Month: September 2006

X-rays solve transport problem

X-ray crystallography has provided new insights into how the microscopic motorised transport system that operates in our cells is powered. The study could have implications for understanding the symptoms of Down syndrome, the neuromuscular condition Charcot-Marie-Tooth disease, and some cancers, all of which arise through some form of breakdown of this system. The work may ultimately lead to possible new treatments for such disorders.

The researchers behind the work are from Duke University Medical Center, the National Institute of Advanced Industrial Science and Technology in Japan, and the Medical Research Council’s Laboratory of Molecular Biology in the UK. They explain that molecular motors are responsible for driving the separation of chromosomes during cell division. This process does not proceed normally in certain genetic disorders and if unchecked can lead to cancer.

Read the full story in my latest news round-up from spectroscopynow.com

Smog Schmog

In his climate-change ain’t happening State of the Union speech of Sept. 25th, Sen. James Inhofe (R-OK) makes the claim that climate change “skeptic” scientists do not get a fair share of media coverage. But, according to DeSmogBlog a quick infomart media search of US papers shows there have been more than 350 mentions of Fred Singer, Willie Soon, Sallie Baliunas, William Grey, Roger Pielke, Richard Linzen and Patrick Michaels.

It seems the infamous gang of climate change “skeptics” got mentioned, on average, once every 5 days in North American major print outlets.

I’m not sure how that compares to the non-skeptics, they don’t say, so I asked Richard Littlemore of DeSmogBlog to expand:

“I presume the argument here is that people who recognize the overwhelming evidence of climate change are getting an unfair amount of media coverage,” he told me, “while the skeptics are being bullied into silence. Woefully, this is pretty much the opposite of what is truly happening.”

He points to a peer-reviewed paper from Boykoff and Boykoff [link is now dead] that wades into the subject in some detail. The short version, according to Littlemore is this: “The climate change discussion in peer-reviewed scientific journals includes no papers whatsoever challenging the theory of anthropogenic global warming (check Oreskes in Science Magazine), while in the mainstream press, cranks like Singer and Soon get their [allegedly] unscientific denials mentioned in more than half the stories.”

Earworms burrow into your brain

I just can’t get you outta my head…is the usual thought when an irritatingly catchy pop song gets stuck on loop in your brain for days on end. A start-up company in East Anglia reasoned that this catchiness might be put to good use in helping people quickly learn a foreign language. Or, at the very least, a couple of dozen keyphrases that will help them get by while on holiday or a business trip abroad.

Programme creator Marlon Lodge found that background music seemed to help his language students remember phrases much better than simply hearing and repeating phrases by rote. Lodge teamed up with his brother Andrew and designed Earworms musical brain trainer (mbt) They reckon the system boosts language retention by up to 80%. I ripped the Earworms Italian CD to my mp3 player and listened every time I went for a run – in an effort to get fit and learn how to order pizza, a gelato, and a cappucino when we went on holiday this year.

It works. Very well. I’d done Spanish and French at school and Italian isn’t so different, but the earworms gave me the necessary extra to be able to confidently book a table, order food and drinks, and find out why the return flight got delayed so badly.

The system uniquely anchors foreign words and phrases into long term memory by hooking them to music. The company reckons it could provide a learning breakthrough for people with poor sight, dyslexia, or attention deficit problems by taking away the need to concentrate on reading phrase books and other academically based language courses.

‘Many people are reluctant to begin learning something new after they leave school, but as Mark Twain once said, ‘My education started the day I left school.’ Earworms is very much about giving people an easy handle on learning, and what easier way to learn than simply by listening to music, something we all enjoy?’ Lodge says.

The program is available for French, German, Greek, Italian, Spanish, and now Mandarin Chinese. More information at www.earwormslearning.com. It would be good to see some solid scientific research on how this system works, perhaps a functional MRI study showing the language centres in the brain lighting up more brightly with music rather than without. I’ll cover any such developments on spectroscopynow.com

Anyway, I just ordered the Spanish disc for next year’s holiday and they sent me Mandarin Chinese too…so, maybe I should think about going a little further afield.

Ciao for now!

Chemists escape browser lock down

WebME chemical structure drawingIs your browser so locked down that you can’t install any plugins or enable Java? Firewall refusing to cooperate with your molecules? Antivirus screaming at your structural efforts?

If so, then you probably find it rather difficult to run some of the chemistry drawing packages available for interactive use on the Web. There is an alternative.

Molinspiration Cheminformatics has released WebME, a molecule editor for creating
and editing molecules within a web browser that doesn’t need Java support and requires no plugins to be installed. The molecular editor is based on Web 2.0 Ajax technology and structure processing runs on serverside rather than on your machine.

The result is a web-based structure-input program with all kinds of potential that is not only platform independent but works with those locked down browsers.

Click to try WebME. In this implementation, the program is being used as the structure input for a molecular property calculator.

It may not have the depth of field of programs like ChemSketch and ChemDraw (yet), nor the bells and whistles of the many other structure packages available. But, the benefits to those behind restrictive user settings (in chemistry libraries for instance) are obvious.

The program is still in the beta stages of development, sitting at version 0.96 whatever that means. It seems nice and smooth to use though, quickly calculates properties and generates a Smiles string that you can then use elsewhere to search for your molecules. I hope they add InChI support soon though that’s the way to go for molecular searching these days.

There is, of course, another application that operates under similar general principles – PubChem sketcher (click the sketch button at PubChem.

Baby poop

It’s not a subject for polite conversatio, but anyone who has ever had to handle a soiled nappy (or diaper as our colleagues Stateside refer to them) will know that baby poop comes in a range of colours (unlike the apocryphal Ford Model T). The BabyPoop lens over on Squidoo offers a kind of litmus test, or more appropriately, a universal indicator paper strip, for the spectrum of options available.

Mustard coloured

 

poop is common for breastfed babies.

Whereas

 

Blue poop can only mean one thing…

Pod, poddy, podd

Apple has got ever so touchy about websites using the term podcast more liberally than its claims to trademark registration would allow. Cease and desist letters have been sent to the likes of Mypodder and Podcastready by the company, according to reports in Wired and The Register.

There are, of course, some bloggers that claim that the term podcast actually has nothing to do with Apple’s brand of mp3 player and that it originates in the phrase “publish-on-demand”-cast. Yeah, right!

Nevertheless, there is no mention of Apple in the dictionary.com definition of podcast: “a Web-based audio broadcast via an RSS feed, accessed by subscription over the Internet” or “to deliver a Web-based audio broadcast via an RSS feed over the Internet to subscribers”. Moreover, despite the term having an obvious etymology in a bastardisation of iPod and broadcast, neither an iPod nor over-the-air broadcasting is need to make or listen to a podcast.

Mark Ramsey of Hear 2.0 reckons it’s time we ditched the term podcast anyway, too few people “get it” he says, and the word should be changed to “audiomag” or something similar. This assertion is made despite the fact that the Ricky Gervais Show is mentioned in the Guiness Book of Records as the most popular podcast, presumably that will change soon with the launch of Sciencebase’s very own Geordie Boffin Podcast. Well, we can all dream, can’t we?

Bizarrely as ever, The Register includes a list of podified words in its report: antipodean, cephalopod, chiropodist, monkeypod, podgy and uropod. They overlooked arthropod, podiatrist, peapod, monopod…some of which point to the fact that pod, the prefix, has its etymology in the Greek word for foot. Maybe it’s time to give it the boot and go with Ramsey’s suggestion, or better still, we could rename them “blogcasts”, no doubt that would open yet another can of bad applies as the trademark owner of that term would more than likely kick up a fuss too.

Top Ten Hot Biologists

Purely in the interests of science, I headed over to flickr to see if I could find a snap of a particular biologist I was writing about today. Couldn’t find a single one, but all the faces that came up got me thinking that perhaps it would be fun and waste a few minutes when I should be working to pull together a list of the top biological totty. So, here it is a whirlwind tour of the world of biologists, in no particular order and no one vetted particularly closely.

Female biologists in action

  • Ninoka
  • Heather
  • Louise and friends
  • Susan
  • Claire
  • Alicia
  • Cerbu
  • Neguin
  • Elinay
  • Beck

For the sake of completeness, and to avoid accusations of sexism, I also gathered together ten male biologists in the field who also featured on flickr.

  • Glyn
  • John
  • Geoff
  • James
  • Dan
  • Alan
  • Bruce
  • Stan
  • Jeff
  • Chuck

I’ll leave it to Sciencebase readers to decide which if any should be in either top ten list. One thing to note, facial hair is common among biologists (but only in the second list).

Tomorrow, physicists on Pixsy.com and then chemists on myspace

Ironically small

An incredibly small item in Saturday’s Times announced that a Voluntary Reporting Scheme – established by DEFRA – in the UK to record and assess the risks posed by nanoparticles has been created. Scientists have welcomed the announcement, apparently. More likely, they are rather peeved that yet another layer of bureacracy has been added to their workload.

According to the paper, “Little is known of the potential risk to health by the creation through nanoengineering of altered particles.” No doubt, UK tabloids and scaremongers will jump on any future pronouncements as an admission of guilt once the first minute risks are revealed. Forgetting, of course, the enormous risks we face every day simply cross the road or jumping in our nanoparticulate-pumping cars.

Interestingly, there is a get out clause for scientists who may wish to peel back that bureacratic layer. The scheme is entirely voluntary!

So, if you’re an “evil scientist” intent on creating a doomsday scenario on a very, very small scale, then you needn’t worry about being risk assessed, just don’t add your research to the database.

Geordie Boffin Science Podcast – #1

UPDATE: I recorded just six episodes, but time pressure and deadlines at the time meant its untimely demise, I may resurrect the Podcast at some point, but I think it would be much better served if I did it as a chats type discussion on science news with colleagues rather than it simply being me reading out the latest blog post.

Geordie Boffin Podcast

Welcome to the first Geordie Boffin Podcast from David Bradley. This irregular and irreverent podcast will bring you audible reporting from the sciences. For most Sciencebase readers this will most likely be your first chance to hear my dulcet tones (and those of my wife) as well as a little effected guitar playing for the intro!

You can play the sound file by using the media player built-in to this post, download the mp3 and stick it on your iPod.

Check out our information sheet for more about the Geordie Boffin Podcast, and for some definitions, in case you’re wondering what any of those three terms actually mean!

Chemical structure lookup service

The NCI CADD Group headed by Marc Nicklaus and colleagues has just launched the Chemical Structure Lookup Service (CSLS). This web-based system allows one you to locate chemical structures in over 70 different public and commercial data sources. Stored within the system is information on over 30 million chemical structures and it provides a simple search interface for looking up chemicals by specific structure as well as by parent structure, and by various identifiers.

There are two mirror sites: http://cactus.nci.nih.gov/lookup/ and http://cholla.chemnavigator.com/lookup/