Free software and open access

This work is licensed under a Creative Commons License.

These are loose notes and links about two somewhat related issues, free software and open access.

Free Software, meaning free as in free speech (not free as in free beer; in Spanish, free as in "libre", not free as in "gratis") is explained in the link above, and in the book Free software, free society by Richard Stallman (the articles that make up that book are available from the GNU site). A related concept is that of Open Source software, but whereas Free Software is also Open Source software, not all Open Source software qualifies as Free Software, and there are important philosophical differences between the two. For details see, for example, Why "Free Software" is better than "Open Source", by Richard M. Stallman, The Open Source Definition, in the original article by Bruce Perens, and The GNU GPL and the Open Source Definition, from Donald K. Rosenberg's Open Source: the unauthorized white papers.

The GNU/Linux phenomenon (see., e.g, Open Source: the unauthorized white papers, Rebel Code, by Glyn Moody ---the above is a link to a review---, Free for All by Peter Wayner, Free as in Freedom by Sam Williams, or Linux, GNU, and freedom, by Richard M. Stallman) has made free software (at least GNU/Linux) a known buzzword. Behind the spread of the GNU project and GNU/Linux there are reasons of convenience, stability, price, ease of customization and control, performance, and philosophical reasons (see the links above for Rosenberg's, Stallman's, and Moody's books).

Loosely related to the above are several efforts to make information available to as many people as possible, to build a "commons" that enhances creativity as well as scientific and social progress and democractic practice. Creative Commons provides several licenses that allow authors to license their work under terms that both offer them protection and at the same time make their work avaialbe to others. ; in this way, the authors' work can be built upon and shared. This is a set of licenses that "(...) intends to help people express this preference for sharing" (from their FAQ).

Licenses from Creative Commons are used by the Public Library of Science, which provides access to free, full text, peer-reviewed scientific journals. Because readers and institutions do not have to pay for access, scientific results can be more widely disseminated, and are accessible to all (with an Internet connection). Somewhat related projects are Samizdat Press, Project Gutemberg and Eldritch Press; the first is more focused on scientific academic works and the later more on general literature.

Free software and open access does affect our work as scientists. Here are a few examples from my own work. Access to source code has speed up my job when writing programs (see, e.g., the README files for the code of the Pomelo tool or FatiGO; in Pomelo-stats-code.tar.gz and FatiGO-stats-code.tar.gz). Access to papers through journals that adhere to open access standards makes dissemination of novel scientific ideas easier and faster. Availability of R, a mature, flexible and extensible language for statistical analysis and graphics allows for easy access to advanced statistical methods; and, of course, the availability of R makes students' and instructors' lifes a lot simpler when teaching stats courses.

A clear example of the positive impact of free software and open source projects in science and technology is provided by the recent field of bioinformatics; here, the major projects/enviornments/tools are all either free software or open source software (e.g., Bioconductor, Biopython, BioPerl, BASE, etc). Without the commitment to make these tools and the underlying code available, use of and research on bioinformatics would be far less developed. Fortunately, these issues are being recognized widely (e.g., Statistical Methods Need Software, by Brian Ripley).

Last, but not least, free software promotes the development of a sense of community; not only do they "turn users into developers" (as the motto of some R conferences says), but free software projects are projects that do indeed belong to the users (the code is there for grabs).

A few relevant pieces

The economy of ideas: selling wine without bottles on the global net, is an early piece by John Perry Barlow where, among other topics, he explains the issues related to "ownership" in the Internet world, and the crucial differences between "material property" (e.g., your house) and "property of a program" or "property of an idea". Whereas "material property" is often of such nature that your owning or using it precludes my owning/using it, that is not the case with "information", "ideas", and "intellectual property": if you share with me code to implement the Fast Fourier Transform, in no way is the output of your FFT routine any worse just because you shared it with me.

Lawrence Lessig is the author of several books that help understand how some of the regulatory changes that affect the Internet and "intellectual property" issues have effects that persist even after you shut down your internet connection, and severely curtail the beneficial effects on democracy, culture, creativity and innovation that the Internet and the Web have brought us. I found his two recent books, The future of ideas and Free culture (freely available in many different formats from from this link), extremely interesting, informative, and worrisome (as well as a pleasure to read).

Developing somewhat similar themes are the two books of Siva Vaidhyanathan, "Copyrights and copywrongs" and "The Anarchist in the Library". Some of the topics discussed in the above books are also covered in the 47-page report (excluding references and notes) FEPP Policy Report: "The progress of Science and Useful arts". Lessig's The future of ideas emphasizes the idea of a "commons"; some of these (and other) issues, with a different emphasis, are also discussed in The Information Commons: A Public Policy Report.

These references show that decisions surrounding "intellectual property", copyrights, P2P, and Internet regulations have serious scientific, cultural, and political consequences that last even after you turn off your modem. In other words, effects that affect the "material world" and extend way beyond the Internet. These are sobering wake up calls about how our current world, and specially our future (the world my daughter will inherit, for example), will be severely affected by changes in law and technology. Additionally, these books show how our choices about Free Software and Open Access have long ranging consequences that extend beyond the realm of software writing or science journals.

Looking at the problem from a very different angle, the short article titled Human rights, human values, and technology: why human rights advocates need to use free software explains why free software (in the sense of "free software" as defined by the Free Software Foundation) is a key piece of the toolbox of human rights researchers and activists.

A very entertaining long article (or short book) about graphical user interfaces and operating systems is In the Beginning was the Command Line, by Neal Stephenson.

And, almost last but not least, in Europe we are currently debating what to do with software patents. Why this is such an issue, what is the current state, and what can be done can be found at the FFII Software Patents in Europe page. [Incidentally, notice that most of the references I mention above are from US authors and most of their comments about the intersection of the law and technology refer to the US. I miss references that are more pertinent to Europe; if you know of any, I'd appreciate if you let me know.]