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I'm a big believer in FOSS (Free Open Source Software), and a physics graduate student. I believe a lot of current researchers are not aware of free solutions to problems that are usually encountered in a lab, and since money is often tight in academia I think it's important.

I also feel like my thesis is the only bit of work I'll do in academia that's truly mine; there's no journal with strict criteria on what I can include.

So do you think it's appropriate to include a section at the end of my thesis, essentially completely separate from the rest of it, containing my views about the state of software in science and solutions to problems? I'm worried that it might seem a bit preachy, but I think that's a problem that can be solved with tone/phrasing.

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    You might want to think about your likely audience reading your thesis. That is, a "lot of current researchers who are unaware" aren't likely to read your thesis. Those who are likely to read will notice (or already know) the software that you have documented you use. And if people aren't noticing what software you used because your particular project only peripherally needed something special, then it seems a bit pointless to spend the energy writing an extra chapter as opposed to supporting your views in other forums. (this applies to any 'soap-box' like topic that adds a chapter.) – Carol Apr 11 '17 at 13:57
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    You could just add a paragraph in the acknowledgements, where you just express your gratefulness to the developers of some of the FOSS projects that have been most useful to you while writing your thesis. That was quite common in my department. – Tim Apr 11 '17 at 14:57
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    A thesis in the sciences should not be about your views. Write a blog post or a letter to the editor. – mbatchkarov Apr 11 '17 at 15:11
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    Can you frame it as acknowledgement? "The author wants to acknowledge the efforts put into free software by volunteers that was used to process data for this thesis, especially the authors of software X,Y and Z for their usefulness in A, B and C processing. The author also wants to acknowledge that this thesis would not have been possible without free software and thus the usefulness of free software for the academic community in general". Its short, to the point and as non-preachy as it gets, and fits into an "acknowledgements" section of the thesis (the wording is open for debate ofc). – Polygnome Apr 11 '17 at 15:42
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    After more than 40 years of Free Software, it seems rather arrogant of you to believe that everyone else is ignorant of it. There can be good reasons to use it. There can be good reasons not to use it as well. Pontificating on it in your thesis really won't sway anybody's opinion. – Jon Custer Apr 11 '17 at 16:31
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I think this is a fairly bad idea, for the following reasons:

  • It's largely shouting in the woods. Let's face it, while you may feel that your thesis is the only piece of work that's "truly yours", it will likely also be the least-read piece of your career. More to the point, your (presumed) target audience (young physicists in other departments) are very unlikely to ever come across your statement. How many PhD dissertations of people you don't know personally have you read to the end?
  • It has a non-zero chance of annoying somebody in your committee. Again, a physics thesis nowadays is mostly there to appease your committee (as few to none outside of the committee will ever read it), so a section that does not contribute to or actively hurts this goal seems like a bad idea. And I would argue that there is a real danger that somebody in your committee is not thrilled about the unconventional political statement in your thesis, as:
  • You may be unable to write it in a way that it does not come across as preachy. I think the pure existence of such a section will be perceived preachy, so no matter how you phrase it, it may always be perceived as such.

So if your thesis (and formal papers, obviously) are bad places to communicate your opinion on science politics, how can you communicate these matters? Most people I know with strong opinions on political matters of science (be they about career models for young scientists, open access, reproducibility, ...) tend to primarily communicate their thoughts over various social media (blogs, Twitter, Facebook), with the occasional invited opinion piece on the topic in a journal or magazine editorial. Every now and then, they are also invited to talk about the issues they care about in seminars or as invited speakers in conferences. Presumably, in some cases, they have just been invited in general and have decided on their own that politics is what they are going to talk about. This strategy reaches substantially more people (even if your blog entry never jumps across 100 views, that's probably still more than your thesis will get in the next 50 years), and from a blog or Facebook entry, people expect opinionated content, so there is much less reason to think less of you (unless they vehemently disagree with your opinion, but in this case no way of communicating your thoughts will help).

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    I read random theses on interesting topics from people I know nothing about. It's sad to see that apparently so few people do :( – Please stop being evil Apr 11 '17 at 18:29
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    What if OP includes a sentence or two in the methodology section saying something like "all software used to process our data is open source. The source code is available at..."? – Kevin Apr 11 '17 at 18:50
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    @thedarkwanderer: How do you even come across these? I don't think I've ever read any thesis except when it was cited somewhere else or someone else suggested that I read it. And even then sometimes I simply failed to find a copy online. Once I think I accidentally found a thesis via a search engine, while doing some background check for my own research, but that seems rare... – tomasz Apr 12 '17 at 3:56
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    @tomasz I live near a University with a library. The library stores paper copies of PhD and Master's thesis of its past students in print. Sometimes when I'm looking for a book on something, something in the PhD library will pop up in the catalog and I will go read it. Otherwise just random postings online (but you are correct that theses are not easily searchable/findable online the same way journals are) – Please stop being evil Apr 12 '17 at 5:14
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    @tomasz When looking at a new topic I find a well-written thesis very helpful, indeed I actively seek out those published by key groups of the new field. They assume less prior knowledge and so for the "newbie" are usually easier to follow and often contain lots of extra information which does not find its way into the final papers for various reasons. Very useful for the less intelligent people like me! – Beetroot Apr 12 '17 at 21:10
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The purpose of a thesis is to show that you can do independent research. Your advisor and your committee members will read your thesis to see if you achieved that goal. Anything in the thesis that does not help them determine that, wastes their time (not too much, as they will probably just skip it, but still it risks annoying people whom you don't want to annoy). Lets be honest, those are the only people who are really going to read your thesis. So you can expect virtually no gain from doing so, as you are not going to reach anyone who might be interested in what you have to say about FOSS, and there is a very real potential of harm to your thesis from doing so.

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I agree with the other answers that it is a bad idea to include a completely separate 'soap-box' chapter of your thesis which is dedicated to your personal political views of FOSS. The key issue is that you are not adding anything that substantiates your thesis. However, I think that if FOSS has legitimately played a substantial role your research project, then there are ways in which you can communicate your point without jeopardizing the integrity of your thesis.

  • Demonstrate the utility: Rather than write an entire chapter, simply demonstrate the utility (point below relevant) of the software in your project. Show your examiners (and any future readers) how you used the software to meet your research goals. 'Do' rather than 'say'.
  • Reference the software: If you are using open source R or Python packages, consider giving credit by referencing the FOSS software that you used (e.g. R example, Python example). The benefit here is that you can tactfully demonstrate the usage of the software, and avoid coming across as just "talking the talk".
  • Acknowledgements: A simple paragraph in your acknowledgements may give you a sense of fulfilment. Not to suggest it's the norm, but I have read several theses in which the student gives thanks to their God and this has not impacted the success of their work. A FOSS paragraph doesn't seem any less appropriate.

I was faced with a similar issue in my thesis, but concerning reproducible research. After consulting my advisers, we came to the conclusion that the fact my entire thesis was entirely reproducible was more than a mere political statement. In fact, many of my research questions, future directions, and implications were centred around this. The key point here is that it wasn't included as a political statement, but to better communicate the research project.

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Isn't there literature that you can cite that can turn this into a scholarly argument, rather than a "soap box" moment? Also, you can put whatever you want in your thesis, but your committee and/or chair need to approve it, so you should discuss with him or her before you go on a tangent.

It seems that using outlets with larger audiences would be helpful, such as a journal article, conference presentation, or other media.

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My suggestion: Instead of putting that in your thesis, write a paper on this issue - a social commentary paper more than a research paper, even if it involves Physics research - and try pitching it to:

  • Professional journals as an opinion column / not-main-matter content.
  • Semi-professional/popular publications which professional societies of physicists issue
  • Some of the conferences you usually submit to - but not in the normal tracks for papers; talk to the organizers and ask for an opportunity to hold a panel discussion on this matter. Or perhaps even suggest a "methodology" session.
  • Some publication dealing with physics research, i.e. with academia and what happens within it. This may be more challenging and it's not clear what the readership would be but it might still be relevant.
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If open source software helped you in your research, write it into the acknowledgement of your thesis. You feel grateful to the contributors, so that's the genuine place where to mention it.

In the main thesis, it is likely off-topic, even if you add some extra section for "FOSS advertising". Also, the acknowledgement will be probably the second most read part of your thesis at all, apart form the abstract.

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I think as many have said here, there might be objections which wouldn't have been there if you hadn't included the "soap box". I would suggest becoming well settled in academia first (gain tenure etc.) and then one day on your own home-page have a section about your personal views on FOSS. This would mean that people who would want to reach out to you and actually follow your views (future students) would get to read them.

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    Why does OP need to wait to get tenure before starting to soapbox? The implication that only tenured professors have interesting things to say or should be listened to is obviously false and quite offensive. I have seen many times graduate students discussing interesting things on their personal web pages or blogs, and would hate to be deprived of such content in the future because of bad advice like that offered in this answer. So I would encourage OP to use such platforms for any kind of soapboxing/activism that they think is worth sharing with the world. – Dan Romik Apr 12 '17 at 0:58
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If it isn't actually part of your thesis target point, you will rightfully be marked down for (1) diverging unnecessarily, and (2) putting unsupported personal opinion in an academic thesis.

You want to do what you say, ask nicely if you can do a vanity publication of your thesis and include it there.

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