O'Really?

December 12, 2007

Mapping the Internet

Internet mapAs of 2007, the Internet is mostly still a wild untamed jungle. Many people have tried to chart the territory, but what should a map of the internet look like?

One of my favourite maps is “The Web Is Agreement” by Paul Downey. Paul’s map has a Tolkien-like Lord of the Rings feel to it, so instead of Microsoft we have Mordorsoft. The all seeing eye of Sauron is Google of course, helping search, but raising privacy concerns.

Paul is not the only cartographer busy drawing maps, Randall Munroe has drawn a nifty map based on Internet Protocol (IP) addresses (available as a poster, for hard-core geeks) and an online communities map, shown at the bottom of this post.

If the atoms of the Internet had numbers, you could organise them into a map like the Periodic Table, just as Mendeleev did. Hence we have The Periodic Table of the Internet by Wellington Grey, which uses PageRank (instead of atomic numbers) as a means of charting the Internet.

Periodic Table of the Internet

And of course there’s some bloke called Tim who, showing his British roots, often draws more abstract maps that look like the London Underground, shown below.

The map is not the territory but you can learn a hell of a lot by looking at the map before you head into the jungle. Using the map below, you’ll find nodalpoint, down South in the warm “blogipelago“, past the “Gulf of YouTube” below. Bon voyage!

November 30, 2007

Burn semantic Web, Burn!

Taking down A.I. town?

Danger! Religious Wars!The Semantic Web is (quote) “a new form of Web content that is meaningful to computers”. It will “unleash a revolution of new possibilities” using a magical “new” artificially intelligent technology called ontology. So says a much-cited article in Scientific American published back in May 2001. Most people who have read this article, fall into two camps: “believers” and “non-believers”. Let me tell you a short story about a religious war between these two groups…

An Old War Story: Chapter 1

This is a work of fiction, though as they say in Hollywood it is “based on a true story”. Characters names are real.

A crusade of semantic web believers, is started by three people called Jim Hendler, Ora Lassila and Tim Berners-Lee. At the heart of their faith is a holy scripture and a suite of sacred technology called the semantic web stack. If people use this technology, the crusaders believe, the Web would be a better place. Search engines like Google, for example, would be even smarter than they already are, because they would intelligently “know what you mean“, when you type your keywords. All this new magic comes from using good old fashioned logic, metadata and reasoning. Better Search Engines is one of the mantras of the semantic web troops as they pour onto the battlefield towards the promised land. Viva la Webolution! Charge!

A counter-attack is launched by the non-believers of this vision of the future. They rally behind a man called Clay Shirky who roars “the semantic web is doomed” at the top of his voice. Many others echo Shirky’s sentiment, including Peter Norvig, Rob McCool, Cory Doctorow and Tim O’Reilly. General Shirky makes powerful allies in battle, and he has a two-pronged attack. “Ontology is over-rated” he jeers. Led by Shirky, the non-believers capture the sacred technology, add their own firewood and put the torch to it in a very public place. The flames leap into the sky, visible for miles around.

“Burn semantic web, burn!” the non-believers cry as they gleefully dance around the fire.

The battle rages, the believers will not take this heresy lying down. They regroup and surge forward again. Death to the blasphemers! With the help of some biologists, they seek revenge using the Gene Ontology as deadly ammunition. The non-believers are confused by this tactic, they don’t know what genes are and neither do the biologists. Unfortunately, the biologists unwittingly find themselves in the middle of an epic battle they didn’t start. There are ugly skirmishes involving logic and graph theory. Dormant and hideous A.I. monsters are resurrected from their caves, where they spent the A.I. winter. These gruesome monsters make the Balrog beast from Lord of the Rings look like a childrens cuddly toy.

From the relative safety of their command centres, the leaders orchestrating the war look on. Many foot soldiers and PhD students have been slayed on the field of battle, tragic young victims of the holy war. Understandably the crusaders are unhappy. Jim Hendler isn’t pleased as he surveys the carnage and devasation. Ora Lassila is also disappointed.

“We never said that, you completely minsunderstood. You are all burning the wrong thing, using fuel we never gave you. You lied, you cheated, you faked, you changed the stakes!”

There is a lull in battle. But confusion reigns, especially among the innocent civilians and bewildered biologists.

(End of chapter 1)

Epilogue

As of the winter of 2007, the semantic web fire is still burning. While I warm myself next to it, using all the juicy metadata as material for my PhD, it is still too early to predict just how useful the technology is going to be. It doesn’t really matter if you’re a “believer”, a “non-believer” or completely agnostic about the semantic web. The religious war beween the two sides tells you more about human behaviour, than it does about the utility of the technology. Optimists profit from making bold claims to get noticed on the battlefield. Critics are more cynical, furthering their own careers by countering the optimists claims. Other people interpret the interpretations of the cynics second-hand. Thanks to cumulative error, or the Chinese whispers effect, everyone gets really upset. The original optimists vision has been changed in ways they didn’t expect.

It’s a very natural and human story amidst all the “artificial” machine intelligence.

Ora, Jim and Tim have done quite well out of the fighting. Google Scholar reckons their original article has been cited nearly 5000 times. That is a lot of attention, in scientific circles, a veritable blockbuster hit. At the time of writing, not even Albert Einstein can match that, and his ideas are much more important than the semantic web probably ever will be. Many good scientists with important ideas can only dream of publishing a paper that is as heavily cited as that infamous Scientific American article. So which do you think would most scientists prefer:

  • Being internationally known and talked about, but misunderstood by large groups of people?
  • Being relatively unknown, ignored but well understood by a small and obscure group of people?

Neither is ideal but I think in most cases, there is only one thing in the world worse than being talked about, and that is not being talked about.

We have reached the end of chapter 1 of this little story. Wouldn’t it be nice if Chapter 2 was less bloody? Perhaps the two sides could focus more on facts and evidence, rather than the beliefs, opinions, marketing, hype and “visions” that have dominated the battle so far. As the winter solstice approaches and the new year beckons, can we give peace, diplomacy and above all SCIENCE a chance?

The Moral of the Story (so far)

The moral of this old war story is simple. Religions of various kinds have been known to make people commit horrendous and completely unreasonable war crimes. Nobody is innocent. So if you don’t like a fight, steer well clear of religious wars.

Acknowledgements

  1. The “burn” idea comes from Leftfield with John Lydon (1995) Open Up “Burn Hollywood, Burn! Taking down Tinseltown
  2. Thanks to Carole for the idea of using fiction to illustrate science see Carole Goble and Chris Wroe (2005) The Montagues and the Capulets: In fair Genomics, where we lay our scene… Comparative and Functional Genomics 5(8):623-632 DOI:10.1002/cfg.442 seeAlso Shakespearean Genomics: a plague on both your houses)
  3. This post, originally published on nodalpoint

November 6, 2007

What’s The Point of Blogging?

I am a hard bloggin' scientist. Read the Manifesto.
Sometimes I wonder what what the point of blogging is and just how much time people (myself included) waste reading and writing them. Let’s face it, most leading scientists are too damn busy to pay much attention to the blogosphere, especially when it descends (as it frequently does) into “uncontrollable verbal discharge”. This unfortunate medical condition is also known as Blogorrhoea. A free-flowing blog is unlikely to directly increase a scientists productivity (as approximated by the infamous h-index), and might even decrease it. Now, we all know that powerpoint can be PowerPointless, so is blogging also a pointless activity? Or to put it another way: Nodalpoint or Nodalpointless?

If you’ve ever wondered what the point of scientific blogging is, you should read the following, (if you haven’t already):

So what the heck, if blogging is fun and helps you communicate ideas with people, why get all uptight about questionable metrics for measuring scientific productivity? Wherever you blog, blog hard, blog fast and enjoy it. At the very least, it will fill the gaping void left on the Web by traditional scientific publishing. Who knows what the other benefits might be?

References

  1. Jorge Hirsch An index to quantify an individual’s scientific research output Proceedings of the National Academy of Sciences. 2005 November;102(46):16569-16572 DOI:10.1073/pnas.0507655102
  2. this post originally on nodalpoint with comments

October 19, 2007

The Webolution Will Be Televised

The American poet and songwriter Gil Scott-Heron once famously remarked that The Revolution Will Not Be Televised [1]. Science has undergone its own quiet revolution since the invention of the Web back in 1990. This has slowly but surely changed scientific communication, not just a Revolution but a “Webolution” [2] if you like. The recent addition of television to the Web means that, to paraphrase Gil, the Webolution will be televised. You can now watch some of the webolution in science, thanks the likes of JOVE (The Journal Of Visualised Experiments), SciVee.TV, Google Video and YouTube. What are these sites like and is their scientific and technical content any good?

(more…)

October 17, 2007

The Luxuriant Flowing Hair Club for Scientists (LFHCfS)

Filed under: Uncategorized — Duncan Hull @ 9:18 pm
Tags: , , , , , ,


Falk Schuch, Andreas Linsner and Kai Jung
Calling all Scientists, is your hair luxuriant and flowing? Perhaps you’re a bouffant bioinformatician, a hairy hacker or share a lab with somebody who is? If this is you, its high-time you joined the Luxuriant Flowing Hair Club for Scientists.

To propose somebody for membership, send email to Marc Abrahams at Harvard University marca /ate/ chem2.harvard.edu. Your email needs to include evidence of your luxuriant, flowing hair (a photo) and your credentials as a scientist. Some current members have impressive hair, see Simon Gregory, Carlisle Landel and Sterling Paramore for examples. Honorary and historical members include Dr. Brian May (Queen guitarist / astrophysicist), Dimitry Mendleyev and Albert Einstein, “Physicist. Bon vivant. A bold experimentalist with hair”.

So, if you are a scientist with a copius coiffure, ask yourself, will you ever get another chance to be in such distinguished company?

September 5, 2007

WWW2007: Workflows on the Web

Don't PanicThe Hitch-hiking novelist Douglas Noel Adams (DNA) once remarked that the World Wide Web (WWW) is the only thing whose shortened form – ‘double-you double-you double-you-dot’ – takes three times longer to say than what it’s “short” for [1]. If he were still with us today, there is plenty of stuff at the 16th International World Wide Web conference (WWW2007), currently underway in Banff, that would interest him. Here are some short, abbreviated notes on a couple of interesting papers at this years conference. They are relevant to bioinformatics and worth reading, whichever type of DNA you’re most interested in.

One full paper [2] by Daniel Goodman describes a scientific workflow language called Martlet. The motivating example is taken from climateprediction.net but I suspect some of the points they make about scientific workflows are relevant to bioinformatics too. Just like the recent post by Boscoh about functional programming, the paper discusses an inspired-by-Haskell functional approach to building and running workflows. Comparisons with other workflow systems like Taverna / SCUFL are drawn. Despite what they say, Taverna already uses a functional model (not an imperative one), it just hasn’t been published yet. The paper also draws comparisons between Martlet and other functional systems, like Google’s Map-Reduce. It concludes that the (allegedly) new Martlet programming model “raises the interesting possibility of a whole set of new algorithms just waiting to be discovered once people start to think about programming in this new way”. Which is an exciting possibility.

Another position paper [3] (warning: position paper = arm waving) by Anupriya Ankolekar et al argues that the Semantic Web and Web-Two-Point-Oh are complementary, rather than competing. Their motivating examples are a bit lame (Blogging a movie? Can’t they think of something more original?) …but they make some interesting (and obvious) points. The authors think that aggregators like Yahoo! Pipes! will play an important role in the emerging Semantic Web. Currently, there don’t seem to be too many bioinformaticians using Yahoo! pipes, perhaps they just don’t share their pipes / workflows yet?

Running in parallel to all of the above is the Health Care and Life Sciences Data Integration for the Semantic Web workshop, where more detailed discussion on the bio semweb is underway. As its a workshop, there are no full or position papers, but take a look at The State of the Nation in Life Science Data integration to get a flavour of what is going on.

Wether functional, semantic, Web-enabled or just buzzword-friendly, there is plenty of action in the scientific workflow field right now. If you’re interested in the webby stuff, next years conference, WWW2008, is in Beijing, China. I wonder if they will mark the 10th anniversary of the publication of that Google paper at WWW7 back in 1998? The deadline for papers at WWW2008 will probably be sometime in November 2007, but around 90% of submitted papers will be rejected if previous years are anything to go by. If you’re thinking of doing a paper, DON’T PANIC about those intimidating statistics, because bioinformatics is bursting full of interesting and hard problems that challenge the state-of-the-art. The kind of stuff that will go down well at Dubya Dubya Dubya.

(Photo credit: Fire Monkey Fish)

References

  1. Douglas Adams (1999) Beyond the Brochure: Build it and we will come
  2. Daniel Goodman (2007) Introduction and Evaluation of Marlet, a Scientific Workflow Language for Abstracted Parallelisation doi:10.1145/1242572.1242705
  3. Anupriya Ankolekar, Markus Krotzsch, Thanh Tran and Denny Vrandecic (2007) The Two Cultures: Mashing up Web 2.0 and the Semantic Web doi:10.1145/1242572.1242684


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Semantic Biomedical Mashups with Connotea


Mashup or Shutup

The Journal of Biomedical Informatics (JBI), will soon be publishing their special issue on Semantic Biomedical Mashups (can you fit any more buzzwords into a Call For Papers?!). Ben Good and friends have submitted a paper on their Entity Describer which extends connotea using some Semantic Web goodness. They’d appreciate your comments on their submitted manuscript over at i9606. As Ben says, their pre-publication turns out to be an interesting experiment “figuring out how blogging might fit into the academic publishing landscape”. If this interests you, get commenting now!

Update: Just spotted this interesting graphic of the Elsevier / Evilsevier logo (snigger), who are the publishers of JBI…

August 7, 2007

Scifoo: Geek Out! Le Geek, C’est Chic…

Deepak Singh and Euan Adie

As well as big famous superstars at Science Foo Camp (scifoo), there is a chance to meet and “geek out” with younger engineers and scientists like Vince Smith, Aaron Schwartz and Vaughan Bell.

Aaron Schwartz and the open library project

On Sunday at scifoo, Aaron (of archive.org) gave a quick demo of the Open Library. Currently this project is taking books that are out of print and not in other book catalogues like Amazon, and making them available online. They are intending to move into archiving scientific journals, so watch that space. I’ve always wondered how the internet archive survived financially, and managed all its interesting projects (like the open library). It’s all funded by some bloke called Brewster Kahle. They provide some great services, like hosting digital artifacts for free, see http://www.archive.org/create/.

Vince Smith, Museums and Drupal

Vince Smith is a “cyber-taxonomist” at the Natural History Museum in London. He’s a world expert on parasitic lice, and uses a multi-site installation of Drupal, see vsmith.info (Hmmm, that drupal skin looks familiar…). Vince uses a drupal module for bibliographic citations, called biblio, looks handy. It’d be nice to have it on nodalpoint? Anyway, anytime spent looking around Vince’s site is time well spent.

Vaughan Bell, Mind Hacker

Vaughan Bell is a clinical psychologist. We chatted about wikipedia and science, as demonstrated by Schizophrenia. He’s also a contributor to a book on MindHacks and blogs at mindhacks.com. My suitcase is full of free O’Reilly book-schwag I filled my boots with on Friday, one of which is Vaughan’s book. Looks like it will be a good read on the plane home, because my brain is in need of some serious “optimisation”.

(Two more geeks, pictured right, but regular nodalpoint readers will know all about them already, Deepak Singh and Euan Adie.)

Theres plenty more I could blog about scifoo, but I’m all foo-ked up, geeked out and mashed-up. It’s time to go home. For more scifoo blogging see www.technorati.com/tags/scifoo, www.nature.com/scifoo and network.nature.com/blogs/tag/scifoo.

References

  1. Aaaaah: Freak Out! Le Freak, C’est Chic…

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August 6, 2007

Scifoo day three: Genome Voyeurism with Lincoln Stein

On day three of Science Foo Camp (scifoo) biologist Lincoln Stein (picture right) gave a presenation on what he calls “genome voyeurism”, using Jim Watsons genome as an example. This session demonsrated the current and future possibilities of individuals having their own DNA sequenced, what has been called “personal genomics“.

Unlike the session on genomics yesterday on day two, where George Church, Eric Lander, 23andme, Sergey and Larry (and even Sergey’s pet dog) are all present, today they are conspicuously absent.

Lincolns presentation starts with a video (see youtube video below) of Jim Watson receiving his genome on a disk from Baylor College of Medicine, Houston. Lincoln tells how Jim puts his genome (stored on a hard drive) next to his Nobel prize medallion in his office. After all the press publicity, Jim deposits the data in GenBank, and it becomes available worldwide. (more…)

Scifoo day two: Good Morning Mashup

Vince Smith, Brian Berman, Paul Ginsparg, Linda Miller, John SantiniSome of the most interesting conversations you have at Science Foo Camp (scifoo) are in the corridors, foo bars and even the bus that shuttles between the Googleplex and the hotel…On Saturday, for example, I ride the bus with David Hawkins who is a laywer working in the area of climate change. He tells me all about the legal issues, how climate modelling works and little on Bjørn Lomborg, who is also here. I tell him about workflows on the web and bioinformatics. We work in completely different areas, and we’d never normally meet. But in a short conversation, we manage to learn a little from each other and find connections. The problems that climateprediction.net face, turn out to be quite similar to the problems that genomics faces in integrating data on the web. When we arrive at the Googleplex, it’s time for Open Science… (more…)

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