[Biopython] Generative AI policy for contributions to Biopython

[Peter Cock]

Dear Biopythoneers,

I have failed so far to convince many of our committer pool to approve
my no AI policy pull request, despite softening it with explicitly
tolerated tool use (outside of the commits themselves) based on the
Python project stance (which I feel is too lax).

https://github.com/biopython/biopython/pull/5241

Some still view the draft as too strict (see the PR and recent linked
PRs, some examples being small AI generated changes that would be
acceptable if from a human). I understand that Michiel favours a more
permissive policy like NumPy or SciPy adopted, based on technical
merits and still expecting human understanding of the code. Given his
long standing and on going substantial contributions to Biopython, his
views carry weight.

A unanimous consensus does not seem to be possible. Might an interim
AI ban with a view to reviewing this in say three years work? Some of
the objections may well be moot at that point. Otherwise we may have
to opt for a majority rule amongst our current maintainers.

Would any of you like to put forward an alternative AI policy draft
pull request based on NumPy and SciPy please (I find the Python
project text too light on detail), including our consensus that the
communications at least should be human written (but possibly computer
translated into English). I think we need something concretely enough
that we can review PRs consistently. One of the advantages of a no-AI
policy is the line for what is or isn't acceptable is much easier to
follow.

In arguing for rejecting AI contributions, I'd focused on the legal
uncertainty argument from a project stewardship perspective (copyright
etc), thinking this was a strong enough point in and of itself. There
are other strong community based-arguments from a project perspective
for rejecting or at least shackling AI contributions including leaving
less room for beginners and mentoring, and very real risks of
maintainer fatigue or burnout. And there are the ethical objections
including unacknowledged plagiarism, excessive energy use, and abusive
collection of training data. And financial too, with the costs of
computers and parts rocketing.

Regards,

Peter


On Fri, Oct 2, 2026 at 11:01 AM Peter Cock <p.j.a.cock at googlemail.com> wrote:
>
> I'd also like a second opinion on merging an AI usage declaration on
> the PR template now:
>
> https://github.com/biopython/biopython/pull/5334
>
> I don't expect the PR template change in itself to be contentious,
> even if we do not yet have agreement on rejecting AI written commits.
>
> Hoping to get AI agents to self-disclose via a directive in our
> contributing file seems worth a try (it has been shown to work on
> other projects).
>
> Peter
>