June 18, 2013

Peter Suber’s Open Access book is now freely available under an open-access license

Peter Suber's Open Access book

Open Access by Peter Suber is now open access

If you never got around to buying Peter Suber’s book about Open Access (OA) publishing [1] “for busy people”, you might be pleased to learn that it’s now freely available under an open-access license.

One year after being published in dead-tree format, you can now get the whole digital book for free. There’s not much point writing yet another review of it [1], see Peter’s extensive collection of reviews at cyber.law.harvard.edu. The book succinctly covers:

  1. What Is Open Access? (and what it is not)
  2. Motivation: OA as solving problems and seizing opportunities
  3. Varieties: Green and Gold, Gratis versus libre 
  4. Policies: Funding mandates (NIH, Wellcome Trust etc)
  5. Scope: Pre-prints and post-prints
  6. Copyright: … or Copyfight?
  7. Economics: Who pays the bills? Publication fees, toll-access paywalls and “author pays”
  8. Casualties: “OA doesn’t threaten publishing; it only threatens existing publishers who do not adapt”
  9. Future: Where next?
  10. Self-Help: DIY publishing

Open Access for MACHINES!

A lot of the (often heated) debate about Open Access misses an important point about open access being for machines as well as humans, or as Suber puts in Chapter 5 on Scope:

We also want access for machines. I don’t mean the futuristic altruism in which kindly humans want to help curious machines answer their own questions. I mean something more selfish. We’re well into the era in which serious research is mediated by sophisticated software. If our machines don’t have access, then we don’t have access. Moreover, if we can’t get access for our machines, then we lose a momentous opportunity to enhance access with processing.

Think about the size of the body of literature to which you have access, online and off. Now think realistically about the subset to which you’d have practical access if you couldn’t use search engines, or if search engines couldn’t index the literature you needed.

Information overload didn’t start with the internet. The internet does vastly increase the volume of work to which we have access, but at the same time it vastly increases our ability to find what we need. We zero in on the pieces that deserve our limited time with the aid of powerful software, or more precisely, powerful software with access. Software helps us learn what exists, what’s new, what’s relevant, what others find relevant, and what others are saying about it. Without these tools, we couldn’t cope with information overload. Or we’d have to redefine “coping” as artificially reducing the range of work we are allowed to consider, investigate, read, or retrieve.

It’s refreshing to see someone making these points that are often ignored, forgotten or missed out of the public debate about Open Access. The book is available in various digital flavours including:


  1. Suber, Peter. Open Access (MIT Press Essential Knowledge, The MIT Press, 2012). ISBN:0262517639
  2. Clair, Kevin. (2013). Kevin Michael Clair reviews Open Access by Peter Suber The Journal of Academic Librarianship, 39 (1) DOI: 10.1016/j.acalib.2012.11.017

May 10, 2012

The Lovelock Laboratory: A fantasy workplace in the West Country

έροτας : love, as described by an implicit heart curve (x²  + y²  − 1)³ − x² y³ = 0

An equation of love (x² + y² − 1)³ − x² y³ = 0

Former Mancunian James Lovelock runs the kind of a laboratory most scientists can only fantasise about working in as they grind through the humdrum bureaucracy of peer-review and never-ending grant applications. Lovelock is fortunate enough to run a completely independent, self-funded lab located in the beautiful West Country. There’s a fascinating interview with him on The Life Scientific with Jim Al-Khalili where he says lots of interesting things about elocution lessons, nuclear power, climate change and his grand theory of planet earth, Gaia [1,2,3]. When asked, he also made this interesting comment about being an indepedendent scientist [4]:

“It’s the most wonderful thing to do [being independent]. I keep on saying that scientists are just like artists if they are creative. If you were an artist, would you want to spend your life in an institute for fine art, quibbling with other academics about the different styles of painting? You’d rather be in your garage doing your masterpiece and selling a lot of art to some tourists to pay the way. That’s been my life as a scientist. ”

The audio file of the broadcast is available for download or just click on the play icon below:

So to become a truly independent scientist, you either need to win the lottery, nobel prize or possibly invent the modern equivalent of electron capture detection to bankroll running a lab from the bottom of your garden.

Well if nothing else, it’s an entertaining fantasy to while away dull moments in the real world…


  1. James Lovelock (2009). The Vanishing Face of Gaia: A Final Warning ISBN:1846141850, Penguin
  2. Andrew Watson (2009). Final warning from a sceptical prophet: James Lovelock fears that humanity faces widespread death and mass migration as Earth’s systems become further unbalanced by climate change Nature, 458 (7241), 970-971 DOI: 10.1038/458970a
  3. John Gribbin and Mary Gribbin (2009) He Knew He Was Right: The Irrepressible Life of James Lovelock and Gaia, ISBN:1846140161, Allen Lane
  4. Matthew Reisz (2012) Free-range thinkers: Independent scholars can confound, complement and challenge the work of their campus counterparts. Times Higher Education

September 8, 2011

UK Riots: Blame it on the Baby Boomers

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].


  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

September 3, 2010

What happens when you teach monkeys to use money?

Capuchin Monkey by Michael RansburgFreakonomics and its successor Superfreakonomics are two books by the economist Steven Levitt and his partner in crime Stephen Dubner that have a common theme running through them (quote):

“People respond to incentives, although not necessarily in ways that are predictable and manifest. Therefore, one of the most powerful laws in the universe is the law of unintended consequences.”

Both books give numerous and often amusing examples of the ways that various incentives often result in unexpected outcomes. They choose a wide variety of animals including teachers, sumo wrestlers, estate agents, bible salesmen and yes, monkeys, to illustrate this point. The second book, Superfreakonomics, finishes with a fascinating epilogue about the consequences of training monkeys to use money, aka “monkeynomics”. When capuchin monkeys (Cebus apella) are trained to exchange money for food, they don’t always behave very rationally [1]. The TED talk about how monkeys mirror human irrationality by the primate psychologist Laurie Santos has more details, see below:

In short, financially trained monkeys make many of the same mistakes (like loss aversionlarceny and endowment effects) that humans do. This research suggests that millions of years of evolution have configured our brains to help us make stupid irrational mistakes, at least when it comes to money. Which provides a great excuse for financial incompetence, whatever kind of animal you are.

If you haven’t already seen the books, they are worth reading and if you’re interested in how investment bankers, capuchin monkeys and other animals make irrational mistakes watch the TED video above.


  1. Lakshminaryanan, V., Chen, M., & Santos, L. (2008). Endowment effect in capuchin monkeys Philosophical Transactions of the Royal Society B: Biological Sciences, 363 (1511), 3837-3844 DOI: 10.1098/rstb.2008.0149

[Creative Commons licensed picture of a Capuchin monkey by Michael Ransburg]

April 1, 2010

Καλό Πάσχα: Happy Easter: Frohe Ostern

Easter Bunny 1 "My arse hurts"... Easter Bunny 2 "What?"Whatever your inclination, it’s difficult to ignore that sandwiched between the Vernal equinox and Beltane, it’s Easter time already. So Happy Easter, Frohe Ostern or Καλό Πάσχα, as they say down south, to all readers of this O’Really? blog.

If you’re gorging yourself on chocolate (see picture right), you might like to consider the food science behind it all thanks to a book [1] by Stephen Beckett published by the Royal Society of Chemistry. Ever wondered why melted chocolate that is put back in the fridge doesn’t quite taste the same? This book will tell you, and a whole lot more besides.

As for the chocolate bunnies, my language skills (german and greek) are a load of old arsch, but the cartoon over on the right roughly translates as follows.

  • Chocolate Bunny #1, with missing posterior: “Mein arsch tut weh!!” (“My arse hurts!!”)
  • Chocolate Bunny #2, with missing ears: “Was?” (“What?”)

Happy Chocolatey Holidays wherever you are…


  1. Stephen T. Beckett (2000). The Science Of Chocolate Royal Society of Chemistry Publihshing DOI: 10.1039/9781847552143
  2. Anon (2010). Book Review of The Science of Chocolate The Science of Chocolate. By Stephen T. Beckett (Nestle Product Technology Centre). Royal Society of Chemistry , Cambridge . 2008. xii + 240 pp. 6 × 9 in. £24.95. ISBN 78-0-85404-970-7. Journal of Natural Products DOI: 10.1021/np100172s

October 8, 2006

Bio-Ignorance: Communicating Biology to Computer Scientists

The Human GenomeMany computer scientists and software engineers are not familiar with basic biology or bioinformatics. Many biologists and bioinformaticians are not familiar with basic computer science or software engineering. This article points to some resources that can help with the former, and asks, what can be done about the latter?

Progress in both computer science and biology is closely linked and dependent on people understanding each others strange language, cross-pollinating ideas and creating technology which hopefully has hybrid vigour. So for example, biologists and bioinformaticians have a healthy apetite for all kinds of better, cheaper, faster and sometimes novel computation. This requires they understand basic computer science and software enginnering. In the other direction, computer scientists often need realistic scenarios to motivate the invention, development and testing of genuinely novel technology. As for the software engineers, more on them later…

It sounds great, but before you can even say the words “inter-discplinary”, there are considerable barriers to communication. The various camps speak different languages, and have radically different cultures. To illustrate this communication breakdown, here is a story from the lab where I work. A while ago, I was discussing the Gene Ontology with a colleague, who shall remain anonymous. This colleague was educated, doing PhD level research and what I’d consider a fairly typical computer scientist. Soon the conversation turned to chromosomes, and they asked me:

“What is a Chromosome?”

Initially I was shocked. How could somebody not know what a chromosome was? Had they never read a newspaper? Never watched the television? Surely, most people have at least a vague idea what a chromosome is? After recovering from the shock, I told this person that according to the Gene Ontology a chromosome is “a very long molecule of DNA and associated proteins that carries hereditary information.” Perhaps this bio-ignorance is an extreme case, but unfortunately, it is all too common. Many computer scientists and software engineers I know stopped studying biology as soon as they possibly could, opting for the so-called “harder” sciences: physics, chemistry and mathematics. Consequently, many (but not all) computer scientists are bio-ignorant. What can we do about it? We really need to understand each other if we are going to make any progress. How can we improve communication between biologists and computer scientists?

Part of the solution to this problem is well-written literature that explains basic concepts quickly and clearly without getting bogged down in jargon or stuck on esoteric details, see the references below for some examples. One of my personal favourites is a little book called The Human Genome: a beginner’s guide to the chemical code of life authored by Jeremy Cherfas. This book is lavishly illustrated and beautifully written, but most importantly of all at 72 pages it is blisteringly concise, so stands a chance of being read by computer geeks and nerds. It is even funny in places, the Nobel laureate and geneticist Thomas Hunt Morgan is amusingly depicted as a red-eyed wild type, just like the fruit flies he studied. Anyway, I lent my copy of said book to my computer science buddy, and they learnt not just what chromosomes are, but also a little bit about why Biology and Genetics are such fascinating subjects.

The literature listed below can help one-way understanding of biology by outsiders, but communication is a two-way street. What about the other direction? Is there any literature that explains computer science and software engineering specifically to biologists and bioinformaticians? I don’t know of any particularly good examples, that are concise, well written and illustrated, but perhaps you do. I’ve frequently found bioinformaticians and biologists misunderstand what computer science is about, and confuse it with software engineering, but that is another story. The moral of this story is, don’t be surprised if people working in different fields to you lack a basic understanding of what you consider fundamental concepts that everybody knows. If they are bio-ignorant computer scientists, you should patiently and tirelessly explain yourself and maybe point to some of the resources below. Maybe we can understand each other just a little better.


  1. Anonymous GO:0005694 Chromosome: A very long molecule of DNA AmiGO! Your friend in the Gene Ontology
  2. Alvis Brazma, Helen Parkinson, Thomas Schlitt and Mohammadreza Shojatalab (2001) All you need to know about biology in twenty pages European Bioinformatics Institute (EMBL-EBI) (A technical introduction, written for EBI employees, but useful elsewhere)
  3. Jeremy Cherfas (2002) The Human Genome: a beginner’s guide to the chemical code of life (isbn:0751337161) Dorling Kindersley (A quick but informative introduction that your granny could understand)
  4. Jeremy Cherfas (2006) International Plant Genetic Resources Institute (IPGRI) public awareness blog IPGRI, Rome, Italy. (Some deserved nodalpoint Google Juice for these news and press releasess)
  5. 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 (A paper describing communication breakdown between two different research “houses”, very possibly the only paper on genomics that will make you laugh. seeAlso Shakespearean Genomics: a plague on both your houses)
  6. John Gribbin Dorling Kindersley’s Essential Science: Human Genome, Global warming, Expanding universe, Food for the future, Digital revolution and How the brain works http://www.dk.com (Some interesting books here)
  7. John W. Kimball Chromosomes Kimball’s Biology Pages (How does John Kimball manage to write so much good introductory material sabout Biology?)
  8. John Bonham, John Paul Jones and Jimmy Page (1969) Communication Breakdown Led Zeppelin (Communication breakdown, it’s always the same, I’m having a nervous breakdown, drive me insane!)
  9. This post was originally published on nodalpoint with comments.

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June 12, 2006

Bend it like Bezier?

Football informatics, theory and practice: Germany 2006

Bayern BallThe frenchman Pierre Bézier knew a thing or two about curves. But as World Cup fever tightens its grip around the globe, it is the footballers in Germany who are showing us just how much they know about the practical science of curving and bending the ball into the goal. Is there any essential curve-theory for World Cup stars like Beckham, Ronaldinho and Thierry Henry to read and brush-up on in their German hotels this summer?

Sports scientist Dr Ken Bray from the University of Bath in the UK hopes that sportsmen and spectators alike will be reading his new book How to Score – Science and the Beautiful Game. This is another popular science book that tries to make fluid dynamics accessible to the layman. In publicising his new book, Ken points out that the new Adidas Teamgeist™ football will unsettle goalkeepers at the World Cup, because the balls move more in the air than traditional ones. This smells of marketing-hype, both for the ball and the book, but it is interesting and topical nonetheless.

Mathematicians and numerical analysts have known for years, the really essential reading for footballers this summer is the famous curves index. These wonderful web pages, free online and completely devoid of hype, describe all the equations for putting the ball in the back of the net in great style. After reading these pages, perhaps World Cup footballers will be able to curve the unpredictable Teamgeist™ ball even more lavishly than before. Just imagine the confusion of a goalkeeper facing a free-kick, when the ball follows a right strophoid curve: y2 = x2(a – x)/(a + x)! This would certainly be more entertaining than the all too predictable and common straight line: y = mx + c that soars over the bar and into row Z of the spectators behind the goal…

Whether scientists, footballers or spectators, we can all enjoy the science of curving at the World Cup in Germany this summer. Bis Bald Berlin!


  1. Bend it Like Beckham: The curve ball free-kick (France 1998)
  2. Bénd it Like Bézier: The Bézier Curve
  3. Bend it like Brazil: A perfect example of a free-kick by Roberto Carlos
  4. Bend it like Euclid: Is a straight line a curve?
  5. Computer Graphics: Curves and Surfaces, Bézier representations
  6. From the beautiful game to the computiful game: Nature catches football fever
  7. Goal fever at the World Cup: Why the first strike counts
  8. This post was originally published on nodalpoint with comments

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