O'Really?

February 15, 2012

The Open Access Irony Awards: Naming and shaming them

Filed under: data mining,publishing,Science,technology — Duncan Hull @ 11:23 am
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Ask me about open access by mollyaliOpen Access (OA) publishing aims to make the results of scientific research available to the widest possible audience. Scientific papers that are published in Open Access journals are freely available for crucial data mining and for anyone or anything to read, wherever they may be.

In the last ten years, the Open Access movement has made huge progress in allowing:

“any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers.”

But there is still a long way to go yet, as much of the world’s scientific knowledge remains locked up behind publisher’s paywalls, unavailable for re-use by text-mining software and inaccessible to the public, who often funded the research through taxation.

Openly ironic?

ironicIronically, some of the papers that are inaccessible discuss or even champion the very Open Access movement itself. Sometimes the lack of access is deliberate, other times accidental – but the consequences are serious. Whether deliberate or accidental, restricted access to public scientific knowledge is slowing scientific progress [1]. Sometimes the best way to make a serious point is to have a laugh and joke about it. This is what the Open Access Irony Awards do, by gathering all the offenders in one place, we can laugh and make a serious point at the same time by naming and shaming the papers in question.

To get the ball rolling, here is are some examples:

  • The Lancet owned by Evilsevier, sorry I mean Elsevier, recently  published a paper on “the case for open data” [2] (please login to access article). Login?! Not very open…
  • Serial offender and über-journal Science has an article by Elias Zerhouni on the NIH public access policy [3] (Subscribe/Join AAAS to View Full Text), another on “making data maximally available” [4] (Subscribe/Join AAAS to View Full Text) and another on a high profile advocate of open science [5] (Buy Access to This Article to View Full Text) Irony of ironies.
  • From Nature Publishing Group comes a fascinating paper about harnessing the wisdom of the crowds to predict protein structures [6]. Not only have members of the tax-paying public funded this work, they actually did some of the work too! But unfortunately they have to pay to see the paper describing their results. Ironic? Also, another published in Nature Medicine proclaims the “delay in sharing research data is costing lives” [1] (instant access only $32!)
  • From the British Medical Journal (BMJ) comes the worrying news of dodgy American laws that will lock up valuable scientific data behind paywalls [7] (please subscribe or pay below). Ironic? *
  • The “green” road to Open Access publishing involves authors uploading their manuscript to self-archive the data in some kind of  public repository. But there are many social, political and technical barriers to this, and they have been well documented [8]. You could find out about them in this paper [8], but it appears that the author hasn’t self-archived the paper or taken the “gold” road and pulished in an Open Access journal. Ironic?
  • Last, but not least, it would be interesting to know what commercial publishers make of all this text-mining magic in Science [9], but we would have to pay $24 to find out. Ironic?

These are just a small selection from amongst many. If you would like to nominate a paper for an Open Access Irony Award, simply post it to the group on Citeulike or group on Mendeley. Please feel free to start your own group elsewhere if you’re not on Citeulike or Mendeley. The name of this award probably originated from an idea Jonathan Eisen, picked up by Joe Dunckley and Matthew Cockerill at BioMed Central (see tweet below). So thanks to them for the inspiration.

For added ironic amusement, take a screenshot of the offending article and post it to the Flickr group. Sometimes the shame is too much, and articles are retrospectively made open access so a screenshot will preserve the irony.

Join us in poking fun at the crazy business of academic publishing, while making a serious point about the lack of Open Access to scientific data.

References

  1. Sommer, Josh (2010). The delay in sharing research data is costing lives Nature Medicine, 16 (7), 744-744 DOI: 10.1038/nm0710-744
  2. Boulton, G., Rawlins, M., Vallance, P., & Walport, M. (2011). Science as a public enterprise: the case for open data The Lancet, 377 (9778), 1633-1635 DOI: 10.1016/S0140-6736(11)60647-8
  3. Zerhouni, Elias (2004). Information Access: NIH Public Access Policy Science, 306 (5703), 1895-1895 DOI: 10.1126/science.1106929
  4. Hanson, B., Sugden, A., & Alberts, B. (2011). Making Data Maximally Available Science, 331 (6018), 649-649 DOI: 10.1126/science.1203354
  5. Kaiser, Jocelyn (2012). Profile of Stephen Friend at Sage Bionetworks: The Visionary Science, 335 (6069), 651-653 DOI: 10.1126/science.335.6069.651
  6. Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010). Predicting protein structures with a multiplayer online game Nature, 466 (7307), 756-760 DOI: 10.1038/nature09304
  7. Epstein, Keith (2012). Scientists are urged to oppose new US legislation that will put studies behind a pay wall BMJ, 344 (jan17 3) DOI: 10.1136/bmj.e452
  8. Kim, Jihyun (2010). Faculty self-archiving: Motivations and barriers Journal of the American Society for Information Science and Technology DOI: 10.1002/asi.21336
  9. Smit, Eefke, & Van Der Graaf, M. (2012). Journal article mining: the scholarly publishers’ perspective Learned Publishing, 25 (1), 35-46 DOI: 10.1087/20120106

[CC licensed picture “ask me about open access” by mollyali.]

* Please note, some research articles in BMJ are available by Open Access, but news articles like [7] are not. Thanks to Trish Groves at BMJ for bringing this to my attention after this blog post was published. Also, some “articles” here are in a grey area for open access, particularly “journalistic” stuff like news, editorials and correspondence, as pointed out by Becky Furlong. See tweets below…

January 2, 2012

Does Android Dream of Electric Sheep?

Filed under: mobile,technology — Duncan Hull @ 1:02 am
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Androids by etnyk. What are they thinking?

With more than three million Android devices activated on the 24/25th December 2011 [1] and something like 200 million (or more?) Android devices in total, there are nearly enough droids around to build a primitive brain.

With all that processing power out there, I can’t help but wonder, like Philip K. Dick did, Does Android Dream of Electric Sheep? [2,3]

References

  1. Andy Rubin (2011) http://twitter.com/Arubin/status/151918325260226561
  2. Philip K. Dick (1967) Do Androids Dream of Electric Sheep?
  3. Ridley Scott et al (1982) Blade Runner

http://twitter.com/Arubin/status/151918325260226561

September 8, 2011

UK Riots: Blame it on the Baby Boomers

Filed under: book review,education,technology — Duncan Hull @ 11:59 am
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What caused the summer riots of 2011 in the UK? Many reasons have been suggested and a long list of possible causes has been drawn up over the summer.  The baby boomer generation should be added to the list of suspects. It is the baby boomers, those born roughly between 1945-1965, that caused the riots – it’s mostly their fault [1].

Riot police looks on as fire rages through a building in Tottenham, north London Sunday, Aug. 7, 2011. A demonstration against the death of a local man turned violent and cars and shops were set ablaze. (AP Photo/PA, Lewis Whyld)

Arson and rioting in Tottenham, August 2011 (AP Photo/PA, Lewis Whyld)

UK riots: a long list of suspects

Who or what can we blame for the UK riots? It’s complicated but we could…

It is hard to conclusively prove that any of these suspects are guilty as charged because the causes of rioting are complex. However, it seems likely that the unequal wealth and influence of baby boomers was a contributing factor in the UK riots. You can read all about it in Mr Willett’s intriguing book [1,2].

References

  1. David Willetts (2010) The Pinch: How the Baby Boomers Took Their Children’s Future – And Why They Should Give it Back ISBN: 1848872313. See full book reviews in The Telegraph, The Times, The Guardian, The Economist, The Daily Mail and New Statesman

May 1, 2011

Myopia, Hubris and Amnesia: Three Reactions to Innovation

Filed under: engineering,philosophy,technology — Duncan Hull @ 9:02 am
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Arthur C. Clarke (1917-2008)According to Arthur C. Clarke [1]:

“New ideas pass through three periods:

  1. It can’t be done;
  2. It probably can be done, but it’s not worth doing;
  3. I knew it was a good idea all along.”

These three stages can be summed up as Myopia, Hubris and Amnesia. Which sounds a bit like the famous misquote (?) by Mahatma Gandhi:

“First they ignore you,
then they laugh at you,
then they fight you,
then you win.”

We are all surrounded by innovations of various kinds. If Clarke and Gandhi are right, we are either:

  • myopically ignoring them…
  • laughing and fighting them hubristically or
  • amnesiacally approving of the winners

Which one are you?

References

    1. Benford, G. (2008). Obituary: Arthur C. Clarke (1917–2008) Nature, 452 (7187), 546-546 DOI: 10.1038/452546a

April 28, 2011

Are machines taking over the planet?

Filed under: economics,engineering,technology — Duncan Hull @ 9:36 pm
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TastyTalk of machines taking over the planet is the stuff of science fiction but if world domination was just a simple numbers game, some machines have already “taken over” from their human masters.

One machine, the particular brand of computer processor found inside all iPhones and lots of other electronic devices, has been quietly spreading around the globe at a phenomenal rate. There are some interesting statistics on just how many of these processors are out there published in an interview with engineer Steve Furber [1]. Here is an excerpt from the interview:

“Around the end of 2007, the ten-thousand-millionth ARM [Advanced RISC Machine] had been shipped, so there are more ARMs than people on the planet. I believe production is currently running at about 10 million a day. It is projected to rise to about one per person on the planet per year within two or three years”.

Those numbers highlighted in bold (emphasis mine) are completely mind-boggling. As humans, we are outnumbered by just one brand of machine! Of course, they are just lots of “dumb” computer chips with no intelligence. But Furber suspects that:

“there’s more ARM computing power on the planet than everything else ever made put together” [1]

So if you could find a way of using all these processors at once, maybe they’d become magically self-aware in a neural network [2,3,4,5]? Cue ominous Terminator theme tune …

References

  1. Jason Fitzpatrick (2011). An interview with Steve Furber Communications of the ACM, 54 (5) DOI: 10.1145/1941487.1941501 (since 2007, numbers have risen to 10 billion in 2008 an another one billion in the first quarter of 2011 alone!)
  2. Steve Furber (2011). Biologically-Inspired Massively-Parallel Architectures: A Reconfigurable Neural Modelling Platform Lecture Notes in Computer Science, 6578 (2) DOI: 10.1007/978-3-642-19475-7_2
  3. Steve Furber, & Steve Temple (2008). Studies in Computational Intelligence Computational Intelligence: A Compendium, 115, 763-796 DOI: 10.1007/978-3-540-78293-3_18
  4. An estimated one million ARM processors give you about 1% of the capacity of the human brain see the details of the Spiking Neural Network Architecture (SpiNNaker) project
  5. James Cameron, et al (1991) Terminator 2: Judgment Day (T2)

[Creative commons licensed picture of Terminator terror by Tasty by cszar]

February 25, 2010

Apache Maven: A Misbehavin’ Build Tool?

Filed under: ChEBI,programming,technology — Duncan Hull @ 11:00 am
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Chocolate Tools by JanneMOne of the many tools we use in our team to manage the development of the ChEBI software is an automated build tool called Apache Maven. Opinions are often divided on whether Maven is a good or a bad thing. Most of them are very subjective, argumentative and often very extended. See why does Maven have such a bad reputation? and 25 things* I hate about Maven for examples.

All this is fairly predictable, and I could add a few tales of Maven woe to the pile myself. But wondering if Maven is any good reminded me of something Bjarne Stroustrup [1,2,3] (one of the people behind the C++ programming language) once said in an article on the problem with programming:

“There are just two kinds of [programming] languages: the ones everybody complains about and the ones nobody uses.”

Actually when you think about it this applies to build systems too, there are two kinds. It also applies to just about any technology you care to name, you can crudely classify them all into two categories:

  1. Those technologies everybody complains about…
  2. … and the rest, that nobody uses.

So is Maven any good? Worth using? Worth the pain? Depends on who you ask. What we can say for sure, is that like many technologies, everybody complains about it.

References

  1. Bjarne Stroustrup (2010). Viewpoint: What should we teach new software developers? Why? Communications of the ACM, 53 (1) DOI: 10.1145/1629175.1629192
  2. Bjarne Stroustrup (2007). Evolving a language in and for the real world: C++ 1991-2006 Proceedings of the third ACM SIGPLAN conference on History of programming languages DOI: 10.1145/1238844.1238848
  3. Bjarne Stroustrup (1993). A history of C++: 1979–1991 The second ACM SIGPLAN conference on History of programming languages DOI: 10.1145/154766.155375

* Only 25? That seems like quite a short list to me.

[CC-licensed Chocolate Tools image by JanneM, some commentary on this post over at friendfeed.]

December 3, 2009

It’s Snowing (JavaScript)!

Filed under: programming,technology — Duncan Hull @ 10:28 am
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You know it’s December when it starts snowing in your web browser. Let it snow, let it snow, let it snow!

Or programmatically:

snowStorm = new SnowStorm();

There was a time, not so very long ago when JavaScript snow would have been “best viewed in browser x”. Thankfully now JavaScript much more reliable, the JBrowse [1] Genome Browser provides a nice example of this in bioinformatics. JBrowse is one of many proofs that JavaScript can be used to take some of the computing load off the server, and do it in the client (web browser) instead, while providing more sophisticated applications for users – not just gimmicks like snow.

References

  1. Skinner, M., Uzilov, A., Stein, L., Mungall, C., & Holmes, I. (2009). JBrowse: A next-generation genome browser Genome Research, 19 (9), 1630-1638 DOI: 10.1101/gr.094607.109

[Creative Commons licensed snowstorm picture by Atli Harðarson, JavaScript SnowStorm code by Scott Schiller, move your mouse around to guide the snowstorm.]

May 26, 2009

Subscribing to O’Really?

Filed under: technology — Duncan Hull @ 4:53 pm
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Feed the WorldJust a quick note about subscribing: if you are a regular reader of this O’Really blog and you don’t already subscribe, there are two ways you can receive automatic notifications when new posts are published here:

  1. Point your feed reader at http://feeds2.feedburner.com/oreally, (the preferred method) or …
  2. Point your feed reader at https://duncan.hull.name/feed/ (the WordPress method) which unfortunately gives unreliable subscriber stats. This  feed is linked to by the blue or orange feed icon (pictured right) you should be able to see in your web browsers address bar.

The first feed, is just the second feed re-routed through the magic of FeedBurner, which gives more useful viewing statistics.

November 6, 2007

What’s The Point of Blogging?

Filed under: technology — Duncan Hull @ 12:07 pm
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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
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