Wednesday, November 28, 2007

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"


Tuesday, November 27, 2007

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!

Friday, November 23, 2007

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.

Wednesday, November 21, 2007

“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).


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.

Tuesday, November 20, 2007

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…!

Wednesday, November 14, 2007

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.

Tuesday, November 13, 2007

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 ( 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.

Monday, November 12, 2007

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.


Thursday, November 8, 2007

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!

Tuesday, November 6, 2007

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!

Monday, November 5, 2007

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.

Friday, November 2, 2007

"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!