Author: David Bradley

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.

Don’t Poison Your Dog This Holiday

Theobromine structure

‘Twas the night before Christmas, when all through the house
Not a creature was stirring, not even a mouse

Well, that may not be quite true, do you know what your dog is doing right now? What about the cat? They’re not rummaging through the presents under the tree are they? You didn’t leave any luxury plain or dark chocolates under there did you? If you did, you could wake up to a quite horrible surprise when Christmas morning comes around. Chocolate makes pets ill! That’s the important seasonal warning being delivered by vets everywhere.

Poisonous chocolatesSo, what’s the problem? Surely a little chocolate snack in the night isn’t going to harm good-old Fido? Well, our vet begs to differ and so do the veterinary toxicology sheets for the chocoholics’ favourite fast-food. Man’s best friend, and several other animals, you see lack a particular liver enzyme that their owners do possess, that breaks down a toxin found naturally in chocolate – theobromine.

Theobromine has nothing to do with the element bromine, rather it is a bitter alkaloid from the seed of the cacao tree, known scientifically as Theobroma. The basic chemical skeleton is a xanthine unit, same one on which several other more well-known natural chemicals are based. The stimulant caffeine (from coffee beans) is a xanthine, for instance, so too is theophylline (found in tea and used in treating COPD and asthma).

Non-chocolate Labrador

Lacking the enzymes to metabolize theobromine leaves dogs exposed to the toxic action of the compound, which can cause vomiting, diarrhoea, hyperactivity, tremors, seizures, abnormal heart rhythms, and in extreme cases death.

So, what are the first signs of chocolate poisoning, what’s the lethal toxic dose, and what should you do if you think your dog has been at the chocolatier’s produce? Well, the first signs of chocolate poisoning are vomiting and diarrhoea, increased frequency of urination, and nausea. A toxic dose that will cause symptoms is about 100-150 milligrams of theobromine per kilogram of body weight, toxic dose could be approximately 250 and 500 mg/kg. A kilogram of milk chocolate will contain about 2 grams of theobromine. So a greedy, little dog is at greater risk of a serious digestive upset than a big gluttonous dog if he or she snaffles a 250 g bar of milk chocolate.

There is no direct way to treat chocolate poisoning in dogs, although inducing vomiting if the animal is caught “brown-pawed” (best left to the vet) is probably a good idea. A dog that has eaten a lot of chocolate will almost certainly require hospitalisation for at least the four days while the theobromine is naturally excreted (It takes about 17 hours for a dog to excrete half of the theobromine in its system, which means this toxin will reach vital organs repeatedly via the blood stream). But, who needs that, or worse, at Christmas? As they say: a gram of prevention is worth a kilo of cure.

For lovers of cats (small, domestic, big, wild) keep the aspirin out of reach. It’s deadly poisonous to felines.

December Chemical Discoveries

In addition to my interview with Chinese chemist Andrew Sun, mentioned earlier this week, the December issue of Reactive Reports features the pick of chemistry news

DNA nanorings DNA Nanorings  A simple approach to making rigid DNA nanorings with tailor-made functionality has been developed by Michael Famulok and his team at the University of Bonn, Germany.

Sunshine superpower Sunshine Superpower  In the depths of the Northern winter, as we approach the shortest day of the year, what could be more welcome than a little sunshine news.

ACS chemical discoveries of 2007 Five Firsts in Chemistry  With 2007 rapidly coming to an end, the inevitable lists are popping up. Not wishing to be left out this holiday season, the American Chemical Society has compiled a Top 5 from its own publications. Oh, and by the way, Sciencebase didn’t want to be left off the wish list either, so I did a Top Ten Molecules of 2007 item just recently.

Ten Computing Tips | Data Recovery

Faster Firefox

Seeing as the holiday season is fast approaching, I thought I’d offer an extra post covering some of the browsing and blogging tips and tricks I run on the Significant Figures site at Sciencetext.com. On that site I used to mainly discuss inappropriate unit conversions, sloppy statistical use, and dodgy typos in the media and still do occasionally.

For instance, there was a lot of press on the comet bigger than the sun issue recently, which interconverted miles and kilometres with astoundingly high improvements in significant figures. Then there was the discussion of how much does Santa Claus weigh…

But, like I say, mostly it’s tips on how to get the most from your web browser, improve security, and boost your blog’s performance. It acts as my personal lab book for all kinds of hacks, so I always have an online reminder of tweaks in case I lose track of how I fixed a particular problem. To follow are some of the most commonly accessed pages on the site, hopefully one or two of them will strike a chords and be of use to Sciencebase readers:

So, there you go, if you plan to use any of these, please backup any important data files first to avoid the need for data recovery and don’t blame me if it all goes horribly wrong, you use them at your own risk. I would be interested to hear how you get on if you do apply any of my hacks.