Category: Chemspy

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!

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.

Firefox-using molecular biologist kinda person? Then, you should check out BioFox (thanks for Bertalan Meskó 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?

It seems it’s now public knowledge that WiChempedia is on its way thanks to Tony Williams at ChemSpider and his colleagues.

“Over the past few weeks I have had a few discussions with a member of the ChemSpider Advisory group regarding a concept to create WiChempedia. I’ve enjoyed these conversations with Alex Tropsha (professor and Chair in the Division of Medicinal Chemistry and Natural Products in the School of Pharmacy, UNC-Chapel Hill),” says Williams in his latest blog post.

Over the past few weeks Williams and his colleagues have been looking at the quality of data on Wikipedia and trying to figure out the best way to mash ChemSpider’s efforts with those of the WP:CHEM team. “Our intention is to deliver wiki-capabilities in ChemSpider and to use the Open Content associated with chemicals and drugs on Wikipedia inside the system,” Williams says, without, he adds, reinventing the wheel or offending the Wikipedians.

“My intention as we work through downloading the data and to check, validate and correct what is sitting on Wikipedia directly for benefit to the community,” adds Williams.

A rather intriguing paper has just been published by the Cambridge-based publishing wing of the Royal Society of Chemistry and highlighted by the scathing, satiricial crew at The Register (don’t visit that link if easily offended). It’s an outrage says The Register, but they’ve given the team a vulgar acronym award for their abbreviation of “copper nanotubes” and “bismuth nanotubes” nevertheless.

I’ll say no more except that apparently “Philip of Cambridge” tipped off The Register about this paper. Now, I’d like to know is “Philip” an aggrieved ex-member of the RSC’s Cambridge staff or is this another of that organisation’s rather adventurous (and some would say pointless) attempts to get its name mentioned in the media in the context of some spurious chemical happening (remember Carol Vorderman in mauveine dyed Victorian costume, or Superman on the side of buses in Hull?)

A new database of antioxidant values for a wide range of foods is now online. The main application will be in ongoing research on the purported health benefits of antioxidants. For example, many fruits and vegetables are known to be good sources of antioxidant vitamins, such as vitamin E, C, and beta-carotene, but these natural foods also contain other compounds, collectively known as phytonutrients, that may contribute to health effects. You can find the ORAC database here.