From mboxrd@z Thu Jan 1 00:00:00 1970 From: Marco van Hulten Subject: good practices in science Date: Fri, 3 Apr 2020 13:54:21 +0200 Message-ID: <20200403135421.5f800ffa@hulten.org> Mime-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Return-path: Received: from eggs.gnu.org ([2001:470:142:3::10]:49808) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jKKu8-0002VE-He for guix-devel@gnu.org; Fri, 03 Apr 2020 07:54:37 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1jKKu6-0004F2-VI for guix-devel@gnu.org; Fri, 03 Apr 2020 07:54:32 -0400 Received: from alfons.uib.no ([2001:700:200:30::141]:36708) by eggs.gnu.org with esmtps (TLS1.0:DHE_RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1jKKu6-00048I-7i for guix-devel@gnu.org; Fri, 03 Apr 2020 07:54:30 -0400 Received: from alfux.uib.no (smtp.uib.no) [2001:700:200:6::a:1f0c] by alfons.uib.no for guix-devel@gnu.org with esmtp (Exim 4.92.3) id 1jKKtz-000yMI-Ro; Fri, 03 Apr 2020 13:54:25 +0200 Received: from 173.92-220-42.customer.lyse.net (localhost) [92.220.42.173]:53944 by smtp.uib.no for guix-devel@gnu.org with esmtpsa (Exim 4.92.3) id 1jKKty-0008NQ-NV; Fri, 03 Apr 2020 13:54:22 +0200 List-Id: "Development of GNU Guix and the GNU System distribution." List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-devel-bounces+gcggd-guix-devel=m.gmane-mx.org@gnu.org Sender: "Guix-devel" To: Guix Devel Hi all=E2=80=94 Are there any natural scientists here? I'm asking because at least in my field not the right tools are used to do the work; I'd like to exchange ideas on how to approach these issues. I am sending this to this list because Guix is an obvious tool for scientific (and other) computing. None of my collegues anywhere in the world have heard of it and they are not interested when I mention it. (Furthermore, brendyyn on #guix suggested this list.) Invasion of privacy has been growing over the years, and getting a spurt during the COVID-19 pandemic (maybe not unlike 9/11). Examples include that here at the university we are expected to use Zoom and Skype, and this was a good moment to push through Microsoft Teams (as a "good replacement for mail"). These are all tools that are not open spec, free software or federated. Very few of my collegues care, and those that do have the opinion (or understanding) that it is too late to do something about it. At the University of Bergen it is expected that we install and use proprietary software on our home network (e.g. MS Teams, Skype and Zoom =E2=80=93 two of these run luckily in Chromium). Except for the integrity = of our scientific results, our privacy and general home security is affected. We have to find ways to mitigate the situation (e.g. laptop dedicated to all the crap on a special subnet). But, in my opinion, such mitigations should not even be necessary in the first place. Especially in an environment of learning and research things should be really different. There are related, even worse, issues outside of academia, like the proprietary COVID-19 tracking apps that several countries are building, mostly independently because "we cannot trust another country's app" (which would be moot point if ...). Discussion of these wider issues would warant a forked or separate thread (or perhaps a different mailinglist). I think it's all connected, but now I'd like to focus on free software and science. When I do science (the ordering and creation of concepts, models, hypotheses and theories; through thinking, programming, simulating, evaluating, discussing and writing), I have a way of working that I think is efficient and in line with the scientific method. In my mind, this must mean that one writes plain text everywhere. This is plain/text for e-mail, LaTeX for papers, code is code, Markdown or similar for most other documents. All this is in version control. You can push, share, collaborate quite easily. Anyone is free to make a pretty PDF of it or do whatever else. Because, of course it is all free as in speech. You know all this. But it doesn't work like this. Collegues don't follow this workflow, and they don't care about freedom. They actually think that Track Changes is the same as version control management. I have some work-arounds for the incompatibility between the workflows. For instance, I write most things in Markdown and use pandoc(1) to convert it to PDF and ODT. The collaborators may use any method to comment on my text and then send it back. They never edit the source, they almost invariably send back a (non-strict OOXML) docx with Track Changes or a PDF with text balloons. In academics, there was recently (in Norway just a year ago) a discussion about open access. The discussion showed that it is very difficult for my collegues to only publish open access =E2=80=93 they consi= der it as a serious problem, even though I would not think twice to publish a paper that restricts its readers. For writing papers I tried the proprietary service Overleaf (and similar) or sending the TeX files, but it doesn't work. They won't use it. They even copy text from a PDF into MS Word and send a Track Changed document in a top-posted HTML e-mail back to me. Some of them expect me to do the same thing (or using Google Docs or Sharepoint or so; sometimes logging in is expected as well). For anyone writing a thesis and having these problems right now: don't think they will go away. It does not even matter if you have your own funding. Most of your partners won't care about anyone's freedom, and you still have to find ways to work with their inefficient workflows. Free software helps a lot dealing with this, but these inefficiencies are not necessary. The inefficiencies arise from naivity about free software and technology, or just not caring and/or trying to follow status quo and writing senseless proposals (with inefficient and non-free tools). This is the state for Earth sciences. My work is appreciated in my field, so I might survive in the system (writing proposals and crap), but these unnecessary inefficiencies are *at least* an annoyance, and it does not appear to get any better. I would like to find a community where I can do science in a good way. I want to use free software and would like to collaborate through version control, IRC, Jitsi, well formatted e-mails. Does such a community exist? I am considering going out of science and focus completely on free software development, even though I have a slight preference of keep on doing science. The switch would for a large part be based on the fact that a different workflow (set of tools) is used for free software development compared with science. Is it crazy to choose your career path based on the tools the people of the respective field is using? If the community of Earth scientist free software users does not exist, is it better in other scientific fields? I guess it may be better in physics, astronomy and some parts of biology, but it will be far from perfect because also the other departments need to live with the universities' policies, right? I realise that I am privileged in even potentially have the option to change my career path, and that a not so unreasonable answer would be "shut up and live with it". But I still also appreciate any other kind of advice. :-) =E2=80=94Marco