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

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I left one comment.

As a more general comment, a No AI policy as is here will require most =
if not all future contributors to do their Biopython development under =
an environment entirely disconnected and divergent from what they would =
be using for anything else they do professionally. (I don=E2=80=99t =
think there=E2=80=99ll be any company or even academic lab in the future =
that can afford not to *require* their software developers to use =
AI-assisted coding. This is already the case in the teams I=E2=80=99m =
involved in, and they are all academic.)

So this will be an interesting experiment in whether and how AI-assisted =
coding policies affect sustainability and viability of projects.

 -hilmar

> On Jul 2, 2026, at 8:02=E2=80=AFAM, Peter Cock =
<[email protected]> wrote:
>=20
> One typo fix later, that's no longer a draft policy - but it is
> waiting on some approval reviews from others with commit permissions
> please.
>=20
> Peter
>=20
> On Mon, Jun 22, 2026 at 9:56=E2=80=AFAM Peter Cock =
<[email protected]> wrote:
>>=20
>> Feedback welcomed on this new draft PR for an explicit no-AI policy:
>>=20
>> https://github.com/biopython/biopython/pull/5241
>>=20
>> I had one interesting comment over the weekend on Mastodon where I
>> asked about the AGENTS file text and if it was too whimsical (humour
>> is even harder with an international audience):
>>=20
>> https://fediscience.org/@pjacock/116782003665914065
>>=20
>> https://illuminant.asjo.org/user/asjo/object/156156
>>=20
>>> I fear it is too whimsical.
>>>=20
>>> It will be appreciated by people who tend to agree, and those who
>>> don't - for whom the message is - will read it as their belief being
>>> ridiculed in an unserious manner.
>>>=20
>>> It is a fun idea, though :-)
>>=20
>> Peter
>>=20
>> On Sat, Jun 6, 2026 at 10:13=E2=80=AFAM Peter Cock =
<[email protected]> wrote:
>>>=20
>>> Assuming no objections I'm planning to merge
>>> https://github.com/biopython/biopython/pull/5229
>>> on Monday (a week for comment seems fine).
>>>=20
>>> Then on to the broader AI policy...
>>>=20
>>> Thanks,
>>>=20
>>> Peter
>>>=20
>>>=20
>>> On Mon, Jun 1, 2026 at 7:31=E2=80=AFAM Peter Cock =
<[email protected]> wrote:
>>>>=20
>>>> I'm proposing some text in the CONTRIBUTING file to spell this out
>>>> this point explicitly:
>>>>=20
>>>> https://github.com/biopython/biopython/pull/5229
>>>>=20
>>>> Suggested changes welcome, ideally on that PR please.
>>>>=20
>>>> I will probably follow that with a draft PR for a general no-AI =
stance.
>>>>=20
>>>> Going back to the start of this thread, I wrote (spelling fixed):
>>>>=20
>>>> =
https://mailman.open-bio.org/pipermail/biopython/2026-April/017113.html
>>>>=20
>>>>> Would anyone like to speak in defense of accepting AI (assisted) =
PRs,
>>>>> and suggest an existing policy you would be happy we adopt or base
>>>>> ours on?
>>>>=20
>>>> Would anyone want to draft a more moderate policy with limited AI =
use?
>>>>=20
>>>> Thank you,
>>>>=20
>>>> Peter
>>>>=20
>>>> On Mon, Jun 1, 2026 at 3:09=E2=80=AFPM Peter Cock =
<[email protected]> wrote:
>>>>>=20
>>>>> This is a real issue - I added that tag to an old issue and with a
>>>>> week it had two likely AI generated PRs:
>>>>> https://github.com/biopython/biopython/issues/2116
>>>>>=20
>>>>> Peter
>>>>>=20
>>>>> On Fri, Apr 24, 2026 at 7:26=E2=80=AFPM Peter Cock =
<[email protected]> wrote:
>>>>>>=20
>>>>>> I just posted this on Mastodon (neither I nor Biopython or the =
OBF use X/Twitter
>>>>>> anymore):
>>>>>>=20
>>>>>> https://fediscience.org/@pjacock/116143426085553346
>>>>>>=20
>>>>>> And that reminded me of an earlier remark I made:
>>>>>>=20
>>>>>>> Seems the recent #GenerativeAI #slop pull requests that I've =
looked at for
>>>>>>> #Biopython have preferentially targeted the "Good First Issues". =
We really
>>>>>>> wanted those to be onboarding ramps for new #OpenSource =
contributors -
>>>>>>> and not for padding anyone's GitHub profile or whatever the =
motivation here is.
>>>>>>>=20
>>>>>>> So I think any formal policy will want to say explicitly #NoAI =
on those issues
>>>>>>> at the very least.
>>>>>>=20
>>>>>> https://fediscience.org/@pjacock/116161804363016972
>>>>>>=20
>>>>>> Peter
>>>>>>=20
>>>>>> On Fri, Apr 24, 2026 at 11:16=E2=80=AFAM Peter Cock =
<[email protected]> wrote:
>>>>>>>=20
>>>>>>> Dear Biopythoneers,
>>>>>>>=20
>>>>>>> We need to set out a generative AI policy for contributions to =
Biopython.
>>>>>>>=20
>>>>>>> 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.
>>>>>>>=20
>>>>>>> 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".
>>>>>>>=20
>>>>>>> =
https://blastedbio.blogspot.com/2025/11/thoughts-on-generative-ai-contribu=
tions.html
>>>>>>>=20
>>>>>>> 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).
>>>>>>>=20
>>>>>>> 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):
>>>>>>>=20
>>>>>>> * 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
>>>>>>>=20
>>>>>>> https://docs.kernel.org/process/coding-assistants.html
>>>>>>>=20
>>>>>>> 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.
>>>>>>>=20
>>>>>>> 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.
>>>>>>>=20
>>>>>>> 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.
>>>>>>>=20
>>>>>>> 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.
>>>>>>>=20
>>>>>>> I therefore very much like this line from the curreth Codeberg =
policy:
>>>>>>>=20
>>>>>>>> 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.
>>>>>>>=20
>>>>>>> =
https://codeberg.org/comaps/Governance/src/branch/main/AI_USAGE.md
>>>>>>>=20
>>>>>>> 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?
>>>>>>>=20
>>>>>>> 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).
>>>>>>>=20
>>>>>>> Thank you,
>>>>>>>=20
>>>>>>> Peter
> _______________________________________________
> Biopython mailing list  -  [email protected]
> https://mailman.open-bio.org/mailman/listinfo/biopython

--=20
Hilmar Lapp -:- lappland.io




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<html aria-label=3D"message body"><head><meta http-equiv=3D"content-type" =
content=3D"text/html; charset=3Dutf-8"></head><body =
style=3D"overflow-wrap: break-word; -webkit-nbsp-mode: space; =
line-break: after-white-space;">I left one =
comment.<div><br></div><div>As a more general comment, a No AI policy as =
is here will require most if not all future contributors to do their =
Biopython development under an environment entirely disconnected and =
divergent from what they would be using for anything else they do =
professionally. (I don=E2=80=99t think there=E2=80=99ll be any company =
or even academic lab in the future that can afford not to *require* =
their software developers to use AI-assisted coding. This is already the =
case in the teams I=E2=80=99m involved in, and they are all =
academic.)</div><div><br></div><div>So this will be an interesting =
experiment in whether and how AI-assisted coding policies affect =
sustainability and viability of =
projects.</div><div><br></div><div>&nbsp;-hilmar</div><div><div><br><block=
quote type=3D"cite"><div>On Jul 2, 2026, at 8:02=E2=80=AFAM, Peter Cock =
&lt;[email protected]&gt; wrote:</div><br =
class=3D"Apple-interchange-newline"><div><div>One typo fix later, that's =
no longer a draft policy - but it is<br>waiting on some approval reviews =
from others with commit permissions<br>please.<br><br>Peter<br><br>On =
Mon, Jun 22, 2026 at 9:56=E2=80=AFAM Peter Cock =
&lt;[email protected]&gt; wrote:<br><blockquote =
type=3D"cite"><br>Feedback welcomed on this new draft PR for an explicit =
no-AI =
policy:<br><br>https://github.com/biopython/biopython/pull/5241<br><br>I =
had one interesting comment over the weekend on Mastodon where =
I<br>asked about the AGENTS file text and if it was too whimsical =
(humour<br>is even harder with an international =
audience):<br><br>https://fediscience.org/@pjacock/116782003665914065<br><=
br>https://illuminant.asjo.org/user/asjo/object/156156<br><br><blockquote =
type=3D"cite">I fear it is too whimsical.<br><br>It will be appreciated =
by people who tend to agree, and those who<br>don't - for whom the =
message is - will read it as their belief being<br>ridiculed in an =
unserious manner.<br><br>It is a fun idea, though =
:-)<br></blockquote><br>Peter<br><br>On Sat, Jun 6, 2026 at 10:13=E2=80=AF=
AM Peter Cock &lt;[email protected]&gt; wrote:<br><blockquote =
type=3D"cite"><br>Assuming no objections I'm planning to =
merge<br>https://github.com/biopython/biopython/pull/5229<br>on Monday =
(a week for comment seems fine).<br><br>Then on to the broader AI =
policy...<br><br>Thanks,<br><br>Peter<br><br><br>On Mon, Jun 1, 2026 at =
7:31=E2=80=AFAM Peter Cock &lt;[email protected]&gt; =
wrote:<br><blockquote type=3D"cite"><br>I'm proposing some text in the =
CONTRIBUTING file to spell this out<br>this point =
explicitly:<br><br>https://github.com/biopython/biopython/pull/5229<br><br=
>Suggested changes welcome, ideally on that PR please.<br><br>I will =
probably follow that with a draft PR for a general no-AI =
stance.<br><br>Going back to the start of this thread, I wrote (spelling =
fixed):<br><br>https://mailman.open-bio.org/pipermail/biopython/2026-April=
/017113.html<br><br><blockquote type=3D"cite">Would anyone like to speak =
in defense of accepting AI (assisted) PRs,<br>and suggest an existing =
policy you would be happy we adopt or base<br>ours =
on?<br></blockquote><br>Would anyone want to draft a more moderate =
policy with limited AI use?<br><br>Thank you,<br><br>Peter<br><br>On =
Mon, Jun 1, 2026 at 3:09=E2=80=AFPM Peter Cock =
&lt;[email protected]&gt; wrote:<br><blockquote =
type=3D"cite"><br>This is a real issue - I added that tag to an old =
issue and with a<br>week it had two likely AI generated =
PRs:<br>https://github.com/biopython/biopython/issues/2116<br><br>Peter<br=
><br>On Fri, Apr 24, 2026 at 7:26=E2=80=AFPM Peter Cock =
&lt;[email protected]&gt; wrote:<br><blockquote =
type=3D"cite"><br>I just posted this on Mastodon (neither I nor =
Biopython or the OBF use =
X/Twitter<br>anymore):<br><br>https://fediscience.org/@pjacock/11614342608=
5553346<br><br>And that reminded me of an earlier remark I =
made:<br><br><blockquote type=3D"cite">Seems the recent #GenerativeAI =
#slop pull requests that I've looked at for<br>#Biopython have =
preferentially targeted the "Good First Issues". We really<br>wanted =
those to be onboarding ramps for new #OpenSource contributors -<br>and =
not for padding anyone's GitHub profile or whatever the motivation here =
is.<br><br>So I think any formal policy will want to say explicitly =
#NoAI on those issues<br>at the very =
least.<br></blockquote><br>https://fediscience.org/@pjacock/11616180436301=
6972<br><br>Peter<br><br>On Fri, Apr 24, 2026 at 11:16=E2=80=AFAM Peter =
Cock &lt;[email protected]&gt; wrote:<br><blockquote =
type=3D"cite"><br>Dear Biopythoneers,<br><br>We need to set out a =
generative AI policy for contributions to Biopython.<br><br>There are =
now multiple recent PRs submitted by new contributors which<br>are =
openly using AI tools, more that I suspect are, and now even AI =
assisted<br>PRs from past contributors (where CV padding or other =
external metrics<br>are unlikely to be driving this). These are =
generally more work to review<br>than human written PRs, and that is a =
growing issue.<br><br>I blogged about my views late last year - ending =
in the line "Right now, I<br>still lean very much to saying no any PR =
using generative =
AI".<br><br>https://blastedbio.blogspot.com/2025/11/thoughts-on-generative=
-ai-contributions.html<br><br>Things will change (both tool =
capabilities, but also the social and legal<br>interpetations) but that =
post still describes my views today - note I did<br>not touch on the =
topic of communications there (see below).<br><br>Recently Linux adopted =
what has been described as a balanced stance<br>treating it as a tool =
with very clear expectations that usage MUST be declared<br>and that the =
human submitter is responsible for (quoting these four points):<br><br>* =
Reviewing all AI-generated code<br>* Ensuring compliance with licensing =
requirements<br>* Adding their own Signed-off-by tag to certify the =
DCO<br>* Taking full responsibility for the =
contribution<br><br>https://docs.kernel.org/process/coding-assistants.html=
<br><br>That is pragmatic but ignores the legal and ethical minefield. =
We don't<br>have a Developer Certificate of Origin (DCO), but I think =
the other<br>points are a bare minimum for any Biopython =
policy.<br><br>Most of my personal open source projects have only had a =
very small<br>number of contributors, and I am comfortable with outright =
rejecting<br>generative AI. I know some of the past/current Biopython =
contributors<br>are more willing to embrace this technology though - so =
I doubt support<br>for a simple ban would be unanimous.<br><br>Speaking =
for a moment as the current Open Bioinformatics Foundation<br>president, =
the board has discussed this and agreed not to try to micro<br>manage =
the member projects. For reference, BioPerl have =
started<br>https://github.com/bioperl/bioperl-live/issues/407 which has =
some<br>excellent points and examples to consider.<br><br>In particular, =
this is not just a code or documentation changes issue - but<br>also =
about the communication around any proposed change: the nature<br>of the =
commit messages, pull request description, and discussion. This<br>ties =
into the maintainers' burden - many of our recent AI generated =
PRs<br>have fairy short code changes but the verbose text is exhausting =
to read<br>and unhelpful. It has sometimes felt like I have been talking =
to an AI agent<br>rather than a human - I actually liked the feeling of =
mentoring a new<br>contributor and guiding them through minor hurdles to =
getting their<br>change accepted, but you lose that with an AI agent =
inbetween you.<br><br>I therefore very much like this line from the =
curreth Codeberg policy:<br><br><blockquote type=3D"cite">All =
communication, that includes: commit messages, pull request<br>messages, =
documentation, code comments and issues (and<br>comments on issues/pull =
requests), that is intended to be read<br>by people to understand your =
thoughts and work must not have<br>been generated with AI. We exclude =
machine translation and<br>tooling that helps with grammar and spelling =
check.<br></blockquote><br>https://codeberg.org/comaps/Governance/src/bran=
ch/main/AI_USAGE.md<br><br>Would anyone like to speak in defence of =
accepting AI (assisted) PRs,<br>and suggest an existing policy you would =
be happy we adopt or base<br>ours on?<br><br>Or should I start drafting =
a more draconian but likely much shorter one -<br>a few lines like this =
in the CONTRIBUTING file and/or PR template: No<br>generative AI to be =
used in any Biopython contributions, with the exception<br>of machine =
translation to/from English (where you might consider including<br>your =
original language text as well).<br><br>Thank =
you,<br><br>Peter<br></blockquote></blockquote></blockquote></blockquote><=
/blockquote></blockquote>_______________________________________________<b=
r>Biopython mailing list &nbsp;- =
&nbsp;[email protected]<br>https://mailman.open-bio.org/mailman/list=
info/biopython<br></div></div></blockquote></div><br><div>
<div><div style=3D"font-family: Monaco; font-size: 11px; orphans: 2; =
widows: 2;">--&nbsp;</div><div style=3D"font-family: Monaco; font-size: =
11px; orphans: 2; widows: 2;">Hilmar Lapp =
-:-&nbsp;lappland.io</div></div><div><br></div><br =
class=3D"Apple-interchange-newline">

</div>
<br></div></body></html>=

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_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython

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