Tag Archives: openscience

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 City, the Rainbow, the Science. And Mafia. A story from Rome.

An half- circle, shiny and huge double rainbow towers the cloudy sky above Rome, in an early December afternoon. A truly heart-breaking view, that lovers and photographers have surely enjoyed. And the landscape of the Eternal City fits wonderfully with the pastel colours of this autumn sky. But the rainbow is not the only dome covering the City, as the clouds you may see in the sky are not the only ones darkening its sky. There is another dome, a real cupola that is oppressing anything here, and the clouds we see at the horizon don’t add any poetry to our life. They are dark, and truly scary. During the last days, a disconcerting serie of news updates have shown us a city we couldn’t just imagine. A huge, impressively organised, and deeply rooted criminal organisation has been found controlling the city. Investigators have discovered a disturbing connection between criminality, city authorities and far-right neofascist organisations controlling the city. A couple of days ago, 37 people were arrested, and the former mayor of Rome, the ultra-conservative and ex-fascist Gianni Alemanno, was charged for mafia conspiracy.

I guess that many foreigners won’t be really surprised of this story, and definitely won’t share my disconcert, since the stereotype linking Mafia and Italy is pretty spread around the world. In deed, in Italy we had a different view. The criminal organisations has always been deemed to be established in Southern Italy only, and massive infiltrations in local governments have never been demonstrated to happen northernmost of Naples before. In the last years, many investigations have found Mafia organisations to cross their historical borders, with huge scandals affecting the wealthy, and more “Continental” Northern Italy. More, many proofs indicate a huge presence of mafia gangs all around Europe, along with their strict control of the drug market in Germany and UK. With this Roman scandal, Mafia has been demonstrated to be all but a “Southern Italy thing” only, and its exclusive interlink with Sicily and Naples has now to be considered a stereotype on its turn.

But why am I talking about this, in a Science blog? I have always kept in high consideration the connotations of Science in politics. Having been a Free Knowledge, Open Science and Public Education activist while at the university, I had many opportunities to reflect about the social importance of an open and democratic Science. Among the many analyses I happened to read, during my university political activity, I have found those connecting the city and the cognitive production particularly interesting. In the so-called post-modern age, cognitive production gets a pivotal and leading role in globalised capitalism. The city, with its connections between universities, research centres, companies and individuals, plays a role in cognitive production that is comparable to the one that the Fordist factory plays in industrial production. Science and the city, the city and society, society and Science. A visceral connection, allowing us to appreciate how much research depends on the city politics, and the extent of science social connotations. That is why I take my time to explain the Roman situation, and I am a bit confident that the understanding of how things work here may be fruitful even for those who live outside this wonderful, and disgraced city.

Synergy vs discord: Rome and Barcelona.

During the last two years, I had the opportunity to work in both Barcelona and Helsinki. I have been in Barcelona for a short visiting at the CRG, and attended a training period at the University of Helsinki. If we want to find a model for a good and effective connection between the city and Science production, Barcelona serves as a perfect example of synergy. Three main universities, associated with three neighbouring science parks, in a perfectly integrated bioregion, made up by the connection between universities, research centres and private companies.

In Rome, the global amount of research groups is quite higher than Barcelona. The three main universities are leaded by the Sapienza University, the biggest athenaeum in Europe. More than 15 public research institutes are spread over the city, accounting thousands employees. Differently from Barcelona, the research institutions are poorly interconnected. I am working at the Santa Lucia Institute as a Bioinformatician from September, and I don’t have a global idea on who is working on bioinformatics in Rome, and where. Very often, these institutions are seriously in competition, because of the small founding provided at government level. More, the lack of communication is worsen by the low number of private companies working in biotech in Rome area. Usually, private companies give a big contribution in the establishment of a well-functioning bioregion, because they know they can grow their business thanks to a proper collaboration network. In Italy is very hard to run a company, even just a small startup, because of the overwhelming bureaucracy, and the heavy tax charged applied to small companies.

Whereas institutions should work to ease the communication between research centres, they do about nothing to ease this process, and they seem mostly aimed at doing the contrary, or rather, adding discord where synergy would be needed. That is why, I can fairly affirm that a real “Roman bioregion” doesn’t really exist.

Mobility, city structure and speculation.

You can understand how much mobility is important only by spending a week or two in Rome. In other cities, things like buses and metros may be taken for granted. The capital of Italy, and the biggest city in the European Union in terms of surface, is provided with only two complete metro lines. The third line, the “C Line”, is not complete yet, and its construction is suffering from endless delays. Moreover, the city has grown dramatically in the latest decades. An infamous policy, aimed at favouring speculation, has let the city to grow uncontrollably. The lack of a proper planning scheme, along with a severe lack of public transportation, render the mobility within the city really adventurous. The effects on Science are clear if we consider the location of research centres. Spread mostly in the outskirts, they are very distant one another. I still remember the discomfort of a couple of colleagues in my laboratory who needed to withdraw some mice at the EMBL in Monterotondo. The Santa Lucia Foundation is located in Southern Rome, whereas the EMBL is in the Northern hinterland. This is the route you’d have to do in order to go with public transportation. Of course, they have chosen to go by car. Just 40 minutes for 50 kilometres.

A science park would be needed, well provided with core facilities, in order to not force a PhD student to transport lab materials and animals by car. Actually, this is what they planned when they have built the structure where the Santa Lucia Foundation is hosted. Unfortunately, right after construction the whole area went out of funding, and half building ran into abandon. Far away from European standards.

The effects on society: critical thinking and democracy improvement.

Science has the potential to prevent society from running into racism and corruption. That is why, I believe, it’s so contrasted in my country. Usually, the city authorities tend to promote science disclosure and cultural events. Unfortunately, the general cutoff that affected public services during the last crisis, didn’t spare cultural activities. Differently from other situations I explored, the city authorities make a small effort to promote the outreach of research institutes, and the same institutes are not putting much interest in communicating with the population.

The effects are disruptive. Italian public opinion is prey for any populistic campaigns. The mafia of Rome made a big effort in convincing the people that gipsies were responsible for terrible crimes, while they were exploiting those communities to impropriate of European fundings allocated for ROM communities integration. The most of the people in Rome, ran into racism, without any capability to distinguish from real datas describing phenomena, and the claims of a corrupted press that aims to the spread of xenophobia.

The antagonist, do-it-yourself and hacker environment.

There is one last thing that is crucial in a good Science policy within a city. Far from institutions and public funding, the volunteering in Science spreading and improvement is fundamental. In this, Rome is fervidly active instead. The state of abandon of many buildings, along with the great spread and establishment of antagonist movement, favoured the occupation of many “centri sociali”, independent and radical community centres. Acting as independent organisations devoted to cultural promotion, they often organise conference and courses. The hacker movement has known a great spread from the 90s, with Indymedia activists, autistici.org an independent service provider guaranteeing data privacy, and quite a lot counter-information websites and community radios. I remember when I joined a linux course at the community centre “Strike SPA“. I ended up learning linux bases and appending the principles of hacker culture. I was barely in my 20s, and running back with my mind, that was most likely the moment when I decided to join bioinformatics. Within the universities, collectives organise self-training courses (autoformazione), and linux- mac- and arduino- user groups are present in all the campuses. No exaggeration in saying that this independent and underground cultural activity impresses a significant improvement of the average cultural level of the city. Of course, it is the demonstration that things could be far better in Rome, if we’d manage to get rid of this suffocating cupola of mafia, misgovernment and corruption.

I really don’t want to show up as the typical endlessly-complaining frustrated Italian. I know that I share my part of responsibility with all my countrymen, and that complaints must make way to the commitment, as we are called to put a huge effort in changing our way to stay together.

I’d rather underline a point. The functioning of a good scientific environment depends a lot on how much scientists are able to fruitfully interact, exchange informations, and collaborate. It’s very linked with the cultural fervidity of a society, and the capability of scientists to get people to understand and appreciate their work. This means, in terms of Systems Theory, that the most important thing in science production is the grade of complexity of the academia-city system. And this must be our main and ultimate aim here in Rome: a better City for a better Science, a better Science to make the City better.

I must confess I really enjoyed that rainbow. In some way, it had somewhat of forgiveness, and looked pretty comforting. As the whole universe told us to chill down, because not everything is lost. As the police crosses the city, people gets arrested, and another judicial blood-bath takes place, we are all in front of a choice. We can either fall asleep, once again, with that awful belief that nothing will change, just to indulge, time to time, to our usual and annoying complaints. Or we can take this as a starting point, a new day, where our commitment gets stronger than our difficulties.

Let me conclude this long article with an expression of solidarity and support to our mayor Ignazio Marino, who is fighting this system since the beginning of its mandate. Marino is a Medical Doctor, who had a professorship at the University of Pittsburg, where he performed the first organ transplant in history in an HIV patient, and authored more than 170 papers. He’s now the man who is supposed to drag the City outside this muddle, and he’s now living escorted after the death threats he received. A man of Science. Not by chance.

Protocols.io, the online open repository for lab protocols.

As many others, I have collected my fair amount of profiles on professional and Science social networks. LinkedIn, Academia, ResearchGate. The real limitation all these web sites share, is that they basically provide you a showcase, in which you can expose yourself to sport your achievements, share your professional profile, and show up as cool as you can. I have always felt that proper tools for collaboration and information sharing in Science were lacking on the internet. Social networking for scientists is limited to a mere activity of results communication and discussion, whereas it could be really useful to have platforms to share datas and protocols.

That is why, as I have heard about protocols.io on Twitter, this project caught my attention immediately. Protocols.io is an online community serving as repository for experimental protocols in Life Sciences. A free, central, up-to-date and crowdsourced protocol database for life scientists. The project is promoted an maintained by ZappyLab, an organisation of scientists whose goal is to provide tools for protocols and lab methods sharing.

Registration is open and pretty simple. Differently from other science communities, you don’t need to provide an “institutional mail address”, any address goes, and this is great for undergrads and graduate students that may have not an official mail address. You subscribe with your mail, and that is enough to make your way to a growing list of lab protocols. You can share your own protocols, deciding whether to make them publicly available or privately shared with you colleagues only. You may also enjoy the benefits of having a smartphone, as ZappyLab provides an application for Android and iOS, available on marketplaces.

At this very moment I am exploring this website, trying to figure out how to deal with it, but it seems pretty simple and user-friendly. Of course, the amount of available protocols is not really high, but this depends on the number of subscribers. The more we are, the more we share, the more protocols will be available.

I cheer up to this project as I think it may represent a great contribution. We always make a big talking about “open science”, “reproducibility” and freedom of knowledge. But most of the times, we limit to blame the publishing groups for their policies of copyright, invoking a major openness. But what are we doing to help Science openness? Sharing your protocols is a fairly good contribution in this, and I hope that you will put your attention and give your contribution to this amazing project.