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Sat Dec 9, 2017, 10:55 PM

Now, THIS is a very cool Ph.D thesis: Francesco Ricci and the origins of chirality.

Life is asymmetric, and why this is so is one of the greatest mysteries of the universe. By asymmetric we are referring to the property that your hands have, they are mirror images of one another, but cannot be superimposed upon one another.

We refer to this property as chirality.

Here is a picture of the two forms of the simple amino acid alanine, with, by convention, the black wedge being representative of coming out of the plane of the page, the dashed wedge representative of being representative of going back behind the plane of the page:



In the laboratory, one can easily make alanine by the hydrogenation, in the presence of ammonia of the symmetric molecule pyruvic acid, with, say for example, a nickel or platinum catalyst. When one does this however, one will get a 50:50 mixture (exactly) of the two molecules above. We refer to such a 50:50 mixture as "racemic."

In living systems, by contrast, which also synthesize alanine from pyruvic acid, one will only get one of these isomers, the S isomer, 100%, exactly.

In fact, one can only synthesize pure chiral molecules in the laboratory (and this has been a subject of vast amounts of research over the last century or so) if one conducts the reaction in the presence of molecules that are also chiral. This is, in fact, what happens in living systems; the vast majority of molecules in living things (other than water) are chiral. But where did it come from? What was the first chiral molecule to exist in the absence of its mirror image, which we call its "enantiomer?"

I have wondered about this a lot while daydreaming over several decades; I've generally assumed with a vague sense, that it somehow resulted from certain types of chiral radiation associated with nuclear decay in cataclysmic stellar events. (Yes, light can be, and often is, chiral.) Here and there, I've pulled some papers down, but none were very satisfactory.

Today, while going through files I collected but never actually read, I came across a recent Ph.D. thesis at Princeton University, written by a young scientist named Francesco Ricci. It's entitled "Theoretical and Computational Studies of Condensed-Phase Phenomena: The Origin of Biological Homochirality, and the Liquid-Liquid Phase Transition in Network-Forming Fluids."

The thesis can be accessed here: Ricci, Ph.D Thesis, Princeton

Very early in the text I came across a concept of which I'd never ever heard, "Viedma ripening" involving homochiral molecules.

Viedma ripening...

Never heard of it.

It doesn't get any better than this, being old and fairly broadly exposed and then run across something from some very charming young guy talking about something about which you know nothing.

I'm going to be pulling up this kid's papers and his references in the next several weeks. Beautiful, very, very, beautiful.

It's going to be a fun Christmas break!

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Response to NNadir (Original post)

Sat Dec 9, 2017, 11:01 PM

1. this was my Achilles heel in org chem - I have a memory like an elephant

can crunch data and see patterns - but I don't do well identifying spacial relationships - my brain isn't wired to "get" stereochemistry all that well.

But somehow I made it through (my PhD was in synthesis of PAH using aryne generation - didn't have to grapple with chirality very often!)

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Response to NRaleighLiberal (Reply #1)

Sat Dec 9, 2017, 11:10 PM

2. Well, those flat molecules are cool too, but dangerous, like when they sit in the chiral grooves...

...of a DNA helix.

Big trouble that...

I did a lot of amino acid chemistry when I was a kid; chiral all the time, but I always wondered, but never had the time to really investigate, where the hell did that chirality come from?

It's one of the great mysteries left, sort of the kind of mystery that one might have wondered about in say, 1890, why is the sun hot?

I'm sure, like how we now know how the sun works, we'll know where chirality comes from, and this kid's thesis is an interesting place to think about it.

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Response to NNadir (Reply #2)

Sat Dec 9, 2017, 11:24 PM

3. well, I appreciate the things you post - takes my mind off the miserable recent politics!

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Response to NRaleighLiberal (Reply #3)

Sun Dec 10, 2017, 11:04 AM

5. Everyone remembers Galileo; few people remember Pope "What's His Name?" other...

...than to recall his unhappy and ignorant relationship to Galileo.

In 50 years the orange ignoramus will be as important to the world as Franklin Pierce is, remembered only by graduate history students in American history and a few trivia buffs, if even them.

Effectively, the uneducated brat is what he has always been and will never rise above, a useless. over indulged carny barker.

When he's gone life will still be chiral; and the planets will still move much as they did in 1610.

I try to keep this in mind, which is why I post these little somewhat obscure notes. Writing them makes me feel better and I am pleased that reading them makes you feel better.

Thanks for your kind words.

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Response to NNadir (Reply #5)

Mon Dec 11, 2017, 06:48 AM

9. The pope's name was Urban VIII and you are slandering him

Urban had known and befriended Galileo for years. Galileo told Urban that he was going to write on the Ptolemaic system versus the Copernican system in his Dialogue on the Two World Systems. Urban, who was well aware that Galileo was an advocate of heliocentrism, asked (not ordered, asked) Galileo to treat the geocentric model with respect and not ridicule. When Galileo did not do this, Urban was displeased. Moreover, Galileo quoted Urban, and put Urban's words in the mouth of a man named Simplicius -- "simpleton" is a good translation. Naturally, Urban really did not appreciate being called an idiot in print. So he had Galileo called before the Papal Inquisition to explain himself. Remember that Henry VIII of England had people executed for less.) So, while the official charge was heresy, the actual charge was lèse-majesté.

Before I go on, a few words about the Papal Inquisition. Don't confuse it with the Spanish Inquisition, a wholly separate organization. The name Inquisition comes from the Latin inquirere -- to look into, or to examine ("inquire" is from the same root). In the Papal Inquisition, defendants had such things as the right to counsel, the right to be told the specific charges against them and their property would not be seized by the Inquisition. Torture was permitted, but only when specifically authorized by the Pope or the head of the Inquisition (at that time, Cardinal Robert Bellarmine) and was to be used only once.

One thing that should be pointed out is that a major part of the Dialogue on the Two World Systems was concerned with a basically flawed theory about tides. Galileo believed that tides were caused by the sloshing back and forth of water in the seas as a point on the Earth's surface sped up and slowed down because of the Earth's rotation on its axis and revolution around the Sun. He advanced this theory because Cardinal Bellarmine called for evidence that the Earth circled the Sun, and Galileo thought this would suffice. Unfortunately for him, the theory is flat-out wrong, and could be shown to be wrong -- for one thing, it said that there should be only one high tide per day, not two. Galileo clearly knew of this problem, but essentially blew it off.

Another thing that should be pointed out is that the Vatican assigned two Jesuits, Christoph Scheiner and Orazio Grassi, to look into Galileo's science. Both had solid credentials as astronomers. However, Galileo had managed to alienate both of them. Schiener was one of the first astronomers to observe sunspots and was, as far as he knew, the first to describe them in a scientific paper. (In fact, the first paper on sunspots was published the previous year by David Fabricius, but his paper was unknown outside of Germany.) Galileo attempted to grab the glory of having first seen sunspots from Scheiner, and compounded this by plagiarizing Scheiner in his own paper.

Grassi and Galileo disagreed on the nature of comets. What made things worse was that Grassi was right and Galileo was wrong. Grassi had observed a comet over a period of time, and had noticed that the moon moved faster in the sky than the comet did; Grassi reasonably (and correctly) assumed that the comet was further from the earth than the moon was. Galileo believed that they were optical illusions in the atmosphere. After several rounds of argument in various pamphlets, Galileo wrote an essay, Il Saggiatore -- "The Assayer" -- attacking Grassi and his theory. This essay is still taught in Italian schools as a masterpiece of polemical writing. Naturally, having been held up to ridicule, Grassi was no friend to Galileo.

No, Galileo brought many of his problems on himself.

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Response to Fortinbras Armstrong (Reply #9)

Tue Dec 12, 2017, 04:37 AM

10. Um...um...um...

I guess, because Newton could not explain the precession of Mercury that gravitation needed papal approval, especially if Newton ridiculed Ptolemy, which I don't believe he did, although he, like many brilliant people, was caustic.

As for the comet, this reminds me of a Lincolnism, wherein he resisted initial calls for the Emancipation Proclamation by noting that it would be "as effective as the Pope's bull against the comet." Of course, Lincoln did issue the proclamation and initially at least, it was as effective as the "Bull against the comet." There is some doubt whether this bull actually existed - it seems to have been promoted by Laplace, who actually worked out many important equations relating to tides, and a hell of a lot of other things about which Galileo could not have known. Fortunately for humanity, Laplace was not threatened by discredited and absurd priests.

I looked up that asshole Maffeo Barberini on Wikipedia - and I had to look him up, because he's a historical curiosity of no moral or intellectual value - which is about as deep as I'm willing to go.

From what I understand, his real problem was that Galileo put his arguments in the mouth of "Simplicio."

This, um, tortured defense of this awful human being, Maffeo Barberini, who took time out of fighting wars for the papacy to threaten Galileo, seems to make an argument that if I call Roy Moore a childish idiot because he is a creationist, and he has me arrested, then it will be my fault.

One hears some pretty incredible historical distortions on the internet, but this one is, I think, a classic.

Barberini was a big factor in the relative rise of English science, since he made science illegal in Italy, more or less, just as Trump will be a factor in the rise of Chinese science, since science no longer needs just for politicians to leave it alone; it needs politicians to support science, which in China they do.

One really can't take the Holy "See" seriously in this case. The case of Galileo and his relationship with the warrior "Prince" Maffeo Barberini is a disgrace to the Catholic faith, although, apparently, in 1993, the church finally conceded that, um, the Pope wasn't an infallible arbiter of the state of the physical universe and that Galileo wasn't a bad guy after all.

I don't think one can "slander" Maffeo. He was a fool with questionable morals and a swelled head, sort of like the orange idiot of today. This is a fact. He is immune to "slander," since slander is a criticism that has no basis in fact.

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Response to NNadir (Reply #10)

Thu Dec 14, 2017, 07:55 AM

11. Did you see the bit where Galileo insulted the Pope?

That's what Urban really objected to. Galileo called him a simpleton in print. And Urban was particularly incensed because he considered Galileo to be a friend.

In England, some years earlier, insulting the king in print was a capital offense. Galileo got off lightly by the standards of his day. Did you also see the bit about Galileo plagiarizing Scheiner? Or that he engaged in what today would be called cyber-bullying of Grassi? Or that he devoted a large part of his book to a theory of the tides that was demonstrably false?

Your ignorant rant about the papacy and Pope Urban is not well done. I could make your points much better because I actually know the history. And while Urban was guilty of several things, he was not a fool, and your calling him one simply shows that you are the fool. Certainly, it shows that you don't know what you are blathering about.

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Response to Fortinbras Armstrong (Reply #11)

Thu Dec 14, 2017, 08:19 PM

12. And, your point is what?

Last edited Thu Dec 14, 2017, 09:27 PM - Edit history (1)

That scientists need to be suppressed, if not threatened with torture, if they have caustic wits?

I don't consider my "rant" about the Papacy to be ignorant, but I do consider threatening scientists because they engage in personally insulting powerful idiots to be ignorance reified.

I note with due contempt that we seem to have another powerful official in this country who thinks it's OK to worry more about insulting attacks on his intelligence than something called "reality."

Science is reality. Irrespective of Maffeo's hurt feelings, the sun does not revolve around the earth.

I feel perfectly justified in holding the opinion that your self congratulation about your knowledge of history comes with a bit of ethical jaundice. If you could make "better" points, I believe you would have made them, but I'm unimpressed.

I will confess that I am spectacularly less interested in the tawdry history of the Catholic Church than I am in the history of science, about which you demonstrate only a very, very, very biased and weak sensibility. Despite my disinterest in church history, I'm very pleased to be aware that the Holy "See" removed the Dialogues from the "forbidden list" in 1835, only 107 years after Newton's death.

As it happens, by pure coincidence, one of the books I'm reading right now is Peter Ackroyd's Revolution, a history of England from "The Battle of the Boyne to the Battle of Waterloo" which deals with Montagu's creation of the Bank of England and its bearing on the famous appointment of Newton to the post of "Warden of the Mint." Sometimes, when historians want to point out what a nasty guy Newton was, they point to his tenure in this office and his fondness for having counterfeiters executed.

As for my alleged grounding in Papal history, I think I made it perfectly clear that Maffeo is one of the least interesting people in history, the only interest in him being in his work on behalf of ignorance which perhaps is worthy of slight consideration today.

Sit around and study Maffeo night and day if you wish and pontificate all you wish about him. I consider that a dullard exercise, but I'm speaking only for myself here: To each his own. Again speaking for myself, I think we have far more important things to which we need to pay concern in the 21st century than defend Popes who died more than 300 years ago.. Medieval minds - and Galileo wasn't one - have very little to do with the present, except to the extent that a dangerous medieval minded super-sensitive reactionary is now in power in a prominent North American country, which risks being set back, much as Italy was set back my Maffeo, into an age of suppression and ignorance.

I'm personally opposed to yet another Maffeo, if you must know.

Have a nice Friday.



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Response to NNadir (Reply #12)

Sun Dec 17, 2017, 02:38 PM

13. My point is that Galileo was not the all-glorious hero that you want to pretend he was.

He was a bully, a braggart and a plagiarist who who published a theory of tides that he must have known was wrong. He publicly insulted a friend and needlessly alienated other scientists. Galileo's theory of tides was demonstrably wrong, as was his theory of comets (which came straight out of Aristotle).

Your saying that Pope Urban VII (who, for some reason, you refer to as "Maffeo", which is like referring to the present pope as "Jorge" -- as the old schoolyard taunt goes, you think you're a wit, and you're half-right) "is one of the least interesting people in history, the only interest in him being in his work on behalf of ignorance" simply shows YOUR ignorance. Urban was politically astute, a patron of the arts. But his real beef with Galileo was that he had been called an idiot in print by someone he thought was a friend. As I said, that behavior would have been a capital offense under Henry VIII of England, and Urban's contemporary Louis XIII of France would lock you up and throw away the key for that sort of thing.

As I said, and you TOTALLY IGNORED, the formal charge against Galileo was heresy, the actual charge was being an asshole.

It is perhaps also worth quoting Stephen Jay Gould, perhaps the most careful historian of science: "All agree that Galileo might have avoided his fate if any one of a hundred circumstances had unfolded in a slightly different manner. He was, in other words, a victim of bad luck and bad judgment, not an inevitable sacrificial lamb in an eternal war between science and religion."

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Response to Fortinbras Armstrong (Reply #13)

Tue Dec 19, 2017, 01:56 PM

14. This determination on your part is unbridgeable.

Last edited Tue Dec 19, 2017, 09:30 PM - Edit history (1)

I fully and totally reject your claim that scientists need to be cute and gracious to their obvious intellectual inferiors to be heroic.

This is nonsense.

While I respect Gould enormously, this does not imply that I buy his logic in this case.

You think science is a social club, maybe like facebook, or a church social club.

I think it's, um, science. Galileo was one of the greatest scientists of his age.

And while I often have respect for dissidents - which in this case you are - I find your dissidence to be without merit.

I have no respect for Maffeo, and you, in my opinion have no respect for science.

The Nobel Laureate Herbert C. Brown held that non-classical carbocations didn't exist. This is incorrect; the evidence that they exist is overwhelming. He was obnoxious and rude about it.

He was also, quite correctly, a Nobel Laureate based on his work on boranes.

There's absolutely nothing I can say to you other than I find your position in these times annoying. You clearly hold no respect whatsoever for science and scientists; something as noted previously, is consistent with the attitude of the orange nightmare in the White House.

Let's call it.

I'll expand my ignore list.

Have a nice life.

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Response to NNadir (Reply #14)

Sun Dec 24, 2017, 08:29 AM

15. Yes, Galileo was a great scientist

He was also a bully, a braggart and a plagiarist in at least one of his scientific papers. He got into trouble because he needlessly insulted his friend, Pope Urban. Your sneer at Urban simply shows your ignorance and prejudice.

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Response to NNadir (Original post)

Sun Dec 10, 2017, 02:05 AM

4. I'm not sure what it all means

other than nuclear power plants are good and alternative energy ain't

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Response to flotsam (Reply #4)

Sun Dec 10, 2017, 01:37 PM

6. What has meaning to a person is wholly dependent on who one is.

If it doesn't mean anything to you, I understand perfectly, even if it means a great deal to me.

Although I'm pleased to be known for my views on energy which I think, for which I would choose to be known - even among people with whom I am not acquainted - I would note that all energy is "alternative energy."

As in most things in life, some alternatives are better than others, and through some effort my views on what is the best alternative are clear enough.

The alternatives chosen by humanity as a whole are poor alternatives, in my view, as is reflected in the concentration of the dangerous fossil fuel waste carbon dioxide in the rapidly degrading planetary atmosphere.

For the week ending December 3, 2017 we're at 406.76 ppm CO2

I'm not sure if that means anything either to you, but if it doesn't, or if it does but sounds like Schadenfreude on my part, I can't help it.

Have a nice Sunday afternoon and evening.

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Response to NNadir (Original post)

Sun Dec 10, 2017, 04:30 PM

7. I found a description of Viedma ripening on a commercial site...

... that's fairly easy reading.

https://www.crystallizationsystems.com/news/january-2017/Viedma-Ripening-in-the-Eyes-of-Cristobal-Viedma

I wasn't bothered that the origins of life's asymmetry seemed random; that it could have gone either way. There are a few science fiction stories where someone is transformed into a mirror image of themselves and begins to starve, or where life on another planet happens to go the other way and is inedible to human colonists. (Ha, ha, as if humans in our present form will ever colonize, let alone visit, other planets...)

It is very interesting if there is some bias in nature.

The abstract of the thesis you linked to is very intimidating in my browser. It's a single high density paragraph, a great wall of science words.

In the actual thesis (which is wonderfully a freely available pdf) the abstract is thankfully broken up into multiple paragraphs and a good invitation to read the rest of the research.



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Response to hunter (Reply #7)

Sun Dec 10, 2017, 08:37 PM

8. Thanks. I recall reading somewhere...

...that there is a very small difference in the thermodynamic stability of L isomers over D isomers, but I’m relying on an ancient and therefore unreliable memory.

I am inspired to get some primary literature on the topic.

I do know that the Murchison metereorite showed a L (largely S) configuration, suggesting that this isomer is universally preferred. The extraterrestrial nature of these amino acids was confirmed by the isotopic ratios of their constituent atoms.

As a result of this finding, I have always held a bias toward panspermia, the speculation that life is widely distributed in the universe as a whole, even if radiation fields are often but not always racemizing.

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