O'Really?

November 2, 2010

Standing on the shoulders of tyrants

Newton (after Blake), by Eduardo Paolozzi, British Library Piazza by chrisjohnbeckett on Flickr.There are at least two ways of looking at the history of Science:

  1. If we have seen farther it is by standing on the shoulders of giants.
  2. If we have seen farther it is by standing on the shoulders of tyrants.

Take Isaac Newton for example, a giant whose shoulders we all stand on today. During his scientific career he employed plenty of tyranny to get ahead. While devising his calculus Newton had a bitter rivalry with his contemporary Leibniz where he exploited his position of power and influence at the Royal Society [1] to discredit his opponents work. Newton was evidently no gentle giant.

Over at the BBC, Marcus du Sautoy charts some of this murky political territory in the first episode of his entertaining Brief History of Mathematics series. The rest of the programmes introduce some of the other colourful personalities involved in the history of “the queen of the sciences”.

So if Newton is anything to go by, many of the giants shoulders we stand on were (and are) terrible tyrants. While friendly and open collaboration is important in Science, cut-throat competition clearly has a place too.

References

  1. Isaac Newton (1671). A Letter of Mr. Isaac Newton, Professor of the Mathematicks in the University of Cambridge; Containing His New Theory about Light and Colors: Sent by the Author to the Publisher from Cambridge, Febr. 6. 1671/72; In Order to be Communicated to the R. Socie Philosophical Transactions of the Royal Society of London, 6 (69-80), 3075-3087 DOI: 10.1098/rstl.1671.0072

[Creative Commons licensed picture of Isaac Newton (after William Blake), by Eduardo Paolozzi, British Library Piazza by Chris John Beckett on Flickr]

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.

References

  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]

September 1, 2010

How many unique papers are there in Mendeley?

Lex Macho Inc. by Dan DeChiaro on Flickr, How many people in this picture?Mendeley is a handy piece of desktop and web software for managing and sharing research papers [1]. This popular tool has been getting a lot of attention lately, and with some impressive statistics it’s not difficult to see why. At the time of writing Mendeley claims to have over 36 million papers, added by just under half a million users working at more than 10,000 research institutions around the world. That’s impressive considering the startup company behind it have only been going for a few years. The major established commercial players in the field of bibliographic databases (WoK and Scopus) currently have around 40 million documents, so if Mendeley continues to grow at this rate, they’ll be more popular than Jesus (and Elsevier and Thomson) before you can say “bibliography”. But to get a real handle on how big Mendeley is we need to know how many of those 36 million documents are unique because if there are lots of duplicated documents then it will affect the overall head count. (more…)

July 27, 2010

Twenty million papers in PubMed: a triumph or a tragedy?

pubmed.govA quick search on pubmed.gov today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it is? (more…)

July 26, 2010

Please Sir, I want some more Science!

Science Online London 2010 (soloconf)Science Online London (#solo10 September 3-4, 2010) is an annual gathering of people interested in the use of web technologies for scientific collaboration and communication.  The organisers at Mendeley, Nature Network and The British Library continue to do a great job of hosting this important gathering, now in its third year:

I’ve been the last two years (2008 and 2009), and it has been worth attending because of the mix speakers, delegates and topics covered. This year includes talks from:

See the impressive full programme here. Reading through the speaker list I wondered, where are all the scientists at science online this year? At the time of writing this, 12 of the 13 speakers are politicians, publishers or journalists with scientist Peter Murray-Rust the odd man out. I’ve nothing against politicians, publishers or journalists but it would be great to have a more balanced event this year. The UK is full of high-profile scientists with blogs who would probably jump at the opportunity to speak at this event. So:

Or as the skeptical Sid Rodrigues said “this looks like fun, needs more nerds though“…

July 15, 2010

How many journal articles have been published (ever)?

Fifty Million and Fifty Billion by ZeroOne

According to some estimates, there are fifty million articles in existence as of 2010. Picture of a fifty million dollar note by ZeroOne on Flickr.

Earlier 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…)

July 7, 2010

Top ten excuses for World Cup football failures (with citations)

NASA Blue Marble 2007 West by NASA Goddard Photo and Video, on FlickrFootball fever grips the globe as we reach the final stages of the 2010 FIFA World Cup in South Africa. Alongside the traditional game where one winning team takes all, leaving 31 losing teams to go home earlier than expected, there is another competition running in parallel. Which losing team can come up with the best excuses for formidable football failure? All manner of feeble and pathetic excuses are offered, but many aren’t backed up with proper citations of peer-reviewed research published in scientific journals. So let’s set the balance straight. Here are the top ten excuses for world cup losers (with citations), using some help from sports scientists [1] and the wikipedian protester demanding that a citation is needed: (more…)

June 22, 2010

Impact Factor Boxing 2010

Golden Gloves Prelim Bouts by Kate Gardiner[This post is part of an ongoing series about impact factors. See this post for the latest impact factors published in 2012.]

Roll up, roll up, ladies and gentlemen, Impact Factor Boxing is here again. As with last year (2009), the metrics used in this combat sport are already a year out of date. But this doesn’t stop many people from writing about impact factors and it’s been an interesting year [1] for the metrics used by many to judge the relative value of scientific work. The Public Library of Science (PLoS) launched their article level metrics within the last year following the example of BioMedCentral’s “most viewed” articles feature. Next to these new style metrics, the traditional impact factors live on, despite their limitations. Critics like Harold Varmus have recently pointed out that (quote):

“The impact factor is a completely flawed metric and it’s a source of a lot of unhappiness in the scientific community. Evaluating someone’s scientific productivity by looking at the number of papers they published in journals with impact factors over a certain level is poisonous to the system. A couple of folks are acting as gatekeepers to the distribution of information, and this is a very bad system. It really slows progress by keeping ideas and experiments out of the public domain until reviewers have been satisfied and authors are allowed to get their paper into the journal that they feel will advance their career.”

To be fair though, it’s not the metric that is flawed, more the way it is used (and abused) – a subject covered in much detail in a special issue of Nature at http://nature.com/metrics [2,3,4,5]. It’s much harder than it should be to get hold of these metrics, so I’ve reproduced some data below (fair use? I don’t know I am not a lawyer…) to minimise the considerable frustrations of using Journal Citation Reports (JCR).

Love them, loathe them, use them, abuse them, ignore them or obsess over them … here’s a small selection of the 7347 journals that are tracked in JCR  ordered by increasing impact.

Journal Title 2009 data from isiknowledge.com/JCR Eigenfactor™ Metrics
Total Cites Impact Factor 5-Year Impact Factor Immediacy Index Articles Cited Half-life Eigenfactor™  Score Article Influence™ Score
RSC Integrative Biology 34 0.596 57 0.00000
Communications of the ACM 13853 2.346 3.050 0.350 177 >10.0 0.01411 0.866
IEEE Intelligent Systems 2214 3.144 3.594 0.333 33 6.5 0.00447 0.763
Journal of Web Semantics 651 3.412 0.107 28 4.6 0.00222
BMC Bionformatics 10850 3.428 4.108 0.581 651 3.4 0.07335 1.516
Journal of Molecular Biology 69710 3.871 4.303 0.993 916 9.2 0.21679 2.051
Journal of Chemical Information and Modeling 8973 3.882 3.631 0.695 266 5.9 0.01943 0.772
Journal of the American Medical Informatics Association (JAMIA) 4183 3.974 5.199 0.705 105 5.7 0.01366 1.585
PLoS ONE 20466 4.351 4.383 0.582 4263 1.7 0.16373 1.918
OUP Bioinformatics 36932 4.926 6.271 0.733 677 5.2 0.16661 2.370
Biochemical Journal 50632 5.155 4.365 1.262 455 >10.0 0.10896 1.787
BMC Biology 1152 5.636 0.702 84 2.7 0.00997
PLoS Computational Biology 4674 5.759 6.429 0.786 365 2.5 0.04369 3.080
Genome Biology 12688 6.626 7.593 1.075 186 4.8 0.08005 3.586
Trends in Biotechnology 8118 6.909 8.588 1.407 81 6.4 0.02402 2.665
Briefings in Bioinformatics 2898 7.329 16.146 1.109 55 5.3 0.01928 5.887
Nucleic Acids Research 95799 7.479 7.279 1.635 1070 6.5 0.37108 2.963
PNAS 451386 9.432 10.312 1.805 3765 7.6 1.68111 4.857
PLoS Biology 15699 12.916 14.798 2.692 195 3.5 0.17630 8.623
Nature Biotechnology 31564 29.495 27.620 5.408 103 5.7 0.14503 11.803
Science 444643 29.747 31.052 6.531 897 8.8 1.52580 16.570
Cell 153972 31.152 32.628 6.825 359 8.7 0.70117 20.150
Nature 483039 34.480 32.906 8.209 866 8.9 1.74951 18.054
New England Journal of Medicine 216752 47.050 51.410 14.557 352 7.5 0.67401 19.870

Maybe next year Thomson Reuters, who publish this data, could start attaching large government health warnings (like on cigarette packets) and long disclaimers to this data? WARNING: Abusing these figures can seriously damage your Science – you have been warned!

References

  1. Rizkallah, J., & Sin, D. (2010). Integrative Approach to Quality Assessment of Medical Journals Using Impact Factor, Eigenfactor, and Article Influence Scores PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010204
  2. Abbott, A., Cyranoski, D., Jones, N., Maher, B., Schiermeier, Q., & Van Noorden, R. (2010). Metrics: Do metrics matter? Nature, 465 (7300), 860-862 DOI: 10.1038/465860a
  3. Van Noorden, R. (2010). Metrics: A profusion of measures Nature, 465 (7300), 864-866 DOI: 10.1038/465864a
  4. Braun, T., Osterloh, M., West, J., Rohn, J., Pendlebury, D., Bergstrom, C., & Frey, B. (2010). How to improve the use of metrics Nature, 465 (7300), 870-872 DOI: 10.1038/465870a
  5. Lane, J. (2010). Let’s make science metrics more scientific Nature, 464 (7288), 488-489 DOI: 10.1038/464488a

[Creative Commons licensed picture of Golden Gloves Prelim Bouts by Kate Gardiner ]

June 9, 2010

World Cup Chemistry: How heavy is the FIFA trophy?

Have you ever wondered how heavy all that Gold and Malachite is in the FIFA World Cup Trophy is?

Professor Martyn Poliakoff from the Chemistry department at the University of Nottingham and his partner in crime Brady Haran over at the fantastic Periodic Table of Videos explain:

Which just leaves one question, who will be lifting it this year? Lúcio? Cristiano Ronaldo? Philipp Lahm? Fabio Cannavaro?  Denis Caniza? Steven Gerrard? Giovanni van Bronckhorst? Iker Casillas? Diego Lugano? John Mensah? Javier Mascherano or A.N.Other?

June 3, 2010

The smell of baking and toasting bread: Entity of the Month

Filed under: ChEBI — Duncan Hull @ 7:47 am
Tags: , , , ,

ToastRelease 69 of Chemical Entities of Biological Interest (ChEBI) is now available, with 584,456 total entities, of which 21,369 are fully annotated to three star level. This months Entity of the Month is the smell of bread (baked and toasted), or more precisely 6-acetyl-2,3,4,5-tetrahydropyridine. The text below is reproduced from the ChEBI website where data is available under a Creative Commons license.

Chemistry, like most other fields of human endeavour, has a tremendous capacity for both good and evil. However, arguably one of the best and most delightful reactions in chemistry is the Maillard reaction.

It occurs when amino acids are heated together with sugar and is therefore a prominent reaction when baking bread or brewing beer: many of the reaction products provide the characteristic flavours of these foods, which we all enjoy so much.While the chemical structures and identities of most of the products of this form of “non-enzymatic browning” are only poorly characterised or unknown, our Entity of the Month 6-acetyl-2,3,4,5-tetrahydropyridine (CHEBI:59533) is an exception. It is a well known aromatic compound, which is responsible for the flavour of white bread, popcorn and tortillas and has an extremely low odour threshold, between 0.02 and 0.06 ng l–1[1]. It exists in a tautomeric equilibrium with 6-acetyl-1,2,3,4-tetrahydropyridine, the two forms usually occurring in foods in a 1:2 ratio.

The compound can be synthesized in a simple three-step procedure. In a first step, BOC-protected 2-piperidone is treated with 1-ethoxy-1-lithioethene in a bid to build up the acetyl side-chain. This results in ring opening and the formation of a linear ketone which, after treatment with toluene-p-sulfonic acid, reforms the heterocycle in the form of an ene-carbamate. Treatment of the latter with potassium hydroxide yields the final product [1].

The Maillard Reaction is named after Louis Camille Maillard, a precocious French physiologist, who first described it in the 1910s. Maillard is also known for his contributions towards the diagnosis of kidney disorders.

The image top right shows freshly toasted bread – and the brown colour (the Maillard reaction is a method for non-enzymatic browning) is indicative of the reaction having taken place and is taken from the Wellcome Trust Image Collection

References

  1. Harrison, T., & Dake, G. (2005). An Expeditious, High-Yielding Construction of the Food Aroma Compounds 6-Acetyl-1,2,3,4-tetrahydropyridine and 2-Acetyl-1-pyrroline The Journal of Organic Chemistry, 70 (26), 10872-10874 DOI: 10.1021/jo051940a
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