PhD blog

Scary article about the World's Busiest PI in Nature this week:

http://www.nature.com/news/2009/090304/full/458022a.html

Back at home taking a break from it all over Christmas. It's been...four days...and I'm already bored silly in the sleepy Hampshire village where I grew up. What did I do here for ten years?* I've already been for a drive in the country, and a walk in the country, which pretty much exhausts the possibilities. Having driven five miles today to get a coffee in the nearest town (An exciting new development - in my day we had to drive fifteen to the city, and I couldn't even drive. That's called Progress.) I decided to pay the local museum a visit to justify the petrol costs a bit more. Now ordinarily these town museums tell you what the Tesco building used to be used for, how many horses the post office used to have, why the pub is called The Angry Badger or other boring things - I only gave this one a chance because my friend had told me in the pub that it had a particularly mangy stuffed bear, and I was curious how that fitted into the local history.

Well somewhat disappointingly it didn't at all, but the museum actually had a vast array of stuffed stuff. In my book, you can't go wrong with a big collection of stuffed animals, and generations of aristocrats with elephant guns have thought the same. Although stuffed animals don't do a lot, I always find this kind of museum very relaxing, as I'm usually the only one there, and I always make a point of checking out the Natural History Museum wherever I go (I'm slightly ashamed to say that it's sometimes the first thing I do in a city) as it's bound to have such a collection assembled by the local eccentric with too much time, money or formaldehyde, so I was amazed that there had been one virtually on my doorstep all this time, cunningly disguised as a museum about the (very dull) town.

Considering the town only has ten thousand people, the collection was very extensive. As well as the bear (named Arthur, apparently) there were all sorts of zebras, black rhinos, two lions, the obligatory huge collection of songbirds in a wooden cabinet, skeletons of extinct kiwi birds, a duck-billed platypus, some echidnas, a selection of marsupials and some alligators. They didn't limit it to zoology either; there were also some fossils from the Burgess shale, various anthropological artifacts and even a mummy and a genuine page from the Egyptian book of the dead. I'm still totally mystified how this is adequately described by ' Haslemere Museum' and I'm still not really sure how all this stuff came to be in this little town. Interestingly (and in using this adjective, I feel like I just became older) the museum was founded by a Victorian surgeon and gentleman by the name of Sir Jonathan Hutchinson, who gives his name to the premature ageing disease Hutchinson-Gilford progeria, which a postdoc in my lab made a mouse model of. Looks like this world back home is even smaller than I thought.

SJP
(Can't wait to get back)

PS - One of the best things about the UK (particularly London) is that museums are almost always free, otherwise I never would have gone in here. I gave them some money when I left, but this policy means you are free to 'pop in' to a museum for a quick look rather than having to make a whole day of it to justify your £10. Probably the worst system is the New York Natural History Museum where you can go in free but you have to actually go and tell the cashier that you're not going to pay and get a ticket certifying that you're officially poor/tight. You probably get put on the FBI's 'Communist List' as a result and will never get a visa again. Do it properly or not at all...

*A rhetorical question really, but of course the honest answer is 'play computer games'. Sadly my computer with 3D acceleration is still in Cambridge.

I've spent some time recently with that all too common bioinformatician's task of writing parsers and file type conversion tools to juggle data between different analysis tools. Whilst doing so I've really begun to like certain features of the Ruby Core API which makes collection handling very intuitive and compact.

Below you'll find a compact example showing three common collection patterns in use: reduce, map and filter.

values = [1.0, 2.0, 4.0, 8.0]
sum = values.inject(0.0) {|acc,val| acc + val}
values = values.map {|val| val / sum}
$stdout.puts values.find_all{|val| val > 0.5}

The above code does the following: accumulate the sum of values in an array containing numeric values. Make a new array containing the values divided by the sum. Output values above 0.5 from this new array to standard output on separate lines.

Read more about collection patterns in Ruby. Enjoy!

A Swissman called Yves Rossy (or the 'Fusionman' as he likes to call himself) will today become the world's first jet-propelled man to fly across the English Channel. If you hear yodling from above around Calais today, you know who's responsible.

Isn't that just the coolest thing??

Update! Fusionman has delayed his flight until tomorrow because of fog over the channel.

Nature is running a nice (so far) series of articles on 'Meetings that changed the world'. SCAMPS didn't make it this time, but the competition is a little stiff - like foundation of CERN, Human Genome Project and a few other trifling things. Anyway this week was about the Asilomar conference on recombinant DNA technology - something I'd read about with interest before and was reminded of today.

In 1972 a crack commando unit was sent to prison by a military court for a crime they didn't commit, and promptly escaped to the Los Angeles underground. One year later, a crack unit of pioneering molecular biologists found that DNA cut with restriction enzymes could be stuck back together in different combinations. This created the field of genetic engineering in Nobel-winning* fashion. As with many discoveries in molecular biology, there were concerns over safety and ethics. What's interesting in this case is that some of the leading scientists in the field actually called for the work to be stopped until the issues had been debated. Even more amazingly, it actually happened. A conference was held within a year of the moratorium, and a consensus was reached that the human race probably wouldn't be devoured by a man-made virus if certain precautions were observed, and research resumed.

I suppose something slightly similar and recent is the addressing of 'will the world end?' questions surrounding CERN. I still think the genetic engineering must have been scarier at the time, with a relatively primitive knowledge of how genes work, and really not knowing what would happen if you shoved some new genes into an oncogenic virus. As someone educated recently in biology, it's hard to really imagine the discoveries and atmosphere leading up to the conference though.

You have to respect the foresight and bravery of these scientists in throwing the future of their research into public debate, recognising that the field would be better served and secured by reaching a public consensus. In the article today, one of them (Paul Berg) reaches some slightly depressing conclusions about whether or not it could happen today, which I'm inclined to agree with. He cites commercial interests as well as unresolvable ethical issues with todays new discoveries - you might also add sensational and inaccurate media reporting (15% of delegates at Asilomar were reporters) as well as competition between scientists in fast-moving fields (can you imagine someone calling a halt to all experimentation in their own, super-hot, research area - and people doing so?). I'm sounding like a grumbling old man so I'll stop short of suggesting things were better in the 1970s - but at least we could have called the A-Team.

Article: Nature 455:290-1

Asilomar Conclusions in PNAS, 1975: http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid...

And because it's great: http://www.youtube.com/watch?v=PIfuaUTH9Y4

* Strictly speaking, the discovery of restriction enzymes won the Prize.

Long time no post. This fantastically fast and light PubMed alternative called Pubget which gives you PDFs and citation files right away just made me break my silence.

Have a look at Pubget.com

The bioinformatics survey that we have spoken before is over.

Same of the inital charts are already available:
Number of entries:

The data will be released soon so it would be possible to analyze them and have at least an initial figure of the bioinformaticians in the world.

I've just discovered on bionformatics zen a survey to collect data about the bioinformaticians around the world and to see what's going on.

The survey is up from the 1st of July and it will be on until the 1st of August.
Everybody who would like to analyze the data can contribute later than that date and the analyzed data should be available from (hopefully) the 1st of September.

The survey is here.

Fill it if you have 5 mins. :)

This entry in the Science magazine news blog outlines a pretty strange motive for someone to go for a career in science: The Power of Poop.

[...] For marine scientist Ellen Prager (left), the moment came 25 years ago when she took a summer job helping researchers who spent a lot of time swimming behind parrotfish with bags in hand to collect poop as it plopped out of their bottoms. "If that was science, I thought to myself, I could do it too," Prager told the audience.

Well Matias and I have been spotting these for a while so I thought this could be an online wall of fame/shame for the worst puns ever to appear in titles of papers in otherwise respectable journals. This was prompted by my discovery today of this - the culprit/genius punster being my supervisor in this case!

http://www.ncbi.nlm.nih.gov/pubmed/9843198

Groan! I also feel that this deserves a special mention.

http://www.ncbi.nlm.nih.gov/pubmed/12509281

Getting a joke like that past the editors is basically the goal of my life.

Anyone else have any favourites?