Jeremy Collings
@jeremycollings.bsky.social
Quantitative ecologist working mostly on modeling populations and communities of plants and critters. Queer. He/him
Pinned
✨Introduction Post✨ Hiya folks. I'm Jeremy. I'm finishing up my Ph.D. at the University of Oregon. I'm passionate about using elegant and creative quant approaches to make inference about populations and communities. Details ⬇️, but I love Bayesian stats, ecological theory, gay stuff, & critters.
Popping on to share that the first project I worked on in my PhD was published recently. Check it out: esajournals.onlinelibrary.wiley.com/doi/full/10....
Environmental context alters plant–soil feedback effects on plant coexistence
Plant–soil feedbacks are thought to mediate outcomes of plant competition through microbially driven positive or negative feedback loops. Plant–microbe interactions are known to depend on the underly...
esajournals.onlinelibrary.wiley.com
August 18, 2025 at 3:34 PM
Popping on to share that the first project I worked on in my PhD was published recently. Check it out: esajournals.onlinelibrary.wiley.com/doi/full/10....
Reposted by Jeremy Collings
Posterior predictive checking of binary, categorical and many ordinal models with bar graphs is useless. Even the simplest models without covariates usually have such intercept terms that category specific probabilities are learned perfectly. Can you guess which model, 1 or 2, is misspecifed? 1/4
August 13, 2025 at 2:34 PM
Posterior predictive checking of binary, categorical and many ordinal models with bar graphs is useless. Even the simplest models without covariates usually have such intercept terms that category specific probabilities are learned perfectly. Can you guess which model, 1 or 2, is misspecifed? 1/4
Reposted by Jeremy Collings
Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories www.biorxiv.org/content/10.1... #jcampubs
August 13, 2025 at 4:49 PM
Stochastic Forces in Microbial Community Assembly: Founding Community Size Governs Divergent Ecological Trajectories www.biorxiv.org/content/10.1... #jcampubs
An algorithm that scientists can use to code up analyses... that is often wrong but prioritizes getting some output out... and is programmed to speak with utter confidence in the output... terrifies me to my core. Systematically... what do we even do about this?
Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.
August 12, 2025 at 6:54 PM
An algorithm that scientists can use to code up analyses... that is often wrong but prioritizes getting some output out... and is programmed to speak with utter confidence in the output... terrifies me to my core. Systematically... what do we even do about this?
Reposted by Jeremy Collings
#Botany2025 ! My talk is in Smoketree D/E today (Mon) at 11:45am, but more importantly, these FANTABULOUS @sunycortland undergrads have posters tonight! Come learn about how polyploidy affects Nicotiana flowers! :) 💖
July 28, 2025 at 4:56 PM
#Botany2025 ! My talk is in Smoketree D/E today (Mon) at 11:45am, but more importantly, these FANTABULOUS @sunycortland undergrads have posters tonight! Come learn about how polyploidy affects Nicotiana flowers! :) 💖
Reposted by Jeremy Collings
Interested in host-symbiont interdependence, eukaryogenesis, and evolutionary transitions in individuality? my first paper just came out! With @gokhalecs.bsky.social and Pete Czuppon, we study when & how individuality emerges in a host-endosymbiont collective doi.org/10.1086/737588 a short thread🧵:
July 23, 2025 at 2:21 PM
Interested in host-symbiont interdependence, eukaryogenesis, and evolutionary transitions in individuality? my first paper just came out! With @gokhalecs.bsky.social and Pete Czuppon, we study when & how individuality emerges in a host-endosymbiont collective doi.org/10.1086/737588 a short thread🧵:
Reposted by Jeremy Collings
How may theoretical ecology & evolutionary theory push microbiology forward?
At Environmental Microbiology, I am commissioning a series of Perspectives exploring that question. Excited to share them in the 🧵 below
The series is open, so do get in touch if you'd like to propose a new contribution!
At Environmental Microbiology, I am commissioning a series of Perspectives exploring that question. Excited to share them in the 🧵 below
The series is open, so do get in touch if you'd like to propose a new contribution!
July 16, 2025 at 2:58 PM
How may theoretical ecology & evolutionary theory push microbiology forward?
At Environmental Microbiology, I am commissioning a series of Perspectives exploring that question. Excited to share them in the 🧵 below
The series is open, so do get in touch if you'd like to propose a new contribution!
At Environmental Microbiology, I am commissioning a series of Perspectives exploring that question. Excited to share them in the 🧵 below
The series is open, so do get in touch if you'd like to propose a new contribution!
Reposted by Jeremy Collings
📢New paper alert ‼️
Excited to share our new paper out now in the @jappliedecology.bsky.social
We evaluated how oil palm plantations affect the community structure of Amazonian birds, with a focus on functional and phylogenetic diversity.
Read more here
tinyurl.com/4ubwjr7s
Excited to share our new paper out now in the @jappliedecology.bsky.social
We evaluated how oil palm plantations affect the community structure of Amazonian birds, with a focus on functional and phylogenetic diversity.
Read more here
tinyurl.com/4ubwjr7s
besjournals.onlinelibrary.wiley.com
July 14, 2025 at 3:50 PM
📢New paper alert ‼️
Excited to share our new paper out now in the @jappliedecology.bsky.social
We evaluated how oil palm plantations affect the community structure of Amazonian birds, with a focus on functional and phylogenetic diversity.
Read more here
tinyurl.com/4ubwjr7s
Excited to share our new paper out now in the @jappliedecology.bsky.social
We evaluated how oil palm plantations affect the community structure of Amazonian birds, with a focus on functional and phylogenetic diversity.
Read more here
tinyurl.com/4ubwjr7s
Reposted by Jeremy Collings
While writing There Is No Place for Us, what I wanted most was for readers to feel the fury I carried throughout my reporting—the outrage, the horror at what this country forces our neighbors to endure.
This review by @lilysanca.bsky.social says everything I hoped the book would convey, and more:
This review by @lilysanca.bsky.social says everything I hoped the book would convey, and more:
You’re Not Angry Enough About Homelessness in America
Homelessness is increasingly caused by soaring rents and low wages, not laziness or personal failures. The solution is strong government intervention to house everyone and to end landlords’ control ov...
www.currentaffairs.org
July 12, 2025 at 1:25 PM
While writing There Is No Place for Us, what I wanted most was for readers to feel the fury I carried throughout my reporting—the outrage, the horror at what this country forces our neighbors to endure.
This review by @lilysanca.bsky.social says everything I hoped the book would convey, and more:
This review by @lilysanca.bsky.social says everything I hoped the book would convey, and more:
Reposted by Jeremy Collings
Here is an article highlight for this recent #BulletinMathBio paper, with a short summary of the paper written by the authors.
smb.org/news/13519509
smb.org/news/13519509
July 12, 2025 at 12:18 AM
Here is an article highlight for this recent #BulletinMathBio paper, with a short summary of the paper written by the authors.
smb.org/news/13519509
smb.org/news/13519509
Writing papers like I'm the Carrie Bradshaw of ecology.
July 11, 2025 at 7:00 PM
Writing papers like I'm the Carrie Bradshaw of ecology.
So now that I have the doctorate, I get to just be a weirdo, right? That’s how it works? Cause I’m gonna go ahead and be weird now if thats cool.
July 10, 2025 at 5:06 PM
So now that I have the doctorate, I get to just be a weirdo, right? That’s how it works? Cause I’m gonna go ahead and be weird now if thats cool.
Reposted by Jeremy Collings
Exciting news, our SPARC proposal has been funded! Our project brings together experts across disciplines and will explore above-belowground coupling/synchrony. Big thanks to @uslter.bsky.social! lternet.edu/stories/thre... 🌱🦠📉🌎
#LTER #SPARC #plants #microbes #SynthesisScience #TeamScience
#LTER #SPARC #plants #microbes #SynthesisScience #TeamScience
Three new SPARC Synthesis Groups demonstrate the value of long-term data collected across ecosystems - LTER
The LTER Network Office is excited to announce that three Scientific Peers Advancing Research Collaborations (SPARC) proposals were funded this year. The three groups will meet in person at the Nation...
lternet.edu
July 1, 2025 at 11:38 AM
Exciting news, our SPARC proposal has been funded! Our project brings together experts across disciplines and will explore above-belowground coupling/synchrony. Big thanks to @uslter.bsky.social! lternet.edu/stories/thre... 🌱🦠📉🌎
#LTER #SPARC #plants #microbes #SynthesisScience #TeamScience
#LTER #SPARC #plants #microbes #SynthesisScience #TeamScience
Idk guys, the idea that 'nature' is some entity that intrinsically heals seems similarly reductionist to medieval European ideas that subjugate the 'wild' as an abode of evil. What if we wrote rich literature that reflects the infinite feelings/relationships one may have w/ their surroundings.
July 9, 2025 at 11:36 PM
Idk guys, the idea that 'nature' is some entity that intrinsically heals seems similarly reductionist to medieval European ideas that subjugate the 'wild' as an abode of evil. What if we wrote rich literature that reflects the infinite feelings/relationships one may have w/ their surroundings.
I've got a lot of thoughts about this blog post (love it). This topic is actually one that I obsess over daily. The metaphorical machine that pumps out unbelievable, sloppy papers that get read as as Truth terrifies me. The senior researchers that act like this isn't the case make me deeply m/sad.
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
Which Kind of Science Reform
What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.
elevanth.org
July 9, 2025 at 11:06 PM
I've got a lot of thoughts about this blog post (love it). This topic is actually one that I obsess over daily. The metaphorical machine that pumps out unbelievable, sloppy papers that get read as as Truth terrifies me. The senior researchers that act like this isn't the case make me deeply m/sad.
I think that I’ve decided to give up entirely on statistical ecology. My new method of inference is going to be putting my hand on a tree and intuiting the parameter values.
July 9, 2025 at 5:22 PM
I think that I’ve decided to give up entirely on statistical ecology. My new method of inference is going to be putting my hand on a tree and intuiting the parameter values.
Late to the party, but love the Stan forum's pride logo. Never been a better time to be a gay Bayesian statistician.
June 9, 2025 at 3:44 PM
Late to the party, but love the Stan forum's pride logo. Never been a better time to be a gay Bayesian statistician.
Reposted by Jeremy Collings
Happy Pride from California Native Plants!
June 1, 2025 at 2:29 PM
Happy Pride from California Native Plants!
Reposted by Jeremy Collings
Your occasional reminder that I maintain a curated list of resources for scientific writers. Is it exhaustive? Heck no. It is useful? I think you'll find it so. scientistseessquirre...
Writing Resources
Writing is a huge part of any career in science, and for many writers – no, for most writers – it’s a daunting challenge. But it’s not a challenge that you have to tackle alone. That’s a lesson I w…
scientistseessquirrel.wordpress.com
May 29, 2025 at 1:53 PM
Your occasional reminder that I maintain a curated list of resources for scientific writers. Is it exhaustive? Heck no. It is useful? I think you'll find it so. scientistseessquirre...
You mean… I actually have to think about the process that I’m studying?!?? 😭😭😭
Ecologists’ endless quest for automatic inference
statmodeling.stat.columbia.edu/2025/05/28/e...
statmodeling.stat.columbia.edu/2025/05/28/e...
Ecologists’ endless quest for automatic inference | Statistical Modeling, Causal Inference, and Social Science
statmodeling.stat.columbia.edu
May 28, 2025 at 9:58 PM
You mean… I actually have to think about the process that I’m studying?!?? 😭😭😭
Reposted by Jeremy Collings
Excited to share our new paper: arxiv.org/abs/2505.06224! We introduce a unified framework for evaluating model representations beyond downstream tasks, and use it to uncover some interesting insights about the structure of representations that challenge conventional wisdom 🔍🧵
May 13, 2025 at 2:15 PM
Excited to share our new paper: arxiv.org/abs/2505.06224! We introduce a unified framework for evaluating model representations beyond downstream tasks, and use it to uncover some interesting insights about the structure of representations that challenge conventional wisdom 🔍🧵
Defended my dissertation yesterday! The weight of it hasn’t totally sunk in yet, but I’m very proud and grateful for all the support I’ve received in my PhD from colleagues, friends, and family.
May 8, 2025 at 9:53 PM
Defended my dissertation yesterday! The weight of it hasn’t totally sunk in yet, but I’m very proud and grateful for all the support I’ve received in my PhD from colleagues, friends, and family.
Reposted by Jeremy Collings
You also can’t learn to write good papers without writing bad drafts (or bad papers) so write your own outlines, drafts, and papers!
If you're a grad student or an undergrad interested in research I need to you listen to me very carefully.
You cannot learn to write good research papers if you do not read good research papers.
Stop asking LLMs to summarize papers for you.
You cannot learn to write good research papers if you do not read good research papers.
Stop asking LLMs to summarize papers for you.
May 3, 2025 at 9:22 PM
You also can’t learn to write good papers without writing bad drafts (or bad papers) so write your own outlines, drafts, and papers!
Reposted by Jeremy Collings
Amy Angert & I are recruiting 2 field technicians for demographic surveys of scarlet monkeyflower in late summer-fall. Please spread word to any potentially interested candidates! jobs.ncsu.edu/postings/217...
Temporary Plant Ecology Field Technician
The Sheth evolutionary ecology lab in the Department of Plant and Microbial Biology at North Carolina State University (Raleigh, North Carolina; USA) and the Angert Lab in the Departments of Botany an...
jobs.ncsu.edu
April 28, 2025 at 1:27 PM
Amy Angert & I are recruiting 2 field technicians for demographic surveys of scarlet monkeyflower in late summer-fall. Please spread word to any potentially interested candidates! jobs.ncsu.edu/postings/217...
Reposted by Jeremy Collings
The great Sally Otto and I are hosting a series of interviews called “Reflections on the history of modeling and theory”, as part of @smtpb.bsky.social. First one drops next week, with Simon Levin. Tune in for great stories, some pearls of wisdom, and the long view on modeling and theory in biology.
Sally Otto (UBC) & @jpodwyer.bsky.social (University of Illinois Urbana-Champaign) interview Simon Levin, James S. McDonnell Distinguished University Professor in Ecology and Evolutionary Biology at Princeton University. Premiering April 14th, 10 AM on SMTPB YouTube! www.youtube.com/watch?v=0TpJ...
Simon Levin Interview
YouTube video by SMTPB
www.youtube.com
April 10, 2025 at 1:39 PM
The great Sally Otto and I are hosting a series of interviews called “Reflections on the history of modeling and theory”, as part of @smtpb.bsky.social. First one drops next week, with Simon Levin. Tune in for great stories, some pearls of wisdom, and the long view on modeling and theory in biology.