Archive for the ‘Scientific Writing’ Category

A Disturbing Note in a Recent SI File

Tuesday, August 6th, 2013

ChemBark InvestigatesA recently published ASAP article in the journal Organometallics is sure to raise some eyebrows in the chemical community. While the paper itself is a straightforward study of palladium and platinum bis-sulfoxide complexes, page 12 of the corresponding Supporting Information file contains what appears to be an editorial note that was inadvertently left in the published document:

Emma, please insert NMR data here! where are they? and for this compound, just make up an elemental analysis…

This statement goes beyond a simple embarrassing failure to properly edit the manuscript, as it appears the first author is being instructed to fabricate data. Elemental analyses would be very easy to fabricate, and long-time readers of this blog will recall how fake elemental analyses were pivotal to Bengu Sezen’s campaign of fraud in the work she published from 2002 to 2005 out of Dalibor Sames’ lab at Columbia.

The compound labeled 14 (an acac complex) in the main paper does not appear to correspond to compound 14 in the SI. In fact, the bridged-dichloride compound appears to be listed an as unlabeled intermediate in Scheme 5, which should raise more eyebrows. Did the authors unlist the compound in order to avoid having to provide robust characterization for it?

ChemBark is contacting the corresponding author for comment, and his response will be posted in full when we receive it.

This story points to very real concerns that young researchers can be instructed and pressured to fabricate data. Would a scientist be so concerned that a journal would reject his manuscript over a piece of missing characterization data that he’d feel pressure to make something up?

Expect more as this story develops…

PowerPoint Peeves and Chemistry Arrows

Thursday, May 23rd, 2013

ChemBark’s ongoing series on PowerPoint advice continues with a look at another one of my irrational pet peeves: the “fat” reaction arrow.

If you are writing reactions in a text box, chances are you’ll use the “rightwards arrow”, Unicode character 2192 (hex). You will probably also choose a font without serifs, because slide text (including atomic symbols) looks better without serifs. Unfortunately, this is how the rightwards arrow is rendered in many sans-serifs fonts:

fat_arrow

I know this is a matter of personal taste, but there is something about that reaction arrow that turns me off. It’s too fat. The same character in Times New Roman looks much better. She has a graceful elegance relative to her Calibri cousin. Consequently, if you want to stick to Unicode characters for writing out reactions, I advocate writing everything in a sans-serif font, then changing the arrow to Times New Roman. You many also need to adjust its font size to make it look right:

fat_arrow_fix

And while we’re on the subject of arrows, there is no need to use the double-headed arrow symbol U+2194 (↔) to indicate an equilibrium. Remember, the double-headed arrow typically separates resonance structures. Instead, use U+21c4 (⇄) or U+21cc (⇌). These characters don’t always appear on the maps in Office, but you can copy and paste the symbols into your text. A full listing of arrow characters is here.

The F Word

Tuesday, July 24th, 2012

You may have noticed that I don’t typically use profanity on this site. It’s not that I have anything against swear words—there is plenty of profanity in the comments here—I just don’t think you get enough bang for the buck with them in long pieces of prose. Written down, I find swear words are usually more distracting than effective at communicating ideas. In contrast, I find profanity to be much more useful in conversation, where you can shape the meaning of words phonetically.

So…what the hell I am babbling about? Well, it turns out that I have the dubious distinction of being the first person to use the “F-word” within the pages of Nature Chemistry. N-Chem has been playing down a man following Neil Withers’ move to Chemistry World, so Stu Cantrill has asked a few bloggers to help out with the monthly Blogroll column. Chemjobber wrote it last month, and I had the honor of writing it for the August 2012 issue. My contribution went live this morning.

Given that my use of profanity in a prestigious chemistry journal could raise some eyebrows, I wanted to take a couple of minutes to defend it. By “it”, I mean this:

Dr Rubidium, an analytical chemist who blogs at the Journal of Are You Fucking Kidding, contrasted several cases of homicide by the paralytic agent succinylcholine with its medical use in life-saving tracheal intubations (http://go.nature.com/bFQFv6). Although that post was shockingly free of swear words, an ode to tetracyanoethylene (TCNE) on Carbon-Based Curiosities was as vulgar as it was informative (http://go.nature.com/AmOzuB).

As I understand it, the purpose of the Blogroll column is to promote interesting items and discussion on chemistry blogs to a wider audience (e.g., to stodgy old-timers who believe the Internet is full of garbage). Usually, the column covers any major subjects from the previous month and is then rounded out with one or two smaller items. My first draft for the column was due June 20th, and the major event that stuck out from the month previous was the splendid Favorite Toxic Chemicals carnival hosted by ScienceGeist.

I read through all of the contributions to the carnival, and the one that stuck out as the best was this one on succinylcholine. Naturally, I wanted to make this the example post of the column, but the name of its parent blog is the Journal of Are You Fucking Kidding. The traditional citation given to posts featured in the Blogroll column is (name of blogger) at (name of blog), so if I were to use it, Nature Chem was going to have to publish “Fucking”, censor the name of the blog, or change the typical citation format.

The more I thought about it, the more strongly I felt Dr. Rubidium’s post deserved to be the #1 representative of the carnival; it really is an interesting, well-written piece. My only question, at that point, was how to deal with the swear word. The three options, as I saw them, were to call the blog:

(1) the Journal of Are You Fucking Kidding

(2) the Journal of Are You F-cking Kidding

(3) JAYFK

I ended up leaning towards option 1, because it was the proper, full name of the blog. You can’t replace a word in a proper name with a synonym or scrubbed letters without taking something away from the name. “F-cking” is different from “Fucking”. Since Dr. Rubidium often abbreviates her blog’s name as JAYFK, I thought option 3 was also fine, but less clear.

At this point, I e-mailed Stu (the editor) a couple of days before my draft was due and asked permission to use the F word. The ruling was not immediate; Stu conferred with the rest of the editorial team, and the decision was made that “Fucking”, in this context, was fine. One good point that was raised in their discussion was that some unsuspecting readers might be more offended by clicking a link to “JAYFK” rather than just seeing the F word in the text of the journal.

While I think the proper name argument alone is strong enough to win, I would also raise the point that this variation of the F word is among the most benign. Dr. Rubidium uses it as an adverb to modify “kidding”. To me, this embodiment should count as less offensive than its use as a gerund.

Once the succinylcholine post was chosen as the centerpiece, I decided to highlight Excimer’s tetracyanoethylene post, because in addition to its being informative and entertaining, I could juxtapose this truly vulgar piece against the JAYFK post. And while there were a number of other really nice posts that could have been mentioned, the whole column is only 300 words, so I had to be picky. Sorry. For the closing part of the column, I thought that the traditional old fogeys who only read journals and never read blogs might have their interest piqued by the latest round of discussion of the death of organic synthesis. That’s always a topic that gets people going.

Anyway, that’s the behind-the-scenes tour for this month’s (possibly offensive) Blogroll column. At the end of the day, will people care about one swear word in a chemistry journal?

If so, they can f— off.

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

A Tale of Two Textbooks, Then & Now — RVW #2

Wednesday, June 6th, 2007

In the second part of his series, Retread lays out his first impressions of Jones vis-à-vis his previous orgo text in grad school, English & Cassidy.

The book for my first Organic Chemistry course (’58 – ‘59) was English and Cassidy, 2nd edition, ‘56.  Jones is the 2004 edition.

………………………………………English & Cassidy            Jones

Pages (text only)                442                          1323
Page size  (inches)            9 x 6                         10 x 8
Text width                          4.5                           5.25
Text height                         7.0                           8.50

The most striking difference is the graphics.  There were only six 3-dimensional representations in the first 100 pages of Cassidy, while Jones has TNTC (too numerous to count).  It is hard to find a page in Jones without one.

The tone is completely different.  Jones is chatty and conversational.  “Remarks for the Student” in E&C begins as follows:   ”It is usually taken for granted that the student who  takes up the study of organic chemistry has a thorough knowledge of first-year college chemistry.”  Not too warm and fuzzy.

One of the very best things about Jones, is that he tells you what is hard, and what you must learn. “The (R, S) convention looks a bit complicated.  It is easier than it appears right now, but it just must be learned and cannot be reasoned out.”   Repeat this advice 50,000 times and you’re through med school.  There is no reason the appendix is on the right, the heart is on the left, speech is usually in the left hemisphere  etc. etc.  Jones also tells you what looks  hard but really isn’t — drawing cyclohexane in the chair form for instance.

Another very good thing about Jones (which may seem rather trivial) is that when he points you back, he gives you a page number to go to.  On retirement from medicine, I indulged a lifelong taste for math by auditing some math courses (number theory, abstract algebra,  algebraic geometry) at the local colleges.   Math books almost never repeat anything.  You are referred back to theorem 10.3 (and have to hunt for it).   There are hundreds of theorems, corollaries etc. in the average upper level math book.  It gets irritating unless you have a completely flawless memory.

Also, math books don’t usually tell you what’s really important, and what will be used later.  Not all results are equally crucial for the argument.  On reading it for the first time, you can’t tell the wheat from the chaff.  Jones is excellent at this.

In one sense, the two books can’t be compared, just as stereos back then and now can’t be.  I worked all summer as a supermarket checker at $1/hour before entering college in ‘56 and bought an RCA Victor record player to take with me for $140.  The richest man in the world back then could not buy sound of today’s quality no matter what he was prepared to spend.

However today’s convenience store worker would have to work considerably more hours to buy Jones (167.74) and the answer book (80.59) than I would have had to for English & Cassidy back then.  I asked the student checking me out how anyone could afford books like
these.  He said that often students bought a single textbook and shared it.  Shades of the 19th century Ghetto.  My grandfather told me how there were people who could only read Hebrew upside down, or at a 45 degree angle, because 4 – 6 students would sit around the  same table and study the same page at the same time.

One final point.  Despite the dryness, formality, lack of graphics etc. etc. not much harm was done.  I liked the book back then as did most of us.  This includes Jones himself (Yale ‘59), who almost certainly used the book, as English and Cassidy were Yale professors and the first edition came out in ‘49.

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Unsolicited Suggestions for C&EN

Wednesday, May 16th, 2007

As you know by now, I’m a C&E News superfan. In this week’s edition, editor-in-chief Rudy Baum discusses how he spices up the cover of our favorite chemistry magazine by insisting on variety.  That’s why I like it when he cuts the leash and lets the art editors (directors?) play with the covers. On May 7th, we saw the third (by my count) fancy cover since the 2006 redesign.  The blue and white title bar made a triumphant return, and the cover sported the most centrally-located address label that I can remember (yet required no ugly white box):

Now is probably as good a time as any to unload all of the comments and suggestions I’ve been saving for C&EN:

As much as I hate to say it, I’ve really liked the new “C&EN Photo Gallery” section.  I’m torn, because while I like nice pictures, I am also troubled by some PI’s insistance on finding a pretty picture FOR EVERYTHING. That said, there are times when the crux of an experiment can be explained by a nice picture. Also, some pictures bankrupt of scientific value still have artistic merit.

I think a regular reader/commenter on ChemBark took one of the pictures featured in this week’s gallery. I don’t want to out him/her, but would the mystery photographer enter and sign in, please?

I’d like to see more opinion in C&EN, especially the point-counterpoint pieces. There is a simple method for selecting good pairs of chemists to fight in print. First, the people have to be recognized experts on the subject in question.  You can’t pick a random idiot, but you also can’t pick a big name in a tangential field just because he’s a big name. Second, it’s best if the people you pick are jerks who don’t care about upsetting anyone. Don’t pick writers who mince words—diplomatic writing is less informative and less entertaining.  Give us a duel.  We want to know why someone is wrong, and we don’t want to sift through BS to find out.

My most radical suggestion: C&EN should sponsor a chemical song parody contest.  They could run a full-page call for submissions over several weeks, then post the best songs (top 50?) online and give prizes to the top 5.  I’m sure the contest would drive plenty of traffic to the online edition, and the feature would stand a good chance of getting picked up by Fark, Slashdot, and Boing-Boing.  If money is what motivates the powers that be, think about how this would increase site traffic, and consequently, ad revenue.

That’s it for now, but prepare for a big Big BIG BIG C&E News post on Friday.  Big.

BIG.

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