PRBB research: a cleaner air improves lung function

The exposition to pollution from diesel vehicles makes people with asthma worsen and the lung capacity of the general population decrease at a faster rate. These are the conclusions of two international studies published in the New England Journal of Medicine, in which Nino Kunzli and Mark Nieuwenhuijsen, from CREAL and IMIM-Hospital del Mar, have participated.

The first study analyses 4,742 Swiss people during 10 years and shows for the first time in adults that the improvement in the air quality slows down the lung function ageing. Kunzli says: “we knew that the lung function degradation in smokers is slowed down when they quit. Now we know that ‘quitting’ pollution has the same result”.

The second article studies the decrease in the lung function in 60 adults with asthma after walking for 2h on Oxford Street, full of buses and diesel vehicles, which liberate 100 times more particles than petrol motors. The study demonstrates empirically for the first time that even short exposures to diesel reduce lung function, worsen asthma symptoms and increase lung inflammation. According to Nieuwenhuijsen, “with 2.5 millions of asthmatics in Spain, where 30% of vehicles are diesel, it is important to know the risks of the exposition to this pollutant”.

Art and science go hand by hand

During the evenings, when it gets dark, a surprising phenomenon occurs at the inner square of the PRBB: the back wall of the conference hall becomes a big screen in which audiovisuals are exhibited. The show can be watched from the square or from the balconies.

As a result of the collaboration with the Centre for Contemporary Culture of Barcelona Barcelona (CCCB), a cycle of projections starts this December. “Cultural reflections at the PRBB” is an open window to the art and culture, which allows us to enjoy CCCB productions of very diverse contents. The cycle starts with “The century of cinema”, homage to ‘the seventh art’ in commemoration of its 100th anniversary. For each new projection, there will be a presentation by the author or an expert, and a glass of cava will be offered to the assistants.

Alternating with the “Cultural reflections”, there will be also the projection of the series “One month, one artist”, a cycle that the CCCB dedicates to an audiovisual creator each month. From the PRBB we will also be able to enjoy this other initiative and to watch the work of authors with an interest to experiment and innovate with new formal and thematic languages.

Helping science whilst playing videogames

(another article from the December issue of el·lipse)


Researchers at the Research Unit on Biomedical Informatics (GRIB) at the IMIM and the UPF have invented a surprising and revolutionary computational initiative, the www.ps3grid.net platform. This will allow those interested in participating to put their own videogame console at the disposal of high-level international science.

In only a few seconds, users can download the program from the website http://www.ps3grid.net/live onto a 1 GB pen drive and insert it into their Playstation 3 (PS3). The PS3 will then be connected to the PS3GRID server, which will use the powerful Cell processor included in the new console to make scientific calculations. To go back to a videogame, you just need to restart the PS3.
Thanks to the Cell processor, molecular calculations will be carried out 16 times faster than with a normal PC. According to Fabritiis, "the combined computational force of all the PS3s reaches the features of a powerful supercomputer, given that there are now 3 million PS3s in the world". And this big calculation capacity is essential for the simulation of the behaviour of microscopic biomolecules, which needs the designing of complex algorithms.

The project is already under way and at the moment there are some 130 machines connected, all of which are located outside Spain. But more are needed in order to increase the calculation capacity. This initiative will allow society to be a participant in the exciting world of basic biomedical research.

“The fly” returns to stardom

(article from the PRBB newspaper el·lipse, December issue)

It is the biggest genomic comparison in history, and it has allowed to start understanding the evolutive processes that have taken place during the last 100 years in Drosophila, the most used insect model organism.

The IMIM researchers Charles Chapple and Roderic Guigó, director of the Bioinformatics and Genomics programme of the CRG, have been co-authors of the article in Nature that compares the genomes of 12 out of the 1,500 species of Drosophila. The study, done by an international consortium of more than 100 institutions, has revealed, amongst other things, sequences that have been preserved through the years and that are probably important for the organism. Within the consortium, Charles Chapple has studied the genes that codify for selenoproteins. This part of the study has given rise to an unexpected finding.

Selenoproteins are implied, amongst other things, in the protection against oxidative stress and toxic effects of selenium. So far it was thought that these proteins were essential for animal life. But this study identifies one of the analysed species, Drosophila willistoni, as the first animal which does not contain selenoproteins. Why this organism has lost selenoproteins is still a mystery, but the group has already started to study the possible reasons and consequences.

The major difficulty of the project, says Chapple, was that “the amount of data was inhuman”. But it’s been worth it. Taking into account that about 61% of the human genes implied in diseases have an equivalent in Drosophila, this study can be an important step to their understanding.

Doing one’s beat for the Earth

Everyone!!!! Please add dothegreenthing.com to your favourites (or even better, sign up with them to receive 2 emails per month with the news) and take a look at it every month. As they say, all you have to do is do it. And the videos are very funny!!

Notes on the 1st European Forum on Science Journalism

So, the time has come for me to tell you about the highlights of the 1st European Forum on Science Journalism that took place in Barcelona last week… There were about 250 people from all countries in Europe and so much going on, I don’t know where to start!

Perhaps I will start by the very beginning; the opening ceremony on Sunday December 2, at the CosmoCaixa Science Museum. I had not been there for years, since long before it was renewed in 2004 – it is really amazing, a very nice museum both inside and outside. Definitely worth visiting if you’ve never been there – and revisiting if you already have!

The forum itself started the next day, with the introduction of Quentin Cooper, from BBC Radio4, who fantastically livened up the two days of conferences. An important basic realisation of the forum was that “To be is to be perceived” – and pretty much all we perceive nowadays, we do through the media. So, it follows the importance of our* field. For example, Hans Peter Peters, a researcher and communicator from Jülich Research Centre, showed a few examples of occasions in which the media had made people familiarise themselves with science concepts – such as cloning during the Dolly years, or plaque tectonics during the ’95 Japan earthquake. But the media has not only a role in ‘educating’ the general public in science, but also in guiding policy makers.

Steve Miller, professor in science communication at UCL, was in charge of presenting the results of the Special Eurobarometer on Scientific Research in the Media. (He appeared a second time during the meeting, graphically explaining to the audience his last Nature publication about giant extrasolar planets, without a powerpoint presentation and using a balloon and an orange instead!). The results of the Eurobarometer were quite encouraging: most people do trust the media coverage of science and are mildly interested in it. BUT most people (and this was the journalists’ main problem, too) found science difficult to understand. So this is one of the bottlenecks, and as Steve mentioned more ‘News and views’ pieces in the specialised journals would be very useful to give journalists a better idea about the article they were reporting on. Other useful initiatives would be more educational science programs in TV; programs for journalists to spend time (e.g. 1 month) with scientists, in their labs; and media training for scientists, who mostly complained of a lack of support. In essence, trying to ‘bridge the gap’ and bring both communities closer together.

But according to Tim Radford, writer at The Guardian, there isn’t such a great difference between science and journalism. They both require the same process: your boss asks you to do something (or you have an idea), you research into it, you write it up, and you try to publish it!  (having been a scientists before a would-be-journalist, I can agree with that!)

We heard talks about science communication at very different levels. More than 1 billion people have access to internet nowadays, and there was a whole section dedicated to science in the internet, in which Sabine Cretella, from Wikimedia, called for all experts (scientists) to add or edit information about their subjects in wikipedia, which is, she said, “as good as its editors are”. We saw how to deal with science and children from Marc Goodchild, from the children’s BBC programs, who knows children learn through doing and who is betting for teaching science through consoles and other media the children like and trust. We also had the opportunity to see different ways to deal with the hot issue of climate change from TV stations from Sweden, Australia and the UK, where they took advantage of social networking and the knowledge that people generally only change their habits when their mates do. One website and one sentence I really liked from this session: dothegreenthing.com and “We are the people we have been waiting for”!

Alan Leshner, the CEO from the American Association for the Advancement of Science (AAAS), summarised what we learned at the forum by saying that “understanding the nature of science is more important than knowing the details”. People must understand what is scientific and what is not, what does it mean to do research, the scientific process, etc. These are the important concepts, and not the molecular details.

Finally, we heard some ’success stories from EU research’. Moderated by Patrick Vittet-Philippe, from the EC, we heard EU-funded researchers talking about their investigations into intelligent sensors integrated into textiles, smart safety technologies for safer road transport, the Noah’s ark project to save Europe’s cultural heritage from climate change, the Earth observation system CarboAfrica, and the TARA environmental observatory adventure through the Arctic drift.

This exciting forum was organised by the EC. And what are they doing for science communication? Well, first of all, any scientists getting EC grants for research must commit to communicate to the public and the media their results. And there’s soon to be a call for proposals for precisely the things that the forum showed are most needed: training the journalists in science and training the scientists in communication.

(… I might need both types of training ….! :)



*(allow me to include myself in this community I am just joining!)

Sign the petition for OA

Here’s a petition for the EU to guarantee public access to publicly-funded research results. Please join!! Whether you are a scientists, a librarian or a member of the public, you have the right of accessing this information (and if you are a scientists, then you also have the obligation of sharing your results).

Believe what you see? Think twice

On November 8, I mentioned a talk taking place in Barcelona entitled “Artistic creation and brain”, and that the speaker would be introduced by Mara Dierssen, a neuroscientist who works at the CRG and who had recently organised a ‘brain fair’ about the illusions of the brain. Well. Here’s an excerpt of what happened on that day (taken from the PRBB newspaper I write, el•lipse):



It is possible to see a hand which is obviously fake and have the feeling that it is your own; or to think that your nose is more than 1’5 meters. The more than 350 visitors to the scientific fair “Brain illusions”, celebrated last October 28 at the Sala 2 Razzmatazz, are now conscious of how the perception of our body is something easy to manipulate.

This fair, which took place within the context of the Science Year, was organised by Mara Dierssen, from the CRG, and was financed by the Spanish Foundation for Science and Technology (FECYT) and the CRG. The centre also helped with the organisation, together with science journalist Guillermo Santamaria, who worked on the production, and several neurobiology, interactive communication and physiology research groups who came to be part of this initiative.

The fair had several aims. On the one hand, to bring neurosciences to the streets, through experiments that surprise and make one question things. Secondly, to get scientists and patient associations closer, in order to establish contacts: this objective was met with a future collaboration between UPF researchers and an association of autistic children. Finally, to emphasize the close relationship between science and art, several unknown young music groups were given the chance to play in public (incidentally, they had been discovered by Mara and her collaborators via MySpace!). During the celebration there was also a première of a music theme composed by a girl with Down Syndrome (DS). This fact inspired collaboration between the Catalan Foundation for Down Syndrome and the rock group in which Dierssen sings. Children with DS will write the lyrics of the songs, and the group will compose the music.

SciDev: science, technology and the developing world

Here’s a website to add to your bookmarks. SciDev: News, views and information about science, technology and the developing world. For all the science news you won’t find in the general media, but that affect a great deal of people and should be of interest to us all. Also, this week it’s SciDev 6th anniversary! A big congratulations from here.

And if you are interested in science communication, SciDev offers a very complete guide full with articles, links, etc. that is very worth checking out here.

BTW, I will soon post a summary of the 1st European forum on science journalism that I attended yesterday and Monday – there were quite a few interesting people and some food for thought!

Vote for the best of the web

I have seen that The Scientist is organising a ‘competition’ for the best Laboratory and Video Web Sites, in order to recognize lab leaders and members who devote their time to developing creative and informative Web sites.
There has already been a pre-selection by 7 judges, based on 60 nominations received, of the top 10 web sites that use cutting edge online tools to collaborate, communicate and broadcast their research. Is yours amongst them? You can check it (and also browse around the web sites and have a vote) here.
Winners will be announced in early December at The-Scientist.com.

The Steve project

The Steve project is (from wikipedia) "a list of scientists with the name Stephen or a variation thereof (e.g., Stephanie, Stefan, Esteban, etc.) who support evolution, originally created by the National Center for Science Education".

I have seen them with their T-shirts (see image) in meetings, and you can go here to hear their "Steve song"

:)

Some tips on communicating science to the public

As I wrote in October 26, an interactive EMBO Science & Society Session on how to communicate controversial scientific topics was held at the PRBB conference hall a month ago. I couldn’t attend but have had a chance to see some of the talks that were recorded, and I think there were some useful tips for all scientists who are interested in talking about their work to the general public (which should be ALL scientists!). As Patrick L. Taylor, from the Children’s Hospital Boston and Harvard Medical School, wrote in a commentary in Nature a couple of weeks ago, “public engagement can directly affect research” and “public involvement is inevitable, whether invited or not”. So, if you are a scientist, you’d better be prepared to get the public on your side…

Here are some notes to help you. They are mostly words from award-winning documentary maker and media consultant Eric May, who talked at the workshop at the PRBB about “Dealing with difficult (scientific) topics in public”. They seem obvious, but I think one needs to hear them and think about them every now and then…

“Failure to communicate is always the fault of the communicator”
“It is not what you know, but how you express it, that is decisive in your audience understanding it”
“If you know something, it is very hard to imagine that other people don’t know it” – but you must! The language you use must be clear, you must never use jargon. Use simple sentences and strong statements (journalists won’t spend forever listening to you, they are looking for the one or two sentences they can take with them).

“You must think of your audience”- how they feel, what they are likely to think. One of the main issues May emphasized was the need to express ideas in terms of ‘shared values’, such as fears, dreams, hopes, disappointments, etc. If you can, find a story, ordinary people who are or could be affected by what you do. Make people trust you and share in the understanding of the wonder of scientific developments. Finally, “ask yourself, as a human being, what is it that interests you about what you are doing?” If something deeply interests you as a human, it will likely interest others, too.

Next week I’ll be attending an European Forum on Science Journalism which will take place in Barcelona. I’m sure I will be hearing some exciting talks and I will sure post the highlights here!

CRG symposium personal summary

So, here are some of the (few) talks I could hear at the CRG Symposium which took place at the PRBB about 10 days ago, and a brief explanation of (what I understood about) them.

Peter Fraser, from the Babraham Institute, gave the first talk, which was about the “transcription factories”, an interesting concept he’s been talking about for a while. Many genes, often genes that are related to the same biochemical pathway or that are regulated by the same transcription factor, ‘meet together’ while being transcribed, they co-localise in so-called transcription factories. He has looked for the genes that co-localise with  and  globin genes using a genome-wide 4C technique and he has found hundreds of them, which interestingly were spread over all chromosomes.

Angus Lamond (University of Dundee) talked about nucleolar dynamics. He’s analysing the nucleolar proteome at the level of protein organization and dynamics: he called this a ‘second generation’ proteomics strategy (as opposed to a first generation which would not include dynamics, but only ‘a list’ of the proteins found there). The nucleolus is a subcompartment in the nucleus where ribosome biogenesis takes place, and it is itself subdivided into 3 regions. So far, Lamond’s group has analysed about 3,000 proteins, and found 407 that are ‘nucleolar’, 234 of which were not annotated at GO as nucleolar (which exemplifies how bad is still the annotation in this gene ontology). For studying the dynamics they are comparing the nucleolus proteome of cells at different temperatures.

Other speakers included, amongst many others, Robert Singer, from the Albert Einstein College of Medicine in New York, who has done FRAP (fluorescence recovery after photobleaching) of mRNAs at the transcription site to study their dynamics in living cells; Miguel Beato, director of the CRG, who talked about hormone nuclear receptors and chromatin remodelling; Raúl Méndez, also from the CRG, who talked about translational control through cytoplasmic polyadenylation; and Tony Kouzarides, from the Gurdon Institute in Cambridge, who talked about histone modifications and the mapping of methylation sties in the genome.

“In 10 years we could be creating artificial miniorgans”

This is an article that I published in the PRBB monthly journal “el•lipse”. It explains what Mark Isalan, a group leader at the CRG, is doing (as I promised in my last entry).


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To generate artificial life might not be as much science-fiction as we may think. The gene network engineering group, from the systems biology program at the CRG, is already making small steps towards that goal. The six people who work under the direction of Briton Mark Isalan – and who represent five different nationalities – have spent the last year working in several projects that will eventually make it possible to create an artificial miniorgan (say, a gland). This miniorgan, which would have some functionality and which could in the future have some clinical application, could exist in less than 10 years, says Isalan.

But for the moment, the daily task of the group is working out the basics. The group focuses on three main lines of research. One is protein engineering – constructing proteins with new properties - and in particular engineering customised zinc fingers (a type of molecular structure able to bind DNA) so that they can bind any desired DNA sequence. One of Isalan’s main scientific contributions so far was actually being part of the team who discovered the protein-DNA recognition code for Zinc fingers, i.e. which aminoacids recognise which nucleotides. This code has been essential for the posterior zinc finger engineering. The second line of research of the group is synthetic gene network construction, which consists on joining together carefully selected genes and regulatory sequences in order to construct artificial 'circuits' that can sense particular conditions or signals within a cell, and respond accordingly – just as electrical circuits do. Finally, the group has developed a new way of delivering DNA containing gene network constructs to specific locations within a mammalian cell population. With this technique, which is called PCR bead transfection and uses magnetic beads, they can transfer a specific DNA construct to a single selected cell within a population. The group, formed only by biologists, also uses the help of some computer scientists at other groups at the PRBB, such as Ricard Solé (GRIB), Luis Serrano (CRG) and James Sharpe (CRG), to do some computer modelling and test their network hypotheses.

By combining these lines of research, the group intends to achieve several aims. Scientifically, their work should help finding out the ‘design principles’ underlying complex biological systems, such as the development of an organism, the formation of the stripes present in some animals, etc. by artificially re-creating the pathways involved in these processes. But their work also has more practical applications. For example, they are working on a biotechnology application of their engineered networks within the EU project Netsensor, in collaboration with Luis Serrano and other European groups. This project consists on introducing into cells a construct that will correct a carcinogenic mutation only if it senses that this is needed. The construct carries an artificial sensor gene network, and a customized Zinc finger nuclease to cut and repair the p53 gene, a gene usually affected in cancer.

“The p53 nuclease Zinc finger is my favourite result so far; we engineered this enzyme to do something we couldn’t do before”, says Isalan of his discoveries since he joined the CRG, a year ago. This is one little step towards what would be Isalan’s dream: to cure a disease using one of these gene networks. Again, optimistically, he thinks we’ll only have to wait a decade.

Decomposing complex science

Luis Serrano is the coordinator of the Systems Biology programme at the CRG, one of the centres at the PRBB. In a talk he gave last Wednesday at the park, he mentioned some interesting projects his lab is working on. One of the most exciting ones, for me, was the global quantitative understanding of a free living organism for the first time ever. For this they have chosen Mycoplasma, the smallest free living bacteria, with only 689 genes. They are doing all sort of things with it: GFP constructs of all genes to look at their in vivo localisation, K.O. of all genes to decipher their functions, microarrays to understand gene expression, pulldown of complexes, metabolism studies, protein-protein interaction studies, electron microscopy, NMR, … everything that can be done, really! The idea is to put all the information together in a computer in order to have a complete model and be able to make simulations and hypotheses. If this works, will we be able to say, for the first time, that we understand 100% how an organism functions and that we are able to predict the consequences of any change in the system with a high confidence? It sounds like science fiction, but it might not be impossible….!

Talking about science fiction, but a more practical type, Serrano briefly touched on another area in his lab, which is new therapies such as the “doctor in the cell” or the “living pill”. In brief, the first one (the “doctor”) would be a genetic system that monitors the status of the cell, checks whether everything is OK and finds out and solves what has gone wrong. They are doing this in collaboration with another group at the CRG, that of Mark Isalan (I’ll tell you more about his work another day). The “living pill”, as I understood it, would be modified bacteria that can get into a cell and integrate as mitochondria (recapitulating Nature, since it seems mitochondria come from intracellular bacteria) so they can be used as a vehicle for gene therapy. Pretty cool, eh?

By the way, it has just been announced that Luis Serrano has been nominated a member of the Royal Spanish Academy of Sciences. He’s the last of the less than 200 members elected since the Academy was created in the XVI century…!

e-repositories in Spain

Yesterday I received a wealth of information about several interesting e-repository initiatives going on in Spain that I would like to share with you. After seven years living in England, I am so out of date with all Spanish initiatives; I have a lot to learn! This was at this year’s TSIUC meeting, which took place in Barcelona. TSIUC (Trobada de Serveis Informàtics de les Universitats de Catalunya) are meetings to debate the uses of IT in Catalan universities, and this year it was the turn of e-repositories. So here’s the summary.

e-repositories, for those of you unfamiliar with the term, are online collections or databases of documents, to say it simply (they offer other interesting services, but this is the basis). The speakers at the meeting presented several initiatives, mostly about institutional repositories of research (papers), but also about some collective repositories (at a local or national level), and about repositories of websites or educational resources. Whatever the subject, OAI-PMH (the Open Archives Initiative Protocol for Metadata Harvesting) was the star of the day – this is definitely the common protocol everyone is using. Open Access is (finally, happily) in vogue!

It seems there are about 447 European repositories – and only 17 are Spanish. Se we still have a long way ahead of us. But things are moving. In 18 months there has been a 150% increase in the number of repositories in Spain (from 13 to 31). And as I mentioned yesterday, the PRBB makes the full-length PDF version of all articles published by the PRBB centres accessible from the PRBB website, via a search-engine that can retrieve them. Not quite a repository, but at least something to make sure the work being done here is publicly accessible.

Here are some other examples of such an initiative that were introduced at the meeting. The CBUC (Catalan University Libraries Consortium) presented some of their ongoing and future projects:

- TDX (or TDR), a repository for full length PhD thesis from universities of all over Spain, which contains now nearly 5,000 thesis.
- Recercat, a cooperative repository of digital documents that include research from universities and research centres of Catalonia. It includes more than 3,800 documents, amongst preprints, working papers, reports, final papers, etc. All of them under a creative commons license.
- Raco (Catalan Journals in Open Access) is a cooperative repository where the full-text from articles of scientific, cultural and erudite Catalan journals can be consulted freely. It currently contains 144 Catalan journals and more than 37,000 articles


Alicia López Medina came from Madrid to tell us about a repository by the Madroño consortium (the equivalent to the CBUC in Madrid) which is called e-ciencia. It is also a cooperative repository, fed by seven independent institutional repositories. In total, they contain nearly 17,000 full length documents.

We also had a visitor from La Rioja, Marta Magriñá Contreras, who presented Dialnet, a Hispanic scientific production diffusion portal. They not only store articles published by external journals, but they also host about 170 journals published by universities or non-for-profit associations.

And talking about journals, RECyT (Spanish Repository for Science and Technology) is a set of services with the aim of helping Spanish scientific journals to be more professional and international. There is a public zone in RECYT (Library) where quality-proved Spanish scientific journals can be hosted and there is a private zone (User Home) that provides an editing tool to help publishing (including peer review, etc.). RECyT is an initiative of the FECYT that was presented by José Manuel Báez.

They also introduced other non-scientific repositories, which I won’t go into but were also interesting. I’ll finish with a take home message that I came out of the meeting with: the way to preserve things is not to keep them locked away, but to have so many copies of them that it’s impossible for all of them to disappear. Or, as Thomas Jefferson put it “… let us save what remains: not by vaults and locks which fence them from the public eye and use in consigning them to the waste of time, but by such a multiplication of copies, as shall place them beyond the reach of accident”.

Regretfully, scientists are still not boarding this ship. Several international reports show that most of them are not aware of these initiatives or of their advantages (such as more visibility for their papers, the assurance that their papers will be preserved indefinitely, etc.). So, I think one essential thing to do in parallel to the technical improvement of the repositories is to get authors enthusiastic about these open archives.

Open Access at the PRBB

As a service to all members of the PRBB centers, as well as any external visitors interested in the research taking place on them, a search engine is going to be re-launched at the PRBB website that will allow to search for articles published by any scientist associated with any of the six PRBB centers, i.e. IMIM, CEXS-UPF, CRG, CMRG, CREAL and IAT. This search engine will retrieve a PDF copy of the full-length article, which will be freely and immediately accessible to the reader.

This initiative is similar to that of self-archiving articles in institutional repositories in parallel to publication in journals, a practice that is very common nowadays all over the world. More and more academic institutions, libraries and other organizations are creating open access institutional repositories as a way to manage and disseminate the intellectual output of their faculty; to preserve, archive, and provide access to the work being done on their premises. The U.S. National Institutes of Health, for example, ask researchers, on a voluntary basis, to make a copy of each paper freely available online, perhaps on their institute's Web site; and five research councils in the United Kingdom have made self-archiving within 6 months of publication mandatory, as have other research funding agencies. The brand-new E.U.-funded European Research Council also supports the idea of self-archiving.

The PRBB initiative of linking the PDF articles to the search engine is not an institutional repository, but it is an alternative and simple way of ensuring a major visibility of the work being done. As scientists, we are particularly dependant on ready and unrestricted access to our published literature, the only permanent record of our ideas, discoveries and research results. And having such advanced communication resources as the Internet, it would be foolish not to use them to share our research in an equally advanced way. We are all aware of the importance of increasing general awareness of our work, and of how a faster and wider sharing of articles and research data stimulates the advance of knowledge.

What about the journal´s copyright?

At the moment, most journals retain the full copyright of the articles they publish, although according to the most authoritative resource on journal policy for self-archiving, more than 90% of journals allow some form of self archiving [1]. Furthermore, awareness is growing by authors and their funders that assigning full copyrights to publishers may not be in their best interests. That is why universities, governments, and other organizations are suggesting that authors now retain their copyrights and then grant publishers a license to publish the work. After the article is published, the author will have nonexclusive rights to reproduce, distribute and deposit their work, including posting it in their website, as well as create derivative works. Ways of reaching this arrangement are suggested for example by The Scholarly Publishing and Academic Research Coalition (SPARC) in the US, and The Joint Information Systems Committee (JISC in the U.K. and SURF in the Netherlands), who propose that authors include an “authors’ addenda” in their publishing agreements, asking publishers to grant them this right.

Another way for authors to retain the copyright of their published articles is to publish them directly with Open Access publishers, such as PLoS and BioMed Central. The Open Access movement provides free access to peer-review articles for everyone via online journals, giving the articles a huge visibility, and it also allows authors to keep the copyright of their work. As of February 2007, the Directory of Open Access Journals (www.doaj.org) lists 2,563 journals with 126,293 articles. In the last years, the Open Access movement has grown and received support from the major funding agencies in both the US and Europe, who now require that the results of research being funded by them is made freely available within a short time, usually not more than 6 months.

Another recent initiative to impulse the free distribution of research is coming from the UK. This is UK PubMed Central, a website that will give free access to most biomedical research conducted in the UK. This initiative is led by the Wellcome Trust, the world´s major biomedical funding agency. According to the Wellcome Trust director, Mark Walport, “Medical research is not complete until the results have been communicated” and “this is a great opportunity for research to be made freely available…”. The Wellcome Trust also says in its position statement that it supports unrestricted access to the published output of research as a fundamental part of its charitable mission and a public benefit to be encouraged wherever possible.

Finally, and despite the journals´ current restrictions, it is common practice for scientists to have links to their own published articles on their websites. A study in 2005 showed that the final version of more than one third of articles in high-impact journals were freely available online. This is the result of an ever-growing ideology that we at the PRBB share: the belief that it is fair that the results of publicly-funded research be also public and available for everyone, both scientists and the general public; that a faster and wider dissemination of information such as that possible through the internet fuels the advance of knowledge; that it is this knowledge upon which future scientific activity and progress are based; and that scientific progress is both a right and a necessity for our society and we as scientists have the obligation to do what is in our hands to stimulate it. We believe that the search engine of the PRBB will be a good step in this direction.

Catalan Science Week

November 9th to 18th is the Science Week in Catalonia (the region of Spain to which Barcelona belongs to). This is a celebration that occurs every year, but this time it coincides with the “Barcelona Ciència”, a celebration of science that lasts the whole year – a very scientific 2007 indeed!

Anyway, during these days there are lots of scientific events directed to the general public, with an emphasis on children and youngsters: games, conferences, workshops, exhibitions and courses on different topics related to science, including global climate change, stem cells, recycling, nanotechnology, physics, zoology, chemistry, engineering, botanic, sustainability, meteorology, materials science, mycology, archaeology, and many more. There’s something for everyone! Many museums, universities and research institutes are involved in this initiative, which aims to get science closer to the society.

Enjoy!

Artistic creation and the brain

This year Barcelona is celebrating the ‘Science year’ and plenty of science-related conferences and events are taking place all over the city. Within this framework, a series of talks called “El(s) futur(s) de la ciència” (The future(s) of science) are being organised.

The next one coming is entitled “Artistic creation and brain”. The talk, in English with simultaneous translation to Catalan, will be given by Samir Zeki, from the University College de Londres. He will be presented by Mara Dierssen, a neuroscientist who works at the CRG (and who is very involved with science communication to the public – she recently organised a very successful and fun ‘brain fair’ about the illusions of the brain).

The talk will be next Thursday, November 22, at 7pm at Palau de la Virreina (La Rambla, 99). I’ll do my best to be there, it promises to be interesting!

Symposium on genomic regulation

The CRG (one of the centres located at the PRBB) is organising for the 6th consecutive year an annual symposium in which they invite some of the worldwide leading experts in a particular field. This year, the 6th CRG Symposium is on genomic regulation and it’s entitled “Executing the Code”. It will take place this weekend (November 9 and 10) at the PRBB Conference Hall, and it will bring together 18 worldwide experts grouped in 6 sessions which go from nuclear dynamics analysed through screening techniques, to global gene regulation, chromatin, RNA processing and translational regulation, to end up with small RNAs regulators.

I’ll try to escape to some of the talks and report on some exiting news. Keep you posted!

Red-haired Neanderthals?

A study just published in Science and in which Jaume Bertranpetit (a geneticist from the CEXS-UPF, one of the centres at the PRBB) has collaborated, shows that Neanderthals varied significantly in pigmentation levels, potentially to the scale observed in modern humans. Analysing the sequence of a gene which regulates pigmentation (MC1R) in the fossils of two Neanderthals, they found a variable that does not exist in the studied current populations but that is similar to that found in red-haired Europeans nowadays. This suggests that Neanderthals may have had clear skin and a hair colour somewhere between blonde and red. This is the first time that an external physical trait of this extinct human species has been identified.

"Watch me do this experiment"

Today I have discovered a new tool that the fantastic internet world offers for sharing scientific discoveries, and I thought I would share it with you. It’s called JoVE – Journal of Visualized Experiments, and it’s an online video-publication for biological research.

Here you can see ‘video articles’, i.e. you watch a video of interviews to scientists, or of scientists explaining their findings to you or, even better, showing their experiments to you: you see the graphs and figures you would see on a paper, but also the real experiments, you see how they do them hands-on. They include step-by-step instructions and discussions about possible technical problems. They seem to be mostly about new laboratory techniques, which I guess are the type of experiments that can benefit more from this type of tool, because it’s some times difficult to imagine them without visualising them.

For example, there are demonstrations of ‘simple’ techniques, such as how to window chicken eggs for developmental studies , or the dissection of Drosophila ovaries. But there are also some more complicated ones, such as the thin sectioning of slice preparations for immunohistochemistry or a microfluidic device with groove patterns for studying cellular behavior .

I invite you to browse the journal – you might finally learn an experimental protocol you did not know how to do – and even to submit your own videos.

Share the (science) love!

FP7 – European money for science and society

Following on from INFOBIOMED's European recognition, let me tell you what I have recently learned about European funding for science.

Last Monday I went to an informative session to find out about the possibilities of getting funding from the FP7 (short for 7th Framework Programme for Research and Technological Development) from the European Union (EU). For those of you who are not familiar with this, this is the EU's main instrument for funding research in Europe. It gives funding for things like improving training and career development of researchers, specific projects and ideas (projects must generally involve groups from different countries or have a European projection), or infrastructures.

The Framework Programmes are usually renewed every 3 years, but this one, the 7th, will run for longer: from 2007-2013. Another novelty of this year’s programme (well, it seems it started last year, but this year it’s more consolidated) is that there’s a specific funding for the area “Science and Society”. This is aimed at bridging the gap between science professionals and those without a formal science education and at promoting a taste for scientific culture in the general public – just what I am trying to do here at the PRBB! This area alone counts with a budget of € 330 million for the seven years. (Actually, the general budget of the FP7 has increased significantly since FP6, from 4 to 7 billion €/year, which is good news!)

The next call for proposals, we have been told, is starting this same week, and we will have until next spring to present our ideas, which should be on one of the topics that will be open for proposals (not all topics are covered each year). Some of the initiatives that could be funded by the area of Science and Society, for example, include projects aimed at triggering the curiosity of young people for science and at reinforcing science education at all levels. Or they could be related to the role of women in science and how to improve gender issues. Oscar López Lorente, one of the Spanish national Contact Points for Science in Society, also explained to us that the encouragement of societal dialogue on research policy is another key issue, and that the FP7 wants to stimulate both the media and civil society organisations (including charities) to become more involved in research, debating and promoting shared values, equal opportunities and societal dialogue.

So, it seems there’s an opportunity for us all to work together making science a powerful tool for the improvement of our society. Anyone want to join? I’m ‘open for proposals’.

European recognition

I have just been informed that a project coordinated by the GRIB (the Research Unit on Biomedical Informatics of the PRBB) has been selected Project of the Month (October 2007) by the European Commission. My congratulations to all the people involved!

The GRIB is a mixed unit, formed by groups belonging to two of the centres located at the PRBB: the IMIM and the CEXS-UPF.

The project, INFOBIOMED, is a European network of excellence (NoE) which has lasted 42 months (ending in June 2007) and which had its final review in Brussels last 28th of September. The excellent results of the review have prompted the award.

The aim of INFOBIOMED was to consolidate European Biomedical Informatics (BMI) as an emerging integrative discipline born from the close collaboration between Bioinformatics (BI) and Medical Informatics (MI). Their synergy should foster individualized healthcare and facilitate the discovery of novel diagnostic and therapeutic methods.

Some of the network achievements, with the support of their € 4.850.000 budget, include the International Symposium on BMI in Europe that they organised at the PRBB last June, and an European BMI Gateway (a repository with information and the latest news on BMI in Europe) that they have created.

Although the EC funding for the NoE is officially ended, the INFOBIOMED Consortium has already committed to continue developing activities addressed to the BMI community in order to set a durable structure to enable collaborative research and to support the consolidation of BMI as a crucial scientific discipline for future healthcare. If you are a researcher in the BI, MI or BMI fields, please do join the initiative to contribute to the consolidation and development of a BMI research capacity in Europe!

Web of Knowledge workshop in Barcelona

Hi there, hope you had a good weekend. Here's another interesting thing coming up soon at the PRBB.

You may know that in Spain, all research centres, universities and hospitals have free access to the Web of Knowledge through the FECYT (Spanish foundation for science and technology).

The Web of Knowledge is something all scientists are (or should be) familiar with. It is a dynamic, integrated environment that provides them with one single source for high quality scientific content and the tools to access, analyze, and manage research information (articles from scientific journals, books, patents, etc.) - an essential task for researchers.

The Web of knowledge is due to start a new interface next January 1st, 2008. The FECYT is organising two formative sessions in Barcelona to explain the use of the Web of Knowledge databases and its new interface. One of the sessions will take place at the PRBB conference hall on Tuesday, November 13th, from 10am to 1,30pm. The previous day at the same time there will be another session at the conference hall of the ‘Edifici de França’ of the UPF (Estació de França).

If you are around and interested in learning more about the Web of Knowledge, please reserve a place by sending an email to presentacionwok@fecyt.es

Sunday 28th: science and the public at PRBB

Good morning,

If you are in Barcelona this weekend and you are interested in science communication to the public, you probably are interested in this.

This Sunday October 28th, an interactive EMBO Science & Society Session on how to communicate controversial scientific topics will be held at the PRBB Auditorium. This session is entitled “Dealing with difficult topics in public: A communication workshop on controversial issues in science” and will go on from 5pm to 7:30pm. Entrance is free and the session is open to both scientists and the general public.

Louis-Marie Houdebine (Institut National de le Recherche Agronomique, Paris), creator of Alba, the "glowing" rabbit, teams up with award-winning documentary maker, Eric May in this session which will count with presentations, discussion, exercises and practical advice on communicating research and "managing" research communication outside scientific circles.

This session is part of the EMBO Members Workshop entitled “Frontiers of Molecular Biology” that is being held in Barcelona this weekend (October 26-29), and which has been organised by two researchers at the PRBB, Juan Valcárcel (CRG) and Francesc Posas (CEXS-UPF), together with two other EMBO members from Barcelona.

Welcome to prbbnews!

This is my personal blog about what's going on at the Barcelona Biomedical Research Park (PRBB), one of the largest biomedical research clusters in Southern Europe. The PRBB is located in Barcelona, and it gathers together six public research centres:

-Municipal Institute of Medical Research (IMIM)

-Department of Experimental and Health Sciences of the Pompeu Fabra University (CEXS-UPF)

-Centre for Genomic Regulation (CRG)

-Centre of Regenerative Medicine in Barcelona (CMRB)

-Centre for Research in Environmental Epidemiology (CREAL)

-Institute of Advanced Technology (IAT)

This large scientific infrastructure that is also physically connected to the ‘Hospital del Mar de Barcelona’, a public hospital.

Here you will find some news of what is happening at the PRBB bulding, both scientifically and socially. I will also include some news or commentaries on communication and society that I think might be of interest to people - always related to science. Please note that although I work at the PRBB and this blog is mostly about it, these are after all my personal views and opinions, and not those of the PRBB.

Do come and visit often to get some of the latest news, and know that your comments will always be welcome!

See you again soon!