Chemistry – Page 23 – David Bradley

Watery Typo Leads to Salvation

Water salvation, photo by David Bradley

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 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.

Brain Scan Reveals Cultural Differences

Magnetic resonance imaging

I’ve just finished writing a news article for the SpectroscopyNOW.com MRI ezine and wanted to expand on some of the implications of the work here. The item describes the results of recent research that purportedly show differences in how born-and-bred Americans differed from immigrant East Asians tackling a simple visual test based on displayed sequences of boxes and lines.

The functional magnetic resonance imaging (fMRI) study looked at differences in activity between 10 Americans and 10 East Asians while they carried out that task. Apparently, they found significant differences depending on whether or not the volunteers were working out the solution to the task based on individual lines or the lines in the context of others. The volunteers were also asked to complete a questionnaire about their cultural attitudes. The research doesn’t intend to imply that either group did better or worse than the other, this is simply about different regions of the brain lighting up during the task and whether that might be correlated with differences in cultural heritage.

It’s interesting work and the researchers claim to have shown for the first time that a person’s cultural upbringing and the extent to which one identifies with those cultural influences can affect brain activity patterns when faced with a specific task.

In the current study, however, the researchers seem to make the rather sweeping generalisation that American culture values the individual and so emphasizes the independence of objects from their context, while East Asian culture tends to emphasize the collective and the interdependence of objects based on context. This, they say, explains why they see such a big difference in brain activity between the two groups of volunteers, the Americans focusing on the individual aspects of the task and the East Asians seeing the collectiveness of the boxes and sticks in the sequence.

My first thought while writing the news item, was whether or not their initial assumptions about cultural stereotypes remains valid in an increasingly globalised world. Do Americans focus on the individual and do East Asians think more in terms of society as a whole? More to the point the study was carried out with just ten individuals from each culture. Yes, those two groups may have different attitudes and aptitudes, but are those results statistically significant?

How random was the choice of the ten East Asians. Apparently, they were people coming to the USA to live! Does that make them “typical” of their fellow countrymen? I would suggest not at all. People who leave their home country are often very different from their stay-at-home counterparts in attitude and outlook . Perhaps these ten individuals had a very different cultural attitude to their former countrymen. Indeed, what if by virtue of their wishing to emigrate to the USA had coloured their whole outlook and notions of their own culture. Maybe they carried out the task in a way they hoped would be more American, or conversely, maybe they tried to be more East Asian to help the researchers. Similarly, who’s to say anyone taking part in such experiments behaves as they normally would given that they’re stuck in a noisy MRI machine being put under pressure to perform.

fMRI is a powerful tool. The burgeoning list of results it generates grows day by day and I will continue to report them for the ezine assuming they are worthy of reporting. The present results are intriguing, but I do feel that they are stretching the perceived prowess of fMRI a little too far. To my mind, there is an enormous gulf between demonstrating some difference in brain activity while a a few individuals carry out an esoteric task and correlating that with alleged cultural differences, especially given the circumstances of those who are supposed to have essentially polarised outlooks.

PaperID – An Open Source Identifier for Research Papers

As a journalist, I receive a lot of press releases that cite “forthcoming” papers. Depending on the publisher one can usually find the paper in a pre-press state on their website. However, it’s often the case that the DOI does not go live at the same time as the embargo expires on the press release, and so I might legitimately publish an article about the research I cannot use the DOI as the reference and must use the direct URL for the paper. Unfortunately, some publishers then move the paper when the paper publishes, so the link I used ends up broken.

Moreover, this cannot be useful for authors themselves in that a paper that does not make the grade at the International Journal of Good Stuff and ends up being resubmitted to the Parochial Bulletin of Not So Good Stuff will gain a different identification code along the way.

Will Griffiths on ChemSpider was recently discussing the possibility of an OpenURL system. I think we could go one step further.

A simple standardized way of generating a unique identifier for each and every paper that would be transportable between different phases of the publication process from submission to acceptance and publication, or rejection and resubmission elsewhere, would be a much better way of registering papers. The identifier would be created at the point when the final draft is ready to be mailed to the first editorial office in the chain, perhaps based on timestamp, lead author initials, and standard institution abbreviation. It could be the scientific literary equivalent of an InChIkey for each research paper.

There would have to be a standardized validation system, so that authors were sure to be using the right system, but that could be established relatively painlessly through the big institutions, be networked and have cross-checking to avoid duplicates. And, of course, be open source, open access.

The possibilities are endless, PaperID would create an electronic paper trail from author through preprint, in press, to online, and final publication. It might even be back-extended into the area of Open Notebook Science and equally usefully into archival, review, and cross-referencing.

DOI is useful most of the time OpenURL sounds intriguing, but PaperID could be revolutionary.

18 Handpicked Online Periodic Tables

Periodic table tattoo

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 renowned 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.

Cooking Pizza During Your Lecture

We’ve all sat through lectures, talks, and symposia that went on too long, some of us may even have been guilty of overrunning! Blogging chemist Andrew Sun was worried about this problem and hunted across the Internet in search of a countdown timer that could be run on one’s desktop to alert a speaker to the time they have left. Unfortunately, while there are many timers available online, most of them are either less than serious or else relate to cooking pizza and boiling eggs. He wanted something a little more dignified, that would not look out of place in a scientific symposium and wouldn’t embarass him in front of his Professor.

So being as intrepid a scientist as ever there was, Sun decided to write his own application to do the job for him so here is LectureTime courtesy of Dr Sun ready for free download. The LectureTime readme file) is here.

You can read more about the tool on Sun’s blog here. Please give it a try and let us know how you get on or if you have any problems in the comments box below. Of course, you can still use LectureTime to boil an egg or cook pizza, just don’t do it during your lecture!

Nature’s Missing Crystal – Found It!

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 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.

PubMed Central Submission Now Mandatory

The US’s National Institutes of Health (NIH) has a Public Access Policy that is set to become mandatory following President Bush’s approval on Dec 26th 2007. This change will mean that NIH-funded researchers will be obliged to submit an electronic version of any of their final, peer-reviewed manuscripts to PubMed Central, as soon as the paper has been accepted for publication in a journal.

Many researchers are pleased with the move and Peter Suber outlines the implications in detail in the January issue of the SPARC Open Access Newsletter. Citing the cons are several of the non-OA publishers who claim that NIH has no rights over the intellectual property of the science it funds and that research papers should remain the copyright of the publishers. They argue that the value added by the publication process will effectively be handed over to PubMed Central by the submission process without compensation. Others argue that the publishers have had it too good for many years.

There remain several outstanding issues which will no doubt be argued over in the months to come.

Chemical Irritation

Not so much a chemical information post today as a diatribe against natural terminology used by the countless chemophobes out there.

I had a query this morning from a reader asking whether adding bleach to the water used with their cut, fresh flowers would reduce fungal infections and so somehow prolong their bloom time. I suspect there’s probably a drop of truth in the idea, but in trying to find a definitive answer I found a gardening type page that discussed the issue.

In it, the author of the item, Marion Owen (whom I am sure is a lovely person) asserts that, “If you don’t like to use chemicals to prolong the life of your cut flowers, there are “natural” alternatives.” She then goes on to list various chemicals that one might add – a penny, aspirin, lemon-lime soda, bleach, lemon juice, sugar, bleach, and listerine. At this point, I’m not worried about whether my blooms stay blooming lovely or not, but am taken aback by how she seems to be defining the word chemical. She’s not alone, of course, millions of people make similar assertions about detox diets that avoid chemicals (so, what do you eat when you’re on a detox diet, raw energy?)

Anything Marion and her readers might add to a vase of flowers is made from chemicals. The flowers themselves are made from chemicals (proteins, carbohydrates, fats, water, minerals etc), lemon juice (water, citric acid etc). Even the water itself (dihydrogen monoxide)!

But, more to the point it’s that use of the word “natural” with which I take umbrage, natural usually preserved for non-synthetic chemicals (although there is no actual distinction in nature between natural and synthetic, humans are “natural” after all). Maybe she meant to specific agrichemicals or chemicals produced by the industry for the specific purpose of reducing mould and extending bloom life. Wouldn’t you rather use something designed specifically for the job rather than adding a random selection of household chemicals to the vase. What, if the bleach and that carbonated lemon-lime drink react, catalysed by the copper penny, to produce some noxious vapour? At best, the flowers would more likely fade faster, but you might also get a nasty whiff of something when you lean over to catch their scent!

Anyway, how can adding aspirin be considered a natural alternative to adding chemicals? Of course, you might use sap from the cricket bat willow (Salix alba) which contains salicylic acid, the active metabolite of aspirin, but that would still be adding chemicals to the flowers, natural or not, and the very process of extracting the sap, is that natural?

Of course, the whole activity of cultivating blooms, hacking them from their plant and sticking them in a vase and leaving them to die with no chance of producing offspring is in itself not an entirely natural thing to do. But, how do you segregate anything humans do from the natural world in the first place? Human intellect and activities are as much a part of the natural world as the very flowers we admire, the insects that would normally pollinate them, the moulds and microbes that grow on them and apparently shorten the blooming lives, the insects and fungi that will rot them on our compost heaps, and the soil bacteria that will feed on them producing the right conditions for next year’s flowers.

Plasticine, Salt, and Melting Snow

Salt water ice freezing

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?)

Biology with Firefox

Firefox-using molecular biologist kinda person? Then, you should check out BioFox (thanks for Bertalan MeskÃ³ of ScienceRoll for the tip off).

Code bioFOX integrates various bioinformatics tools into the Firefox web browser, allowing users to analyse genes without all the hassle of retrieving data from NCBI or Swiss-Prot and can then manipulate the information via various tasks including: Translation of a nucleotide sequence, blast search (For eg. blastn, blastp etc.) of the desired nucleotide/protein sequence, calculation of properties (like PI, charge, molecular weight, AT/GC content etc.) of a protein/nucleotide sequence, conversion between formats (Genbank, Fasta, Swiss-Prot etc.), and prediction of sequence for sub-cellular localization (PREDOTAR, TargetP, pSORT etc).

Maybe chemical connector Tony Williams is reading this and thinking…How might a Firefox Plugin be used to provide chemists with similar levels of information manipulation and functionality via their databases, such as ChemSpider?