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Ben Farmer, PhD

@benfarmer.bsky.social
377 followers 576 following 23 posts

Senior Scientist with Coastal Eco-Group, interested in coral reefs and persistence. Fascinated with the ecology of diseases, microbes, and seascapes 🦠 🌊

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Reposted by Ben Farmer, PhD
Gwênlyn Glusman (she/her) ☸️ @gwenlyn.bsky.social · 04/10/2026
I have modernized and enhanced the NSF COA generator tool. Results now update dynamically • Published under more than one name? Covered! • Other people share your name? No problem! • You prefer searching by ORCID? Go ahead! Give it a try. Feedback, bug reports, feature requests are MOST welcome! 🧪
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Ben Farmer, PhD @benfarmer.bsky.social · 02/10/2026
So excited to share that I applied to both the LSRF and PRFB postdoc programs this week! Was a whirlwind but exciting to be submitting grants again.
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Prof Gavin Yamey MD MPH @gavinyamey.bsky.social · 01/10/2026
When Musk AND Rubio said “not a single person” died as a result of shutting down USAID, I wanted to vomit An estimated 700,000 people died (500,000 were kids) within a year of USAID being “put in the wood-chipper” Studies by Brooke Nichols at BU and by CGD researchers estimated a similar number
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Chrystal Starbird @drstarbird.bsky.social · 01/10/2026
And… I am SO excited to share the first research preprint from my group! In this paper we determined several cryoEM structures to visualize the entire cell-to-cell bridging complex formed by TAM receptor and ligand, bringing into 3D a common graphical depiction. www.biorxiv.org/content/10.6...
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Josef Uyeda @pseudacris.bsky.social · 28/09/2026
If you're submitting a reference letter for a PRFB, I was surprised to not see any option for deleting and reuploading, which contradicts the info provided in the email requesting it. In fact, as soon as you select the file it is uploaded and you can't change it. Was fine for me, but beware.
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allie igwe @anigwe.bsky.social · 23/09/2026
Finally published! Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils www.microbiologyresearch.org/content/jour...
microbiologyresearch.org
Redundancy maintains microbial ecosystem functional potential despite taxonomic shifts between serpentine and nonserpentine soils
Environmental filtering and buffering are complementary processes responsible for stabilizing ecosystem services across landscapes. The extent to which either of these processes structures microbial c...
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Reposted by Ben Farmer, PhD
Center for Biological Diversity @biologicaldiversity.org · 26/09/2026
The Trump administration is trying to undo the 2001 #RoadlessRule, clearing the way for road construction and logging across more than 44 million acres of wild, natural forests. And they have only given the public a short time to weigh in. Tell the Forest Service to protect national forests 🌲⬇️
act.biologicaldiversity.org
Protect the Roadless Wild
The Trump administration just released its plan to undo the landmark 2001 Roadless Area Conservation Rule and strip protections from nearly 45 million acres of wild, national forest and 70,000 miles o...
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Dr. Nyssa Silbiger @nsilbiger.bsky.social · 25/09/2026
New paper! 🪸🌊 As reefs shift, the communities that replace corals can reshape the chemical environment around them. Laurel shows how community metabolism creates “chemical legacies” that alter coral physiology. @aslo.org aslopubs.onlinelibrary.wiley.com/doi/10.1002/...
aslopubs.onlinelibrary.wiley.com
Community metabolism generates chemical legacies that alter coral physiology
Coral reefs are among the world's most diverse ecosystems and contribute substantially to ocean productivity and the carbon budget. Disturbances are shifting reefs to altered community states, yet ho...
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UBC Oceans @ubcoceans.bsky.social · 03/09/2026
Having found a mysterious killer of sea stars, scientists see an ingenious way to stop it. @rhizalyssa.bsky.social www.theglobeandmail.com/canada/artic...
theglobeandmail.com
Having found a mysterious killer of sea stars, B.C. scientists see a way to stop it
To halt a bacterial illness that killed billions of marine animals, researchers look to viruses
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SK Winnicki, PhD 🏳️‍⚧️ @skwinnicki.bsky.social · 22/09/2026
Separating the forebrain from the hindbrain is such a useful way to conceptualize adrenal responses ("fight or flight" limits the function of the forebrain and midbrain in favor of hindbrain function) very neat to see data showing they're separate from very early development on
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⚡⚡MAD DOCTOR IMPOSSIBLE⚡⚡ @impossiblephd.bsky.social · 21/09/2026
*Frothing at the mouth with excitement* HEY GUESS WHAT, YOU DON'T HAVE ONE BRAIN, YOU HAVE TWO! med.stanford.edu/news/all-new...
med.stanford.edu
Human brain is two separate organs, Stanford Medicine-led research finds
Stanford Health Care delivers the highest levels of care and compassion. SHC treats cancer, heart disease, brain disorders, primary care issues, and many more.
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Ed Yong is offline @edyong209.bsky.social · 17/09/2026
Briefly popping my head back in to unveil the cover of my upcoming book, LIFE BEYOND MEASURE: Nature's Hidden Wonders at Every Scale. It’ll be out on April 6 in the U.S. and April 29 in the U.K. and you can pre-order it right now! www.penguinrandomhouse.com/books/757705... 1/
A book cover featuring a beautiful closely cropped portrait of an Anna's hummingbird. The cover says LIFE BEYOND MEASURE: Nature's Hidden Wonders at Every Scale, by Ed Yong. The image also says US: 4/06/27 and UK: 4/29/27
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ESA Journals @esajournals.bsky.social · 17/09/2026
New findings from #TheScientificNaturalist in our journal "Ecology" ⬇️
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Joshua Rivera @jmrivera.bsky.social · 14/09/2026
it is wild how, if you go far enough up the chain, every AI has humans greasing the wheels, maintaining the illusion
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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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Jun B. Cai @junbcai.bsky.social · 07/09/2026
Defending my dissertation in five days 🎓🪸 September 11 at 1 PM (PST) In-Person: Cordley Hall 1316 Zoom: beav.es/JunCai YouTube: beav.es/IBLive
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Woods Hole Oceanographic Institution @whoi.edu · 08/09/2026
Can science save coral reefs from the impacts of ocean warming and disease? 🪸 Scientists and engineers at the newly established WHOI Schiller Center for Reef Solutions are conducting research to do just that! Learn more from the Cape Cod Times: go.whoi.edu/cct-schiller 📸 Dan Mele © WHOI
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The Coral Reef Research Hub @coralreefresearch.bsky.social · 07/09/2026
PAID INTERNSHIP: Coral and Sponge Restoration with i.care in the Florida Keys Learn more here: icareaboutcoral.org/interns/ #coralreefs #coralrestoration #coralreefinternship #internship #coral #marinescience #marineinternship #reefrestoration #marinebiology
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 11/08/2026
It's so annoying multiple folks have made tools to help compile the data. A couple examples: db.systemsbiology.net/gestalt/cgi-... and bib.experiments.kordinglab.com/nsf-coa
db.systemsbiology.net
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Jon Aguiñaga @jon-aguinaga.bsky.social · 12/08/2026
Been working on my NSF PRFB proposal for what seems like weeks now. Thankful for the examples provided in @jrossibarra.bsky.social 's github page (github.com/RILAB/statem...). The current call is AI in biology, and fortunately thats a lot of what I do, so I'm giving it a shot!
github.com
statements/fellowships at master · RILAB/statements
Successful Job Applications and Grants. Contribute to RILAB/statements development by creating an account on GitHub.
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Smith Fellowship @smithfellows.bsky.social · 27/08/2026
Smith staff will hold an open office hour on September 10 from 10:00–11:00 a.m. PT to answer lingering application questions. Drop by anytime during the hour; as with in-person office hours, others may be present while your question is discussed. Register below to add the session to your calendar:
zoom.us
Welcome! You are invited to join a meeting: Office Hour with Smith Staff. After registering, you will receive a confirmation email about joining the meeting.
Office hour open to all for questions related to 2027 Smith Fellowship applications
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PLOS Biology @plosbiology.org · 30/08/2026
Pathogens sense #stress hormones in the gut and use them to regulate motility and virulence. Weston Whitaker explores a new @PLOSBiology.org study which transfers this pathway to a #probiotic bacterium, redesigns it to drive programmable outputs 🧪 Article plos.io/4zI6itm Primer plos.io/4qE1npb
A schematic diagram for engineering catecholamine-responsive control in Escherichia coli Nissle 1917.
(A) Wild-type E. coli Nissle encodes a QseBC two-component system closely related to that of enterohemorrhagic E. coli (EHEC), but showed minimal transcriptional responses to the catecholamines norepinephrine and epinephrine under the conditions tested. In EHEC, catecholamine-responsive QseBC signaling feeds into the native flhDC promoter, which is embedded in a broader network of global and flagellar regulation, including an apparent sigma-28-dependent promoter core. Srivastava and colleagues transferred EHEC qseBC into E. coli Nissle and reconstructed its transcriptional output by tuning constitutive qseBC expression, truncating the native promoter, replacing the apparent sigma-28-dependent core with synthetic sigma-70-dependent promoters, and restoring a QseB-associated motif. The resulting circuit retained catecholamine responsiveness while producing a larger and more consistent transcriptional response that could control a reporter or therapeutic cargo, yielding a portable catecholamine-sensing module. (B) Future circuit architectures could combine catecholamine-sensing with additional disease-relevant physiological inputs and use amplification, logic, thresholding, or memory to process these signals. Such circuits could couple therapeutic production to particular physiological conditions or generate a retrievable record of signals encountered in the gut. Figure created in Adobe Illustrator.
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Laura-Li Jeannot @lljeannot.bsky.social · 03/08/2026
🐠📣 New paper alert! 🦀 📣 Cryptofauna doesn't react uniformly to nutrients: cryptobenthic fishes are better able to capitalize on extra nutrients near seabird colonies, likely boosting larger piscivores; when rats are present, inverts thrive instead ▶️ doi.org/10.1002/ecy....
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Deb Houry @drdebhoury.bsky.social · 28/08/2026
One year ago today, I resigned from CDC alongside Dan Jernigan and @drdemetre.bsky.social . We walked out, but we did not walk away from public health. Today, we reflect on why we spoke up and what it will take to build a stronger CDC for the future. www.statnews.com/2026/08/28/c...
statnews.com
We quit the CDC last year. The problems we protested remain
How disease spreads and the risks and benefits of interventions are questions for science, not for ideology.
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Hannah Richter @hannah-richter.bsky.social · 28/08/2026
Reports about the Tibet-Nepal flood have been devastating—and confusing. Here's the whirlwind story of how scientists around the world pieced together the cascade of events. @science.org: www.science.org/content/arti... #flood #hazard #naturaldisaster #landslide
science.org
How scientists unraveled the cause of the devastating flood in Tibet and Nepal
Global cooperation revealed a landslide, not a glacial collapse, likely initiated the cascade of events
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SharkScience @sharkscience.bsky.social · 17/08/2026
Evidence of a Potential Nursery Area for the Great Hammerhead Shark, Sphyrna mokarran, in the Largest Coral Reef System of the Southwestern Atlantic 🦑🦤🐟🦈 onlinelibrary.wiley.com/doi/10.1002/...
onlinelibrary.wiley.com
Evidence of a Potential Nursery Area for the Great Hammerhead Shark, <fi>Sphyrna mokarran</fi>, in the Largest Coral Reef System of the Southwestern Atlantic
We present evidence suggesting that the Abrolhos Bank functions as key habitat for early life stages of Sphyrna mokarran. Kernel density estimation revealed spatially structured aggregations, with ne....
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Rae Radford @raeradford.bsky.social · 17/08/2026
100% #BookSky
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Ocean Hoptimism @oceanhoptimism.org · 08/08/2026
Pssst. It’s not the sand that’s the problem. Sea levels are rising. Storms are intensifying. And we keep replacing sand to defend development built beside a coastline that was never static. The ocean is changing. How long will we keep rebuilding the past instead of adapting to the future?
sfgate.com
Surf spot Tamarack State Beach lost most of its sand in less than 2 weeks
The beach had recently undergone a sand replenishment project.
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Ocean Hoptimism @oceanhoptimism.org · 08/08/2026
Gen Z is going crabbing—and we are SO here for it. 🦀🌊 Fresh air. Cheap seafood. New friendships. Less screen time. And women and nonbinary folks claiming space in a traditionally male pastime. Turns out touching grass is great. Touching the ocean? Even better.
sfgate.com
This San Francisco influencer quit medical school to pursue crabbing
Young San Franciscans are making crabbing cool again.
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Nancy Knowlton @nancyknowlton.bsky.social · 19/07/2026
Baby boom for a species on the brink - My news to me good news for July 18 (cheating by 38 mins) #EarthOptimism www.washingtonpost.com/nation/2026/...
washingtonpost.com
Red wolves, once nearly wiped out, had a spring baby boom in North Carolina
The births are a boon to efforts to revive the species, which was once nearly hunted to extinction.
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Holly Moeller @mixotrophe.bsky.social · 14/07/2026
I'm so #sciencehappy that I wanna do it all again. Let's go for Year 5 of fig-a-day! Starting with the best science week of my life at @nitmb.bsky.social, producing some very cool models for multispecies mutualism, including the #SSRImodel -- because it makes us happy. #figaday 5.001 #year5
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Simon Donner @simondonner.bsky.social · 03/07/2026
Record daytime high temperatures and heat indices are getting all the attention in this N American heatwave, as in the recent European heatwave. As big a health risk is the high overnight temperatures; inability to cool off overnight is a primary driver of sickness and death during heatwaves.
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TeeDixie ✊🏼 @teedixie.bsky.social · 02/07/2026
Wow who’d have thunk it, vaccines work 🤔 Great news to celebrate.
No women aged 20-24 in England have died from cervical cancer for the first time, thanks to the HPV vaccine.
A landmark study funded by Cancer Research
UK shows the HPV vaccine is making cervical cancer increasingly preventable, with researchers highlighting a major milestone: between 2020 and 2024, no women aged 20-24 in England died from the disease.
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dr-skitch.bsky.social @dr-skitch.bsky.social · 24/06/2026
Attending ICRS 2026 in Auckland? Want to learn how we streamline coral genotype tracking? Join us (me, Kim De Luca and @ibaums.bsky.social) for an interactive workshop on Standard Tools for Acroporid Genotyping Database (STAGdb)! #ICRS2026 #CoralRestoration #Bioinformatics #ConservationGenetics
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Jeff Berardelli @weatherprof.bsky.social · 23/06/2026
Marine heatwave developing around Florida, with a Coral Bleaching Warning issued for the Florida Keys! If you’ve been to the beach lately you know we are past the refreshing stage, and have moved onto hot tub stage! Water temps in Florida Bay are as high as 97°F in the silty waters… 1/
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Chris Oakley @quercus62.bsky.social · 19/06/2026
Sad to miss #evol2026 this year but most of my lab will be there. Juan Diego will defend his PhD in October and will be looking for a Postdoc. Stephanie will be presenting a poster on work that she did as an undergraduate and she is looking for graduate programs for Fall of 2027.
Stephen Mills  - Adaptation and Ecology I 6/21/26 at 11:15
Stephanie Tirado Rojas - Poster B06 6/21/26
Juan Diego Rojas Gutierrez - Ecological Genetics 1 6/22/26 at 10:00
Emily lancaster - Poster D17 6/23/26
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Shooti @bambooshooti.bsky.social · 16/06/2026
#ResistanceEarth Don't write off coral reefs just yet. Scientists have identified 64,000 square miles of coral reefs across 71 countries capable of not only surviving but recovering from climate change. Some of these reefs are in areas not previously recognized. www.yahoo.com/news/science...
yahoo.com
Scientists identify 64,000 sq miles of coral reef capable of surviving climate crisis
SINGAPORE, June 16 (Reuters) - Scientists have identified nearly 166,000 sq km (64,000 sq miles) of coral reefs that are capable of surviving and recovering from climate change, three times more than
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Brock Wooldridge @tywooldr.bsky.social · 03/06/2026
A big postdoc project of mine is now out in PNAS! Please take a look if you're interested in marine invertebrates, ancient DNA, inversions over time, genomic erosion, rapid adaptation, and more! (photos thanks to Sarah Ford and Michael Ready) www.pnas.org/doi/10.1073/...
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Wendy the Woke @nomorex61.bsky.social · 05/06/2026
Altman must be feeling a little burnt.
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ICRS International Coral Reef Society @icrs.bsky.social · 01/06/2026
🪸 Happy World Reef Day! Here are some of our favourite coral reef documentaries released recently — the ones that stopped us in our tracks and reminded us exactly why this work matters. What film or documentary has reignited your love for coral reefs and the ocean lately? Share it in the comments! 🎬
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Schmidt Ocean Institute @schmidtocean.bsky.social · 03/06/2026
A moment of discovery! It was a nearly 20-hour dive that the science team will never forget — discovering the first vents in the little-explored #Doldrums Megatransform & Fracture Zone. (Led by Aaron Micallef of @mbarinews.bsky.social ) Read more via YouTube caption: youtube.com/shorts/ocR0l...
youtube.com
A moment of discovery!
YouTube video by Schmidt Ocean Institute
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Lisa @tuexplorer1.bsky.social · 03/06/2026
A nice big hairy slime star for you @echinoblog.bsky.social (they didn't collect it) @schmidtocean.bsky.social dive 929 #Doldrums #MarineLife
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Tressie McMillan Cottom @tressiemcphd.bsky.social · 03/06/2026
Can’t divest, condemn, mock, and abandon young people when they conform and then jail, surveil, deport, track, and kill them if they protestors and *then* wonder why they don’t believe in the system.
What I see on the ground is a divestment from our political system, from electoral politics, from retail politics that have operated as usual for all of young people’s lives with very little material effect. And in fact, the only material consequences most young people can see to political action has been on the side of reclaiming rights — taking away people’s citizenship, right? Making the world less pluralistic and less equal. And so in that sense, I’m not sure that that’s apathy as much as it is an accurate assessment of their political reality, which, to your point, is, “None of us believe in this thing, and yet there doesn’t seem to be anything that we can do about it.” So I separate out the accurate assessment, or diagnosis, of the political problem from whether or not young people feel like they can do something. We have just come off the last three years of really — maybe not a historical high, but a historical moment — a lot of young people organizing, a lot of young activists. And what happened to most of them is surveillance, stigmatization, expulsion, right?
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Adam Kovac @adamjkovac.bsky.social · 02/06/2026
The Trump administration's NSF is removing hundreds of ocean sensors that provide incredibly comprehensive and continual data. This is a loss not only for climate scientists, but marine biologists and industries that rely on the health of those waters. www.scientificamerican.com/article/trum...
scientificamerican.com
Trump administration takes aim at crucial ocean monitoring network
The Ocean Observatories Initiative has been collecting data on physical, chemical, geological and biological conditions in the Atlantic and Pacific Oceans for the past decade
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Dr. Dawn Wright @deepseadawn.bsky.social · 02/06/2026
A shot across the bow by these authors in @pnas.org : "Ecology is not yet ready for AI—and why that matters" www.pnas.org/doi/10.1073/... 🧪 ⚒️ 🌏 🌍 🌎
pnas.org
Ecology is not yet ready for AI—and why that matters | PNAS
Ecology is not yet ready for AI&mdash;and why that matters
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Maggie Wiggin @maggie162.bsky.social · 01/06/2026
My god, Octavia Butler, just miss ONCE
 Page from a book saying:

From EARTHSEED: THE BOOKS OF THE LIVING
Choose your Leaders with wisdom and forethought.
To be led by a coward is to be controlled
by all that the coward fears.
To be led by a fool is to be led
by the opportunists who control the fool.
To be led by a thief is to offer up your most precious treasures to be stolen.
To be led by a liar
is to ask to be told lies.
To be led by a tyrant is to sell yourself and those you love into slavery.
t
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Jessica McKenzie @jessimckenzi.bsky.social · 02/06/2026
in retrospect making twitter and/or facebook integral parts of disaster response and communication was probably a mistake
29. Stop requiring me to have an X account to read the emergency updates that my government posts on X. I am in a hurricane. My house is in a swimming pool, and the swimming pool is in a tree. Emergency services are, for reasons I am not presently at leisure to explore, posting vital safety updates on X. When I try to read the relevant thread, the app tells me I can’t do it unless I create an account, something I would gladly do if a Kia Sorento were not flying at my face. I shall die peacefully here in my swimming-pool tree, knowing that at least I never had to talk to Grok.
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Dr. Lucky Tran @luckytran.com · 02/06/2026
Incredible! Scientists receive a rare standing ovation after announcing that a new treatment can double the survival time for pancreatic cancer, the deadliest cancer which was once considered “undruggable.” When we fund and support science, we can achieve anything! (Video: Dr. Wish Dhillon)
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Ben Farmer, PhD @benfarmer.bsky.social · 02/06/2026
Absolutely shameful to not call the Gulf of Mexico its rightful name. I know NOAA is bound by federal headwinds, but if the lunatic who made this directive is a pedophile fascist who is creating modern day concentration camps, I think the agency has a moral and ethical obligation to resist.
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