Archive for the ‘Hall of Shame’ Category

Sulfuric Acid on Sugar Demo

Thursday, July 5th, 2012

One of my favorite chemistry demonstrations is the addition of concentrated sulfuric acid to sugar, but who in his right mind would handle concentrated sulfuric acid without gloves?

Um, this guy:

No one appeared to get hurt, but I would not endorse the chap’s claim that “if this will get on your hands, you have about [a minute and 10 seconds] until it takes to really react to wash it off”.

B.S.

Stay safe, kids.

 

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
Chemistry-Blog
Pharyngula
David Bradley’s Sciencebase
The Awl

WWWTP? – HF Stupidity on House, M.D.

Tuesday, February 14th, 2012

A concerned labmate brought my attention to a chemical abomination on last week’s episode of the increasingly unpopular television show House, M.D.

Thanks to a very special friend of mine, we can all enjoy video footage of what Hollywood writers believe constitutes a realistic demonstration for a high school chemistry class:

 

Marvelous, isn’t it? Notice how the teacher isn’t wearing a single piece of personal protective equipment—no gloves, no goggles, no lab coat—whilst working in front of a poster that reads “LAB SAFETY RULES”.

Who knows what this demonstration was supposed to be, but the last time I checked, HF wasn’t combustible. In fact, its NFPA 704 flammability rating is zero. Oh well, I doubt the flame coming out of the Bunsen burner is real anyway, seeing as how the dude just picked up the metal with his bare hands. The limp gas line and the fact that the blue flame doesn’t deflect upward when it is tilted are also nice pieces of laziness on the part of the production staff.

If you plan to replicate this experiment at home, I suggest that you work with hydrofluoric acid in plastic containers instead of glass ones. HF is a great etchant for glass and many other materials that contain silicon. Furthermore, if you have an accident and get HF on your skin or in your lungs, you are going to be in a world of hurt. That stuff is nasty and goes right for the calcium in your body. In the event of an accident, you should apply calcium gluconate gel to the affected areas of your skin and seek medical attention immediately. Preferably, not from Dr. Gregory House.

Mailbag: How Not to Clean a Rusty Trunk

Tuesday, June 14th, 2011

Larry the Crystal Guy e-mailed me the following discussion from a science forum.  It’s ancient, but interesting.  The exchange begins with an inquiry from a citizen with a rust problem.  I’ve reproduced the authors’ typos and larger morsels of stupidity unedited…

I have recently acquired a large trunk for sotring things in, however the metal on the edges and corners has gone very rusty, through being sat in a cupboard for a long time.  Anyone have any ideas, or know any good ways for how I can get rid of it?  Cheers!
 
After one board member suggested using vinegar and a second—predictably—told the original poster to search Google, in stepped user lightarrow, a “Hero Member” of the forum:
 
The best chemical I know to dissolve rust is hydrofluoric acid HF. Here in italy is sold in dilute acqueous solution (~10%) to use with textiles. On the other hand, it’s better not to use more concentrated solutions or there is the risk to attack the metal too.  If you want to use it with a piece of metal, you should find a way to make the solution in a gel or sirup form, otherwise the solution slips away and/or dries too quickly. Once, I dissolved a large amount of sugar to that solution for this purpose (but there will surely be better ways than this one); of course the reactivity is lower.
 
Yes, please, don’t use anything more concentrated because it might damage the metal.  And just ignore the mild burning sensation—that just means it’s working.  Ugh.  The next day and several posts later, daveshorts (another “Hero Member”) weighed in with safety concerns:
 
Don’t go anywhere near HF, working in a materials lab for 5 years, this was the only chemical people were actually scared of – a suggested damage limitation measure invovles an axe! If you get it on your skin it will get rapidly into your flesh and then proceed to break down your bones…
 
Affronted, lightarrow defended his advice:
 
I wrote: “dilute acqueous solution (~10%)”. It’s sold in most supermarkets!  I have tried oxalic acid, phosphoric acid and acetic acid (the active chemical in vinegar) and only HF works, unless the rust is thin or in a “good” composition/physical structure. Infact, rust is not a specific compound, it can vary from Fe(OH)3 to FeOOH to Fe2O3..ecc. The first form, Fe(OH)3, is the easiest to remove chemically. But try to dissolve Fe2O3 with vinegar or oxalic acid.   (I have tried).
 
I’ve been to a supermarket in Italy, but I don’t recall seeing 10% HF.  Maybe I missed it behind the gnocchi?
 
Seriously, kiddies…don’t try this at home.  Hydrofluoric acid can do bad, bad things to you (warning: gross).  I would not characterize 10% HF as “dilute”, either.

How Not to Organize a Journal

Saturday, September 4th, 2010

ACS Publications…you are killing me.

The Journal of Physical Chemistry Letters has a very…ummm…original way of organizing its content online.  If you select an issue from the archive, the papers are sorted by subject rather than by page number.  So, scrolling down the contents for April 2010 (vol. 1, pages 1020-1169), you sequentially encounter articles from pages 1288, 1020, 1160, 1107, and 1068.  Huh?

I imagine most people access back issues of a journal in order to find a particular paper—as I did—and not to browse for pleasure.  This predominance can only grow wider as the archive grows older.  What is the purpose of making it hard for people to find a paper by its page number?

And if you’re going to do it this way, why even bother numbering the pages at all?  I haven’t seen the hard copies of this journal, are its pages also not sequential?  That would be interesting.

Or maybe this is how the next generation does things and I’m just getting old.

Bah.

“What’s Wrong with this Picture?” — The Return

Friday, October 5th, 2007

Hello friends.  Remember me?  It’s your ol’ buddy, Paul Bracher.

You’re probably asking yourself, “What brings this guy back from the dead?”  Well, when a postdoc in our lab showed me what arrived in the mail, not only did I roll over in my grave, I decided to resurrect everybody’s favorite chemistry game: “What’s Wrong with this Picture?”

The following 52-page brochure arrived courtesy of Oxford University Press with the following cover.  That’s right…COVER:

 

oxford_univ_press_cover_big

 

Oh. My. God.  The real question is: What’s right with this picture?  Not much.  There are messed up bond angles, aryl Texas carbons, acyl Texas carbons, Rhode-Island carbons, bizzare peroxides, Texas oxygens, Texas nitrogens, and the list goes on.

What the hell is wrong with these people and why the hell is the ACS logo on this piece of garbage?  The O.U.P. editors should be drawn and quartered, and their heads should be displayed on pikes outside of ACS headquarters in Washington.

As if the front cover didn’t offer enough entertainment, the back cover has the following unintentionally humorous statement:

xford (sic) University Press, Inc. publishes works that further Oxford University’s objective of excellence in research, scholarship, and education.

Hooray for excellence.  Anyway, this weekend I’ll probably post on the upcoming Nobel Prize announcement (Oct. 10th).  After that, I might go back into hibernation.  We’ll see.

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