UBERISATION of SCIENCE a Euroscientist Special Issue – April 2016

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UBERISATION OF SCIENCE A EuroScientist Special Issue – April 2016

Table of Content

Introduction ...... 2 Welcome to this Special Issue of EuroScientist on: Uberisation of Science! ...... 2 Editorial ...... 3 One cultural shift away, towards fairer science ...... 3 A changing world ...... 4 Are the disruptions of uberisation a bane or boon for science? ...... 5 From Uber to OpenStreetCab: how data shifts the power back to users ...... 8 Birju Pandya interview: choosing sustainable values to drive research ...... 11 Performing research differently ...... 13 Matters founder Lawrence Rajendran: the Lego approach to scientific publishing ...... 13 When privacy-bound research pays for open science ...... 15 Biological mechanisms discovery by globally-distributed research force ...... 17

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Introduction

Welcome to this Special Issue of EuroScientist on: Uberisation of Science!

Welcome to the special issue of EuroScientist focusing on uberisation of science.

Much has been debated about the impact of technologies on the research and innovation process. The truth is that these changes signify the beginning of a new era. With an increased reliance on geographically-distributed teams, tomorrow’s researchers are going to be able to reach unprecedented scales of collaborations, not just limited to cooperation between well-funded labs. Researchers from wider afield, including from territories with lower level of research funding, will finally be able to more systematically contribute to the great scientific endeavour of the future.

This issue is not limited to the mere technicalities of working across self-organised, distributed teams. It also looks at how, for such scenario to take place, it is essential that we change our outlook on what we mean by collaborating. This may require examining the values driving our future investigations. Aiming for social stability or environmental sustainability, could become the core values, which increasingly influence where future research focuses.

It is your choice whether you want to be part it. Meanwhile, you are invited to share this content as widely as possible so that we can stimulate the debate on these new ways of progressing science.

The EuroScientist team.

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Editorial

One cultural shift away, towards fairer science By Sabine Louët

With scientists’ greater willingness to share and adequate crediting, technology could foster the widest ever scientific collaboration

Picture the future of science. We would live in a world where those who promote secrecy in research, do it at a cost. The cost of subsidising those who favour sharing knowledge freely. In this dual-pronged model, there is a shift in power away from hierarchy, towards self-organisation.

Putting the onus on scientists to choose whether information is private or not gives power back to individuals. It also creates an opportunity for geographically-distributed teams to contribute to a joint aim from across the world at unprecedented scale. This could mean greater involvement of scientists in the lesser funded laboratories, for example from emerging economies.

What technology is about to achieve, is to bring this sharing culture to the next level, by associating scientists who would never had an opportunity to collaborate before.

However, technology alone does not have the power to make change happen. It just facilitates such a move. This shift in attitude towards the scientific and innovation processes requires scientists to muster all the plasticity that their brain can offer. That’s because it takes a lot of will power to step away from the traditional ways of practising science, and to revisit the notion of research competitivity.

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Competitivity might have driven science in recent years. But it does not foster a spirit of collaboration. The trouble is, to be able to take, you need to be able to give. The ‘giftivism’ movement may bring a welcome evolution to the current research culture. This approach advocates giving to others, through radical generous acts, as a means of changing the relationship between people. And, ultimately, it harbours the noble aim to alter the values driving change–away from greed and secrecy. This movement is partly based on the concept that generosity changes our outlook on life, down to the last neural connections.

Regardless of competitivity, one could argue that giftivism has, to an extent, always been part of the scientific culture. Exchange of ideas and perspectives between research collaborators–which involves sharing findings and giving one’s time to the mutually commenting of others’ results or validating other people’s work by taking the time to reproduce it–are just many of the routine aspects of doing research. However, the new piece of the jigsaw is the sheer scale of connectivity between scientists. This opens the door to unprecedented scale of collaboration, which will require more good will than competition.

For this to work, we need a stimulus. One solution is to evolve the credit and reward systems so that it recognises the minutest contributions to the debates, which constitute the essence of scientific progress — be it via nanopublications, blogs or tweets. The formula has yet to be further refined. Let’s hope that it is possible to make most of the new opportunities in a way that provides adequate reward to scientists showing a positive attitude without forcing them into precarity.

Sabine Louët EuroScientist Editor

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A changing world

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Are the disruptions of uberisation a bane or boon for science?

By Fiona Dunlevy Can the scientific endeavour become sustainable as it becomes reliant on distributed teams?

Uberisation is the latest buzzword to describe the disruption of industries by slick digital platforms connecting workers with specific tasks or services. So where does science stand in the brave new uberised world? For every characteristic of uberisation, there is a parallel in the world of research. This raises the question of whether research uberised before Uber even existed? In this article, EuroScientist, looks into whether science was ahead of its time and explores what we can expect in the future.

Precarity on the rise

Industries have been uberised one after another. For example, AirBnB competes against hotels, crowdfunding platforms complement traditional finance tools and an army of specialist workers land computer-based tasks via the likes of Upwork. There are two sides to the on-demand uberisation model. The agile environment fosters innovation and better value as well as a more streamlined user experience. On the flip side, uberisation is pretty dismal regarding workers’ rights and job security.

A worker in the uberised world is the ultimate multi-tasker, cobbling together multiple income streams to keep their portfolio career afloat. Often, they never quite know where their next paycheck is coming from. Labour becoming more casual and job precarity increasing is nothing new, according to Ruth Müller, assistant professor for science & technology policy at the Technical University of Munich, Germany. “The gradual restructuring of labour conditions has been going on for a few decades now,” she says.

Research does not escape this trend. It is being revolutionised by digitally-enabled big data and platforms. “A problem for the researcher is mastering and accessing these new tools,” says Yann Bonnet, secretary general of the Digital Council of France (CNNum), and co-author of a recent report called “Digital work: new trajectories”, examining the impact of digitalisation for workers. As far as permanent salaried work goes, “the age of certainty is over,” says Judith Herzog, CNNum member and report co-author, “the important thing is that people are secure in in their transition, that they have access to appropriate training.”

Increased competitivity

The shift to competitive funding in recent decades has exposed researchers to new forms of precarity. This competition has shifted the goal posts for normal work conditions. “Researchers who work a standard 40 hour week lose out in a culture that normalises overwork,” says Müller, explaining that in this pressure, “rights are implicitly taken away.”

Competing for research grants like Uber drivers compete for jobs has an impact beyond precarity. A less discussed consequence is the rise of risk-free research, says Müller. “The more insecure the working conditions are, the more researchers choose secure, somewhat predictable projects,” adds Müller. She adds: “contracts limited to two or three years exclude certain questions that need longer time frames. This problem is barely recognised in science policy at the moment.” Read this post online: http://www.euroscientist.com/science-uberisation/

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Other experts concur. “Researchers have to follow the money,” says Lidia Borrell-Damian, research and innovation director at the European Universities Association, in Brussels, Belgium. She adds: “the critical issue is that researchers in the labs are not in charge of the research strategy. They have very little leverage.” She agrees that “blue skies research must be better funded in future ; this is what gives the competitive edge.”

Publishing and rewards

Another aspect of scientific life that is changing is how researchers communicate their findings. Scientific publishing is undergoing major disruption, facilitated by a myriad of online platforms. Researchers can now bypass paywalls by sharing articles on ResearchGate and Academia.edu, while anonymously reviewing new papers on PubPeer. According to Borrell-Damian, the rise of these platforms is “having an effect on how research and the careers of researchers are being assessed, with huge consequences ahead.”

This shift in the reward system of science and the resulting pressure on young precarious researchers risks “breeding a generational conflict” with their older, comfortably salaried research bosses, according to sociologist Alan Irwin, professor of science and technology studies at Copenhagen Business School, Denmark.

Already some suggest changing the reward system itself by giving credit to the most elementary contribution to research, as the recently created Matters journal does. Others go one step further by recording everything down to each database query and comments contributing to furthering the scientific debate, as a means to later crediting scientists adequately for their contribution.

Evolving science practice

Research activity can, however, in principle benefit from uberisation. Science is increasingly dependent on collaboration, and outsourcing specialised tasks is an integral part of the process. For example, Science Exchange matches clients outsourcing experiments with service-providing labs through a slick online platform. “We took the idea of what Uber had done to transportation and applied it to contract research organisations (CROs), core facilities and other scientists,” explains Dan Knox, co-founder and chief operating officer at Science Exchange, Paolo Alto, California, USA.

Crowdsourcing external expertise is not new. Innocentive, Waltham, USA has been crowdsourcing solutions to challenges set by their clients for 15 years. They were the foreguard of the uberisation trend in science. Innocentive deals in big ideas and solutions, giving cash prizes to winning tenders. Science Exchange, on the other hand, brokers the outsourcing of laboratory experiments. “Scientific collaboration is as old as science, ” says Knox, “a platform like [ours] that makes it massively more convenient could have a big impact on the [research-based] industry.”

Path to sustainability?

Uberisation brings some further interesting advantages. Allowing labs to complement their funding by partly earning their own money could be the key to survival for many research groups, according to Gilles Mirambeau, an editorial adviser to EuroScientist, who is also professor of molecular biology at UPMC Sorbonne Universités, Paris, France. “The high stakes in labs today is maintaining know-how and personnel,” says Mirambeau. He explains that lack of funding for technicians means that expertise leaves the lab along with the PhD student or postdoc who spent years perfecting the technique.

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Expertise could be maintained, if commercialised. “In the life sciences there a growing tendency for small spin-offs to look for experimental services from small academic groups for a fee,” says Mirambeau, “this should give research groups a means of survival.” Borrell-Damian from the EUA is open to this approach but warns: “these kinds of services can contribute to costs but cannot replace investment in science.” In a further warning, Irwin says that labs selling laboratory services risk “losing the ethos of science.”

Breaking monopolies

Uberisation is also about ordinary people holding the power to collaborate and break monopolies, according to Remy Oudghiri, sociologist at Sociovision, in Paris, France. For example, crowdfunding of sciencecould allow “ordinary people to give money to causes that make sense to them.”

Some scientists has thus been able to raise limited research funding. That’s the case of Angelica Menchaca, a PhD student in bat evolution and ecology at the University of Bristol, UK. She successfully crowdfunded her research to the tune of €6,200 ($7,000), using the platform Experiment.com. As a Mexican student studying in the UK, Menchaca receives a stipend for living expenses but no money for the research itself. “I used the money for field trips and DNA analysis. It funded the first chapter of my thesis,” says Menchaca, “You have to create your own opportunities to succeed in science.”

The solution, not the problem

Academia has traditionally been a place where researchers were insulated from money worries. But those days are long gone. And every little revenue stream could help researchers hold their heads above water and keep research groups intact. According to Oudghiri, we must ask “how science can use uberisation to move forward.” Clearly, “uberisation is one radical solution and the opposite to [employing] civil servants and full stability,” says Mirambeau. The challenge now is to further leverage uberisation for the good of science and scientists; keeping the best bits while sensibly jettisoning the bad.

Fiona Dunlevy

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A changing world

From Uber to OpenStreetCab: how data shifts the power back to users By Anastasios Noulas Greater transparency and value for money needed in tech-disrupted industries Call it as you like. A car sharing, car hiring or simply a taxi service. There is no difference on the ground. Uber’s main competitors are taxi and minicab companies in hundreds of cities worldwide. Over the past couple of years, the California-based company has grown to serve a billion journeys in 2015, with tens of thousands of vehicles crawling the globe’s biggest cities every moment. Every kilometer driven in an Uber taxi adds an extra little piece to an ever growing market share in an industry that is worth hundreds of billions. But is there a way for taxi customers to get the fairest deal as prices are no longer static? And can policy makers get greater value from publicly available data to inform their decisions?

Technology answer to disruption

There are almost a thousand minicab operators in a city like London. Meanwhile, the galloping urbanisation process is expected to lead to more than 60% of the earth’s population living in cities by 2030. In addition, global mobility looks unstoppable. Therefore, it does not come as a surprise that disruptions in urban transport would also spark controversy.

As new technologies emerge to transform traditionally operating industries, there are changes in norms. The most controversial in the Uber case has been the introduction of a volatile pricing landscape for taxi journeys: Uber’s “surge pricing” experiment. It varies journey prices in real time in accordance to the service’s perceived balance between passenger demand and driver supply. Passengers and drivers alike now find themselves in an entirely new marketplace. Read this post online: http://www.euroscientist.com/science-uberisation/

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In this marketplace, the cost of a taxi journey is not as predictable as previously. Worse, the control over price is in Uber’s hands. New technologies like those developed by Uber are able to disrupt its market. However, alternative technologies can also provide innovative solutions to circumvent the challenges associated with this disrupted market.

Power back to consumers

Knowledge is power, Sir Francis Bacon once said. In the 21st century, the new proxy to power is data. No better examples are state-operated large scale surveillance programmes like the one orchestrated by the National Security Agency in the USA. Other examples range from the organised corruption, recently revealed by the revelation of the Panama Papers, to the establishment of monopolies by Google for online search, Amazon for online retail and Facebook for online social interactions.

To counter these emerging trends, the disclosure of information based on the analysis of data has been the simplest, yet most effective, mean of not maintaining a fair society in economic and political terms, during periods of accelerated change.

Guided by this principle, we have built a technology solution to introduce transparency in taxi fares and help give power back to customers. This is how we have developed OpenStreetCab. This app is the result of a collaboration between three European Universities–namely Cambridge and Lancaster, in the UK, and Namur, in Belgium. It aims to equip passengers with knowledge of the different prices available for different taxi services, in real time.

Launched in New York City, USA, in March 2015 and more recently in London, UK, OpenStreetCab, has been enthusiastically received by thousands of mobile users, It also has enjoyed the endorsement of taxi drivers and technology gurus alike.

Data-driven knowledge

The concept of OpenStreetCab is simple. Users submit a query with information on their intended taxi pick up and drop off locations. The app provides almost instantly estimates of the costs incurred by major providers for their journey. It is powered by the lawful release of open datasets that describe taxi mobility. Thus, OpenStreetCab’s mission is to understand the new complexities emerging in urban transport. It has been designed to empower urban travellers with the knowledge required for making informed choices, as they navigate the city.

The millions of taxi professionals and minicab companies worldwide can also expect benefit from OpenStreetCab. It has the potential to provide the traditional taxi ecosystem with the tools to face the competition by Uber by giving them transport intelligence. It thus enables them to remain competitive in the face of the Uber behemoth. As Uber no longer has the near monopoly over data intelligence for transport, much like Google has done for online search over the past two decades.

A first step in this direction, starts with the introduction of minicab operators in the app’s search results. We also aim to keep the community of small transport players strong by providing intelligence solutions supporting their operations. We are planning to offer services to help them optimally deploy their drivers throughout the city, to help with quicker pick-ups for example. We also plan to offer better methods to facilitate communication between local cab companies and their customer base.

Our vision is that OpenStreetCab’s services will only remain relevant in the long term, if there is a diverse global market of intelligent taxi providers.

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Customer value from data

OpenStreetCab’s work can also be placed in a broader context. Services whose concept relies on open data have been blossoming across multiple economic sectors. In the sphere of the sharing economy, the presence of Inside Airbnb has shed a new light regarding the reality of those involved in providing hospitality via the service operator. The result is an eye opener. One of the myths this data helps debunk is that AirBnB is for hosts–which only occasionally rent the homes in which they live–as often rentals are run like a business.

When it comes to public transport, there has been a plethora of cases where open data sets have provided unprecedented insights into how city dwellers move. More importantly, these datasets also open the door to informing how transport services can be optimised.

Despite these notable efforts, citizens, policy makers and governments need to keep advocating for more data openness. They also need to continue endorsing the existing efforts seeking to harvest value from data. This will help our transition towards a world where technology is dominant while helping services to remain competitive and fair.

Anastasios Noulas

Anastasios is lecturer at the Data Science Institute at Lancaster University, UK, and OpenStreetCab co-founder.

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A changing world

Birju Pandya interview: choosing sustainable values to drive research Interview by Sabine Louët Moving away from a transaction-based towards a trust-based approach to social project financing Birju Pandya is a specialist of the gift-economy. In this gift-based approach, what is of value is higher purposes, such as progress in social or environmental protection, not merely financial gains. Pandya defines gift culture as follows: “it’s the engagement of people between one another in an unconditional way, moving away from a transaction- based approach relationship to a trust-based approach”. For him, it is offering no strings attached. “I have been playing around with ways of incorporating that into my own life and offering it to groups that I work with for about ten years now”, he adds.

Specifically, he specialises in introducing the gift culture to the world of finance. Prior to this, Pandya was a consultant with McKinsey & Company. He is based in Berkley, California, USA. Until now, he has been involved with social and ethical financing organisations. Among others, he has been working with Armonia— a private equity firm specialising in ‘regenerative investing’ using nature-based solutions—RSF Social Finance—a social fund focusing on food & agriculture, education & the arts, and ecological stewardship—ServiceSpace—a non-profit, which provides an umbrella for generosity-driven projects—and Nessel Development—which develops housing that is beyond sustainable. He has noticed that there are already organisations in Europe following this approach, including Awakin, in London, UK and the Lunt Foundation, in Brussels, Belgium.

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values, based on long-term relationships. This leads to what he describes as inner transformation in terms of redefining what values support the well-being of all. This in turn, may shift the way we live and interact with each other.

Gift culture in academia

Even if academia is different from finance, Pandya thinks that “the impetus behind much of the original trust of academia was in effect information being free.” However, he admits that he as seen more recently “how the nature of research is starting to skew and bend to the will of the capitalist paradigm, that we are part of, and so, so much of the research happening seems to be driven by monetisation.”

In research and innovation, he believes, the easiest way to success is not necessarily to encourage technological progress but also inner progress—i.e. defining the values to drive progress before starting to research or innovate. . For him, organisations and people across the world may find benefit in “seeing the world with new eyes.” He further explains: “there is a growing movement of people who are living a life that is more based on voluntary simplicity now, inviting in ways of living that are more connected to earth, more connected to their community members, more connected to their own inner nature”. “I find that there are tremendous opportunities for bringing non- transactional approach to all of these things”, he adds.

Resistance against rewiring

Pandya explains that he sees in gift culture as “the invitation for a person to rewire [their] own mind,” both metaphorically and biologically. If we want to live in a sustainable society, he believes, we first need to start rewiring ourselves to redefine what values drive us. Rewiring one’s brain without immediate survival reason is difficult. The same applies to changing the way organisations are run. “I see it in myself and, certainly, I’m not surprised when I see it in culture and in systems”, he says.

By starting to change perspective, the benefits become obvious. “What I have discovered is that there are many sources of capital that I was not tracking previously that I am now starting to grasp, as my own neurology starts to shift.” While there may be resistance, for him, the ongoing results are well worth the effort.

Video editing and cover text Charline Pierre and Lena Kim.

Interview by Sabine Louët, EuroScientist editor.

Photo credit: Birju Pandya

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Performing research differently

Matters founder Lawrence Rajendran: the Lego approach to scientific publishing Interview by Sabine Louët

Research findings should be published as a series of individual observations, linked together Lawrence Rajendran, known as Lawrie, featured in the world’s top 100 scientists in 2009, recipient of many awards and honours. As an expert in the cell biology of Alzheimer’s disease, he is also one of the founding members of the International Society for Extracellular Vesicles (ISEV). He is currently Velux Stiftung professor for systems and cell biology of neurodegeneration, at the University of Zurich in Switzerland and the CEO of Matters.

Science publishing without story-telling

Rajendran is both interested in science and science communication. With the creation of Matters, he wants to change the way we communicate science. His goal is to increase the crowdsourced dimension in science by encouraging teamwork. He has identified constraints associated with the storytelling approach in current scientific papers. Instead, he believes scientists should be able to submit all kinds of observations to help link orphan, negative, confirmatory and contradictory data together. He is in favour of triple-blind peer review to ensure that the observation is scientifically solid.

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“I came up with this idea something like seven years ago” says Rajendran. He started to wonder about irreproducibility of science, incentives associated with scientists publishing on high-rated journals to help their carriers and the need for stories to publish observations. “Every piece of the data that you publish needs to fit into a coherent story. And this is where I challenge this notion: why do we have to tell stories?” he asks.

Sharing observations as a Lego Puzzle

For him, the solution is to come up with a system that allows scientists to publish single observations. He explains that there is no reason to eliminate negative data, for example. This is why he created Matters, “A place where I can say “look, I think A leads to B, this is my hypothesis, and when I experiment it, I find a positive result, I should be able to publish it. I find a negative result, I should be able to publish it. And then I can come back, I shouldn’t be asked extra additional things,” he explains before adding: that it would remove the risks that researchers are dishonest in the way they report their findings.

Opening up connections between findings

The Matters platform then makes it possible to connect individual observations. “You can say that it is a single data for example. Now, once you published this, someone else who is interested in this can add their observations and say: “you know what, I also find it in my system’,” explains Rajendran. He adds that Matters works with node and edges that connect.

Anybody can provide information, whether it’s a confirmatory observation or a contrary result. “Once you do it like a Lego puzzle, you also allow other researchers to extend it with their own observations.” he says. Because the publishing platforms are now dedicated to large stories and renowned scientists, he says, “much of the data that we have, could be the piece of the puzzle of somebody else. But we have these interesting observations we never ever publish.”

For him, “the complexity will be reflected in the way that people attach their observations.” This will not only make it possible to open up results across scientific disciplines but also to wider audiences. He concludes: “It’s my duty and responsibility to tell the public what we find.”

Interview by Sabine Louët, EuroScientist Editor

Video editing and cover text Charline Pierre and Lena Kim.

Photo credit: Lawrence Rajendran

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Performing research differently

When privacy-bound research pays for open science

By Barend Mons A new open science business model charges those who want to keep information private to subsidise those who share it

In theory, open science should involve students and scholars from developing regions too. Yet, there is still an imbalance between developed and developing countries, as research is not yet truly open. Colleagues in developing countries are often relegated to the position of second-tier scientists, partly living from intellectual and financial charity from developed countries.

In many cases, they are penalised by sub-optimal Internet access and insufficient research funds to subscribe to pay- walled scientific literature. Meanwhile, the advent of open access journals only partly solves their problem. They now need exceptions to publication fees, just like HINARI, a joint initiative between WHO and publishers, is an exception to reading fees.

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To support open science, it is time to radically change the business models for scholarly communication, way beyond just open access articles. The idea is to draw the line very differently, following a new logic. Only those who wish to keep research discoveries private, pay. Others have free authorship and copyright if they are prepared to share their knowledge without restrictions.

This logic would introduce a bias towards greater and faster sharing of scientific discovery and give a boost to open science. And more importantly, it could open the door to millions of scientists from developing regions to take part to future advances in research. Opening science further

In this scenario, researchers in developing countries are treated exactly the same way as colleagues in the most advanced scientific power regions. So how would this work? First, scientists publish their elementary findings or concepts in FAIR format, for instance as nanopublications. Following these principles, not only data become citable, but individual assertions, such as annotations, do as well. These are all nano-contributions to open science. That is to say, if the person making these assertions makes them open.

This approach can be facilitated if scientists adopt the unique researcher identifier scheme, defined by ORCID. Indeed, any of their online interactions can be recorded via their ORCID. Thus, making it possible for them to be credited–and in time rewarded–for their contribution to open science.

Second, we redefine what research objects actually are. We recognise that in open science all results of scientific activity are again potential sources of knowledge discovery. This includes any form of querying that is recorded, tweeting, blogging, data publication and ultimately narrative communication from person to person. Once these principles are established, all scientific activity that is made available in the public domain–i.e. fully open for anyone to re-use–should be free.

Sharing versus closing

However, we all know free does not really exist. It is a euphemism for ‘others paid for it.’ So who pays for it in this model? The people having ownership of new knowledge, but consciously choosing to not share it. Obviously, not sharing data, information or knowledge–at least temporarily–can be justified by valid underlying reasons. For example, to preserve the privacy of patients, protect national security or guarantee a commercial advantage.

These people, institutions or companies deriving knowledge, who do not share, could conceivably pay a new kind of ‘tax’ to support the furthering of open science. This tax is justified by the fact that also ‘private knowledge’ is partly built on public knowledge available for sharing that we have collectively paid for.

To illustrate how it could work in practice, see our case study, focusing on disease mechanism discovery. This is not very different from dual licensing in open source software. In such case, if users do not want to share their additional code, because it is to be re-used within a proprietary software product, they have to pay.

A great opportunity to make great strides in this direction is offered by the recently announced European Open Science Cloud, a virtual environment to store, share and re-use their data across disciplines and borders.

To me, the proposed approach would be more just a model, than the current open access model, where people publishing in open access need to pay. The new model would request that people keeping things private collectively subsidise the open realm of our knowledge creation. This logic calls for the development of closed as well as open services, business models and partnerships in science.

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Barend Mons Barend is professor in bio-semantics at the department of human genetics at the Leiden University Medical Centre, The Netherlands, and and co-head of the Dutch Techcentre for Life Sciences. Disclaimer: This is a vision for the future: all elements to make this happen are there, but connecting them will still be a major effort, but worthwhile. This is also the personal opinion of Barend Mons as a scientist and cannot be quoted as the formal opinion of the High Level Expert Group for the European Open science Cloud, of which I am a member.

Photo credit: John Vetterli (CC BY-SA 2.0)

Performing research differently

Biological mechanisms discovery by globally-distributed research force By Barend Mons

Case study: a new open science model applied to disease pathways discovery

A new open science approach could soon change the way we think about research. It is based on charging those keeping discoveries private to subsidise those who publicly share their findings. Here, we examine how this new way of handling scientific findings could work in practice. To illustrate this approach, we take the example of discovery of biological mechanisms underlying health and disease.

Our research with the Biosemantics Group Leiden performed in close collaboration with the Dutch bioinformatics start-up EURETOS, based in Delft, has led to the development of the privately owned EURETOS Knowledge Platform (EKP). This is a very valuable collection, or graph, of 60 million unique so-called Cardinal Assertions, derived from over 80 data sources as of January 2016. The graph features relations between two concepts—dubbed triples (including ‘concept A’, ‘relation’ and ‘concept B’)— relevant for health and diseases, such as genes, proteins, chemicals, diseases, tissues and physiological process.

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By removing all redundancy from the triples, the data engineers of EURETOS have narrowed them down to Cardinal Assertions. What makes them valuable is that they are presented with their complete provenance—that is, the reference to the evidence from the scientific literature for each assertion. In turn, the linked provenance makes it possible to for humans to judge the validity of these Cardinal Assertions.

Privately versus publicly held findings

Using the EKP in a safe, fire-walled environment obviously costs money. This proprietary resource is available can be accessed subject to paying a license fee. Private clients, such as pharmaceutical companies and clinicians, would typically use it. They can safely query the database and avail of the convenience of the in-built workflows system to explore and validate or invalidate the Cardinal Assertions.

How can such resource be relevant to further open science?

A copy of the entire EKP of Cardinal Assertions is also available in an open access version for academics, provisionally called DKP. This version is accessible via a registration to enable tracking users via their ORCID number as a means to reward their contributions to open science. In fact, DKP has been established as a public-private partnership between EURETOS, and the data analysis service provided by the Dutch Techcentre for Life Sciences (DTL), based in Utrecht. By being part of this partnership, EURETOS thus supports the open science credo by providing the DKP, available free of licensee fee to DTL users.

Of course there should be mutual benefit. The academic community is expected to adopt and support the EURETOS approach, by publishing every query, annotation and addition in open access. In turn, the company, like everyone else, can use these public findings to improve their content, workflows and general service offering. Obviously, this is subject to annotators and contributors making their contribution available in open access. If they decide they want any kind of restrictions, they will have to pay and revert back to using the commercial EKP version.

New open science scenario

This is where the opportunity for developing and developed country scientists alike could arise.

Let’s take the example of Jeanine, a clinical geneticists at a large academic centre. She has a patient with Intellectual Disability (ID) and performs genome sequencing. All genes known to be associated with ID appear intact. But she notices in the sequenced genome of one of her patients that a gene called DRAXIN shows a major deletion, which may mean that it is affected in its expression and makes the wrong protein or none.

The trouble is that DRAXIN and ID do not have any direct co-occurrence in the current scientific literature. Nor in the 80+ databases encompassed in the EKP. Using classical literature search, there is no connection or obvious indirect relations. However, when looking at possible indirect associations between the gene and the disease, the EKP predicts a reasonable chance that DRAXIN could be playing a role in brain development and mental retardation.Indeed, DRAXIN appears to be strongly associated with concepts, such as forebrain development, axon chemotaxis and neutron migration. These are all concepts that can be easily connected to mental retardation and intellectual disability.

The prediction power stems from the 60 million connections stored in the database, as opposed to 8 millions connections documented by the National Center for Biotechnology Information (NCBI) database, which is not from openly available life science literature databases, such as PubMed.

Further, in the NCBI database, the abstract of the corresponding research paper does not contain the literature supporting this connection while the full text is behind a paywall. This is not a problem for jeanine because she is lucky

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enough to be at and institute with an expensive subscription that enables here to retrieve the full text. Herein lies the rub for open science. The very fact that Jeanine–whose activity is tracked via her ORCID number and connected to her institution–searched the EKP for the new combination of DRAXIN and Intellectual disability is a piece of information of great value.

An identical query related to a potential relation between DRAXIN and ID, could potentially be done by many independent clinical geneticists around the world.

On the record

This repeated number of searches is recorded by the system and could thus produce a signal to be investigated further by the wider scientific community. And the signal could easily picked up first by a scientist from a developing country in DKP. The nanopublication of Jeanines’s first query is a way of documenting her contribution to the association via her own ORCID number and her institution. Meanwhile, there is also a time stamp associated with the query, attesting that she could be the first to think about such association

If Jeanine decides that she is quite interested in these relations, she can then automatically request, from her EKP account, a human readable article explaining the rationalisation of all indirect connections between DRAXIN and ID. Typically, these connections arise via other genes, proteins metabolites, drugs, and physiological processes, such as axon guidance and forebrain development. This advanced workflow, for instance, suggests that DRAXIN is involved in neurogenesis. However, the computer generated article does only give a very low chance (13%) to the prediction that DRAXIN may be directly involved in intellectual disability. These many indirect connections include 8 associated sub- diseases, such as Down syndrome, Backwith-Wiedemann syndrome and X-linked mental retardation.

Based on this relatively vague connection, she decides to publish the article via her chosen open access channel for anyone to read, comment on or claim. This also means that all other clinical geneticists or biologists working on DRAXIN for instance posting the same query will now see the published article and may become reviewers.

As long as this all remains in full open access, it contributes to open science and should ideally be free –namely subsidised by restricted science. In this scenario, Jeanine’s goal is not to increase her impact factor but to help patients. Therefore, she does not have any desire to keep this article to herself, as sharing may help quicker discovery of more genetic causes for ID.

Like Jeanine, any researcher from across the globe, who gets really interested in this link and its rationale outlined in the article can claim the EKP/DKP computer generated association as their research hypothesis. They could then decide to do more research on it.

Should they have access to a wet laboratory, they could for example perform experiments where the DRAXIN gene is prevented from being expressed in zebrafish embryos and find that they do not develop a brain. This mean that they have contributed additional evidence to support the hypothetic link between DRAXIN and ID.

Then, they can start writing a standard article about this hypothetical relationship, with the option to include the results of their labora-tory experiments. Even if scientists do not hace ready access to wet lab facilities of expensive equipment, they could be the first claimant of the hypothesis and seek collaboration to prove it.

Should Jeanine opt retrospectively to become one of the authors of a formal publication, she is expected to contribute to the publication fee–akin to an Open science Tax–or an open access article publication fee.

Credit for contribution

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Another way that developing country scientists could contribute is in annotating the database. Any triple from the EKP/DKP platform is available to be annotated by any researcher identified through their ORCID number. Annotations include both critics on existing assertions and negative results. We will soon be ready to invite millions of students and experts from around the world to annotate and improve triples with proper predicates, nuances and comments. Again if they decide to keep their annotations to themselves, they would have to pay and/or have to use the fee-based EKP.

Any open annotation using open tools like the Open RDF Knowledge Annotator (ORKA) would also be credited as one of the actions contributing to further opening science. If two concepts like a drug and a disease are co-occurring in a text and are new to EKP/DKP, according to specialised text mining tools such as Utopia Docs, they can be served up as an RDF triple in ORKA.

Students can make a name for themselves as annotators. Once more, internal annotations–keeping knowledge about certain triples private–should be paid for. We could imagine business models where annotators contributing a given number of open annotations, build up credits that allow them to do a given number of private annotations; again a model that does not put colleagues in developing countries at a disadvantage.

New business model

For this solution to work, all kinds of paid services could subsidise the free services associated with publication of findings made available for sharing and further testing. For example, users have the option to do micro-payments to preserve the confidentiality of queries in DKP. They can also choose to buy private subscriptions to EKP workflows from EURETOS. There might be many other ways of generating additional revenues.

In essence, all actions that contribute to open science in this system should be free or rewarded accordingly, potentially financially in some cases. For example, any action can be automatically recorded on its authors’ CV– particularly via systems like VIVO, which recognise the unique research identification number ORCID. Thus, sharing is subsidised by not sharing; in many cases for good reasons.

I invite all scientists concerned to get together and make this happen sooner rather than later.

Barend Mons

Barend is professor in bio-semantics at the department of human genetics at the Leiden University Medical Centre (LUMC)

Disclaimer: This is my personal opinion as a scientist and cannot be quoted as the formal opinion of the High Level Expert Group for the European Open science Cloud, of which I am a member, nor attributed to LUMC, Dutch Techcentre for Life Sciences (DTL) or EURETOS. I am an independent scientific advisor to EURETOS without any financial arrangements or other forms of participation in this initiative.

Photo credit: Sabrina Campagna (CC BY-NC-ND 2.0)

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