Wednesday, February 25, 2009

Accepting Submissions for the Worst Named Reaction

Usually, in my extensive experience, named reactions work pretty well. I mean they wouldn't be famous reactions if they worked like shit. Right?

That brings me to the Reimer-Tiemann reaction. This thing sucks. In my particular case, the reaction was a complete disaster. Here is a generic version of the reaction if you are not familiar with it (everyone out there except Jason).

In an effort to optimize this reaction, I consulted a recent review. Here are some of the accolades from the article.

"Even 105 years after its discovery, conditions for the Reimer-Tiemann reaction cannot said to have been optimized. This is not too surprising for a reaction in which a quantitative yield has never been reported, and in which useful yields of 3-10% are not unususal."

Nice. I guess I should have consulted this before embarking on a route invoving the "Reamed"-Tiemann reaction. Any other suggestions for the worst named reaction?

Monday, February 16, 2009

Talk About a Mad Scientist

Carl Djerassi is pissed.

I don't think that you want to piss this guy off. For a chemist, he looks like he could kick some ass. He is pissed because Trost failed to reference the isolation of bryostatin in his recent Nature paper on its total synthesis. I'll let Carl speak for himself:

"who isolated the bryostatins? Who established their structures? Who initially pursued their anticancer activity? Without these achievements, the synthesis would simply constitute chemical acrobatics that never would have been accepted by Nature.

These decade-long efforts by G. R. Pettit's group at Arizona State University are concealed by reference to a generic review article authored by others. There are a couple of "et al." references that also mask Pettit's name. This demeaning treatment of the key work of earlier investigators in the field of natural products by chemists who then undertake the total synthesis of the molecule in question is unfortunately all too common—either because of sloppiness or as a discreet attempt to eliminate any reference to the initial discoverers.

Trost's treatment of Pettit is particularly egregious given the well-known fact in the chemical community that the spectacularly laborious decade-long efforts of one of the heroes of marine natural products chemistry—the person who personally collected the bryozoan, isolated the bryostatins, established their constitution, and pursued their anticancer activity against all odds—were terminated through a draconian closure of his laboratory by the new administrators of Arizona State University."

I love organic chemistry pissing contests. I think that Djerassi could definitely kick Trost's ass. And when was the last time Trost developed a drug that 100 million people use daily?

no love for Barry, sorry Mike

Saturday, February 14, 2009

Maggots, Fly Eggs, and Rodent Hairs

Sounds delicious!


We can thank the FDA for our yearly intake of about 1-2 pounds of this delicacy per year. I was recently enlightened about the FDA guidelines relating to bug parts in various foods. Here are some real "limits" on shit that is allowed in your food.

"Tomato juice, for example, may average “10 or more fly eggs per 100 grams [the equivalent of a small juice glass] or five or more fly eggs and one or more maggots.” Tomato paste and other pizza sauces are allowed a denser infestation — 30 or more fly eggs per 100 grams or 15 or more fly eggs and one or more maggots per 100 grams.

Canned mushrooms may have “over 20 or more maggots of any size per 100 grams of drained mushrooms and proportionate liquid” or “five or more maggots two millimeters or longer per 100 grams of drained mushrooms and proportionate liquid” or an “average of 75 mites” before provoking action by the F.D.A.

The sauerkraut on your hot dog may average up to 50 thrips. And when washing down those tiny, slender, winged bugs with a sip of beer, you might consider that just 10 grams of hops could have as many as 2,500 plant lice. Yum.

Giving new meaning to the idea of spicing up one’s food, curry powder is allowed 100 or more bug bits per 25 grams; ground thyme up to 925 insect fragments per 10 grams; ground pepper up to 475 insect parts per 50 grams. One small shaker of cinnamon could have more than 20 rodent hairs before being considered defective.

Peanut butter — that culinary cause célèbre — may contain approximately 145 bug parts for an 18-ounce jar; or five or more rodent hairs for that same jar; or more than 125 milligrams of grit.

In case you’re curious: you’re probably ingesting one to two pounds of flies, maggots and mites each year without knowing it"

Friday, February 13, 2009

La Clair hexacyclinol, again

A few years ago James La Clair published a synthesis of hexacyclinol, and it was immediately met with skepticism. Rychnovsky studied the NMR data for the natty-P and others and via comparison proposed a new structure, that was eventually made by Porco and proved to be both the compound in question, and have the Rychnovsky proposed structure.

La Clair commented in Nature: "La Clair now says that he and Porco may have made two different molecules that happen to have very similar NMR spectra."

As far as I know La Clair has not done any more in this area, to defend himself or otherwise, which is odd considering he claimed to have more than a gram of the material in question on hand.

Today in Org. Lett. a paper came out specifically examining this problem of the different compound-same NMR spectra issue.

Where 2 is the Rychnovsky proposed correct structure, and 1 is the original La Clair claimed structure.

This seems to me to be a lot like backhanding La Clair right in the face while calling him a bitch.

That and flogging a dead horse.

Thursday, February 12, 2009

I shouldn't post this

I have a feeling this post is a bad idea, but I have a few things a need to get off my chest. As a grad student, I had an idea of how science is done. People do work in the lab, write up their impeccable results, and then submit their work to a peer reviewed journal. Once in the journal's hands, the editor sends the paper to a number of the author's "peers" who evaluate the paper closely for scientific merit. Once these peers decide that the science described is accurate and important, they accept it. If not, the paper is rejected. As the three loyal Mad Scientists readers know, that idea is purely fiction.

Here is what really happens. Often, incompetent people do sloppy work and then submit it to third rate journals in a language that barely resembles English, and the paper is accepted and published with virtually no peer review. Why? Because these idiots work for a boss who has to publish to get funding and promotion, and third rate journals have to publish something.

Why do I care? Because I keep getting these horrible papers from my boss who is the one who is supposed to be peer reviewing them. He just cut-and-pastes my comments to the editor and as a result his workload is greatly diminished. But I have to read this crap and today I've had enough. While I guess this stuff is supposed to be confidential, since I was not formally told that, I have decided to post a slightly edited to protect the innocent version of my comments to the editor of this prestigious journal. Enjoy!

"While the science is sound, the language used to describe the work is difficult to understand and rife with grammatical errors. I count at least 15 examples in this brief manuscript where the authors have left out an essential article, such as a, an, or the.
For example:
- …XXXXXs operate through Zn-dependent mechanism.
- …there is urgent need for more useful drugs.

In many cases, singular forms of words are used where plurals are required.
- XXXXXs are well validated anticancer target.
- The choice of cap groups was based on the XXXXXs previously reported by us and other group.

In other cases, a complete sentence is almost impossible to understand.
- We also investigated the ability of this set of compounds to block the cancer cell growth as their potential utility in cellular level with the special attention towards pancreatic cancer.
- The results have impinged upon cancer drug discovery research, predicting the restriction of the use of isoxazole moiety near XXXXX catalytic region.

I cannot accept this manuscript for publication in its current form. The work should be rewritten with a critical eye focused on the myriad grammatical errors and cumbersome language. The peer review process is essential for the dissemination of important and timely scientific knowledge. I am proud to review the work of my colleagues, when I feel they have spent an ample amount of time on the finished product. However, when insufficient time is spent simply proofreading a manuscript, then my time is wasted reading an unfinished product. In order to conserve everyone’s limited time, I encourage the authors to proofread their work prior to submission in the future."

Tuesday, February 10, 2009

Blue Ice

Why does some ice look blue?

and some ice looks white?

It turns out that it all has to do with the frequencies of light absorbed by water molecules. The vibrational modes that are absorbed by the O-H bonds in water fall in the red end of the visual spectrum. So water absorbs red light and blue is transmitted. But we only see it if the ice is sufficiently thick and the light is passing through the ice so as to absorb more red and transmit more blue.

For once, vibrational spectroscopy is useful.

Wednesday, February 4, 2009

more great proofreading errors

I was flipping through that paper based laxative C&EN this morning on the train to work, and this caught my attention from the corner of my eye. I don't know if seeing errors readily means I'm becoming better at my job, or the asshole I always swore I would never be, but it seems to happen a lot.

look off to the right there

For people who don't know what the error actually is, it's a subtle, but very very important, mistake. When I got in, I showed it to a South Korean Professor that is here in the lab on sabbatical, and he said "Wow, they should get the Nobel prize!", then winced when he recognized the company as South Korean, and then quietly cursed under his breath. Once a prof, always a prof.

Monday, February 2, 2009


For years now I've wished there was a good science spelling dictionary in MS Word, and have even had discussions about how MS has really dropped the ball be essentially having no science/engineering version available. I've used the add feature in Word to build my own, but it's tedious and every now and again the custom dictionary file ends up getting lost or erased when a major incident takes place or I swap/upgrade computers. For some reason I never remember to back that shit up.

Azmanam, an enterprising grad student, went to the effort to create his own decent list, he developed it and collaborated with Antony Williams of to further increase the volume to ~104,000 words!

If you want this little gem go to, read about it, and download it.

I tried the instructions included in the zip, and some of the tips on the site with no success. Being trapped with a relatively old Mac at work is not helpful some days. To work around the issue, and greatly simplify things, I opened the new file and the existing custom dictionary, copied the contents of the new file, pasted into the old dictionary, saved, and was done.