Author: David Bradley

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

A Billion Light Years from Home

Cosmic death star (Credit: NASA et al)

Have you ever come across this kind of description of an astronomical event:

“…astronomers have witnessed a supermassive black hole blasting its galactic neighbor with a deadly beam of energy…Both galaxies are situated about 1.4 billion light-years away from Earth…The offending galaxy probably began assaulting its companion about 1 million years ago…”

How can that be? asks Sciencebase reader Adam Azman. If the event is at a distance of 1.4 billion light years from Earth it will have had to have started its journey from that point in space to reach us 1.4 billion years ago, yet, the article tells us the event only began 1 million years ago? It seems quite paradoxical, but according to Dave Mosher, author of the article Galaxy Blasts Neighbor with Deadly Jet, the explanation is quite simple and essentially glosses over Einstein’s theory of relativity to help astronomers talk about the times and distances as if there were a fixed universal frame of reference.

“Most astronomers,” Mosher told Sciencebase, “refer to time relative to Earth when they say something happened. E.g. as an observer on Earth 1 million years ago, the event would have just been getting started. They avoid stating it happened 1.401 billion years ago because of the quirkiness of relativity…in other words, just because light appears to be 1.401 billion years old doesn’t mean it actually is… there’s too much fudge factor to be certain. It’s more accurate AND precise to say the light reached Earth 1 million years ago.” He admits that the issue sometimes “fries his brain”, and told Sciencebase that he is “really going to start putting an explanatory graph in my stories from now on… there’s no way around it.”

Meanwhile, Azman, a chemistry student at the University of North Carolina Chapel Hill, had also done some digging of his own and had spoken to Bryan Preston, a political blogger who often writes about cosmological matters. Preston’s explanation is close to that of Mosher, “The ‘million years ago’ bit is a reference to ‘as seen from earth’ – if we’d had a Hubble telescope a million years ago, we could have seen this event begin,” he says, “But the event actually happened 1.4 billion years ago and it took the light that long to get to us to see it in the first place.”

Preston adds that, “if we’d been technologically advanced a million years ago, we’d have used that technology to see the start of the Death Star’s bombardment of its neighbor. To have seen it all happening when it actually happened, we’d have had to be at the scene, 1.4 billion light years away from Earth.”

These timelines can be confusing and are a constant source of letters to the editor for popular science publications and space websites. “For instance,” adds Preston, “we name supernovae by the year they were observed to have blown up, hence SN1987A. But that star was 100,000 light years away, so it actually blew up 100,000 years ago, but we just saw it blow up in 1987 because it took the light 100,000 years to get here.”

It’s all relative, you see?

Popular Science Discoveries This Year

Happy New Year 2008

No science blog would be fulfilling its annual duties if it didn’t provide an end of year round up of what’s been hot and what’s been not in the past year. So, I activated Alex King’s excellent Popularity Contest plugin (new version out now) to find out what Sciencebase readers have been reading the most on the site over the last 365.256363051 or so days. So, here’s the top ten.

  1. Potato powered mp3 player – a video spoof on lighting a bulb with a lemon battery, don’t try this at home!
  2. How does salt affect the boiling point of water – a perennial question in science class.
  3. Obesity gene – is hereditary to blame for overweight?
  4. The secret of Newton’s laws explained with Lego – If only Newton had been made of plastic. Enjoy the falling apples.
  5. Chemistry News – Regular round up of chemical discoveries
  6. Sniffing out our sense of smell – Olfactory inlet
  7. Christmas rose and hellebrigenin – Christmas chemicals
  8. People caught pubic lice from gorillas – Ewwww, gross!
  9. Egg in a bottle – Yes, air pressure alone is enough to force a hard-boiled egg without its shell into a bottle
  10. Viagra and steroids – Drug testing and elder Congressmen

Not included in this list are archive articles from the legacy version of Sciencebase, which used to go under the name of Elemental Discoveries, you can check out a stack more popular science writing via the archive index page.

All the best for 2008!

Science Blogs, Favourites of 2007

Science OPML

In an effort to keep Sciencebase bubbling along during the holiday season, I figured a quickie post listing some of my favourite science blogs from this year might be interesting. Blogs come and go, of course, and my newsreader account is in constant flux with new blogs that catch my attention briefly getting pole position and then dropping off.

However, I remembered that there is a quicker way for you to grab a recent snapshot of my feed favourites and that is with my newsfeed OPML file (right-click and save the link with an “.opml” extension. You can then import it into any compatible news aggregator, offline (Snarfer) or online (Google Reader) with minimal fuss. Or use an OPML editor to edit it, it’s entirely up to you. My science OPML file is up to date, relatively speaking, although I may have added or removed a few feeds from my own aggregator in the last few days. Anyway, it’s as good as it gets at this time of year.

Meanwhile, a growing list of blogs with a genetics, DNA, and health theme can be found on the DNA Network. At the time of writing, my good friends Ricardo Vidal and Hsien-Hsien Lei are busy creating a new website for the Network that will feed on all the RSS files from the member blogs (I should admit, Sciencebase is a member of the Network). It’s difficult to single out any of the other blogs in the DNANetwork for specific attention, Ricardo and Hsien’s are superb, and so are many of the others. So. once you’ve trawled through my science OPML, do check out the DNA Network too.

Chemistry’s Sun Rises in the East

Andrew Sun Chemistry Blogger

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.