Italian Minister of Health authored the preface of a book supporting homoeopathy.

War on Science, yet another chapter. I think that anyone working in Science or caring about it, and anyone who aims to a growth in the public opinion’s awareness on the scientific issues of global interest, tends to spend some time to contrast hoaxes, misconceptions and anti-scientific propaganda. The most of the times, you end up returning references to the documents published by health and science officials to those ones claiming that “official science” is lying. If someone affirms that vaccines cause autism, or are potentially harmful for the child’s health, you may consider responding with data provided by health institutions. Likewise, if someone is keen to promote homoeopathy as a real cure, some documents published by the NIH, FDA or WHO, and proving its flat inefficacy, could turn out really useful. Basically, the most of the times, national and international health institutions are on your side, providing you and the whole public opinion with referenced data and clear positions in favour of  “official” biomedical science. But what happens if a national health institution turns its way, and starts supporting one of the major scientific hoaxes ever, such as homoeopathy?

This disturbing scenario has just become reality in Italy. The Minister of Health in charge, Beatrice Lorenzin, authored the preface of a book supporting homoeopathy, entitled In Praise Of Homoeopathy (Elogio della omeopatia) and written by Giovanni Gorga, president of an association of enterprises producing and delivering homoeopathic products. Even if the official position of the Ministry in matter of homoeopathy has remained unchanged, and homoeopathic products are sold in Italy as “medicals without any approved therapeutic indication“, this clear stance of the Minister Lorenzin generates concerns in the Italian scientific community.

The Italian non-profit organization CICAP, devoted since yeas to counteract the diffusion of anti-scientific information in Italy, has presented an open- letter to ask the Minister to clarify her position about the real efficacy of homoeopathic products, and to publicly declare that there are no evidences supporting it. The International Association of Italian Researchers (AIRI) is spending as well to spread this letter and rally the support of Italian researchers.

Being an ecologist and a radical leftist, I am very far from being a Beatrice Lorenzin’s supporter. Forty-four years old, serving as minister of health since the formation of the government led by Matteo Renzi in the spring of 2013, Beatrice Lorenzin grew her political career within the right-wing coalition led by Silvio Berlusconi. Anyways, I have always considered her a very reasonable woman and a politician of rare quality in the awful italian political landscape (not a big medal, actually). I am in fact pretty surprised by this awkward fail, and I still comfy that anything could be fixed.

I would limit to consider this fact as the usual yet another strange thing coming from Italy, or one of the many events stating how difficult the relationship between science and governance is, but I fear that something more serious is on the way. In the neo-liberal West, governments are all about economy, and the promotion of private sector has become the only concern of administrations of any political area. The last April, bloomberg published an insight pointing out that homoeopathy constitutes a billionaire market in the United States. I fear that the only element we don’t consider about this matter, is how much money an hoax could generate. Even if it is pretty clear that homoeopathic products have no effect on human health, it is still able to generate consent and to turn it into business and jobs. And a disturbing question comes along: will governments shut a wealthy sector for ethical reasons?

Applying phylogenetics and bioinformatics to NF-kB studies

To anyone having to do something with immunity studies, the nuclear factor kappa-light-chain-enhancer of activated B cells, will sound really familiar. The NF-kB is a protein complex deputed to initiate the transcriptional response to external stimuli, such as stress, citokines, antigens, bacteria, free radicals or UV light irradiation. Expressed in active B cells, it is the protagonist of the immune response at molecular level.

For quite a long time, its evolutionary characterization has been rather neglected, since no homologous sequence is found. Actually, I often happen to realize that biomedical studies tend to keep quite far from evolutionary approach. Biomedicine is about to understand processes happening here and now, and it often aims to quickly find a reliable therapeutic approach for the disease of subject. So many factors to study, so little time. This shifts biomedical studies away from the influence of evolutionary biology. A real pity, as Catriona MacCallum  pointed out on PLoS Biology in 2007, since the contribution of evolutionary biology to biomedicine has a big, almost unexplored potential.

Recently, NF-kB and NF-kB-like proteins have been discovered in “basal” marine animals and non-metazoans, allowing the study of the early evolution of this nuclear complex of extraordinary importance for human health. John R. Finnerty and Thomas D. Gilmore from the University of Boston published an interesting paper on this topic just a few months ago, and I dare to introduce it here for two main reasons.

Beyond the clear scientific interest of their work, representing one of the few and really valuable evolutionary approaches to an all-biomedical subject, and highlighting deep conservation and repeated instances of parallel evolution in the sequence and structure of NF-κB in distant animal groups, which suggest that important functional constraints limit the evolution of this protein, it also provides an explanation of how to easily apply phylogenetic and bioinformatic approaches even without a previous hard training.

The authors run on the double track of reporting a scientific result, and introducing the reader to some simple (but still effective) computational tools that more or less anyone may use to implement phylogenetics in his/her work, rendering Methods for Analyzing the Evolutionary Relationship of NF-κB Proteins Using Free, Web-Driven Bioinformatics and Phylogenetic Tools a very interesting reading for both bionformaticians who need to communicate with experimentalists, and people working with NF-kB.

The article is part of the methodological book NF-kappaB. Methods and Protocols edited by Michael J. May and published by Springer Protocols.

Happy birthday mr. GNU

It was the early eighties, a day like any other at the MIT. And a printer was not working. The Artificial Intelligence Laboratory programmer Richard Stallman did his best to fetch the source code of the driver from the manufacturer to fix it, but there was no chance. The code was closed, and this was definitely a huge problem. Because if we give up sharing our work, we cease to work for the common good. And this should never happen in science.

All of a sudden, something as simple as the possibility to modify a driver became the symbol of an epic struggle. The struggle between greed and generosity, individualism and solidarity, profit and redistribution, patents and free knowledge and, to some extent and in a more philosophical fashion, between capitalism and anti-capitalism.

It was the September 27th 1983, and Richard Stallman was announcing his challenge to the world: ensure that the source code flows freely. The GNU project was born.

Over the years, a huge crowd of any kind of programmers joined the movement, rising the flag of free knowledge as a means for the redistribution of wealth, and for the spread of democracy. A lot of admirable and romantic ideals that shocked the world as they proved to be effective enough to beat up the informatics bad guys. Although the efforts of software majors to promote their closed and patent- based way to software, the free software movement has been the one to dictate the metrics and trace the groove of many aspects of the evolution of IT market. The encounter with Torvald’s kernel linux, the birth of the main distribution projects, the extension of free software principles to all the aspects of cognitive production that led Lawrence Lessig to found Creative Commons in 2001. Year by year, open source software have spread over, becoming the standard for almost everything that is leading the internet nowadays,  including Google and Facebook.

A lesson that we still need. Openness is fair, and it is productive. As the debate on Open Science spreads up, the example of Free Software still traces a way we must follow.

The Catalan scientists' support for Independence and Science production in post-modern Europe

The day of truth has come for Catalonia. The region surrounding Barcelona will meet a crucial election tomorrow in which the people will decree whether following within the Spanish State or going further with the negotiations to separate from Madrid and build and independent state. Differently from the UK in the Scotland affair, anyways, the Spanish government doesn’t grant any right for Catalans to decide about their own destiny, and a victory of the pro-independence front (that is largely expected) will drag the region into a dramatic situation of political stalemate. As you may expect, the discussion is very heated, as anyone is questioning about the many aspects that the independence implies.

Sometimes a link is better than thousand words, especially if it will redirect you to the Catalan News Agency website, one of the most complete resources for updates from Catalonia in English, where you can make up your mind about this complex matter. On this blog, I think we’d better focus on the implications of a possible declaration of independence over the Catalan research system, that is one of the most growing and dynamic in Europe. A swift browse on the Catalan bio- region official website will return a fair picture of the vitality of this area in Science production, accounting for hundreds companies that have doubled in the last decade and hundreds research groups included in dozens of research centres, hospitals and universities. A swift calculation attests that one worker out of four in Catalonia is employee in Research and Development area at any level.

It is not surprising that the 11 internationally renowned Catalan scientists’ declaration in favor of the independence from Spain had an explosive effect on the electoral campaign. On September 22nd, scientists like Jaume Bertranpetit (UPF evolutionary biologists known for its studies in human genome evolution), Xavier Estivill (CRG Group Leader working in non-coding RNA and diseases) and the Princeton professor Joan Ramon Resina, signed a document in which they affirm that voting for the independence “is the best option to maintain the good work and the consensus achieved through many years” and that the new Catalan state will have the opportunity to “increase the resources that science requires and provide the state structures to guarantee the consolidation and growth of the research system“.

Catalan scientists basically blame the Spanish government on two main points. First, according to the document signatories, Spain didn’t support enough science, having cut the national funding way too much to guarantee a good competitiveness of the Spanish research. In this, there is also a matter of redistribution. The criteria adopted from the Spanish Ministry of Science are claimed to be not meritocratic and to respond to mere political interests. Second, the same structure of Spanish academia is argued to be not satisfactory in terms of dynamism and effectiveness, as a major autonomy in the decisions for universities and research centres is strongly advocated.

I have not enough information to propose opinion of mine, and after my short experience here in Barcelona I can just appreciate the huge potential this area has in Science. Anyways, we may try to find an interpretation, and even realise that what is going on in Catalonia is just the reflection of something far more extended.

About ten years ago, the Marxist philosophers Antonio Negri and Michael Hardt proposed that, in the current postmodern age, the production strategy changed from a Fordist factory- based structure into a city- based network. The idea starts from the assumption that technological advancements moved cognitive work to the centre of industrial production. The city thus become the “factory” of the new era, because of its role in interconnecting individuals, research centres, facilities and small enterprises in a peer production cluster. Any city- factory is included in the network and the network is regulated over a large scale, ideally over a global scale, but more realistically over a continental scale. While during the modern age the system’s core was a conjunction of industrial areas that were interacting at national and international level, in the post- modernity the system is based on productive clusters, the cities, interacting at continental and global level. The consequences in politics are pretty clear. National states end up ceding power downward to those institutions that are able to govern the single peers, and upward to those organisations acting at a continental or global level. This is strikingly evident in Europe, and we can tell that it is the main force driving the European integration. During the last decades many national states have reformed their structure to grant a major autonomy to local and city governments and, on the other side, the birth of the Euro displaced the economical governance towards the UE institutions.

Actually, Negri and Hardt’s view has been deeply controverted by those who claim that it is not fully capable to draw a realistic picture of the whole system, and that it just works, to some extent, in describing the quaternary sector of economy. Even if most of these critics may have sense, we can still rely on this city-factory model, since our interest in this discussion is limited to scientific production. What Catalan scientists have understood is that their future challenges will be played both locally, over the Barcelona area, and more widely over the European Research Area. The city needs a full decisional autonomy to freely interact with the other peers at European and global level, in a game that is getting way too hard for the dated and cumbersome Spanish state, that is not able to be a good teammate anymore.

No one can really tell how it will end. Tomorrow, a large pro- independence majority is expected, but even a defeat won’t most likely stop the growth of the separatist sentiment, so deeply rooted in the new generations. The controversy between Barcelona and Madrid will drag on for years, bringing along the symbolic meaning of how Europe is changing.

There is a funny word pun that Catalans use to remark their sense of belonging to their own land. In Catalan, you just need to move a single letter to transform the sentence I live in Catalonia, Visc a Catalunya into the catch Long live Catalonia, Visca Catalunya. The only personal comment I can add is that I am overjoyed to have the possibility to give my tiny contribution to such a thrilling scientific environment. And in any case, and with any political scenario, I will keep trying to do my best as researcher and citizen to keep Science growing on this side of the Mediterranean. Because whether Spain or not, jo visc a Catalunya, visca Catalunya.

Organising the European #PlantScience Retreat 2016 in Barcelona.

There is no better way to come back to my blog writing than by announcing a couple of novelties. As someone may remember,at the beginning of January I joined the Centre for Research in Agricultural Genomics (CRAG) in Barcelona as PhD student. Along with other PhDs at the CRAG, I am volunteering for the organisation of the 2016 edition of the European Plant Science Retreat, that will be held here at the CRAG at the beginning of next january.

The European Plant Science Retreat (EPSR) is an international scientific congress organized each year by a team of local PhD candidates. The idea came in 2007 when PhD candidates from three European research schools in Plant Science (EPS in The Netherlands, IMPRS in Germany, and SDV in France) initiated an international collaboration to improve research, training and education of plant science PhD candidates in Europe. Yearly since 2008 this network organizes a congress “by and for” PhD candidates in the different associated institutes, which have highly related and complementary thematic.

This year, the EPSR will count its 8th edition, and after having been successfully placed in Netherlands, Germany, Belgium, France and UK, this is gonna be the first meeting in the Mediterranean, and there is no better context than the ultra- vivid and prolific scientific environment of Barcelona.

We are now working on any aspect of the organisation, from the fundraising to the selection and invitation of the speakers, in a very challenging, but still instructive activity that we are putting side by side with our ordinary PhD bustle.

As for now, I can share with you the link of the provisional epsr website, that will redirect you on the active profiles on the main social networks. Updates will come very soon and I will return on this from time to time on atcgeek too.

I told you that I had a couple of novelties. Well, the second one it’s more about me. My first paper has been accepted and it is next to be published online. With a bit of patience I will be able to tell you how, some time ago, in Rome, we used to evaluate how good exercise is in a clinical picture of cancer cachexia.

Snapshot of a day like any other.

Wake up very early, of course sleepy, and stoned as fuck. The website has to be finished before noon, next congress brochure has to be sent even earlier. Fingers flowing fast on the keyboard, images, text, typo, adjustments. Why the fuck is the department mail not working? It’s time to collect your stuff already, destination university. Bus is not coming, metro is not coming. Metro is now coming, but is full, hot and smelly. Now I remember why I was so keen to leave this city. Come across a guy from your hood. He’s telling about his awful job at labor union. Now I remember why I was so keen to leave this country.

One-hour briefing with the head of Neurobiology to discuss the website. Lot of ideas, no time to realise them. Crossing the Sapienza campus, overwhelmed by memories. Meet some friends, call some other friends. See you in a few hours. And then straight to San Lorenzo Biochemistry labs to hail your master thesis supervisor. He looks older. Then wait for your friends, write down a couple of lines in a university library. Silence, anyone is studying here. Very pretty young girl around me. Actually anyone looks very young here. I look older. Fuck you everyone.

I am now sitting on a bench, faculty of Psicology. A police helicopter is smashing my brain and tearing apart what is left of my mental health. They are controlling a protest from above. This damn city is ruled by mafia and these retards spend thousands Euros to chase protesters. But there is nothing really strange about my day today. You know that you are a PhD student if you spend the most of your days trying to work ambitious projects in a very hostile environment. And during your holidays.

Getting back to blog.

Dear Fabio, welcome to your PhD. An this means welcome to whole genome analyses, cryptic pipelines, hundreds of python code lines, thousands of documentation pages. And Plant Biology. Yeah, Fabio. Welcome to all this. What? Did you believe that some time for blogging could be spared during your PhD? Well, you was not that wrong. But not right away.

I start this short blog post with this pretty outspoken message the Universe sent me in the latest months. The few readers I rallied during a little more than one year of blogging, may have noticed that my update rate has dramatically decreased.

Starting a PhD is never easy, and I must confess that my introduction to the lab has been pretty though, and I had to spend my big efforts to link up with this new situation. Of course, this little blog bone the brunt. Luckily, I have managed to find my way in my PhD project and the very first results are coming out.

From now on, I will have more time to share my thoughts here as I used to do some months ago. Let me just thank you for the interest in this silly diary once again.