Back in the 1980's when I first encountered (mostly) American creationists on the emerging Internet, one of their arguments from personal incredulity was that 'no-one can explain' why amino acids occur naturally in two stereo forms, yet only one is found in nature (therefore God did it!).
This 'problem' for evolutionary biologist now seems to have dropped out of favour with creationists, probably because, as more and more former creationists realise they've been fooled, only the lower tail-end of the IQ bell curve remain, and this phenomenon, known as chirality, is a little difficult to understand and requires a modicum of understanding of chemistry.
Basically, at the heart of an amino acid is a carbon atom with four different atoms of groups attached. This structure can be thought of as a pyramid with a triangular base (known as a tetrahedron) with the carbon atom in the centre and each of the four atoms or groups at each point of the tetrahedron. These groups can be attached to the carbon in two separate ways so that one is a mirror image of the other. These are known as chiral forms or stereo-isomers. No matter how you rotate one, it can never be the same as its opposite chiral form.
These chiral forms have the same chemical properties and the same physical properties apart from one - the way they interact with polarised light. One form causes the plane of polarity of polarised light to rotate in one direction, the other in the other direction; so they are also known as optical isomers.
The chiral forms of amino acids are prefixed with 'D' or 'L' (upper case; Dextro and Laevo (right and left)) according to the physical structure, or 'd' and 'l' (lower case) according to which direction they rotate the plane of polarity of polarized light.
ChatGPT explains it more succinctly:
Please explain the phenomenon of chirality as it applies to amino acids. Chirality is a fundamental concept in chemistry and refers to the property of molecules that are not superimposable on their mirror images. In other words, chirality describes molecules that exist in two non-superimposable mirror image forms, known as enantiomers. These enantiomers are often referred to as "left-handed" and "right-handed" versions of the molecule.The creationists argument went something along the lines of: if abiogenesis is true, there should have been two forms of life since each is equally possible, but one couldn't eat the other because they couldn't assimilate the 'wrong' chiral forms, therefore something must have 'decided' to create life from just the L-forms. Regardless of the non sequitur, and the childish teleology, creationists, as they do today, thought that raising an 'unanswerable' gotcha! question about science rendered the entire thing false, so their god wins by default, so they never need to bother with evidence.
Amino acids are the building blocks of proteins and are themselves chiral molecules. They consist of a central carbon atom (the alpha carbon) bonded to four substituents: a hydrogen atom, an amino group (NH2), a carboxyl group (COOH), and a variable side chain group (R group). It's this R group that gives each amino acid its unique properties.
In the context of amino acids, chirality arises due to the presence of the alpha carbon bonded to four different substituents. This arrangement creates a carbon atom with a tetrahedral geometry, which results in two possible spatial arrangements of the substituents around the central carbon atom.
For most naturally occurring amino acids, except for glycine, the alpha carbon is a chiral center. This means that they can exist in two distinct enantiomeric forms: L-amino acids and D-amino acids. In the Fischer projection, the configuration of amino acids is often represented with the amino group at the top, the carboxyl group at the bottom, and the R group extending horizontally. In the L-form, the amino group is on the left side, while in the D-form, it's on the right side.
It's important to note that in biological systems, proteins are composed exclusively of L-amino acids. This homochirality is a fundamental aspect of biochemistry, and deviations from this can have significant impacts on biological function. For instance, D-amino acids can be found in certain bacteria cell walls and are sometimes used as signaling molecules, but they are not typically incorporated into proteins in the same way as L-amino acids.
Overall, chirality in amino acids is a critical aspect of their structure and function, influencing everything from protein folding to enzymatic activity and molecular recognition in biological systems.
But now that god-shaped gap has been closed by scientists working at the Scripps Institute, La Jolla, CA, USA, who have just published two papers explaining how homochirality evolved. Sadly, both papers, one in Nature and the other in PNAS are both behind paywalls, so only the abstracts are available. However, the research is explained in a Scripps Research news release:
How molecular “handedness” emerged in early biologyThe abstracts to the two papers give more technical details:
Scripps Research chemists fill a major gap in origin-of-life theories.
Molecules often have a structural asymmetry called chirality, which means they can appear in alternative, mirror-image versions, akin to the left and right versions of human hands. One of the great mysteries about the origins of life on Earth is that virtually all of the fundamental molecules of biology, such as the building blocks of proteins and DNA, appear in just one chiral form.
Scripps Research chemists, in two high-profile studies, have now proposed an elegant solution to this mystery, showing how this single-handedness or “homochirality” could have become established in biology.
The studies were published in the Proceedings of the National Academy of Sciences on February 5, 2024, and in Nature on February 28, 2024. Together, they suggest that the emergence of homochirality was due largely to a chemistry phenomenon called kinetic resolution, in which one chiral form becomes more abundant than another due to faster production and/or slower depletion.
Graduate student Jinhan Yu and postdoctoral research associate Min Deng, PhD, were the first authors of the two studies.There have been many proposals for how homochirality emerged in specific molecules—specific amino acids, for example—but we really have needed a more general theory.
Professor Donna Blackmond, PhD, corresponding author of both papers John C. Martin Chair
Department of Chemistry
Scripps Research, La Jolla, CA, USA
The conundrum of homochirality
“Origin of life” chemistry has been a busy field for much of the past century. Its practitioners have discovered dozens of key reactions that plausibly occurred on the early, “prebiotic” Earth to produce the first DNAs, RNAs, sugars, amino acids and other molecules that sustain life. Missing from this body of work, however, has been a plausible prebiotic theory for the emergence of homochirality.
Ordinary chemical reactions that produce chiral molecules tend to yield equal (“racemic”) mixes of left- and right-handed forms. Outside of biology, this mixing typically doesn’t matter, as both forms usually have similar or identical properties. Within biology, though, as a consequence of extensive homochirality, it is commonly the case that only the left- or the right-handed form of a chiral molecule has useful properties—the other may be inert or even toxic. Thus, cells often guide reactions to yield specific chiral forms, using highly evolved enzymes.There has been a tendency in the field to ignore the chirality issue when looking for plausible reactions that could have made the first biological molecules. It’s frustrating, because without reactions that favor homochirality, we wouldn't have life.
Professor Donna Blackmond
The prebiotic Earth would not have had such enzymes, though—so how did homochirality ever arise?
A paradoxical result
In their study in Proceedings of the National Academy of Sciences, Blackmond and her team addressed this problem for amino acids. These small organic molecules are used as building blocks for proteins by all living things on Earth, but exist in biology in just the left-handed chiral form.
The researchers specifically sought to reproduce homochirality in a central process in amino acid production called transamination, by using a relatively simple, plausibly prebiotic chemistry that excludes complex enzymes.
In early tests, the team’s experimental reaction worked, and yielded amino acids that were enriched for one chiral form versus the other. The problem was that the favored form was the right-handed form—the one that biology doesn’t use.
When they did that, the reaction no longer preferentially made right-handed amino acids. In a striking example of kinetic resolution, it instead preferentially consumed and depleted the right-handed versions—leaving more of the desired left-handed amino acids. It thus served as a plausible route to homochirality for amino acids used in living cells.We were stuck for a while, but then the light bulb went on—we realized we could do part of the reaction in reverse.
Professor Donna Blackmond
Tying it all together
For the Nature study, the chemists explored a simple reaction with which amino acids in the earliest life forms might have been linked together into the first short proteins (also known as peptides). The reaction had been published earlier by another researcher, but had never been investigated for its ability to produce homochiral peptides from racemic or near-racemic mixes of amino acids.
Once again, the chemists ran into what seemed to be an insurmountable obstacle: They discovered that in forming peptide chains of amino acids, the reaction worked faster for linkages of left-handed with right-handed amino acids—the opposite of the desired homochiral peptides.
Still, the team persevered. Ultimately, they discovered that when one type of amino acid in the starting pool of amino acids had even a moderate dominance of the left-handed form—as their other study made plausible—the faster reaction rate for left-handed-to-right-handed linkages preferentially depleted right-handed amino acids, leaving an ever-greater concentration of left-handed ones. Additionally, the left-right-left-right peptides had a stronger tendency to clump together and fall out of solution as solids. These kinetic resolution-related phenomena thus ended up yielding a surprisingly pure solution of almost fully left-handed peptides.
To Blackmond, the seemingly paradoxical mechanisms uncovered in these studies offer the first convincing and broad explanation for the emergence of homochirality—an explanation that probably works not only for amino acids, she says, but also for other fundamental molecules of biology such as DNA and RNA.
“Prebiotic access to enantioenriched amino acids via peptide-mediated transamination reactions” was co-authored by Jinhan Yu, Andrea Darú, Min Deng and Donna Blackmond.
“Symmetry breaking and chiral amplification in prebiotic ligation reactions” was co-authored by Min Deng, Jinhan Yu and Donna Blackmond.
SignificanceSo, yet another of creationism’s favourite gaps has been closed by science and no god(s) shown to be needed. Creationism's god of the gaps arguments are never more than arguments from ignorant incredulity and the false dichotomy fallacy - if science can't explain it, God did it!
While much progress has been made in developing prebiotically plausible synthetic chemical routes to RNA, DNA, and peptides, as well as in prebiotic metabolic pathways, the question of the emergence of biological homochirality has often been left unexplored. Our work suggests that modern biological transamination may have evolved from a prebiotic half-reaction in reverse, effecting a kinetic resolution of racemic amino acids that preferentially leaves behind the proteinogenic amino acid enantiomer. This reaction joins several other recently reported prebiotically plausible kinetic resolutions that have been shown to produce enantioenriched sugar and amino acid building blocks. Kinetic resolution may be seen as an effective means of imparting stereochemical control that preceded and aided the development of highly selective asymmetric biocatalysts.
Abstract
The kinetic resolution of racemic amino acids mediated by dipeptides and pyridoxal provides a prebiotically plausible route to enantioenriched proteinogenic amino acids. The enzymatic transamination cycles that are key to modern biochemical formation of enantiopure amino acids may have evolved from this half of the reversible reaction couple. Kinetic resolution of racemic precursors emerges as a general route to enantioenrichment under prebiotic conditions.
Jinhan Yu, Andrea Darú, Min Deng, and Donna G. Blackmond
Prebiotic access to enantioenriched amino acids via peptide-mediated transamination reactions
Proceedings of the National Academy of Sciences; 121 (7) e2315447121. DOI: 10.1073/pnas.2315447121
Copyright: © 2024 The authors.
Published by PNAS. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Abstract
The single chirality of biological molecules is a signature of life. Yet, rationalizing how single chirality emerged remains a challenging goal1. Research has commonly focused on initial symmetry breaking and subsequent enantioenrichment of monomer building blocks—sugars and amino acids—that compose the genetic polymers RNA and DNA as well as peptides. If these building blocks are only partially enantioenriched, however, stalling of chain growth may occur, whimsically termed in the case of nucleic acids as “the problem of original syn”2. Here, in studying a new prebiotically plausible route to proteinogenic peptides3,4,5, we discovered that the reaction favours heterochiral ligation (that is, the ligation of L monomers with D monomers). Although this finding seems problematic for the prebiotic emergence of homochiral L-peptides, we demonstrate, paradoxically, that this heterochiral preference provides a mechanism for enantioenrichment in homochiral chains. Symmetry breaking, chiral amplification and chirality transfer processes occur for all reactants and products in multicomponent competitive reactions even when only one of the molecules in the complex mixture exhibits an imbalance in enantiomer concentrations (non-racemic). Solubility considerations rationalize further chemical purification and enhanced chiral amplification. Experimental data and kinetic modelling support this prebiotically plausible mechanism for the emergence of homochiral biological polymers.
Deng, M., Yu, J. & Blackmond, D.G.
Symmetry breaking and chiral amplification in prebiotic ligation reactions.
Nature 626, 1019–1024 (2024). https://doi.org/10.1038/s41586-024-07059-y
© 2024 Springer Nature Ltd.
Reprinted under the terms of s60 of the Copyright, Designs and Patents Act 1988.
The lessons from the history of science is that no god-shaped gap was ever closed and found to require a god in the explanation, yet they are somehow able to convince themselves that their latest gap, real or imaginary, will be the one where their god is finally found to reside.
The god-shaped gap/false dichotomy fallacy only works on scientifically illiterate, parochial cultural chauvinists, of course, so the puzzle is why they think they're ever going to work on people who understand science and who have a broader, more enlightened understanding of the world. But then logic is not a noted creationist strong point either.
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