments have shown that one of the important building blocks of the car—iron—can be produced by heating naturally occurring minerals like hematite to temperatures which are found in some locations on earth. What’s more, iron can be shown to form thin sheets under pressures which are known to occur in certain geological formations ….’

If this seems far-fetched, then note that even the simplest self-reproducing cell, which has 482 genes,15 has a vastly higher information content than a car, yet self-reproduction is a pre-requisite for neo-Darwinian evolution.

Essential building block missing—cytosine

The evolutionary biochemist, Robert Shapiro, published a detailed study of the ‘prebiotic’ synthesis of cytosine in the Proceedings of the NAS.16 Previous studies of his had noted that neither adenine17 nor ribose18 were plausible prebiotic components of any self-replicating molecule, but the problems with cytosine are even worse. Together, these studies raise serious doubts about whether a prebiotic replicator with any Watson-Crick base pairing could have arisen abiotically.

Shapiro noted that not the slightest trace of cytosine has been produced in gas discharge experiments, and nor has it been found in meteorites. Thus, he notes, either it is extremely hard to synthesise, or it breaks down before detection. So ‘prebiotic’ productions of cytosine have always been indirect, and involve the methodology alluded to above. That is, cyanoacetylene (HC≡CC≡N) and cyanoacetaldehyde (H3CCOC≡N) have been found in some spark discharge experiments. Organic chemists have obtained pure and fairly strong solutions of each, and reacted each of them with solutions of other compounds which are allegedly likely to be found on a ‘primitive’ earth. Some cytosine is produced. This then apparently justifies experiments trying to link up pure and dry cytosine and ribose to form the nucleoside cytidine. However, these experiments have been unsuccessful (although analogous experiments with purines have produced 2% yields of nucleosides),19 despite a high level of investigator interference.

Unavailability of cytosine precursors

Shapiro also critiqued some of the ‘prebiotic’ cytosine productions. He pointed out that both cyanoacetylene and cyanoacetaldehyde are produced in spark discharge experiments with an unlikely methane/nitrogen (CH4/N2) mixture. The classical Miller experiment used ammonia (NH3), but NH3, H2O and hydrogen sulfide (H2S) greatly hindered cyanoacetylene and cyanoacetaldehyde formation. However, most evolutionists now believe that the primitive atmosphere was ‘probably dominated by CO2 and N2.’20

Furthermore, cyanoacetylene and cyanoacetaldehyde would undergo side reactions with other nucleophiles rather than produce cytosine. For example, cyanoacetylene and cyanoacetaldehyde both react with the amino group, which would destroy any prebiotic amino acids. And there is one destructive molecule which is unavoidably present: water. Cyanoacetylene readily hydrolyzes to form cyanoacetaldehyde (t½ = 11 days at pH 9, 30°C),20 although one should not count on this as a reliable source of cyanoacetaldehyde because cyanoacetylene would more likely be destroyed by other reactions.20 And cyanoacetaldehyde, while more stable than cyanoacetylene, is still quite quickly hydrolyzed (t½ = 31 years at pH 9, 30°C).21

The implausible production scenarios and likely rapid destruction means it is unrealistic to assume that the concentration of cyanoacetylene and cyanoacetaldehyde could remotely approach that needed to produce cytosine.

Instability of cytosine

As pointed out above, cytosine is deaminated/hydrolyzed (to uracil) far too rapidly for any ‘hot’ origin-of-life scenario. But it is still very unstable at moderate temperatures—t½ = 340 years at 25°C. This shows that a cold earth origin-of-life scenario would merely alleviate, but not overcome, the decomposition problem. And a low temperature also retards synthetic reactions as well as destructive ones.

On single-stranded DNA in solution, t½ of an individual cytosine residue = 200 years at 37°C, while the double helix structure provides good protection—t½ = 30,000 years.22 Such C→U mutations would be a great genetic hazard, but cells have an ingenious repair system involving a number of enzymes. It first detects the mutant U (now mismatched with G) and removes it from the DNA strand, opens the strand, inserts the correct C, and closes the strand.22 It seems that such a repair system would be necessary from the beginning, because a hypothetical primitive cell lacking this would mutate so badly that error catastrophe would result. And the far greater instability of cytosine on single-stranded nucleic acid is yet another problem that proponents of the RNA-world must account for.

Also, cytosine is readily decomposed under solar UV radiation, which requires that prebiotic synthesis should be carried out in the dark.21

An efficient prebiotic synthesis of cytosine?

This was claimed by Robertson and Miller.23 They rightly disagreed with a previous suggested synthesis of cytosine from cyanoacetylene and cyanate (OCN) because cyanate is rapidly hydrolyzed to CO2 and NH3. Instead, they heated 10-3 M cyanoacetaldehyde with various concentrations of urea ((NH2)2CO) in a sealed ampoule at 100 oC for five hours with 30-50% yields of cytosine. Urea is produced in spark discharge experiments with N2, CO and H2O.

However, Shapiro criticised this experiment on the grounds of the unavailability of cyanoacetaldehyde and instability of cytosine, as above. Robertson and Miller avoided the latter problem by stopping the reaction after five hours. But in a real prebiotic world, such a reaction would most likely continue with hydrolysis of cytosine.

Shapiro also shows that urea is too unstable to reach the concentrations required (>0.1 M). Urea exists in equilibrium with small amounts of its isomer, ammonium cyanate, and since cyanate is hydrolysed readily, more urea must convert to maintain the equilibrium ratio (K = 1.04 x 10-4 at 60°C).21 Robertson and Miller’s sealed tube thus provided a further example of unacceptable investigator interference, because this prevented escape of NH3, thus unrealistically retarding cyanate and urea decomposition. In an open system, ‘half of the urea was destroyed after 5 hr at 90 oC and pH 7’,21 and t½ is estimated at 25 years at 25°C.21

The usual cross-reaction problem would intervene in the real world. For example, urea can react with glycine to form N-carbamoyl glycine,21 which would remove both urea and amino acids from a primordial soup.

Also, the primordial soup would be far too dilute, so Robertson and Miller propose that seawater was concentrated by evaporation in lagoons. But this would require isolation of the lagoon from fresh seawater which would dilute the lagoon, evaporation to about 10–5 of its original volume, then cytosine synthesis. However, such conditions are geologically ‘rare or non-existent’ today.24 Concentrating mechanisms would also concentrate destructive chemicals.

The conditions required for cytosine production are incompatible with those of purine production. Therefore this scenario must also include a well-timed rupture of the lagoon, releasing the contents into the sea, so both pyrimidines and purines can be incorporated into a replicator.

Shapiro’s materialistic faith

Shapiro concluded:

‘the evidence that is available at the present time does not support the idea that RNA, or an alternative replicator that uses the current set of RNA bases, was present at the start of life.’ 25

But unwilling to abandon evolution, he suggests two alternative theories:

1. Cairns-Smith’s clay mineral idea,13 which seems to be driven more by dissatisfaction with other theories than evidence for his own.

‘Cairns-Smith cheerfully admits the failings of his pet hypothesis: no-one has been able to coax clay into something resembling evolution in the laboratory; nor has anyone found anything resembling a clay-based organism in nature.’26

[Update: recent research shows more difficulties with this idea: Darwin’s warm pond idea is tested, 13 February 2006:

‘Professor Deamer said that amino acids and DNA, the “building blocks” for life, and phosphate, another essential ingredient, clung to the surfaces of clay particles in the volcanic pools.

‘“The reason this is significant is that it has been proposed that clay promotes interesting chemical reactions relating to the origin of life,” he explained.

‘“However,” he added, “in our experiments, the organic compounds became so strongly held to the clay particles that they could not undergo any further chemical reactions.”’]

2. Life began as a cyclic chemical reaction, e.g. Günter Wächtershäuser’s theory that life began on the surface of pyrite, which Stanley Miller calls ‘paper chemistry’.27

‘Wächtershäuser himself admits that his theory is for the most part “pure speculation”.’28,29

Shapiro’s dogmatism is illustrated in his interesting popular-level book Origins: A Skeptic’s Guide to the Creation of Life in the Universe, where he effectively critiques many origin-of-life scenarios. But he says, in a striking admission that no amount of evidence would upset his faith:

‘some future day may yet arrive when all reasonable chemical experiments run to discover a probable origin of life have failed unequivocally. Further, new geological evidence may yet indicate a sudden appearance of life on the earth. Finally, we may have explored the universe and found no trace of life, or processes leading to life, elsewhere. Some scientists might choose to turn to religion for an answer. Others, however, myself included, would attempt to sort out the surviving less probable scientific explanations in the hope of selecting one that was still more likely than the remainder.’30

Conclusion

  • No plausible prebiotic synthesis of cytosine yet exists.
  • Vital ‘building blocks’ including cytosine and ribose are too unstable to have existed on a hypothetical prebiotic earth for long.
  • Even if cytosine and ribose could have existed, there is no known prebiotic way to combine them to form the nucleoside cytidine, even if we granted unacceptably high levels of investigator interference.
  • Building blocks would be too dilute to actually build anything, and would be subject to cross-reactions.
  • Even if the building blocks could have formed polymers, the polymers would readily hydrolyse.
  • There is no tendency to form the high-information polymers required for life as opposed to random ones.

Related Articles

Further Reading

References

  1. Science and Creationism: A View from the National Academy of Sciences, Second Edition, <http://books.nap.edu/html/creationism/index.html&gt;, 28 July 1999. Return to text.
  2. <http://books.nap.edu/html/creationism/origin.html&gt;, 28 July 1999. Return to text.
  3. Aw, S.E., The origin of life: A critique of current scientific models , Journal of Creation 10(3):300–314, 1996. Return to text.
  4. Thaxton, C.B., Bradley, W.L. and Olsen, R.L., The Mystery of Life’s Origin, Philosophical Library Inc., New York, 1984. Return to text.
  5. Bird, W.R., The Origin of Species: Revisited, Thomas Nelson, Inc., Nashville, Tennessee, Vol. I Part III, 1991. Return to text.
  6. Larson, E.J. and Witham, L., Leading scientists still reject God, Nature 394(6691):313, 1998. The sole criterion for being classified as a ‘leading’ or ‘greater’ scientist was membership of the NAS. [See also National Academy of Science is godless to the core — survey — Ed.] Return to text.
  7. For example, the NAS teacher’s guidebook Teaching about Evolution and the Nature of Science, National Academy Press, Washington DC, 1998. This has been shown to be severely flawed by Sarfati, J.D.Refuting Evolution, Master Books, Green Forest, AR, USA, 1999. Return to text.
  8. Sarfati, J.D.Origin of life: the polymerization problemJournal of Creation 12(3):281–284, 1998. Return to text.
  9. Thaxton et al., Ref. 4, p. 51. Return to text.
  10. See Mills, G.C. and Kenyon, D.H., The RNA world: A critiqueOrigins and Design 17(1):9–16, 1996. Return to text.
  11. Larralde, R., Robertson, M.P. and Miller, S.L., Rates of decomposition of ribose and other sugars: Implications for chemical evolution, Proc. Natl. Acad. Sci. USA 92:8158–8160, 1995. Return to text.
  12. Levy, M and Miller, S.L., The stability of the RNA bases: Implications for the origin of life, Proc. Natl. Acad. Sci. USA 95(14):7933–38, 1998. Return to text.
  13. The evolutionist A.G. Cairns-Smith has raised the same objections against the typical ‘origin of life’ simulation experiments in his book Genetic Takeover and the Mineral Origins of Life, Cambridge University Press, New York, 1982—see extractReturn to text.
  14. Thaxton et al., Ref. 4, ch. 6. Return to text.
  15. Fraser, C.M., et al., The minimal gene complement of Mycoplasma genitalium, Science 270(5235):397–403, 1995; Perspective by Goffeau, A., Life with 482 genes, same issue, pp. 445–446. Return to text.
  16. Shapiro, R., Prebiotic cytosine synthesis: A critical analysis and implications for the origin of life, Proc. Natl. Acad. Sci. USA 96(8):4396–4401, 1999. Return to text.
  17. Shapiro, R., The prebiotic role of adenine: A critical analysis, Origins of Life and Evolution of the Biosphere 25:83–98, 1995. Return to text.
  18. Shapiro, R., Prebiotic ribose synthesis: A critical analysis, Origins of Life and Evolution of the Biosphere 18:71–85, 1988. Return to text.
  19. Orgel, L.E. and Lohrmann, R., Prebiotic chemistry and nucleic acid replication, Accounts of Chemical Research 7:368–377, 1974; cited in Cairns-Smith, Ref. 13, pp. 56–57. Return to text.
  20. Shapiro, Ref. 16, p. 4397. Return to text.
  21. Shapiro, Ref. 16, p. 4398. Return to text.
  22. Lindahl, T., Instability and decay of the primary structure of DNA, Nature 362(6422):709–715, 1993. Return to text.
  23. Robertson, M.P. and Miller, S.L., An efficient prebiotic synthesis of cytosine and uracil, Nature 375(6534):772–774; correction 377(6546):257. Return to text.
  24. Shapiro, Ref. 16, p. 4399. Return to text.
  25. Shapiro, Ref. 16, p. 4400. Return to text.
  26. Horgan, J., In the beginning, Scientific American 264(2):100–109, 1991; quote on p. 108. Return to text.
  27. Horgan, Ref. 26; Miller cited on p. 102. Return to text.
  28. Horgan, Ref. 26; Wächtershäuser cited on p. 106. Return to text.
  29. Sarfati, J.D.Ref. 8, extensively critiques one of Wächtershäuser’s latest experiments that supposedly supports his theory. Return to text.
  30. Shapiro, R., Origins: A Skeptic’s Guide to the Creation of Life in the Universe, Penguin, London, p. 130, 1986,1988. Shapiro then wishfully continues: ‘We are far from that state now.’Return to text.

Is Water the Solution to how Life began?

Is Water the Solution to how Life began?

From: EarthAge


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

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 whylife 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”  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:

It 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, that are all 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.” 8

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.  

For more on why the raw materials on earth cannot produce life, see Life, DNA, and Proteins.9  See also the links below.


*   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 a condensation reaction. (See t the fourasterisks below)  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 tohydrolyze 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.

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., MT, 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

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