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Konrad Hinsen

@khinsen@scholar.social
mastodon 4.7.3
  • Open on scholar.social

Researcher at CNRS. Computational science, in particular computational biophysics. Metascience, in particular the evolution of science in the digital era.

Favorite hash tags:
#DoughnutAcademia
#Emacs
#GlamorousToolkit
#Guix
#Pharo
#CommonLisp
#ReproducibleResearch

1266 Followers
387 Following
50 Posts
Joined April 30, 2022
Web:
https://khinsen.net/
Blog:
http://blog.khinsen.net/
Digital garden:
https://science-in-the-digital-era.khinsen.net/
ORCID:
https://orcid.org/0000-0003-0330-9428
Open post
Konrad Hinsen @khinsen@scholar.social
· 2mo ago
Replying to
Related: "Why computer modeling should become a popular hobby" https://www.qrg.northwestern.edu/papers/Files/simhobby-local.htm (h/t @akkartik@merveilles.town) Written 30 years ago, this article assumes that convivial modeling software will become widely available. The opposite has happened: even modeling software for professionals (computational scientists) is no longer convivial.
qrg.northwestern.edu
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago

Lettre ouverte : Arrêtons l’adoption naïve des technologies de l’IA dans le milieu universitaire

https://aeporreca.org/blog/lettre-ouverte-adoption-ia/

Traduction française d'une lettre ouverte internationale (par @olivia@scholar.social et al.) que vous pouvez signer dans l'original en anglais ici;

https://openletter.earth/open-letter-stop-the-uncritical-adoption-of-ai-technologies-in-academia-b65bba1e

aeporreca.org
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago

RE: @kristoff@hachyderm.io

All I knew about Zig before reading this post is that it's a programming language in the C/C++/Rust subspace. I have no opinion at all about the language. But this post almost makes me want to use it, just because of its credible long-time plan to become and remain community-managed technology.

hachyderm.io

Loris Cro ⚡: "Contributor Poker and Zig's AI Ban https://krist…" - Hachyderm.io

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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@slava@mathstodon.xyz @andnull@social.nouveau.community I see the fundamental problem in a neglect of the integration domain (see this paper by @stephenrkell@recurse.social: https://doi.org/10.1145/1639950.1640051) In a better world, every programming language would plug into an infrastructure for polyglot software assemblies. Since that infrastructure doesn't exist, PL implementers make minimal replacements according to their perceived needs.
doi.org
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago

Interesting remark by @k9ox@mastodon.radio in the FedWiki Matrix room: "I don't mind wiki being unreliable but I want to know why it isn't."

This looks like a good framing for reproducibility issues in science as well. If something is not reproducible but it is generally understood why, that's OK - not nice, perhaps, but it's possible to work around it. But if you can't reproduce a result that everybody believes to be reproducible, that's a problem.

CC @danielskatz@fediscience.org

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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago

You can now sign up for the next session of the MOOC

"Reproducible Research II: Practices and tools for managing computations and data"

which opens on May 5th.

https://www.fun-mooc.fr/en/courses/reproducible-research-ii-practices-and-tools-for-managing-comput/

fun-mooc.fr
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago

"Hallucinated citations are polluting the scientific literature. What can be done?"

http://doi.org/10.1038/d41586-026-00969-z

After lots of technicalities:

"In some cases, hallucinated citations might serve as a sign that the entire paper is fabricated, whether by an individual or a paper mill, a business that sells authorship slots. But the extent to which fabricated papers are contributing to the fake-citation problem is unclear."

doi.org
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@zimoun@social.sciences.re The issue I see with the current arrangement plus the advertising for it is the implicit message: Here's a nice new feature, but you will have to abandon manifests, and list your packages on the command line instead. For me, manifests as part of a version-controlled project are an essential feature for reproducibility. So *I* am not going to use this nice new toy. But others will put convenience of deployment over reproducibility. The same people who like conda. @civodul@toot.aquilenet.fr
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago

"Even more troublingly, other researchers say, the fake papers were then cited in peer-reviewed literature. Osmanovic Thunström says this suggests that some researchers are relying on AI-generated references without reading the underlying papers."

Does this still surprise anyone?

https://www.nature.com/articles/d41586-026-01100-y

nature.com
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago

RE: @gvwilson@mastodon.social

An interesting view on software use in science. What this means is
- gain in efficiency: less software to maintain, less friction in collaborations, etc.
- fewer but more critical points of failure - potentially offset by improvements in funding and governance, but I am probably dreaming
- reduced epistemic diversity: the chosen few software packages determine which scientific methods become consensual

mastodon.social
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@glyph@mastodon.social My take is that boilerplate results from the idea of general purpose programming languages, supposed to cover all application domains. So one way out is DSLs. But a multitude of languages creates new challenges, e.g. learnability and interoperability. LLMs pretend to transform human languages into general purpose programming languages. Which works for small and well-defined problems, but is risky for large or poorly understood problems. 1/2
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@glyph@mastodon.social I see a place for intermediates. Semi-formal languages, a bit like controlled natural languages (e.g. http://attempto.ifi.uzh.ch/site/) But I suspect that there is no way around the statistical approach behind LLMs for compiling a database of patterns. The patterns expressed today in boilerplate. 2/2
attempto.ifi.uzh.ch
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@toxi Today, I see public research culture, quite similar in spirit to early FLOSS culture, evaporate in much the same way, for similar reasons.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@bzg Here's a tool that does roughly that: https://github.com/khinsen/swh-checkout More proof-of-concept than for wide-scale use, if only because it has Guix as a dependency. But I do use it from time to time. @andrewnez
GitHub

GitHub - khinsen/swh-checkout: Download a single commit of a Git repository, using the Software Heritage as a fallback

Download a single commit of a Git repository, using the Software Heritage as a fallback - khinsen/swh-checkout

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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@hipsterelectron I agree that the categorization is a bit too extremist. But the list is a good starting point for doing one's own explorations. @civodul
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
The most surprising for me is Anubis.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@smallcircles Better comms practices is where I'd start as well. For example: if you consider yourself a community project rather than a software vendor, don't make a Web page that advertises a project, make a Web page that showcases a community. @johannab
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@aartaka If you launch a petition, I'll sign it! For foreigners learning Russian, putting the dots on the ё is a big help. What's the point of having a near-perfect correspondence between phonetics and spelling but leaving out the final touch? The only excuse I would accept is wabi-sabi. 😉
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@jack Then you should have posted this link instead: https://ia.wikipedia.org/wiki/Interlingua 😉
ia.wikipedia.org
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@civodul Fortunately there are efforts to (slowly) liberate the EU from such imposed restrictions: https://www.eurohpc-ju.europa.eu/advancing-european-sovereignty-hpc-risc-v-2025-03-06_en
eurohpc-ju.europa.eu
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@simon This looks like a special case of the principle that "people without LLMs" and "people with LLMs" cannot collaborate in the long run. Different priorities, different skills, different time scales.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to

@smallcircles I have made various attempts in the past to explain to FLOSS communities that they need to have at least their users implied in their governance, and ideally even more distant stakeholders. With little success.

The typical reaction is one of

  • Users get our work for free, they have no right to complain.

  • Users can join our community, e.g. by contributing to documentation, and then they have a say as well.

@johannab

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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@screwlisp Unix interoperability is at a very low level: character streams. Every programming system support character streams. CL conditions are standard CL, but CL-only. Much less interoperable than character streams. And then, even inside the CL universe, I think your scheme requires interoperable programs to use the same conditions, i.e. have a common dependency. Maybe I got that wrong though. @dougmerritt
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@plexus@toot.cat Here is an explanation by @k9ox@mastodon.radio, who coined the term: http://found.ward.bay.wiki.org/view/debt-metaphor-explained
found.ward.bay.wiki.org

debt metaphor explained

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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@SReyCoyrehourcq@social.sciences.re You can, but it has to be a local file, not a URL or a SWHID. @zimoun@social.sciences.re @civodul@toot.aquilenet.fr
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@aartaka@merveilles.town In addition to all the suggestions already made, let me add the meta-suggestion: all the ideas that people will come up with once they have the possibility to do lightweight GUI apps. So whatever constraints you consider acceptable now, be prepared for people complaining about them in the near future.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@civodul@toot.aquilenet.fr Of course, *I* don't have a problem with all of that. I just added --unsafe-channel-evaluation to my "update-guix" script. Problem solved. So maybe the workaround (for preventing frustration) is just to add this hint to the error message, if that's easily doable. @zimoun@social.sciences.re
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@civodul@toot.aquilenet.fr I am one of those who use 'channel-with-substitutes-available'! For manifests, I would impose restrictions only when loaded from a URL That doesn't make anything worse than now for anyone. @zimoun@social.sciences.re
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@zimoun@social.sciences.re So... channel files run in a sandbox even if they are local files? That sounds like an unnecessary restriction likely to break many of them. I thought they were isolated only when loaded from a URL (or SWHID). @civodul@toot.aquilenet.fr
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Open post
Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@civodul@toot.aquilenet.fr This looks very nice! Now if only "guix shell" could also download a manifest file... via a SWHID of course. All the convenience of curl ... | sh without the problems.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@kingcons@tiny.tilde.website I was shocked by the size of Plan 9. This makes it an excellent pedagogical resource indeed.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@jackdaniel Wow, congratulations!
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@interstar@artoot.xyz That's a credible vision. Personally, I don't believe in unrestricted natural language for software. Its interpretation is always context dependent. With today's coding agents, the agent supplies the context statistically, without asking for confirmation. That's not reliably enough in general. I'd expect future coding agents to turn natural language into a semi-formal language with explicit context, to let a human proofread. @glyph@mastodon.social
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@flomaraninchi Et juste quelque pouets plus tard, je vois cet excellent exemple: https://mathstodon.xyz/@jonmsterling/116448938967012441
mathstodon.xyz
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@screwlisp It all depends on what you consider the key features of Unix pipes to be. Chaining operations is something you can do with function calls. Is that already "the same as Unix pipes"? For me, Unix pipes are about just-in-time composability between independently written programs. You don't get that with your condition hack because there needs to be a prior agreement on the conditions in all candidate components. @dougmerritt
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@lain_7 Indeed. There were in fact lots of practices to manage information on paper, some very sophisticated. Luhmann's Zettelkasten has become famous. Also Leibniz' paper slip cabinet, although it isn't very clear how he used it. And many others. @aartaka
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago

Formation "Construction et animation d'une communauté autour du développement d'un logiciel libre"

30 juin - 2 juillet à Autrans

La formation est ouverte et gratuite à tous les membres des laboratoires de recherche académique en France.

https://animeopensource.sciencesconf.org/

animeopensource.sciencesconf.org
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@aartaka That's what Ivan Illich calls "radical monopolies" (in his 1973 book "Tools for conviviality"): technologies that people can no longer opt out of because society at large has decided to adopt them. However, before you decide to fight against radical monopolies, keep in mind that agriculture is one as well! As are fridges, or the power grid. For me, the priority is understanding and then equilibrating the power structures that each radical monopoly creates.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@aartaka I wonder how realistic this description is. When I look at how people of my parents' generation worked (those I knew well enough), I note that they all wrote drafts by hand on paper before turning to the typewriter. I also remember when word processing arrived in my own life, around 1983. It made my writing a lot better, because outlining first and then iteratively refining the outline is how I work best. I am not going back to typewriters!
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Konrad Hinsen @khinsen@scholar.social
· 6mo ago

"Reliable research in the social and behavioural and sciences"

A collection of four (paywalled) articles on reproducibility and replicability in the April 2 issue of Nature:

https://www.nature.com/collections/idajfifcfg

nature.com
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@brembs I'd say they are more than distractors, as they actively exploit the weaknesses of the ever more failing reviewing system.
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Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@aartaka If the goal is a neat copy for sending to someone, yes. For personal notes, you write with generous line spacing, and then you can do minor corrections But not what I do on my computer. Which is why I hardly write on paper any more. Just short notes like shopping lists.
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Open post
Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@deech I expect FLOSS projects to move into one of two categories: those that attract the Jeff Dean archetype and those who reject it.
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Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@jonmsterling I expect similar issues with attempts to automate science in other disciplines. Today's hand-written scientific software should serve as a warning example: it is almost never possible to check that it does exactly what the informal papers and equations suggest it does. AI scales that problem up by a huge factor.
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Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@zimoun@social.sciences.re In general, it's a lot less boilerplate-like than a channel file. And yet, *most* manifest files just list packages by name. Maybe there is a useful intermediate level that can be put into a sandbox. @civodul@toot.aquilenet.fr
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Open post
Konrad Hinsen @khinsen@scholar.social
· 6mo ago
Replying to
@csantosb@sigmoid.social Indeed. The code that handles this fallback is exactly what my little Guile script exposes for other uses. That's why Guix is a dependency. @bzg@floss.social @andrewnez@mastodon.social
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Konrad Hinsen @khinsen@scholar.social
· 4mo ago
Replying to
@civodul@toot.aquilenet.fr Looks OK for users who need only the main Guix channel. Not good enough for me: I also have guix-science plus my personal channel. @zimoun@social.sciences.re
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Konrad Hinsen @khinsen@scholar.social
· 5mo ago
Replying to
@jonmsterling I am less pessimistic about democratic project governance in the long run. But it's inherently slower than a dictator, and these projects will need a lot of time to develop a consensus on LLMs. One problem I see is divergent views on LLMs among core contributors. I doubt that people with such divergent views can effectively collaborate. Meaning that the outcome is one group leaving the project.
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