Year: 2008

Chemical Sensitivity

This week’s Spinneret post actually points you to my latest Alchemist column on ChemWeb.com but also goes into a little more detail on one of the items reported there regarding pesticide contamination.

First off, Environmental research gets a boost from NIH in the form of a $6.8million grant to establish three DISCOVER centers to study the effects of environmental pollutants. Crystallography reveals the cellular machinations of the humble hydrogen peroxide molecule in The Alchemist this week, while fatty samples suggest that all of us harbor at least one pesticide or other persistent organic compound in our tissues. In environmental news, researchers have turned to gold to help them convert biomass into a useful chemical feedstock, while in theoretical studies it still matters, relatively, that electrons and nuclei are massively and speedily different. Finally, crystals behaving badly in supramolecular chemistry could herald new approaches to technological problems.

Read current issue of The Alchemist here.

Anyway, back to the contentious item on global contamination, which referred to news that almost everyone in Spain, and putatively the world, may be contaminated with at least one pesticide. I did have some misgivings about reporting on this and my concerns were brought into sharp relief by an Alchemist reader friend who happens to be a retired organic chemist with a great deal of experience.

He points out that the item on finding persistent organics in blood serum should really be put into perspective. “The fact that many of these studies find mainly halogenated compounds may well simply reflect the exquisite sensitivity of the detectors used in capillary gas chromatography to halogen,” he says, “these devices will pick up nanomolar concentrations of compounds containing chlorine or bromine.” He also asks whether strict controls were used by the investigators in this research and points out that work in this area submitted for regulatory filing requires stringent controls beyond simply showing a peak that has roughly the same Rf as a suspected pollutant.

More to the point, however, he questions the significance of finding traces of DDT or even DDE in serum. “If this were truly perilous the landscape should be littered with victims,” he says.

40320, Such a Significant Figure

40320, Such a Significant Figure

I am currently writing a post about pico and femto satellites for Sciencebase, these devices are tiny compared to the enormous one tonne behemoths many of us would picture if asked to visualise an artificial satellite (more on that later). Anyway, the earth’s escape velocity at sea level from a standing start was a figure I needed to hand while writing the piece.

I found a value in metres per second, converted to kmh and did a quick search with Google Toolbar just to get some references and to confirm my calculation. The kmh value, as you may have guessed, comes out at about 40320. However, Google’s auto-suggest offered me a search for the phrase “40320 plain bob major”, which was odd, to say the least, but would have been the obvious figure to a bell-ringing friend of mine. He would have immediately spotted it as an astoundingly long peal of bells. In fact, this very long peal was rung in 1963 in Loughborough, England, using eight tower bells in all possible permutations 8 multiplied by 8 factoria (8×8!) would come to 322,560 blows. Apparently, it took more than 18 hours to ring the changes all the way through.

Of course, the peal of 40320 arises because of the 8 factorial connection, 8×7×6×5×4×3×2×1 (8!) and has nothing to do with earth’s escape velocity, but it hooked me on a bit of guided searching looking for other significant mentions of the number 40320.

40320 is the number of minutes in 4 weeks and so February with its usual 28 days, should be designated “International Factorial Appreciation Month” according to one author (except in leap years, such as 2008, of course).

Kentucky 40320 is a spot on Ford Hampton Road in Kentucky, USA.

Item 40320 in the SigmaAldrich catalog of chemicals is 2,2-dimethylglutaric acid and bug number 40320 in Ubuntu Linux – “devhelp starts with an “empty” page area, which is not redrawn”, whatever than means, apologies to Ubuntu fans, I’ve not been there, nor done that yet.

The PubMed ID (PMID) 40320 points to a paper in the August 1979 issue of the journal Tijdschr Diergeneeskd entitled “Relationship between the presence of meconium in newborn lambs and postnatal pH and blood gas tension levels” and Tinyurl page 40320 displays a scan of a cheque for $950 with the filename bloodmoney.jpg.

Assuming Rudolph is at the front, there are 40320 ways to arrange the other eight reindeer (this simply relies on the 8! value mentioned earlier and could apply to clusters of any eight objects). It ignores “Olive the other reindeer”, you know the one who used to “laugh and call him names”. At the time of writing there were 207 cars listed for sale according to Google that had 40320 miles on the clock and just 5 with that same number in kilometres, while according to Cancerwise, 40320 women will be diagnosed with uterine cancer this year.

40320 is the item number for a “please shower” sign at BackyardGardener.com and BIOS 40320 is the Aquatic Conservation course covering global freshwaters, science and policy at University of Notre Dame.

Most of these various facts are totally unrelated, except those invoked by 8! Amazing what you learn writing about femto satellites. If you have any other fascinating examples of the number 40320 please give them a mention in the comments box below.

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?)

An Amply Adequate Sufficiency of Tautology

Sign with sharp edges

As Russ Swan of Laboratory Talk pointed out in reference to my previous post on the redundancy of the phrase “male semen”, there are numerous other examples around. For instance, the phrase HIV virus is equally redundant as it literally says, “human immunodeficiency virus virus”, likewise ATM machine (automated teller machine machine), PIN number (personal identification number number) and the Sierra Nevada mountain range (Snowy mountain range mountain range). There are lots more everyday examples of interlanguage tautologies of the latter kind on Wikipedia

But there are plenty of examples in science and technology. For instance, this patent title – RAID array configuration synchronization at power on is just one of many examples that cite the acronym RAID followed by the word array, as if RAID standing for “redundant array of independent disks”. Ironic indeed that the phrase itself contains the word redundant.

HIV virus shows up countless times throughout the media, and no less in scientific journal article titles, such as this one – Prevalence of HIV virus among patients, I even saw the phrase “female girls” in one reference on the subject of Rett syndrome. And, there are plenty of examples along the lines of LED display, LCD display, and DC current.

Not quite a pure rhetorical tautology, the graphics acronym TIFF is often accompanied by the word “file” as in a TIFF file, which literally means “tagged image file format file”. Same goes for the phrase pertaining to Adobe’s almost ubiquitous and much-maligned “PDF format”, which expands to “portable document format format”. Then there are phrases like DOS operating system (disk operating system operating system), Windows NT technology, (Windows New Technology technology), BASIC code (Beginners’ All-purpose Symbolic Instruction Code code), and ISDN network (Integrated Services Digital Network network).

There’s a nice extensive, long itemised listing of redundant tautologies to be found located here, but is there any purposeful point to drawing your attention to these phrases? Not really, but they’re great fun to find so if you discover any others please let me know via the comments box.

Airborne Germs and Handwringing

How to avoid colds

Just before the Christmas break, right as my annual winter festival cold kicked in and I was up to my neck in end of year deadlines, I posted a link to a press release in my Geeky Bits science extra column. That page is a repository of the less worthy, but hopefully interesting stuff I come across. Occasionally, I see an intriguing headline, give it a click, give the text a quick read through, add the item to the Bits, and thinking nothing more of it, just as one might with a del.icio.us or StumbleUpon post.

However, one regular Sciencebase reader, Churchill Fellow Grace Filby, was somewhat taken aback by my highlighting a timely press release from the London School of Hygiene and Tropical Medicine (University of London) – and described it as “a load of misguided nonsense”. Unfortunately, there is no online feedback or comments form on that LSHTM press release through which we could open a public debate on its content.

The press release was entitled – “If you don’t want to fall ill this Christmas, then share a festive kiss but don’t shake hands” – not the snappiest of titles but almost certainly one attempting to catch the wave of festive spirit seeing as it was released on December 19. However, both the title and the subheading of the press release (“The fight against all types of infections, from colds and flu to stomach bugs and MRSA, begins at home, with good hand hygiene, says first review of hand hygiene in the community.”) perhaps places too much emphasis on hand hygiene as opposed to the problem of airborne pathogens, believes Filby.

First off, Filby says that the press release “deflects the public’s attention away from a major source of germs which is the air we breathe…handwashing is only a part of it.” She adds that, “It is the germs arriving in the air that need disinfecting or freshening before the germs land on surfaces that could be touched by hands and passed to other people.” Even the British government appears to be acknowledging this to some degree, according to The Times on Christmas Eve in a bulleted item on how air disinfection units can kill MRSA, and C difficile.

The press release states: “But a report just published warns that we may be far more at risk of passing on an infection by shaking someone’s hand than in sharing a kiss.” As far as we can see, the full text of the original 38-page report cited in the release the word kiss or kissing occurs only once. It’s almost as if the press office hoped to catch media attention with the mistletoe and seasonal kissing theme regardless of the science reported in the report itself. Moreover, there is nothing much about handshakes or shaking hands either.

There are several other dubious details about handwashing: “but we believe that this targeted approach to home hygiene…” Is “believe” valid in a heavyweight scientific document of this sort, asks Filby.

The press release concludes that, “Handwashing with soap is probably the single most important thing you can do to protect yourselves and your loved ones from infection this Christmas.” Probably – that’s good, but we also need to deal with airborne germs. Whatever would Florence Nightingale have said? There are plenty of other risk factors out there and ways to reduce the chances of succumbing to winter bugs, such as walks in the fresh air, healthy eating, and more contentiously vitamin C or zinc supplements, although the jury is still out on the benefits of those.

Regardless, the main problem is that the press release ignores the primary source of respiratory infection which occurs from carrier to the next victim before pathogens ever fall onto a surface. In the case of many winter bugs, they spread quickly through sneezes or coughs when people don’t cover their noses and mouths.

Of course, Filby and I could put on our cynical hats at this point and come up with some kind of plausible explanation as to why hand hygiene as opposed to air hygiene is considered important. “Perhaps it is worth noting that funding for research on air hygiene wasn’t forthcoming whereas for hand hygiene there are plenty of interested parties – soap manufacturers, handwash products and water companies,” says Filby.

Hand hygiene is obviously part of the story and in the pre-Xmas rush for headlines one could forgive the LSHTM for highlighting it, but a broader perspective on all-round hygiene education and the promotion of other aspects of hygiene, as opposed to simple hand-wringing in the washroom, would have made more sense.

Learn to Let Go of Your Spam Folders

Ignore spam

In the spirit of recent posts about conversational spam and other such topics, I thought I’d let you into a little secret. My blog comment spam folder fills up every day but thanks to Akismet you never get to see the spam on the blog itself. Same goes for my GMail account spam folder (I route all email through it for that very reason). You probably find the same. Several hundred spam comments every day and the same again in email spam. It can get out of control during the holiday season when you’re not there to check every day. So, what do with it all?

You have two options: you could quickly scan page after page of spam, which can add up to a lot of time each week looking for false positives (and that’s even if you are greasing the spam) or you could simply learn to let go of your spam folders.

Both Akismet for comment spam and GMail for email spam automatically delete the contents of their respective spam folder once entries reach a certain age. The trick is not to be tempted to keep checking the spam folders, just in case. Just let the filters do their job and ignore the contents. If there are false positives, so what? 99.999% of the stuff that is filtered (once you’ve trained the system by properly assigning definite false positives and false negatives early on) is most certainly spam.

Do you really need to wade through page after page of ads for “lager beasts”, “vI@ gera gel”, and “dr@gs Rx online”? No? Me neither. Just learn to let go and you will feel a weight lifted from your shoulders. After I got back online following the Christmas break (other winter solstice festivals are available), Sciencebase had accumulated 14052 spam comments. One click on “Delete All” removed the whole lot from the blog’s database.

I am sure some readers will have found that no amount of training prevents a regular slurry of false positives, so for those poor unfortunates you may have to ignore this advice.

For those with a 99.9999% miss rate, the forget-about-it approach is such a powerful exercise in self control, it’s almost Zen, although I’m sure the psychologists in the audience will have something to say about that (in fact please do, but make sure your comments don’t look spammy).

Biology with Firefox

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?

Medline on Facebook

For those who care about such things as online social networking, and if you’re reading this blog, I assume that could be you, there is now a Facebook application available that allows you to cite your journal publications (provided they are listed in PubMed).

You can add the Medline Application (yes, I realize PubMed and Medline are not synonymous, but that’s the name the authors used) – by following this link.

I’ve added a few of my publications from Science, Nature RDD, Drug Discovery Today and PNAS, they’re listed towards the bottom of my profile below my Flickr gallery.

Chemical Language Translated

Gold Book Logo

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