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endonuclease.bsky.social

@endonuclease.bsky.social
9 followers 53 following 8 posts

Just a student, so please forgive my naive questions.

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Reposted by @endonuclease.bsky.social
worm @rfksbrainworm.bsky.social · 02/10/2026
If you ever wondered why visible light is those particular wavelengths, it's because life evolved to see in the narrow range where water is transparent
Diagram of absorption of emf by water. There's a gap right that dips in the 500 nm range
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conputer dipshit @davidcrespo.bsky.social · 01/10/2026
point for my strategy of never reading the chain of thought. you might as well ask the model why it did what it did, the answer‘s not going to be any less bullshit
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Mark A. Hanson @hansonmark.bsky.social · 26/09/2026
To close: it's crazy to worry about profit motive in author COI declarations, but not journal editing itself. The damage this was causing was apparent before AI. The power to enact change lies with funders. Funders can use the same mechanisms they already use to support non-profit journals. 14/14
direct.mit.edu
The strain on scientific publishing
Abstract. Scientists are increasingly overwhelmed by the volume of articles being published. The total number of articles indexed in Scopus and Web of Science has grown exponentially in recent years; ...
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bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 24/09/2026
aaRSID, an engineered pyrrolysyl-tRNA synthetase platform for multi-probe proximity proteomics www.biorxiv.org/content/10.64898/20…
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endonuclease.bsky.social @endonuclease.bsky.social · 24/09/2026
sorry if any of these are common knowledge already, i just came across your thread while scrolling and i don't know much about this field!
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endonuclease.bsky.social @endonuclease.bsky.social · 24/09/2026
very cool!!! any reason you decided to look at embryonic development in particular for this regulation? i wonder what the biological advantage is -- timing? upon cessation of transcription are ncRNAs quickly degraded? lots of interesting angles :)
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Dan Luu @danluu.com · 18/09/2026
There's no point at which turning your brain off will work: danluu.com/brain-off/
In early 2025, I started seeing people turn off their brain as they use LLMs1. They would have an LLM take an action (summarize text, write some code, etc.), and just assume that it worked2. This generally didn't work in early 2025 and the result was often quite silly.

As LLMs have gotten better, I've seen more of this. Sometimes, people will try to get the LLM to write some code for them and basically just assume that it works3. Sometimes there's a human in the loop and, if the thing doesn't work, they'll ask the LLM to figure out the problem and solve it. Niklas Gruhn calls some variants of doing this being a meat proxy.4

Being a for loop meat proxy works better than it did in early 2025 and the software I've tried that's developed like this sometimes actually sort of works. Not well enough that I'd want to use it or that it's successful, but I'm impressed at how effective being a meat proxy is in September 2026. You could even imagine LLMs improving enough that brain-off meat-proxy development produces average quality software in the foreseeable future.

Let's say that happens. What reason is there for the company to employ the meat proxy? The company can just run the LLM in a loop and lay off the employee. There's no point at which this methodology will work for the employee5.
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conputer dipshit @davidcrespo.bsky.social · 19/09/2026
now this is fun. guest post on Terry Tao's blog by the great Grant Sanderson of 3Blue1Brown arguing that we should "give novel and compelling motivated explanations academic credit similar to what generating new proofs of open problems has had historically."
terrytao.wordpress.com
If math is more than proof, we need to better celebrate the rest of it
[This is a guest post by Grant Sanderson. This blog post was initially written in a different file format and converted using AI. — T.] A sentiment echoing throughout the mathematics communit…
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Robert Arkowitz @robertarkowitz.bsky.social · 06/09/2026
www.biorxiv.org/content/10.6...
biorxiv.org
Weak interactions drive selective proteome demixing and tune the differential response to environmental perturbations
The intracellular space is a crowded environment where macromolecules perform distinct tasks despite pervasive "non-specific" interactions. Whether these interactions are functionally relevant and how...
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 27/08/2026
Nuclear size is genetically controlled and influences cell fate www.biorxiv.org/content/10.64898/20…
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Molecular Cell @cp-molcell.bsky.social · 28/08/2026
Online Now: Intragenomic homologs with distinct phase behaviors broaden the range of cellular stress responses Online now:
dlvr.it
Intragenomic homologs with distinct phase behaviors broaden the range of cellular stress responses
Guan et al. show that bacteria use protein homologs with different material properties to regulate biomolecular condensates. By tuning the abundance of these proteins in heterotypic assemblies, bacteria balance condensate dynamics and stability, thereby maintaining fitness during stress.
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endonuclease.bsky.social @endonuclease.bsky.social · 17/09/2026
really interesting system! if mechanism is more through length than sequence, why do you think you're seeing conservation?
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Thibaut Brunet @thibautbrunet.bsky.social · 02/09/2026
🚨 New preprint alert! 🚨 Choanoflagellates reorganize their global cytoskeletal architecture within seconds to explore confined microspaces. This is the main PhD work of the amazing @maitefreired.bsky.social www.biorxiv.org/content/10.6... A tread 🧵⬇️
biorxiv.org
Rapid repurposing of microvillar content drives a flagellate-to-amoeboid switch in the closest relative of animals
Animal cells extensively remodel their cytoskeleton during differentiation and can notably switch between two major motility modes: flagellum-based swimming and actin-based crawling. We previously sho...
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Christian Landry @christianlandry.bsky.social · 10/08/2026
I wrote this short piece on a paper that profoundly impacted my PhD more than 20 years ago! rdcu.be/fyr4C
rdcu.be
The genetics of complex gene expression phenotypes illuminated
Nature Reviews Genetics - Christian Landry reflects on a 2002 study by Brem, Yvert and colleagues, which combined yeast genetics and genome-wide expression profiling to reveal the genetic...
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bioRxiv Cell Biology @biorxiv-cellbio.bsky.social · 24/08/2026
Kinetic Control of Nuclear-encoded Mitochondrial mRNA Localization and Local Translation www.biorxiv.org/content/10.64898/20…
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Kevin Forsberg @kvnforsberg.bsky.social · 02/07/2026
Humans and bacteria share strategies to defend against viruses. We wondered: could they use each other's genes? Yes, both can! Bacteria can use human immune genes to defend against phages AND Human cells can use bacterial genes for viral defense. www.biorxiv.org/content/10.6...
biorxiv.org
Bacterial and human exonucleases mediate interkingdom antiviral immunity
All kingdoms of life have developed strategies to limit viral infection. In humans, interferons induce a suite of antiviral factors that collectively provide immunity. Some human immune genes are homo...
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Cell Metabolism @cp-cellmetabolism.bsky.social · 25/06/2026
Online now: The metabolic basis of regulated cell death
dlvr.it
The metabolic basis of regulated cell death
Regulated cell death (RCD) relies on finely tuned cellular programs traditionally understood to be regulated by cellular signaling. In this review, Tang and colleagues propose cellular metabolism as a gatekeeper of RCD, coordinating context-specific cell death programs across pathophysiological settings.
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Suckjoon Jun’s lab at UCSD @junlab.bsky.social · 18/06/2026
5/ Why would a cell hold its growth below capacity? Because the setting that buys faster growth costs survival. GTP up: faster growth, dies under antibiotics. GTP down: slower growth, endures. Wild-type sits at a regulated balance. Growth and survival pull against each other.
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endonuclease.bsky.social @endonuclease.bsky.social · 30/05/2026
are you using some sort of app to compare responses to a prompt across different models? ive always been interested in doing something like that!
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conputer dipshit @davidcrespo.bsky.social · 04/05/2026
we need to teach kids to have thoughts and articulate them. the aims of education have not changed!
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Sternberg Lab @sternberglab.bsky.social · 12/05/2026
1/9 New preprint from the Sternberg Lab in collaboration with the Nishimasu Lab! We uncover how the DRT3 antiphage immune system pairs two reverse transcriptases, one RNA-templated and one protein-templated, to build a double-stranded DNA effector. doi.org/10.64898/202...
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Andy Masley @andymasley.bsky.social · 10/05/2026
The key thing about this is that saying "cars don't even work" undercuts your ability to criticize cars, because you need to reckon with the fact that the reason they're popular is that on some metrics they work so uniquely well
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bioRxiv Biochemistry @biorxiv-biochem.bsky.social · 06/05/2026
TIR-like NADases act in bacterial immunity and the RNA vault www.biorxiv.org/content/10.64898/20…
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Jonathan Friedman @labfriedman.bsky.social · 20/04/2026
Check out our highlight of the most recent example of subcellular mitochondrial specialization in @currentbiology.bsky.social. Be sure to also check out the beautiful work from David Sherwood's lab www.cell.com/current-biol...
cell.com
Mitochondrial biology: Specialized powerhouses pack a punch
A new study reveals that a specialized population of mitochondria in the Caenorhabditis elegans uterine anchor cell is remodeled and enriched in machinery needed for optimal local energy production to...
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Vivek Mutalik @vivekmutalik.bsky.social · 03/04/2026
📣Huge preprint 🔔 Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
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Jens Hör @jenshoer.bsky.social · 21/03/2026
Excited to share the first preprint from the lab! We show that ApeA defends against RNA phage infection by cleaving the phage genome: www.biorxiv.org/content/10.6...
biorxiv.org
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conputer dipshit @davidcrespo.bsky.social · 22/03/2026
I think this Terry guy might be onto something www.dwarkesh.com/p/terence-tao
Terence Tao

I think AI has driven the cost of idea generation down to almost zero, in a very similar way to how the internet drove the cost of communication down to almost zero. It’s an amazing thing, but it doesn’t create abundance by itself. Now the bottleneck is different. We’re now in a situation where suddenly people can generate thousands of theories for a given scientific problem. Now we have to verify them, evaluate them. This is something which we have to change our structures of science to actually sort this out.

Traditionally, we build walls. In the past, before we had AI slop, we had amateur scientists have their own theories of the universe, many of which were of very little value. We built these peer review publication systems to filter out and try to isolate the high signal ideas to test.

But now that we can generate these possible explanations at massive scale, and some of them are good and a lot are terrible, human reviewers are already being overwhelmed. Many journals are reporting that AI-generated submissions are just flooding their submissions.

It’s great that we can generate all kinds of things now with AI, but it means that the rest of the aspects of science have to catch up: verification, validation, and assessing what ideas actually move the subject forward and which ones are dead ends or red herrings. That’s not something we know how to do at scale. For each individual paper, we can have a debate among scientists and get to a consensus in a few years. But when we’re generating a thousand of these every day, this doesn’t work.
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Claus Wilke @clauswilke.com · 11/03/2026
Interestingly, we can also predict model performance based on simple dataset statistics, such as how variable site means are and how many variable sites there are in a dataset. High variability of site means and intermediate number of variable sites imply good model performance. 4/
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endonuclease.bsky.social @endonuclease.bsky.social · 06/03/2026
since a lot of people studying phage defense use escapers to study the mechanism of sensing infection, does that imply that there might be a lot of defense systems that sense essential phage proteins that can't be identified this way?
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endonuclease.bsky.social @endonuclease.bsky.social · 06/03/2026
i see, that makes sense!
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endonuclease.bsky.social @endonuclease.bsky.social · 06/03/2026
and also, if there are no phage mutations that could bypass this protease activated CBASS, would it still be possible for phages to adapt to it or develop a counter defense somehow?
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endonuclease.bsky.social @endonuclease.bsky.social · 06/03/2026
hello! i am a student who's trying to learn more about studying phage defense right now. i'm sorry to bother you, but i was wondering if you could explain why this would mean that you couldn't find escapers? for instance, might a mutation in the phage protease (maybe for recognition) escape defense?
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