O'Really?

February 15, 2012

The Open Access Irony Awards: Naming and shaming them

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 Elsevier, recently  published a paper on “the case for open data” [2] (please login to access article). Login? Register? 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 more. 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…

December 20, 2011

Happy Christmas Lectures 2011: Meet your Brain with Bruce Hood

Bruce Hood

An animated Bruce Hood. Creative Commons licensed picture by Dave Fayram

The holiday season is upon us which means it’s time for the Royal Institution Christmas lectures. This year the lectures are on the meaty subject of how our brains work and are delivered by psychologist Professor Bruce Hood from the University of Bristol [1,2]. Broadcast over three episodes at 8pm on BBC4  (27th, 28th and 29th December) the talks will also be freely available online afterwards, see trailer.  Here’s the blurb on the first episode: What’s in your head?

Why does your brain look like a giant walnut, how does it fit in enough wiring to stretch four times around the equator and why can a magnet on your head stop you in mid-sentence? In the first of this year’s Christmas Lectures, Professor Bruce Hood gets inside your head to explore how your brain works. He measures the brain’s nerve cells in action, reads someone’s mind from 100 miles away and reveals how the brain ultimately creates its own version of reality.

The second episode is titled Who’s in charge here?

Your brain is constantly being bombarded with information, so how does it decide what to trust and what to ignore, without you even being aware? Professor Bruce Hood leads us through the second of this year’s Christmas Lectures – testing the limits of our memory, finding out how we learn, how our brain takes shortcuts and why multi-tasking can be dangerous. Bruce will make you say the wrong thing and fail to see what’s right in front of you. Can you really believe your eyes? Possibly not.

The final episode is Are You Thinking What I’m Thinking?

Have you ever seen a face in a piece of burnt toast, or given your car a name? Why do you feel pain when someone else is hurt? Why are people so obsessed with other people? In the last of this year’s Christmas Lectures, Professor Bruce Hood investigates how our brains are built to read other people’s minds. With a little help from a baby, a robot and a magician, Bruce uncovers what makes us truly human.

This year the Royal Institution have relaunched their website at richannel.org and made some of the previous lectures available at richannel.org/christmas-lectures. Hopefully Santa will eventually get around to adding many more lectures from this fantastic series to the archive soon.

This will (probably) be the last post of the year at O’Really, so if you’ve visited, thanks for reading during 2011. It’s been an eventful twelve months, with not much time for blogging, maybe that will change next year…

Wherever you are, whatever you’re up to, have a happy holidays and a prosperous 2012.

References

  1. Hood, B., Willen, J., & Driver, J. (1998). Adult’s Eyes Trigger Shifts of Visual Attention in Human Infants Psychological Science, 9 (2), 131-134 DOI: 10.1111/1467-9280.00024
  2. Hood, B. (2009) Supersense: From Superstition to Religion – The Brain Science of Belief. ISBN:1849010307

September 22, 2011

I Can’t Get No Job Satisfaction

I can't get no satisfaction

Rock and Roll: The ultimate in job satisfaction?

Job satisfaction is like a complex mathematical equation that needs to be balanced. There are many factors that contribute to the mix, both good and bad. Hopefully the good things about a job will outweigh the bad. But what are the good things that contribute to the elusive but crucial job satisfaction?

Daniel Pink, argues that motivation is key to job satisfaction. If you provide the right motivations to people in an organisation, not always large financial ones [1], then their job satisfaction is more likely. According to Pink, the three key motivations are:

  1. Autonomy: The desire to be self-directed.
  2. Mastery: The urge to get better at doing things and be recognised for it
  3. Purpose: The sense that your work makes a difference and maybe even makes the world a better place somehow.

Pink explains how these factors work in another one of those beautifully animated RSA videos below:

So if like Mick and Keith, you can’t get no (job) satisfaction [2], it’s probably worth aiming for more autonomy, mastery and purpose in your work.

References

  1. Ariely, D., Gneezy, U., Loewenstein, G., & Mazar, N. (2009). Large Stakes and Big Mistakes Review of Economic Studies, 76 (2), 451-469 DOI: 10.1111/j.1467-937X.2009.00534.x
  2. Jagger, M. & Richards, K. (1965) (I Can’t Get No) Satisfaction Decca Records

August 15, 2011

Wikipedia: I Fought the Lore and the Lore Won

"The age of nations is past. It remains for us now, if we do not wish to perish, to set aside the ancient prejudices and build wikipedia..."Fighting the lore of wikipedia is an increasingly futile battle but there are people who resist using and improving the online encyclopedia. The remarkable thing is that some of this resistance comes from the scientific and academic communities, two groups of people who are supposedly concerned with the dissemination of knowledge.

Wikipedia is the lore

With around 300 million visitors each month, wikipedia is firmly in the top ten of most trafficked websites in the world. But you don’t get 300 million visits without attracting some critics, many of whom object to wikipedia’s inaccuracies and the anonymity of some its contributors. What many critics object to is that wikipedia is the lore. That is not the law, but the lore, as in folklore. Like folklore, wikipedian knowledge often comes handed down by word of mouth, copy-and-paste and other questionable practices. The trouble with lore is, it can sometimes be unreliable, based on hearsay, gossip and urban myths rather than hard facts and knowledge favoured by scientists and academics. To some people, wikipedia is a lore which should be fought in every way possible.

Fighting the lore of wikipedia

Professor Neil Waters is one of many examples of an academic who has fought the lore of wikipedia. Water’s students were infamously told that they can’t cite wikipedia in their work [1]. They are still free to use it, but are forbidden to cite it, because of the lack of academic rigour. Wikipedia, the argument goes,  is a “tertiary source” rather than a primary one and therefore not suitable for serious research.

But people like Patricia Dooley have pointed out that academics fighting the use of wikipedia is hypocritical. In a small study published [2], she found that some university faculty members (the “two-faced professoriate” [2]) depend on Wikipedia in their teaching and published research despite the fact that they often discourage their students from using it. Are critics of wikipedia in the academy hypocrites fighting a losing battle?

Has the lore of wikipedia won?

As with many keywords, if you Google just about any scientific term, wikipedia will be in the first page of results. Here are some examples, taken from by Darren Logan’s why wikipedia is important in science:

At the time of writing, 90% of the search terms above have a wikipedia page as their very first Google hit. So, when it comes to accessibility and visibility, the lore of wikipedia is winning.

Improving the lore of wikipedia: Don’t fight it, edit it

So wikipedia is winning but many articles with scientific content are incomplete, inaccurate or just plain wrong. What should scientists do about it?  Rather than discouraging students to use it, wouldn’t it be better if academics and scientists encouraged their students to correct it? Fusing the lore of wikipedia with the law of science in this way is perhaps, the “greatest ever opportunity for public engagement”.  Ornithologist Alexander Bond is the latest in a long line of scientists arguing exactly this case [3]. Where wikipedia is wrong, he suggests that scientists have a duty to make sure that it is accurate and up to date:

“Regardless of the academy’s views on Wikipedia, it will remain a resource used by students, researchers and the public for the near future. Academics should appropriate Wikipedia as a teaching and outreach tool, resulting in higher quality information, more engaged students and a better-informed public.”

So if you’re a scientist or any other kind of academic, there is plenty of help and advice on hand [4] and many different wiki-projects to get involved in. Don’t fight the lore, edit it.

References

  1. Neil L. Waters (2007). Why you can’t cite Wikipedia in my class Communications of the ACM, 9, 15-17 DOI: 10.1145/1284621.1284635
  2. Patricia L. Dooley (2010). Wikipedia and the two-faced professoriate WikiSym ’10 Proceedings of the 6th International Symposium on Wikis and Open Collaboration DOI: 10.1145/1832772.1832803
  3. Alexander L. Bond (2011). Why ornithologists should embrace and contribute to Wikipedia Ibis, 153 (3), 640-641 DOI: 10.1111/j.1474-919X.2011.01135.x
  4. Darren Logan, Massimo Sandal, Paul Gardner, Magnus Manske, & Alex Bateman (2010). Ten simple rules for editing Wikipedia. PLoS computational biology, 6 (9) PMID: 20941386
  5. Sonny Curtis et al (1959) I Fought The Law (and the Law Won) as covered by The Clash:

[Acknowledgement: thanks to wikipedian Paul Gardner for posting the Bond paper on the journal picks. Image above via wikipedia.]

July 1, 2011

Anything that calls itself a Science, probably isn’t…

Way Cool Science Stuff by Mark A. Hicks www.markix.netScience, is a big word that gets used and abused with reckless abandon. Virtually any discipline can award itself extra kudos by adding the magic S word at the end. For example, which sounds weightier, sports studies or sports science?

This phenomenon has been noticed many times before, for example, the philosopher John Searle once remarked that:

Science has become something of an honorific term, and all sorts of disciplines that are quite unlike physics or chemistry are eager to call themselves ‘sciences‘.

A good rule of thumb to keep in mind is that anything that calls itself a science probably isn’t.” –see [1,2]

So let’s make a list. Starting with things that probably aren’t a Science because they call themselves one:

We could carry on for ages with this list and eventually include:

So are maths, physics, chemistry, biology etc real sciences™ too? Using Searle’s definition, it’s difficult to say. To avoid confusion, it might be a good idea to use a subjects non-scientific original name (“biology” rather than “life science”) that way, we know (paradoxically) they are real sciences. Probably.

References

  1. John R. Searle (1986). Minds, Brains and Science (1984 Reith Lectures) Harvard University Press ISBN:0674576330 (see also audio from the BBC Reith lecture archive) not  Speech Acts: An Essay in the Philosophy of Language. Cambridge University Press. ISBN:052109626X (as originally stated in the first version of this post)
  2. Fuller quotation: “Science has become something of an honorific term, and all sorts of disciplines that are quite unlike physics and chemistry are eager to call themselves ‘sciences’. A good rule of thumb to keep in mind is that anything that calls itself ‘science’ probably isn’t — for example, Christian science, or military science, and possibly even cognitive science or social science. The word ‘science’ tends to suggest a lot of researchers in white coats waving test tubes and peering at instruments. To many minds it suggests an arcane infallibility. The rival picture I want to suggest is this: what we are all aiming at in intellectual disciplines is knowledge and understanding. There is only knowledge and understanding, whether we have it in mathematics, literary criticism, history, physics, or philosophy. Some disciplines are more systematic than others, and we might want to reserve the word ‘science’ for them.”
  3. Peter J. Denning (2005). Is computer science science? Communications of the ACM, 48 (4) DOI: 10.1145/1053291.1053309

June 19, 2011

Sunday at the Lab with Uri Alon

Ah Sunday, a day of rest, recuperation and roasted food

Unless you’re a scientist, that is, in which case you might be working. If that’s you, this one goes out to all you committed high-calibre, driven scientists [1,2,3] who are spending this Sunday working at the laboratory bench. The amusing little ditty below is written by biologists Michael Elowitz and Uri Alon, and performed here by Uri Alon.

I kissed my wife and kissed farewell
I must go down to run my gel
I’m going to spend another Sunday at the lab

My wife said “Uri, you’ve got to promise,
you love me more than doing Science”
I said “Honey, can we discuss this another day?”
I’m going to spend another Sunday at the lab

My mum said “Son, don’t waste your life,
go home and spend time with the wife
you must have heard this from your father
why can’t you be more like your brother?
No son of mine spends Sundays at the lab.”

My dad said “Son, you need a shrink”
The shrink said son “you need a drink”
Those Rorschach spots reminded me of blots
He said “Oh God, you obviously have an obsessive compulsion
to spend all your Sundays at the lab”

My wife she left me
My mum disowned me
The shrink pretends he doesn’t know me
Because I can’t be myself
Without some buffer on the shelf

So if you need me, you can phone me at the lab
I’m going to spend another Sunday
I’m going to spend another Sunday
I’m going to spend another Sunday at the lab

References

  1. Elowe J (2010). Workaholism: between illusion and addiction. L’Encephale, 36 (4), 285-93 [Boulomanie : entre illusion et addiction] PMID: 20850599 DOI: 10.1016/j.encep.2009.12.002
  2. Overbaugh, J. (2011). 24/7 isn’t the only way: A healthy work–life balance can enhance research Nature, 477 (7362), 27-28 DOI: 10.1038/477027a
  3. Anon (2011). The 24/7 lab: Nature’s readers comment online Nature, 477 (7364), 280-280 DOI: 10.1038/477280c

July 15, 2010

How many journal articles have been published (ever)?

Alexandria Library Interior by Mindy McAdams on FlickrEarlier this year, the scientific journal PLoS ONE published their 10,000th article. Ten thousand articles is a lot of papers especially when you consider that PLoS ONE only started publishing four short years ago in 2006. But scientists have been publishing in journals for at least 350 years [1] so it might make you wonder, how many articles have been published in scientific and learned journals since time began?

If we look at PubMed Central, a full-text archive of journals freely available to all - PubMedCentral currently holds over 1.7 million articles. But these articles are only a tiny fraction of the total literature – since a lot of the rest is locked up behind publishers paywalls and is inaccessible to many people. (more…)

September 10, 2009

July 24, 2009

Escape from the impact factor: The Great Escape?

The Great Escape with Steve McQueenQuite by chance, I stumbled on this interesting paper [1] yesterday by Philip Campbell who is the Editor-in-Chief of the scientific über-journal Nature [2]. Here is the abstract:

As Editor-in-Chief of the journal Nature, I am concerned by the tendency within academic administrations to focus on a journal’s impact factor when judging the worth of scientific contributions by researchers, affecting promotions, recruitment and, in some countries, financial bonuses for each paper. Our own internal research demonstrates how a high journal impact factor can be the skewed result of many citations of a few papers rather than the average level of the majority, reducing its value as an objective measure of an individual paper. Proposed alternative indices have their own drawbacks. Many researchers say that their important work has been published in low-impact journals. Focusing on the citations of individual papers is a more reliable indicator of an individual’s impact. A positive development is the increasing ability to track the contributions of individuals by means of author-contribution statements and perhaps, in the future, citability of components of papers rather than the whole. There are attempts to escape the hierarchy of high-impact-factor journals by means of undifferentiated databases of peer-reviewed papers such as PLoS One. It remains to be seen whether that model will help outstanding work to rise to due recognition regardless of editorial selectivity. Although the current system may be effective at measuring merit on national and institutional scales, the most effective and fair analysis of a person’s contribution derives from a direct assessment of individual papers, regardless of where they were published.

It’s well worth reading the views of the editor of an important closed-access journal like Nature, a world champion heavyweight of Impact Factor Boxing. So their view on article-level bibliometrics and novel models of scientific publishing on the Web like PLoS ONE is enlightening. There are some interesting papers in the same issue, which has a special theme on the use and misuse of bibliometric indices in evaluating scholarly performance. Oh, and the article is published in an Open Access Journal too. Is it just me, or is there a strong smell of irony in here?

References

  1. Philip Campbell (2008). Escape from the impact factor Ethics in Science and Environmental Politics, 8, 5-7 DOI: 10.3354/esep00078
  2. Philip Campbell (1995). Postscript from a new hand Nature, 378 (6558), 649-649 DOI: 10.1038/378649b0
  3. John Sturges (1963) The Great Escape

February 11, 2009

Janet Street-Porter on the Internet Revolution

Janet Street-PortableI’m not much of a fan of Janet Street-Porter, neither am I a regular viewer of the BBC Money programme but right now they are screening an interesting series of three half-hour programmes on the impact of the internet on newspapers, books and television. It’s a familiar tale of the power-and-money struggle between old media and new media that, if the first programme is anything to go by, is worth watching. Here is the blurb from the first episode in the series, billed as Media Revolution: Stop Press?

Former national newspaper editor Janet Street-Porter investigates how papers are coping with falling circulation, advertising revenues and the growth of the internet, and asks if newspapers can survive in their current form. In her quest to discover what the future holds for her beloved newspapers, Janet visits newsrooms, printing plants and even spends a morning as a papergirl. With contributions from national editors, advertising gurus and a rare interview with media mogul Rupert Murdoch, Janet examines if papers can survive as new multimedia information giants.

There are some interesting parallels between the changes described in this programme, and scientific media, especially the scientific journal publishing racket.

Scientific Media Revolution?

The story of the current revolution in scientific and technical publishing is perhaps just as interesting (and more important) than the one being told on the money programme. Just think of it, why scientists publish, the emergence of peer review, how Robert Maxwell made his fortune from the Pergamon Press, the impact factor game, the birth of the Web (in a scientific laboratory), the growth of Google, the copyright wars, open-access publishing, social software, the rise and fall of publishing empires (and technology companies), the vanity journals, scientific blogs and wikis, software showdowns, how all this change affects producers and consumers of science and technology, both now and in the future. A juicy subject, worthy of broadcasting on any media (old or new). You would need a lot more than three half-hour programmes to cover this particular ongoing epic, so who is going to tell that story?

Anyway, the series is worth a look (if you haven’t already seen it) at least according to me  (others disagree see also no paper is the future). It is also available on iPlayer for up to a week after first broadcast – Thursday 5th, 12th and 19th February 2008 – for each episode in the UK only, unless you go through some kind of proxy.

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