You republican-face!

According to a study that you can read in Rule and Ambady, PLoS one 5 (2010) e8733, it turns out that American citizens are quite good at guessing the political affiliation of people just by looking at their faces. One more clue suggesting that the incredibly complex homo sapiens sapiens maybe is not so much.

Scientific neo-liberalism

In a very nice personal opinion article at EMBO Reports, Laurent Ségalat, research director at the CNRS Center for Molecular and Cellular Genetics at Lyon, draws a lot of worrying parallelisms between the mechanisms and ways of thinking that led us to the present financial crisis and those prevalent in the present scientific system. It is worth noticing that the article is published in a journal of the Nature group, one of the greatest beneficiaries of the actual status quo. The vision presented in the article is undoubtedly pesimistic and serious, but Ségalat also tells us what could be the solution: The funding agencies should decrease the pressure on scientists for achieving short-term goals.

A DOI for researchers

It has arrived to me by many channels (e.g., this Nature editorial) that a number of important organizations, including Thomson Reuters, Nature Publishing Group, Elsevier, ProQuest, Springer, CrossRef, the British Library and the Wellcome Trust, have set up an initiative to develop a system to assign a unique digital identifier to everyone in the research business. The name of the initiative is ORCID and it already has an official web page.

As the well-known DOI system does in relation to the unique identification of research papers, the new ORCID system aims to remove ambiguities in name spelling, cultural differences in name order, inconsistent first-name abbreviations or the use of different alphabets, hence assigning a unique digital ID to every researcher. Although this is a very nice feature that we all would like to see working soon, such a digital ID system allows for more interesting and far reaching applications: One of them, which is mentioned in the Nature editorial, is that our unique ID could be attached not only to scientific papers, but also

to data sets they helped to generate, comments on their colleagues’ blog posts or unpublished draft papers, edits of Wikipedia entries and much else besides.

So that

This kind of ‘microattribution’ could ultimately make it possible for each researcher to have a constantly updated ‘digital curriculum vitae’ providing a picture of his or her contributions to science going far beyond the simple publication list.

This could eventually result in a change of the ways of evaluating scientific output, as the Nature editorial concludes:

But perhaps the largest challenge will be cultural. Whether ORCID or some other author ID system becomes the accepted standard, the new metrics made possible will need to be taken seriously by everyone involved in the academic-reward system — funding agencies, university administrations, and promotion and tenure committees. Every role in science should be recognized and rewarded, not just those that produce high-profile publications.

Ironically, this idealistic foresight comes from the journal that everybody desires to precisely boost their CV with high-profile publications.

I already use the less ambitious ResearcherID by Thomson Reuters, and I am really willing to try ORCID.

Emptying and filling of the Mediterranean sea

In García-Castellanos et al., Nature 462 (2009) 778-782, a group of scientists from the Spanish CSIC and the French CNRS tells us a wonderful story. It seems that, around 5.6 million years ago, the Mediterranean sea was almost dry, because it had been geologically separated from the Atlantic and Indic oceans and it had evaporated. The rivers that still poured into the Mediterranean sea, such as the Nile, excavated deep canyons when falling to the bottom of the sea at their deltas, and the existence of these canyons is one of the data that allow us to conclude that the sea was dry. Then, about 5.33 million years ago, the Atlantic waters found a way via the Gibraltar Strait and refilled the sea very rapidly. And what does ‘very rapidly’ mean? It means that 90% of the water flowed at a rate 3 orders of magnitude larger than the Amazone river, excavating the Gibraltar Strait rock at 0.4m per day, refilling the sea at 10m per day and finishing the task in a time between a couple of months and a couple of years!

Manifiesto ‘En defensa de los derechos fundamentales en Internet’

LANGUAGE NOTE: I apologize to my English-speaking readers (if any) for the post in Spanish. The reason is that the Spanish Government is trying to pass a Law to enforce intellectual property in the internet, containing several points that reduce the rights of the citizens. This is a joint declaration written by a number of journalists, bloggers, users, professionals and creators in the internet, against this silly move by the Government.

Ante la inclusión en el Anteproyecto de Ley de Economía sostenible de modificaciones legislativas que afectan al libre ejercicio de las libertades de expresión, información y el derecho de acceso a la cultura a través de Internet, los periodistas, bloggers, usuarios, profesionales y creadores de internet manifestamos nuestra firme oposición al proyecto, y declaramos que…

1.- Los derechos de autor no pueden situarse por encima de los derechos fundamentales de los ciudadanos, como el derecho a la privacidad, a la seguridad, a la presunción de inocencia, a la tutela judicial efectiva y a la libertad de expresión.

2.- La suspensión de derechos fundamentales es y debe seguir siendo competencia exclusiva del poder judicial. Ni un cierre sin sentencia. Este anteproyecto, en contra de lo establecido en el artículo 20.5 de la Constitución, pone en manos de un órgano no judicial -un organismo dependiente del ministerio de Cultura-, la potestad de impedir a los ciudadanos españoles el acceso a cualquier página web.

3.- La nueva legislación creará inseguridad jurídica en todo el sector tecnológico español, perjudicando uno de los pocos campos de desarrollo y futuro de nuestra economía, entorpeciendo la creación de empresas, introduciendo trabas a la libre competencia y ralentizando su proyección internacional.

4.- La nueva legislación propuesta amenaza a los nuevos creadores y entorpece la creación cultural. Con Internet y los sucesivos avances tecnológicos se ha democratizado extraordinariamente la creación y emisión de contenidos de todo tipo, que ya no provienen prevalentemente de las industrias culturales tradicionales, sino de multitud de fuentes diferentes.

5.- Los autores, como todos los trabajadores, tienen derecho a vivir de su trabajo con nuevas ideas creativas, modelos de negocio y actividades asociadas a sus creaciones. Intentar sostener con cambios legislativos a una industria obsoleta que no sabe adaptarse a este nuevo entorno no es ni justo ni realista. Si su modelo de negocio se basaba en el control de las copias de las obras y en Internet no es posible sin vulnerar derechos fundamentales, deberían buscar otro modelo.

6.- Consideramos que las industrias culturales necesitan para sobrevivir alternativas modernas, eficaces, creíbles y asequibles y que se adecuen a los nuevos usos sociales, en lugar de limitaciones tan desproporcionadas como ineficaces para el fin que dicen perseguir.

7.- Internet debe funcionar de forma libre y sin interferencias políticas auspiciadas por sectores que pretenden perpetuar obsoletos modelos de negocio e imposibilitar que el saber humano siga siendo libre.

8.- Exigimos que el Gobierno garantice por ley la neutralidad de la Red en España, ante cualquier presión que pueda producirse, como marco para el desarrollo de una economía sostenible y realista de cara al futuro.

9.- Proponemos una verdadera reforma del derecho de propiedad intelectual orientada a su fin: devolver a la sociedad el conocimiento, promover el dominio público y limitar los abusos de las entidades gestoras.

10.- En democracia las leyes y sus modificaciones deben aprobarse tras el oportuno debate público y habiendo consultado previamente a todas las partes implicadas. No es de recibo que se realicen cambios legislativos que afectan a derechos fundamentales en una ley no orgánica y que versa sobre otra materia.

NOTA: Este manifiesto fue redactado conjuntamente por periodistas, bloggers e internautas, en una maratoniana sesión durante la tarde-noche de ayer. Si estás de acuerdo, difúndelo por todas las vías que puedas.

The most powerful computers in the world

I read in New Scientist, that the latest top500 list has been released. The top500 list gathers the 500 most powerful general-purpose supercomputers, and it is like the Oscars of the high-performance computing field. Arguably, a portion of the interest for building faster supercomputers lies not in the science that can be made using them, but precisely in scaling some places in the top500 list. Moreover, the fact that a lot of work is presently being done in specific-purpose computers (opposite to general-purpose), such as the blazingly fast Anton machine build by the D.E. Shaw group for performing molecular dynamics (and only molecular dynamics), has made the top500 list a bit less relevant than in previous years, when general-purpose computers were the almost ubiquitous player.

Nevertheless, and having these qualifications in mind, we can extract some interesting fact from the list:

• The fastest supercomputer is Jaguar (see the above photograph), running at 1.8 petaflops, i.e., performing a thousand billion (1000000000000) floating point operations per second.
• The fastest supercomputer and the third one (Kraken) are both located at the same place: the Oak Ridge National Lab, in the USA.
• The three fastest supercomputers are in the USA. The fourth one is in Germany and the fifth one in China (a promising new player).
• The fastest Spanish machine is, of course, MareNostrum, running at approximately 60 teraflops and ranked at the 77th place in the list.
• Among the 500 supercomputers in the list, 277 are in the USA. UK is the second country with the largest number of supercomputers in the list: it has 45.
• Spain has 6.
• The aggregated power of the 500 supercomputers in the list is about 28 petaflops, of which the USA machines represent 16 petaflops, and the British ones about 1.5 petaflops. Germany, with fewer machines than UK (“only” 27) is the second country in aggregated power, with 2.3 petaflops.
• Spain amounts to around 0.2 petaflops.

Now we are starting to fold

I read today, in Thukrai et al., JACS (2009) ASAP article, a new simulation that succeeds in folding a small peptide/protein using classical force fields (OPLS-AA this time). I did not trust that such simplified descriptions of the potential energy of these complex molecules could be enough to produce roughly correct folding simulations. Now I am beginning to be convinced that, at least for short polypeptides, classical force fields are good enough for folding. Let’s see what happens when this scales up.

It’s not the government, it’s the private sector

Since the centre-left government of the PSOE came to power in Spain in 2004, the total expenditure in science and innovation (i.e., public + private) has doubled. The 1.1% of the GDP that Spain spends now in scientfic research is not close enough to the 1.8% which is the European average, but it is a great advance that has been much welcome by the Spanish scientific community in the recent years.

Now, using the global recession as an excuse, the government is probably going to reduce (or, luckily, keep unchanged) the science budget for 2010. This is a bad decision, which in fact is opposite to all public speeches the President, José Luis Rodríguez Zapatero, has produced in the past months, and it is also opposite to the choices that the rest of developed countries are making. Therefore, it is not surprising that the scientific community has strongly complained about these plans, and even that a wide movement in internet has been produced around the campaign “La ciencia española no necesita tijeras“, in English: “Spanish science does not need scissors“.

Today, I read an editorial in Nature echoing the same complaint.

I have to say that I agree that it is a silly decision not to increase the public efforts in science and innovation in these recession times. It seems the only choice to get to an economic model more resilient to financial fluctuations. I am also prepared to criticize the government for this in the strongest terms, however, I must say that I think that the amount of research that is done in the public sector in Spain is not the biggest problem. In fact, the public expenditure in research and innovation in Spain is above the average of the European Union. What is keeping the total numbers low is the incredibly small effort that the Spanish private sector makes in research: One astonishing datum is that the research budget of only one firm, Nokia, is four times the sum of research budgets of the 21 Spanish firms that spend the most money in innovation.

Learning languages by watching subtitled films

Anybody who has watched some films in a foreign language (known by the watcher, but without being completely fluent in it) must have noticed that watching it with subtitles in the same foreign language is much better than watching it with subtitles in the watcher’s mother tongue. Well, in Mitterer and McQueen, PLoS one 4 (2009) e7785, two Dutch researchers have actually tested this fact in a controlled scientific experiment. It is clear that the datum can be used to improve learning methods of foreign languages.

The placebo dilemma

In Eippert et al., Science 326 (2009) 404, I read about a direct measure, in the spinal cord, of the placebo effect. It opens new ways to address such a relevant issue as pain control, but also it sets me off thinking about one moral problem that I call the placebo dilemma:

The fact is that a lot of medicines work completely (or partially; partially probably all of them) via placebo effect. I.e., they alleviate the sypmtoms that are bothering you, just because you believe they will. Additionally, I believe that another important factor that influences the effectiveness of placebo medicines is that the degree of some symptoms are so difficult to monitor by our very minds that we may perceive that they have increased or diminished their intensity just if we look at a nice picture or if we start thinking about another thing. All of us have experienced this.

Of course, if the medicine we are taking is composed at the molecular level by just water and sugar, like in the case of homeopathic ‘medicines’, or if the ‘doctor’ never touches us and never gives us anything to eat, drink or inhale, like some shamans, then the whole effect of the ‘medicine’ (if there is any) must be placebo.

Note however that this does not mean they do not work. In fact, in many cases, and probably too in many cases of ‘traditional’, ‘western’ medicine, they do work. They alleviate your symptoms. They fix your problems. They make you happy. (The above paper, for example, shows that the placebo effect is very real.)

Of course, if you know that the ‘medicine’ is water and sugar, and you know that the only way in which it could alleviate your problems is via you believing it will, then you probably will not believe it will, and the ‘medicine’ will not work for you. (It is very difficult to voluntarily force oneself to believe something that one knows it has no empirical basis; or at least it is very difficult for me.)

And here it comes the moral dilemma:

Imagine you are a doctor and a patient comes to ask you for medical advice. Imagine you know (because you have read conclusive scientific studies) that the symptoms the patient presents can be easily cured via placebo effect just handling him a flask with water and sugar in it and telling him it contains a powerful drug called ‘homeopatol’.

Then you have to choose between two paths both of which are morally wrong in most people minds: either you lie to the patient or you let the patient suffer.