– I recently registered for the Spring ACS National Meeting in New Orleans.  My talk will probably be the worst disaster to hit the city since…uhhh…nevermind.  In all seriousness, I look forward to the four days of wall-to-wall chemistry, since I really didn’t get the chance to consume that much in Boston.  It will also be interesting to see what’s going on with the reconstruction efforts following Katrina.  I assume that all of the debaucherous elements of the city will have been restored by April.  Is anyone else going?

–  The Crimson got to this story about a month late.  Someone’s moving to MIT…or not (?)  I really don’t get why there is any confusion here; the people being quoted are seemingly the ones who should know exactly what’s going on.

–  Later this week, Prof. Dr. E.J. Corey will sell and sign copies of his newest book in Harvard’s historic chemistry library.  I wonder if he’ll take personal requests.  “Professor Corey, could you please make this one out to ‘the greatest chemist of all time’?  Thanks.”

–  Retread has passed along the next installment of his Rip Van Winkle series, and I shall post it in short order.

Thanks for reading,
Rudy Paul 

When Roger Kornberg won the Nobel last year for transcription crystallography, a stink erupted not over whether his work was worthy of recognition, but whether it was chemistry.  But that’s old news. The big story this week is this year’s Nobel, and I know that the person who still reads this blog daily despite the fact that it’s never updated is interested in hearing revised odds for tomorrow’s winner.

I’m kind of torn about my final pick. On one hand, I’m thinking about adopting the same approach I used pre-2005 when I guessed that metathesis would win every year. My new perennial guess would be GFP/fluorescent probes, because I’m still of the opinion that these guys absolutely deserve to win it. It’s less a question of “if” and more a question of “when”—GFP and similar probes are ubiquitous in research nowadays.

On the other hand, given the stink made in the media over biology getting shoe-horned into the chemistry prize last year, I think the Swedes might feel some pressure to pick a pure chemist this year (Palladium couplings, anyone?). As Excimer points out, the stars might be aligned for the more physical achievements this time around due to the composition of the Nobel committee. That, plus the fact that the last two prizes have been organic and biological, means that this year’s prize stands a good chance of having some element of physical flavor, which GFP has none of.

So, in a nutshell, just about anyone could win the Nobel this year. My pick is GFP, but I expect to be surprised.

Now, back to the odds. I’ve revised them a little bit from earlier this year, thanks to reader input and personal changes of heart. Remember that these numbers address the question of who will win the Prize, not who should win it. As always, feel free to share your criticism in the comments. Also, my judgment is very probably impaired due to the fact that I’ve been inhaling a large quantity of thiols over the past several months.  Forgive me.

The Field (everything not listed below), 3-1
Molecular Studies of Gene Recognition, Ptashne, 15-1
Nuclear Hormone Signaling, Chambon/Evans/Jensen, 15-1
Fluorescent Probes/GFP, Tsien/Prasher/Shimomura, 15-1
Modern Surface Chemistry, Somorjai/Ertl/Whitesides/Nuzzo/+/–, 15-1
Transition-Metal-Catalyzed Cross-Couplings, Suzuki/Heck/Sonogashira/Tsuji/+/–, 17-1
Instrumentation/Techniques in Genomics, Venter/+, 19-1
Biological Membrane Vesicles, Rothman/Schekman/+, 19-1
Techniques in DNA Synthesis, Caruthers/Hood/+, 19-1
Molecular Structure of the Ribosome, Steitz/Moore/Yonath/+/–, 29-1
Telomeres & Telomerases, Blackburn/Greider/Szostak, 29-1
Application of Lasers to the Study of Chemical Reactions, Zare, 39-1
Bioinorganic Chemistry, Lippard/Holm/Gray/+/–, 39-1
Mechanistic Enzymology, Walsh/Knowles/Abeles, 49-1
Combinatorial Chemistry/DOS, Schreiber/+, 49-1
Pigments of Life, Battersby/+, 49-1
Global Warming, Thatcher/Gore, 99-1
Development of the Birth Control Pill, Djerassi, 99-1
Development of Chemical Biology, Schultz/Schreiber/+, 99-1
Molecular Modeling and Assorted Applications, Karplus/Houk/Schleyer/+/–, 99-1
Contributions to Organic Synthesis, Evans/Danishefsky/Nicolaou/Ley/Trost/Stork/Wender/Kishi/Overman/+/–, 149-1
Fluorocarbons, Dupont/Curran/–, 199-1
Dendrimers, Frechet/Tomalia/+, 199-1
Application of NMR to Organic Chemistry, Roberts, 199-1
Understanding of Organic Stereochemistry, Mislow, 199-1
Mechanical Bonds and Applications, Sauvage/Stoddart/+, 199-1
Self-Assembly Whitesides/Nuzzo/Stang/+/–, 199-1
Nobel Gas Reactivity, Bartlett/+, 199-1
Tissue Engineering, Langer/+, 199-1
Contributions to Bioorganic Chemistry, Breslow/Eschenmoser/+, 199-1
Molecular Recognition, Dervan/+, 399-1
Development of Nanotechnology, Lieber/Whitesides/Alivisatos/Seeman/+/–, 399-1
Astrochemistry, Oka, 399-1
Zeolites, Flanigan, 399-1
Molecular Machines, Stoddart/Tour/+/–, 499-1
Studies in the Origin of Life, Miller/Orgel/+/–, 99999-1

Past Awards & the “Pre-Nobels”
Past Nobel Prizes in Chemistry
Lasker Award for Basic Research
Wolf Prize in Chemistry
Welch Award in Chemistry
Kyoto Prize
Von Hippel Award
Science Magazine’s Breakthroughs of the Year

Stories
The History of GFP
History of Pd-Catalyzed Cross-Coupling Reactions
History of Telomeres and Telomerases
A Really Biased History of the Global Warming Issue
History of Noble Gas Compounds

Buzz in the Blogosphere
ChemBark: 2007-1
Derek Lowe, In the Pipeline: 2005, 2006, 2007
Sceptical Chymist: 2006
Curious Wavefunction: 2006, 2007
Endless Frontier: 2006-1, 2006-2, 2006-3
Carbon-Based Curiosities: 2007
The Chem Blog: 2007

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:

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. 

Sleeper is one of the great Woody Allen movies from the 70s. Woody plays Miles Monroe, the owner of (what else?) a health food store who through some medical mishap is frozen in nitrogen and is awakened 200 years later. He finds that scientific research has shown that cigarettes and fats are good for you. A McDonald’s restaurant is shown with a sign “Over 795 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 000 Served”.

Rip returned from the 100-year birthday blowout and band camp and began attacking a giant pile of accumulated unread journals. In the 9 August Nature (p. 630 - 631) he was amazed to read criticism of a 64-step, 22-year synthesis of an exquisitely complex molecule (azadirachtin) — a molecule for which it is easier to count the number of optically inactive carbons than the optically active ones. Back in the 60s, we were all impressed with how Woodward got the five asymmetric centers in one of the six-membered rings of reserpine (which was in use as an antihypertensive at the time, and whose fairly common side effect of depression was one of the clues leading to the amine theory of affect). Rip was surprised to find that the criticism was not that the synthesis was incorrect, but that the project shouldn’t have been done at all. Apparently, a significant body of organic chemists think this way.

Political correctness has left us with few groups that are safe to disparage. With apologies to one of them (Christians) I’ve got to ask, “What would Woodward do?”

Rip’s father went into the hospital shortly after his 100th, and is getting out 1 Sep, so it may be a while before he can respond to what this post brings forth.

Retread

Two things:

1. The ACS is coming. Lots of good talks. I previously floated the idea of a ChemBark BBQ, and after further thought, that will not be happening. It has zero to do with money. It has something to do with time/organzation. And it has lots to do with the fact that while 98% of you are probably great people, 2% of you probably can’t be trusted. That means if 20 of you were to come, there’d be a 33% chance of something really nasty happening to the Dawghouse. That’s too risky.

1a. Drinks or dinner at a neutral location is a much better option. Everyone’s got to eat, right? I’ve got no problems treating fellow 98-percenters to pitchers of beer in Harvard Square or whereever people fancy. And I have no idea what other meet-ups the blogosphere has planned. It’s probably easier if we combine forces. How does Wednesday sound?

2. I can easily see this semi-blog-hiatus continuing for a while. I realize that stinks, but those are the breaks. As Retread is gone for a spell as well, that will mean posting will be sparse. If anyone wants to join Retread in taking a turn at posting, feel free to send a prospective post my way. You needn’t use your real name so long as you keep the gloves on.

That’s it. And…commence complaining…now.

Updates:

Creepy Internet Meet-up details are here.  Tuesday night, 11pm around the Convention Center.  Wednesday evening, 7:30pm, in Harvard Square.

The special C&EN Boston blog is up.  Nature’s Sceptical Chymists, Chemistry World, The Chem Blog, and Mitch are here too (links on sidebar at right).

Two people have contacted me about the possibility of advertising on ChemBark. As you know by now, I really don’t like the idea of having ads on this site. I don’t want to be perceived as having conflicts of interest when writing, holding down a second job, or personally profiting off a site that the rest of you contribute to as well. Still, it seems kind of silly to turn down money when it could go to something worthwhile, much like Kyle has done over at The Chem Blog. So, if any of you care, feel free to weigh in on the idea of ChemBark’s running ads. There are two options:

Option #1 — No ads of any sort on ChemBark.

Option #2 — Ads on ChemBark, with all proceeds (after I report the money as income and pay taxes on it) going to the Reeve Foundation.

Why the Reeve Foundation? Well, it’s a charity that is run well and has a mission that I ardently support. Also, I don’t want to get into arguments about what charity should get the money. If you don’t like the Foundation, vote option #1.

Option #2 involves a little trust on your part. First, you’d trust me not to smear advertising feces all over the place and ruin your reading experience. Second, in order to keep this operation completely legit, ad revenue would go into my pockets as income, I would pay taxes on it, and then you’d trust me to cut a check to the Reeve Foundation. I’d scan the checks and post them here. It’s simply too hard to set up a tax-free charitable operation and worry about all of that legal junk and paperwork.

If option #2 wins, I’ll eventually come up with some sort of advertisement policy. All ads would clearly be labeled as such. No popups. No ugly text lists. I’d start by waiting for advertisers to contact us as they are now. If a vendor or some author wanted to put a 100×100 box on the sidebar for a month, that’d be cool. Buying ads on specific posts would be an option too. We might even have an option for cheap classified ads if people wanted to sell old technical books or run personals in search of hot chemical romance.

That said, if the level of support falls too short of unanimous and enthusiastic, it ain’t happening.

Allow me to apologize in advance for writing such a long article. I know that most of you have neither the time nor inclination to read lengthy posts, but parsing these ideas into smaller sections would create problems in that the complete picture would be missing.

Princeton’s Hire: Legitimate News, Not “Gossip”

As you know by now, the news to which am I referring is that Princeton University offered a tenure-track faculty position to a graduate student in the chemistry department at Harvard. I stand behind the validity of this information and the other facts presented below. While as a general rule you can count on the accuracy of the information that I post to this site, the same cannot be said for the info that visitors leave in the comments. Read anonymous comments with a healthy dose of skepticism.

The first task that I’m faced with is to defend this story as legitimate news rather than personal gossip. A lot of people improperly label some of the news in our field as “gossip” simply because the stories have aspects that portray people or organizations in a negative light. The real criterion one should use in identifying gossip is not negativity, but relevance. Gossip is news that bears only a loose connection to chemistry or the culture of our field. Gossip often focuses on issues like sexual orientation, romance, personal finance, health, addiction, and criminal history. There is very little or nothing for us to learn, as chemists, from gossip.

The story here is clearly not gossip. The news is of interest to the community not just because it deals with a top department and the subject of getting a job in academia, but because this particular hiring process marked a substantial deviation from the norm. I have stated before and adamantly maintain that it has become increasingly uncommon over the past four decades for grad students to be offered assistant professorships, especially without the expectation of pursuing postdoctoral study. Many commenters have listed examples of professors who did not complete a postdoc (e.g., Evans, Denmark, Whitesides), but these cases only support my argument. The last such hire that comes to mind is Liu in 1999; the rest occurred many moons ago. In my opinion, that qualifies as rare.

At this point, the discussion splits into two subjects: postdocs and hiring practices.

Postdoctoral Study: A Valuable Learning Experience or a Waste of Time?

From my perspective, the most interesting questions raised by this hire deal with the pros, cons, and necessity of pursuing postdoctoral study. As commenter Metastable said:

This interesting string of comments (much more interesting with Professor Reichman’s involvement) brings up a very important question: what is the point of a postdoc? Many scientists (named by Professor Reichman and others above) have had incredibly successful careers without one. And, it certainly is not the norm in many other disciplines (economics is one that rapidly comes to mind).

.

It seems to be a protracted holding pattern for future scientists, consuming their more creative years. A case could be made that it allows the young scientist to gain experience, but is another 2-3 years working in someone else’s lab really all that valuable? And, is the research environment that much more complicated than 20 years ago, before the postdoc became a “requirement.”

The vast majority of people seeking a career in academia complete a postdoc, and a lot of commenters have left great reasons for doing one. Allow me to review some of them:

1) Expertise — Postdoctoral study is the highest plateau of the education continuum (grades 21-23, or so). During a postdoc, you will pick up a new set of skills and gain experience with a new research problem. A postdoc is a chance to broaden your base of knowledge in preparation for dealing with the world’s ever-growing emphasis on “interdisciplinary” research.

2) Sustained Productivity — Doing a postdoc allows you to demonstrate that you can switch research problems and be productive in a short time span, exactly what you will be expected to do as an assistant professor. In this regard, getting publications out of your postdoc will make you less risky from the standpoint of a university’s trusting you to set up a successful lab of your own.

3) Networking — Working at a new school for a new advisor will hopefully expand your “network” of colleagues. You will gain new contacts in the form of both labmates and professors. You will establish mutually-beneficial intellectual relationships that will last a lifetime. If you’re lucky, some doors may open in terms of finding a job, whether in academia or industry. And as mentioned in the comments, having another letter of recommendation will also help you get hired. Such a letter might be of greater importance to those with graduate advisors who are not well known (or liked) in the community.

4) Exposure to a New Environment — Whenever you change schools, you are exposed to different styles of management, ethical standards, social norms, experimental techniques, safety procedures, and regional cultures. Broadening your horizons will allow you to sample different “ways of doing business” from which you can pick and choose what you think works best when the time comes to set up your own lab.

5) Publications — Doing a postdoc will allow you to build a deeper record of publication. In addition to the papers that you will publish in your new lab, a postdoctoral stint will allow time for your grad school work to make it through the review process. Longer publication lists are definitely a good thing in terms of impressing future employers and securing funding.

6) Buying Time — There’s often not a lot of time left over for writing original proposals when you’re busy trying to write your Ph.D. thesis. Doing a postdoc gives you some time to decompress following the thesis crunch, sink your teeth into a new set of research problems, consult acquaintances on job hunting, and write proposals with renewed intensity.

Of course, these good things come at a cost: spending yet another two or three years in school when you could, in theory, be building your own research program. As Metastable said, these two or three years come in the prime of your life. Furthermore, it’s not guaranteed that you will have a good experience during your postdoc; you are taking a risk whenever you enter a new job.

I’m going to go out on a limb and say that the consensus opinion of the community is that the good things about doing a postdoc outweigh the bad, because the overwhelming majority of people who wish to enter academia complete a postdoc. Given the recent news, should we question the value this path? Does undertaking postdoctoral training actually enhance the quality of an assistant professor? Are there any worthwhile data that support this claim? If not, why does almost every chemist planning to enter academia do one?

A lot of people make a big deal about exploring new areas as your professional development progresses. Obviously, such a perception did not hinder the candidate in the present case, as she did her undergrad and grad work at the same school for the same advisor. It’s also interesting to note that when referring to his not seeking a postdoctoral position after grad school, George Whitesides told C&EN, “If you have a reasonably good taste about what’s new, then you might as well go it.” (C&EN, 26/3/2007, p. 20). If this is true, then is it the schools or the candidates themselves who are hesitant about bypassing postdoctoral training? Surely we can all agree that doing a postdoc is not a prerequisite for success as an assistant professor.

At the end of the day, I don’t know if we have enough data to answer most of these questions with any degree of satisfaction. Where do we even start? What is the best metric for “success” as an assistant professor? Furthermore, a number of potential confounding factors hinder proper analysis of this issue. For instance, the grad students who are offered assistant professorships are not randomly sampled—they are, presumably, the cream of the crop. I suppose we are forced to base our analysis largely on anecdotal evidence. Feel free to provide some data…

Fellow grad students out there: do you have any classmates who applied for academic jobs straight out of grad school? If so, were these applications targeted to a specific school or did they cast a wider net (the size typical of a postdoctoral candidate going academic)? Professors out there: do you see a lot of applications from grad students? In cases where you do see these applications, did the candidates have contacts at the school or were they especially encouraged to apply, i.e., were they recruited in any way?

The more information the better, but you needn’t use names. They don’t add much to the conversation and they get people riled up.

The Competition for Academic Talent

A second line of discussion that relates to the Princeton story centers on the techniques that departments use when competing for academic talent. Intellectual ability is a precious commodity, and schools want to attract candidates who will build fantastic research programs, win grant money, and increase the prestige of the institution.

In terms of measurable compensation, schools can offer candidates higher salaries, more lab space, more start-up funding, and lighter teaching loads. Each school also has intangible benefits it brings to the table, such as a desirable geographical location, high perception of prestige, friendly/congenial atmosphere, and access to better instrumentation. These are much harder to control—capital improvements can take years, cultural changes in a department can take decades, and geographical changes will almost never occur. Finally, there are also “negative” tools that departments can use, like peer pressure. (Yes, this actually happens.)

At the end of the day, the schools with the most money and prestige usually have the advantage. They can offer the candidates better financial packages, access to better facilities, more talented pools of students, and better brand names. These schools can also go after established superstars. For instance, Harvard is well known for recruiting talented professors from “rival” departments.

We see plenty of analogies in major sports. Successful teams in big markets, like the New York Yankees and Manchester United F.C., are more successful at attracting superstar players because they can offer them more money and historically better chances of contending for championships. Less successful teams in smaller markets find themselves having to scout less established players in hopes that one of them pans out. The upside, of course, is that they spend less money on player contracts.

What are some of the tools that smaller departments use? The first one is timing. Schools with fewer resources typically conduct their interviews and make subsequent offers earlier in the hiring cycle than the more prestigious schools. In doing so, the smaller departments apply pressure to the candidates they have targeted. The hope is that these candidates will accept a position instead of waiting for offers from better schools and risking not getting hired at all. Sometimes, the candidates must decide whether to accept offers before they’ve even finished all of their other interviews.

A second tool that smaller schools can use is what we saw happen in the case of Princeton: you can go after younger talent. Again, we see the same thing in sports. Perennially decent teams with lower positions in the draft will gamble on underclassmen (or even high schoolers) that they probably would have no shot at drafting as college seniors. It is often the case that departments don’t wait for young talent to come to them. Instead, they gather intelligence and invite prospective talent to apply.

The issue of hiring young talent in sports has prompted massive debate. Should academia should consider the same questions? How young is too young? Will young talent develop better in college (a postdoc) or in the pros (as an assistant professor)? Many national governments and leagues (e.g., NBA and EPL) have passed legislation preventing teams from “robbing the cradle,” an action that speaks to the importance of the issue.

So, will we see more early hires? I wouldn’t be surprised. What actually surprises me is that we haven’t already seen more.

The Tangential Details and Related Public Perception

At this point, I believe that I have sufficiently established the legitimacy and importance of the story. It would be remiss of me if I did not address the somewhat provocative tangential details that were raised in the discussion threads. I’m not here to make any judgments or add to either the concern or praise (let’s not forget that there was lots of it) expressed in the comments. I think it is self-evident that, as David Reichman put it, “NO CHEMISTRY DEPARTMENT HIRES SOMEONE BECAUSE THEIR MOTHER IS THE PRESIDENT OF ANOTHER UNIVERSITY OR BECAUSE THEIR PARENTS USED TO BE FACULTY MEMBERS IN A UNRELATED DEPARTMENT.” In the same vein, I’ll reprint part of an excellent comment left by Slapshot:

2) Proposals
Evaluating a potential prof candidate solely on the available info (published papers and rumors) is also very silly indeed. The most important thing for a department are the ideas the incoming new person brings to the table — the awesome, new, outside-the-box chemistry the person proposes to do. If someone is eager and ready to the mental work of a prof coming out of grad school — they better get the chance to it before they realize they can take their brains and jump ship to a hedge fund. Talk about bad for science. Seriously, why waste time in a post-doc running more columns and learning how to run a gel or a laser if you don’t need to do that to do your chemistry???

.

3) The person in question.
I don’t know for sure but have heard from friends at Harvard and Stanford that this person is absolutely stellar scientifically and also that she’s super nice. Really, based on the amazing things I’ve heard I wasn’t surprised to see the link above to the Princeton seminar series page. But… that’s just a seminar. To get an offer you have to have much more than a couple of JACS papers and good talk. You have to be brilliant, see (2).

That said, there is an interesting general point we should explore regarding the importance of “whom you know” in terms of finding jobs. While it won’t be 100% responsible for getting an offer, can having friends or well-connected professors help you get a foot in the door? Do some professors “go to bat” for their students more than others? If so, is that “unfair”? Does it partially erode the perception of meritocracy if everyone is not subjected to the same application process?

It’s no secret that some advisors have better track records in terms of their students finding academic positions at good schools. Why is this? Is it better letters of recommendation, better contacts, more encouragement to apply for academic jobs, better research, better training? Along the same lines, some schools (Harvard is one) seem to disproportionately hire alumni of the school. Is this a coincidence? I don’t know, but again, you can point to a number of possible confounding factors.

Regarding the hiring of female assistant professors, I think we can all agree that the under-representation of female professors in the sciences has schools especially intent on hiring qualified female candidates. This focus was intensified following the professional lynching of Larry Summers, and every issue of C&EN has classified ads that end with something akin to “University of X is an Equal Opportunity/Affirmative Action Employer and applications from women and underrepresented minority group members are especially encouraged.” Without delving into a discussion of the merits of affirmative action, we must accept that affirmative action is now endorsed across most of our field. The reality is that it’s both a blessing and a curse, because while more minority candidates will be hired, there will also be more people who think that anytime a minority is hired it’s just because they’re a minority. Regardless, it will be interesting to see if schools make recruiting minority graduate students a key tool in diversifying their faculties, especially in the sciences.

The Experimental Nature of the “Princeton Post”

A few commenters asked why I brought up this specific story if I just wanted to talk about postdocs and hiring practices. Well, this piece of news is what drew my attention to the subject. It is a fact of life that interesting discussions are almost always started by stories in the news. It took 9/11 to direct more attention to terrorism. It took global warming to direct the world’s attention to carbon emissions. It took Christopher Reeve’s accident to direct national attention to spinal cord research. If we speak purely in hypothetical terms without any basis in reality, fewer people are going to care. There is nothing unfair or irresponsible about examining hiring practices in the context of the Princeton news.

A number of commenters also took umbrage at how I approached this story and these issues in a sort of “open thread.” Some of the people who agree that these issues are worthy of discussion and analysis believe that I should have provided more direction to focus the discussion. In hindsight, I am inclined to agree. When I originally wrote this post, I was under the impression that more people were aware of the news. Quite a few people brought it up in discussions around here and word had traveled outside of the department. Most news is reported on ChemBark juxtaposed with my take on the subject. That creates a bias that influences the ensuing discussion. I thought this was the perfect opportunity to see what happens when I don’t bias the presentation of information, but allow commenters on “equal footing” with each other to bring out the news and discuss it themselves. I clearly labeled the post as an experiment and asked commenters to be civil and analytical. Obviously, some weren’t.

I’ll regard the experiment as a failed success. It was successful in that it succeeded in sparking a spirited discussion where we were actually discussing important issues. And for the first time, a professor at a top-ten department chose to leave a signed comment. That said, the success was overshadowed by a number of negative aspects, some of which were a direct result of the “experimental” method of presentation. While the news eventually took control of the threads, it took 48 comments to get on track. From that point, there was a mix of interesting comments, vapid comments, insulting comments, and utter garbage. Obviously, not all readers can be trusted to be civil in the comments. I’m learning here and will adapt accordingly. In this regard, I appreciate when people voice their opinions on how to improve this site, even if it is in the form of rude and threatening comments directed at me.

ChemBark as a Chemical News Medium

ChemBark is many things. It is part serious. It is part silly. It is a place people come to read about important issues in our field. It is a place people come to make jokes and have fun. Much like a newspaper has a front page and a comics section, ChemBark has posts that lie on different levels of seriousness. The unifying theme is that they all have something to do with chemistry.

Clearly, bona fide chemistry news falls within the purview of this blog, and the fact that some posts contain original reporting is one of the biggest reasons people come to this site. The “news” at ChemBark extends beyond commentary on research reports into areas like the political, cultural, ethical, and managerial aspects of research in chemistry. When discussing these topics, I steer clear of discussing personal information that is irrelevant or of little relevance to any larger story. I know a lot of you know or want to know about things like chemists’ places of residence, sexual orientation, romantic affairs, and other sensitive personal business. I don’t discuss such information here.

I enjoy writing posts, and part of this enjoyment comes from being able to use the blog to draw attention to issues that I think are interesting and merit discussion. I have limited time to devote to the site, so I generally focus on issues and stories that have been overlooked by the more traditional media. There is no need for me to post on things that are already covered somewhere else. That’s why there aren’t many reviews of research papers here. If you want to read about research, you can open JACS or Angewandte and read the original reports. For coverage of most of the significant events in the world of chemistry, you can crack open your weekly copy of C&EN.

Of course, publications like C&EN and Chemistry World usually limit themselves to stories that portray our field in a positive light. Unfortunately, not all of the aspects of research in chemistry are positive. There will always be matters of scientific misconduct, ethical dilemmas, dirty politics, misappropriated funds, and petty bickering. These sorts of issues are pervasive in our community and we should not feel ashamed to learn about them and discuss them. Part of the job of the media is to serve as a watchdog. Despicable acts like scientific misconduct merit coverage and significant follow-up attention. It is sad that the paper media in our field either don’t share this view or don’t have the time, money, space, or inclination to apply constant pressure and get to the bottom of things. It is ridiculous to think that ChemBark is contributing to a problem or doing more harm than good when we report on a negative or provocative story. No scientist should feel that ignorance is bliss or that discussing interesting news is counterproductive.

Finally, let me also point out that there are plenty of positive posts on ChemBark, too (1 2 3 4 5). A lot of people conveniently forget that.

ChemBark as a Venue for Analysis and Discussion

It is one thing for me to post news or analysis, but unlike with traditional media, on a blog, all readers have the chance to respond and start a discussion. ChemBark is not just a publication, it’s a community.

As Josh Finkelstein, a senior editor at Nature, said in the latest Nature Chemistry Podcast, “Chemists are generally quite social animals.” The problem is that for many important “hot button” issues, the only places you can find these discussions are around water coolers or over lunch tables—venues that are closed to the public. Why not discuss these issues on a bigger scale? That’s part of what ChemBark is about: being a water cooler for everyone who’s interested in discussing important chemical news. It doesn’t matter if you’re in a big department or a lone alchemist—anyone can participate.

I have accepted the fact that there will be bumps in the road as I try to steer ChemBark to becoming a respectable place for discussion about technical and cultural issues in chemistry. Due to the lack of transparency in our field and the concentration of power in a small elite class, we are fighting a massive activation barrier in reaching that goal. We live under a cloud of fear. Students fear their advisors. Professors fear their colleagues. Authors fear their reviewers. Reviewers fear revenge. People don’t want to run the risk of being honest and upsetting someone because they think it will come back to bite them…and they might be right. Long gone are the days when chemists would intellectually spar over fascinating research with little regard for anything but the truth. Grizzled physical organic chemists still sing songs of the epic battles over nonclassical carbocations (the followers of Winstein vs. the followers of Brown). Although tempers often flared and feelings were often hurt, there is no question that these debates pushed the field to improve its experiments and solve the problem.

But, like I said, those days are gone. Now, if we want our culture to change, the progress will have to be slow and steady. If ChemBark falls too far outside of the current cultural norms, people will just ignore it. I manage ChemBark accordingly. First, I favor depth in coverage as opposed to breadth. Only a small percentage of the posts on ChemBark are “hot button” topics. If I came out with guns blazing against every problem and injustice in the world of chemistry, this site would be viewed as a joke. Second, while I would like for everyone to feel safe in signing their names to their comments, I realize that this is going to take some time. While I comment using my real name, I allow anonymous comments because not granting anonymity would stifle any sort of meaningful discussion. The trade off, of course, is that there’s an element of hypocrisy in how ChemBark seeks to be an “open forum” but allows people to hide behind anonymous screen names. Last, I realize that I’m a lowly graduate student with zero clout or power in our field. The “Paul Bracher” brand name is worth nothing, and correspondingly, offers this blog nothing. The only way that I can build credibility for this site is to manage it responsibly by being fair and addressing issues in a professional manner—especially the controversial ones.

One philosophical stand that I’ve made is to allow nearly complete freedom of speech in the comments. The comments are a big part of this site and we’ve already seen how great comments can be informative and thought provoking. This is exactly the reason that the comments exist. As I agree with Potter Stewart that censorship “is the hallmark of an authoritarian regime,” the only comments I delete are spam and those that stray so recklessly deep into personal ground that the information is both offensive and worthless. I welcome you to identify comments that you think should be deleted.

A consequence of all this leeway is that comments will sometimes venture into areas that hurt people’s feelings. Sometimes, commenters crack hurtful jokes. Sometimes, completely legitimate comments hit a little “too close to home.” I am resigned to the fact that providing an open forum will inevitably mean that “good” people will occasionally be hit with shrapnel, but getting mad at me for these comments is like getting mad at your department’s administration for funding social hours and parties. After all, people come to these events and discuss rumors and crack insulting jokes. At the same time, plenty of people participate in intelligent, thought-provoking conversations. The comments that rub you the wrong way are the price we pay for all of the “good things” that the freedom of commentary brings.

What you should remember is that—ChemBark or no ChemBark—these conversations are still taking place behind closed doors. I personally think the “open” system afforded by blogs is better than the “closed” system that is currently in operation. First, the closed system is unfair to the individuals being discussed because not only can they not defend themselves, they have no idea they are even a subject of discussion. On ChemBark, everyone has access to the same information and can either choose to join the discussion or just observe. The current system affords no such courtesy. Second, the current system is inefficient. With a select few individuals holding these discussions, there are fewer brains actively analyzing what is going on. When you open the discussion to the entire community, everyone can raise points and learn from it.

One aspect of the comments that probably goes overlooked is that I am one of the biggest losers as far as allowing anonymous commenting is concerned. First, I receive the “blame” for many of these anonymous comments because I am the one who provides the open forum. Second, many (most?) anonymous attacks on this blog are leveled at me. Some commenters have attacked me using multiple user names to make it seem that the dissatisfaction is widespread. Third, people comment anonymously to mask perceived conflicts of interest. For instance, by their IP addresses, I know that some of the attacks leveled at me come from friends and colleagues of people discussed in news stories. If you knew that at the time, you would probably reduce the weight of their opinion relative to an unbiased casual observer. Still, I allow the comments to stay and don’t “out” the people who left them. While I don’t dish out anonymous vitriol, I take more of it than anyone.

Getting back to the “hot button” issues discussed on ChemBark, do we have to discuss these topics? The simple answer is “yes.” A lot of Web 2.0 efforts that should enjoy success are initially doomed for failure because they are too restrictive. There is already a resistance in our field, for whatever reason, to embracing Web 2.0 technology. Since we are already attracting a small number of people, it would be stupid to further discourage participation by requiring registration, banning anonymous comments, narrowing the scope to ridiculously specific subsets of our field, or attempting to cater to too many people by barring discussion of interesting but provocative issues.

I think it’s also fair to say that most of the opinions expressed on ChemBark regarding provocative issues are actually representative of more widely-held opinions in our field. For instance, I think the outrage expressed in the blogosphere over the Sames-Sezen situation mirrored that in the world of research. I think it is also clear that views in the blogosphere have shaped, to a degree, some of the stories run in C&EN, Chemistry World, Science, and Nature. Aside from the SSS, opinions expressed in the blogosphere regarding the 2007 Nobel Prize (1 2) were reported in the print edition of Nature. I don’t think the editors would have done this if our views were not representative of a larger population of chemists.

I’d like to think that ChemBark is doing some good things and that it is not simply a “time sink” blog, as one commenter put it. I am pleasantly surprised that the site receives a lot of Google traffic for technical questions, like the general procedure for HATU coupling. There is clearly an audience for technical information in chemical blogspace. I am also encouraged that people refer visitors to ChemBark’s discussions of cultural issues in our field, like the order of authors on papers or how to improve peer review. Where else can you find analyses of these issues that are open and accessible to all who wish to voice their opinion? And as far as humor is concerned, I would hope that people appreciate and enjoy the posts and comments on ChemBark that are made in jest. You guys crack me up, and I thank you for it.

Risk Management

A question that is occasionally raised in comments is whether ChemBark could damage my prospects for a career in chemistry. It is something I have considered at great length, and I have arrived at the unsurprising conclusion that running this blog has the potential to both help and hurt me. ChemBark is a genuine reflection of my personality because I have elected to run the site in as honest and straightforward a manner as possible. I use my real name, strive for 100% factual accuracy, and openly share my personal opinions and the reasons behind them. The downside of sharing all of this information is that some people will be turned off by my personality and opinions. For example, I get the distinct impression that some of you do not appreciate my frankness and willingness to explore politically incorrect questions. I suppose this could hurt my chances of landing a job in some places, but I’d rather miss out on these jobs than be hired and have to pretend that I’m someone I’m not.

On the flip side, there is also the small prospect that this blog could end up helping my career. On the off chance that potential employers stumble across ChemBark, I would hope to come across as reasonably intelligent, creative, logical, and someone who loves chemistry, loves teaching, and cares about the managerial aspects of research (advising, administration, ethics, etc.). It should also be noted that ChemBark and its predecessor have damn good track records of finding interesting stories and getting the facts right. At times, we may have even outclassed the coverage of C&EN, Science, Nature, and the New York Times. The commentary on ChemBark, while opinionated, is kept as clinical as possible. I don’t swear. I don’t launch personal or ad hominem attacks. I take the time to substantiate my opinions with facts and reason, and I provide an open forum for public dissent should anyone wish to disagree. What news medium publishes every single piece of correspondence the editors receive, including attacks against them which are untrue and personally insulting?

I also want to address the concern that my candor could result in the ultimate demise of this site:

I’m kind of annoyed that no one else besides Paul was willing to say anything after this. Are we afraid someone will pull the plug, Trost-style?

Rest assured; there is only one person who can “pull the plug” on this site—me. One of the things I enjoy about ChemBark is that it’s something over which I have complete editorial control. I can ensure that the site addresses issues I feel are important and adheres to the principles I espouse in life because I run everything. In the future, it may become necessary for me to either suspend or terminate my participation on ChemBark. Should that happen, I will give you a full report on the reasons necessitating the action. In the meantime, everyone deserves a hobby, and ChemBark is mine.

Concluding Remarks

In theory, academia exists to enhance our understanding of the world. Critical examination and honesty should take precedence over personal advancement, popularity, pride, and political correctness. We should not fear starting discussions about interesting news, ideas, and theories simply because the scrutiny may stray into areas where people will have their ideas challenged or feelings hurt. Sadly, in the current politicized climate of chemical research, many chemists are resigned to an existence where speaking critically and honestly is limited to the shadows cast by privacy and anonymity. Such a system is shamefully inefficient, and as scientists, we should seek alternatives that allow us to embrace our analytical roots and thoughtfully examine our lives.

Reaching that goal is a big part of what ChemBark is all about. In the meantime, if I don’t get back to acting like I don’t take this blog that seriously, everyone is going to get upset.

A series of comments on the first half would be rather disjointed, so I’ll put just one in now and then. Here’s today’s: I wrote my Junior paper on the Grignard reagent, and it seemed obvious that no one knew what was going on back then. From the discussion on p. 236, it seems like not much has changed. Any comments?

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There wasn’t much response to the request for examples of chemical serendipity in the last post, so here are two from medicine to get the discussion going.

Interns don’t get much sleep. On a three-month surgery rotation, it was 36 hours on/12 off, but to get a weekend off, call was bunched so that in one 7-day stretch, it was 5 nights on/2 nights off, making 24 of 168 hours off call. Most nights we got 3-4 hours of crummy sleep. According to legend, Mary Walker was one such intern who in 1934, fell asleep during a lecture on myasthenia gravis (a disease characterized by muscle weakness, which can affect the ability to breathe, hence the “gravis”) for which there was no known treatment. She woke up after the lecture, walked up to the great man and asked how to treat myasthenia. The great man, irritated, said — “It’s just like curare poisoning”, so she went off to the library, looked up curare poisoning, found the treatment (physostigmine), administered it to a myasthenic and became famous.

Few of the drugs first used to treat neurological disease were discovered rationally. The first drug for epilepsy (bromide ion) was thought to work by decreasing libido, as epileptics were thought to be sexually overwrought. Things improved in the 30s with the discovery that seizures could be induced by electric shocks administered to the brain. Zillions of hapless rabbits were shocked while pumped full of various drugs. If the drug increased the current required for seizures, it was a potential anticonvulsant. This is exactly how Dilantin was discovered. Cruel, but at least rational.

Science marches on, and it was soon discovered that drugs getting into the brain (which is mostly fat) had to be soluble in lipids (which meant they weren’t too soluble in water). So potential drugs were first put into amphipathic (soluble in water and lipids) solvents, like soap. Soap is basically a bunch of long chain (12-18 carbons) carboxylic acids. One such solvent was 2-propylpentanoic acid (valproic acid).  Many drugs put into it seemed to work pretty well. Fortunately, someone had the brains to do a control, and found that the actual anticonvulsant was valproic acid (and a very useful one it was — although like everything else in medicine, not without side effects). A case of not throwing out the bathwater. Anything similar in chemistry?

Retread

When I think back on why I became a chemist, I always point to my 10th-grade chemistry class. Our teacher, Dr. Liebermann, was absolutely fabulous. He developed an engaging, rigorous two-year AP Chemistry course with great lecture notes and a detailed laboratory component. The focus was on really understanding the general principles at play, and the massive lab reports and essay questions on tests forced us to understand what was going on. A month into his class, I was certain that I would become a chemist.

But that decision probably had deeper roots. I knew that I wanted to go into math or science in 7th grade, when I had the legendary Vern Williams for math. Before that, in elementary school, I religiously watched Mr. Wizard’s World and would mess around with those experiments in our kitchen. Finally, this periodic table has dominated the landscape of my (old) bedroom since 3rd or 4th grade:

With pictures and small blurbs about each of the elements, it’s still the best periodic table poster I’ve come across. My father brought it back from a trip to England, and I think the Royal Society still sells it. The yellowed pieces of packing tape are a testiment to the sentimental value I hold for the poster. I had to piece it back together after my sister ripped it in a violent rage circa 1992.

Whenever I go back home to Virginia and see the poster, I always chuckle at how funny it is that the periodic table was the last thing I saw at night for nine straight years, and sure enough, now I’m a chemist.

Fortunately (for me) the Army was short of neurologists in 1968, so with just one year of residency (instead of the usual three) under my belt, I was sent to one of their best hospitals (Fitzsimons) to work under an excellent and seasoned neurologist (Col. Halbert Herman Schwamb — whose name alone scared the hell out of me).

The tour of duty in Vietnam was one year for everyone, so docs who had been there for their first of two years got their pick of where to go for their final year.  Naturally, Fitzsimons was one of their top picks, so the place was full of them.

What in the world does this have to do with molecular biology?  The army had something called the ‘body count’ which meant the number of Viet Cong (and possibly civilian) bodies they could find.  It gave a number, which was increasing with each passing month.  It showed we were winning.  However, not one of the returning two-year docs I talked to (and I talked to a lot of them) thought we were winning.  Most thought we were losing, and badly.  They were, of course, right.  The point is that what we could not measure was far more important than what we could.

Consider the following terms from molecular biology: nonsense codon, noncoding DNA, Junk DNA.  Two of them are downright pejorative.  All imply that anything in our DNA not coding for an amino acid going into a protein is unimportant.  As most of you probably know, the four bases of DNA (A, T, G, and C) are read in groups of three (these are the codons) giving 64 possibilities.  The 3/64 not coding for an amino acid are called nonsense codons.  They tell the protein making machinery (the ribosome) to stop and start on another protein.  The 3 codons are just as vital for life as the other 61, or we’d just be one big protein.  Calling them nonsense always seemed peculiar to me.

Noncoding DNA means DNA which doesn’t code for an amino acid going into a protein.  The implication is that it doesn’t code for anything else.  Of our 3.2 billion positions in DNA, perhaps 2% codes for amino acids going into proteins.  The rest has been called ‘junk DNA’ — again the implication is that it does nothing.

You have doubtless heard that we are 98.5% chimpanzee.  What this means is that our proteins are 98.5% similar (e.g. they have the same sequence of amino acids in 98.5% of positions).  Again, the proteincentric view is dominant here—proteins are all that you have to know.

Now, we all love chemistry or we wouldn’t be here reading this.  Consider Independence Hall and Monticello from the chemical point of view.  They’re both made of bricks, and a chemical analysis of them could certainly figure out that one set of bricks came from South Jersey and the other came from the Virginia piedmont.  However, the most sophisticated chemical analysis can not tell us why the two buildings look so different.

Why not?  Chemistry can’t deal with the way the bricks are put together.  You can do a lot with bricks if you stack them just right (and the chemical nature of the bricks doesn’t matter very much for this).

However, for at least 30 years, minor differences in proteins were thought to determine the differences between a man and chimp.  In fact, it was seriously stated at one point, that chemically man and chimp weren’t different enough (as far as their proteins were concerned) to be considered separate species.

Well, we are, and the determining difference lies in the 98% of the DNA which does NOT code for protein.  In some way (which we are just beginning to find out) it determines which protein is made where, how much of it is made, and when it is made.  Molecular biology is definitely still in the hunter gatherer stage at this point.

That’s enough for now.  The details are emerging and including things like epigenetics, microRNAs, RNA interference, and even in bacteria metabolite control of mRNA translation into protein (look up the work of Breaker at Yale if you’re interested).

**The answer is Henry Mosely who died at age 27 in the battle of Gallipoli in 1915.  Moseley used X-ray diffraction to show that each element has an atomic number. With this tool he was able to fill the six remaining gaps in the periodic table (at the time) and to put some order into the rare earths.  After that, the British (and everyone else) decided that brains like that shouldn’t be used as cannon fodder.

At my father’s recent 79th Rutgers reunion ( yes his 79th ! ) I met an 87 year old graduate.  I asked him where he served in the war (because just about every male in his generation did).  He said that he didn’t.  I asked him how come. The answer — “I was making penicillin for Merck.”

Retread