Author Archive
Introductory Sections (for a Paper or Your Thesis)
by Phil on Nov 18 2009 (7975 Views)
Long-term Experiments
by Phil on Oct 23 2009 (6333 Views)I recently read this Nature article, where is described what is probably one of the longest experiments ever to be conducted. A population of E. coli was kept for 20 years (!) in a nutrient solution (low on glucose), and samples were taken and deep-frozen after 2000, 5000, 10000, 15000, 20000 and 40000 generations. The authors sequenced the genome of the sample bacteria to investigate the rate of mutations.
Up to generation 20K, the number of mutations grew steadily to a total of 45. The adaptation to the environment, however, only increased strongly in the beginning. It was concluded that the most beneficial mutations were the first to occur. After generation 20K, a change in the mutT gene caused a rapid increase in the mutation rate to result in 653 mutation at generation 40K, but with a neutral signature, i.e. no further adaptation.
What I find most fascinating about this extreme long-term experiment is the confidence of the researchers that it would be possible to analyze the genes at a later point; this was not at all self-evident in the late '80s! In addition, some work had to be done each day, for twenty years. What if the power had failed for a week or so? Of course, this unique opportunity to watch evolution as it happens is very intriguing.
An experiment that took even longer was awarded this year's Ig Nobel Prize in medicine: Donald L. Unger of Thousand Oaks, CA, cracked the knuckles of his left hand, but not his right hand, every day for 50 years to see if knuckle-cracking leads to arthritis. After this time, both hands were fine, so he concluded: "While a larger group would be necessary to confirm this result, this preliminary investigation suggests a lack of correlation between knuckle cracking and the development of arthritis of the fingers." Apparently, the experiment must be repeated.
Vice President of Research resigns at ETH
by Phil on Sep 21 2009 (6137 Views)Another case of scientific fraud has been uncovered, unfortunately at my home university, ETH Zurich.
Quote from the official e-mail: "More than ten years ago, as has just been confirmed by an internal investigation, research data was falsified in a research group then headed by Peter Chen, who is now Vice President Research and Corporate Relations. It would be extremely difficult to find out exactly who manipulated the data."
As a consequence, Chen steps down as head of research of ETH at the end of the month. He will continue working as a professor.
Apparently, somebody in his group had falsified spectra, which was proven by a repeating pattern in the background noise, as well as by the fact that the results could not be reproduced. The spectra were obtained by "zero-kinetic-energy photoelectron spectroscopy" of hydrocarbon radicals. At the time a doctoral student and a postdoc were involved in the project, however, the lab books and some raw data are missing. The two publication in question were withdrawn. Additionally, the student withdrew his doctoral thesis, but retracted the withdrawal later. As of now, it has not been possible to prove the guilt of a specific person, and all people involved deny falsifying the data.
http://www.ethlife.ethz.ch/archive_articles/090921_Peter_Chen_Ruecktritt_MM/index_EN
Leaving the Lab
by Phil on Aug 17 2009 (4861 Views)After 3+ years of manual labour (not counting undergrad studies) it is time to leave the hood and write up the thesis. I must say, it's been a very good time, with good colleagues in the lab and also some reasonable results. I now have about two weeks left to finish the stuff that I'm currently working on.
After all this time, it will feel strange to leave my workspace behind and move to a desk. I know my hood so well, the way all the labware is sorted, that I could probably set up a column blind-folded. Time to move on! From now on, I'll be spending my days in front of the computer screen. In the beginning, I expect the paperwork to be a nice change, but I'm pretty sure that it will get boring really quickly. For my future career, I cannot imagine having a desk job, although I'm sure the point will come where I'll have no choice. The writing time will give me a taste of that future.
Looking back, somehow I feel that I have not accomplished very much during my PhD. It seems to me that I could have obtained the same results in much less time. Some of the problems I encountered now seem pretty trivial to me, so I ask myself why I spent so much time on them. I guess it's always like that in retrospect...
Anyway, I'll add a picture of a kitten (taken from here).
Condensed Print Format
by Phil on Jun 19 2009 (7948 Views)My boss has pointed out this piece of news covered by C&EN. Apparently, starting from July, all ACS journals will be printed in a "rotated and condensed" format, that is two pages on one printed page in landscape format. This is an effort to reduce printing and distribution costs.
In my opinion, this change is just one further step towards purely electronic journals that are not printed at all. I think this will deeply affect the way we present our data and how we look at formatting. Preparing a manuscript in a way meant for printing is different from one which will never appear in print. Some may welcome this change because it saves paper, others will probably miss the possibility of flicking through a new issue of JACS. Although I rarely go to the library to pick up a printed journal, I admit to reading printouts very often (see this post).
Update: Apparently, in 2010 the print versions will stop completely, with the exception of JACS, Acc. Chem. Res. and Chem. Rev. See also Nature News.
Talking to Guests
by Phil on Jun 18 2009 (3821 Views)Whenever a guest speaker is invited to my institute, it is the custom for a few members of our group to speak with him/her about their projects. Normally you have a time slot of about 15 minutes.
It is always a good idea to check the guest's home page first, in order to find out what topics he will be particularly interested in. For instance, somebody doing research in a biological field will not want to know all the details of my synthesis. On the other hand, a synthetic chemist will not be interested in the invasive mechanism of the bug I'm fighting. By now I have a small presentation of abot 20 slides, of which I will focus on the ones most interesting to the guest.
I always like it best when the guests show some interest and ask questions. In those cases I stop giving a "talk" and enter into the discussion. Sometimes the questions are really hard to answer, but they are always very interesting because they look at my work from a new angle. If I get into a real discussion, the usual quarter of an hour seems like a very short time! It can be a pity to have to stop a good conversation because other people are waiting on the other side of the door, waiting to see the guest.
Printing
by Phil on May 25 2009 (3548 Views)Most of the printing of our group (~30 people) is done on just one laser printer. I often find myself walking from the lab to the group library, where the printer is located, and back because of paper jams or printing orders that have misteriously vanished into the digital nirvana. This is making me crazy! Somehow I am unable to proofread a manuscript on my computer screen, so I always need a printout. Maybe I should try and get my own printer.
This leads me to my question: Do you often print papers for reading, or do you always read the PDFs directly? I try to read most things directly, but the papers I cite the most, I also keep in printed form.
Puns
by Phil on Apr 24 2009 (3557 Views)Angewandte is kind of famous (or infamous) for the puns in the graphical abstract subheadings. I came across this one:
Kaim, Hosmane, Záliscaron, Maguire and Lipscomb, ACIE, Early View: To "B" or not to "B",
which is about average for an ACIE pun. Fair enough. Further down the page there was this one:
Winchester, Whitby and Shaffer, ACIE, Early View: To Bi or not to Bi.
Seriously, are we running out of puns?
Elemental analysis
by Phil on Apr 19 2009 (8202 Views)What analytical data are necessary to characterize a new compound in organic synthesis? In the times before NMR, melting points, elemental analysis and IR used to be the available methods (and UV, if applicable). Nowadays, EA isn't required by the journals anymore andv IR is probably going to disappear soon. Additionally, the significance of melting points is quickly decreasing because mostly people take the product as it comes off the column without recrystallizing it. Are we losing something there?
A number of people argue that the ability to get crystalline compounds is essential to be a good chemist, so recrystallization should always be done if possible. As a reward, you get EA-pure solids that are also easy to handle and may give you the occasional X-ray crystal structure (if you want to grow crystals). On the other hand, an additional effort is required: you need substantial amounts of material, which is no problem in a short synthesis, but can be a problem if it takes twenty steps to get to the product. If I have tediously made 50 milligrams of a material, I don't really want to give ten away to be burned.
I wonder if elemental analysis is still a necessity today. In most cases you get all the information you need from NMR (identity and purity). What EA gives you is confirmation that your compound is pure as well as dry. Still, is it worth the trouble or just a waste of time? I suppose it all depends on the kind of research you're doing. If you are "target-oriented", as medicinal chemists like me are, I do not think it is worth it, as long as the final compounds being tested are pure. I suppose this is being sloppy, but I want to get a series of compounds in a reasonable amount of time. It might be a bit different in a total synthesis project, where the focus is on the pathway rather than the target compound per se.
