For more information on why leaves turn red in autumn, check out this page from Wisconsin University. Science Made Simple has a nice explanation too as does Dr David Wilkinson from Liverpool John Moore’s University, and the USDA.

As an adjunct to this PNAS has just published a paper that reveals the enzymiccascade that controls abscission, the process that determines how and when plants actually shed their leaves:

S. K. Cho, C. T. Larue, D. Chevalier, H. Wang, T.-L. Jinn, S. Zhang, J. C. Walker (2008). Regulation of floral organ abscission in Arabidopsis thaliana Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0805539105

Autumn Leaves is a jazz classic about the bittersweet symphony that’s life. My singing group Big Mouth cover it in a medley of standards. I’ve created a playlist of the other songs we cover, on Youtube, these are either original versions or, as Jon points out, oddities.

This is an updated post Sciencebase from November 2006. Hope you enjoy my new photos too, top one is a snap I took in the English Lake District one autumn, the second leafy view is of a tree at Anglesey Abbey in Cambridgeshire.

Autumn Leaves

• DBpedia for Chemists
• Drug Design on the Playstation
• Google Science Dot Com
• Open Notebook Science
• PaperID - An Open Source Identifier for Research Papers

I’ve imported all Chemspy blog content as it stood on April 4, 2008, so you can access the Chemspy archive in the Sciencebase chemspy category. Hopefully, the few dozen Chemspy posts won’t stream into the RSS feed, doesn’t look like they have yet, as they’re all simply date-stamped with their original post dates dating back to early 2007. Apologies for any glitches. At some point, I will migrate the Chemspy newsfeed over to Sciencebase too, so please subscribe to the Sciencebase feed (there is a chemistry category) to keep up to date with Chemspy updates.

Spying on the Chemical Spy

In the world of pharmaceuticals we discover that there might be yet another string to the bow of aspirin-like drugs, this time in the fight against breast cancer. There’s good chemical news for those hoping to save Gulf Coast Wetlands from the rampages of the coypu with the discovery of a chemical lure, The Alchemist also hears of a novel system of surfactants and gelating agents that can form separate compartmentalized structures resembling the organelles in a living cell. You might care to have a drink with The Alchemist this week in celebration of a clearer understanding of why some drinks, such as ouzo, form cloudy emulsions with water. There’s more on the ouzo effect in my SpectroscopyNOW story on the subject where an independent team working in parallel have used NMR to take a look at these rare and peculiar emulsions.

Finally, a little kitchen chemistry could give your French fries a little je ne c’est quoi.

Speaking of haute cuisine…also on this week’s SpectroscopyNOW, I report on how Portuguese scientists have identified a whole range of smelly molecules found in wild edible mushrooms. It’s pioneering work that will allow the food industry to ensure it is not being fobbed off with cheap mushrooms when a more expensive variety is what they ordered. The results could also be used by biotechnologists to engineer specific flavours into easily cultivatable varieties of mushroom. Two points arose as I was writing the item: The first is that overall mushrooms smell of nothing more complex than 1-octen-3-ol, which the researchers describe helpfully as having a mushroom-like odour. Secondly, the notion of cultivating wild things is at odds with the whole ethos of wild mushrooms, surely?

Either way, it’s hopefully an interesting read. Now, pass the ketchup for my mushrooms and fries, would ya?

French Fries, Wild Mushrooms and Ouzo

In the realm of physical chemistry (or is it chemical physics?) there was almost theological interest in this week’s Alchemist. Having written about water glass and how low-temperature studies of aqueous phase changes are helping scientists to explain this anomalous and yet ubiquitous material it was a simple spellcheck-induced typo that drew the most interest from The Alchemist’s email newsletter readers.

Wave after wave (pardon the pun) of correspondents got in touch almost as soon as the newsletter was dispatched to point out that I, Uberpedant Taskmaster General had been hoist by my own petard. In describing water’s fascinating properties I described its ability to interact act at a fundamental level with many other materials as being related to its “powerful salvation properties”. Like I said, my petard was well and truly hoist. Of course, some would say it was a baptism of fire to describe water thus, but that would be nothing but hot air with an earthy stench. Thus having shoehorned allusions to all four classical elements into that last sentence, I stand
before
you hands
up and head
bowed, seeking solvationI stand before you hands up and head bowed, seeking solvation!

Meanwhile, back with the chemistry news. I also report in The Alchemist on a new approach to engineering goats to produce medicinal milk which has been devised in Pennsylvania. The research could be good news for people with diabetes. Then there’s the finding that a well-known anticancer compound also used as an antiparasitic drug could turn out to be an even better multitasker operating as it does as an effective antiviral against HIV.

Also this week, a multitude of awards from the National Academy of Sciences for diverse chemical discoveries. You can read the list of winners on the Chemweb site, together with links to the juicy bits on how much money they got, in other words.

Finally, in the legendary world of organic synthesis a wartime effort to synthesize quinine may have been vindicated while Canadian chemists have constructed nanoscopic gas cylinders from barium organotrisulfonate that come with temperature-controlled valves for trapping hydrogen and carbon dioxide. And, speaking of which, I have a hopefully typo-free but far more controversial item on the whole issue of carbon footprints, climate change now live on the Sciencebase blog.

Watery Typo Leads to Salvation

Earlier this year organic chemist Adam Azman contacted me to ask if there is a free or open source chemistry dictionary available for word processors. Well, a quick search revealed only paid-for dictionaries so he set about creating his own from scratch.

“It took me the better part of a month,” Azman told Chemspy, “but I’ve made my own and I want
it to be as open-source as possible. Chemspy Sciencebase is now hosting Azman’s efforts ready for free download zipped chemical dictionary file here). The chemistry dictionary is in standard “.dic” format and instructions for installing it on Microsoft Word OpenOffice can be found in the download together with licensing information (it’s creative commons).

Azman concedes that it is not yet perfect and focuses mainly on organic chemistry words. “It almost certainly contains at least one error and misspelled word that sneaked through,” he confesses, “I tried to get as many of the conjugations as possible (-e, -es, -ed, -ing, -tion, etc), but probably missed several.” He also points out that it employs only US spellings.

“I don’t know how helpful it will be to an average chemist,” Azman told me, “but organic chemists should love it. From the organic perspective, I did not systematically go through and list every iterative derivative of every compound (methylbenzene, ethylbenzene, dimethylbenzene, fluorobenzene,
etc.),” he adds, which could be something of a limitation compared to the paid for program which has 1,800,000 words compared to the 8000 or so entries in Azman’s dictionary. However, he did vet his list using the current ASAPs of JACS, JOC, and OL to catch some of the iterations he missed initially. “There are a surprising number of typos in those articles,” he points out.

Personally, I’ve had a medical dictionary running in my word processor for years, but this organic dictionary will complement that nicely and save me a lot of repeated add to dictionary clicks when writing around the subject of organic chemistry.

Azman is currently working on automating the iteration process with an Excel expert and as soon as that task is complete we’ll let you know so you can download the .dic file and install into your word processor.

Free Download: Chemistry Dictionary for Word/OpenOffice

Keywords: Open Access Chemistry Dictionary, Open Source Chemistry Dictionary, Microsoft Word Chemistry Dictionary, OpenOffice Chemical Dictionary.

This item originally appeared on Chemspy.com, but the Sciencebase server is more robust and will cope better with the download traffic, especially once we upgrade to the ChemSpider augmented version of the chemistry dictionary which is currently being created by Adam and ChemSpiderMan Antony Williams.

Chemistry Dictionary

Where online do you turn, when you are looking for a periodic table?

The domain name PeriodicTable.com - reveals a superb online periodic table with an obvious website name and the option to buy a poster printout.

For more on what Periodic Tables mean and their underlying formulations check out Periodic Table Formulations by Mark Leach

Berkeley nuclear chemist Mitch Garcia who runs ChemicalForums.com, would, as would many other chemists turn straight to Mark Winter’s Web Elements this seminal online PT has become the guide to elemental discoveries and has been in existence almost beyond living memory (in net-years). However, he also points out that there is more nuclearcentric PT on the Lawrence Berkeley Lab site that provides all the decay properties for all the isotopes.

An interactive PT aimed squarely at NMR spectroscopists is offered here and with a click tells you how many isotopes for each element and whether or not it is NMR active. A click of the arrow then spells out the spin, abundance, quadrupolar moment, and typical relaxation time information.

If you are after pretty PT, then the slightly overblown version from the Royal Society of Chemistry is nice enough at Visual Elements.

A single site offering a conventional PT in six different languages (English, Dutch, French, German, Italian, Spanish) can be found at LennTech.com.

The American Chemical Society has an interactive PT, although I’m not entirely sure what makes it any more interactive than any of the others. It too is available in different languages, however, including Chinese, English, French, German, Japanese, Russian, and Spanish.

On the other hand, there is something about the Dynamic Periodic Table that gives it the edge on the word interactive in that there are various sliders and tabs that allow you to alter the way the Table is displayed depending on the elemental properties you wish to study. It is even available in Swahili for those chemists south of the Sahara.

It was inevitable that I’d have to mention the ubiquitous Wikipedia, which under the chemical jurisdiction of Martin Walker also provides a straightforward PT for the masses. In fact my good friend Michael Engel and several other practicing chemists point out that they invariably stop off at Wiki for elemental information and if that fails simply Google what they’re after to find the data.

If you are looking for yet another interactive periodic table, then try this one from designers TouchSpin. Originally, it was referred to as portable, perhaps it could be saved to your PC or a USB stick, but there seem to be no references to this now. Anyway, a much more obvious way to make a PT portable is simply to print it (colour or b&w), what you gain in tangibility you lose in interactivity of course.

If you want interactivity and portability then the Periodic Library will slip into a tiny space on your Windows hard drive taking up a mere 264 kilobytes or thereabouts. The website shows a PDA in its iconography but doesn’t specifically mention a PDA version.

To combine your penchant for coffee table books with your love of periodic tables turn to the infamously offline wooden periodic table, which is not only a period piece by definition but metaphysically the absolute zenith in coffee table information repositories.

A rather staid but internationally definitive PT is that found on the IUPAC website. Given that IUPAC ultimately decides on the names of the elements this has to be the place to go for absolute elemental knowledge.

Anything but staid, is the real cutting edge in online periodic tables, the Second Life PT from Andrew Lang and Jean-Claude Bradley [no relation] of Drexel University sponsored by ACS.

There are, of course, hundreds if not thousands of variations on the Periodic Table theme, many of them cranky beyond belief, others tailored for specific groups of scientists such as physicists and geologists, others in 3D that attempt to show more information than conventional flat Tables, and yet others that are not so much PTs as simply entertaining. The obviously named AllPeriodicTables.com provides yet more information and conventional online version of the interactive PT. This one has an environmental bent.

For more on the philosophy underlying the periodic table take a look at the work of Eric Scerri.

If you’re interested in how the chemical elements were named, then this etymology of all the elements is rather useful.

If I’ve overlooked an online periodic table you find particularly useful in your research field let me know in the comments.

18 Handpicked Online Periodic Tables

Diamond is not unique! Nature’s missing crystal discovered! A crystal as beautiful as diamond! Those were the themes running through dozens of articles in the media about a discovery made by Japanese mathematician Toshi Sunada of Meiji University. The original press release proclaimed that he had discovered a theoretical crystal structure with the same symmetry properties as diamond but with handedness, or chirality, and that this knocked the crown from diamond’s uniqueness.

Unfortunately, he soon discovered just how embarrassing press attention can be as chemists and crystallographers began filling his email inbox with messages alerting him to the existence of the exact same structure he was “predicting” already having been found. I asked Sunada about what happened.

“After my article appeared [in Notices of the American Mathematical Society; PDF file] a few people pointed out the oversight,” he told me, “They were rather sympathetic to that the difference of culture between mathematics and other sciences that leads to such ignorance.” He adds that although he hadn’t been aware of the known crystal structure until his modelling constructed it before his eyes, the people who contacted him were unaware of the history of his work in this area stretching back a decade. The original work that led to the discovery of the structure was done by AF Wells in the mid-1970s.

It highlights just how far apart different fields in mathematics and the sciences are despite efforts by various agencies and funding bodies to attempt to build multidisciplinary bridges. The debacle reminded me of how it took a mathematician colleague to point out to Harry Kroto and his colleagues that the structure of the all-carbon molecule buckminsterfullerene and the symmetry laid bare by their spectra was suggestive of a truncated icosahedron, a soccerball, in other words!

It makes me wonder what other
discoveries
have we missedwhat other discoveries have we missed because the sciences are no longer as joined up as they were in the heyday of the nineteenth century polymaths like Faraday. Put another way how much money is wasted re-inventing the wheel. Without wishing to criticise Sunada or the referees of the original paper, but if a chemical colleague happened to have seen his structural simulations they might have spotted th fatal flaw in the argument that much sooner. Perhaps the Scandinavian idea of hot-desking should be introduced into labs, hot-benching you might call it, to boost the potentially innovative cross fertilisation of ideas. Or, how about a cross-disciplinary approach to peer review, send to two experts and an additional referee in another field entirely if the paper claims true novelty.

Anyway, back to Sunada’s work. It may at first seem that here was merely a mathematician modelling something that chemists and materials scientists already knew, but although one half of his discovery was not a discovery at all because the structure was already known, one aspect of his work could save chemists a lot of searching in vain. “My result pins down that there are only two crystals having these properties,” he told me.

You can read more about Sunada’s discovery in my SpectroscopyNOW column this week.

Nature’s Missing Crystal - Found It!

Why do they grit the roads with rock salt in winter? What does the salt do to the water to reduce ice on the roads? Is this somehow related to how salt affects the boiling point of water? Keywords to search for: colligative properties, boiling, freezing, ions, solutions, solvent, Raoult’s law

Meanwhile, I’ll let Plasticine models from Ithaca and cheesy music explain:

Incidentally, if it is too cold, no amount of salt will prevent the roads freezing, but if climate predictions are to be believed then that will not be a problem for much longer. (Unless the computer models are all wrong and we are heading for another ice age…now where did I put that hot-water bottle?)

Plasticine, Salt, and Melting Snow

During my time at the Royal Society of Chemistry (do I sometimes make it sound like a prison sentence?), I watched in awe as my old mucker Andrew Wilkinson helped reformulate the IUPAC book of chemical definitions commonly known as the Gold Book. That mighty auric tome is online and searchable with a click these days. And is as useful as ever to chemists looking for a quick description for a jargon word.

Take chiral, for instance: “Having the property of chirality“. Hmmm. So, look up chiral: “The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non-superposable on its mirror image; such an object has no symmetry elements of the second kind.” Such a crisp and easily comprehended definition. Not.

Obviously, there is a need for technical definitions, but somtimes such definition simply complicate something that could be just as easily described often with a single word. Chiral = handed. (The clue’s in the word itself, which comes from the Greek for hand and I’m pretty sure the scientist who coined the term did so to save us all the trouble of talking about non-superimposable mirror image objects (you know, like hands and gloves?). Indeed, many a chemistry student would grasp the concept much faster and many a lay reader of a scientific paper would understand if such terms were explained in parallel with their simpler analogue. So, for all you non-chemists, here’s a Boxing Day list together with links to their technical definitions if you need the fully Monty,

• Chiral - handed
• Hydrophobic - water hating
• Hydrophilic - water loving
• Micelle - microscopic bubble
• Cyclodextrin - starch rings
• Mass - how much stuff
• Isotope - same element, different mass
• Bond - a link between atoms
• Organic - made with carbon
• Inorganic - made without carbon
• Lipid - Oily or fatty natural molecule
• Morphology - shape
• Half life - Time taken for value to half
• Second Life - Virtual meeting place

Obviously, these simple definitions gloss over the finer details, but isn’t that the point of a glossary? “Professionals often face difficulties explaining these terms to lay people because they are too aware of the exactness of the concept, emphasizing both the morphological and functional aspects,” says chemist Andrew Sun, recently interviewed in Reactive Reports. There are many more I use in writing for a non-technical audience, but some jargon words are quite stubborn. Are there any good, simple definitions for the following?

• Polymer
• Sublime
• Catalyst

Chemical Language Translated

Many of you will know chemist Andrew Sun from his On the Road blog and from his occasional but insightful comments on the Sciencebase site. I recently interviewed him for the Reactive Reports chemistry webzine and you can read the result there in the current issue. I edited his answers to fit the magazine for length and housestyle but I’ve reproduced his full answers to one or two poignant questions here exclusively for Sciencebase readers.

How do you think being a chemist in China differs from working in “The West”?

I don’t know very much how people doing chemistry in the west. I get an impression from videos of lab work posted online. But one difference I am very sure is that we do not have enough money and we do have a poor academic system. Most students still have to pay tuition at the MS stage. The campus scholarship can only pay for a dinner with your friends, and we have far fewer, or no, third-party scholarships here). In the PhD phase public subsidies can still hardly cover the cost of living. Bosses (supervisors) cannot be too nice to their students because they are also running out of money. To apply for more funds and get promoted in a badly designed academic system they have to publish enough papers in high quality journals. They have to publish more in less time so they need more unpaid PhD students working harder.

China pours the world’s second largest bucket of money into science according to statistics, but one should also consider the fact that no NMR machines, no TEM, SEM, AFM sets, neither other instruments, are manufactured in China. Bosses have to buy these from abroad (CNY 1.00=USD 0.13=EUR 0.10, plus taxes) - and regain the cost by charging several hundred per sample for characterization requests. (Cryo-TEM, which is widely used in the study of soft matter, cost CNY 2000 per sample here!) Money thus goes two ways to both buying the instruments needed and to paying the usage fees.

In addition we have a weak chemical industry here which cannot provide qualified reagents. So to conduct a delicate synthesis with less failures in less time, one trick is to buy your reagents from Alfa Aesar, Sigma Aldrich, etc. who charge your boss more. Not to mention the local glassware - we cannot find any tight ground glass joint from local manufacturers. Oftentimes PhD are forced to manipulate impure reagents in a leaky glove box, with minimal budgets to test their products for sure, yet still having to publish in journals with high impact factors.

As such PhD students in China are a depressed group and we hear of suicides among PhD chemists from time to time (in one case the poor guy synthesised a few milligrams of potassium cyanide and…). That’s why now lesser MS grad students are moving on to a PhD. In fact most of the MS students aren’t truly working for science; they are only working for the degree which could mean a slightly better salary than a BS degree in the job market. So most MS students go to find a job once they get their degrees, and yet a large number pursue their career of science abroad. So we have the brain drain problem - obviously the above mentioned situation in China is not attractive enough of them to come back in the future.

However I’m still hopeful because everything is getting better, not worse. Therefore I chose to stay in China during my PhD period.

What more can chemists around the world do to work towards a global chemical community? How might certain more restrictive governments be persuaded of the benefits of such international collaborations?

First it is important for them, both the chemists and the governments, to realize the benefits of international collaborations; not only why, but practically how. Currently with limited communication, for example, a US scientist can hardly know why he/she should cooperate with a Chinese scientist for a project. More communication and understanding between chemists from different countries are needed to start any collaboration. The growing online chemistry community could provide such chances. But currently Chinese chemists who actively participate in the online community are rare; I know no one else except me.

Governments might consider much more, for example the ‘leakage’ of knowledge or secrets. However I believe the advantage of collaboration can outweigh the shortcomings which can be overcome by carefully designed policies and contracts. I guess the Chinese government should welcome global collaborations because we are currently much weaker and have a lot to learn from others. But currently the extent of this is much smaller than I’d hope for. There is still much to change.

For more Reactive Profiles, grab the site’s chemistry interview feed.

Chemistry’s Sun Rises in the East