iiinova — where your digital self keeps evolving

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JL Weissman @jlw-ecoevo.bsky.social · 28/09/2026

Two weeks left to apply for these postoc positions! We seek two postdocs interested in 1) building trait prediction models capable of resolving complex microbial traits from genomes and metagenomes, and/or (2) building mathematical models of microbial community dynamics in the human microbiome.

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 22/09/2026

Another fabulous example of cooperative interactions within microbial communities!

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Kevin England @kevinengland.bsky.social · 13/09/2026

🦠My fav. "mini-discoveries" in this paper: 45% of ribosomes are engaged in translation! Ribosome hibernation is a consequence, not a cause, of ribosomes becoming disengaged from translation during (p)ppGpp prod.! NahA hydrolyzes (p)ppGpp much more strongly in Mg than Mn, unlike hydrolysis by Rel!

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Kevin England @kevinengland.bsky.social · 13/09/2026

Our paper (and my first first-author) is out! The alarmone pGpp inhibits translation through GTP depletion academic.oup.com/nar/article/... 🦠🚨🤠 @narjournal.bsky.social

academic.oup.com

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JL Weissman @jlw-ecoevo.bsky.social · 10/09/2026

My lab is hiring two(!) postdocs interested in (1) building trait prediction models capable of resolving complex microbial traits from genomes and metagenomes, and/or (2) building mathematical models of microbial community dynamics www.microbialgamut.com/mGAMUT_postd...

microbialgamut.com

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 22/08/2026

Absolutely tickled I’ll be defending in the “lambing pentagram“ room

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CNY ASM @cnyasm.bsky.social · 17/08/2026

Do you live in Central New York and have FOMO watching everyone post from a conference in New Zealand? Don't. We have New Zealand at home — minus the jet lag and 20 hours in a middle seat in economy. Plus one thing NZ can't offer: the CNY ASM Fall Meeting --> tinyurl.com/CNYASM

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Katie O'Reilly @drkatfish.bsky.social · 06/08/2026

Summer mayfly swarms are a highly visible reminder of the progress made to improve the health of the #GreatLakes - even if it is sometimes gross to wake up to streets, cars, and everything else covered in a carpet of bugs www.statenews.org/section/the-...

statenews.org

Mayflies' return to Ohio isn't just a nuisance — it's a good sign for Lake Erie

An entire generation grew up without mayflies. But the pesky bug's return this summer points to a healthier Lake Erie .

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Warren Currie 🦠🦐 @drplanktonguy.bsky.social · 05/08/2026

Pleased to announce publication of our collaborative #GLEON data paper in Limnology and Oceanography Letters. The Zooplankton International Geospatial dataset has 🦐 zoop+ data on 311 lakes. Huge effort over 7 years from 143 authors at 101 institutions in 37 countries. 🎉 dx.doi.org/10.1002/lol2...

dx.doi.org

The Zooplankton International Geospatial dataset: A global repository of spatiotemporal freshwater zooplankton community composition data from lakes and reservoirs to support ecological research

Zooplankton transfer substantial energy in aquatic food webs and are used as indicators of environmental change. Syntheses of zooplankton community dynamics globally require datasets that span a wide....

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 05/08/2026

New preprint! Me and @sophiaaredas.bsky.social spent weeks on the Lake Guardian to bring YOU 🫵 new insights on cyanobacterial-heterotroph relationships across Lake Erie. What did we learn? (a thread) www.biorxiv.org/content/10.6...

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Cameron Thrash @jcamthrash.bsky.social · 05/08/2026

Cyanobacterial cohorts structure the diversity, abundance, and metabolism of heterotrophic bacteria in Lake Erie www.biorxiv.org/content/10.6... #jcampubs

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 11/07/2026

Just needed to darken the outlines of a few maps today…turned into three hours of package installation hell 🤬

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samuel mehr @mehr.nz · 07/07/2026

inspired by @russpoldrack.org's AI policy for his lab, last night I drafted up this AI policy and came up with an initial set of use case suggestions for my lab

General principles
Here are a few key principles that govern our use of AI in scientific work.
AI tools are not necessarily useful. Despite what you might have heard in OpenAI's advertising, using AI tools is the wrong choice for many tasks. Alternative and often more old-fashioned tools will do a better job for quite a few specific things (see this instagram feed for a variety of examples); one should never assume that an AI tool is the default "best thing to try". Moreover, because verifying AI results can be time-consuming, there are plenty of cases where you'll spend less time learning how to do X (i.e., by working on it yourself) rather than having Claude do X and then spending weeks to painstakinly confirm that it worked.
AI usage does not absolve you of your responsibility for your own science. We are responsible for the science that we produce, both from an ethical standpoint and a practical one. Any errors in your work are your responsibility, any security risks caused by AI usage (see below) are your responsiblity, and so on. Just as you must debug the outputs of your analysis code, the outputs of any/all AI usage must be carefully verified.
AI usage requires disclosure. The decision to use (or not use) AI tools for any aspect of the scientific process is one that requires discussion with all leaders of a project. This is both for scientific reasons (i.e., we ourselves must know what our project invovles) and practical ones: many scientific societies and jouranls require the disclosure of AI usage.
AI tools may present security risks. Many commercially available AI tools, especially free ones, do not provide substantive protections regarding inputs provided by users. Put another way, you don't know what will happen to the text, data, images, or anything else you show a third-party AI tool. This may present substantial security risks.
AI is not for scientific writing. Papers are the primary end product of our science. Scientific writing distills our thinkin…

How to handle AI usage
Like many things in our lab, it's best to be vocal. You should always feel free to raise the possibility of AI usage on a project. For any potential use case, chat with your labmates, your collaborators, and Sam about it. Discussion with external-to-lab collaborators can be particularly important given the issue of disclosure, mentioned above; you may not be aware of what AI tools collaborators are using, unless you've asked.
You should also be skeptical of the utility of AI for a specific task (not least because of the billions of dollars being thrown at selling AI subscriptions to universities and other institutions). One thing to consider might be whether the use case is something that would actually be useful for you to master yourself. For example, a common web element that turns up in tons of online experiments would probably be worth your figuring out how to code up from scratch, since you'll use it often in online experiments and figuring it out may help you come up with new ideas for how to design a game. In contrast, an esoteric web element that you'll use for one experiment and never again might be a better fit to farm out to Claude.
With the above General Principles in mind, we do not have any blanket policy about where AI should and shouldn't be used in research, with the clear exception of drafting text for manuscripts, grant proposals, posters, reports, or any other text-based scientific product: AI tools should never be used for writing, i.e., no copying and pasting of text directly from an LLM is appropriate, without explicit discussion and agreement prior to generating the text.
Other use cases are worth considering, however, and should be considered freely. Some good and bad examples follow, based on the principles above (we should populate more examples as they come up).

Some potential examples of AI usage
AI as a cheap web developer. If you're coding up a gamified experiment it can be quite difficult to learn a whole bunch of web development from scratch. Claude will be better at this than you, and that's fine: we are not a web development lab, we're a cognitive science one, so it's not essential that you become a super-proficient dev. Vibe-coding web stuff is a pretty decent use case. (But you must very carefully ensure that whatever AI tools code up for you behave exactly as you expect them to, e.g., if you've vibe-coded a specific form of randomized experiment, you'll need to check that the randomization is being carried out appropriately).
AI as a code reviewer. You might try using an AI tool to figure out why your CSS isn't displaying properly or to help debug code in general. (But you must never provide participant data to a third-party LLM, as this would be a data security risk; and you must always double- and triple-check the tool's output, just as you would with a human code reviewer or if you were trying out tips from Stack Exchange).
AI as a search engine. You might try using an AI tool to discover types of models or analysis approaches that you hadn't heard of before, or to turn up obscure research papers. (But you'll need to verify the output carefully with trusted sources, to ensure accuracy; and you should never, ever treat AI-generated search results as an objective and accurate summary, as they are far from unbiased and are often inaccurate, especially when it comes to scientific questions — try asking Gemini whether music makes you smarter).
AI as a sketch pad. You might try using an AI tool to generate ideas for what to put in a scientific figure, or come up with creative different layouts, which you then use as inspiration for figures you create yourself. (But you should not provide data to an LLM and ask for figures to be produced for you, since this often leads to laughably bad outcomes; it also would not be r…

Some bad examples of AI usage
AI as a data analyst. You should not provide a dataset to an AI tool (this is a security risk) and you should not ask an AI tool to write analysis code for you from scratch. Analyses done without statistical understanding are worse than no analyses at all. While it's OK to use an AI tool to help debug your analysis code, your development as a statistical analyst is part of your scientific development, so it's a bad idea to farm this out.
AI as a literature reviewer. You should not use AI to generate reference lists or summarize whole fields of literature for you. AI tools notoriously cite papers that do not exist, and they recapitulate well-known biases in science (e.g., citing more male authors than female ones).
AI as an illustrator. We are fundamentally opposed to the practice of AI models appropriating human artists' work to produce generative imagery and so we do not support its use for scientific work. The reputational risks associated with embarrassing errors in generative imagery are also substantial. We are lucky to have grants available to us that can be used to pay illustrators and graphic designers for work, and we regularly hire folks like this. Talk to Sam if you have a design need on a project that you'd like us to fund; it's a much better call than using AI.

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 23/06/2026

My paper on bacterial communities just got cited as the primary citation for QGIS in a paper about bat viruses 💀 the AI slop has reached even me.

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Hannah Reich @hannahgreich.bsky.social · 12/06/2026

It’s out! There are so many fun back stories with this project’s origin story & how it reshaped my career trajectory. For now, plz welcome my lab’s culture collection of #Symbiodiniaceae associated bacteria! & the many siderophores they produce! 🧪 doi.org/10.1093/fems...

doi.org

Widespread siderophore production among Symbiodiniaceae-associated bacteria

Abstract. Nutritional exchanges fuel the evolutionary and ecological dominance of multi-partner symbioses among reef-building corals and microbial associat

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 05/06/2026

#Ecologists 🗣️ I need your help! If you had abundance data of species across two treatments, how would you rigorously test which species were differentially abundant? I DON'T want common methods in microbial ecology as they assume compositionality, while my data is absolute abundance.

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Kevin England @kevinengland.bsky.social · 19/05/2026

Incredibly fascinating work by the Landick and Darst labs: ppGpp regulates pausing of elongating RNA polymerase via allosteric inhibition, competitive inhibition at the active site, and depletion of GTP levels #microsky

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Keila Stark (she/her) @keila-stark.bsky.social · 13/05/2026

Sharing some fun, ongoing trait-based phytoplankton work with @elenalitchman.bsky.social and @chrisklausmeier.bsky.social at #ASLOSIL26 today at 17:45 in room 520E!

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Physalia-courses@ONLINE @physaliacourses.bsky.social · 12/05/2026

Boost your multivariate data analysis skills! Join us for the GLLVMs in R (7–10 July) online course with @vdveenb.bsky.social Learn model-based multivariate analysis of ecological communities using GLMs, GLMMs, JSDMs & model-based ordination in R with gllvm www.physalia-courses.org/courses-work...

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Jay T Lennon @jaytlennon.bsky.social · 05/05/2026

"When energy is scarce, evolution selects dormancy" Commentary by Chris Kempes in @pnas.org www.pnas.org/doi/10.1073/...

pnas.org

When energy is scarce, evolution selects dormancy | PNAS

When energy is scarce, evolution selects dormancy

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 05/05/2026

Excited to be attending and connect with y'all!

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Ben Zipperer @benzipperer.org · 25/04/2026

So far, AI is having limited effects on employment. 95% of AI-using companies report that AI isn't changing their headcount, with equally small shares reporting AI-driven increases and decreases.

Table 4 from The Microstructure of AI Diffusion: Evidence from Firms, Business Functions, and Worker Tasks, April 2026, by

KATHRYN BONNEY, CORY BREAUX, EMIN DINLERSOZ, LUCIA FOSTER, JOHN HALTIWANGER, AND ADITYA PANDE

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 24/04/2026

Watch your back Alison Roman, I just made Buttery Lemony Potatoes with Chili Oil Tinned Mackerel and Soft Herbs

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 24/04/2026

Anyone know what happened to the world's supply of metapolyzyme? Catastrophic phage infection??

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Antonio Camargo @apcamargo.bsky.social · 15/04/2026

It’s that wonderful time of year again. A new GTDB release is out :)

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 26/03/2026

Unbelievably grateful that I get to work with these folks at the Lake Superior National Estuarine Research Reserve!

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Mariko Bennett @nachoriko.bsky.social · 24/03/2026

I defended my PhD 10 years ago today. That was the least remarkable thing that happened that day. Sharing something I wrote about it last year. Since then "the horrors persist but so do we." And with dignity.

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 23/03/2026

Just a moment of gratitude: every industry scientist I've reached out to (even cold-calling on LinkedIn!) has been willing to chat with me, and been incredibly generous with their time, contacts, and advice. Makes a scary job search feel so much more welcoming!

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Chenxin Li, PhD @chenxinli2.bsky.social · 20/03/2026

I just had that conversation earlier this week. The college dean is deciding if they will (dis)continue the bioinformatics training program for grad students. An argument for discontinuation is that students will use GenAI to help them code, so they don’t need to learn bioinformatics.

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Chris Kenny, PhD @chriskenny.bsky.social · 20/03/2026

Doing a lot of testing of AI agents with my team these days. Pulled together a new package, wf, which helps install and manage agent skills from within #rstats (A great time to be at Princeton DDSS; our team has an intro to Claude workshop today and an intro to Posit Assistant workshop next week!)

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 16/03/2026

Those who know me know how big a deal this is for me... Spent a few hours using Github Copilot in VS Code to prepare a new shiny app that complements our recent UniFrac paper! Excited to release this soon, including my code, skill files, and reflections on AI coding (from a certified AI-grump).

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 09/03/2026

I always try and present like I'm about to tell you the juiciest gossip about bacteria

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 08/03/2026

WOAH!! Catherine Lozupone and Rob Knight cited my paper!! this is actually mind blowing to the microbial ecologist nerd that I am 🤯🥳🤓 Huge credit to Jianshu Zhao for an incredible innovation www.biorxiv.org/content/10.6...

biorxiv.org

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 24/02/2026

I finally spent some time sprucing up my personal website. Feel free to see what I've been up to! gus-pendleton.github.io

gus-pendleton.github.io

Augustus Pendleton

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Francisco Rodriguez-Sanchez @frodsan.bsky.social · 18/02/2026

Periodic reminder that we should avoid testing the Normality of the response variable. For a linear model, what matters is the Normality of residuals (and not that much). Visual checks better than test. #statistics

A Shapiro-Wilk test of the response variable concludes very significant deviation of Normality. But residuals of linear model consistent with Normal distribution.

Visual check of the linear model with DHARMa

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 13/02/2026

Learned a very painful statistics lesson today (after investing a whole day of analysis)

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Nandita Garud @nanditagarud.bsky.social · 12/02/2026

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

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Augustus (Gus) Pendleton @augustuspendle1.bsky.social · 09/02/2026

Survived the 50km Winona Tourathon last Saturday, all in sub-zero temps! Skied an hour longer than planned but super happy with my 5th-place finish.

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