Large-Scale Open Access for Research and Outreach

Paul Ginsparg is being honored as a Champion of Change for the vision he has demonstrated and for his commitment to open science.

In 1991, before the WorldWideWeb, before the general population was even aware of the internet, physicists had already begun to share pre-publication versions of their articles via email.  As a research staff member at Los Alamos National Laboratory, I was concerned that this private sharing unintentionally gave privileged access to more established researchers. To help rectify the situation, I set up a centralized automated repository and alerting system, making cutting-edge full-text articles accessible to anyone with internet access.   For the initial group of high energy theoretical physicists, the system had the immediate positive effect of democratizing the exchange of information within an entire global research community.

By 1993, the advent of the WorldWideWeb suggested ever broader possibilities, with research communication for all fields ported to the new on-line medium.  The arXiv system itself quickly grew from a few hundred submissions per year to many tens of thousands, and moved to the Cornell University Library in 2001. Its growth continued to accelerate, and it now receives close to 100,000 new open access submissions per year (see graphs.) With nearly a million open access articles in the repository, and hundreds of millions of full-text downloads per year, it serves as the primary daily information feed for global communities of researchers in physics, mathematics, computer science, and related fields. Its proof-of-concept served as the prototype for many other modern open access systems that disseminate scientific research results.

When the general public arrived on the internet by the mid 1990's, there emerged intriguing possibilities for engaging beyond the professional research community.  Scientists write articles in order to have them read, hence the more readers the better. Research output, like any public good, becomes more valuable the more it is used.

Twenty years ago, I began discussing with officials at NSF and DOE the possibility of creating open repositories for the articles that result from federally funded research. In 1997, biologists (and by then as well mathematicians and computer scientists) interested in how physicists were sharing on-line information set up a series of discussions which ultimately led to NIH's PubMedCentral repository (on whose initial advisory board I served) and, a decade later, to the NIH mandate to deposit. The OSTP policy memorandum expanding this mandate to other large federal funding agencies, making "the results of federally funded research freely available to the public within one year of publication" is thus welcome progress, and perhaps the time delay can eventually be reduced. arXiv.org already plays an extremely valuable role in giving access to federally-funded research articles to the general public; conventional news sites and blogs link directly to multiple articles, frequently bringing in hundreds of thousands of readers to popularly accessible articles.

My own work has remained focused on making these systems so useful to researchers that they participate spontaneously, and so (like YouTube) no mandate has ever been required. Most recently, in collaboration with computer scientists (at Cornell, Rutgers, and Princeton), I've been implementing a variety of new "big data" datamining tools for the purpose of analyzing usage and information genealogy, using arXiv's unique combination of open access texts and twenty years of longitudinal usage data. Some of the results of this work will go on-line in a new experimental interface later this year, with improved ability to track both long- and short-term trends through the literature, a new recommender system to help users cope with information overload, and new interdisciplinary means of information navigation and discovery. This work should further clarify the benefits to both the research community and the general public of having fully open access research text aggregated and treatable as computable objects.

Continued growth in distributed network databases, new interoperability protocols, machine-readable document standards, and relevant ontologies will build on these components to catalyze more rapid scientific progress, and provide integration of educational resources for the general public.

Paul Ginsparg is a Professor of Physics and Information Science at Cornell University.

Most of the Smartest Bioengineers Work for Someone Else

Drew Endy is being honored as a Champion of Change for the vision he has demonstrated and for his commitment to open science.

In ways we often barely understand, natural organisms, from piping plovers on Long Island to banana slugs among California’s redwoods, reproduce, struggle, or thrive across amazingly diverse environments.  Yet despite this sparse understanding, we already partner with biology to make many necessities.  Foods, medicines, fuels, and materials are increasingly manufactured by domesticated or re-engineered organisms: Insulin for treating diabetes is made with re-engineered microbes, and organic mushrooms grown by natural wood fungi that eat sawdust.  Forty years after its inception, genetic engineering now underlies about two percent of our domestic economy.

Yet, most of what we might make with biology has not been imagined or created.  For example, researchers just figured out how to store archival digital copies of books, including Shakespeare, in chemically synthesized DNA, a molecule so tiny that many millions of books could be stored in mere thimbles.  Meanwhile, much of nature’s biodiversity is being lost or increasingly threatened by growing populations and expanding consumption.  These natural ecosystems are essential for the wellbeing of our environment and are also the source of almost all biotechnology innovations.  We don’t so much engineer biology from scratch as repurpose and refine nature’s existing materials.

Thus, a fundamental challenge confronting everyone, directly or indirectly is to learn to work in better partnership with nature and each other, to make the things we need without destroying ourselves or the environment.  “Open science” in every respect, including sharing of ideas, unfettered access to all research literature and data, and freedom-to-use basic biological materials, is central to making this progress.

In this spirit, we started the BioBricks Foundation (BBF) in 2003 as a public-benefit charity with a long-term mission of helping to advance biotechnology to benefit all people and the planet.  Tom Knight, then at MIT, had already led the way by teaching how free-to-use technical standards could enable radical, global collaboration. Students in Australia could suddenly take a fragment of natural DNA encoding a microscopic protein-based “balloon” that causes cells to float or sink, and refine it into a standard “biobrick” part.  Researchers everywhere could then readily take that BioBrick balloon, and stack it with many other similarly standardized genetic parts to more easily solve innumerable problems. 

Since 2003, the BBF has focused on improving open and free-to-use standards that support biological engineering.  We have leveraged seed funding from the National Science Foundation to create cooperative partnerships between universities and companies to develop high-quality, standard biological parts.  We created a legal tool, the BioBrick Public Agreement (BPA), which allows researchers in academia and industry to easily share free-to-use our standard biological parts.  We are now using the BPA to give away many of the best standardized creations from our labs, including genetic switches and amplifying logic gates, so that others can more quickly solve pressing problems.

As Bill Joy, Co-Founder of Sun Microsystems reportedly observed, “No matter who you are, most of the smartest people work for someone else.” “Joy’s Law” applies to bioengineering in almost every way possible. No matter where you are, most of the smartest biologists work for somebody else.  Thus, most of the biological discoveries you need for a given problem will be housed somewhere else.  Needs and opportunities will exist somewhere else, and the world’s biomanufacturing capacity, distributed across the world’s bread, yogurt, cheese, and brewing facilities, is controlled by someone else. Most of the people who need to use and trust your work won’t ever meet you. In all, tools for sharing will form the foundation of our future bioeconomy. 

Drew Endy is a Bioengineer at Stanford University.

Open Access: The Pathway to Innovation

Jack Andraka is being honored as a Champion of Change for the vision he has demonstrated and for his commitment to open science.

When I was 14 a close family friend, who was like an uncle to me, succumbed to pancreatic cancer.  When the disease hit so close to home, I felt like I needed to know more.  So I went online and started reading through the available information and what I discovered was eye opening.  A big reason for the dismal pancreatic cancer survival rate is that there is no inexpensive, simple way to detect it early.

I was sure there had to be a better way. But as I started to research online (using the teenager’s favorite sources, Google and Wikipedia) I started running into problems. I would find an article I needed, I would click to start reading, and then a new window would pop up informing me that if I wanted the paper, it would cost $35. The first thought that came to mind was, “Who in their right mind would pay $35 for 11 pieces of paper???”

Now I can answer my question as to why anyone would pay $35 for 11 pieces of paper: It’s scientific knowledge.  

Because of the high demand for the newest and best scientific research, the major publications have successfully — yet subtly — commoditized this knowledge.  Publishers are basically discriminating based on whether or not you or your school can afford to access.  This tier-based approach for the dissemination of knowledge — I believe— is incredibly detrimental to the entire field of science.

Scientific research benefits from the open sharing of knowledge. When I was working on a diagnostic test for pancreatic cancer, there was one key paper… but imagine if I didn’t have access to that paper. I might never have had the idea that led to my success. That to me, that is the fundamental problem with scientific journals: they prevent the democratization of innovation.

Google and Wikipedia were the sites I relied heavily on to gather most of the information I needed.   But it was by no means easy. I still had to send out hundreds of emails and pay hundreds of dollars to get access to those articles. Imagine if we removed the cost barrier. If the flow of scientific knowledge was unrestricted no matter what your age, race, or how much money you had, how would that impact your ability to do quality scientific research?

Then the only restriction would be was what was in your head. That’s the ONLY way to include the billions of future innovators: to make access to articles free. If we did, can you imagine the possibilities?  The best ideas in the world usually come from the most unexpected places!  When you deny open access you deny people like me the ability to innovate. You are leaving behind billions of potential innovators and innumerable amounts of world-changing innovations.

People’s minds must be free, and that means the minds of all, not the minds of a select few. A scientific discovery is like a grain of wheat. A grain of wheat is just a singular grain, unless of course you cultivate it and let it grow, and then you have many grains of wheat that will continue to multiply. A scientific discovery is in itself just a singular discovery unless you allow others to see it and add their input and creativity. Then, you have a scientific revolution.

We have our grains; so now the question is what will we do with them?

I for one am supporting the Fair Access to Science and Technology Research Act (FASTR) in its efforts to promote open access. You’ll find me giving talks in person around the world and through social media about the importance of open access to innovation and STEM.

Jack Andraka is a Maryland High School Student.