Chemistry Blog

Jul 26

Dangerous Chemistry Sets

From: SMBC – Fear Itself


Jul 20

Cargo cult science in the Gulf, news at 11

Credit: WKRG/Mediaite

The Gulf oil tragedy has already shown the ignorance of some reporters about chemistry. However, a Mobile TV station and their chemist has taken it to new heights when they blamed the oil spill for (likely) bad glassware.

WKRG is a local TV news station in Mobile, Alabama; they sent intrepid reporter Jessica Taloney to collect samples of local beach water. (See video of story below.) They asked a local lab to analyze the samples for oil and grease; the lab owner and analytical chemist, Bob Naman, suggested that the level of oil and grease should be pretty close to 5 ppm.

Of course, all the samples showed the presence of oil and grease, with amounts up to 200 ppm. While these results are not particularly surprising, the result of one sample was not obtainable because the chemist claimed that the sample exploded during the extraction. Rather than blame the broken separatory funnel on a star crack or a lack of venting, the chemist said that “We think that it most likely happened due to the presence of methanol, or methane gas, or the presence of the dispersant Corexit.”

No. This is just wrong. Having actually shaken separatory funnels full of mixtures of water and flammable solvents (including methanol!) on a daily or weekly basis for about 10 years now, I have yet to see any of them explode. Surfactants like Corexit are not known for being particularly explosive, especially at room temperature.

I think it is far more likely to be coincidental; in addition, wouldn’t a true explosion have left much less of the funnel? Heaven help us. (When the reporter obtained another sample from the same area 4 days later, the oil and grease concentrations were at the 1 ppm level. Not explosive enough? (That’s a joke, non-chemists.))


Jul 18

Finding a Postdoc Position is a Difficult Journey but here are 15 Tips to Help You Along the Way.

My impression, from the anecdotes of others as well as my own experience, is that finding a postdoctoral position is a widely unknown and undiscussed process that one learns about via “trial by fire.” For example, Mitch wrote about the surprises he experienced during his interview last January.

Unlike applying for college or graduate school, there is no formal application process for obtaining a postdoc. From what I have been told it more closely resembles the job search process, but for further complication, many postdoc openings are not advertised and only become available when the right applicant inquires. In an effort to support future postdoctoral hopefuls, I am going to expand on Mitch’s prior post with insight and advice I acquired through trial and error and gleaned from the stories of others. It is a long list but hopefully some of this information will be helpful.

Get your foot in the door…
1. Begin your search one to two years before graduation. A few professors shared this insight with me after they learned I began my postdoc search only nine months before my own graduation (oops). It makes sense now when I think about it because potential advisors need time to allocate money, resources and a project for your estimated date of arrival.

2. Find four or five research groups you are interested in working with. I focused primarily on finding groups working in the flavor of research I am interested in. Other searchers may prioritize location. Another variable, more important than either, is whether the lab you are interested in will serve as a stepping stone for your long-term professional goals.

3. Write a cover letter to each professor. This letter should include a brief overview of the research you have conducted and why you are interested in their work. I recommend subtly incorporating the skills, tools, and ideas you would bring to their research. I would also mention a willingness to pursue external funding sources or to request recommendations for any fellowships they may know that you could apply for.

4. Ask your advisor to send a short email on your behalf. It is not unusual for a top research professor to get several postdoctoral applications each week. Regardless of how good your qualifications may be it can be difficult to differentiate your email from the others. If your advisor is willing, have them send a truncated recommendation email saying something like, “I have a spectacular graduate student that is interested in being a postdoc in your research group and you would be a fool to pass them up. They will be sending you their CV and cover letter shortly.” If the professors know each other it can be huge advantage in your favor and sometimes this email is all it takes to get an offer.

5. Send an email with cover letter and CV attached. Example email text: “I am a fifth year graduate student in the …. research group at the University of …. This email is to express my interest in joining your research group as a postdoc starting in Month 201x. Attached are a cover letter and curriculum vitae. Letters of recommendation are soon to follow. I am happy to provide any other information you may find helpful.”

6. Send a hard copy of the cover letter and CV. Even if your email gets ignored you can pretty much guarantee that a physical letter will at least be opened and your name will cross the professor’s mind at least one more time.

7. Wait for a reply. Hopefully you hear back from the professor with good or at least a neutral (not no) reply. In the best case scenario you get a job offer or an interview. If they do not extend an invitation for a campus visit, you can insist on paying for your own visit and offer to give a talk. This option of course depends on how badly you want the position, as well as the state of your bank account. My theory is that it would be much more difficult to say no after a person has demonstrated that they are highly interested and competent (assuming you demonstrate these qualities). If you do not hear back in several weeks you should send a follow up email asking for an update on the postdoctoral position.

You have planned a visit. Before you go…
8. Do your homework. Looking into the research group’s goals and methods should be a no-brainer. It is unlikely that you will get a pop quiz on their research. However, your general dialog with the adviser and group members will flow much better and you will leave a better impression. Nothing says “I have a scientific mind” like asking a really insightful question. If possible, think of a proposal or direction they could shift their research. They might not want to pursue your ideas but it does show that you have them.

9. Have a one hour talk prepared. Instinctively you might feel the need to include as much of your PhD work as you can cram into an hour but it is much more effective to present a small subset of your research with a coherent storyline. This talk should also be tailored in a similar manner as your cover letter as to clearly demonstrate skills/tools/ideas you can bring to their research.

During the visit…
10. Consider how to dress. This is a point where I respectfully disagree with Mitch. If you are someone that is comfortable or enjoys wearing a suit by all means look more professional. However, I am not willing to sacrifice my comfort for appearance. The more relaxed I am the better I will perform in both my presentation and one-on-one meetings. For my postdoc interviews (and defense) I wore a nice pair of jeans and a suite coat.

11. What to expect. Your visit will most likely be comprised of a lab tour, possibly a short campus tour, a meeting with the adviser/grad students/postdocs, lunch and a presentation (either to the group or the entire department). Not necessarily in that order. If there are in-house collaborators, a meeting with them can be expected but thanks to Mitch I now know that you might also be asked to meet with other professors in the department.

12. Be prepared for a long, energy consuming day. You will likely be putting in an 8-hour day of constant discussions. I have heard rumors that when veteran professors are interviewing a candidate they will set up a meeting in the morning and one at the end of the day. The reason they do this is to first catch you in the morning to see how awake and energetic you are, and then at the end of the day to see if you are the same way. It is a method of finding out who you really are. It is very difficult to keep up a facade for 8 hours. Also if you can keep up your energy that entire time you are probably going to get a lot of work done.

After your visit…
13. Send a follow-up email. A few days after the interview I sent a follow-up email thanking the professor and their group members for their time, reemphasized my interest in their research group and closed by asking for updates on the position. If I did not hear back within a month I sent a second email asking for an update.

14. Funding. Even if you have received an offer that includes full financial support it is still a good idea to apply for postdoc fellowships not only for the money but also the prestige that comes with receiving a fellowship. Most advisors are willing to help you write a proposal based on their work or an original proposal idea. Whether or not you get the fellowship you will still learn a lot about your future projects.

15. Making a decision. Believe it or not, this might be one of the more difficult parts of the process. If you only receive one offer out of several attempts it greatly simplifies your decision. However, if you get a few offers it may be more difficult. This is the time to ask some honest questions about your future advisor and group members. Will they help you find a job? Do they like the area? What is it like working their? Many of us also have to consider the two body problem. Can my significant other find a job there?

The final advice I will give is that the process is so individualized that you should consult everyone you can that has undergone their own postdoc adventure. If others have any more information to share, please do so.

Jul 13

Common Student Difficulties in Organic Chemistry

While cleaning out my newly assigned “war room” (the setting where I’ll strategize on how best to torture students this fall), I came across some fairly interesting documents that were buried in far corners of crowded file cabinets.  They’re nothing personal or discriminating (sorry TMZ), but I saw them as material I could use in upcoming classes.

One of the several I found, titled “Common Student Difficulties in Organic Chemistry,” caught my attention more than the others.  The document, which appears to have been assembled using a typewriter (for the unfamiliar, you can find information about typewriters here), lists problems students encounter while navigating through the dreaded “O Chem”.  In any case, at the bottom of the page, in bold, is the following message:

If you start to get into trouble in this course review this sheet.  Knowing what has gone wrong allows you to fix it.

This closing interested me from a historical perspective.  Did enough students bomb the course to warrant this document’s assembly?  Did the professor discover this or a similar list at an ACS meeting and felt it was prudent to include it in his/her course?  Did the document actually help students better understand the course material?

Although I can speculate until the cows come home, I’m throwing it out to you, the blogosphere.  Do you agree with this list?  Would you change anything on it?  I’m curious to see what the blogger generation thinks (FYI, I believe this list was developed in the 1980′s).

  1. Lack of organization
  2. Difficulty in keeping up with lecture while taking notes
  3. Failure to finish exams
  4. Inability to manipulate three-dimensional structures on paper
  5. Too little drill – lack of repetitive practice
  6. Falling behind
  7. Poor problem analysis
  8. Inability to see and mentally manipulate three-dimensional objects
  9. Insufficient energy and/or motivation for the challenges of this course

Jul 09

Chemists Purposely Withholding Information

I once saw an undergraduate setting up a reflux in my lab, and I could tell immediately it wasn’t going to work. The undergraduate didn’t take enough precautions to ensure that the liquid wouldn’t leak out from the joint connecting the round bottom flask and the condenser. I debated whether I should say anything, but decided that the reagents weren’t expensive enough to warrant my involvement. I also knew that once he made this mistake he would never make it again. The next morning when he came into lab his reagents were a black char at the bottom of his flask. Apparently, chemists not freely sharing all their techniques has historical precedences as professor Martyn Poliakoff explains below.


Jul 06

A Chemist Doing Biology

My postdoctoral research has just begun (started 1.5 months ago) and it will heavily rely on using mice. Thus far I have imaged, dissected, injected, xenografted, castrated, you name it and I’ve already done it or will be doing it to mice. As chemists we are sheltered from the bloody side of science. Sure some chemists on the biological side may have done cell culture or a gel here and there, but most chemists don’t handle things that bite you while your injecting the nanoparticles you made to monitor the progress of the cancer you gave them weeks earlier. Because of this I will be making a series of posts tagged a Chemist Doing Biology chronicling my adventures into Biology.

Brief background: I am a Chemist not a Biologist, my PhD was equal measures of nuclear/radio-chemistry, materials chemistry, organic synthesis, and electronic circuit design (sigh). My new research group is all chemists even though we are in the Pharmacology department. My first task in the group, take the graduate student’s Gd-encapsulated nanoparticles and inject them into mice. Then extract the lymph nodes and get ICP-AES data. A daunting task for a chemist to accomplish, especially with no biologists in the group or anyone having in vivo experience.

Fortunately, I found a happy biology graduate student willing to take her research time to teach me how to do the injection/dissection of the poor mice. When the day arrives, the chemistry graduate student and I whisk the biologist down to the animal cages. We gown up, bring our nanoparticles and chemical reagents in a box, we show the biologist the mice and proceed to the procedure room. We give the mice anesthesia, hand the biologist our nanoparticles and hope for the best. It is at this moment where the disconnect between hardcore Biologists and hardcore Chemists becomes evident.

Biologist, “Can you hand me the syringe?”

Chemists, “They don’t keep the syringes in the procedural room?”

Biologist, “No. Where are your surgical tools, I thought you wanted to extract the lymph nodes?”

Chemists, “I thought you would bring the surgical equipment since you were going to show us how to dissect?”

Biologist, “That’s not how it works. All my mice are immune compromised, so I don’t want to risk using my equipment with wild type mice.”

Mitch to the chemistry grad student in my best postdoc voice, “Well, you better go find some equipment if you want to get your experiment done today.”

Grad student flies out in search of a miracle. I do my best to laugh off the situation with the biologist. The biologist is taking it well, but I was definitely embarrassed. After 10 minutes the chemistry graduate student returns with syringes, needles, scissors, and cutting blades.

Biologist picks up scissors, “These are not surgical scissors, these are to cut paper I can’t use these.” Looks at our cutting blades, “Is that a box cutter? That definitely won’t work on something as small as a mouse. You’re going to have to order real surgical equipment.”

Although that day went horribly wrong at least we learned what would be needed for the next attempt. Last month we used our new surgical tools and performed the dissection of the mice as we originally planned with the biologist. The data from that experiment is amazing and compliments the graduate student’s in vitro work beautifully. The paper is already done and waiting for the PI to submit to Angew.

Next Time: My first tail vein injection and the story of the fainting biologist.


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