Archive for March, 2007

Scientists have been pretty good about developing standards to ease communication across scientific disciplines, but we have yet to decide on a standard protocol for determining the order of authors on papers. Since papers are widely regarded as the principal metric of scholarly achievement, maybe it’s time we did.

If you asked anyone what position they’d want in an author list, the general consensus would be first. Knowing nothing else about a paper, most of us would assume that the first author made the most important contributions. In the majority of chemistry labs, the first position is usually granted to the researcher who took primary responsibility for conducting experiments, writing the paper, and shepherding the project to completion. The remaining junior authors are usually listed in descending order of perceived scientific contribution, until you get to the principal investigator, who almost always goes last (1 2 3).

But making the above assumption can lead you astray, as that’s not the way all chemists do it.  Although it has become decreasingly common for the principal investigator to take first authorship (1 2 3), some young professors are continuing this trend.  It seems to be more common in organic synthesis than in other areas.  My understanding of this practice was that it simplified finding papers out of a particular research lab back when papers were sorted alphabetically in literature indexes.  While the advent of computerized literature searches has rendered this advantage obsolete, the practice of some PIs “going first” persists.  Perhaps it is simply a matter of tradition, or maybe a means of senior authors “protecting their brand,” since long author lists are usually shortened to “First Author, et al.”

What do other types of scientists do?  Astrophysicists list authors in descending order of contribution (1 2), which means that the advisor is usually the second author listed.  While this system seems the most fair to me, I can see how some bosses might lament the prospect of getting lost in long author lists.  When I’m scanning through ASAP alerts, after the title, I usually glance quickly at the end of the author list to see where the paper came from.  In this respect, the PI going first or last is rather convenient.  An astrophysics professor I talked to here said that he usually assumes that the last author on a paper was the guy who drove the rest of the team to the telescope.

While the practice of listing authors in alphabetical order is exceedingly rare in chemistry, it turns out to be standard protocol in the economics community (1 2 3). Does anyone else find it disturbing that, when left to their own devices, economists will revert to academic communism? Isn’t there something to be said for providing incentives for hard work?  Oh well.

Aside from author order, there is also the wacky issue of joint authorship. Sometimes author order assignments are so troublesome that people choose to indicate joint first-authorship. While it is occasionally seen in Angewandte Chemie, it has actually been banned from JACS:

JACS does not permit equal or partial authorship designations. JACS assumes that all authors have made substantial contributions to the work.

I’ve got no problem with having these notices of equal contribution; I’m not sure why JACS does.  The issue of joint authorship is so important to some authors that they actually published addition/correction notices to set the record straight (1 2).

Finally, I’d be remiss if I didn’t link to Jorge Cham’s Ph.D. comic strip that illustrates what the order of authors really means.  There’s more than a bit of truth in it.

So…what style do I advocate? First, any of the above styles is acceptable.  It’s a personal decision that is determined at the sole discretion of the PI.  So long as the community knows how each PI operates, there won’t be any problems.  That said, I like the PI-last format—with a twist.  With the PI-last ordering, the people in the trenches have added incentive to get papers out and the PI gets to stand out too. My twist is that I think the first pages of supporting information for any paper should contain a short summary of each author’s contributions. This way, anyone who wants to know who did what can find out.  The added detail would be a double-edged sword, because with each credited contribution comes the added burden of being responsible for the integrity of the data.  Assigning responsibility in this manner would make it harder for fraudsters and sloppy researchers to hide behind their colleagues.  Furthermore, I think this list should be followed by a signed statement from each author asserting that, to the best of his or her knowledge, the results are authentic, are accurate, and were obtained in an academically honest manner.  It would be naive to think that this simple change would solve all of our community’s problems, from inflated yields to outright fabrication, but it might make some people think twice about going down those roads.

The ACS Spring National Meeting is here, and the chemical blogosphere seems to have it well covered:

• C&EN Chicago Blog
• Sceptical Chymist
• Nature News
• ChemistryWorld Blog
• Chem-bla-ics
• The Chem Blog

I’m expecting full-scale coverage of everything-GMW, as the Big Guy is in Chicago to collect the Priestley Medal.  I hope some of you will make it to his autograph session, sponsored by ACS Pubs, on Tuesday from 12:30-2 pm.  He’ll be signing copies of the March 26th issue of C&EN, although I’d also imagine he’d be amenable to signing meeting programs, lab notebooks, or packages of Nutter Butters (seriously, the man lives on these things).  You’ll never know if you don’t ask, and more importantly, we’ll never know if you don’t show up and blog about it.

Have fun.

Whether you like it or not, one of the principal reasons the government supports scientific research is to strengthen our ability to wage war. Scientific discoveries often open avenues for new and improved weapons, and making sure that our military technology is the most advanced in the world is vital to our national security. While military power alone is not a sufficient condition for maintaining our superpower status, it is a necessary condition. Part of our job as scientists is to use our knowledge to ensure that the “good guys” have the most advanced technology in the world when it comes to efficiently killing humans. Yes, this thought is a little revolting, but having scientists collaborate with the military is one of the best ways to ensure the protection of our political and social ideals.

The announcement that the US will begin developing a new model of nuclear warhead seemed to completely bypass the major news outlets. At least, no one made a fuss about it. I don’t know how much of an improvement the new design is over the old one, but it seems that the change is oriented more toward safer handling than greater yields.  That said, I wouldn’t be surprised if there’s more to the story.  I don’t expect the Army to go around advertising what exactly they’re hoping to accomplish. Congress needs to know, but that can be done behind closed doors. Suffice it to say, if the leap is significant, I think that the money used to fund the project would be money well spent. It will be interesting to see what Congress has to say when hearings open this month.

I’ve always wondered where the US stands in terms of the active development of chemical weapons. I know the Army has publicized the fact that it’s trying to destroy large portions of its stockpile, but it probably doesn’t want anyone to know whether it’s researching ways to create more potent chemical weapons.  Whether for tactical or strategic purposes, I simply presume that in some secret lab, the government continues to sponsor research on lethal chemistry.

And that’s a good thing. Do you think the bad guys wouldn’t use a powerful chemical weapon if they had access to it? No way. In both times of war and of peace, we should constantly challenge ourselves to develop new and improved chemical and biological weapons so that: 1) they are available if we need them and 2) we can develop effective counterweapons in case the enemy makes them first. Saying that the development of weapons of mass destruction is wrong and pursuing a strategy of self-imposed ignorance will solve nothing. We can’t afford to let our enemies seize the initiative on any of these fronts.

If you don’t want to participate, that’s understandable—I personally wouldn’t like testing compounds on mice all day—but be glad (as I am) that there are people who have decided to work in these areas.

This graphic was made in very bad taste.  I’ve posted it here as an example of the kind of poor attempts at humor that will not be condoned on ChemBark.  If you have examples of similarly poor attempts at humor regarding chemistry or life in graduate school, please make me aware of them so I may post them as a public service. Thank you.

• Remember that rhodamine spill in our lab? The bill for the clean up came to a whopping $2436.
  .
• Question for the synthetic chemists: if you measure a yield of 98.5%, do you report it as 98% or 99% in the substrate table? And by “do you” I don’t mean “does one”, I mean “do you” .
  .
• I like it when C&EN plays around with its cover.  The March 12th cover is particularly cool, because the change is so subtle you probably missed it. If you look closely, the title lettering is transparent, so the red you’re seeing is from the Chinese flag. I think the only other time they’ve strayed from their new redesign was with the cerulean 2006 Pharma Review cover.
  .
• Finally, can you think of any chemical feuds other than those listed below? The first group contains “academic” debates, while the second group contains “ethical” disputes. The names below sometimes just refer to the “face” associated with each side; they aren’t all one-on-one conflicts.

………………Nonclassical Carbocations (Brown vs. Winstein)
………………Nanotechnology (Whitesides vs. Drexler)
………………Origin of Life (Miller vs. Wächtershäuser)

………………Woodward-Hoffmann Rules^* (Corey vs. Woodward)
………………Nonlinear Effects in Asymmetric Catalysis (Córdova vs. Blackmond)

* Note the error in the caption to the first photo.

A few people have already mentioned that they plan to be in Boston this August for the ACS National Meeting.

Question 1: Are you going?

Question 2: Would you be interested in attending a BBQ at ChemBark Corporate Headquarters? It’s a five minute walk from the Harvard T (Boston’s version of the subway/Metro/Tube/El/BART/MARTA).

Other options would also work, like going to happy hour at a downtown bar, putting together a team for a pub quiz, or staying up for an all-night game of poker. I suppose we could even develop a creepy scavenger hunt where you have to trek around Boston restaurants taking digital pictures of famous chemists eating dinner. There’d be a point system: Nobel Laureates = 10, Priestley Medalists = 7, tenured professors at top 10 schools = 3, etc.

Post your thoughts in the comments. You needn’t use your real name…yet. Depending on what goes down, some form of RSVP might be in order. We don’t want a disgruntled copy editor from ACS Pubs to come heavy and spray the place with bullets. Also, I’d prefer that the Czech mafia not use this event as an opportunity to whack me.

And whatever you do, don’t start dropping hints that you need a place to stay; I’m very particular about the people I allow to sleepover at the Dawghouse.

The finals of the Intel Science Talent Search ended last night in Washington, DC. Old fogies like me know the contest as the Westinghouse, a competition open to high school seniors who have completed scientific research projects. The girl who won top honors this year built an instrument for collecting Raman spectra, in her home, for $300. Now, if she would just go ahead and make a 400 MHz NMR spectrometer for ChemBark Labs, I’ve got a check for $400 with her name on it.

The Westinghouse/Intel competition has been running since 1942, and you might recognize some of the people who’ve reached the finals:

Andrew Streitwieser (STS ‘45)
Martin Karplus (STS ‘47)
Ronald Breslow (STS ‘48)
Walter Gilbert (STS ‘49)
Roald Hoffmann (STS ‘55)
Eric Lander (STS ‘74)
David Liu (STS ‘90)
Paul Bracher (STS ‘98)

Those are some pretty big names in chemistry. Andy Streitwieser’s story is particularly remarkable. It’s been about six years since I’ve read his autobiography, so I might have a couple of the details wrong, but it goes something like this:

Streitweiser and his friends loved chemistry so much that they built a rudimentary lab in his basement. While thumbing through the literature, he came across a JACS paper that described the reaction of fluorene with sulfuryl chloride but didn’t report the position at which the molecule was chlorinated. Streitweiser repeated the preparation and found that the melting point of his product matched that of 2-chlorofluorene, which had been reported previously. Maybe it doesn’t sound like such a big deal now, but it was 1944, he was in high school, and he was working in a lab that he built himself. You gotta love it.

Streitwieser wrote up his results, and at the tender age of 17, he published a communication/note in JACS. The institutional address printed in the journal was his home address in Queens. The only time I’ve seen something even close to as cool as that is when Gunter Wachtershauser listed his Yahoo! e-mail address on a paper in Science. L0Lzzz!!111!1!

Streitwieser would grow up to become a true hero in the field of physical organic chemistry, spending over 50 years on the faculty at Berkeley. He kept (keeps?) an entire print collection of JACS in his office, and before the advent of pubs.acs.org, it was not uncommon for students to stop by when the library was missing issues they needed. Even when Streitwieser was in his office, his secretary would tell the students to just go in and grab whatever they needed. Streitwieser, renowned for his intense concentration, would sit there like a statue despite being in the presence of someone rummaging through his book shelves. Weird.

Anyway, if you read through that paper from 1944, you will notice a familiar name in the acknowledgments: Ed Kosower. A classmate of Streitwieser’s at Stuyvesant, Kosower also grew up to become a fantastic chemist. They even co-authored a sophomore organic textbook together (with Clayton Heathcock). The book is superb, but it’s unfortunately out-of-print. I heard that the reason the fourth edition is the last is that the authors refused to acquiesce in the publisher’s wish to add color graphics. You’ve got to give those guys credit for not selling out the Old School.

Some commenters in a previous thread took umbrage at the fact that I admit to judging people by their grammar. Well, I do, and I’m not going to change anytime soon. I’ll put poor grammar on par with poor hygiene, dressing like a slob, and bad table manners—while they don’t automatically invalidate a person’s ideas, they will cause me to treat anything the person says with more skepticism than usual. With respect to the four errors I found in the first paragraph of this recent paper from Org. Lett., the misplaced apostrophe in “Evan’s” was the most aggravating. While the chemistry in the paper was good, as The Chem Blog has noted, the authors’ lack of attention to detail was borderline disrespectful. I expected more from one of the most storied labs in synthetic organic chemistry.

A lot of people will complain, “So what if I make a few mistakes? Why don’t you focus on the ideas?” That’s the thing: I want to focus on your ideas, so why don’t you stop whining and learn to write properly? The rules of grammar are not up for discussion—just follow them out of courtesy to your readers. Grammatical errors are distracting and will cause them to lose sight of what you’re writing. If you are someone who has no trouble reading documents riddled with mistakes, that’s great, but when you are writing, you aren’t writing for yourself.

While grammar shouldn’t be the sole criterion for evaluating intelligence, I will admit to judging some things by a relatively obscure set of criteria. For instance, I have a list of favorite subjects for judging textbooks and course packets. One of the first things I do to determine the quality of a sophomore organic textbook is to look in the index for phenol. As you all know, phenol is more acidic than “standard” aliphatic alcohols. If you took a survey, most people would ascribe this fact to a resonance effect by drawing the following structures:

There are a number of variations on this theme, including drawing out all of the unhybridized p orbitals and showing that an orbital on oxygen containing a lone pair can overlap with the pi system, thereby allowing for increased delocalization of the extra negative charge density.

It turns out that an inductive effect—not a resonance effect—is the predominant reason for the increased acidity of phenol relative to aliphatic alcohols. Whereas aliphatic alcohols have a C(sp³)—O bond, the carbon to which the hydroxyl group is bonded in phenol is sp² hybridized. The increased s-character of the carbon orbital used to form the C—O bond makes it more electron withdrawing, which leads to greater stabilization of the conjugate base of the alcohol. For the purpose of comparison, look at the pK_a of phenol compared to that of enol tautomer of acetone:

Even though you can only draw two resonance forms showing delocalization of the extra negative charge in the conjugate base of the enol (vs. four for phenol), the acidities of the two protons differ by less than an order of magnitude. For those interested, these data come from Evans’ Chem 206 lecture notes (Lecture 20, restricted access), where the point is hammered home in glorious detail. Professor Evans’ PowerPoint slides should be framed and displayed in the Smithsonian.

While we’re discussing phenol and errors, let me also use this example to illustrate one of the main problems with Wikipedia. Wikipedia is great, but it is home to a number of edit-happy users who think they know more than they actually do. If you look at the discussion page for phenol, someone actually addressed the resonance vs. inductive effect argument, but was unceremoniously (mis)corrected by another user, who references an incorrect explanation on the Internet. Thus, the main article (as of today) gives the incorrect (resonance > inductive) explanation:

Phenol has a limited solubility in water (8.3 g/100 ml). It is slightly acidic: the phenol molecule has weak tendencies to lose the H⁺ ion from the hydroxyl group, resulting in the highly water-soluble phenoxide anion C₆H₅O⁻. Compared to aliphatic alcohols, phenol shows much higher acidity; it even reacts with NaOH to lose H⁺ whereas aliphatic alcohols do not. This is due to orbital overlap between the oxygen’s lone pairs and the aromatic system, which delocalizes the negative charge throughout the ring and stabilizes the anion. This effect is attenuated, however, due to oxygen’s relatively high electronegativity. ^[1]

God knows that we in the chemical blogosphere love the Wikipedia, but read it with skepticism.

This concludes today’s lesson. Your homework for the weekend is to find all of the grammatical errors in this post. For extra credit, find an error in a chemistry article on Wikipedia, fix it, and brag about having done so in the comments. Class dismissed.