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Hi all</div>
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Thanks for the interesting conversation. Like João and Michiel, I would also argue against a total ban, but rather in favour of a policy that allows AI to be used in some contexts, by some people, adhering to some conditions.</div>
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BTW, I write "we" below, for convenience not because I consider myself part of the BioPython developer community, I'm just an interested user.</div>
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There are two main reasons I think AI use should be allowed under agreed upon conditions. First, AI can already pass the Turing Test with natural language so there's no way we're going to be able to detect AI-written code going forward if it's created by a
human who tells the AI to make its contributions look human. A ban may actually incentivize deceptive behaviour and make things worse. Second, the AI tools are so powerful that, in the right hands, they offer the possibility of getting things done at high
speed and without sacrificing quality.</div>
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It might be interesting for people to think about this from the following perspective: if you interviewed a programmer and they performed the way the AI does today, would you hire them? A few years ago when I first tried getting ChatGPT to write some code
for me, I decided to "interview" it, and I would never have hired someone who behaved in that way. Today the answer is completely the opposite, I'd hire the person on the spot. But I would know (or quickly learn) that that person needs to be carefully supervised.
And if they made the kinds of mistakes AI makes today, I wouldn't fire them, I'd get better at managing/supervising them and assigning them tasks.</div>
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So we could consider a policy that instead of a ban says that we welcome contributions that have been made with the assistance of an AI but you must follow some rules. And that the BioPython community reserves the right to summarily reject or completely ignore
contributions which violate or appear to violate any of these conditions.</div>
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Rule #1 would be that you have to declare AI usage.</div>
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We could insist that people (or those not known to the BioPython community?) using an AI must provide a transcript of the AI sessions. I've done this in several recent projects for accountability and review reasons. It's actually difficult to get Claude code
to write a verbatim transcript with the inputs and outputs (excluding diffs along the way).</div>
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I would encourage known contributors who understand the rules and are experienced enough programmers to use AI as much as they like. I'd do this for sure, even if just privately, because it doesn't make sense to forbid very good and experienced programmers
from responsibly using what is basically a power tool to help get things done. That would be like telling a carpenter they can't use an electric drill because in the wrong hands a drill can be dangerous.</div>
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I have no idea to what extent people on this mailing list have been using a tool like Claude code but if you haven't, I would strongly encourage you to give it a go. I'm not an overly excitable person but I find the capabilities of Claude code to be quite incredible.
Not just for writing new code but also for debugging and investigating results. It's also capable of being incredibly dumb. And of course its code sometimes has bugs which may be difficult to detect, just like human code. Using it requires careful thought
about how to structure code and tests, and insisting that it prove to you that it has done what you asked. But this is the way we work when programming in isolation and with each other on human teams. So to me this level of carefulness is already fairly normal.</div>
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Sorry for so many words!</div>
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Regards,</div>
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Terry</div>
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<b>From: </b>Biopython <biopython-bounces@biopython.org> on behalf of João Rodrigues <j.p.g.l.m.rodrigues@gmail.com><br>
<b>Date: </b>Saturday, 25. April 2026 at 02:06<br>
<b>To: </b>Peter Cock <p.j.a.cock@googlemail.com><br>
<b>Cc: </b>biopython <biopython@biopython.org><br>
<b>Subject: </b>[ext] Re: [Biopython] Generative AI policy for contributions to Biopython<br>
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Hi Peter, </div>
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I lean towards limiting but not banning AI contributions. Fully automatic contributions by agents should be banned, but the reality is that we cannot police what people use to work on code. We can, however, ban contributions from people that violate our "rules".</div>
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Beyond a policy, some other ideas:<br>
- review our contribution guidelines, to make it explicit to incoming devs what we expect of them (maybe this is redundant with the policy);</div>
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- maybe include an AGENTS.md file (<a href="https://github.com/agentsmd/agents.md" data-outlook-id="185bdda4-4c00-41b8-8c8a-018f352bbfd3">https://github.com/agentsmd/agents.md</a>) to at least provide some guidance to people wanting to use agents to help them
work on our codebase;l and flag when they do so (tag, etc);</div>
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- and add an explicit checkbox/agreement to the pull request template indicating that the human user is responsible for the contribution under penalty of ban from future ones.</div>
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Cheers,</div>
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João </div>
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<div class="gmail_attr" style="direction: ltr;">A sexta, 24/04/2026, 12:16, Peter Cock <<a href="mailto:p.j.a.cock@googlemail.com" data-outlook-id="870454cb-982a-4e68-a330-7c5cbdebfc1c">p.j.a.cock@googlemail.com</a>> escreveu:<br>
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<div class="gmail_quote">On Fri, Apr 24, 2026 at 12:51 PM Markus Piotrowski<br>
<<a href="mailto:Markus.Piotrowski@ruhr-uni-bochum.de" target="_blank" rel="noreferrer" data-outlook-id="7bd3ca84-f0b5-4b00-8a44-5f24289d176a">Markus.Piotrowski@ruhr-uni-bochum.de</a>> wrote:<br>
><br>
> Dear Peter,<br>
><br>
> While I also tend to strongly restrict or even forbid the usage of AI in<br>
> Biopython,<br>
<br>
Thank you - and as one of top top contributors that carries weight<br>
and is encouaraging.<br>
<br>
> ... I wonder how you really can prevent this. A careful submitter<br>
> can mask the AI signs in his/her code so that I will go undetected. So<br>
> wouldn't it be better to allow the usage under strong restrictions and<br>
> conditions (and I agree with the those that you have mentioned,<br>
> including the "good first issues" in your other e-mail) to encourage<br>
> potential contributors to be transparent about the of use of AI?<br>
><br>
> I'm unsure about this, but I wanted to include this topic into the<br>
> discussion.<br>
><br>
> Best<br>
> Markus<br>
<br>
That is a real worry, and I think Andrew and Bastian have given good answers.<br>
<br>
Thank you,<br>
<br>
Peter<br>
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<a href="https://mailman.open-bio.org/mailman/listinfo/biopython" target="_blank" rel="noreferrer noreferrer" data-outlook-id="4fea60ca-bcbb-42e1-8759-8045cf8a96ca">https://mailman.open-bio.org/mailman/listinfo/biopython</a><br>
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