ChemBark

Sometime last year, my girlfriend DVR’d a copy of this commercial for Garnier Fructis shampoo because she saw it had chemistry in it and because she is awesome:

If you pause the video at 0:13, you will notice quite a few chemical atrocities:

Basically, nothing is right. Note the surfeit of Texas carbons. I also love the asymmetry of their elemental fluorine, though maybe those things labeled “F” are atoms of fruit? And what is up with that ideal gas law? You’d think they’d be able to get a structure for biotin in there, considering how big they wrote the word on the chalkboard. Argh…

Anyway, great catch by the ol’ g/f…whom I am now happy and proud to call my fiancée.

Antipope John XXIII

Is anyone else loving this papal conclave?  It’s so refreshing to hear people actually speaking Latin. The constant parade of cardinals in the news just brought to mind a quick story from grad school:

At a weekly meeting of teaching assistants, one of the profs I taught for told us about a professor who came to the department as a visitor to teach sophomore organic chemistry. On the first day of the semester, he introduced the course’s teaching assistants and finished by saying that he was the pope, the TAs were his cardinals, and you never go directly to the pope.

As with the infamous Guido letter, it is always interesting to hear of a professor embracing his villainy. Habemus jerkface.

First they ignore you,
then they laugh at you,
then they fight you,
then they join you,
then everybody wins.

Mahatma Gandhi posted that piece of advice on his blog shortly before his death in 1948, and it still holds true today.

After admitting that chemistry faculty typically roll their eyes at blogs and that he personally doesn’t have time for them, Phil Baran—or, more precisely, the Baran Lab at Scripps—has established the newest chemistry blog on the Internet. Baran and his lab are at the top of the game of organic synthesis, so this is a major development for academic chemistry. Their participation can do nothing but lend legitimacy to an activity that has been robustly and repeatedly poo-pooed by the respected Old School of our field.

The establishment of the Baran Lab’s blog fell out of the ongoing post-publication review of IBX-promoted benzylic oxidation at Blog Syn, a relatively new site that focuses on checking synthetic procedures in the vein of Organic Syntheses. Post-publication peer review is something familiar to the chemical blogopshere. Previous examples include the questioning of the science in the “Arsenic Life” paper, the exposure of duplication by Breslow in the “Space Dinosaur” saga, and the experimental investigation into the oxidation-by-NaH paper in JACS. Blog Syn takes post-publication review of synthetic procedures to the next level by coordinating replication of the procedures among a group of bloggers who compile and compare their results for all to see and discuss.

Last month, Blog Syn decided to examine a method for IBX-promoted benzylic oxidation published as part of Baran’s graduate work in K.C. Nicolaou’s lab. What started as a straightforward effort to test the (questioned) reproducibility of the reaction quickly evolved into a vigorous and thoughtful discussion of both the merits of anonymous bloggers’ questioning peer-reviewed research and of the reaction itself. Baran and the first author of the paper have participated actively in the generation of data and its analysis, and the most recent development appears to be improved mechanistic insight as to how the reaction might work.

Those interested in this specific reaction can check out the discussion for themselves, but all chemists can appreciate the value that blogs and other Web 2.0 venues offer in terms of advancing scientific knowledge and enriching our understanding of chemistry. While blogs may often engage in journalism that is a little rough at the edges, the ease of online publishing has helped to provide open venues for meaningful discussion, to give voice to important ideas, and to democratize power in a field where many grumble that power is overly centralized. What Blog Syn has started is a great service to the field of organic chemistry, and I look forward to the wealth of material that the Baran Lab can bring to the table in its own addition to the blogosphere.

Great stuff!

Edit to add: This great post by Rich Apodaca at Depth First places Blog Syn in historical context among similar experiment-based efforts in the chemical blogosphere. The post also offers an interesting analysis of the role that blogger anonymity plays.

Edit: Another (similar) great analysis and comment thread in this post by DrFreddy at C&EN‘s blog.

I enjoy watching the field of supramolecular chemistry just about as much as I enjoy following the movement of professors among chemistry departments. Thus, it should come as no surprise that J. Fraser Stoddart is someone who passes across my radar with some degree of regularity. Sir Fraser has been a pioneer in using organic chemistry to build supramolecular structures that can function as rudimentary devices, and many of the systems developed by his lab are impressive synthetic feats.

While it is not uncommon for big-named professors to jump from one school to another, it is less common to find full news stories that cover these events. In the case of Stoddart, he seems to have a precise method for deciding where to migrate:

Here’s what Stoddart said in 2000 regarding his move from Birmingham to UCLA:

Stoddart came to UCLA from England’s University of Birmingham, where he was head of the school of chemistry and professor of organic chemistry.

“I tried to get collaborators to work on a molecular computer in Europe, but I drew a blank,” Stoddart said. “It was all a dream until I came to UCLA.”

“I liken Southern California today to Paris in 1900, which was the place to go if you were an artist,” Stoddart said. “When I was working in England in the ’90s, I felt that the place to make things happen as a scientist was Southern California, and I have been proved right.”

And here’s what he said in 2007 regarding his move from UCLA to Northwestern:

I have had the opportunity to visit both Southern California and Chicago in this century. While I cannot comment on their resemblance to Paris in 1900, these cities and the science they foster appear quite different to me. I wonder where the next Paris of Nanotech will be?

Yesterday, Science magazine published what are effectively two death certificates for arsenic life (1 2). These twin papers delve back into the experiments first conducted on the GFAJ-1 bacterium that led Felisa Wolfe-Simon and coworkers to conclude that this organism can grow using arsenic instead of phosphorus.

In the newest reports, Redfield and coworkers were more fastidious than FWS in their experimentation and reported that the presence of arsenate did not affect the growth of the bacterium when phosphate was limiting. They also found no covalently incorporated As in the DNA of GFAJ-1. Erb, et al. found similar results. You can read the papers for yourselves, but suffice it to say that these are findings that jive with everything we know about biochemistry excluding the one paper published by Wolfe-Simon. The only reasonable analysis is that until bona fide experimental evidence to the contrary is presented, there are no organisms we know of that can function by substituting As for P in their DNA.

To follow up on one of my earlier posts, unfortunately, Felisa Wolfe-Simon *still* does not get it. The first rule of getting out of a hole is to stop digging. Giving a statement like the following to USA Today does not help FWS’s cause:

The “new research shows that GFAJ-1 does not break the long-held rules of life,” says the editorial statement by Science. The bacteria, “is likely adept at scavenging phosphate under harsh conditions, which would help to explain why it can grow even when arsenic is present within the cells,” it says.

Wolfe-Simon says in response, “There is nothing in the data of these new papers that contradicts our published data.” Her team hopes to submit more data on the microbe for publication within a few months, she suggests.

Her latest collaborator also decided to pick up a shovel in commenting to the Washington Post:

Wolfe-Simon, now on a NASA fellowship at the Lawrence Berkeley National Laboratory, is collaborating with senior scientist John A. Tainer on wide-ranging studies of the bacterium. In an interview Saturday, Wolfe-Simon and Tainer said that they had produced tentative results in the Berkeley lab almost identical to the original results at a U.S. Geological Survey laboratory, and that they were busy finishing the research and preparing another paper.

Tainer said the two new studies in Science may have come to different results than theirs because of the methodologies used, the precision used to detect arsenates and the provenance of the cells. He said the authors of the two new papers “may well regret some of their statements” in the future.

“There are many reasons not to find things — I don’t find my keys some mornings,” he said. “That doesn’t mean they don’t exist. The absence of a finding is not definitive.”

Wolfe-Simon and her numerous collaborators had made samples of GFAJ-1 broadly available after her initial results caused a storm of controversy, but she and Tainer said they may have been contaminated or modified in transit.

Even the Catholic Church admitted it was wrong when faced with the overwhelming evidence that the Sun does not revolve around the Earth. And we’ve just discussed scientific megablunders with regard to Ronald Breslow and the space dinosaurs paper: when you are spectacularly wrong, you need to admit it for people to let you move on. Denying or ignoring your mistakes prolongs the story.

The second rule of getting yourself out of a hole is to grab a life-line if someone offers you one. Wolfe-Simon could have easily jumped on the “good news” of the GFAJ-1 story by embracing the bacterium’s remarkable resistance to arsenic—which was verified. Instead, it appears as though FWS has doubled down behind the initial report. I’ll keep an open mind when she presents her newest results, but I don’t expect much.

As an aside, it is interesting to note that Science (with a capital “S”) got dragged through the mud again. As if publishing the flawed initial report wasn’t bad enough, the magazine was forced to publish the Redfield and Erb papers prematurely because Redfield broke the embargo on her own paper at a decided to present the results yesterday at a popular conference on evolution. What a mess for Science!

JACS has removed Ronald Breslow’s “Space Dinosaur” paper from its Web site. Users who click to view the PDF are greeted with the following message:

10.1021/ja3012897
This article was removed by the publisher due to possible copyright concerns. The Journal’s Editor is following established procedure to determine whether a violation of ACS Ethical Guidelines to Publication of Chemical Research has occurred.

This is an interesting move by the editors. While the paper has not yet appeared in print, its presence on the ASAP site constitutes “official” publication. There is something unwholesome about making the paper vanish. After all, isn’t that why we have addition/correction notices? Otherwise, why wouldn’t we go just into the original documents and change them?

Update (9:05 PM) — The guide “Notice to Authors of JACS Manuscripts” verifies that the ASAP version constitutes official publication of the paper:

Authors must consider that the publication date for a paper is the date of first disclosure, either the Just Accepted date, ASAP date, or date on which the issue is posted on the web.

I guess it is possible to un-ring a bell.