« Proprietary Software Poisons Science

Aleksa Sarai

free software licensing peer review programming research science

13 November 2015

Before I start, I’d like the make the record clear: I am not a GPL, GNU or FSF zealot. Most of the code I’ve written is licensed under the MIT License (but that’s a story for another day), and I don’t understand the thinking of people who use the GPL for every single piece of code they’ve released as free software.

[EDIT: Since writing this blog post, I have become a bit of a GPL zealot. So this is no longer a valid portrayal of my views – though the rest of the article still is a fairly accurate summary of my concerns with proprietary software and science.]

I agree with Linus Torvalds on the question of the purpose of the GPL, that what matters is the collaboration aspect of the GPL:

My argument for liking GPL version 2 […] is that I give you source code, you give me changes. We’re even.

So it doesn’t really make sense to GPL code for which you don’t forsee (or intend) community development. If you want your code to just exist, why not just place it under the MIT license or Unlicense it so that people can use it for any project?

The Problem

But anyway, back to scientific research and my grievances with proprietary code being used to produce results that then must be peer reviewed. One of the main principles behind all of science is reproducibility. Most papers outline “what their code basically does”, which makes sense if you’re outlining an experimental setup but simply doesn’t make sense for code. As any developer will tell you, what you think your code does and what your code actually does are usually two very different things.

For that reason alone, all code used in scientific papers should be released as free software (and copyleft, to make sure that anybody who uses it in future research must also make their improvements free software). But of course, it’s not that simple.

And, to be perfectly honest, most of the code I’ve seen that’s written by researchers isn’t particularly pretty anyway. It’s a whole mess of no comments and spaghetti code. Since I’ve been a programmer for a while, I tend to think of my code as being cleaner (here is some code I wrote for my current research). So you shouldn’t assume that code written by a researcher would be useful for any other purposes (as it was written with a single purpose in mind, and usually it was hacked together so it only just works). Matthew Alger shares this view, and he makes a very good point: research builds on research and if you want other people to build on your code it needs to be readable. In my opinion, apart from experience, feedback from other developers is one of the best ways of improving your code quality.


When you are part of a research group, you are generally paid in some form. Thus, you are employed by the university. This means that all code you write is no longer owned by you, since it was written using university resources and time. As such, one would need to convince universities to release as free software all code their researchers write that is used in papers. This is unlikely to go well.

One could also make the case that any data used by that code which is not in public domain (and is vital to the code running properly) should also be public. I’m not sure I’d agree with that view, since what’s important in reproducibility is knowing what the method was, so you could go get your own data and follow that method – as well as check that the method is valid.

But the bottom line is that it’s unlikely that any reasonable university would spend money to then release as free software the code that was written for that money. However, most researchers’ code doesn’t have any real applications that would give it any intrinsic monetary value (it’s very … pragmatically written).

A New Hope License?

While there is a very large population of licenses available to your local neighbourhood researcher, none of them are really suited to solving this problem. Sure, you could go overkill and use the GPL (which is what I did), but it doesn’t actually cover the main problem – people using the code to produce results that are then published aren’t required to distribute the source code.

Clearly the only possible solution is a new license. What I would like in a license, which would solve this problem and be a step in the right direction in this new world of computational science (where code has become your method) is the following:

  1. All four freedoms (as defined by GNU) must be provided to all users of the software, and all readers of publications that made use of the software.

  2. The license must be copyleft, any derivative works must be licensed under this license and cannot be relicensed under any circumstances.


Obviously, this license is quite similar to the GPLv2 (it is copyleft and is designed to uphold all four user freedoms). However, it provides an additional requirement to all users of the software: if a user uses the software to produce a publication they must provide the same freedoms under this license to any readers of that publication.

In my opinion (although I’m unsure if this should be in the license), you should not charge any extra fees to the readers of the publication. If it was published in a journal, then any journal fees should be considered to have covered both the paper and any resources in the paper. While I don’t agree with JSTOR and other such publishers’ views on freedom of information, at least it’s unreasonable for them to claim they should be paid extra for code they don’t host or provide.

You should probably note that I’m not a lawyer, and that these three clauses may not be sufficient to adequately ensure that research remains reproducible as we continue to create more and more software. I am considering getting legal advice to see whether this license should be drafted, if you’re interested in seeing this become a real license shoot me an email: cyphar@cyphar.com.

But what about other licenses?

So, there are some licenses which attempt to fix this problem. The first one I found was the CRAPL. As far as a free software license goes, it’s very shoddy. It’s main purpose is to allow peer reviewers to verify the results given in a paper. While this is the problem we’re trying to solve, I don’t like the fact that it’s selective and that derivative works require permission from the original author (or even papers using the original code). The general public (even people who find the paper on arXiv) should be allowed to modify and run the code.

There was a document written by someone at Stanford discussing this, but they stated things that are simply not correct (emphasis added):

Two of the most common types of open licenses that rescind copyright are those designed for code (for example, the GNU Public License or GPL and the Berkeley Software Distribution or BSD license) or media (for example, the family of Creative Commons licenses).

This is utterly false, none of the given licenses rescind copyright, that is not their purpose. In addition, the proposal given in the paper is not actually a proper license – it’s a description of a scholarship method that will ensure researchers release their code as free software and doesn’t actually solve the problems we’re discussing. However, it would be nice if all scholarships had a requirement that code written as part of the research had to be made free software.

So, I couldn’t find a proper license (that had been written by a lawyer) which solved the problem we’re trying to solve while simultaneously providing people with the rights under traditional free software. Clearly this is an important issue, and I haven’t heard much discussion about this topic in the academic community – which is slightly troubling.

Unless otherwise stated, all of the opinions in the above post are solely my own and do not necessary represent the views of anyone else. This post is released under the Creative Commons BY-SA 4.0 license.

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