Criticism of “Homochirality and the Origin of Life”[1] by Hugh Ross

Hi Hugh,

I recently came across this tweet:

Ross 01

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).

  1. 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.
  2. 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.”
  3. 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.
  4. “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.
  5. [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.]

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. […] 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.
  6. 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. [2]
  7. 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.
  8. 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.
  9. 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. [6]
  10. 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. [7]
  11. 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.

@takethatchem

References

  1. 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).
  2. J. E. Hein, D. Gherase, D. G. Blackmond Top. Curr. Chem. 2013333, 83-108; DOI: 10.1007/128_2012_397.
  3. J. Cohen Science 1995267, 1265-1266; DOI: 10.1126/science.7871419.
  4. E. Rubenstein, W. A. Bonner, H. P. Noyes, G. S. Brown Nature1983306, 118; DOI: 10.1038/306118a0.
  5. L. Barron J. Am. Chem. Soc. 1986108, 5539-5542; DOI: 10.1021/ja00278a029)
  6. D. A. Singleton, L. K. Vo J. Am. Chem. Soc. 2002124, 10010-10011; DOI: 10.1021/ja027129o.
  7. T. Satyanarayana, S. Abraham, H. B. Kagan Angew. Chem. Int. Ed. 2009, 48, 456-494; DOI: 10.1002/anie.200705241.

 

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An Interview with Biblenauts’ Tyler Lolong

by @TakeThatDarwin

Hey, Tyler. Thanks for agreeing to answer a few questions about Biblenauts, which gives me an excuse to talk about Biblenauts on my Twitter account, which I enjoy doing.

For the past year and change, you’ve written and drawn Biblenauts, a Monday-Wednesday-Friday webcomic that explores the Old Testament. Is this your first webcomic? How do you stick to your schedule so — ah ha ha — religiously? And how did you decide that a webcomic was the best means of exploring the Bible in this way?

I started doing comics in college, where I had a five-day- a-week strip in the student paper. It was awful and I loved it. That strip got me used to following a deadline pretty quick. After that I did a comic called Pomophobia for a couple years while suffering through grad school and developing Biblenauts. That comic is still at pomophobia.com, if anyone’s interested. Fae and Basie show up.

I love making comics, and I love the Bible, so combining the two just made sense. A ton of folks have adapted the Bible, including cartoonists, but I don’t know of too many adaptations that followed a newspaper-strip style, doing bits and pieces over time. I like the intimacy a comic strip brings, and how that intimacy contrasts with the bombast of the sword-and-sandal epic. I also love how comic strips can quickly switch between 2014-09-08-Whats-Eden-You-Page-04storytelling and one-shots, which is useful when dealing with a collection like the Bible that’s made up of more than just stories.

The characters of Fae and Basie were prominent in the first few comics, but have since faded into the background and become a sort of Greek chorus, appearing only to deliver the occasional punchline or bit of editorializing. (Fae’s comment at the end of the Sodom and Gomorrah story was especially brilliant.) How much was their role intended to change from the beginning, and how much just sort of organically happened?

Biblenauts is inspired by (ripping off) Superbook, an anime that adapted the Bible for a Japanese audience. It featured two kids and a robot traveling to Bible times to learn lessons about genocide and the importance of cleaning your room. Originally I wanted to do a straight-up parody, with my present-day characters as the main focus, and had a whole prelude chapter written out. But then I realized I was sixteen pages in before I got to “in the beginning,” and I decided that maybe my Bible comic should focus on the Bible.

I really liked the characters, though, and their chorus function is very useful, so they stuck around. Currently they spend a lot of time in the background because the Bible characters steal the stage. When I hit later books like Judges, which has minimal characterization, Fae and Basie will have a bigger role to play.

One of the things you do remarkably well is highlight both the admirable and less-admirable aspects of various Biblical characters, thereby humanizing them and bringing them to life. Your interpretation of Jacob, for one, is clever but deceptive, almost Odysseus-like. How much of your characterization do you think is textually supported?

Do you think a first-time Bible reader would come away with similar impressions of these characters? Would a Bible scholar?

This question is complicated, because different traditions and different scholars disagree on how to interpret the text. I like to think I hew pretty close to the text, but the Bible is so intertwined with my identity that I can’t claim any sort of objectivity.

While I stand by my readings, they’re not meant to be scholarly. I pull mainly from the text, but also from pop culture, folklore, midrash, and scholarship. My version of Joseph is likely different from what most modern readers will take from the text, because I took it from extra-biblical traditions that depict Joseph as feminine. And sometimes I go with a particular translation just because it’s funny.2015-08-24-The-Wrestler-Page-04

Your portrayal of angels is MEGA otherworldly. What influenced your decision to make them so different from the traditional dude-but-with-wings image?

In my mind, the best pop culture version of an angel I’ve come across is Madeline l’Engle’s A Wind in the Door, which features a cherubim made up of a pulsing mass of wings and eyes. I used to stare at that novel’s cover art. I like her take on angels because they resemble the otherworldly depictions you see in texts like Ezekiel. When that prophet  approaches divinity, he has trouble describing what he sees. I wanted to approximate that.

In your earliest comics, the serpent in the Garden of Eden is a talking snake rather than, as people seem to automatically assume, Satan. How did so many people come to the conclusion that the serpent is Satan, and why did you avoid that reading? Are there any other instances you’d like to point out where you break ranks with modern-day Bible interpretations?

That interpretation really shows the power of tradition. The text never refers to the snake as anything other than a snake, but enough people made the connection with the Christian concept of the devil that we started to read him into the story. I felt that shoving 2015-10-26-Absents-Speak-Louder-Than-Words-Page-11the devil in would add little to the story, so I left the snake a snake. Though Fae found a way to shove Jesus into that story, so maybe the whole thing is a wash.

You warned your readers about the story of Dinah early on, and probably with good reason. It’s one of those stories that really highlights the difference in values between us and the authors of the Old Testament — while it’s a fascinating revenge story, it totally treats the rape victim as a MacGuffin who drops off the radar as soon as she’s set up the conflict between the male characters. Your thoughts?

Yeah, the true horror of that story, for me, is that no one asks Dinah what she thinks. She never gets to speak. If that story pisses anyone off, I highly recommend Anita Diamant’s The Red Tent, which goes through most of Genesis from Dinah’s perspective.

While your affection for the Bible as literature is obvious, I get the impression — pardon me for saying so — that the affection is kind of one-sided, and that you are probably not the audience the Bible’s authors intended thousands of years ago. What do you think?

I’m not an ancient Israelite, no. I doubt the Bible’s authors and editors would like me very much.

How do you feel about the people who maintain that they can draw meaningful lessons from a sola scriptura reading of the Bible without understanding the culture from which it came?

Depends on the lesson. Do you use the Bible to make the world a better place, and to bring you closer to God? Then go for it. Do you use the Bible to devalue other people, and justify hatred? Then we have a problem.

Anyone who claims they’re just following the Bible is lying, though. We all come to it from a tradition, even just by existing in the Western world. We all have biases which affect our reading. You have to examine how your view of the world colors your interpretation, and vice versa.

You started Biblenauts more than a year ago and have, at this point, made it most of the way through Genesis. What does the future hold for Biblenauts? Will you be skipping ahead at any point? Is the New Testament in the cards?

Well, Exodus is next, naturally. I plan to focus mainly on the narrative material, but the format of a comic strip lets me jump out of a story and play with whatever I want. I do want to put at least a little of every book of the Tanakh in the strip, but some may need to be peppered in with others. I doubt anyone would want a full year of just Psalms.

Thanks so much for your time, Tyler.

Thanks for the opportunity!

Tyler Lolong has a Patreon. Give him money.

Why We Expanded

By @TakeThatGMOs

What can 140 characters do? 140 characters can make you divorce your wife of 30 years. 140 characters can suspend you from school. 140 characters can make you look like an absolute genius, or you can cram creationism into those precious 140 characters and that can make you look like an absolute idiot. Whatever you do with your 140 characters, you need to remember how powerful they are.

140 characters, however, is not enough to explain everything in detail. Then again, some argue that these people are a lost cause, they’re simply serving the purpose of being an example. But more often than not, I find myself arguing with people who are on the fence, and who sometimes do change their opinions. Other times, I find myself arguing with more confident people, and therefore having to use a buttload of tweets.

The way we fight pseudoscience, by direct arguing, is the best way to do it. It is, however, rarely done by people. And so that’s why we’re there. We have faced criticism for the way we do it and the platform we do it. We have focused on Twitter only and have left many, many other people on other platforms to spread their pseudoscience.

We therefore came to the realisation that, as the TakeThat phenomenon was catching fire and rapidly expanding, we had to expand too. We chose to start this with a blog, as it’s only an extension to what we do. We can provide reflections on relevant news, explain complex topics, argue, provide opinions, give insights and even breakdown the week in detail. There’s so much more we can do with a blog, and we can provide our experience in doing it.