O'Really?

April 28, 2010

Philip Campbell on Science Facts and Frictions

Filed under: publishing — Duncan Hull @ 6:28 am
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Philip Campbell: Will you pay for good online stuff, Dammit? (Libraries do, thankfully)As part of the Gates Distinguished Lecture Series editor Philip Campbell is giving a public lecture at 6.30pm tonight titled Science – facts and frictions at Emmanuel College, Cambridge. The abstract and text below is reproduced from talks.cam.ac.uk:

‘Climategate’, MMR vaccine, GM crops, stem cells – these are examples of public debates in which science and scientists have come under attack. And yet the processes of science were no different in kind from those in calmer territories, such as cancer research, where the public not only trusts researchers but directly donates half a billion pounds every year in their support. Why are there such contrasts? And what can scientists and others do in response to such attacks? The talk will offer some suggestions.

As Editor-in-Chief of Nature, Philip Campbell heads a team of about 90 editorial staff around the world. Dr. Campbell takes direct editorial responsibility for the content of Nature editorials, writing some of them. He is the seventh [1] Editor-in-Chief since the journal was launched in 1869.

Dr. Campbell’s role as Editor-in-Chief of Nature publications (of which there are many editorially independent journals and several websites) is to ensure that the quality and integrity appropriate to the Nature name are maintained, and that appropriate individuals are appointed as chief editors. He sits on the executive board of Nature’s parent company, Nature Publishing Group.

According to the accompanying press release from the University, Campbell:

“is particularly interested in groups of scientists who regularly produce blogs in order to help the public and journalists gain access to their perspectives on scientific developments and controversies.”

So, if you’re in or near Cambridge tonight, this talk is open the public and looks like it will be enlightening.

[Update, some interesting things mentioned in this talk in no particular order:

Refererences

  1. Philip Campbell (1995). Postscript from a new hand Nature, 378 (6558), 649-649 DOI: 10.1038/378649b0
  2. Daniel Sarewitz (2004). How science makes environmental controversies worse Environmental Science & Policy, 7 (5), 385-403 DOI: 10.1016/j.envsci.2004.06.001

July 23, 2009

Josh the Java Junkie

Filed under: programming — Duncan Hull @ 12:18 pm
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Joshua Bloch at scifooOne of the people I enjoyed seeing at Science Foo Camp this year was Joshua Bloch. Josh is a Java Junkie [1,2,3] and software engineer at Google. When he wasn’t playing harmonica around the foo camp fire (see picture right), he was giving interesting talks about optical illusions, some of which can be found in his book Java Puzzlers. So I bought the book, and have been doing a puzzle a day to keep the doctor away. Most of the puzzles in this book are short Java programs that behave in ways you would not expect. The one below is a nice example:

public class Indecisive {
    public static void main(String[] args) {
        System.out.println(decision());
    }

    static boolean decision() {
        try {
            return true;
        } finally {
            return false;
        }
    }
}

What does this program do? Return true or false? Perhaps it does both or something else completely? Does it even compile? Can’t decide? Welcome to public class Indecisive…

References

  1. Joshua Bloch and Neal Gafter (2005). Java Puzzlers: Traps, Pitfalls, and Corner Cases (isbn:032133678X) Addison-Wesley
  2. Joshua Bloch (2006). How to design a good API and why it matters OOPSLA ’06: Companion to the 21st ACM SIGPLAN symposium on Object-oriented programming systems, languages, and applications, 506-507 DOI: 10.1145/1176617.1176622
  3. Neal Gafter (2008). Is the Java Language Dying? Neal Gafter’s blog: Thoughts about the future of the Java Programming Language.

July 13, 2009

Science Foo Camp 2009: Scifoo Day Two

Filed under: conferences — Duncan Hull @ 6:30 pm
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Theodore Gray (of Wolfram Research) with super-soluble sodium acetateThe fourth International Science Foo Camp (scifoo) 2009 has just concluded. Here are some very brief and incomplete notes and links from some of the sessions on the second day (Saturday), see the scholarly kitchen for a report on the first day. With seven parallel sessions, most people at this event miss most (six sevenths) of the sessions, but here is a summary of the (one seventh) sessions I managed to get to:

  • Larry Page ran a session on Making Artificial Intelligence happen. In brief, Larry argued that not enough people are working on this problem. Marvin Minsky joined in talked about his book The Emotion Machine. I’d write more about this, but Larry asked for what he said to be off-the-record so he could speak more freely.
  • Following on from this Harry Collins and Lee Smolin ran a session titled: The Social Nature of Knowledge, Science and Artificial Intelligence. As David Colquhoun pointed out in the session, you “need to be something of a sado-masochist” to attend a session on the sociology of Science but there was some interesting discussion on the Science (truth?) vs. Belief (religion) debate. Henry Thomspson pointed out: some argue that “Knowledge is true belief” which can make it hard to distinguish between Science and Religion. Jamie Heywood described his simple “truth formula” where truth = cost to make a claim divided by the cost to disprove claim.
  • Next up Douglas Kell did a session on Data-driven Science. This discussed the relationship and balance between hypothesis driven science (hypothetico-deductive) and data driven science (via inductive reasoning and machine learning for example) [1]. Attendees in this session included Tony Tyson (Director of the Large Synoptic Survey Telescope), Craig Rowell (BioRad), George Poste, Julia Lane (NSF), James Wilsdon (Royal Society), David Colquhoun, Nat Torkington, the six-minute-genome guy from Halcyon Molecular whose name I can’t remember and Annalee Newitz. Much of the discussion was about the over-reliance on hypothesis driven science (e.g. 92% of NIH R01 grants have to be hypothesis-driven) which can make the “fishing-trip” or “data-driven” science difficult to do. One conclusion from this presentation was that both types of science are required and complementary.

Then it’s time for lunch, not just any old food, but some yummy Google Food.

  • In the afternoon, I ran a session on The Invisible Scientist: Personal Digital Identity on the Web, Problems and Solutions. After a short set of introductory slides we discussed some solutions to identifying scientists digital contributions, not just electronic journal publications but wiki edits, blog posts, software development, ontology and database curation etc. Participants in this session included Cameron Neylon, Julie Lant (NSF) who will reuse some of my data in a report she is writing (Yay!), Nicola McCarthy (Senior editor of Nature Reviews Cancer), Shirley Wu, Michael Rogan, Mackenzie Cowell and Chris Holmes. The last time I was at Science Foo Camp (back in 2007) I felt slightly phased by the stellar company (nobel prize winners, billionaires, entrepreneurs, silicon valley A-listers, venture capitalists, artists, policy makers, movers and shakers) that I didn’t present anything. I’m very glad I made the effort this year, it forced me to think harder about the problem of digital identity (and solutions), which included a useful chat with Googler Ben Laurie (a cryptography person) who gave me the lowdown on OpenID, PKI and the like. Very useful stuff – thanks Ben and thanks to everyone who turned up at my session.
  • The second session of the afternoon was on Google Wave with Cameron Neylon. I won’t say too much about this, because it will probably be blogged by Cameron and others – but it was an interesting peek into some of the current strengths and weakness of this software – especially from the point of view of scientists.
  • The last two sessions of the day, I stayed in the Lightning Talks organised by Nat Torkington (see blog). These were great, probably my favourite part of scifoo this year. Each speaker got a very strict five minutes, including Natahan Wolfe, Ben Fry on visualisation, George Dyson on Darwin, Christopher Stumm on astronomical metadata, Adam Summers on fish, Linda Stone on unhealthy computing, Ed Lu, Brian Uzzi and Fiorenzo, Shelley Batts, Larry Weiss, Saul Griffith, Chris DiBona on telemedicine, Joshua Bloch on Java puzzlers, Christian Bok on poetry and Gregory Benford.

In the evening there were further demonstrations and talks, including sodium acetate crystals (ChEBI:32594) (with Theodore Gray – see picture above) and a talk by Bob Metcalfe (of Metcalfe law fame) on the “Enernet: Internet Lessons for Solving Energy”. One of the take home messages from this is that the energy industry should be much more decentralised (like the internet is). Bob argued that the huge centralised powerplants we have today are beginning to look as dated and obsolete as mainframe computers.

So in summary, saturday at scifoo was a fantastic action-packed day, started early in the morning and went on late into the night. It’s almost impossible to capture it all in a blog post, so if you’re interested my scifoo 2009 photo set on flickr has more details. My mind has been blown into lots of little pieces again – thanks to all the organisers and participants for another great day.

References

  1. Kell, D., & Oliver, S. (2004). Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era BioEssays, 26 (1), 99-105 DOI: 10.1002/bies.10385

July 8, 2009

California Googlin’

Filed under: lyrical — Duncan Hull @ 3:27 pm
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The Googlin' Gate BridgeSo, I’m going to San Francisco and on to the Googleplex in the heart of Silly Valley, California for Science Foo Camp (scifoo) 2009. As I put the Flowers In My Hair (what’s left of it) and confirm my booking at the Hotel California I’m not just California Dreamin’ but California Googlin’. Just how many American and Californian musical clichés it is possible to cram into one blog post and accompanying iPod playlist? Now there’s no shortage of lyrics to choose from, which is handy because it is a long journey from the UK to California and I’m extremely bored waiting for a flight westwards. So with a little help from a well known search engine and just like in the novel High Fidelity by Nick Hornby here is a (personal) top twenty-ish all time greatest hits:

  • Let’s start with The Beatles since they played their last ever gig in San Francisco (at Candlestick Park), so it seems appropriate. On Get Back Paul McCartney sings

    Jojo was a man who thought he was a loner

    But he knew it couldn’t last

    Jojo left his home in Tucson, Arizona

    For some California grass

    Get back, get back, back to where you once belonged

  • And what better to follow with than some Beatles-inspired rivalry in the shape of The Beach Boys who when they’re not Surfin’ USA they are singing about California Girls

    I wish they all could be California

    Girls, girls, girls yeah I dig the…

    I wish they all could be California Girls

    Are The Beach Boys possibly the band with the most cliches-per-album in the history of mankind?

    (more…)

April 17, 2009

The Unreasonable Effectiveness of Google

Filed under: Googleology — Duncan Hull @ 4:00 pm
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GoogleVia the Official Google Research Blog at the University of Google, Alon Halevy, Peter Norvig and Fernando Pereira have published an interesting expert opinion piece in the  March/April 2009 edition of IEEE Intelligent Systems: computer.org/intelligent. The paper talks about embracing complexity and making use of the “the unreasonable effectiveness of data” [1] drawing analogies with the “unreasonable effectiveness of mathematics” [2]. There is plenty to agree and disagree with in this provocative article which makes it an entertaining read. So what can we learn from those expert Googlers in the Googleplex? (more…)

April 2, 2009

Upcoming Gig: Science Foo Camp (scifoo) 2009

Filed under: awards — Duncan Hull @ 10:57 am
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Google Classic: Please Allow 30 Days for your Search ResultsIn my inbox this morning, an intriguing email from Timo Hannay, Tim O’Reilly and Chris DiBona:

Duncan,

We’d like to invite you to join us for Science Foo Camp (or “Sci Foo”), a unique, invitation-only gathering organized by Nature, O’Reilly Media, and Google, and hosted at the Googleplex in Mountain View, California.

Now in its fourth year, Sci Foo is achieving cult status among those with a passion for science and technology. Nobel laureate Frank Wilczek wrote of last year’s event:

“SciFoo is a conference like no other. It brings together a mad mix from the worlds of science, technology, and other branches of the ineffable Third Culture at the Google campus in Mountain View. Improvised, loose, massively parallel–it’s a happening. If you’re not overwhelmed by the rush of ideas then you’re not paying attention.”

As before, we will be inviting about 200 people from around the world who are doing groundbreaking work in diverse areas of science and technology. Participants will include not only researchers, but also writers, educators, artists, policy makers, investors, and other thought leaders.

The format is highly informal: all delegates are also presenters and demonstrators; the schedule is determined collaboratively on the first evening; and sessions continue to be organized and re-organized throughout the weekend. This creates a unique opportunity to explore topics that transcend traditional boundaries, and discussions are of a kind that happens at the best conferences during breaks and late into the night. Of course, there will also be time to have fun and relax at Google’s legendary campus.

Sci Foo 2009 will run from about 6pm on Friday, July 10 until after lunch on Sunday, July 12. Campers need to make their own way to and from the event, but Google will provide accommodation and meals, and there is no registration fee. For those who don’t have cars, there will also be free shuttle buses between the hotel and the Googleplex.

Please RSVP  etc

We hope to see you at the Googleplex in July!

Tim O’Reilly, O’Reilly Media
Chris DiBona, Google
Timo Hannay, Nature

About Nature Publishing Group

Nature Publishing Group (NPG) is dedicated to serving the information and communication needs of scientists and medics. NPG’s flagship title, Nature, first published in 1869, has now been joined by over 80 other titles, among them the Nature research journals, Nature Reviews, Nature Clinical Practice and a range of prestigious academic journals including society-owned publications. It also operates the leading scientific website, Nature.com, and a range of innovative online services, from databases to collaboration tools and podcasts.

About O’Reilly Media

O’Reilly Media spreads the knowledge of innovators through its books, online services, magazines, and conferences. Since 1978, O’Reilly has been a chronicler and catalyst of leading-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying “faint signals” from the alpha geeks who are creating the future. Whether it’s delivered in print, online, or in person, everything O’Reilly produces reflects the company’s unshakeable belief in the power of information to spur innovation. An active participant in the technology community, the company has a long history of advocacy, meme-making, and evangelism.

About Google Inc.

Google’s Philosophy – Never settle for the best “The perfect search engine,” says Google co-founder Larry Page, “would understand exactly what you mean and give back exactly what you want.” Given the state of search technology today, that’s a far-reaching vision requiring research, development, and innovation to realize. Google is committed to blazing that trail. Though acknowledged as the world’s leading search technology company, Google’s goal is to provide a much higher level of service to all those who seek information, whether they’re at a desk in Boston, driving through Bonn, or strolling in Bangkok.

About Foo Camps

The “Foo Camp” meeting format has been pioneered by O’Reilly (see when geeks go camping). In this context, “Foo” originally stood for “Friends Of O’Reilly“, but it is also a meaningless ‘placeholder word’ commonly used by computer programmers, rather like the term ‘X’ in algebra. The success of O’Reilly’s original technology Foo Camps has stimulated a wide range of similar events, from Science Foo Camp to Disney’s Pooh Camp.

Obviously I’m thrilled to bits to receive such an email, I’ve been to scifoo once before and it was a fantastic mind-blowing experience. This time, I’m invited as a consolation prize for being a runner-up in the international science blogging challenge 2009 which challenged younger scientists to get a senior scientist to blog. I managed to convince Douglas Kell and David DeRoure to start blogs, so thanks are due to them for entering into the spirit of the competition. This year, the first prize was won by Russ Altman and Shirley Wu at Stanford University, congratulations Shirley and Russ, it will be good to compare scientific blogging notes with you both.

Now, it would have been good to win this prize, but the invite above is probably one of the best runner-up prizes I’ve ever had. Thanks are due to the competition judges Cameron Neylon, Peter Murray-Rust and Richard P. Grant for organising the competition. Thanks also to Tim O’Reilly, Timo Hannay and Chris DiBona, see you in the Googleplex!

[More commentary on this post over at friendfeed]

October 31, 2008

Defrosting the Digital Library

Filed under: web of science — Duncan Hull @ 7:21 am
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Bibliographic Tools for the Next Generation Web

Sunset Ice Sculptures by Mark K.We started writing this paper [1] over a year ago, so it’s great to see it finally published today. Here is the abstract:

“Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.”

Biotechnology and Biological Sciences Research CouncilThanks to Kevin Emamy, Richard Cameron, Martin Flack, and Ian Mulvany for answering questions on the CiteULike and Connotea mailing lists; and Greg Tyrelle for ongoing discussion about metadata and the semantic Web nodalpoint.org. Also thanks to Timo Hannay and Tim O’Reilly for an invitation to scifoo, where some of the issues described in this publication were discussed. Last but not least, thanks to Douglas Kell and Steve Pettifer for helping me write it and the BBSRC for funding it (grant code BB/E004431/1 REFINE project). We hope it is a useful review, and that you enjoy reading it as much as we enjoyed writing it.

References

  1. Duncan Hull, Steve Pettifer and Douglas B. Kell (2008). Defrosting the digital library: Bibliographic tools for the next generation web. PLoS Computational Biology, 4(10):e1000204+. DOI:10.1371/journal.pcbi.1000204, pmid:18974831, pmcid:2568856, citeulike:3467077
  2. Also mentioned (in no particular order) by NCESS, Wowter, Twine, Stephen Abram, Rod Page, Digital Koans, Twitter, Bora Zivkovic, Digg, reddit, Library Intelligencer, OpenHelix, Delicious, friendfeed, Dr. Shock, GribbleLab, Nature Blogs, Ben Good, Rafael Sidi, Scholarship 2.0, Subio, up2date, SecondBrain, Hubmed, BusinessExchange, CiteGeist, Connotea and Google

[Sunrise Ice Sculptures picture from Mark K.]

September 4, 2008

Famous for fifteen people

Filed under: web of science — Duncan Hull @ 2:47 pm
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Marilyn Monroe by Andy Warhol (and oddsock)The artist Andy Warhol once said:

“In the future everybody will be world famous for fifteen minutes”.

This well worn saying has been quoted and misquoted in hundreds of different ways in the forty years since Warhol first coined it [1].

Bad Scientist Ben Goldacre, in his keynote speech* at Science Blogging (sciblog) 2008, highlighted one of these deliberate misquotes, which he attributed to NTK.net (Need To Know: Britain’s most sarcastic high-tech weekly newsletter). It goes a little something like this:

“On the internet everybody can be world famous for fifteen people“.

This wonderful expression captures the nature and scale of science blogging on the internet today in a nutshell. Personally, I think it also sums up much of the spirit of the Science Blogging 2008 conference as well. In total, around eight groups of fifteen people, attended the conference. It was physically impossible to talk to all of them in one day, especially since I had to slink off early at 7pm, but I did manage to meet the following people: (more…)

August 7, 2007

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

Filed under: informatics — Duncan Hull @ 9:54 pm
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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

Filed under: informatics — Duncan Hull @ 10:30 pm
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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…)

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