Zach Marin
@zacsimile.bsky.social
hardware x software in microscopy | postdoc in Ries Lab | http://zacsimile.github.io | 🇺🇸 in 🇦🇹 | he/him | views are graphical projections
Happy to share the first preprint out of the Nomburg lab! Many aspects of cellular immunity are shared across the tree of life. Here, we show that some of these conserved aspects of cellular immunity are mirrored by conserved effectors of immune antagonism. Thread below! 1/15
bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2w agoConserved folds enable immune antagonism across the tree of life https://www.biorxiv.org/content/10.64898/2026.07.21.739742v1
Nature did a short piece on our preprint about how LLMs will affect the practice of science; my more detailed thread is below.
Scientists using LLMs will ‘do more, less well’, modelling study predicts
Research suggests that the combination of incentives to publish and the use of large language models will lead to more papers, but they will be less refined.
nature.com
Carl T. Bergstrom@carlbergstrom.com · 2w ago1. We—@eduede.bsky.social, @mjcrockett.bsky.social, Kevin Gross, and I—have a new preprint on the arXiv today, based on ideas that emerged during an @sfiscience.bsky.social workshop in November 2024: The unintended consequences of large language models as a labor-augmenting technology in science.
[0/1] Excited to share our new preprint DECODE-Plex! After many people efforts, we developed a deep-learning framework for multi-channel SMLM, enabling simultaneous localization and color assignment of densely packed emitters across multiple channels. biorxiv.org/content/10.6...
Thoughts on the various Trump administration proposals to revamp US science funding - and what they all have in common:
The Assault On Science Funding Continues
science.org
1. The new Trump / Kratsios plan for US science appears explicitly designed to destroy US universities. Diverting money to tech donors is probably just a bonus. Gift link.
Trump’s Plan for Science: More Money for A.I., Less for Universities (Gift Article)
Michael Kratsios, President Trump’s science adviser, proposed overhauling how the government funds research. Democrats said Mr. Trump’s actions had weakened science.
nytimes.com
Listening to Music to Make Microscopes To Listen To Music To www.youtube.com/watch?v=qJ5D...
Big City (Everybody I Know Can Be Found Here)
YouTube video by Spacemen 3 - Topic
youtube.com
FlatMux: an optimized microscope system for multiplexed 2-photon imaging of neuronal activity with voltage sensors. www.nature.com/articles/s41...
A versatile platform for two-photon neuronal population voltage imaging across cortical depths - Nature Methods
FlatMux is an optimized microscope system for multiplexed two-photon imaging of neuronal activity with genetically encoded voltage sensors. The flexible system is demonstrated in a variety of scenario...
nature.com
We need to change norms around sexual harassment Yesterday Tessa West spoke up about a sexual harassment complaint she filed against John Jost. Not only is he a senior colleague in the dept of psychology, but he is one of the most prominant figures in the field of social and political psychology.
the degree to which they want to destroy one of the jewels of the American republic—our exceptional research universities—is just gobsmacking
Ben Allen@evodynamics.bsky.social · 3w agoCongrats we just made it impossible to come here for a PhD www.bostonglobe.com/2026/07/16/m...
Excited to see this collaboration now in print. Dye chemistry meets AI-designed proteins. Three small, orthogonal tags; lifetime modulation; split versions. Request the free dyes at dyes.janelia.org www.science.org/doi/10.1126/...
De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging
Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostabilit...
science.org
As an AI hater, it's with deep regret I inform you that I agree. Claude Code is very useful.
Giuseppe Navarria@techdesign.rocks · 3w agoLinus Torvalds clarifies the Linux Kernel position on AI use. It's not one to be celebrated but, if you're an engineer, as I've been saying, it's one to be understood. source: lore.kernel.org/linux-media/...
The end of this article correctly touches on what Corey Doctorow calls reverse centaurism (www.theguardian.com/books/2026/j...), where humans end up working in service to AI rather than the other way around. By using LLMs to write articles, we force reviewers to screen for machine made errors.
The Reverse Centaur’s Guide to Life After AI by Cory Doctorow review – the real price of artificial intelligence
A vivid and entertaining polemnic on the economics of the tech revolution, filled with righteous ire
theguardian.com
Samuel Moore@samuelmoore.org · 3w ago"The propagation of AI slop [...] is making science less trustworthy. But in parallel, AI enthusiasts are telling the world that the remedies should all be easy to automate, creating the impression that journals can not only catch more errors but also do it more efficiently and cheaply."
Manuscripts with women as corresponding authors are less frequently sent out for review at Science. The ones reviewed receive less favorable reviews by both male and female reviewers.
Javi Ibarrondo@jibarrondo.bsky.social · 3w agoEditorial and peer review dynamics at elite general science journals | Science Advances www.science.org/doi/10.1126/... 🧪
An analysis of public comments on a White House proposal to change the way federal contracts and grants are doled out shows widespread opposition. www.statnews.com/2026/07/15/t...
Flood of comments on White House grantmaking overhaul is largely negative, analysis shows
An analysis of public comments on a White House proposal to change the way federal contracts and grants are doled out shows widespread opposition
statnews.com
I have taken the powermeter that was on the optics table and which you were probably saving for later Forgive me it was useful so sensitive and so fast
Thanks for the kind words, but equal (if not greater) credit goes to @benpatrickwill.bsky.social for helping us by identifying the AI slop to begin with. Highly recommended read - particularly for the unbelievably disgraceful use of GenAI faces. nobreakthroughs.com/the-scientis...
The Scientists That Don't Exist
Ghostly websites publishing science press releases are filling up with AI-generated content — and the ghosts of scientists that don't exist.
nobreakthroughs.com
Altmetric@altmetric.com · 4mo agoThanks again @benpatrickwill.bsky.social - we owe you an update. Scienmag and Bioengineer have been removed from the Altmetric dataset. AI has a role to play in the world, but AI-journalism slop, concealed or not, is not it. New attention page: www.altmetric.com/details/1845...
Hunh. AI search becomes a lot less useful if you can't access to 20% (blog.cloudflare.com/application-...) of all websites. Are we heading back to web directories? www.adweek.com/media/publis...
Publishers Are Preparing to Opt Out of Google Search
The nuclear option is gaining traction as web traffic collapses and Google refuses to negotiate with content creators
adweek.com
When I explain to peeps how much we do in research labs for how few $$, they simply don’t believe me. I once explained it to a famous person from Pixar, he looked me square in the eye and said “You mean all the cancer, vision, and Alzheimer’s grants work that way? You’ve gotta be %#ing kidding me!”
Jason Rasgon@vectorgen.bsky.social · last mo.The NIH is an ENORMOUS bargain for the American people. Do folk think that private industry will do the background slog work for drug discovery for 250K direct costs?
I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...
My Peer Review of The 1%
I wanted to like QED's new 1% ranking. I don't.
open.substack.com
A newly identified species of fungus attacks the famous “zombie mushrooms” that control ants.
The ‘Parasite of Parasites’ Has Been Discovered in the Tropical Forests of Borneo
A newly identified species of fungus attacks the famous “zombie mushrooms” that control ants.
wrd.cm
Thermo Fisher now has a page up in response to our observations. They flatly deny that images were manipulated or fabricated while repeating that images were "optimized for presentation and clarity on the website", no lie, six times. www.thermofisher.com/us/en/home/l...
thermofisher.com
Reese Richardson@reeserichardson.bsky.social · 2mo agoThe Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
🔬 Happy to share our new paper showing that fluorophore brightness open a new dimension in SMLM microscopy ! Thanks to all authors @laurent-le.bsky.social S. K. Sreenivas @emmanuelfort.bsky.social ! @ismolab.bsky.social @instlangevin.bsky.social @cnrs.fr rdcu.be/fmIeD doi.org/10.1038/s415...
🔬🚀 It's out! Run 100s of imaging experiments before touching a microscope. #VLab4Mic reproduces them in silico from PDB/AlphaFold to help you image right first time. From rockstars Damián Martínez & Bruno Saraiva, inaugural preprint of @mariodelr.bsky.social new lab www.biorxiv.org/content/10.6...
Mario Del Rosario@mariodelr.bsky.social · 2mo agoCongratulations to Damián Martinez, Bruno Saraiva, @taylashakespeare.bsky.social, @wmarkbates.bsky.social, Dylan Owen, @christlet.bsky.social and @henriqueslab.bsky.social We hope VLab4Mic helps researchers design better experiments and ask better biological questions 💻 vlab4mic.henriqueslab.org
We present: Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution www.biorxiv.org/content/10.6...
Hello #world, meet 1,000× Expansion Microscopy. A small gel would grow to the size of an Olympic swimming pool, while amino-acid-scale distances become visible with ordinary light microscopy. Led by Helena Hu from @eboyden3.bsky.social's lab, in collab with us. Story: www.biorxiv.org/content/10.6...
Meet MagLuc: a magnetically-controlled luminescent protein. This is a foundational tool for remote control of biological processes, also known as "magnetogenetics". Can you tell when the magnetic field turns on and off? From @mariaingaramo.bsky.social and the team at @nonfictionlabs.bsky.social
This. "When academics in more comfortable political climates declare it unethical for the rest of us to remain and to fight, they undercut the solidarity necessary to help move toward the kind of world they want to see." www.insidehighered.com/opinion/view...
How Not to Talk About Colleagues in Texas, Florida (opinion)
We’re not fighting a lost cause.
insidehighered.com
Yes, Swiss scientist Fritz Zwicky coined the term “dark matter” which is impressive, but he also coined the term “spherical bastard” to describe people who are bastards no matter which way you look at them, and I think that should be celebrated more.
This isn’t the first time. He told someone he was “feeling blue” about the results of this study - www.nytimes.com/2020/04/15/s... - and then he didn’t publish them. As far as I know this hasn’t come up in congressional oversight. Pretty wild.
M.L.B. Employees Become the Subjects of a Huge Coronavirus Study (Published 2020)
nytimes.com
Gregg Gonsalves@gregggonsalves.bsky.social · 4mo agoJay Bhattacharya pulls a study because he doesn’t like the conclusions. I cannot explain how bad this is and how it reeks of the stench of ideological zealotry and has no basis in science. www.nytimes.com/2026/04/22/u...