naturepoker
@binomicalabs.org
Binomica Labs independent researcher by day, warehouse worker by night Small thoughtful science #phylogenetics #archaea #evolution #bioinformatics #phage @naturepoker@genomic.social http://naturepoker.wordpress.com https://orcid.org/0000-0002-6977-5440
AI companies scraping websites at scale is a real problem. But a proposed NY law could make it harder for libraries, journalists & researchers to preserve the web and investigate the powerful. That's why we've joined @eff.org & others in a letter to Gov. Hochul. blog.archive.org/2026/08/04/i...
Internet Archive to New York: Don’t Kill the Good Bots in the Fight Against Bad Bots | Internet Archive Blogs
blog.archive.org
Normally I avoid company-associated lectures but this one looks genuinely interesting. Apparently aeonophile is a thing! Never heard of the term before, but I'm sure we've all asked the microbial life span question before. 🦠🧫 www.zymoresearch.com/pages/aeonop...
Aeonophiles: Can an individual microbial cell live for a million years? | ZYMO RESEARCH
Explore how aeonophiles survive for millennia and what they reveal about evolution and biotechnology.
zymoresearch.com
New #ISEPpapers #PrePrint! Skiaviridae: a large DNA virus family that persistently infects thraustochytrid protists www.biorxiv.org/content/10.6... by Jessica Latimer et al. #Protists #Viruses #Microbes
LLM in coding discussions in public sphere is just completely broken. Don't ship things you couldn't build yourself. One would think this wouldn't be a controversial take, but apparently it is.
#rustlang has an official LLM policy. Pretty sensible - everything boils down to "you can't copy paste LLM output without any work and call it a contribution". QC requirements are higher for LLM generated code, also common sense. blog.rust-lang.org/inside-rust/... Also this part cracked me up:
Picked up a refurbished Keychron Q2 on the cheap... And going into it without high expectations, wow this is genuinely different from the generic cooler master I've been using. Brown switches are not as noisy as I expected too. This thing also weighs a ton despite the size.
I genuinely can't find a legit, not-xerox pirate copy of Rilke's letters until 1910 anywhere on the usual online channels. Had to order a used library copy from eBay to get a halfway decent version. I think this is the second time I had this experience with a major international literary figure.
It's raining even more than earlier in the morning. Enjoying the view but not looking forward to wading through all this soon. #nyc
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
pnas.org
Academics need to understood that just their presence doesn't do jack for anyone- it's always about the project. 'I existed in xyz lab' wont get you a job cleaning dishes in real world. Hiring someone to do X and then changing your mind 4 months into the process is just screwing the person over.
Hmm what is this I hear about RAM prices beginning to fall, what with more and more datacenter deals falling through and getting cancelled? Could we actually get some reprieve at some point?
🖥️🧬
Rob Patro@robp.bsky.social · last wk.New preprint🚨(*long* time coming)! We introduce seqproc: an efficient, flexible, and concise tool for describing and transforming sequencing-read geometry. The aim: make complex protocols easy to specify & transform without giving up speed or accuracy. www.biorxiv.org/content/10.6... 🧵
This unattributed 2020 viral video of a sea lion chilling half-underwater is the timeline cleanse you *need*. But it's also a great intro to a discussion of how pinnipeds (walruses, seals, sea lions) SLEEP, especially when they're too far away from a safe "haul out" location. Let's talk about it.
This is not at all a good way to use the tool, but I love it nonetheless. Feeding linux shell output directly to #julialang -e module env for inline plots without repl. 2 seconds to plot because of module compilation, but maybe I can keep a precompiled env just for inline figs 😆
Looks like @stcmicrobeblog.bsky.social is back from summer hiatus. Thoughtful post as ever - I love the comparison between manipulation of concepts toward an end versus comprehension in the question of artificial and human intelligence. smallthingsconsidered.blog/schaechter/2...
STC, Writing & Me
by Roberto — It's time to get back into the swing of things at STC. Our vacation is over.
smallthingsconsidered.blog
Quick film photography snap from my trip to Washington DC National Gallery. It was a welcome relief from everything outside those walls.
Whoa, playing around with helix and #rustlang - the pair's really made for each other. There's no setup. Just run 'rustup component add rust-analyzer' and pull up :config to add 'display-inlay-hints=true' and it's ready to go. I feel like I've been playing on hard mode all this time har har.
Housekeeping like this can matter with Julia, since a package update means recompilation with some downtime. If you're immediately sketching out ideas that could really get in the way. Granted, you don't necessarily have to update environments that are already working well enough.
Another derp moment for me. All this time I've been manually updating global Julia envs as I go. Meanwhile all I had to do was just bash loop the .julia/environments directories with a julia --project=@"$n" 'using Pkg; Pkg.update();' Sigh. #julialang
It kind of sucks to suddenly come up with a fun question for an ISMB talk I attended three whole days ago, and author/presenter contact info is nowhere to be found :-/
Wildfire smokes haven't cleared up yet. Looking forward to the supposedly pretty big thunderstorm later this morning. #nyc
Wow, arriving in nyc to some blade runner hellscape. The wildfire smokes are thick enough to be painful, and all lights are casting permanent traces in the air. Apparently this is an improvement over how things were during the day.
The preprint was already exciting but this awesome single-virus paper from @joshuasweitz.bsky.social lab is now published in a great journal! phys.org/news/2026-07...
Scientists find hidden individuality in viral infections
An international team of researchers developed a new way to uncover hidden differences in how viruses infect and destroy individual microbial cells—solving a biological puzzle that has persisted for m...
phys.org
Joshua Weitz@joshuasweitz.bsky.social · 3w agoBacteriophage continue to have so much to teach us. It's in our interest to understand how they work and impact human & environmental health. New joint work led by @mariandm.bsky.social & @rantahan.bsky.social inferring single-cell latent period & burst size heterogeneity from population dynamics.
Ahhh good times at ISMB is over - time to head back to the sweltering warehouse lab in the city. I'll definitely try to return for the 2027 - wow what a fun & educational conference.
@wheelerlab.org is talking about his effort to build a resource for protein dynamics (PDB for MD). MDRepo is a repository to store simulation data. This is really needed to push the needle in design, function and more. Please help make it successful by sharing your MD data. #ismb2026 🌐 mdrepo.org
