Let the four freedoms paradigm apply to ecology
Trends in Ecology & Evolution, 27 (6):
310--311 (2012)DOI: 10.1016/j.tree.2012.03.009
Abstract
n 1985, Richard Stallman, one of the most brilliant minds in computer science, founded the Free Software Foundation and launched the concept of ‘copyleft’, the opposite of copyright. The aim, outlined in the GNU Manifesto (http://www.gnu.org/gnu/manifesto.html, 1), was to make software programs ‘free’ as in ‘freedom’.
The famous ‘four freedoms’ expounded by Stallman 1 are: (i) the freedom to run the program for any purpose; (ii) the freedom to study how the program works and adapt it to one's own needs; (iii) the freedom to redistribute copies; and (iv) the freedom to make improvements to the program and release them to the public. Thus, the whole (scientific) community benefits from software development. These freedoms are also inherent in several free software licenses, the GNU General Public License (GPL) being one of the most popular.
Approximately a quarter of a century after Stallman put forward his ideas, William K. Michener and Matthew B. Jones, in an article in TREE2 focusing on the analysis of ecological data, stated that: ‘analytical processes are fundamental to most published results in ecology’. Explicit reference to the analytical procedures adopted in generating scientific results is crucial for reproducibility, yet these processes are rarely documented in published ecological papers 2. Scientific workflow applications, such as Kepler (https://kepler-project.org), attempt to address the problem 2, but are only partially successful because the underlying algorithms may still be opaque.
In our view, the explicit use of Free and Open Source Software (FOSS) with availability of the code is essential for completely open science: ‘scientific communication relies on evidence that cannot be entirely included in publications’, but ‘anything less than the release of source programs is intolerable for results that depend on computation’ 3.