Chemistry Blog

Feb 25

Peer review and the new media


I attended a Macintosh Users Group recently. (Yes, I am a Mac user.) This meeting was unusual. Natali Del Conte, a tech writer for CNet and CBS, was the featured speaker. She talked about being authentic, social networking, and how technology has changed how we get information. She argued that gone are the days that information is simply pushed to us and that Walter Cronkite is the most trusted name in news.

A detail I have come to think more about is what we know. I remember that stomach acid was thought to cause ulcers, but Marshall and Warren have received a Nobel prize for their discovery of the role of Heliobacter pylori and its role in peptic ulcers.

Mitch (Feb 08) and azmanam (Feb 02) have posted on congressional misunderstanding of science and false or poor science reporting, respectively, but I don’t think chemists are as cognizant of the accuracy or correctness of textbooks or peer reviewed papers. There have been a few cases in which errors have entered the chemistry world.

I wrote the the archivist at the Oregon State University Library inquiring about whether there was any correspondence regarding a paper Pauling published (there wasn’t). I wondered what the referees may have said.  Now, I have been thinking how this is like the comments to a blog post. One of the really interesting things about the new media, is errors can be pointed out. They can be argued and open to everyone.

I have been thinking about how our ideas of atomic theory have evolved. In doing so, I have been reading a fascinating series of transcripts from recordings deposited at the Center for History of Physics of the American Institute of Physics.

It was interesting that some people thought Niels Bohr had confused the literature with his papers. However, overall, what I liked was how these transcripts contained the personalities of the scientists, their interests, and in some cases their ideas (or biases) about topics being discussed. I felt these transcripts from leading scientists were like our modern internet (although generally without the details of the science).

Our modern internet has no rules. It can be difficult to sort out the wheat from the chaff. We need to learn who to follow and who to ignore. Peer reviewed journals only give the filtered result. The referees reports are confidential. Comments are not published except in blogs. Now that science is moving toward electronic publication, would a new model for scientific publication improve the scientific world?

Just to note that this is not unusual in chemistry. Organic Synthesis has long provided a kind of review for a select set of procedures. I don’t foresee H.C. Brown’s papers becoming ignored, but independent reports could prove useful. Similarly, critical steps to improving yields  would be helpful. You can find examples of this in the Organic Chemistry Forums.

Should online journals allow comments? Would it be useful? How could it be done? Would it be science?

Feb 23

Eating Carbon Nanotubes



Fathi Moussa

Lon Wilson

Last year I covered Khodakovskaya et al.’s paper regarding the benefits of growing tomatoes in carbon nanotubes (CNT).[CB] At the time I was concerned with the potential health risks associated from eating carbon nanotubes, but today in ACS Nano my concerns are alleviated. A paper from Lon Wilson’s and Fathi Moussa’s research groups discusses the effects from administering oral doses of carbon nanotubes (concentrations as high as 1g of CNT per kg body weight) to Swiss mice.[ACS Nano] The authors summarize their work the best.

CNT materials did not induce any abnormalities in the pathological examination. Thus, under these conditions, the lowest lethal dose (LDLo) is greater than 1000 mg/kg b.w. in Swiss mice.


So feel free to eat all the CNTs you want in lab, assuming they are not functionalized, you do it only once, and you limit yourself to single walled carbon nanotubes. I think partly because the results of the oral administration of CNTs went without any interesting side effects to present, the authors also looked into what happens when you inject CNTs into the peritoneal cavity of mice.

The image on the left is the control while the image on the right is 14 days after injecting mice with CNTs at a concentration of 1g CNT per kg of mouse. Although it looks sickly, the mice injected with the high concentration of CNTs did not die. Well…, not from the CNTs anyways.

Link to paper: In Vivo Behavior of Large Doses of Ultrashort and Full-Length Single-Walled Carbon Nanotubes after Oral and Intraperitoneal Administration to Swiss Mice (ACS Nano)

Mitch

Feb 18

Wisconsin-Madison Lab Fire


A graduate student at the University of Wisconsin-Madison suffered burns and the loss of their favorite chair due to a fire that was started in the lab. A small lab fire usually wouldn’t make for interesting news, but see if you can spot something strange in the redacted narrative from the Madison Fire Department.

E4 found dry chem extinguisher activated, smoke, dry chem created haze on fire floor. found burned cushion chair in stairwell that was pushed there from room where reportedly students were working with chemicals that were spilled on to a chair that then started on fire. students came up with the idea to use a dry chem extinguisher as well as push the burning chair down the hallway to the stair well. It was reported to us that (deleted) was one of the students who was already at the UW hosp being treated for burns to his hand. E4 saw no one on the fire floor upon arrival.



The student took a burning item out of the laboratory and put it in the stairwell. A follow up revealed the student was worried about other chemicals in the lab catching on fire, but to the best of my knowledge most laboratories are designed to contain a lab fire. If the fire had gotten further out of control and caught the hallway and stairwell on fire, Madison might be missing a building today.

For future reference young graduate students the correct method for dealing with a burning chair in lab is the following. Rush to the safety shower and turn the flow of water on, then with a non-flammable object push the chair under the shower. Do not transport flaming objects outside the lab!

The chemical that started the fire was ethanol. Apparently the student was cleaning a pipette with an open flame nearby. As the student was shaking the pipette dry, a few drops of ethanol landed onto the chair and caught on fire.

The fire department received the call at 11:17 pm.

More media coverage: UW student burned in lab fire (The Cap Times)

Mitch

Feb 15

Android Spectroscopy


I was jealous when I saw Joel write about his boss using his iPhone’s light source for experiments (finally, a really useful science iphone app). I knew I had to one-up him for no other reason then I am a Google Android user. Below is a video of an app I made; the app will scroll through the visible spectrum. In the video the glass contains red wine.

During the video you can see the wine absorbing blue light when the camera pans over the glass for the first time. Next time it pans over the red wine the light is green and still not transparent, but as the light was turning yellow the solution became more transparent. By the end, the light was red and it transmitted through the wine just fine.

If I had an other Android phone on hand I probably could have made a quick and dirty visible spectrometer.

Mitch

Feb 13

Biology professor allegedly involved in shooting


Suspect in UAH shooting - credit Huntsville Times, Dave Dieter

News broke this afternoon that there was a shooting at the University of Alabama in Huntsville’s Shelby Hall. It took me a while to find that this is (among other things) the home of UAH’s chemistry department. While CNN hasn’t filled in the details, the Huntsville Times already has reported that biology Professor Amy Bishop was taken into custody and her husband has been detained for the deaths of 3 faculty members and the wounding of 3 others.

While stunning and tragic, this would not have rated a post except for the alleged reason for the shooting: denial of tenure. According to the New York Times:

WAFF, the NBC affiliate in Huntsville, quoted university officials as saying the professor began shooting after learning at the faculty meeting that she was being denied tenure…

Dr. Bishop had told acquaintances recently that she was worried about getting tenure, said a business associate who met her at a business technology open house at the end of January and asked not to be named because of the close-knit nature of the science community in Huntsville. “She began to talk about her problems getting tenure in a very forceful and animated way, saying it was unfair,” the associate said, referring to a conversation in which she blamed specific colleagues for her problems.

Wow. Denial of tenure must be crushing for an assistant professor, especially since the process must seem protracted, random and unfair (at times). The really surprising detail is that (allegedly) she brought a gun; that’s an indication of a willingness to use violence and a certain level of forethought as to the potential outcome of the meeting. (CORRECTED: see update below.) Academic science is high pressure indeed.

My (our) thoughts are with the families of the victims.

UPDATE: From the AP:

University spokesman Ray Garner said Saturday that the professor, Amy Bishop, had been informed months ago that she would not be granted tenure. He said the faculty meeting where she is accused of gunning down colleagues was not called to discuss tenure.

Feb 12

This Message Will Self-Heal in 3, 2, 1…



Cassandra Fraser

Recently, Cassandra Fraser’s group reported on a very cool property, reversible mechanochromic luminescence, observed in an easy to make material.[JACS] The molecule of interest is the difluoroboron complex of avobenzone (BF2AVB), that UV absorbing molecule in your sunscreen minus the boron and fluorines.

In broad general language, mechanochromic luminescence describes the ability of some materials to change colors after scratching under UV light. The image below shows BF2AVB coated on weighing paper (A), a cotton swab is used to write “Light” (B), the surface is hit with a heat-gun (C), the surface is ready to be written on again with a cotton swab (D).

The image brings up all kinds of creative ways to write secret messages, especially as the letters will fade over time even without using a heat gun. But before the CIA intelligence wonks in the audience get ahead of themselves the material doesn’t seem to be completely reversible at room temperature without annealing.

…even a small mechanical perturbation, such as a slight touch with the tip of a cotton swab, changed the green-blue BF2AVB film emission to yellow. The yellow emission gradually reverted back to green again at room temperature, with much faster recovery at elevated temperature. The written regions were no longer readable after annealing.



The field has, in short order, gotten tantalizingly close to a 100% reversible mechanochromic luminescent material at room temperature. Congrats!

Link to article: Polymorphism and Reversible Mechanochromic Luminescence for Solid-State Difluoroboron Avobenzone

Sam covered one of the first entrants to reversible mechanochromic luminescence a year ago: reversible mechanochromic luminescence is cool

Mitch

Update and Correction: Cassandra Fraser has corrected me, apparently the wording of the paper was just awkward to my ear, the material is fully reversible at room temperature!

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