Just in case you hadn’t spotted this (among other naturejob listings), Nature Chemical Biology is looking for a locum (temporary) editor. All the details are here – the most important one, perhaps, being the deadline of March 17th. The only down side is that you’d have to put up with my dumb jokes all day long…
Catherine (associate editor, Nature Chemical Biology)
1. What made you want to be a chemist?
When I was twelve years old, I reasoned that if I only knew what matter was made of, I would understand “Life, the Universe, and Everything”. Chemistry not only seemed to provide an answer to this big question but, luckily, the recipes to make fun explosives.
2. If you weren’t a chemist and could do any other job, what would it be – and why?
I guess being an artist would be an attractive alternative although I think I lack talent. Both the art that artists can create and the molecules that chemists can make, are truly novel.
3. How can chemists best contribute to the world at large?
Chemistry is different from biology and physics in that it creates new things. Chemistry has changed the world with the invention of new molecules and reactions. Just consider antibiotics, the discovery of nuclear fission, the polymerase chain reaction, cracking or the industrial synthesis of ammonia. All these achievements and many others had a profound impact on the world. The next big challenge for chemists is just around the corner: Solving the energy problem of our planet!
4. Which historical figure would you most like to have dinner with – and why?
Emil Fischer, a master of chemical intuition and an organic synthesis genius. I wonder why and how he was so much ahead of his time.
5. When was the last time you did an experiment in the lab – and what was it?
In 2004 I had a relatively small group, but was convinced a certain molecule would be a good catalyst. It was Easter Sunday; nobody was in the lab and so I made it myself. It involved a Grignard reaction and an acetalization. Unfortunately, the catalyst was pretty much inactive…
6. If exiled on a desert island, what one book and one CD would you take with you?
B.K.S. Iyengars’s “Light on Yoga” and Bach’s St. Matthew Passion.
Ben List is in the Department of Homogenous Catalysis at the Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany, and develops new concepts for catalysis.
Posted on behalf of the Prospective Professor
When I started the process of finding a job, I assumed that the most challenging aspect would be the endless grilling during the interviews. I imagined that during my individual meetings with faculty members they would challenge my basic chemistry and biology knowledge, test me on my familiarity with their work and just generally attempt to check the integrity of my fundamental scientific knowledge. I expected that the proposal defense seminar (or “chalk talk”) would be filled with impossible questions, many that could only warrant the answer, “That’s an interesting question, I will have to look into that” (read as, I have NO idea).
I’m happy to report that the experience was nothing like this. People were excited to meet me and tell me about their department. Most started the meeting by saying, “Do you have any questions about our department that I could answer for you?” It was in less than 50% of the cases that we actually got around to talking about science. And while I wouldn’t call the “chalk talks” easy, I can honestly say that it was only on the rare occasion when I didn’t have an answer to a question or that I felt that people were “testing” me instead of being genuinely curious about my ideas.
It turns out that despite the huge amount of concern I poured into the interviews, I hadn’t recognized what would be the most challenging aspect of the job hunt: Deciding which job to accept.
There are so many factors to consider ranging from the quality and number of grad students, to instrumentation availability and collegiality of the faculty. I have to take into account the start-up and salary offers, teaching requirements, fundability of the institution, space availability, and the mission of the department. Next, I must decide if a chemistry department, biochemistry department or medical school would best fulfill all of my needs. And this is before I start to ponder the more personal issues such as location, cost of living, and personal relationships. How do I weigh each of these issues so that they are represented adequately in my final choice?
…
If I knew the answer to this question, I would have already made my decision!
Posted on behalf of Retread
Much of the training of budding neurologists in the 60s was concerned with how to perform a good neurological exam and interpret the results. Various constellations of abnormalities pointed to different regions of the nervous system and the history often told us what sort of trouble was present there. Essentially we were inferring abnormalities of structure from abnormalities of function.
Why not just look? We had only two ways to do so back then (1) sticking a needle in an artery and injecting a dye which X-rays couldn’t pass through (radio-opaque dyes – if you don’t already know what they are, think of what you’d want to synthesize) – this had a 1–5 % stroke rate at the time (2) injecting air via a spinal tap and taking X-rays subsequently (I’m not kidding).
The advent of computerized axial tomography (CAT scans) and MRIs (magnetic resonance imaging) changed all that. We were able to directly look at structure without a decent exam. Not only that – problems could be picked up before they produced changes in function (e.g., earlier).
Naturally, neurologists were panicked, thinking that we would soon become the buggy whip manufacturers of medicine. Somehow, telling my colleagues that MRIs showed the essential correctness of quantum mechanics didn’t help, producing only blank stares and decreased referrals.
Telling the man in the street that spectroscopy alone shows the correctness of quantum mechanics (sharp absorption and emission lines show that only certain energies of molecules and transitions between them are permissible) just doesn’t cut it. But everybody knows what an MRI is.
Forget the wave nature of light (for today). Think of photons as baseballs travelling at various speeds (I know, light has but one speed and its frequency determines its energy just as the speed of a baseball determines its kinetic energy). Throw the baseball at a window. If you throw it fast enough (high kinetic energy) it goes through, if you throw it slowly it doesn’t. Everybody knows that.
Not so with the light used for MRI. They are radiowaves and contain around one millionth of the energy of visible light, yet they go right through our skull and brain rather than bouncing back. Why? The only way we can get them absorbed by our brains is to place ourselves in a strong magnetic field in the scanner. The magnetic field essentially creates two new energy levels so close together in energy that the tiny energy difference between them matches the energy of the radiowave permitting it to be absorbed. Without absorption, no pictures. Certainly counterintuitive, but used every day all over the world. Quantum mechanics rules (but weirdly).
Retread
I’m sure that some of you may have noticed that the signature to my Friday post on ‘Reactions’ finally had a link in it to Nature Chemistry.
This is the first incarnation of the Nature Chemistry website and just covers the basics at this point. It will be fleshed out with a lot more details in a couple of months’ time, but at least you can now see the colour…
Stuart
Stuart Cantrill (Chief Editor, Nature Chemistry)
Posted on behalf of the Rookie Rocky
I still remember most research institutions that I interviewed with told me that my job would be 40% teaching, 40% research, and 20% service. What they did not manage to convey though, is that actually another 200% of the job for a junior faculty member goes to grant writing. A perfect example is this, the second semester in my rookie year as an assistant professor: I am off teaching duty. However, if you think I have one more free minute than last year, think again. Actually, don’t think again – I don’t have time to wait, because another grant is due tomorrow!
The reason for my long absence from the Sceptical Chymist is purely because my time is almost all caught up by non-stop grant writing, revising, re-writing, and submitting in the never-ending grant application cycle. As most starting academics do not have large amounts of external support (this may have started changing, as some lucky ones do have a significant amount), junior faculty members tend to apply for everything they can find because (1) the competition is so keen, and you never know whether your proposal might wow a particular group of reviewers, and (2) the amount of such support usually is relatively small. Thus, even if you get some grants funded, each one does not help that much in paying your bills. This results in many short proposals built on similar ideas with only slightly twisted applications or directions. On the top of that, the effort to put together even one of these small grants is extensive. I’m not sure what people with larger groups do; in a public school like mine, I have to collect over twenty different forms and files for a small grant application, including a budget, justification, CVs, letters, research plans, approvals…etc., etc. You keep navigating among ten different offices on campus and talking with people who are in charge of contracts, IP, safety, budgets… Toward the end, getting the grant out of the door becomes the only goal. Is there anything else that makes you feel better than finally sending these 100-page paperweights that you have read and modified a hundred times to someone else and making it his/her burden?
…
Well, getting a phone call saying your effort actually paid off would definitely be better. Keeping my fingers crossed…
This is just a quick blog to mention a thought-provoking article that Peter Murray-Rust wrote for Nature recently, which discusses chemists’ contributions to open-access data and software. The article is now available for free, for a limited period of a month – so if you haven’t seen it, click here to have a look.
I’d love to hear your thoughts about this – do you agree with Peter that all chemistry data and software should be open access?
Andy
Andrew Mitchinson (Associate Editor, Nature)
As you will have noticed, today is Friday, and that brings with it a new Reactions piece to the Sceptical Chymist – but this one will be slightly different to the previous 52. That’s right, we’ve racked up a whole year’s worth, and so ‘Reactions’ is celebrating its first birthday!
Apart from finding out what people would want to be if not chemists, one of my favourite things is finding out who they would invite to dinner. A quick survey of the last year shows that the most popular dinner guest is Leonardo da Vinci (with 5 votes). Following on closely is Jesus (4 votes), then Feynman, Einstein, Darwin and Mozart were popular choices (each with 3 votes). Isaac Newton and Nelson Mandela were each picked twice and it’s worth noting that a few US presidents made the cut, John Adams and Abraham Lincoln – and although nobody thought to invite John F. Kennedy, his brother Robert was. Have a surf through the older entries – it’s quite interesting. I would suggest that the strangest choice was made by Mark Green…
So, at this point, I want to ask you – the readers – some questions. Please leave your responses as comments to this post, and I encourage all of you to join in.
Should the questions change?
‘Reactions’ will continue, but we wonder if some of the questions are wearing a bit thin at this point – our least favourite is probably number 3, ‘how can chemists best contribute to the world at large?’ because most people say the same sort of things… Of the other questions we currently use, are there some that you really like (or dislike) and if so, why? Do you have suggestions for other questions that you would like to see us asking?
Who would you like to see featured?
As has been commented on, it’s obvious that there are a lot more male than female chemists featured in the ‘Reactions’ series. I don’t know the total numbers of chemists that we’ve asked to participate, or the gender breakdown of those, but the only criterion we have in terms of who gets featured, is those that say ‘yes’. A very large number of ‘Reactions’ e-mails go unanswered, and a lot of people do say ‘no’. I would imagine we have asked more men than women, but not in the proportions ultimately featured on the blog.
If you have any suggestions of who you would like to see featured, either in terms of subject area, or specific chemists, we’ll see what we can do. Again, however, there is no guarantee someone will agree to be featured.
Normal service will be resumed next week, Ben List, who has just had a paper published in Nature, will be answering the current set of six questions.
Stuart
Stuart Cantrill (Chief Editor, Nature Chemistry)
If a picture is worth a thousand words, what’s a journal cover worth?
Well, in 2007, when I was on a paper that was lucky enough to be featured on the inside cover of Angewandte Chemie, it was 1000 Euros (that’s almost $1500). If our artwork had been judged to have been worthy for the real cover, i.e., the one on the outside, it would have cost 1800 Euros – I don’t know how the prices have changed since then. It’s a similar story at Chem. Commun. – one of my papers made it to the inside cover back in 2005, and I think a ‘contribution’ was made to the production costs – I don’t recall how much that was.
There has been some debate on journal cover art – some journals do have it and some don’t. Some charge for it and some don’t. Most authors in my experience are quite eager to have their work featured on a journal cover – it’s a big glossy colourful advert for their work – and occasionally they make for nice posters too!
When establishing a new journal, especially here at NPG, it’s another part of the process that needs some careful thought. A ‘pre-launch’ cover can be used on sample issues and in marketing campaigns to raise awareness of the journal in the community – in this case, the cover is not only an advert for the work it depicts, but the journal itself.
The reason I bring this up is that we’ve just finalized our ‘pre-launch’ cover for Nature Chemistry. Just like the other Nature research journals, on the cover of each issue we will have artwork that is related to the content inside – usually one of the research papers. Obviously we have no inside content yet – and so we had to think of an image that says ‘chemistry’ – and be inclusive of as many of the sub-fields as possible… not easy, and unless you just slap a stereotypical periodic table or a cheesy line-up of glassware containing pretty coloured liquids on it, there’s a bit of thought involved. And you also want something that is visually striking.
I think we’ve checked a lot of the boxes and have a very good cover – you’ll start seeing it on the web and at some conferences in the near future (and I’ll fill you in on the details of exactly what the image is and where it came from when it goes public…).
Stuart
Stuart Cantrill (Chief Editor, Nature Chemistry)
Posted on behalf of Retread
An incredible article appeared last month in the journal Science. If it can be verified and if it applies generally, our conception of just how genes coding for protein are turned on will be radically changed (yes, there are many other kinds of genes other than those coding for proteins). If DNA compaction, nucleosomes, histones, lysine methylation and demethylation, the histone code, nuclear hormone receptors (particularly the estrogen receptor), DNA glycosylase and topoisomerase aren’t old friends have a look at the first comment on this post for the background you need. Don’t worry, there is plenty of chemistry to follow.
Some histone code modifications are reversible, particularly acetylation of the epsilon amino group of lysine. Enzymes acetylating histone lysines are called histone acetylases, those removing it are called histone deacetylatases (HDACs). However, lysine methylation was thought to be permanent until ’04 when several enzymes able to demethylate lysine were found. One such enzyme is called LSD1 (it has nothing to do with the hallucinogen). It removes the two methyl groups from lysine #9 of histone #3 (H3K9me2). If this modification is present on a nucleosome near a gene, the gene is silenced, so the methyls must be removed so the protein it codes for can be made.
The estrogen receptor + estrogen complex bound to the ERE (the estrogen response element – a 15 nucleotide DNA sequence) triggers H3K9me2 removal. The process of demethylation is oxidative (how else would you split a nitrogen to hydrocarbon bond?). Hydrogen peroxide is produced, a loose cannon which oxidizes the juicy electron-rich bases of DNA nearby, forming in particular 8 oxo-guanine, as guanine is the most easily oxidized DNA base. Since 21% of the DNA bases in our genome are guanine, H2O2 doesn’t have far to look. This calls in some fairly heavy artillery (DNA glycosylase to remove the 8 oxo-guanine, topoisomerase IIbeta to unwind the DNA so it can be repaired, the repair enzymes, etc, etc…). Naturally this opens up the compacted DNA structure around the gene allowing RNA polymerase II to do its work transcribing the estrogen responsive gene into mRNA (once the damage is repaired).
So according to this paper, estrogen turns on gene transcription by damaging DNA. This is fantastic (if true). There’s more. The estrogen receptor is but one member of a group of proteins called nuclear hormone receptors. The name comes from the fact that other hormones (progesterone, androgen, thyroid, glucocorticoids, mineralocorticoids) have their own proteins that turn on (or turn off) genes the same way. Subsequently it was found that some vitamin metabolites (vitamin D3, vitamin A) have similar receptors even though they aren’t hormones. The human genome contains 48 such proteins. Less than half of them have known ligands. Those with known ligands have their finger in just about every metabolic pie in the cell.
One final point. It has been estimated that 8-oxoguanine is formed 100,000 times each day in every cell. Perhaps its formation is physiologic rather than pathologic. Where does that leave antioxidant therapy, which has been touted to do everything but cure hemorrhoids? Well, one such trial was done on 29,000 Finnish men at high risk for lung cancer (they were smokers) [New England J. Med. vol. 330 pp. 1029-1035 (1994)] Alpha tocopherol (one antioxidant used in the study) didn’t decrease the incidence of lung cancer, and there was an 18% higher incidence of lung cancer among the men receiving beta carotene (another antioxidant). In medicine, theory is great but data trumps it every time.
Retread