Archive for February, 2007

Here are some interesting posts from last month that I meant to write about but never got around to doing so:

Excimer classified the chemistry advisors at his school into two schools, sparking passionate discussion.

Paul at TotallySynthetic wrote about some of the reasons that keep him excited about chemistry.  On this subject, I am surprised at how many of my classmates started out in love with chemical research but slowly decided to pursue careers away from the bench.  I guess a big part of any schooling is figuring out not just what you want to do, but what you don’t want to do.  Also, not everyone grew to hate research; some people simply found things that they enjoyed more.

Dr. Free-Ride examined whether blogging is a “service activity” in the context of academic contributions.  Hmmm…that reminds me.  I am no longer a blogger; I’m the editor-in-chief of ChemBark, an Internet publication that serves the public interest. (Zzzzzz….)

And A Synthetic Environment continues the enjoyable parade of Top 5 lists.  Please resist the urge to make puerile jokes about Ellen Swallow Richards.

Speaking of things I never got around to writing about, I’ve got to resurrect those remaining Chemmys.  Also slated for discussion: “Forgotten Genius”, my response to The Chem Blog, some tidbits of chemical grammar, and the upcoming Intel Science Talent Search.

And holy cow…here’s a late addition to the clippings from Everyday Scientist.

Ready for another round of what’s wrong with this picture?  Good.  Take a look at this ad for ACS Publications that ran in the last edition of C&EN (Feb. 19, p. 33, click for full image):

I’m not particularly upset that Dr. Julian isn’t wearing gloves, and I’m not going to whine about the bright sources of light in the background that make this an awful photograph.  This time, my beef is with the caption:

In 1948, Percy Julian developed a new way to synthesize hydrocortisone, which is still used to treat rheumatoid arthritis; 45 articles published by Julian are in the ACS Legacy Archives. 

As far as I know, Julian never came up with an original synthesis of hydrocortisone (or cortisone, for that matter).  What Julian is famous for making is Reichstein’s Compound S, which Upjohn later found a way to oxidize to cortisone using a microorganism.  In fact, once Upjohn discovered the process for selective oxidation at the 11-position, there were many routes to cortisone, not just through compound S.  Julian’s route through steroids isolated from soybeans was not as effective as Syntex’s route through the Mexican Yam, since this species of yam produced a greater yield of the steroid precursors.  Julian eventually quit his job as director of the Soya Products Division at Glidden so that he could work with the Mexican Yam.

While we’re busy correcting things, the 45 articles by Julian that the ACS claims to have in its “Legacy Archives” include two addition/correction notices.  Thus, the correct value for the number of articles he published with the ACS is 43, two of which he later amended.  Feel free to check my math.

So, let’s recap:

1.  Julian did not make hydrocortisone in 1948.   He reported the partial synthesis of Compound S in 1951 (submitted to JACS in 1950).  I don’t know what 1948 has to do with anything.

2.  Julian never came up with an original, complete route to hydrocortisone.  Upjohn’s fermentive oxidation of the 11-position of steroids made it possible to take Julian’s route to Compound S all the way to cortisone.  This process was developed in 1951/2.  (Although he did not make the key discovery, Julian should be praised for predicting that this amazing transformation would eventually be discovered.)

3.  Julian/Glidden applied for a patent on the “Preparation of Cortisone” on September 9, 1950, but it was one of those pie-in-the-sky deals.  They never actually made the key transformation, and basically said so in the patent: “The present invention is not concerned with the introduction of the 11-keto group, nor with the formation of the acetyl group in the 17-position of the molecule, but is concerned with the other conversions and reactions mentioned.”

3b.  In light of this important fact, it is amazing that Julian was inducted into the Inventor’s Hall of Fame for this particular patent.  Why not choose one of his many other inventions?

4.  The ACS Legacy Archives contain 43 (not 45) articles by Percy Julian.

Do not leave with the wrong impression; Percy Julian was a truly excellent chemist.  But the fact that the ACS didn’t even bother to get its facts right suggests that this full-page ad was more about pandering to a perceived need to participate in Black History Month than about honoring an excellent chemist.  In the future, I hope that the ACS publishes an ad that accurately reflects Julian’s wonderful contributions to our field, and I hope it doesn’t wait until next February to do so.

When you go to Harvard, there are many things that you come to enjoy: the quality of the research facilities, the amount of money that flows into the department, the rigor of the courses, and the intelligence and motivation of most of your coworkers. The problem is that “most” does not equal “all”—there are plenty of people here who are just plain asshats.

Take, for instance, the big news in our lab last week. Someone spilled a massive amount of a pink dye in one of our instrument rooms, and it didn’t take long before it was being tracked all over the place. The dye, probably a derivative of rhodamine, was somewhat soluble in water and the melted snow on everyone’s shoes exacerbated the problem. I can’t do the development of this story justice, so let me show you clippings from the ten or so e-mails sent to our students-only list over the course of a couple of hours:

Admin: ***Please DO NOT ENTER the AFM room without first drying the soles of your shoes. Bring paper towels, or something appropriate to clean the soles of your shoes before you *leave* the room as well. Shoe covers would be the best bet, once you’ve dried your shoes before entering…It is frankly beyond my ability to understand how whomever did this could be so abusive of our facilities, especially in one of the more expensively equipped rooms on the entire campus. Accidents happen. Ignoring, and thereby perpetuating and extending them, absolutely should not. Ever.

Lab Safety Officer #1: As safety officers for the lab, LSO #2 and #1 need to know the identity of the pink dye that spilled in the AFM/ITC room. We suspect that it is Rhodamine due to its solvatochromism in methanol (and that it was probably *not* Ru-bipy); however, we absolutely have to know what it was for the sake of all our safety and for reporting the spill to the department…Please send LSO #2 and/or LSO #1 an e-mail detailing what happened if you know anything about it. We promise to keep your identity and this information confidential.

Admin: LSO #1, our safety officer, has been working with Department Safety Officer #1 regarding the dye spill in our AFM room. It now appears the prime suspect is rhodamine; not ruthenium. We still do not know for sure, but the concensus opinion remains that we are not facing toxicity issues. However, DSO #1 wishes to be appropriately cautious, so Triumvirate will be here this evening to do a professional cleaning of the AFM room. Meanwhile, it will be off limits to all personnel. I regret any inconvenience. LSO #1 is now reviewing the MSDS for rhodamine with FAS safety people, and with LSO #2 will complete any necessary documentation related to the spill. It is not clear to me at this point how much effort will be (or ought to be) expended to precisely identify the spilled compound.

Department Safety Officer #1: Dear Admin and Lab Safety Officers, As you know, a rhodamine spill occurred in M2xx (AFM room) on Friday afternoon. It is unknown which specific rhodamine was spilled. Triumvirate was brought in to clean the floor in M2xx and the areas where rhodamine contamination had spread due to foot traffic (hallways, restrooms, lab floors). Upon further investigation, it was discovered that almost all of the surfaces in M2xx are contaminated with rhodamine. This includes benchtops, computers, monitors, and instruments. Random Lab Guy #1 turned off most of the instrumentation, the chairs will be disposed of, and the floor is in the process of being cleaned. Your group should use damp paper towels or cloths to wipe down all surfaces in the room before use of the room continues. A mild soap solution may be more effective for some surfaces. Researchers should wear gloves and eye protection when doing this. Contaminated material should be disposed of in the yellow hazardous waste bags outside of M2xx. These bags can be taped shut, tagged with a hazardous waste label, and placed in your hazardous waste cabinet. It appears as though the contamination was not due to a single incident, but extended use of rhodamine in M2xx. No rhodamine should be used in this room until we work out a Standard Operating Procedure for future use.

I kid you not: professional HAZMAT people came, in bunny suits, to clean up this spill. Thus, because some jackass was a super-slob and would not fess up so that we could be sure what chemical was spilled, the lab is probably going to end up spending thousands of dollars for this clean up. Thanks, jerk.

Here’s a picture of our new pink floor.  Unfortunately, it was taken post clean up and doesn’t really do the mess that much justice. The entire room, which contains over a million dollars worth of equipment, still needs to be wiped down; when you spray Windex on any surface, the liquid quickly turns bright magenta. Anyway, I hope the person who committed the evil deed is cursed with low yields and/or failed fabs.

What are the (obvious) take-home messages?

1. Wear gloves and glasses—you never know what your labmates have done to your workspace.

1a. Major-league asshats are everywhere; no place is immune.

2. Try to be careful and not spill things.

3. Sometimes people spill things. No big deal. When you spill something, clean it up. If the spill is really bad, ask for help.

4. If you walk away from a mess, but a department safety officer later asks what the mess is, speak up. Your dignity is not worth the thousands of dollars it costs to decontaminate a room of unknown hazardous waste. Everyone else knows it was you, anyway. You look like a bigger jerk for continuing to deny it.

Argh. 

From their Web site:

“Scientific Publishing at a Non-Profit Organization: or How to Get Your Name in Every Issue of JACS”
Presented by Sonja Krane, Ph.D.
Managing Editor, Journal of the American Chemical Society
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Dr. Krane, will talk about working in the scientific publishing industry. In February 2006, Dr. Krane joined the American Chemical Society staff, serving as Managing Editor of JACS, the society’s flagship journal since 1897. Based in Salt Lake City, Utah, she works closely with Editor-in-Chief Professor Peter Stang and the editorial staff to manage and streamline the manuscript submission and review process. Her responsibilities include evaluating manuscripts for their fit within the scope of JACS, adjudicating minor ethical issues, representing the journal in correspondence with editors, authors, and reviewers, and developing initiatives to sustain and enhance the standing of JACS at the forefront of international chemistry journal. Dr. Krane is an alumnus of the Department of Chemistry, receiving her Ph.D. in 2004 with Koji Nakanishi. Her graduate studies centered on the characterization of a variety of plant (Ginkgo biloba) and animal (slow loris, gaur) derived natural products, as well as the synthesis of retinoid analogs for investigating activation of the signaling protein Rhodopsin.

I imagine that the question and answer period could be quite interesting.  Or maybe not (San Francisco ‘06, anyone?).  In case people run out of things to ask, how about: 

1. When do publications go directly into print without going through ASAP first?  Who makes the decision?
2. Under what circumstances does JACS allow the online edition to be edited?  When are edit notices placed in PDF files and when are they not?
3. How often does JACS find it necessary to sanction authors for ethical offenses?  What are the most common punishments?
4. Do you think the peer-review system is broken?
5. Is JACS planning to do anything cool with its Web site, like adding a news blog or online review or comment system?
6. How much money does a technical editor at JACS make?  What about the production staff and copy editors in Ohio?

So it looks like you’re in for a real treat, Columbians.  Enjoy, and let us know how it goes.

James Sherley, the MIT professor who went on a hunger strike in protest of MIT’s decision not to grant him tenure, finally broke his fast on Friday.  He lasted a whopping 12 days, although it should be noted that he was still ingesting liquid nourishment and probably snuck in a couple of Snickers bars when nobody was looking.

I applaud MIT for not giving in to Sherley’s ridiculous demands and the professor himself for his will to live.  In addition to losing his battle for tenure and his pride, Sherley said he lost 20 pounds.  I suppose that counts for something.

As part of the ChemBark 2.0 Initiative (set to launch in mid-2018), I want to transfer most of the chemistry-related posts from the old blog on to this one.  Since A Synthetic Environment has been firing off a bunch of top 5 lists, this seems like a good time for a blast from the past: my list of the top 10 organic chemists ever…

Here’s my list of the top 10 organic chemists of all-time, without regard to nationality or sub-specialty. I’m sure that the list is biased towards academic chemists, because their triumphs tend to be more heralded, but I’m sure most of them took plenty of money from industry, too.

10. George Olah

Olah was a giant in the field of physical-organic chemistry and the study of reactive intermediates. With his development of superacids, he was able to study carbocations and essentially end the debate about the existence of nonclassical ions. He has also been celebrated for his work in organofluorine chemistry and organic synthesis.

9. Carl Djerassi

The “Father of the Pill,” Djerassi’s synthesis of the progestagen norethindrone had huge medical and societal consequences–people of the ’60s and ’70s should thank him for all of the uninhibited sex they enjoyed. He is also one of the poster boys (along with Marker and Julian) for using plants as sources of steroidal starting materials needed for industrial syntheses.  Because Djerassi’s pill work can be viewed as a nice, tight package with a profound practical application, I think he’s still got a good shot at picking up a Nobel Prize someday.

8. Paul D. Bartlett

The Bartlett Lab was a physical organic powerhouse, and Frank Westheimer said Bartlett “dominated that field for perhaps four decades.” Bartlett hammered home the concept of using kinetic and stereochemical studies to determine mechanisms, and he elucidated the two-step mechanism of electrophilic additions to olefins and the free radical mechanism of certain polymerizations. He also made important contributions to the study of carbocation stabilization (he synthesized 1-bromonorbornane), hydride transfer, and kinetic vs. thermodynamic control of reactions. Perhaps most importantly, Bartlett is credited with changing the way organic chemistry is taught by introducing the mechanistic perspective that we use today.

7. Sir Robert Robinson

The man made the field of natural product synthesis popular. While he might be condemned for this today, for the latter half of the 20th century, the field drove the discovery and development of new reactions in organic chemistry. His one-step synthesis of tropinone is legendary, and he made fundamental contributions to the structural elucidation and synthesis of steroids, alkaloids, and dyes. He is also credited with inventing the arrow formalism (electron pushing) approach to drawing reaction mechanisms.

6. Jack Roberts

Roberts made numberous contributions to the field of physical-organic chemistry, including his studies of cyclopropylcarbinyl systems and molecular rearrangements. Roberts played a major role in popularizing the use of MO theory among organic chemists and he coined the terms “nonclassical carbocation” and “benzyne.” More importantly, the man essentially brought NMR to organic chemistry. In addition to showing chemists how to use the method to elucidate structure, he pioneered the use of isotopic labels to monitor reaction mechanisms. Despite the fact that NMR is still the single most useful method for the characterization of organic compounds, he hasn’t yet been rewarded with a Nobel Prize. I ask you, where is the justice?

5. H.C. Brown

Sure he won the Nobel Prize for his work with hydroborations, but his contributions to physical-organic chemistry were just as important as those to synthesis. His epic battles with Saul Winstein over the nature of carbocations (classical vs. nonclassical) forced chemists at the time to think critically about how to disprove a mechanism and the existence of a particular reactive intermediate. Of course, Brown’s position on nonclassical ions proved to be wrong, but he made the field better nevertheless.

4. Adolf Johann Friedrich Wilhelm Ritter von Baeyer

Trained by Bunsen and Kekule, Baeyer would go on to win the Nobel Prize in 1905 for his work on aromatic compounds and dyes, which were important at the time for the chemical industry. He is especially famous for his work with indigo. He also synthesized phenolphthalein, fluorescein, and barbituric acid. He studied lactams, terpenes, purines, and polyacetylenes, and conducted seminal work on ring (Baeyer) strain. He also introduced the concept of tautomerization. Baeyer did it all, including training three future Nobel laureates (Fischer, Buchner, and Willstatter) and numerous other famous chemists.

3. Emil Fischer

The German chemist is responsible for developing a number of fundamental synthetic methods, including the Fischer indole synthesis, the Fischer oxazole synthesis, and Fischer esterification. Fischer laid the basis for the entire field of carbohydrate chemistry. His proof of the structure of glucose was a tour de force and don’t forget about his Fischer projections (and his lucky guess). He essentially gave his life to chemistry, as the compounds he worked with literally drove him insane.

2. E.J. Corey

The man is a machine, churning out countless total syntheses, new reaction methods, and well-trained chemists with frightening efficiency. In 2002, he was dubbed “the most cited author in chemistry” by the ACS. His progeny populate both the upper levels of academia and the pharmaceutical industry, and at 77, he’s still going strong.

1. R. B. Woodward

The man is a legend–he revolutionized the fields of structural determination, organic synthesis, and physical-organic chemistry. The Nobel Committee essentially bestowed a lifetime achievement award on him with the ‘65 Prize for “outstanding achievements in the art of organic synthesis,” and he would have won a second in ‘81 for orbital symmetry had he not died in 1979. Some, including Woodward himself, thought that he deserved to share in the ‘73 Prize for the “chemistry of organometallic compounds.” On top of all this, he could drink any other chemist under the table. Salud.

Others meriting consideration (in no particular order): Gilbert Stork, Sir Christopher Ingold, George Hammond, Linus Pauling, Donald Cram, Jean-Marie Lehn, Justus von Liebig, Sir Derek Barton, William von Eggers (the “Bull”) Doering, August Wilhelm von Hofmann

Commenter suggestions: Percy Julian, Grignard, Pasteur, Winstein, Sharpless, Dervan

The bubble fusion investigation at Purdue University is now complete, and the school has reached the conclusion that no scientific misconduct occurred.  What is unclear is what exactly was being investigated.  The case centers around an exciting experimental result reported in 2002 that neutron emission and nuclear fusion occurred following the collapse of bubbles in deuterated acetone.  Many researchers have been unable to reproduce the results, and many of them think something fishy might have been done to the data.

The Purdue news release said that the inquiry was raised internally, but Ken Suslick, a chemistry professor at UIUC, admits he contacted the administration at Purdue to suggest that the 2002 report was fraudulent.  The conclusion that most people are drawing is that Suslick’s questions were not among the questions investigated by Purdue.  Instead, it appears that the investigation centered on whether the P.I. should have put his name on more (!) papers.  We’ll never know exactly, because Purdue is claiming that it has already said too much:

Purdue’s policy on integrity in research requires that all allegations of research misconduct be reviewed under procedures that ensure strict confidentiality. The policy states:

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“The mere suspicion or allegation of wrongdoing, even if totally unjustified, is potentially damaging to a person’s career. Consequently, no information about charges of a lack of integrity in research may be disclosed except to the appropriate university and federal authorities.”

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However, in the interest of ending speculation regarding Purdue’s inquiry, Dr. Taleyarkhan has agreed to allow the university to confirm the existence of the internal review and disclose its final result, according to Joseph L. Bennett, vice president for university relations at Purdue. “Professor Taleyarkhan cooperated fully throughout the inquiry,” Bennett said.

Scientists are going to have to get together and decide what information should and should not be released at the conclusion of investigations into alleged scientific misconduct.  Steadfast silence, regardless of the circumstances and outcome of an investigation, seems unacceptable.

Some form of the bubble fusion report should be made public so that the community knows what questions were examined and how thoroughly.  What have they got to lose?  If the evidence led the panel to conclude that no scientific misconduct occurred, then they should be confident that the scientific community will reach the same conclusions with the same information.

Along the same lines, if you are going to fund your research with taxpayer dollars, the taxpayers have a right to know what is going on.  If you want all of this business to be private, raise private funds. I would hate to see the government stymie scientific creativity by imposing burdensome oversight of publicly-funded research, but if scientists can’t decide how these investigations should be handled, Congress will step in sooner or later.

Yesterday, Drew Gilpin Faust was named the first female president of Harvard University in its 371-year history. I’m glad that Harvard finally lost its virginity in this regard. Now, can we please stop dwelling on the issue?

While being a woman probably helped her candidacy, I don’t think that the Corporation was intent on having a female president at any cost. Faust got the job not because she is a girl, but because she was among the most qualified candidates. She appears to have the skills and now the reins are deservedly in her hands. Not that she 1) cares or 2) reads this blog, I wish her luck and success.

Now Harvard can finally move past the ugly way its faculty dealt with Larry Summers. While his brusque management style ruffled the faculty’s feathers, instead of dealing with that issue directly, a large faction of professors opportunistically used his comments on women and science as a springboard for an all-out media campaign for his ouster. He was thrown to the wolves—shameful behavior by an academic body that is supposed to value having a diverse set of hypotheses to fuel healthy academic debate.

I am a little concerned with regard to what the presidency of Drew Gilpin Faust will mean for science at Harvard. While I have no reason to believe she will be an enemy of science, her background is in the history of the Civil War and I wonder if she is in tune with the needs of scientists. The last time I checked, Harvard’s expansion into Allston wasn’t going to include a billion-dollar institute for 19th-century American history. Perhaps that’s why I was hoping that Thomas Cech would be elected, but the Nobel laureate in chemistry pulled his name from consideration. In fact, the most disturbing aspect of this presidential selection process was that so many talented candidates (both male and female) withdrew their names from consideration.

The truth is that there were worse options for scientists. I had expected the popular Dean of the Law School, Elena Kagan, to win in the end. If she had, I think it is safe to say that it would have extinguished all hope of the Law School’s moving to Allston. Harvard desires to expand its science divisions and develop institutes for things like stem cell research, and the best place for these new buildings is as close to the Yard as possible. Scientists benefit from being around other scientists, where they can share instrumentation and exchange ideas. This is especially important for “interdisciplinary” research, like the kind that we’ll probably see at the proposed Origins-of-Life Institute.

The problem is that there’s no open space in Harvard Square. One solution is for the Law School to move to a brand new campus in Allston, near to the current location of the business school. This would leave plenty of room for expansion of the science departments, and it makes sense because there is no reason that HLS needs to be close to the Yard. They are an isolated, self-sustaining community, whereas the College counts on science professors and grad students to teach courses in the vicinity of the Yard.

To make a long story short, the Law School put up a big stink when the Summers administration floated this idea, and Larry backed off. I hope Faust gives the issue a second look, because if she doesn’t, it is going to stink for the future generations of grad students who will have to hop on a shuttle bus to teach orgo lab.