Re: [Biopython] Generative AI policy for contributions to Biopython

Dear Peter,

While I also tend to strongly restrict or even forbid the usage of AI in 
Biopython, I wonder how you really can prevent this. A careful submitter 
can mask the AI signs in his/her code so that I will go undetected. So 
wouldn't it be better to allow the usage under strong restrictions and 
conditions (and I agree with the those that you have mentioned, 
including the "good first issues" in your other e-mail) to encourage 
potential contributors to be transparent about the of use of AI?

I'm unsure about this, but I wanted to include this topic into the 
discussion.

Best
Markus

Am 24.04.2026 um 12:16 schrieb Peter Cock:
> Dear Biopythoneers,
>
> We need to set out a generative AI policy for contributions to Biopython.
>
> There are now multiple recent PRs submitted by new contributors which
> are openly using AI tools, more that I suspect are, and now even AI assisted
> PRs from past contributors (where CV padding or other external metrics
> are unlikely to be driving this). These are generally more work to review
> than human written PRs, and that is a growing issue.
>
> I blogged about my views late last year - ending in the line "Right now, I
> still lean very much to saying no any PR using generative AI".
>
> https://blastedbio.blogspot.com/2025/11/thoughts-on-generative-ai-contributions.html
>
> Things will change (both tool capabilities, but also the social and legal
> interpetations) but that post still describes my views today - note I did
> not touch on the topic of communications there (see below).
>
> Recently Linux adopted what has been described as a balanced stance
> treating it as a tool with very clear expectations that usage MUST be declared
> and that the human submitter is responsible for (quoting these four points):
>
> * Reviewing all AI-generated code
> * Ensuring compliance with licensing requirements
> * Adding their own Signed-off-by tag to certify the DCO
> * Taking full responsibility for the contribution
>
> https://docs.kernel.org/process/coding-assistants.html
>
> That is pragmatic but ignores the legal and ethical minefield. We don't
> have a Developer Certificate of Origin (DCO), but I think the other
> points are a bare minimum for any Biopython policy.
>
> Most of my personal open source projects have only had a very small
> number of contributors, and I am comfortable with outright rejecting
> generative AI. I know some of the past/current Biopython contributors
> are more willing to embrace this technology though - so I doubt support
> for a simple ban would be unanimous.
>
> Speaking for a moment as the current Open Bioinformatics Foundation
> president, the board has discussed this and agreed not to try to micro
> manage the member projects. For reference, BioPerl have started
> https://github.com/bioperl/bioperl-live/issues/407 which has some
> excellent points and examples to consider.
>
> In particular, this is not just a code or documentation changes issue - but
> also about the communication around any proposed change: the nature
> of the commit messages, pull request description, and discussion. This
> ties into the maintainers' burden - many of our recent AI generated PRs
> have fairy short code changes but the verbose text is exhausting to read
> and unhelpful. It has sometimes felt like I have been talking to an AI agent
> rather than a human - I actually liked the feeling of mentoring a new
> contributor and guiding them through minor hurdles to getting their
> change accepted, but you lose that with an AI agent inbetween you.
>
> I therefore very much like this line from the curreth Codeberg policy:
>
>> All communication, that includes: commit messages, pull request
>> messages, documentation, code comments and issues (and
>> comments on issues/pull requests), that is intended to be read
>> by people to understand your thoughts and work must not have
>> been generated with AI. We exclude machine translation and
>> tooling that helps with grammar and spelling check.
> https://codeberg.org/comaps/Governance/src/branch/main/AI_USAGE.md
>
> Would anyone like to speak in defence of accepting AI (assisted) PRs,
> and suggest an existing policy you would be happy we adopt or base
> ours on?
>
> Or should I start drafting a more draconian but likely much shorter one -
> a few lines like this in the CONTRIBUTING file and/or PR template: No
> generative AI to be used in any Biopython contributions, with the exception
> of machine translation to/from English (where you might consider including
> your original language text as well).
>
> Thank you,
>
> Peter
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