I recently came across this tweet:
Needless to say that I was very intrigued. Of course, homochirality was, at some point, a big mystery for those thinking about the origin of life, but in 2017, the veil has been lifted on the fundamental mechanisms that allow enantiomerically pure compounds to form spontaneously. I therefore had a look at your post, and was quite unpleasantly surprised. Here are the things I take issue with, listed in order of appearance, not importance. Each particular point is numbered. This will make it easier, should you wish to reply to this post (I hope you will).
- The date of the blog entry is November 7, 2011. Why does your tweet call it “latest blog”? Have you really not written anything since? The fact that you still consider it up to date in 2017 is quite a problem, as we will see later.
- “Life requires homochirality in certain molecules.”
Do we know that? I don’t think we do. We actually have no idea about life other than that which we observe on Earth. I would suggest replacing that sentence by “Life as we know it uses its main chiral building blocks in a homochiral fashion.”
- “When scientists failed to demonstrate a naturalistic explanation for homochirality via terrestrial chemical pathways, they turned to astronomical mechanisms.”
This is factually incorrect. Both terrestrial and astronomical factors have been taken into account from a very early stage. I will say more about this later.
- “However, research continues to prove fruitless […]”
That is of course a blatant lie. Over the last 40 years, chemistry has advanced enormously (and often serendipitously) to provide us with the definitive certainty that the appearance of homochirality is possible and understandable, both spontaneously on Earth or caused by non-terrestrial chemical or physical influences. Details about this will be presented in later points.
- “[research] instead, makes it clear that supernatural design is a much better explanation for the existence of life-essential homochirality.”
That is the second lie in the same sentence. You know very well that no scientific research has ever pointed to a supernatural explanation. As a physicist, you also know that no scientific research can ever point to a supernatural explanation. This is the first occurrence of the “god of the gaps” fallacy in this blog. Lack of knowledge is lack of knowledge, not knowledge of an alternative explanation.
[Side note: I’m only past your introductory paragraph, and I’ve already listed 5 criticisms. This will be a long post.]
- “Any molecule with four different chemical groups attached to a central carbon manifests two distinct three-dimensional configurations. Chemists refer to these mirror image configurations as left-handed and right-handed. Such molecules are said to be chiral.”
That definition is both incorrect and incomplete. The first sentence is the definition of a stereogenic carbon atom. Molecules that contain multiple stereogenic carbon atoms are not necessarily chiral. Chemists also don’t use the terms left- and right-handed anymore. We haven’t done so for decades, it’s completely archaic and useless. Finally, your definition leaves out stereogenic atoms other than carbon, helical, axial, and planar chirality. Never mind, we can go on assuming that we will limit all of the following points to the particular case of chirality caused by the presence of one or multiple stereogenic carbon atoms.
- “Life chemistry demands homochirality”
No Hugh. Chemistry does not demand anything. This is simply what we observe. It is an observation that living organisms are composed of proteins made from l amino acids, it is not a necessity or a demand. Let me also give a tip to the writer you’re trying to be: do not use nouns as adjectives, it’s considered poor style.
- “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.”
That is wrong. Proteins can form from either enantiomer of the amino acids, or mixtures of both enantiomers. Once again, the correct thing would be to say that living organisms only use and produce proteins made from one enantiomer of the amino acids. The exact same comment applies to the following sentence (“Likewise, DNA and RNA molecules cannot assemble unless all pentose sugars are 100 percent left-handed or right-handed.”). Fortunately, you’re not incapable of getting it right, as the sentence “All organisms on Earth manifest only left-handed chiral amino acids and right-handed pentose sugars.” shows. It is indeed an observation of a fact, not a fundamental necessity. Despite the last sentence being correct, I recommend you use a nomenclature recommended by IUPAC to designate enantiomers instead of using left- and right-handed.
- “Homochirality presents a challenge to atheists, agnostics, and others who try to explain the origin of life via purely natural mechanisms.”
They’re called scientists, regardless of their spiritual beliefs. One does not have to be an atheist or agnostic to enquire scientifically about the origin of life. To present this as a question of the religious being opposed to unbelievers is both a strawman argument and divisive.
- “[…] demonstrating how homochirality arises […] is the simplest problem”
Well no, it isn’t. And if it were, you’d have a strange way of relegating the the topic of your post to the rank of a minor question.
- “But, as Fuz and I documented in our book, Origins of Life, no possible terrestrial pathways exist for producing the homochiral molecules required for life’s emergence.”
This statement is the fundamental falsehood that undermines the whole validity of your blog post. It is very clear nowadays that homochirality can be the result of purely terrestrial phenomena. The emphasis is deliberate: I am not stating that it is the case, but I’m refuting your statement that there are no pathways.
The “purely terrestrial” pathway to homochirality would involve a phenomenon called spontaneous absolute asymmetric synthesis. This process is now well-known and well-understood. Its result is the formation of a product that is either enantiomerically enriched, or even pure, starting from either achiral or racemic substrates. I will not detail the mechanisms behind this here, but they are most commonly of two types:
– they involve phase changes and the enantiomeric selection is due to the formation of conglomerate crystals;
– they do not involve phase changes and the enantiomeric selection is due to a phenomenon of asymmetric autocatalysis which results in amplification of the enantiomeric excess.
The peculiar aspect of spontaneous absolute asymmetric synthesis is that it is a stochastic phenomenon. In the absence of any external influences, it is impossible to predict which enantiomer will be favoured during the process. If the process is repeated a large number of times, an equiprobable outcome for either enantiomer is observed.
The logical consequence of this would be that, if homochirality emerged spontaneously on Earth without any outside influences, the enantiomers that we observe (the handedness, as you call it) is the product of chance. Nature uses one of the two possible forms, without there being a reason why.
A concise review dealing with this topic has been published by Hein, Gherase and Blackmond. 
- “Organic chemist William Bonner once declared: […]”
You fail to explain 3 things about this quote:
– It is taken from a news article (albeit published in Science magazine) and not a peer-reviewed paper. As such, it is not bound to present conclusions that strictly follow from experimental data and is merely a statement of personal opinion.
– Bonner was convinced one had to look towards outer space and therefore oriented his research projects in that direction. His statement is a justification of his research interests, and says nothing about the possibility or impossibility of there being other explanations for the origin of homochirality.
– Bonner’s most influential work is from the 1980s and this particular interview was from 1995. Over 20 years later, we have a much better and deeper understanding of, among other things, the phenomena mentioned in point 11. This is also your only reference on the topic, meaning that you neither cite proper research publications nor contemporary work. Given the large amount of research done in the area of prebiotic chemistry, this superficial treatment is more than inadequate.
Most importantly, the question whether an initial enantiomeric excess occurred on Earth or elsewhere is of no importance whatsoever. Neither one of the two possibilities would support your claim that supernatural forces are a necessity.
- The rest of your post deals with different (more or less recent) accounts of chiral molecules found in space or produced using circularly polarised light.
Circularly polarised light (CPL) is known to be capable of inducing absolute asymmetric synthesis. The difference with the spontaneous version described in point 11 is that now, in the presence of a physical chiral influence (CPL displays ‘true’ chirality according to the definition given by Barron), the outcome of absolute asymmetric synthesis is no longer stochastic: the enantiomer (or handedness, as you call it) obtained in the experiment is determined by the circular polarisation of the light source. What is the implication of that? It means that if the initial absolute asymmetric synthesis process happened in space where CPL is effective, then the observed preference for an enantiomer would not be random.
- When commenting the enantiomer ratios found in experiments and on meteorites, you falsely claim that the low preferences that are observed mean that such phenomena cannot explain homochirality on earth. This is not true. It is well understood that both mechanisms responsible for spontaneous absolute asymmetric synthesis, i.e. asymmetric autocatalysis and crystallisation of conglomerates, can give rise to asymmetric amplification. An initial infinitesimal imbalance in the ratios of enantiomers can give rise to very high final enantiomers in just a few cycles of the same reaction. A very striking example has been published by Singleton. 
- The false assumption that in order to explain homochirality on Earth, all biologically relevant chiral molecules need to come into existence in enantiomerically pure is all pervasive throughout your blog post. This is of course not necessary. For instance, in an asymmetric catalysis-driven scenario, the existence of a single catalytically active species in enantiomerically enriched form is sufficient to account for the formation of one or many other chiral molecules. If you factor in non-linear effects, the initial species does not even need to be enantiomerically pure. 
- Finally, from a scientist to a former scientist, your list of references is a shambles. It looks like it came from bad OCR software and much of it needs to be deciphered before one can use it. Please give the references the attention that they deserve.
This post has grown quite long. Given the extraordinary amount of published science concerning each of the points made here, it could have grown to the size of a book. However, its objective has never been to review all known science or to teach current prebiotic models to the readers.
The objective of this article is to show that all your claims of impossibility are wrong. Ultimately, your whole blog post amounts to a fallacious “god of the gaps” argument. You point out our ignorance on a number of topics, and conclude that a supernatural explanation is therefore more reasonable.
However, I have shown that (i) we are not as ignorant as you claim we are, and (ii) we know that the appearance of homochirality is not at all at odds with the fundamentals of science. Thus, despite the fact that we don’t know the exact nature of the events that led to the emergence of homochirality, we do know all the mechanistic aspects that can lead there. If a reasonable explanation is to be found, then it will be found within this framework. Incidentally, and I’m sure you’ll agree, humanity has found explanations for many of the natural phenomena that used to puzzle our ancestors. None of these explanations have ever required a supernatural force. Helios’ chariot doesn’t pull the sun, lightning is not the product of Zeus’ anger and thunder is not the result of Thor bringing down his hammer. There is no reason to think that this will ever be necessary, and the arguments you have brought forward in your blog post certainly don’t imply the necessity for a supernatural explanation either.
- http://reasons.org/explore/blogs/todays-new-reason-to-believe/read/tnrtb/2011/11/07/homochirality-and-the-origin-of-life (Retrieved on 13 December 2017).
- J. E. Hein, D. Gherase, D. G. Blackmond Top. Curr. Chem. 2013, 333, 83-108; DOI: 10.1007/128_2012_397.
- J. Cohen Science 1995, 267, 1265-1266; DOI: 10.1126/science.7871419.
- E. Rubenstein, W. A. Bonner, H. P. Noyes, G. S. Brown Nature, 1983, 306, 118; DOI: 10.1038/306118a0.
- L. Barron J. Am. Chem. Soc. 1986, 108, 5539-5542; DOI: 10.1021/ja00278a029)
- D. A. Singleton, L. K. Vo J. Am. Chem. Soc. 2002, 124, 10010-10011; DOI: 10.1021/ja027129o.
- T. Satyanarayana, S. Abraham, H. B. Kagan Angew. Chem. Int. Ed. 2009, 48, 456-494; DOI: 10.1002/anie.200705241.