Archive for the ‘Attempted Humor’ Category

WWWTP? – Mohawk Edition

Thursday, February 14th, 2013

Bobak “The JPL Mohawk Guy” Ferdowsi dyed his hairdo several weeks back to celebrate the discovery of chloromethane on Mars:

Very nice, though I’m not a big fan of the atomic radii. That turquoise chlorine atom should be huge—4 times the diameter of the red hydrogens.

You just can’t trust engineers these days…

Happy Thanksgiving

Thursday, November 22nd, 2012

Happy Thanksgiving from the staff of ChemBark!

As a service to PIs everywhere, the editor is compelled to remind those of you who are grad students and postdocs that “Thanksgiving is a dinner, Christmas is a day.”

That is all.

Breslow and Dinosaurs in JACS, Oh My

Thursday, April 12th, 2012

You all know that origin-of-life research is near and dear to my heart, and you’re probably sick of how often I lament that the problem has not taken root in chemical academia despite the fact that it almost certainly requires a chemical solution. One of the few PIs at a top university who has dabbled in the field is Ronald Breslow, University Professor at Columbia and a past president of the ACS. Breslow just published this little diddy as a perspective in JACS:

First of all, how often do you see a single-author paper in JACS anymore? It is kind of refreshing. It also means that you can attribute 100% of the content to Breslow, including the ChemDraw structures:

What the hell is that? If I drew that structure on a slide in grad school, my committee would have eviscerated me.

Anyway, let’s get down to the science. Breslow’s premise is that you can take alpha-methyl amino acids found in non-racemic mixtures in meteorites—generated by selective destruction of one enantiomer by circularly polarized UV light—and “use” these compounds to generate non-racemic mixtures of sugars (which are also found as moieties in nucleic acids). Since meteors hit the early Earth with great frequency, maybe one or more of these chiral amino acids was the origin of life’s homochirality. It is an interesting idea and one worth keeping in mind. We could argue all day about how unlikely the scenario is, but this field needs to collect more neat ideas accompanied by simple demonstrations. That said, I take issue with the premise of the paper as outlined in the Introduction:

In 1969 a carbonaceous chondritic meteorite landed in Murchison Australia carrying many organic compounds. These compounds were apparently able to survive the frictional heating as the meteorite passed through our atmosphere since they were initially at ca. 10K, and chondritic meteorites are pieces of rock, with low thermal conductivity, from the asteroid belts that surround the sun. When the meteorite was split open the interior was still cold enough to freeze water.

Among the compounds identified were the amino acids alanine, valine, aspartic acid, glutamic acid, proline, and leucine, which were racemic, with equal mixtures of the L and D forms, along with achiral glycine. However, five amino acids were found that had methyl groups instead of hydrogens on their alpha positions (Figure 1), and these had a range of small excesses of the enantiomers originally described as the L amino acids (in modern terminology they are the S enantiomers). Since that time, these and other α‐methyl amino acids with small excesses of the S enantiomer have been found in the Murchison, Murray, and Orgueil meteorites (ref 1).

The whole point of why the Murchison meteorite is so interesting is that while the “natural” amino acids in it were initially thought to be racemic, subsequent analyses revealed them to have enantiomeric excesses.  I could be missing more recent analyses, but I don’t think so. Breslow should check out these seminal papers (1 2) and revise his background before the paper is “truly” published in JACS.

It is things like the odd ChemDraw structures and completely wrong information in the background that make me question the quality of peer review in JACS (and in all of chemistry, for that matter). I think one should also question the fairness of the editors, for I cannot imagine that this paper would have made it anywhere near publication in JACS if the author were Assistant Professor Joe Schmoe from Sunny Valley Technical College. But that said, the editors of JACS are the sole arbiters of what is “worthy” of publication in JACS, so I’ll just accept it and move on.

Normally, I wouldn’t blog about an otherwise run-of-the-mill paper about the origin of life, but this paper has really taken off in the world of popular science thanks to what amounts to a poetic thought by Breslow used to close the paper:

An implication from this work is that elsewhere in the universe there could be life forms based on D amino acids and L sugars, depending on the chirality of circular polarized light in that sector of the universe or whatever other process operated to favor the L α‐methyl amino acids in the meteorites that have landed on Earth. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.

Since you are a reader of blogs, you will recognize this paragraph for what it is: a silly piece of fluff meant to close an otherwise esoteric piece on a humorous note. I’ve got no problem with that. We can argue over whether the joke is funny, but the attempt at humor is obvious…

…except to the staff in the ACS Pressroom, for they issued the following press release to promote the paper. I am copying it here verbatim because these things are intended for distribution—and because it is ridiculous.

Could “advanced” dinosaurs rule other planets?

Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth
Journal of the American Chemical Society

New scientific research raises the possibility that advanced versions of T. rex and other dinosaurs — monstrous creatures with the intelligence and cunning of humans — may be the life forms that evolved on other planets in the universe. “We would be better off not meeting them,” concludes the study, which appears in the Journal of the American Chemical Society.

In the report, noted scientist Ronald Breslow, Ph.D., discusses the century-old mystery of why the building blocks of terrestrial amino acids (which make up proteins), sugars, and the genetic materials DNA and RNA exist mainly in one orientation or shape. There are two possible orientations, left and right, which mirror each other in the same way as hands. This is known as “chirality.” In order for life to arise, proteins, for instance, must contain only one chiral form of amino acids, left or right. With the exception of a few bacteria, amino acids in all life on Earth have the left-handed orientation. Most sugars have a right-handed orientation. How did that so-called homochirality, the predominance of one chiral form, happen?

Breslow describes evidence supporting the idea that the unusual amino acids carried to a lifeless Earth by meteorites about 4 billion years ago set the pattern for normal amino acids with the L-geometry, the kind in terrestial proteins, and how those could lead to D-sugars of the kind in DNA.

“Of course,” Breslow says, “showing that it could have happened this way is not the same as showing that it did.” He adds: “An implication from this work is that elsewhere in the universe there could be life forms based on D-amino acids and L-sugars. Such life forms could well be advanced versions of dinosaurs, if mammals did not have the good fortune to have the dinosaurs wiped out by an asteroidal collision, as on Earth. We would be better off not meeting them.”

What. The. Hell. Some booger-eating PR guy on 16th Street jumped to the end of the manuscript and took Breslow’s joke at face value. Then, his/her editor never thought to question the idea, and sent the press release out in the weekly PressPac. Now, the ACS is the laughing stock of the world of scientific publishing and popular science writing.

I guess we’ve learned nothing from the NASA/Wolfe-Simon/Arsenic Life episode. Why the hell do these things always seem to happen to origin-of-life chemistry?


See also:

Just Like Cooking
David Bradley’s Sciencebase
The Awl

Estructuras de QuímDibujar

Sunday, April 1st, 2012

Una cuestión muy importante cuando usted está enseñando a la química orgánica es la manera de dibujar estructuras químicas correctamente. Es muy fácil. Todo lo que tienes que hacer es tomar la estructura ChemDraw y añade un montón de acentos al azar. Por ejemplo:

Siguiente lección: cómo traducir recetas sintéticas

Armpitin – “A Peerless Contraceptive”

Wednesday, March 21st, 2012

This article from 1965 might be the first example of the publication of a purely farcical chemistry paper in a respectable journal. This article also appears to have completely eluded the attention of blogs, most likely because bloggers were especially lazy in the 60s. The unmistakable quality of the paper is certified by a consequent letter to the editor, in which a concerned member of the Canadian Medical Association wrote:

I was appalled to read J.S. Greenstein’s Very Original Article on “Armpitin”…I am very sorry to observe that the official journal of Canadian doctors has published this article.

The paper describes the development of armpitin as a powerful contraceptive agent. While the author provides a structure for a portion of the molecule, he refuses to provide the full details of its synthesis because he “intends to make a fortune.”

The results seem unsurprising. I would wager that a majority of us have collected anecdotal evidence that a repetitive string of NOs can be very effective at preventing pregnancy. The author reports he serendipitously stumbled into the field of contraceptives while designing deodorants. One deodorant led to a noticeable increase in libido without concomitant increase in pregnancy. His initial studies proceeded from there:

With typical male self-assurance, we undertook to examine the females for the causative factors leading to their infertility. We employed every known gross anatomical, histological, histochemical, biochemical, endocrinological, physiological and psychological test of reproductive capacity and could find no evidence of malfunctioning of the female reproductive systems and accessory structures. We could only conclude, reluctantly, after months of exhaustive investigation, that the females were normal in all respects, and that we should turn our attention to the males.

When we took the trouble to examine the ejaculates obtained by masturbation, artificial vagina, or by post-coital recovery from the site of deposition, the answer to the enigma stared back at us through the narrow barrel of the microscope tube: THERE WERE NO SPERMATOZOA IN ANY OF THE SEMEN SAMPLES.

Yeah, this paper was actually published in a respectable journal—and in 1965, when by all accounts, people were humorless. (There is simply no other rational explanation for the popularity of Jerry Lewis.) What shocks me more than anything is that the content of the paper is 98% pseudo-legitimate technobabble and only 2% punchlines, yet the editor allows the damn thing to go on for 5 pages. That said, the list of references is particularly amusing. The author acknowledges “A. Gabriel” for divine inspiration in the form of a personal communication, and also cites a paper on orgasm by C. Men as well as a child’s guide to erotica by M. Goose.

While I regularly advocate that Carl Djerassi should be recognized by the Nobel Committee, I don’t think that Dr. Greenstein’s seminal contribution rises to the same level.