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Gareth (Gary) Trubl

@gtrubl.bsky.social
255 followers 188 following 28 posts

Dad; Staff scientist at Lawrence Livermore National Lab; first generation PhD; He/Him pronouns; I study climate change, soil viruses, ecology, microbial ecophysiology, biogeochemistry, and astrobiology using meta-omics combined with stable isotope probing

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Gareth (Gary) Trubl @gtrubl.bsky.social · 30/09/2026
www.nature.com/articles/s41...
nature.com
Rethinking soil microbiome interventions through an ecological lens - Nature Reviews Microbiology
Microbial interventions offer sustainable opportunities to enhance soil health and ecosystem functioning, but they can also have unintended ecological consequences. This Comment explores their benefit...
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Jonathan Eisen @phylogenomics.bsky.social · 24/09/2026
Job: Assistant Professor of Plant Pathology at @ucdavis.bsky.social. Great department. Great university. Great students. Really great colleagues. recruit.ucdavis.edu/JPF07904
recruit.ucdavis.edu
Assistant Professor of Plant Pathology
University of California, Davis is hiring. Apply now!
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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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Manuel Kleiner @manuelkleiner.bsky.social · 08/09/2026
We are looking to hire a microbiology laboratory research technician here at NC State in Raleigh, NC. If you have experience in microbiology and/or LC-MS/MS please consider applying. Please repost! jobs.ncsu.edu/postings/234...
jobs.ncsu.edu
Microbiology Laboratory Research Technician
The Kleiner Lab at North Carolina State University is seeking a Research Technician to support research focused on complex microbial communities, microbial symbioses, and metaproteomics. Reporting to ...
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Joint Genome Institute @jgi.doe.gov · 21/08/2026
From our FY26 Functional Genomics call: Jane Fudyma will pair real-time VOC flux measurements with metatranscriptomics to identify the active genes and pathways behind VOC cycling, revealing the microbial drivers of desert VOC gases. Full portfolio: jointgeno.me/FGFY26
Congratulations
to our CSP Functional Genomics Call recipients!

Jane Fudyma
University of Arizona

Integrating soil VOC fluxes and metatranscriptomics to define microbial functional traits across plant-driven nutrient and moisture gradients in arid soils.
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Katharine Hayhoe @katharinehayhoe.com · 14/08/2026
I talked about wildfires, fossil fuels, clean energy and the possibility of a better future with CBC News yesterday. With a few audio cameos from Mr Jekyll 🙀 Watch here:
youtu.be
Climate change 'loading the dice' for extreme weather, says climate scientist
YouTube video by CBC News
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Digital Brain @yourdigitalbrain.bsky.social · 11/08/2026
A 65-year-old man with a severe antibiotic-resistant E.
sinapti.ca
CRISPR-armed phages help treat a severe superbug infection - Sinaptica
A 65-year-old man with a severe antibiotic-resistant E. coli infection showed significant improvement after receiving experimental treatment with bacteriophages
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Albert Ruhí @albertruhi.bsky.social · 08/08/2026
We're hiring an ecologist at UC Berkeley! The Dept. of Integrative Biology is hiring a tenure-track Assistant Professor in Ecology. Plants/algae, invertebrates, microbes, or marine systems a priority. Come join us!! Apply by Oct 5, 2026. aprecruit.berkeley.edu/JPF05489 PS: Please share!
aprecruit.berkeley.edu
Assistant Professor –Ecology- Integrative Biology
University of California, Berkeley is hiring. Apply now!
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Global Soil Biodiversity Conference 2026 @gsb2026.bsky.social · 03/08/2026
📰 Special Issue: New research reveals that predator control of microbivorous fauna enhances microbial turnover and promotes soil organic matter stabilization, highlighting the importance of intact soil food webs for long-term carbon storage. www.sciencedirect.com/science/arti...
sciencedirect.com
Predator control of microbivorous fauna is required to enhance microbial turnover and SOM stabilization
Soil organic matter (SOM) stabilization is increasingly attributed to microbial processing and the formation of microbial necromass, yet these pathway…
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Gareth (Gary) Trubl @gtrubl.bsky.social · 01/07/2026
Excited to share our latest paper! We developed 18O-SIP-viromics to track new virion production in soils. Most persist without replicating, creating a stable genetic reservoir, while new viral diversity is linked to a subset of hosts. @jgi.doe.gov journals.asm.org/doi/10.1128/...
journals.asm.org
Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics | mSystems
Soil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those...
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Nature Microbiology @natmicrobiol.nature.com · 29/06/2026
Out Now! Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils #MicroSky
go.nature.com
Mobile genetic elements shape microbial diversity and functions in thawing permafrost soils
Nature Microbiology, Published online: 29 June 2026; doi:10.1038/s41564-026-02391-7An 8-year soil meta-omic time series shows how mobile genetic elements shape permafrost microbial diversity and impact a range of functions, including carbon and nutrient cycling.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 29/06/2026
Such a great conference!
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Elaine Luo @oceanmicrobes.bsky.social · 16/04/2026
New publication out @natcomms.nature.com! We identify novel viruses that actively infect highly productive chemoautotrophs, and reveal key trophic interactions and virus-host dynamics that impact microbial carbon cycling in aphotic environments. www.nature.com/articles/s41...
nature.com
Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs - Nature Communications
In this study, Luo and colleagues identify previously unknown viruses that actively infect highly productive chemoautotrophs. These findings provide new insights into key trophic interactions and&nbsp...
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/04/2026
Divergent successional patterns and infection dynamics in virion and transcriptionally active soil viral communities following phosphorus amendment and wet-up Huge effort by Grant Gogul! www.biorxiv.org/content/10.6...
biorxiv.org
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Cameron Thrash @jcamthrash.bsky.social · 15/04/2026
The Microbiology and Geochemistry of the Shallow‐Water Hydrothermal Vents of the Gulf of Naples, Italy enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/... #jcampubs 🌊
enviromicro-journals.onlinelibrary.wiley.com
The Microbiology and Geochemistry of the Shallow‐Water Hydrothermal Vents of the Gulf of Naples, Italy
This study investigated the interplay between fluid geochemistry and microbial diversity in the shallow-water hydrothermal vents of the gulf of Naples, Italy. We found that hydrothermal fluid chemist...
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Cameron Thrash @jcamthrash.bsky.social · 25/03/2026
13C-Labeled Single-Cell Raman Sorting Reveals Sulfur-Driven Dark Carbon Fixation in Coastal Sediments academic.oup.com/ismecommun/a... #jcampubs
academic.oup.com
13C-Labeled Single-Cell Raman Sorting Reveals Sulfur-Driven Dark Carbon Fixation in Coastal Sediments
ABSTRACT. Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized in situ activities. In t
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Cameron Thrash @jcamthrash.bsky.social · 09/03/2026
Illuminating the newly produced viruses within the virosphere with BONCAT and single virus genomic sequencing technologies academic.oup.com/ismecommun/a... #jcampubs
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Gareth (Gary) Trubl @gtrubl.bsky.social · 23/02/2026
We said goodbye to Buddy. We will cherish the 15yrs he shared with us. Buddy was here for many milestones: engagement, college graduations, wedding, bringing our kids home, cross-country moves, buying a house. He lived with us in 4 different states & 9 different homes. I miss him terribly.
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Paul Carini @uncultured.carinilab.com · 20/02/2026
New preprint! We propose "anergiobiosis" to describe microbial life at thermodynamic limits as a way of separating the physiological state from questions about aeonophilic extremophile specialization. ecoevorxiv.org/repository/v... #Microbiology #Extremophiles #SubsurfaceMicrobiology #MicroSky
ecoevorxiv.org
Anergiobiosis: a testable framework for microbial life under extreme power limitation
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Scientific American @sciam.bsky.social · 18/02/2026
After initially rejecting Moderna’s application for review, the FDA will now consider the mRNA flu shot
scientificamerican.com
FDA agrees to review Moderna mRNA flu vaccine in dramatic reversal
After initially rejecting Moderna’s application for review, the FDA will now consider the mRNA flu shot
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Prof Chris Jackson @seismatters.bsky.social · 11/02/2026
😂
One on left is a black dog and above it the words “Reality”. Below it is “I chased a squirrel” 

One the right is a black dog and above it says “LinkedIn”. Below it says, 

Proud to announce that I effectively executed a rapid-response squirrel displacement strategy to mitigate potential yard intrusions.

Humbled by the unwavering support of my family and local stakeholders.

This experience reinforced the importance of vigilance, ownership, and continuous improvement.

Looking forward to scaling this impact in future engagements.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 30/01/2026
The closet genes that I am aware of are in Simon (2016) & Consuelo's (2020) papers, but I am not up-to-date with marine virus work. There have been some recent soil virus papers on N (mostly N2O), but when I think N & soil viruses I look to Christina Hazard & Graeme Nicol. That is the best I can do.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 29/01/2026
>90% of viral genes are unknown, so that makes sense. Viruses move genes and have bycatch all the time. We are finding more and more genes that viruses carry. Viruses drive genetic mutation and they tend to hold onto genes that are efficient, or so we think.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 28/01/2026
Super cool! I'd love to include viruses in this work.
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Nature Communications @natcomms.nature.com · 22/01/2026
#Ecology & #Microbiology Some microbes use atmospheric trace gases as energy and carbon sources, sustaining primary production in caves @greening.bsky.social
dlvr.it
Microbial aerotrophy enables continuous primary production in diverse cave ecosystems - Nature Communications
Metabolic strategies of cave microorganisms are poorly studied. Here, the authors show that cave microbes use atmospheric trace gases hydrogen, carbon monoxide and methane as energy and carbon sources, sustaining primary production and revealing how life can thrive in oligotrophic and dark ecosystems.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
Read the behind the paper communities.springernature.com/posts/uneart...
communities.springernature.com
Unearthing the Viral Secrets of a Changing Landscape
Thawing permafrost is reshaping landscapes and releasing carbon—and soil viruses may play a hidden role. By uncovering ~10,000 new Arctic soil viruses, we reveal unseen players shaping microbes and ca...
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
ssDNA viruses spanned multiple major phyla, dominated by Cressdnaviricota, with representatives of Microviridae, Parvoviridae, and Inoviridae. They were strongly enriched in fully thawed fen habitats, revealing peatland soils as a vast, largely unexplored viral reservoir.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
We compared two quantitative library prep methods: one targeting dsDNA only & one capturing both ssDNA & dsDNA. Both recovered similar dsDNA viral communities, but only the latter revealed the hidden diversity of ssDNA viruses in soil. Both library prep methods are available @jgi.doe.gov
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
Viral genomes encoded 811 putative auxiliary metabolic genes (AMGs), nearly half linked to carbon processing. Both viral diversity & the abundance & diversity of virus-encoded AMGs increased along the permafrost thaw gradient, suggesting expanding potential for viruses to modulate host metabolism.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
We predicted microbial hosts for 38% of viral populations, largely dsDNA viruses, spanning 9 archaeal & 36 bacterial phyla, including key carbon-cycling taxa. The ssDNA viruses were predicted to infect bacteria & microbial eukaryotes.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
Across a natural permafrost thaw gradient, we used optimized soil viromics to quantitatively recover ~10,000 mostly novel ssDNA and dsDNA soil viruses. Viral communities were highly habitat specific, with most viruses endemic to a single thaw stage (palsa, bog, or fen).
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
New paper published in @natcomms.nature.com! Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient doi.org/10.1038/s414... www.nature.com/collections/... @sullivan-lab.bsky.social
doi.org
Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient - Nature Communications
The potential roles of viruses in microbial-induced permafrost thaw, which is accelerated by climate change, are unclear. Here, Trubl et al. sample a permafrost thaw gradient and identify thousands of...
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Innovative Genomics Institute @innovativegenomics.bsky.social · 17/12/2025
Out now in Nature Communications, from IGI's Jill Banfield (The Banfield Lab) and collaborators: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses Read here: www.nature.com/articles/s41467-025-…
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George O'Toole (he/him/his) @geiselbiofilm.bsky.social · 16/01/2026
Summer REU in biofilms! Pls share. www.binghamton.edu/centers/biof...
binghamton.edu
Research Experience for Undergraduates (REU) | Biofilm Research Center | Binghamton University
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Gareth (Gary) Trubl @gtrubl.bsky.social · 16/01/2026
This was a hard read. I strongly disagree with "many of the recommended policies, including lockdowns, social distancing, school closures, wearing masks & vaccine mandates, lacked robust confirmatory evidence and remain the subject of debate about their overall benefits and unintended consequences"
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Joshua Weitz @joshuasweitz.bsky.social · 12/01/2026
Viruses transform microbes, populations, & ecosystems. In new work jointly led w/@tn-marine-micro.bsky.social + more, we find a link between enhanced viral infection and productivity 50 meters below the surface in the otherwise nutrient limited Sargasso Sea. a 🧵 www.nature.com/articles/s41...
"Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea"
https://www.nature.com/articles/s41467-025-67002-1
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Gareth (Gary) Trubl @gtrubl.bsky.social · 13/01/2026
I am grateful to collaborators, mentors, field assistants, & funding support that made this possible. A special thanks to our editor and reviewers. Honored that this paper was selected as an Editors’ Highlight. www.nature.com/ncomms/edito...
nature.com
Client Challenge
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Gareth (Gary) Trubl @gtrubl.bsky.social · 13/01/2026
I also wrote a Behind the Paper piece reflecting on the fieldwork, the challenges of soil viromics, & the long road from peat cores to viral genomes. communities.springernature.com/posts/uneart...
communities.springernature.com
Unearthing the Viral Secrets of a Changing Landscape
Thawing permafrost is reshaping landscapes and releasing carbon—and soil viruses may play a hidden role. By uncovering ~10,000 new Arctic soil viruses, we reveal unseen players shaping microbes and ca...
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Gareth (Gary) Trubl @gtrubl.bsky.social · 13/01/2026
Soil viruses are notoriously hard to study, but we used an optimized viromics workflow to explore how viruses change across a natural permafrost thaw gradient. We quantitatively captured ssDNA + dsDNA viruses, revealing ~10,000 mostly novel viruses & their roles in C cycling.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 13/01/2026
A big milestone, my final PhD paper is finally out! Started lab work in 2017 & bioinformatics via a DOE SCGSR fellowship @jgi.doe.gov with @simrouxvirus.bsky.social @sullivan-lab.bsky.social doi.org/10.1038/s414...
doi.org
Client Challenge
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Aaron Whiteley @aaronwhiteley.bsky.social · 08/10/2025
Our work on the Panoptes antiphage system is published! Here we find that Panoptes "watches" the cytosol for phage immune evasion proteins–captured in this illustration by Clair Huffine of Insight Illustrations. A beautiful example of the effector triggered immunity paradigm.
Illustration depicting a bacterium under assault by phage. The bacterium “sees” phage immune evasion proteins and protects itself using a newly described antiphage system called Panoptes, named for the many-eyed mythical giant Argus Panoptes. Credit: Clair Huffine Insight Illustrations LLC
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Dr. Kat Napaaqtuk❄️ @napaaqtuk.bsky.social · 06/10/2025
I have a fabulous undergrad who has a lot of experience with QIIME2 & using R to analyze microbiome data. She is looking for a job starting in January. Would love to learn more bench and field skills (will be getting some in her last 2 months). Open to academic, industry, government jobs in the US.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 24/09/2025
I know. I always support open access, but it was over 4K & we do not currently have the funds for that. I did put a preprint before on Zenodo which is updated doi.org/10.5281/zeno...
doi.org
Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication
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Gareth (Gary) Trubl @gtrubl.bsky.social · 20/09/2025
Same! Now, let's see if I still get requests to do "16S metagenomics"...ugh.
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Gareth (Gary) Trubl @gtrubl.bsky.social · 19/09/2025
New paper alert with @alexjprobst.bsky.social. enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
enviromicro-journals.onlinelibrary.wiley.com
Clarifying Terminology in Microbial Ecology: A Call for Precision in Scientific Communication
The rapid evolution of microbiology as a field of research has led to the introduction of new terminology and the adaptation of existing terms. However, inconsistencies in the use of these terms, inc...
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Michael E. Mann @michaelemann.bsky.social · 13/09/2025
“This Is the Greatest Threat to Our Human Future” | @peterhotezmdphd.bsky.social and I discuss with @nextbigidea.bsky.social about our new book, #ScienceUnderSiege: nextbigideaclub.com/magazine/gre...
nextbigideaclub.com
This Is the Greatest Threat to Our Human Future
Co-authors Michael Mann and Peter Hotez share 5 key insights from their new book, Science Under Siege: How to Fight the Five Most Powerful Forces that Threaten Our World.
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Prof Peter Hotez MD PhD DSc(hon) @peterhotezmdphd.bsky.social · 03/09/2025
Register today www.bakerinstitute.org/event/scienc...
Baker Institute
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Joshua Weitz @joshuasweitz.bsky.social · 04/09/2025
Super team of physicians, scientists, and public health experts come together with a single message: RFK must go. "It is time to reverse course and begin rebuilding the public health infrastructure overseen by CDC. Kennedy has proven himself unwilling and ill-prepared to lead that effort. " 👇
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Helen Branswell 🇨🇦 @helenbranswell.bsky.social · 15/08/2025
This point isnt being made enough. Last week’s attack on the #CDC could have been a slaughter. www.statnews.com/2025/08/15/c...
statnews.com
The CDC shooting was public health’s Jan. 6
“In RFK Jr.’s America, it will never be safe to practice public health or medicine," write an epidemiologist and a former CDC staffer.
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Science & Technology Policy at Rice University's Baker Institute @stpolicy.bsky.social · 15/08/2025
Save the Date! Sept. 9 @ 12pm. @bakerinstitute.bsky.social with @stpolicy.bsky.social will host Drs. @peterhotezmdphd.bsky.social & @michaelemann.bsky.social to discuss their new book, "Science Under Seige". Come hungry, lunch will be served! Register here: www.bakerinstitute.org/event/scienc...
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