Thursday, June 28, 2007

Poetic Chemistry

Today at the Sceptical Chymist, Catherine wrote an interesting post on poetry in the scientific literature. One of the comments contained a link to this 1971 JOC paper, which is written in quite a unique style. I suggest that you take a look.

Also, as Catherine suggested, I tried to write some chemistry/biology related haikus, and here are my attempts.

For the chemists:

Stirring at reflux
Overnight. Leaky tubing
Flooded his office

(As a side note, that didn't ever happen to me, but a post-doc in my lab managed to flood the office below his lab with some tubing that wasn't properly secured. That office luckily belonged to one of the nicest faculty members here).

For the biologists:
Oh dear western blot
where is my protein hiding?
not on the membrane

Tuesday, June 26, 2007


Today was my first time trying out confocal microscopy, and I enjoyed it quite a bit. Seeing stained cells through the microscope was pretty amazing. Unfortunately the camera doesn't capture the images quite as well as the human eye, but I wanted to share one of the pictures that I captured today.

Monday, June 25, 2007

Visualization of Single Electrons

Yes, you can believe your eyes. The above image has captured the movement of a single electron through liquid helium, with a velocity of 6 cm/s. Researchers at Brown University have captured these traveling electrons on film in a recent Journal of Low Temperature Physics article. (You can also watch a movie on the Maris group website).

How does this work? Well, the Pauli Exclusion Principle tells us that a free electron injected into liquid helium would experience some repulsion from the atom's own bound electrons. Thus, the electrons are encapsulated by so-called "electron bubbles." Electron bubbles can't be seen under normal pressure because of their tiny size (on the order of 10-23 cm2, but utilizing soundwaves to explode and expand the electron bubbles, Guo and Maris were able to actually see the movement of electrons through a 6.8cm long helium cell that was kept at an extremely low temperature (1.3o K which is approximately -457o F or -272o C). Although most of the observed bubbles traveled in a straight line, some of them followed a snakelike path, most likely following a superfluid vortex.

One question still remains--Where are these electrons coming from? As the authors point out, the liquid helium cell does not contain a source of electrons. One theory is cosmic rays might cause ionization of helium atoms, producing UV photons. As these photons hit the cell wall, it is possible that electrons could be ejected into the helium due to the photoelectric effect. A simpler explanation might be that some other kind of charged particles (such as muons) simply ionize helium atoms, producing positive and negative particles. While most of these charged particles would recombine, some might escape, allowing researchers to track their movement.

Tuesday, June 19, 2007

Comic Clumsiness

My husband pointed out the Periodic Table of Comic Books this morning, and while I haven't had a chance to check out all of them, so far my favorite one is this Wonder Woman strip. I just love the end, where Wonder Woman says, "The hydroxo gas is transforming you into an electron and me into a proton."

Also, I thought I'd share some of my clumsiness with you. Today in Cardio Camp! I somehow managed to tear my deltoid ligament and am now restricted to hobbling around on crutches for the next few weeks. Right now I'm not sure how this will affect my labwork, but maybe I found those comic books just in time...

Monday, June 18, 2007

Top 200 Drugs...

As my boss pointed out earlier this month, the Njardarson group (Cornell) currently has a listing of the 2006 top 200 generic and brand name drugs with structures. You can download the pdf files for your own pleasure or have them blown up to poster size as my group did. (The posters currently reside in our group breakroom, so that even at lunchtime, we never totally leave the realm of medicinal chemistry). It's amazing how many of the drugs that I recognized by name--and of course now it is handy to know their structure. Who knew that the estradiol analog found in many birth control pills contains an alkyne (ethinyl estradiol) that (according to wikipedia) was apparently key in creating a compound resistant to degradation by the liver? Or that the brand name drug Klor-Con (#153 on the list), which made $160,000,000 last year is actually only KCl?

Absorption of Polyphenols from Black Tea,,,

Yay! According to a study in J. Agric. Food Chem., I can once again start drinking my black tea with milk.

Wednesday, June 13, 2007

Getting Closer to Open Access?

While reading C&EN today, an advertisement promoting the ACS AuthorChoice free access option caught my eye. Maybe I am just a little behind the times, but I didn't actually know that something like this existed (and looking at the release date, it has been around almost a year). Basically, in exchange for a fixed fee (ranging from $1,000 to $3,000, paid by the author(s) or their funding agencies), the ACS allows unrestricted internet access to an author's article published in an ACS journal. This is different than the ACS Articles on Request policy which I had previously heard about; through this FREE policy, the ACS gives authors a URL that they can email out to colleagues. In this way authors can distribute up to 50 free copies of their published work, and after 12 months access to articles is unrestricted through this unique URL. Of course, Wiley journals have a similar policy (with a similar price, but limited to only the biomedical journals) called Wiley Funded Access Service.

Looking at the list of published ACS AuthorChoice Articles, I was slightly surprised to see that only 24 papers have been published in this way. Apparently the fee, while not too hefty in my opinion, prevents most authors from choosing this option. Hopefully with time, we will see more open access articles available through programs like ACS AuthorChoice and Wiley Funded Access Service. Although I like the idea of peer-reviewed open access and hope that it becomes the wave of the future, something in me says that it will be a long journey...

On a related note, these posts at In the Pipeline and Chemistry Central
discuss the important role that open access journal articles play for those in the field with no literature subscription (such as the retired on unemployed).

Sunday, June 10, 2007

Chemistry in my life...

While reading one of my favorite non-chemistry magazines the other day, I came across the advertisement pictured above for the Lexus RX hybrid. In the closeup picture, you can see why I've decided to include it here. Whenever I see chemical information or structures in real world situations, it makes me excited that non-chemists are getting a little exposure to what I work with every day. Usually the chemistry isn't great (and sometimes it doesn't even make sense), but at least our industry is getting some recognition. Although I tried to find some connection between the structures pictured and hybrid cars, I couldn't find one. Any ideas?

Saturday, June 9, 2007

Pictures from Sao Miguel

My husband took most of the pictures while we were on our vacation in the Azores. While I took only about 200 pictures, he snapped approximately 1,000. He is the more advanced photographer, but it is hard to make any picture of such a beautiful landscape look bad, so most of the pictures that I took turned out pretty nicely too. Sorting through the pictures to pick out the "best" ones is difficult, but you can see a small selection below. I've left out some of the more stunning ones (taken by my better half of course), so that he will have a chance to post them himself.
Lagoa do Fogo Lagoon of Fire

cliffs down to the Atlantic

São Miguel


baby volcano

one of the many small "ports"

I also have to add that our accommodations were absolutely wonderful: Casa Vitoriana in Ponta Delgada, Quinta das Queimadas in Nordeste, and Quinta Altamira in Caloura (near Água de Pau).

Thursday, June 7, 2007


Looking through the literature, you see some papers with twenty-plus authors and others with only two or three. Maybe it is just a difference between papers coming out of industry versus those produced by academia. Sometimes I have to wonder if all twenty authors really contributed much at all to a six page paper, or maybe it is just a system of "you pat my back and I'll pat yours" (or "I'll include you on this publication if you include my name on your next one"). On the other hand, how many key people were left out of the typical two author paper? Does the undergrad who helped synthesize a key compound (through a method you carefully worked out for weeks beforehand) get left out of the author list? How about a visiting scientist that contributed ideas and demonstrated new techniques to a group? Is she kept on a publication because of the contribution of original ideas and thoughts, or do you leave her off because she didn't physically complete any of the actual experiments?

Is it enough to contribute time/manual labor? Is it enough to contribute only ideas? Or is it necessary for one to contribute both to be worthy of authorship? I've heard people say that it's only really necessary to look at the first and last author of an article, and if that's the case the debate over authorship doesn't really matter.

I'm for citing ALL of those involved in a project, no matter how small a part they played (meaning inclusion as authors, in the acknowledgments or in the references section under "personal communication"). What are your opinions?

Back from vacation

I'm officially back from vacation! Expect some pictures from the Azores soon. Until then, I'll catch up on some reading ;o)