I didn't make it to the essay about Mendeleev that I mentioned earlier today... got sidetracked by an interesting comment piece by Professor Raymond Tallis in today's Times about the public's perception of science. It's definitely worth a read and can be found here.

This led me to Sense about Science - a charity that provides a bridge between the front lines of science and the general public. The section on making sense of chemicals should be mandatory reading for everyone...

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

Posted by Stuart Cantrill at 04:20 PM | Permalink | Comments (1) | TrackBacks (0)

Just a quick post about a couple of papers I saw while surfing through Angewandte Chemie earlier today.

The best porphyrin structure I've seen for a while is right there in Early View - Harry Anderson and cohorts in Oxford have used a porphyrin to template the formation of a conjugated octaporphyrin ring (thought I'd mention this before carbon-based curiosities get a hold of it... I'll see about getting our blogroll updated as ChemBark needs a direct link as well...).

Other than that, there's an essay about Mendeleev that will keep me occupied on the train this evening, 100 years since he died apparently...

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

Posted by Stuart Cantrill at 10:27 AM | Permalink | Comments (1) | TrackBacks (0)

Have you ever considered how far chemistry has come in such a short space of time? As a News & Views editor, I get to look through the really old issues of Nature, searching for interesting snippets that can go into our ‘100 Years Ago’ section. It’s a real eye-opener to see how little we knew in 1907, and it sometimes makes me nostalgic for a more innocent age. So, I thought I might indulge myself (and hopefully you too) by picking out some choice chemistry from the February 21, 1907 issue of Nature.

In the ‘Letters’ section, there was the latest correspondence in a long running debate about the conditions required to rust iron. There seemed to be a consensus that oxygen and water were required, but more controversially some people thought that carbonic acid was also necessary. And how could it be explained that iron immersed in potassium dichromate solution doesn’t corrode?

Chemists were still very interested in explaining the properties of materials such as leather or wood, so it comes as no surprise to find a letter describing a chemical test for the strength of wheat flour. To be precise, the author was trying to find a physical parameter to explain why different flours give different sized loaves from the same quantity of flour. The answer depends on the amount of carbon dioxide liberated upon the addition of yeast; this in turn depends upon the amount of sugar in the flour — another mystery is solved!

Medicinal chemists and those of a pharmaceutical bent may be interested to hear that a plant growing on the plains around Kuala Lumpur had apparently been identified as a cure for ‘the opium habit’. Quite sensibly, however, the author comments that “it would be premature to express a definite opinion until a larger quantity of the material is available for chemical analysis”. It’s hard to imagine how they could have successfully analysed it in 1907, but you’ve got to give them full marks for enthusiasm.

So, what to conclude from all this? One thing that strikes me is that people back then seemed much more willing to debate issues in the open — the arguments about rust had been rumbling on for weeks, with many disagreements and new revelations appearing all the time. Somehow, that doesn’t seem to happen so much now. Have scientists become more secretive, or polite? Or is research nowadays more competitive, so that people are less inclined to disclose their results freely?

Posted by amitchinson at 11:51 AM | Permalink | Comments (1) | TrackBacks (0)

[Welcome to a new (and hopefully regular) feature on our little chemistry blog here. 'Reactions' will feature chemists answering questions ranging from why they entered the field to what reading material they would like to be stranded on an island with... - Stuart]

1. What made you want to be a chemist?

Like many who choose to study chemistry at university, an excellent and enthusiastic school teacher.

2. If you weren't a chemist and could do any other job, what would it be - and why?

If I was miraculously granted the ability to do any of them well (unfortunately I have severe limitations in all the qualities required!) then prime minister, rock star, footballer.

3. How can chemists best contribute to the world at large?

By changing it for the better. This can be in obvious ways - introducing new technologies that contribute to solving global problems like pollution, energy needs, health and sustenance etc - and in less obvious ways, such as improving the way the general public understand the world, thereby making it safer by removing the influence of religions and other superstitions on societies and individuals.

4. Which historical figure would you most like to have dinner with – and why?

Jesus or Einstein. So many questions...

5. When was the last time you did an experiment in the lab - and what was it?

Back in 2002 I was particularly excited about a compound one of my group was preparing at the end of a long synthetic sequence. It was a friday night and I was impatient to see the NMR of the product. So I worked up her reaction without asking and spent all Saturday and Sunday running chromatography columns to try and isolate it. Needless to say, I never got it and by the end of the weekend and half-a-dozen columns later there was nothing left. Jenny Wong, bless her, didn't say a thing - at least not in my presence! - and went back and did the 15 step synthesis again (this time without telling me when she put the final reaction on!).

6. If exiled on a desert island, what one book and one CD would you take with you?

'Card College' by Roberto Giobbi - I'd finally have time to study! [Leigh is a magician as well as a chemist - Ed.] - and any live bootleg of Elvis Costello from the 80s.

David Leigh is in the School of Chemistry at the University of Edinburgh and works on synthetic molecular motors and machines.

Posted by Stuart Cantrill at 07:19 AM | Permalink | Comments (1) | TrackBacks (0)

Catherine’s entry on toys (here) reminded me of clothing and accessories items I had seen earlier. Kyle at Chem Blog has been selling T-shirts, mugs, wall clocks or postal stamps – which are legal in the US and everything. I didn’t even know that was possible, but I just checked and found out that, in several (all?) countries, you can indeed customize stamps.

The folks at YellowIbis also make T-shirts featuring chemical structures. They picked molecules particularly relevant / amusing – so you can let everybody know that you’re cool as *insert menthol structure*, wear a green jumper showing the structure of a “lucky” 18-crown-6-ether for Saint Patrick’s Day, or alternatively you might want to give this T-shirt to a labmate.

In particular, I’d come across the made with molecules jewellery line, representing the actual structure of certain molecules influencing our behaviour (such as neurotransmitters or hormones). In a less obvious way – except for the DNA ones – the design of these items at Sci Wear also refers to chemical substances, each piece containing the actual microscopic picture of a molecule.

Which molecule would you like to wear? Personally – and you might say I’m biased – I can’t decide between the caffeine necklace and the chocolate (theobromine) earrings...

Anne

Anne Pichon (Intern, Nature Reviews Drug Discovery)

Posted by Anne Pichon at 04:56 AM | Permalink | Comments (5) | TrackBacks (0)

This is my first post...it's all very exciting...so here goes! Has anyone been listening to crusading environmental chemist Jim Lovelock recently?

Bizarrely I fell asleep to his voice on Sunday night then woke up to it again in the morning (on Radio 4 of course). Lovelock strongly believes that nuclear is the only viable energy option for the future, because climate change is ‘past the point of no return’ and renewable energy is underdeveloped. Read a Times review of his latest (and rather pessimistic) book and find out why he says wind farms aren’t green.

Five ways to save the world on BBC2 Monday night presented high tech solutions to climate change. What do people think about these ideas, or about nuclear power for that matter?

Samia

Samia Mantoura (Intern, Nature Physical Sciences)

Posted by Samia Mantoura at 05:17 AM | Permalink | Comments (2) | TrackBacks (0)

Hi everybody,

As Stuart mentioned, a bunch of us NPG chemists got together recently to chat about all things related to Nature and chemistry. While we were gathered together, our thoughts naturally turned to the blog, and to brainstorming about different features that could make the Sceptical Chymist more fun and interesting for everyone (Is it possible, you say? Hard to believe, but it's true...). This entry is thus the first to venture forward into new territory. This feature is basically the same as the 'Journal Club' included as part of Nature's Research Highlights, except that we get to pick the scientist, so that's more fun for us. And, more to the point, the online posting means that we can all chime in about the paper, or at least more quickly check it out ourselves through the magic of links. We'll be contacting more of you in the weeks and months to come, but in the meantime, please enjoy this highlight, courtesy of an excellent scientist and all-around nice guy:

Chemically engineered extracts as an alternative source of bioactive natural product-like compounds

by Lopez et al., PNAS 2007, 104, 441-444

Everybody agrees that structurally diverse compound collections are necessary as sources for bioactive molecules. To find new drugs, industrial research seems to particularly enjoy mining synthetic collections using elaborate cheminformatic tools to go and buy the best candidates for testing, a management optimized strategy to shoot for the average while missing the innovative. On the other hand many synthetic chemists favor the view that natural products are the best innovative source of bioactives. Is there anything else in sight, for a change? The report by Lopez et al. on "chemical engineering" of natural product extracts refreshes bioactive discovery in a particularly simple and elegant manner. These authors report an experiment in which a crude natural product extract is reacted with hydrazine to effect chemoselective derivatization of carbonyl groups, which are abundant in natural products, to hydrazones and nitrogen containing heterocycles. In this manner, they create a new brew of compounds which, in contrast to natural products, contains nitrogen rich functional groups that are particularly favorable for bioactivity, thus providing for what Nature had obviously forgotten. This new witch's brew is then tested directly for biactivity to guide isolation of active compounds. In their example, the authors found an antifungal aromatic compound containing a pyrazole group apparently derived from the reaction of hydrazine with a simple flavone. Although the paper is only sketchy about the details, it is a great experiment, which, to my knowledge, is new. With such a simple setup, there is little doubt that many will follow in this path to discover new chemical wonders.

Jean-Louis Reymond

University of Bern

Bern, Switzerland

Catherine (associate editor, Nature Chemical Biology)

Posted by Catherine Goodman at 10:27 AM | Permalink | Comments (1) | TrackBacks (0)

Hi all,

I don't know how it's possible, since I'm pretty convinced that it's still early-mid January, but somehow our March issue has gone live. This issue is jam-packed with interesting science, including zebrafish-insect hybrids, vitamins gone wild, and click chemistry crossed with kinases (try saying that three times fast!).

In addition, we have (as always) our editorial, which for this month focuses on the unique challenges of publishing in interdisciplinary fields. In our experience, these challenges primarily arise from the different interests and expectations of widely varied scientists, whether in a collaborative or author/referee relationship. In putting together the editorial, we heard a few anecdotes of scientists from different fields trying to coordinate their sense of what aspect of a research project is most interesting, or what conclusions are reasonable based on a given data set. Do you have any experiences that stem from this intellectual divide? Or do you have any advice for scientists looking to get started in your field? Or, most importantly, what would you do with your own fish-insect hybrid?

As always, thanks for reading!

Catherine (associate editor, Nature Chemical Biology)

Posted by Catherine Goodman at 06:44 PM | Permalink | Comments (0) | TrackBacks (0)

Hi everyone, this is my first entry so I thought I’d blog about… well, blogging.

Last week I attended a talk by Tony Hey, from Microsoft. He was speaking about e-science and, among other things, talked about CombeChem, an EPSRC project based at the University of Southampton. A small part of the project (see this BBC news article last year) involves replacing the traditional notebook by a digital form. The degree of privacy of the digital lab book could be determined by the user (only themselves? their research group? their university?). Of course the ultimate openness in science is Jean-Claude Bradley’s Open Notebook Science initiative at Drexel University, where he and his group use a wiki as a lab notebook (UsefulChem) and make all their data publicly available. Bill Hooker at 3 Quarks Daily also refers to it in his trilogy about the future of open science, where his posts progress from Open Access to the research literature (here), to the “openness” of data (here), to a fully open practice of science (here).

Nobody can really predict what the future of science will look like. But for now, would you consider blogging about your unsuccessful experiments - those that will never make it into a paper or thesis - to make them available to everyone?

Anne

Anne Pichon (Intern, Nature Reviews Drug Discovery)

Posted by Anne Pichon at 05:09 AM | Permalink | Comments (4) | TrackBacks (0)

I was just talking with Catherine, and we can't remember if "a week in the library will save you a day in the lab" or if "a week in the lab will save you a day in the library"? I guess if you're starting a new project, maybe it's best to set up a whole bunch of experiments to see what works (steering clear of the dogma you’d find in published papers). But if you're nearing the end of a total synthesis, you probably want to play it safe with your milligram/sub-milligram quantities of your natural product and spend a bit more time in the library trouble-shooting problems...

What about other quotable quotes? Was RB Woodward right ("A scientist has to work very hard to get to the point where he can be lucky.") or was Ralph Waldo Emerson right (“Shallow men believe in luck. Strong men believe in cause and effect.”)? (The Google fight results are closer than you'd think...) Is time on your side or does time pass more quickly as your Ph.D./post-doc progresses?

What do you think/what's your scientific philosophy? Does it match up with the prevailing philosophy of your lab? What other quotes (or song lyrics) come to mind when you think about the last six months of your scientific research?

Unfortunately, we aren't able to set up a poll on the blog, so we'll have to do it the old fashion way - please leave us a comment with your thoughts...

Joshua

Joshua Finkelstein (Senior Editor, Nature)

Posted by Joshua Finkelstein at 03:09 PM | Permalink | Comments (4) | TrackBacks (0)

I must admit, I really enjoy riding the bus to work - it's not just because of the unusual people you tend to meet on public transportation (though that's half the fun), but because the rides are long enough for me to skim through various journals to see if there's anything I want to read later on in the day. Normally there are a few things that catch my eye, and I'll set them aside for a lunch break (or while I'm waiting for the bus at the end of the day). But my plan to quickly skim through this week's Science failed completely - it's jam-packed full of interesting articles, and I needed to set aside a few hours to read through them all.

It's a special issue focused on 'Sustainability and Energy,' two topics that are obviously important these days - it starts out with a few 'Profiles' of major players in the field (I especially enjoyed reading the ones on Dan Nocera, Jay Keasling, and James Dumesic) and then there's a number of 'Perspectives' (I'd recommend starting with the ones by Whitesides & Crabtree and Stephanopoulos).

Reading through this material made me feel like (somewhere along the way) I should have had a class or two that focused on the chemistry/biochemistry of energy research. Before I started working at Nature, I hadn't really been exposed to this topic in much detail, despite taking (what felt like) dozens of classes in my undergraduate days. Those classes tended to focus on 'pure' chemistry/shy away from applications, and the graduate classes I took were fairly specialized/on completely different topics...

One of my undergraduate physical chemistry classes had both chemists and civil engineers in it, and I remember that the questions asked by the civil engineers ("Is this why cement dries on the outside first?") generally annoyed the chemists - is this a clash of the two cultures (i.e., science vs. engineering), or were my experiences the exception and not the rule?

Do you think we are doing enough to make sure that future generations of chemists are prepared to tackle important problems in energy research? Sure - you could argue that applied chemistry is the domain of the chemical engineers and that chemists shouldn't learn this sort of stuff at the undergraduate level. But shouldn't we be doing more to expose undergraduate chemists to important topics involving applied chemical research (for example, by requiring chemistry majors to take a chemical engineering class or two)?

Joshua

Joshua Finkelstein (Senior Editor, Nature)

Posted by Joshua Finkelstein at 12:42 PM | Permalink | Comments (2) | TrackBacks (0)

I've spent the last few days in Boston in the company of many of the other self-confessed chemists who work for Nature Publishing Group. We've been thinking of ways to focus and improve our coverage of chemistry and some of the changes you will see relatively soon - here on the blog and also a rejuvenated chemistry portal on nature.com.

The reason I'm writing about this? - Well, my first title was going to be 'Brainstorming in Boston', but then I got to thinking about what the collective noun for chemists is? See the Wikipedia entry for a general list - one of my favourites has always been a 'murder' of crows.

So, chemists of the world, how best to describe us collectively? A quick search on Google found suggestions such as 'solution' or 'aliquot' - but surely we can do better?! We could even break it down by field... what do you call a group of organic chemists, or physical chemists? (I'm talking collective nouns here - not collective insults...!!).

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

Posted by Stuart Cantrill at 05:00 AM | Permalink | Comments (10) | TrackBacks (1)

While all of us are familiar with a certain amount of brevity (via acronyms, such as ASAP) in our daily writing, it seems that the internet chat lingo and texting revolution is finally starting to catch up with even me, for whom writing this blog is by far the most technological thing I've ever done (even my email software knows that :) is a smiley face!). And now that I'm starting to tell people things 'BTW' or to send them emoticons, I've been thinking more about what could be done with this shorthand.

What I've come up with is labicons. Chemicons? I don't have a perfectly catchy title, so you all will have to make some good suggestions. Anyway, the point is that chemists don't have a great way to communicate without spelling out all kinds of things. Here are the new abbreviations I've thought of,

\/ = Extraction (or extract)
|| = Running a column
[] = Running a TLC
() = Stir/stirbar
C- = Round bottom flask (look sideways) (this one, to be fair, is not much more concise than RBF)
L! = Measuring something (probably liquid)
ooo = reflux/heating in general (get it? It's the bubbles)
XX = Crystallize/crystallization

I can't figure out 'rotovap,' which seems like the major remaining thing that chemists stereotypically do.

Now, you might be wondering when you would use these silly things, but I think they will really come in handy. For example, imagine you (as a professor) are off at a conference, and you get an email from your student about a problem in the lab. The whole thing could be wrapped up quite quickly:

Student: My rxn didn't go. ??
Prof: Did you ooo?
Student: Yes. No XX.
Prof: Try \/, EtOAc
Student: Thanks!

Or, for students who are meeting up with friends for a beer after a hard day in the lab, but work in different buildings:

Josh: Ready?
Stu: Got to ||
Josh: OK. I'll [] till then

Or, for people in the same lab that want to complain about a labmate without being heard:

Stu: I can't find my C-!
Josh: Check with Terry. He took all my ().
Stu: Argh...

You get the idea. Well, see what you think (and definitely chime in if you figure out how to say rotovap!). In the meantime, I'm off to ooo my lunch...

Posted by Catherine Goodman at 01:36 PM | Permalink | Comments (6) | TrackBacks (0)

I went to visit my sister recently, and her daughter has a toy pancreas. No, really! For a children's toy, it's pretty non-descript: it's similar in shape and size to a yellow squash, but (I think) has a little face on it. Somehow, I am not able to enlighten you with a picture (the all-powerful internet has failed me), so you'll have to imagine it. Not only is it funny that she plays with it in general, but that she, at 4 years old, could quite happily request it. "Mom! I want my pancreas!" or "Mom! Jack took my pancreas!" Actually, it's starting to sound like an episode of ER...

Hospital dramas aside, I also knew about these stuffed microbes, which are equally hilarious. I think what's happening is that someone who feels very strongly about increasing the numbers of scientists in the US (or anywhere, really) has decided that targeting high school students is not working. The kids are already turned off to science at that point. So, they think, let's start earlier. Get these 4-year olds to appreciate the difference between the Ebola virus and sleeping sickness! Get them to love their kidneys, and we'll have a new generation of microbiologists and doctors ready to go. Even the physicists have their mascot...

In all this, though, I wonder: where are the chemists? I did find a Marie Curie finger puppet, but I think we need to step it up in order to really promote chemistry among our kindergarteners. The problem, of course, is to identify chemistry-related items that could be translated into plush toys. Individual atoms may be difficult to make interesting, since they would all be quite similar. What about glassware? Wouldn't every child love a stuffed round bottom flask? I think molecules would also work, but manufacturers might balk at all the little pieces...

What do you think would make a good toy? And, more importantly, what have I done with my pancreas?...

Catherine (associate editor, Nature Chemical Biology)

Posted by Catherine Goodman at 06:24 PM | Permalink | Comments (5) | TrackBacks (1)

Looking for something to read while you're waiting for the rotovap to free up or the PAGE gel to finish running? You might want to take a look at yesterday's issue of Nature, which has a number of chemistry/chemical papers. In addition to the paper by Serreli et al. that Katharine and Stuart mentioned, there's a News & Views piece from Steven Nolan on Craig Forsyth's recent ACIE paper and a paper from Stern et al. that describes miniature, ultra-sensitive sensors that can detect unlabeled antibodies at concentrations below 100 femtomolar (and can monitor the cellular immune response in 'real-time').

There's also a cool paper involving the TRPA1 channel - TRP channels respond to "temperature, touch, pain, osmolarity, pheromones, taste, and other stimuli," and the TRPA1 channel specifically responds to a range of structurally-diverse compounds, including mustard oil, acrolein, and icilin.

In Macpherson et al., the authors used 'click chemistry' to show that derivatives of mustard oil and cinnamaldehyde covalently bound to the TRPA1 channel. They used mass spectrometry to identify fourteen TRPA1 cysteine residues that reacted with iodoacetamide, three of which were required for normal channel function. From a chemical standpoint, this might not seem all that surprising, but this is apparently the first ion channel known to be activated by this mechanism, and I think it's interesting to see how "tuning TRPA1 to respond to covalent modification by reactive compounds ... [enables the nervous system to] directly assess the noxious environment of sensory neurons." For those of you teaching biological/bio-organic chemistry courses, this might make a good test question - it's a nice 'real world' example of how understanding basic organic chemistry can be used to explore how an enzyme works...

Joshua

Joshua Finkelstein (Senior Editor, Nature)

Posted by Joshua Finkelstein at 02:57 PM | Permalink | Comments (0) | TrackBacks (0)

CNN is now covering David Leigh's molecular 'information ratchet' that was inspired by Maxwell's demon (which Katharine wrote about here yesterday)...

I do despair about the communication of science to the public when the story contains statements like this:

"His mechanism traps molecular-sized particles as they move. As Maxwell had predicted long ago, it does not need energy because it is powered by light."

Is there any hope!?

Stuart

Stuart Cantrill (Associate Editor, Nature Nanotechnology)

Posted by Stuart Cantrill at 07:38 AM | Permalink | Comments (2) | TrackBacks (0)

I was asked if Dave Leigh's latest paper in this week's Nature was all that special after all - Leigh claimed to have recreated James Clerk Maxwell's famous thought experiment about the second law of thermodynamics and a demon (read the news story I wrote here). But in reality, Leigh didn't actually recreate the demon, he made a molecular machine that can force a system to go against chemical equilibrium after being inspired by Maxwell. Is that so special?

Some would say yes, very much so. And not just by battling against equilibrium. The complexity demonstrated in Leigh's system is unprecedented. His machine cleverly traps the ring of his rotaxane at one binding site on the axle when light is shone on the system, skewing the ratio of molecules with the ring on one site or the other away from equilibrium. Easy to say, but the synthesis I was told by one eminent person in the field, "outstrips anything that a traditional synthetic chemist can achieve."
Are complex systems like Leigh's the future for chemistry? If chemistry begins to re-create natural processes with mechanical machines, rather than just mimicing natural molecules, what will this mean for the field as a whole? Exciting times beckon.

Katharine Sanderson, (physical sciences reporter, Nature)
ps this is my first post, and while my credentials are being checked I am going undercover as Stuart Cantrill

Posted by Stuart Cantrill at 10:03 AM | Permalink | Comments (0) | TrackBacks (2)