good practices in science

[Marco van Hulten]

Hi all—

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
– 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 – they consider
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.  :-)

—Marco