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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>

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!

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

The Urey-Miller research actually goes against abiogenesis

Contemporary research has failed to provide a viable explanation as to how abiogenesis could have occurred on Earth. The abiogenesis problem is now so serious that most evolutionists today tend to shun the entire field because they are ‘uneasy about stating in public that the origin of life is a mystery, even though behind closed doors they freely admit that they are baffled’ because ‘it opens the door to religious fundamentalists and their god-of-the-gaps pseudo-explanations’ and they worry that a ‘frank admission of ignorance will undermine funding’.

Abiogenesis was once commonly called ‘chemical evolution’, but evolutionists today try to distance evolutionary theory from the origin of life. This is one reason that most evolutionary propagandists now call it ‘abiogenesis’. Chemical evolution is actually part of the ‘General Theory of Evolution’, defined by the evolutionist Kerkut as ‘the theory that all the living forms in the world have arisen from a single source which itself came from an inorganic form’.

Darwin recognized how critical the abiogenesis problem was for his theory. He even conceded that all existing terrestrial life must have descended from some primitive life-form that was originally called into life ‘by the Creator’. But to admit, as Darwin did, the possibility of one or a few creations is to open the door to the possibility of many others! Darwin evidently regretted this concession later and also speculated that life could have originated in some ‘warm little pond’ on the ancient earth.

The ‘warm soup’ theory

Although seriously challenged in recent years, the warm soup hypothesis is still the most widely held abiogenesis theory among Darwinists. Developed most extensively by Russian atheist Alexandr Ivanovich Oparin (1894–1980) in his book, The Origin of Life, a worldwide best seller first published in 1924 (the latest edition was published in 1965). Oparin ‘postulated that life may have evolved solely through random processes’ in what he termed a biochemical ‘soup’ that he believed once existed in the oceans. The theory held that life evolved when organic molecules that originally rained into the primitive oceans from the atmosphere were energized by forces such as lightning, ultraviolet light, meteorites, deep-sea hydrothermal vents, hot springs, volcanoes, earthquakes, or electric discharges from the sun. If only the correct mix of chemicals and energy were present, life would be produced spontaneously. Almost a half century of research and millions of dollars have been expended to prove this idea—so far with few positive results and much negative evidence.

What sequence?

Oparin concluded that cells evolved first, then enzymes and, last, genes. Today, we recognize that genes require enzymes in order to function, but genes are necessary to produce enzymes. Neither genes nor cells can function without many complex structures such as ribosomes, polymerase, helicase, gyrase, single-strand–binding protein and scores of other proteins. Dyson concluded that Oparin’s theory was ‘generally accepted by biologists for half a century’ but that it ‘was popular not because there was any evidence to support it but rather because it seemed to be the only alternative to biblical creationism’.

The Miller–Urey research

Haldane, Bernal, Calvin and Urey all published research in an attempt to support this model—each with little, if any, success. Then, in 1953 came what some then felt was a critical breakthrough by Harold Urey (1893–1981) of the University of Chicago and his 23-year-old graduate student, Stanley Miller (1930–). Urey came to believe that the conclusion reached by ‘many’ origin-of-life researchers that the early atmosphere was oxidizing must have been wrong; he argued instead that it was the opposite, namely a reducing atmosphere with large amounts of methane.

Their ‘breakthrough’ resulted in front-page stories across the world that usually made the sensational claim that they had ‘accomplished the first step toward creating life in a test tube’. Carl Sagan concluded, ‘The Miller–Urey experiment is now recognized as the single most significant step in convincing many scientists that life is likely to be abundant in the cosmos.’ The experiment even marked the beginning of a new scientific field called ‘prebiotic’ chemistry. It is now the most commonly cited evidence (and often the only evidence cited) for abiogenesis in science textbooks.

The Miller–Urey experiments involved filling a sealed glass apparatus with the gases that Oparin had speculated were necessary to form life—namely methane, ammonia and hydrogen (to mimic the conditions that they thought were in the early atmosphere) and water vapour (to simulate the ocean). Next, while a heating coil kept the water boiling, they struck the gases in the flask with a high-voltage (60,000 volts) tungsten spark-discharge device to simulate lightning. Below this was a water-cooled condenser that cooled and condensed the mixture, allowing it to fall into a water trap below.

Within a few days, the water and gas mix produced a pink stain on the sides of the flask trap. As the experiment progressed and the chemical products accumulated, the stain turned deep red, then turbid. After a week, the researchers analyzed the substances in the U-shaped water trap used to collect the reaction products. The primary substances in the gaseous phase were carbon monoxide (CO) and nitrogen (N2). The dominant solid material was an insoluble toxic carcinogenic mixture called ‘tar’ or ‘resin’, a common product in organic reactions, including burning tobacco. No amino acids were detected during this first attempt, so Miller modified the experiment and tried again.

In time, trace amounts of several of the simplest biologically useful amino acids were formed—mostly glycine and alanine. The yield of glycine was a mere 1.05%, of alanine only 0.75% and the next most common amino acid produced amounted to only 0.026% of the total—so small as to be largely insignificant. In Miller’s words, ‘The total yield was small for the energy expended.’ The side group for glycine is a lone hydrogen and for alanine, a simple methyl (–CH3) group.

Oxygen: enemy of chemical evolution

The researchers used an oxygen-free environment mainly because the earth’s putative primitive atmosphere was then ‘widely believed not to have contained in its early stage significant amounts of oxygen’. They believed this because ‘laboratory experiments show that chemical evolution, as accounted for by present models, would be largely inhibited by oxygen’. Here is one of many examples of where their a prioribelief in the ‘fact’ of chemical evolution is used as ‘proof’ of one of the premises, an anoxic atmosphere. Of course, estimates of the level of O2 in the earth’s early atmosphere rely heavily on speculation. The fact is, ‘We still don’t know how an oxygen-rich atmosphere arose.’

It was believed that the results were significant because some of the organic compounds produced were the building blocks of much more complex life units called proteins—the basic structure of all life. Although widely heralded by the press as ‘proving’ that life could have originated on the early earth under natural conditions (i.e. without intelligence), we now realize the experiment actually provided compelling evidence for exactly the opposite conclusion. For example, without all 20 amino acids as a set, most known protein types cannot be produced, and this critical step in abiogenesis could never have occurred.

In addition, equal quantities of both right- and left-handed organic molecules (called a racemic mixture) were consistently produced by the Miller–Urey procedure. In life, nearly all amino acids that can be used in proteins must be left-handed, and almost all carbohydrates and polymers must be right-handed. The opposite types are not only useless but can also be toxic (even lethal) to life.

Was there a methane–ammonia atmosphere?

According to many researchers today, an even more serious problem is the fact that the atmosphere of the early earth was very different from what Miller assumed. ‘Research has since drawn Miller’s hypothetical atmosphere into question, causing many scientists to doubt the relevance of his findings.’ The problem was stated as follows:

‘… the accepted picture of the earth’s early atmosphere has changed: It was probably O2-rich with some nitrogen, a less reactive mixture than Miller’s, or it might have been composed largely of carbon dioxide, which would greatly deter the development of organic compounds.’

A major source of gases was believed to be volcanoes, and since modern-day volcanoes emit CO, CO2, N2 and water vapour, it was considered likely that these gases were very abundant in the early atmosphere. In contrast, it is now believed that H2, CH4 and NH3 probably were not major components of the early atmosphere.

Although the composition of the atmosphere of the early earth is now believed to have consisted of large amounts of carbon dioxide, this conclusion still involves much speculation. Most researchers also now believe that some O2 was present on the early earth because it contained much water vapour, and photodissociation of water in the upper layers of the atmosphere produces oxygen. Another reason is that large amounts of oxidized materials exist in the Precambrian geological strata.

Yet another reason to conclude free oxygen existed on the early earth is that it is widely believed that photosynthetic organisms existed very soon after the earth had formed, something that is difficult for chemical evolutionary theories to explain. A 2004 paper argues from uranium geochemistry that there were oxidizing conditions, thus photosynthesis, at 3.7 Ga.37 But according to uniformitarian dating, the earth was being bombarded by meteorites up to 3.8 Ga. So even granting evolutionary presuppositions, this latest research shows that life existed almost as soon as the earth was able to support it, not ‘billions and billions of years’ later. Even if the oxygen were produced by photodissociation of water vapour rather than photosynthesis, this would still be devastating for Miller-type proposals.

Early hopes not realized

Modern replications of the Miller–Urey experiment using a wide variety of recipes, including low levels of O2, yield even lower amounts of organic compound than the original experiment. To solve this problem, some researchers have speculated that small, isolated pools of water achieved the required level of concentration. The same problem remains: No feasible method exists to account for this source. Some even speculate that ‘submerged volcanoes and deep-sea vents—gaps in the earth’s crust where hot water and minerals gush into deep oceans—may have provided the initial chemical resources’.

To duplicate what might have happened in a primordial soup billions of years ago, scientists would need to mix the chemicals currently believed to be commonly found on the early earth, expose them to likely energy sources (usually speculated to be heat or radiation), and see what happens. No-one has performed this experiment, because we now know that it is impossible to obtain relevant biochemical compounds by this means. The Miller–Urey experiment held great hopes for the materialists, which have now given way to pessimism:

‘Soon after the Miller–Urey experiment, many scientists entertained the belief that the main obstacles in the problem of the origin of life would be overcome within the foreseeable future. But as the search in this young scientific field went on and diversified, it became more and more evident that the problem of the origin of life is far from trivial. Various fundamental problems facing workers in this search gradually emerged, and new questions came into focus … . Despite intensive research, most of these problems have remained unsolved.

‘Indeed, during the long history of the search into the origin of life, controversy is probably the most characteristic attribute of this interdisciplinary field. There is hardly a model or scenario or fashion in this discipline that is not controversial.’

Some of these major problems will now be reviewed.

Functional proteins can exist only in very narrow conditions

To produce even non-functional amino acids and proteins, researchers must highly control the experiment in various ways because the very conditions hypothesized to create amino acids also rapidly destroy proteins. Examples include thermal denaturing of proteins by breaking apart their hydrogen bonds and disrupting the hydrophobic attraction between non-polar side groups. Very few proteins remain biologically active above 50ºC, or below about 30ºC, and most require very narrow conditions. As any molecular biologist knows from daily lab work, the pH also must be strictly regulated. Too much acid or base adversely affects the hydrogen bonding between polar R groups and also disrupts the ionic bonds formed by the salt bridges in protein.

Cross-reactions

Miller had to deal with the fact that the common cross-reactions of biochemical reaction products cause destruction or interfere with amino acid production. All compounds that interfere with bonding must be isolated or they will destroy the proteins.

This is no small problem. Many organic compounds, such as ethanol and isopropyl alcohol, function as disinfectants by forming their own hydrogen bonds with a protein and, as a result, disrupt the proteins’ hydrophobic interactions. Alcohol swabs are used to clean wounds or to prepare skin for injections because the alcohol passes through cell walls and coagulates the proteins inside bacteria and other cells. Also, heavy metal ions such as Ag+, Pb2+ and Hg2+ must be isolated from proteins because they disrupt the protein’s disulfide bonds, causing the protein to denature. As an example, a dilute (1%) AgNO3 solution is placed in the eyes of newborn babies to destroy the bacteria that cause gonorrhea. Many heavy metal ions are very toxic if ingested because they severely disrupt protein structure, especially enzymes.

Another problem is that many of the other compounds necessary for life, such as sugar, also react strongly with amino acids and affect amino acid synthesis. For example, Miller and others had to use a sugar-free environment in their experiments. Miller stopped his experiment after just a few days, but if it had been allowed to go on, would the compounds he produced be destroyed or would they produce more complex amino acids?

The Miller–Urey experiments produced many other compounds aside from amino acids, as toxic compounds such as cyanides, carbon monoxide, and others.

Undirected energy is disruptive

A critical question, ‘How much energy was necessary?’ has been much debated. However, all forms of energy can disrupt protein, including all of those forms postulated to be important in abiogenesis, such as UV and lightning.

Many speculate that ultraviolet light was the source used to create life, but UV is highly toxic to life, and is, in fact, often used to destroy life (thus UV lights are used in hospitals to kill micro-organisms). The intensity of the destructive long wavelengths exceeds that of the constructive short ones, and the quantum efficiency of destruction is much higher than that for construction as well. This means that destruction of amino acids is four to five orders of magnitude higher than construction.

In Miller’s UV experiments, he used a select wavelength to produce amino acids and screened out other wavelengths because they destroy amino acids, which are very delicate and readily break down under natural sunlight.

The Miller–Urey experiment also had strategically designed traps to remove the products from the radiation before they could be destroyed.

Miller’s research has, for the reasons discussed above, helped us to better understand why life could not have emerged naturally. In a summary of the famous Miller–Urey origin-of-life experiment, Horgan concluded that Miller’s results at first seemed to

‘… provide stunning evidence that life could arise from what the British chemist J.B.S. Haldane had called the “primordial soup.” Pundits speculated that scientists, like Mary Shelley’s Dr. Frankenstein, would shortly conjure up living organisms in their laboratories and thereby demonstrate in detail how genesis unfolded. It hasn’t worked out that way. In fact, almost 40 years after his original experiment, Miller told me that solving the riddle of the origin of life had turned out to be more difficult than he or anyone else had envisioned.’

Creating life in a test tube also turned out to be far more difficult than Miller expected. Scientists now know that the complexity of life is far greater than Miller (or anyone else) imagined in 1953, prior to the DNA revolution.

Life is far more complex than Miller believed

About the same time as Darwin, T.H. Huxley proposed a simple, two-step method of chemical recombination that he thought could explain the origin of the first living cell. Both Haeckel and Huxley thought that just as salt could be produced spontaneously by mixing powered sodium metal and heated chlorine gas, a living cell could be produced merely by mixing the few chemicals they believed were required. Haeckel taught that the physical basis of life is a substance he called ‘plasm’ of different types such as ‘colourless’ and ‘also red, orange, and other kinds of protoplasm’ that were comparable in complexity and texture to a pot of glue or cold jelly.

Haeckel also believed that the first single cell owed its ‘existence to spontaneous creation’ from inorganic compounds, primarily ‘carbon, hydrogen, oxygen, and nitrogen’. As late as 1928, the cell was still thought to be relatively simple, and few scientists then questioned the belief that life commonly developed from relatively simple to relatively complex forms. They also thought evolution was ‘the formation of new structures and functions by combinations and transformations of the relatively simple structures and functions of the germ cells.’

We now also realize, after a century of research, that the eukaryote protozoa, believed in Darwin’s day to be as simple as a bowl of gelatin, are actually enormously complex. Molecular biology has demonstrated that the basic design of the cell is

‘… essentially the same in all living systems on earth from bacteria to mammals. … In terms of their basic biochemical design … no living system can be thought of as being primitive or ancestral with respect to any other system, nor is there the slightest empirical hint of an evolutionary sequence among all the incredibly diverse cells on earth.’

The polymerization problem

The Miller–Urey experiment left many critical questions unanswered. Chemicals do not produce life; only complex structures such as DNA and enzymes produce life. Also, even if the source of the amino acids and the many other compounds needed could be explained, how these many diverse elements became aggregated in the same area and then properly assembled themselves must still be dealt with. This problem is a major stumbling block to all abiogenesis theories because

‘… no one has ever satisfactorily explained how the widely distributed ingredients linked up into proteins. Presumed conditions of primordial earth would have driven the amino acids toward lonely isolation. That’s one of the strongest reasons that Wächtershäuser, Morowitz, and other hydrothermal vent theorists want to move the kitchen [that cooked life] to the ocean floor. If the process starts down deep at discrete vents, they say, it can build amino acids—and link them up—right there.’

The amino acid assembly problem is complicated by the fact that amino acids are able to bond in many locations by many kinds of chemical bonds. To form polypeptide chains requires restricting the links to only peptide bonds, and only in the correct locations. All other bonds must be prevented from being formed, no easy task. In living cells, a complex control system involving enzymes exists to ensure that inappropriate bonds do not normally occur.

Information content

Another major reason the Miller–Urey experiments failed to support abiogenesis was that, although amino acids are the building blocks of life, a critical key to life is the information code stored in DNA (or, as in the case of retroviruses, RNA), depending on the sequence of nucleotides. This in turn provides the instructions for the amino acid sequences for the proteins, the machinery of life. Michael Polanyi (1891–1976), former chairman of physical chemistry at the University of Manchester (UK) who turned to philosophy, affirmed a very important point—the information was something above the chemical properties of the building blocks:

‘As the arrangement of a printed page is extraneous to the chemistry of the printed page, so is the base sequence in a DNA molecule extraneous to the chemical forces at work in the DNA molecule. It is this physical indeterminacy of the sequence that produces the improbability of any particular sequence and thereby enables it to have a meaning—a meaning that has a mathematically determinate information content.’

Another huge problem is that information is useless unless it can be read. But the decoding machinery is itself encoded on the DNA. The leading philosopher of science, Karl Popper (1902–1994), expressed the huge problem:

‘What makes the origin of life and of the genetic code a disturbing riddle is this: the genetic code is without any biological function unless it is translated; that is, unless it leads to the synthesis of the proteins whose structure is laid down by the code. But … the machinery by which the cell (at least the non-primitive cell, which is the only one we know) translates the code consists of at least fifty macromolecular components which are themselves coded in the DNA. Thus the code can not be translated except by using certain products of its translation. This constitutes a baffling circle; a really vicious circle, it seems, for any attempt to form a model or theory of the genesis of the genetic code.

‘Thus we may be faced with the possibility that the origin of life (like the origin of physics) becomes an impenetrable barrier to science, and a residue to all attempts to reduce biology to chemistry and physics.’

The chirality problem

What Sarfati calls a ‘major hurdle’ is the origin of homochirality, the fact that all amino acid biomolecules with rare exceptions (such as some used in bacterial cell walls) are all left-handed; and with rare exceptions, all sugars, including those in nucleic acids, are right-handed. Those produced in a laboratory are a half left-handed and half right-handed mixture called a racemate. Even in the laboratory, chemists use pre-existing homochirality from a biological source in order to synthesize homochiral compounds. Chiral molecules are dissymmetric—they exist as mirror images of each other, just as the right hand is a mirror image of the left hand (the word chiral comes from the Greek word for ‘hand’). The problem is left-handed sugars and right-handed amino acids can be toxic and prevent abiogenesis. Furthermore, most all enzymes are designed to work only with right-handed sugars and left-handed amino acids. All attempts to solve the chirality problem, including magnetochiral dichroism, have failed.

Conclusion

It is now recognized that the Miller–Urey line of research is simply a ‘revival of the antique notion of spontaneous generation’ because it

‘… suggests that given the primordial soup, with the right combination of amino acids and nucleic acids, and perchance a lightning bolt or two, life might in fact have begun “spontaneously”. The major difference is that according to what biologists customarily called spontaneous generation, life supposedly began this way all of the time. According to the “soup” suggestion, by contrast, it began this way only once in the immeasurably distant past.’

We must conclude, as Ridley did, that the early forms of life, and how natural selection could shape them, are ‘so obscure at the primordial stage that we can only guess why complexity might have increased’.

From: Creation Ministries

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