ElShamah - Reason & Science: Defending ID and the Christian Worldview
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ElShamah - Reason & Science: Defending ID and the Christian Worldview

Otangelo Grasso: This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, biodiversity

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1Homochirality Empty Homochirality Sat Nov 16, 2013 11:48 am



Homochirality, a unresolved issue


Tan, Change; Stadler, Rob. The Stairway To Life:
In all living systems, homochirality is produced and maintained by enzymes, which are themselves composed of homochiral amino acids that were specified through homochiral DNA and produced via homochiral messenger RNA, homochiral ribosomal RNA, and homochiral transfer RNA. No one has ever found a plausible abiotic explanation for how life could have become exclusively homochiral.

A. G. CAIRNS-SMITH Seven clues to the origin of life, page 40:
There are CONVENTIONS in the universal system, features that could easily have been otherwise. The exact choice of the amino acid alphabet, and the set of assignments of amino acid letters to nucleic acid words - the genetic code - are examples. A particularly clear case is in the universal choice of only 'left-handed' amino acids for making proteins, when, as far as one can see, 'right-handed' ones would have been just as good. Let me clarify this.
Molecules that are at all complex are usually not superposable on their mirror images. There is nothing particularly strange about this: it is true of most objects. Your right hand, for example, is a left hand in the mirror. It is only rather symmetrical objects that do not have 'right-handed' and 'left-handed' versions. When two or more objects have to be fitted together in some way their 'handedness' begins to matter. If it is a left hand it must go with a left glove. If a nut has a right-hand screw, then so must its bolt. In the same sort of way the socket on an enzyme will generally be fussy about the 'handedness' of a molecule that is to fit it. If the socket is 'left-handed' then only the 'left-handed' molecule will do. So there has to be this kind of discrimination in biochemistry, as in human engineering, when 'right-handed' and 'left-handed' objects are being dealt with. And it is perhaps not surprising that the amino acids for proteins should have a uniform 'handedness'. There could be a good reason for that, as there is good reason to stick to only one
'handedness' for nuts and bolts. But whether, in such cases, to choose left or right, that is pure convention. It could be decided by the toss of a coin. 
My comment: Conventions depend on decisions. Decisions are made by minds.
A. G. CAIRNS-SMITH: It is one of the most singular features of the unity of biochemistry that this mere convention is universal. Where did such agreement come from? You see non-biological processes do not as a rule show any bias one way or the other, and it has proved particularly difficult to see any realistic way in which any of the constituents of a 'probiotic soup' would have had predominantly 'left-handed' or right-handed' molecules. It is thus particularly difficult to see this feature as having been imposed by initial conditions.

A. G. CAIRNS-SMITH genetic takeover, page53
It is commonly believed that proteins of a sort, or nucleic acids of a sort (or both) would have been necessary for the making of those first systems that could evolve under natural selection and so take off from the launching platform provided by prevital chemical processes. We have already come to a major difficulty here: Much of the point of protein and the whole point of nucleic acid would seem to be lost unless these molecules have appropriate secondary/tertiary structures; and that is only possible with chirally defined units. As we saw, the ‘abiotic‘ way of circumventing this problem (by prevital resolution of enantiomers) seems hopelessly inadequate, and ‘biotic’ mechanisms depend on efficient machinery already in action.

Homochirality Originates from the Handedness of Helices 2020 November 20
Homochirality is a common feature of amino acids and carbohydrates, and its origin is still unknown.

On the possible origin of protein homochirality, structure, and biochemical function December 26, 2019
How L-chiral proteins emerged from demi-chiral mixtures is unknown.The lack of understanding of the origins of the breaking of demi-chirality found in the molecules of life on Earth is a long-standing problem, and models to date either focused on the RNA world hypothesis, which does not explain how RNA became chiral, or the use of chiral templates (e.g., chiral crystal surfaces). The alternative view due to Dyson conjectures that metabolism, likely from proteins, came first, followed by replication. But how did the ultimately homochiral proteins responsible for metabolism emerge from the short peptides that formed spontaneously and probably contained a mixture of D and L amino acids? The foldamer hypothesis suggests that such oligomers acted as templates to catalyze the synthesis of likely demi-chiral proteins. Other mechanisms such as molecular mutualism or the spontaneous peptide formation from aminonitriles might have been operative. By whatever means, we assume that, somehow, proteins, whose lengths range from 50 to 300 residues, were generated.

Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation 30 November 2018
The origin of homochirality in L-amino acid in proteins is one of the mysteries of the evolution of life. Experimental studies show that a non-enzymatic aminoacylation reaction of an RNA minihelix has a preference for L-amino acid over D-amino acid.

The origin of biological homochirality along with the origin of life January 8, 2020
How homochirality concerning biopolymers (DNA/RNA/proteins) could have originally occurred (i.e., arisen from a non-life chemical world, which tended to be chirality-symmetric) is a long-standing scientific puzzle.

Earthly life has the remarkable property that virtually all proteins are constructed only from left-handed amino acids, whereas the nucleic acids RNA and DNA utilize only righthanded sugars in their structures. Terrestrial organisms cannot utilize right-handed proteins (with a few exceptions) or lefthanded sugars in their biochemical processes; they would starve to death if such wrong-handed materials were the sole food source. Yet, abiotically produced amino acids such as those in meteorites and the Miller–Urey experiments are a roughly equal mixture of left-handed (l) and right-handed (d) molecules (there is one meteorite in which there is a modest excess of left-handed amino acids). Furthermore, chemical production of polymers such as proteins or nucleotides does not prefer a particular handedness when the starting molecules are a mixture of l- and d-enantiomers. 1

Chirality selection on some rocks cannot be cumulated enough through some mysterious filtration process to justify the homochirality in a living organism, not even with highly selective lab procedure.

Dr. Stanley L. Miller, University of California San Diego
The original study raised many questions. What about the even balance of L and D (left and right oriented) amino acids seen in your experiment, unlike the preponderance of L seen in nature? How have you dealt with that question?
All of these pre-biotic experiments yield a racemic mixture, that is, equal amounts of D and L forms of the compounds. Indeed, if you're results are not racemic, you immediately suspect contamination. The question is how did one form get selected. In my opinion, the selection comes close to or slightly after the origin of life. There is no way in my opinion that you are going to sort out the D and L amino acids in separate pools. My opinion or working hypothesis is that the first replicated molecule had effectively no asymmetric carbon. 2

Is an abiologic origin of chirality as is found in (2R)-2,3-dihydroxypropanal (D-glyceraldehyde), and also in amino acids, sugars, etc., possible? 3

The origin of the homochirality of amino acids is still an unsolved issue. There must have been a definite process to ensure that the sequence-based mechanism functioned in the RNA world. Future experiments will provide insights regarding the basis using which this mystery can be solved. 4

Enantiomers are molecules that are mirror-images of each other. Today, amino acids and sugars exist in only one enantiomeric form in most biological systems on earth. This homochirality remains one of the greatest unsolved mysteries to scientists. 5

However, the question of the origin of biological homochirality remains as yet unanswered. 6

left and right-handed molecules of a compound will form in equal amounts (a racemic mixture) when we synthesize them in the laboratory in the absence of some type of directing template.


Several mechanisms have been proposed for elucidating the origins of the chirality of organic compounds, such as circularly polarized light (CPL) (3) and quartz (4); however, a suitable amplification process for chirality is required to reach single-handedness of biological compounds (biological homochirality)

Mirror Image Catalysis Chiral molecules
When alanine is produced in a laboratory under normal conditions, a mixture is obtained, half of which is (S)-alanine and the other (R)-alanine. The synthesis is symmetrical in the sense that it produces equal amounts of both enantiomers.

Now suppose that we want to make a protein that involves 100 amino acids (this would be a short protein – most are at least three times as long). Amino acids exist in two chiral forms that are mirror images of each other, called L and D forms. These two forms appear in equal numbers in prebiotic simulation experiments, so that the probability of getting one or other of the forms is roughly 1/2. However, the great majority of the proteins found in nature contain only the L-form. The probability of getting 100 amino acids of L-form is, therefore, (1/2)100, which is about 1 chance in 10^30.

Nature is chiral

One may well think that both forms of chiral molecules ought to be equally common in nature, the reactions should be symmetrical. But when we study the molecules of the cells in close-up, it is evident that nature mainly uses one of the two enantiomers. That is why we have – and this applies to all living material, both vegetable and animal – amino acids, and therefore peptides, enzymes and other proteins, only of one of the mirror image forms. Carbohydrates and nucleic acids like DNA and RNA are other examples.

Thus the enzymes in our cells are chiral, as are other receptors that play an important part in cell machinery. This means that they prefer to bind to one of the enantiomers. In other words, the receptors are extremely selective; only one of the enantiomers fits the receptor's site like a key that fits a lock. (This metaphor comes from another Nobel Laureate in Chemistry, Emil Fischer, who was awarded the Prize in 1902.)

Since the two enantiomers of a chiral molecule often have totally different effects on cells, it is important to be able to produce each of the two forms pure.
Quantifying the Left - Handed Amino Acid Dilemma: The Tale of the Snail

Life only uses the left handed variety. All 20 amino acids that are used in life all exhibit this characteristic except glycine. The left handed and right handed isomers react
chemically the same, and are virtually impossible to separate. Moreover, when death occurs, the left handed isomers over time spontaneous reverse into the right handed
variety, a process called racemization. proceedings from a conference where papers were being presented trying to find a way to synthesize pure left handed amino acids, and all met with failure.
Asymmetry at the molecular level in biology
One of the greatest challenges of modern science is to understand the origin of the homochirality of life: why are most essential biological building blocks present in only one handedness, such as L-amino acids and D-sugars? Efforts towards understanding this phenomenon ultimately have to rely on the effect of a chiral, external influence that, at some point during the evolution, has driven certain systems towards specific chiralities. Several possible chiral fields have been suggested, with scenarios based on circularly polarized light in photochemistry, the electroweak interaction, vortex motion and external electric and magnetic fields. However, to date only few of these scenarios have been experimentally demonstrated.
Darwinism refuted
The question of how proteins can pick out only the left-handed ones from among all amino acids, and how not even a single right-handed amino acid gets involved in the life process, is a problem that still baffles evolutionists. Such a specific and conscious selection constitutes one of the greatest impasses facing the theory of evolution.

Enantioselection of supramolecular chirality by external fields
Naturally occurring biological molecules are made of homochiral building blocks. Proteins are composed of L-amino acids (and not D-amino acids);
nucleic acids such as DNA have D-ribose sugars (and not L-ribose sugars). It is not clear why nature selected a particular chirality. Selection could have
occurred by chance or as a consequence of basic physical chemistry.

Explanation of the homochirality of amino acids in the biosphere is one of the most important mysteries in the origin of life



life uses only left-handed amino acids in the construction of proteins


Proteins cannot assemble unless all the chiral amino acids (20 out of the 21 bioactive amino acids are chiral) are either 100 percent left-handed or 100 percent right-handed. Likewise, DNA and RNA molecules cannot assemble unless all pentose sugars are 100 percent left-handed or right-handed. All organisms on Earth manifest only left-handed chiral amino acids and right-handed pentose sugars.


One of the most difficult problems for the materialistic scenario on the origin of life is something called molecular chirality. The building blocks of DNA and proteins are molecules which can exist in both right and left-handed mirror-image forms . This "handedness" is called "chirality." These mirror-image chemicals are referred to as dextrorotary (dextro-form) and levorotary (levo-form)

In all living systems the building blocks of the DNA and RNA exist exclusively in the right-handed form, while the amino acids in virtually all proteins in living systems, with very rare exception, occur only in the left-handed form.

The dilemma for materialists is that all "spark and soup-like" experiments produce a mixture of 50% left (levo) and 50% right-handed (dextro) products. Such a mixture of dextro and levo amino acids is called a "racemic mixture." Unfortunately, such mixtures are completely useless for the spontaneous generation of life.

Complex molecules such as DNA and proteins are built by adding one building block at a time onto an ever-growing chain. In a "primordial soup" made up of equal proportions of right and left-handed building blocks, there is an equal probability at each step of adding either a right or left-handed building block. Consequently, it is a mathematical absurdity to propose that only right-handed nucleotides would be added time after time without a single left-handed one being added to a growing DNA molecule. Sooner or later an incorrect, left-handed nucleotide will be added. The same goes for proteins. Every time another amino acid is added to the growing chain of amino acids the chances are virtually certain that both right and left-handed amino acids will be added.

With unguided or undirected chemistry, a primordial ooze consisting of right and left-handed building blocks can only result in the production of DNA and proteins composed of a mixture of right and left-handed building blocks.

This dilemma has enormous implications for the materialistic scenario.30 For a living cell to function properly, it is absolutely necessary for it to contain the correct three-dimensional structure in its DNA and proteins.

This correct three-dimensional structure is in turn dependent upon proteins built from a pure mixture of left-handed amino acids and DNA built from right-handed nucleotides. Consequently, if even one nucleotide or amino acid with the incorrect "handedness" is inserted into a DNA or protein molecule, the three-dimensional structure will be annihilated and it will cease to function normally.
1. Earth Evolution of a Habitable World, second ediction page 152
2. https://web.archive.org/web/20080518054852/http://www.accessexcellence.org/WN/NM/miller.php
3. https://en.wikipedia.org/wiki/List_of_unsolved_problems_in_chemistry
4. http://labquimica.files.wordpress.com/2011/02/homoquiralidad.pdf
5. http://microbewiki.kenyon.edu/index.php/Origins_of_a_Homochiral_Microbial_World
6. http://www.cnrs.fr/Cnrspresse/n386/html/en386a11.htm

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2Homochirality Empty Re: Homochirality Sun Dec 08, 2013 5:04 am




Handedness: Left and Right

a . “Equally disappointing, we can induce copying of the original template only when we run our experiments with nucleotides having a right-handed configuration. All nucleotides synthesized biologically today are right-handed. Yet on the primitive earth, equal numbers of right- and left-handed nucleotides would have been present.” Leslie E. Orgel, “The Origin of Life on the Earth,” Scientific American, Vol. 271, October 1994, p. 82.

u “There is no explanation why cells use L [left-handed] amino acids to synthesize their proteins but D [right-handed] ribose or D-deoxyribose to synthesize their nucleotides or nucleic acids. In particular, the incorporation of even a single L-ribose or L-deoxyribose residue into a nucleic acid, if it should ever occur in the course of cellular syntheses, could seriously interfere with vital structure-function relationships. The well-known double helical DNA structure does not allow the presence of L-deoxyribose; the replication and transcription mechanisms generally require that any wrong sugar such as L-deoxyribose has to be eliminated, that is, the optical purity of the D-sugars units has to be 100%.” Dose, p. 352.

b . An important exception occurs in a component in cell membranes of eubacteria. There, the amino acids are right-handed. This has led many to conclude that they must have evolved separately from all other bacteria. Because evolving the first living cell is so improbable, having it happen twice, in effect, compounds the improbability. [See Adrian Barnett, “The Second Coming: Did Life Evolve on Earth More Than Once?” New Scientist, Vol. 157, 14 February 1998, p. 19.]

c . Recent discoveries have found that some amino acids, most notably aspartic acid, flip (at certain locations in certain proteins) from the normal left-handed form to the right-handed form. Flipping increases with age and correlates with disease, such as Alzheimer’s disease, cataracts, and arteriosclerosis. As one ages, flipping even accumulates in facial skin, but not other skin. [See Noriko Fujii, “D-Amino Acid in Elderly Tissues,” Biological and Pharmaceutical Bulletin, Vol. 28, September 2005, pp. 1585–1589.]

If life evolved, why did this destructive tendency to flip not destroy cells long before complete organisms evolved?

d . Many researchers have attempted to find plausible natural conditions under which [left-handed] L-amino acids would preferentially accumulate over their [right-handed] D-counterparts, but all such attempts have failed. Until this crucial problem is solved, no one can say that we have found a naturalistic explanation for the origin of life. Instead, these isomer preferences point to biochemical creation.” Kenyon, p. A-23.

u Evolutionists who work in this field are continually seeking a solution. Occasionally, someone claims that it has been solved, but only after checking the details does one find that the problem remains. In Germany, in 1994, a doctoral candidate, Guido Zadel, claimed he had solved the problem. Supposedly, a strong magnetic field will bias a reaction toward either the left-handed or right-handed form. Origin-of-life researchers were excited. Zadel’s doctorate was awarded. At least 20 groups then tried to duplicate his results, always unsuccessfully. Later, Zadel admitted that he had dishonestly manipulated his data. [See Daniel Clery and David Bradley, “Underhanded ‘Breakthrough’ Revealed,” Science, Vol. 265, 1 July 1994, p. 21.]

u James F. Coppedge, Evolution: Possible or Impossible? (Grand Rapids: Zondervan Publishing House, 1973), pp. 71–79.

u A. E. Wilder-Smith, The Natural Sciences Know Nothing of Evolution (San Diego: Master Book Publishers, 1981), pp. 15–32, 154–160.

u Dickerson, p. 76.


3Homochirality Empty Homochirality Fri Dec 13, 2013 4:07 pm





The origin of the homochirality of amino acids is still an unsolved issue. There must have been a definite process to ensure that the sequence-based mechanism functioned in the RNA world. Future experiments will provide insights regarding the basis using which this mystery can be solved.

Enantiomers are molecules that are mirror-images of each other. Today, amino acids and sugars exist in only one enantiomeric form in most biological systems on earth. This homochirality remains one of the greatest unsolved mysteries to scientists.

However, the question of the origin of biological homochirality remains as yet unanswered.

left and right-handed molecules of a compound will form in equal amounts (a racemic mixture) when we synthesize them in the laboratory in the absence of some type of directing template.


Several mechanisms have been proposed for elucidating the origins of the chirality of organic compounds, such as circularly polarized light (CPL) (3) and quartz (4); however, a suitable amplification process for chirality is required to reach single-handedness of biological compounds (biological homochirality)

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4Homochirality Empty Re: Homochirality Sat Dec 14, 2013 7:26 pm






5Homochirality Empty Re: Homochirality Sat Dec 14, 2013 8:50 pm






6Homochirality Empty Re: Homochirality Wed Jan 29, 2014 1:03 pm




Left-Handed Amino Acid Dilemma

In his book, Evolution: Possible or Impossible, James F. Coppedge pointed out problems associated with the fact that proteins utilize only left-handed amino acids. Usually when an amino acid is synthesized in experiments such as Stanley Miller's synthesis producing amino acids from a mixture of ammonia, methane, hydrogen and water by the treatment with an electric spark, a roughly equal amount of D and L isomers are produced. Since the D and L isomers react in the same way, and are the same in all respects chemically and physically except for the physical properties associated with assymetry, it is inconceivable that a random event could account for the formation of a protein with all L isomers.

Coppedge calculated that for an average protein molecule that contained 445 amino acids (of which 35 would be glycine, which is neither D nor L, leaving 410) the probability of random formation with all L isomers would be I chance out of 10123 (2410).

In order to generate an idea of the magnitude of this figure, one could imagine one million protein chains forming per second for one quadrillion years. In that time, only 3.15 x 1028 protein chains would be formed. It is interesting to note physicists use a certain criterion: if the calculated probability for an event is less than 1 in 1041, the results are usually considered out of the realm of possibility.

Coppedge also calculated the probability for formation of a set of 238 proteins, the minimal number which would sustain life. The odds against this event occurring during the history of the earth would be 1 in 1029345, completely out of the realm of comprehension.8




Relevance of coin analogies to homochirality and symbolic organization in biology

The problem of homochirality in biology does not have prominence in ID literature because it is unglamorous and there is hesitation to endorse homochirality as evidence of design because of the fear there will be some future discovery in chemistry that will over turn it. But the sword of uncertainty cuts both ways, and if uncertainty casts doubt on ID, it casts even more doubt on mindless evolutionism. Right now the problem of homochirality is firmly an argument in favor of ID, and future discoveries could favor the ID case even more not less, so let us not be too quick to de-emphasize the homochirality argument.

Life is made of chiral molecules. A chiral molecule can be left-handed or right-handed. Below is a picture of two chiral molecules, the left-handed molecule is the left-handed form of an amino acid found in life:

Living organisms are notoriously 100% left-handed for amino acids and 100% right-handed for DNAs and sugars (thus living organisms are said to be homochiral).

If we apply enough heat to a chiral molecule, it will flip spontaneously from one form to another, just like a coin will flip sides if we apply enough agitation to it. Even at room temperature, given enough time and chance, the left-handed amino acid will become right-handed. Living organisms have huge amounts of built-in cellular machinery to generate and maintain homochirality. When something dies, the amino acids will slowly racemize into mixtures of 50% left and right-handed forms, and that is under the generous assumption the dead organism doesn’t undergo other forms of chemical decay such as hydrolysis, deanimation, depurination, etc. etc.

Every experiment trying to synthesize the pre-cursors of life via some “plausible” pre-biotic chemical soup (like Urey-Miller), creates heterochiral mixtures of molecules (50% left, 50% right handed).

We are conditioned to think that chemistry will drive the organization of atoms to one particular configuration, but the opposite is true of chiral molecules. The natural evolution of chiral molecules is to go toward a 50/50 mix of left and right handed forms like fair coins will tend to go to a 50/50 mix of heads and tails.

IDists were quick to seize on the fact that left-hand and right-handed forms can be treated like symbols. The organization of the symbols into recognizable patterns cannot be due to chance or chemical processes in a pre-biotic soup. In fact, chemical principles will work against symbolic organization into homochirality just like chance process will work against symbolic organization of a set of fair coins to 100% heads. The statistical arguments that were offered at UD for fair coins applies to chiral molecules. Could that be why Nick Matzke didn’t want to give one millimeter of ground on the question of 500 fair coins heads, because deep down, he knew the question was extensible to biology?

Can material/mechanistic processes be a solution to the problem of homochirality? Yes and no. “Yes” in the sense a nano-molecular material machine (a cell) can make homochiral materials, but “no” in the sense that such complex machines can’t self assemble from a pre-biotic soup where chance is the only mechanism available to build such a machine. Why? Homochirality is essential for life. Proteins will not fold properly and likely DNA cannot be read realiably without homochirality. It is the classic chicken and egg paradox. Did life emerge first or did homochirality emerge first?

Some might argue the first life was not homochiral. Well, the problem is this: suppose the first life was heterochiral, how can you guarantee stable protein folding and reliable reading of DNA for the next generation of creatures when the state of the components is unstable. This is almost as bad as suggesting binary data of a working piece of software could be have all the bits randomly flipped and you’d end up with another piece of working software. If heterochiral life emerged, it would quickly self destruct in the next generation.

Chemists have tried in vain to find ways to make pre-biotic soups homochiral, but like starting out with all fair coins heads, it won’t take too much to destroy the symbolic organization even if the system started out organized.

Individual amino acids molecules (monomers) in a pre-biotic soup need a means of assembling into long chains of molecules (polymers). This cannot be done without energy. It is like welding things together (so to speak). Now using undirected energy, Sidney Fox took homochiral amino acids monomers from soy beans (because he couldn’t find such nice homochiral materials from a pre-biotic synthesis experiment :-) ), and then tried to weld them together to form primitive proteins by heating the acids to 200°C for several hours. No matter that we would consider 200°C a temperature more conducive to sterilization (aka killing biological organisms), but in the process of welding the L-amino acids into polymers, many of the L-amino acids became D-amino acids.

Homochirality is an unglamourous form of symbolic organization, but because of its simplicity I like using it to illustrate ID concepts. The symbolic organization of homochirality is also critical to the functionality of life. I’m going bit out on a limb in that the argument could be falsified by some future discovery in chemistry, but isn’t that what science is about? Making falsifiable claims? In any case, I’d rather be on the ID side of the wager than the other side given what is known.

I do not worry so much about some chemist finding a way to make a homochiral pre-biotic soup (yes that would mean a soup of 100% left-handed amino acids, 100% right handed DNAs, and 100% right-handed sugars ). Because even supposing there were some means to start off with a homochiral pre-biotic soup, it cannot stay that way for long and the homochirality will be lost if polymerization takes place using undirected energy.

Though I’ve laid out some technical details as to why life will not arise from dead chemicals, we know this instinctively. A dead dog is far richer in plausible pre-biotic materials than can ever be synthesized in any OOL lab. But a dead dog will stay a dead dog.


1. photo credits : Vanderbilt.

2. There are a few bacteria that like high temperatures. Thermophillic bacteria live at 122°C, but even Fox’s polymerization method would have killed those bacteria. Further, when temperatures are so high or conditions so amenable to random polymerization that free-floating amino acids spontaneously bond to a polymerized chain, that would be lethal also to life.

3. Homochirality in amino acids is only tip of the iceberg in terms of simple symbolic organization of that variety. To that we must add that all the peptide links to form a proptein must be alpha-peptide bonds, not some mix of alpha and epsilon,beta, and gamma bonds (such as happened with Sidney Fox’s experiment above).

4. And what about DNA polymers? When DNA is randomly polymerized in pre-biotic type experiments, you end up get a mix dominated by 2′-5′ over 3′-5′ links, whereas for DNA to be readable it has to be uniformly 3′-5′. Without the homogeneity of homochirality, identical kinds of links, etc., even if life could have miraculously formed without all this, it would quickly self destruct for the next generation.

5. A general rule seems to emerge. Trying to solve one problem for OOL (like amino acid polymerization via heat) create other problems (like creating lethal temperatures and racemizing the amino acids). Pre-biotic soups would be considered toxic. Darwin’s “warm little pond” was not the origin of life but rather a cesspool of death.


8Homochirality Empty Re: Homochirality Mon May 11, 2015 5:32 pm





The origin of the homochirality of amino acids is still an unsolved issue. There must have been a definite process to ensure that the sequence-based mechanism functioned in the RNA world. Future experiments will provide insights regarding the basis using which this mystery can be solved.


Enantiomers are molecules that are mirror-images of each other. Today, amino acids and sugars exist in only one enantiomeric form in most biological systems on earth. This homochirality remains one of the greatest unsolved mysteries to scientists.


However, the question of the origin of biological homochirality remains as yet unanswered.


left and right-handed molecules of a compound will form in equal amounts (a racemic mixture) when we synthesize them in the laboratory in the absence of some type of directing template.


Several mechanisms have been proposed for elucidating the origins of the chirality of organic compounds, such as circularly polarized light (CPL) (3) and quartz (4); however, a suitable amplification process for chirality is required to reach single-handedness of biological compounds (biological homochirality)


9Homochirality Empty Re: Homochirality Mon May 11, 2015 5:35 pm



It seems that neither Baley, nor Tamura present a consistent solution to the chirality problem :


In regard of Baley's paper we read :

An attempt to be explain the origin of homochirality in amino acids has been made by invoking some rather complex chemistry. Researchers have shown that transfer RNA (tRNA), the molecule responsible for binding to amino acids during protein synthesis, does not selectively bind to L-amino acids in solution. So, it has become apparent that the prebiotic soup hypothesis will not explain the origin of homochirality. However, researchers thought that if RNA were bound to a solid substrate, the selectivity of RNA might be constrained, since the molecular configuration would be more limited. So, researchers have hypothesized that homochiral RNA bound to polar mineral surfaces would alter stereospecificity. In fact, this technique has produced up to a 35-60% enantiomeric excess of L-amino acids,5 but not nearly enough to produce any reasonably-sized protein.

And in regard of Tamuras paper :

In another strategy, researchers isolated the amino acid binding site of several tRNAs and modified them to make an "RNA minihelix" that demonstrated a four-fold enantiomeric selection.6 Although impressive compared to previous attempts, such a system would still produce a 20% error rate, which would prevent the formation of anything larger than a small peptide. In addition, the system assumes that the problem of RNA homochirality had already been solved. In addition, the author assumed that some primitive life form would have come up with the minihelix design, instead of stealing it from current life forms, which is what the scientists did.

Furthermore :

(Morrison, R.T. and Boyd, R.N., 1987. Organic Chemistry, 5th ed. Allyn & Bacon Inc. p.150)

Synthesis of chiral compounds from achiral reagents always yields the racemic modification.’ and ‘Optically inactive reagents yield optically inactive products.

and :

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

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.

(Cohen, J., 1995. Science, 267:1265–1266).

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

Organic chemist William Bonner once declared:

I spent 25 years looking for terrestrial mechanisms for homochirality and trying to investigate them and didn’t find any supporting evidence. Terrestrial explanations are impotent or nonviable

http://esppro.mtk.nao.ac.jp/Members_PRE ... dex_E.html

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.

So i have yet to see a convincing answer to homochirality.

Last edited by Admin on Sun Oct 18, 2015 9:23 am; edited 1 time in total


10Homochirality Empty Re: Homochirality Sat May 16, 2015 12:05 pm



Amino Acids and Chiralty


To answer the question of origins we learned that amino acids have been found in various places like on meteorites and have been produced in experiments to simulate the early atmosphere of earth, such as the Miller Urey experiment.[5] The conclusion being that amino acids can form naturally from chemicals, and thus life can form from chemicals (non-life). But recall that even one protein requires a specific combination amino acids, followed by proper folding from other proteins. Without other proteins present how could the amino acid polypeptide chain be folded into a protein? Also, both my textbooks failed to mention that there are over 2,000 amino acids found naturally occurring, but only 20 can be used to build proteins.[6] Were the amino acids from the meteorites and lab experiment the correct 20, or were they just a few of the other 1,980 other amino acids that cannot be used to build a protein?

Furthermore there is an even a greater issue with amino acids called Chiralty. I learned about Chiralty from my personal studies outside of school because it also was not mentioned in either of my biology textbooks. I’ve presented that it takes the proper combination of specific amino acids out of thousands followed by the proper folding of amino acids to create just one protein. But there is a fourth and more important perquisite for amino acids in the polypeptide chain. When the atoms that make up the amino acids fuse together they make two different shaped amino acids, left-handed and right-handed. Just like our two human hands which are completely opposite of each other, amino acids are likewise opposite of each other, mirror like-reflections of one another but not identical, allowing them to fuse together. Interestingly enough when a left-handed amino acid fuses to a right-handed amino acid, they become useless for building a polypeptide chain and therefore useless to building a protein, which is known as being racemic.[7] This phenomenon is called chiralty, which is Greek for handedness.[8]

Here is where it gets interesting; all amino acids used to build proteins in life are all 100% left-handed. There are no right handed amino acids used in life.[9] Equal amounts of left and right handed amino acids called “racemates,” is the product of chemical production of amino acids, which naturally want to bond together. So here are my questions: If all amino acids found chemically are both right-handed and left-handed which naturally want to fuse together making them useless for building proteins, how is it that all proteins found in living organisms have only left-handed amino acids? If life came from non-life, how did the first amino acids, 20 out of 2,000, only left-handed, manage to get in the right combination, and become properly folded to build the first protein?


11Homochirality Empty Re: Homochirality Sat Jun 27, 2015 10:38 pm



The Origin of Biological Homochirality

The implications of the single chirality of biological molecules may be viewed in this context of complexity. Whether or not we will ever know how this property developed in the living systems represented on Earth today, studies of how single chirality might have emerged will aid us in understanding the much larger question of how life might have, and might again, emerge as a complex system.






13Homochirality Empty Re: Homochirality Fri Oct 16, 2015 7:20 pm



Why are amino acids always left handed and sugars always right handed? This latest study indicates the answer is not chemistry, but physics. It might be due to noise vibrations from the chemical fluctuations. This might seem trivial knowledge, but understanding the physics of genetics might be the clue to a breakthrough in origin of life studies.
"Imagine you've got a coin, and it's perfectly made, so it's not biased at all, and you start flipping the coin. Each time you flip it, it keeps coming up heads. So then you say, something must be operating that's causing this to happen . . . you get the same puzzle with these biological molecules, and that's the problem of homochirality."



14Homochirality Empty Re: Homochirality Wed Jan 27, 2016 6:19 pm



More Attempts to Explain Chirality

Despite the hype in some reports, the highly-designed experiments only underscore the problem for origin of life theories.
50 years since James Coppedge focused on the problem in Evolution: Possible or Impossible?, the problem of homochirality still challenges naturalistic theories for the origin of life. Coppedge showed that the probability of getting a single-hand chain of peptides is vanishingly small. He also noted that natural selection cannot be invoked before a system existed capable of accurately reproducing all its parts (ch. 5). Since we last discussed this in October (10/02/14), a few more potential solutions have been offered, some with fanfare.
Discovery demystifies origin of life chirality phenomenon (PhysOrg). The article calls homochirality one of the more “fascinating” of the “unsolved puzzles” in the origin of life “mystery.” A team led by A. Schulman, U of Akron, publishing in Nature Communications, claims that “Mother Nature’s inner workings may not be as complex as we think.” The abstract of the paper, however, shows that the claimed “self-recognition” for the same hand was tested on very large molecular building blocks, like Fe28(μ3–O)8(Tart)16()24]20−, where Tart is tartaric acid. The molecules, furthermore, were wheel-shaped, unlike amino acids. The abstract ends, “We believe that delicate long-range electrostaticinteractions could be responsible for such high-level chiral recognition and selection.”
From Heat and Cold Comes Image and Mirror Image (U of Heidelberg). Researchers in Heidelberg, Germany intelligently designed a catalyst that can synthesize both hands of a compound depending on the temperature. This experiment has little to do with chance in a warm little pond, because it requires the specially-built catalyst, and the problem in origin-of-life theory is not getting the building blocks, but combining them in homochiral polypeptides. There’s only an off-handed remark at the end of the press release about this. “Itcould be a key principle in creating homochiral compounds through a temperature gradient such as observed in polymerisation,” the article says. “Such mechanisms are significant in researching the origin of life.
Chemists Crack the Chirality Code (PhysOrg). Despite the flashy headline, this article is also about intelligent design, not chance. The “code” that the scientists at Trinity College Dublin “cracked” is not the origin of life, but a method chemists can use to intelligently design one-handed products for drug development. The headline, then, is a false lead. The article has nothing to do with the origin of life.
It appears Coppedge’s contention stands: without design, the chance of getting an average sized protein out of all the proteins on earth, made of all left-handed amino acids, is one in 1071.  That’s for one average-size protein. The simplest known living organism has 239 proteins. Coppedge puts that low probability in context:
Saying it another way, the odds are a hundred billion trillion trillion trillion trillion trillion to one against that happening!
That isn’t all.  Even if one did occur, 238 more all-left-handed ones would be needed to work with it, or all would be lost.  Since all 239 would have to be together in space and time, the probability of each of the remaining 238 would be 1/10123.  Those huge numbers would then have to be multiplied together and with the 1/1071 probability of the first one, according to the multiplication rule.  This would give the probability of the needed group of 239 protein molecules being all left-handed.
The number is beyond all comprehension, namely 1 in 1029345.

Since believing that will happen is utterly ridiculous, origin of life research will never get off the ground without solving this mystery. Louis Pasteur said, when he first discovered the chirality phenomenon, “here are here mysteries which prepare immense labors for the future, and from this time invite the most serious meditations of science.”  Incidentally, the sugars in and are also homochiral, but right-handed in those cases (left– and right– being artificial designations for the convenience of classification).
Get to work, secularists. We’re still waiting. Did you notice that intelligence can easily sort and select things of one hand and snap them together quickly? Long before the “intelligent design movement” started, Coppedge said, after stating that natural selection is completely inadequate as a solution, “We find that there is no lessening of confusion until one accepts the logic that “intelligent” systems could not arise without an intelligent Designer.”



15Homochirality Empty Re: Homochirality Fri Jan 29, 2016 3:16 am



The problem of spontaneously producing a simple homochiral compound, say, l-alanine, from racemic reaction systems has not been solved .

Classical mechanisms generally rely on chance for the selection of l-amino and d-sugars by self-replicating systems. Mason has put forward the tantalising speculation that a weak nuclear interaction will stabilise the l-amino acids and their polypeptides over their d-forms. This electroweak advantage is considered too weak to affect the outcome of biochemical evolution. An imaginary flow reactor of a kilometre in diameter and four metres deep would be needed to autocatalyse a change of 10–2 to 10–3 moles of one isomer over 10,000 years if the temperature is kept at ambient. Admittedly a good thought experiment “but it will find no popular primitive Earth scenarios.” 

1) http://creation.com/origin-of-life-critique#endRef12
Mason, S., Origin of biomolecular chirality, Nature 314:400–401, 1985


16Homochirality Empty Re: Homochirality Tue Apr 18, 2017 11:03 pm



Astronomical sources of circularly polarized light and the origin of homochirality.

Possible astronomical sources of ultraviolet circularly polarized light (UVCPL) which might be responsible for enantiomeric selection in interstellar organic molecules are considered, Synchrotron radiation from magnetic neutron stars has been suggested as a possible source of UVCPL. However, synchrotron radiation in these situations is not predicted to be strongly circularly polarized. Very few such sources show optical synchrotron radiation and in the few that do circular polarization has not been observed. Magnetic white dwarfs and white dwarf binaries (Polars) can be highly circularly polarized but any effect on molecular clouds and star formation regions must rely on rare chance encounters. Recent observations show that substantial levels of circular polarization are present in reflection nebulae in star formation regions. This mechanism produces polarized light exactly when and where it is needed in regions where star formation is occurring and organic molecules are known to be present.



17Homochirality Empty Re: Homochirality Sat Feb 27, 2021 8:31 am



All amino acids, except glycine, have at least one carbon chiral, thus, they are optically active. The most commonly used system to classify amino acids is as L-amino acids or D-amino acids. L-amino acids deflect polarized light to the left so they are named as levogyre and D-amino acids deflect polarized light to the right, so they are classified as dextrogyre. However, the Cahn-Ingold-Prelog system is more complete, since some amino acids have more than one chiral carbon. In the Cahn-Ingold-Prelog system all L-protein-amino acids are classified as (S)-amino acids, with one exception L-cysteine is classified as (R)-amino acid. L-isoleucine and L-threonine, in the Cahn-Ingold-Prelog system are classified as (2S: 3S)-isoleucine and (2S: 3R)-threonine, respectively. The L/D-system is an oversimplification.

Isoleucine has two chiral centers, and, therefore four possible stereoisomers: l-isoleucine (S,S); d-isoleucine (R,R); d-allo-isoleucine (R,S); and l-allo-isoleucine (S,R). 2

Isoleucine, an essential amino acid, is one of the three amino acids having branched hydrocarbon side chains.

Branching stiffens large nonpolar side chains. 
The branched side chains of valine, leucine and isoleucine provide hydrophobic bulk yet limit internal flexibility. Stiff side chains are easier to fit into specific positions during the chain folding process. Valine, isoleucine, and leucine are almost always found in the interior of protein molecules. 

For a side chain to be hydrophobic, it must have more than two carbon atoms and no polar groups.   Straight hydrocarbon chains, such as ethyl or propyl are avoided as R-groups.  A straight propyl side chain would be free to wave around in the solvent in an unfolded protein. The γ methylene group and the δ methyl group of a propyl side chain are free to rotate about the connecting C–C single bonds. Consequently, a propyl side chain in the unfolded protein would sweep out a large volume relative to the α carbon. During folding of the protein the propyl side chain would lose most of this freedom as it were packed into the hyrophobic interior. This large loss of side chain entropy during protein folding rules out the use of the propyl group as a side chain.

Homochirality Phenyl10

The β carbon of isoleucine is optically active, just as the β carbon of threonine. These two amino acids, isoleucine and threonine, have in common the fact that they have two chiral centers.

1. https://www.mdpi.com/2073-8994/12/12/2046
2. https://pubs.acs.org/doi/10.1021/acs.chemrev.9b00474


18Homochirality Empty Re: Homochirality Sat Nov 18, 2023 4:20 am



The discussion of purity should have labeled as the homochirality problem and noted that this problem has remained unresolved since the 1800s when Louis Pasteur first recognized the issue. Only one experiment using magnetic materials has come close and even then the environment had to be aligned precisely and only about half of the necessary parts were purified, which means that a halfway purified mix must somehow be transported to a different environment to complete the process without dissolving.


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