Making sense of science

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)

Porphyrin power

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 ViewHarry 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)

A bygone age

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?

Reactions – David Leigh

[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.

Sparkly science

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)

Go nuclear?

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)

What’s black and white and read all over?

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)

People are people, so why should it be…

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)

Anything you’d like to share?

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)

Time is on my side

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)