I can see utility in keeping a human forum going. I do think the “how do I make a circle tree?” technical questions are now likely handled by general LLMs, github copilot, etc., but “is this a good plot for a tree” is still going to be better addressed by humans (“hey, if you show an edge, show bootstrap support for it, even if it’s <50%”, “No, they shouldn’t because….”). We haven’t had a lot of those discussions here lately, but maybe we should start. Bluesky or other social media can also be venues for that sort of thing, but those work better for immediate back and forth but not things people might want to get back to in a few days.
I also worry about fossilization of the field. The training data will always be biased by the past, so if we ask a model “how do I make a workflow for estimating the rate of evolution?” it’s more likely to point to older approaches. As someone who is now one of the older folks, that’s great for me (more citations!) but it makes it harder for newer people to get uptake of their new tools (or even older people who propose new things – would an LLM workflow recognize the importance of “tip fog” when doing rate estimates, or has that not hit the training data yet?). Best, Brian _________________________________________ Brian O’Meara He/Him Professor, Dept. of Ecology & Evolutionary Biology Interim Director, National Institute for Modeling Biological Systems (NIMBioS) University of Tennessee, Knoxville From: R-sig-phylo <[email protected]> on behalf of Jacob Berv <[email protected]> Date: Sunday, September 7, 2025 at 7:42 PM To: Hilmar Lapp <[email protected]> Cc: R Sig Phylo Listserv <[email protected]> Subject: Re: [R-sig-phylo] What kinds of posts is this list needed for in the age of AI? This is an interesting take. I wouldn’t be surprised if it accounts for a drop off in most questions up to a pretty advanced level. I know that my personal use of forums like stack overflow has gone to zero, but before November 2023 was a daily visit. Even google for search is eroding, at least for me personally. The frontier models already know the best strategies for using search engines to find the most relevant information. I have also had good luck in using LLMs to assist in building relatively complex phylogenetic analysis workflows. Maybe this itself is worth some discussion on here. > On Sep 2, 2025, at 5:57 PM, Hilmar Lapp <[email protected]> wrote: > > (Re-titling, but it’s a follow-up to my previous post) > > Incidentally, I notice that the most recent Answer post to Evoldir is from > 2022 (https://evol.mcmaster.ca/brian/Answers.html). > > There’s no reason to speculate that people who ask questions have somehow > become rude and do not post a summary of answers anymore, so the most likely > (and arguably Occam’s razor) explanation seems to be that it’s the asking of > questions that has faded away on Evoldir as well. Indeed, the “Other” > category archive (https://evol.mcmaster.ca/brian/Other.html) bears this out, > at least for the last 4 months that the archive extends to. > > In that context, the asking of questions has persisted here for a little > longer, but in principle has taken the same trajectory. > > This decline in posted questions obviously coincides with the advent of > increasingly powerful LLMs. Correlation doesn’t imply causation, and I don’t > know whether this is what trainees are using now, but I know it’s what I > would try first. As a random experiment, I tried one of the more recent > questions that generated a number of responses here, on model-averaging > corHMM models. > > Original list post: > https://www.mail-archive.com/[email protected]/msg06023.html > My query to ChatGPT (free version): > https://chatgpt.com/share/68b76601-2a80-8001-98ad-7ef4417db345 > > You all judge the answer. > > Anyone interested in examining this with a little more rigor? > > -hilmar > >> On Aug 24, 2025, at 4:44 PM, Hilmar Lapp via R-sig-phylo >> <[email protected]> wrote: >> >> Apologies for chiming in a little late here. I have to say I am (and have >> been for a while) in favor of moving the course announcements out of this >> mailing list into a channel of its own. The main reasons in my mind include >> the following: >> >> - Having a separate channel for course announcements seems to be the common >> mechanism for distribution lists with a wide reach (case in point for our >> field is evoldir). This seems to work well – people interested in receiving >> these announcements opt in, everybody else doesn’t need to take (and >> validate, check, monitor etc) specific action. >> >> - Science has become and will continue to become more interdisciplinary, >> more so than ever in the age of data deluges and AI/ML. This can make it >> difficult to draw a good line between courses that are and those that aren’t >> pertinent to this community. And across this community, we’d probably choose >> different lines. >> >> - It’s a little hard to say right now whether the diminishing frequency of >> on-topic Q&A-style threads is a reaction to course announcements taking over >> more and more and arguably most of the traffic, or an independent trend >> reflecting something else. In the past, we have used frequency of posts as >> evidence supporting the list’s value and usefulness. I still consider this >> very valuable information to have – if this kind of forum is becoming or is >> much less useful than it was in the past, we should be able to see this from >> the list traffic, ideally unencumbered by confounding factors. Perhaps >> chatbots can now utilize the information from the list archives (which are >> public) well enough that most questions get answered this way rather than >> reaching the list as a post. >> >> -hilmar >> > > -- > Hilmar Lapp -:- ORCID:0000-0001-9107-0714 > <https://orcid.org/0000-0001-9107-0714> -:- GitHub:hlapp > <https://github.com/hlapp> > > [[alternative HTML version deleted]] > > _______________________________________________ > R-sig-phylo mailing list - [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > Searchable archive at http://www.mail-archive.com/[email protected]/ _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/ [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/[email protected]/
