naturepoker
@binomicalabs.org
Binomica Labs independent researcher by day, warehouse worker by night
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@naturepoker@genomic.social
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Small thoughtful science
#phylogenetics #archaea #evolution #bioinformatics
@naturepoker@genomic.social
http://naturepoker.wordpress.com
https://orcid.org/0000-0002-6977-5440
Pinned
naturepoker
@binomicalabs.org
· Oct 21
Now that we have pinned posts:
I'm a self-taught biologist in #NYC studying the microbial tree of life with lots of long-read sequencing focus.
Most of my study is self-funded from warehouse and other odd jobs - I'm hoping to document paths to a working class, independent researcher for others.
I'm a self-taught biologist in #NYC studying the microbial tree of life with lots of long-read sequencing focus.
Most of my study is self-funded from warehouse and other odd jobs - I'm hoping to document paths to a working class, independent researcher for others.
Reposted by naturepoker
In our last thread, we left the jelly-enjoyers of Bluesky with a cliff hanger ending, in what one eager onlooker described as soap opera science 😜 ... wait no more, we are back! Grab your popcorn shrimp and come with us on a journey spanning more than...
bsky.app/profile/iwan...
bsky.app/profile/iwan...
Kailua Beach, Hawai’i: The first time I laid eyes on a By-the-wind sailor, I stopped dead in my tracks, dusted the sand off my hands, grabbed my iphone and...
November 10, 2025 at 10:13 PM
In our last thread, we left the jelly-enjoyers of Bluesky with a cliff hanger ending, in what one eager onlooker described as soap opera science 😜 ... wait no more, we are back! Grab your popcorn shrimp and come with us on a journey spanning more than...
bsky.app/profile/iwan...
bsky.app/profile/iwan...
Please tell me this is just a wild guess. Democrats decided to cave in because successfully defending ACA coverage will get rid of a talking point in the midterms?
newrepublic.com/post/202948/...
newrepublic.com/post/202948/...
November 10, 2025 at 9:37 PM
Please tell me this is just a wild guess. Democrats decided to cave in because successfully defending ACA coverage will get rid of a talking point in the midterms?
newrepublic.com/post/202948/...
newrepublic.com/post/202948/...
Reposted by naturepoker
November 10, 2025 at 7:56 PM
Picked up a #Polaroid Sun660 from a curve sale for pocket change. Very happy to see it's working properly with fresh film!
Doubly glad to capture the last of the autumn leaves - I was afraid I wouldn't be able to take them before the rains washed them away.
#analogphotography
Doubly glad to capture the last of the autumn leaves - I was afraid I wouldn't be able to take them before the rains washed them away.
#analogphotography
November 8, 2025 at 9:58 PM
Picked up a #Polaroid Sun660 from a curve sale for pocket change. Very happy to see it's working properly with fresh film!
Doubly glad to capture the last of the autumn leaves - I was afraid I wouldn't be able to take them before the rains washed them away.
#analogphotography
Doubly glad to capture the last of the autumn leaves - I was afraid I wouldn't be able to take them before the rains washed them away.
#analogphotography
Reposted by naturepoker
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:16 PM
Reposted by naturepoker
Raise a glass for Rosalind Franklin tonight and honor her memory and scientific contributions
NYT obituary of Jim Watson.
A long and fairly balanced view of a complicated man who participated in one of the greatest discoveries in biology.
[Gift Link]
www.nytimes.com/2025/11/07/s...
A long and fairly balanced view of a complicated man who participated in one of the greatest discoveries in biology.
[Gift Link]
www.nytimes.com/2025/11/07/s...
James Watson, Co-Discoverer of the Structure of DNA, Is Dead at 97
www.nytimes.com
November 7, 2025 at 9:12 PM
Raise a glass for Rosalind Franklin tonight and honor her memory and scientific contributions
Ok I think I'm set for the winter.
November 7, 2025 at 10:50 PM
Ok I think I'm set for the winter.
Reposted by naturepoker
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
November 6, 2025 at 1:13 AM
Fantastic talk by @vikramshivakumar.bsky.social Mumemto—Scalable multi-MUM finding for pangenomes
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Papers biorxiv.org/content/10.1101/2025.05.20.654611 & doi.org/10.1186/s13059-025-03644-0
Code: github.com/vikshiv/mume...
Very efficient pangenome visualization tool, revealing synteny and variations!
Reposted by naturepoker
Second day of Genome Informatics #GI2025 began with the session “Genome Assembly and Sequence Algorithms" Yun William Yu presented “Average-case Analysis of Seed-Chain-Extend under Random Mutations"
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
November 6, 2025 at 2:19 PM
Second day of Genome Informatics #GI2025 began with the session “Genome Assembly and Sequence Algorithms" Yun William Yu presented “Average-case Analysis of Seed-Chain-Extend under Random Mutations"
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
genome.cshlp.org/content/33/7/1175
providing theoretical guarantees for the popular seed-chain-extend
Reposted by naturepoker
Wow! 😮🤩
There's a new interactive map of Every Known Road in the Roman Empire!! 🤓
itiner-e.org
We might have to have a lie-down.
There's a new interactive map of Every Known Road in the Roman Empire!! 🤓
itiner-e.org
We might have to have a lie-down.
November 6, 2025 at 5:07 PM
Wow! 😮🤩
There's a new interactive map of Every Known Road in the Roman Empire!! 🤓
itiner-e.org
We might have to have a lie-down.
There's a new interactive map of Every Known Road in the Roman Empire!! 🤓
itiner-e.org
We might have to have a lie-down.
Reposted by naturepoker
Have any of my followers implemented a "flipped classroom" for an upper division Environmental Micro (or related) course? I am planning a re-work for my current class for next fall and considering a flipped modality.
November 4, 2025 at 6:49 PM
Have any of my followers implemented a "flipped classroom" for an upper division Environmental Micro (or related) course? I am planning a re-work for my current class for next fall and considering a flipped modality.
Check this out - first image of a new Halococcus species I discovered with collaborators. Still figuring out the scheme to name the darn thing.
Independent research & amateur biology FTW.
🧫🦠🧪
Independent research & amateur biology FTW.
🧫🦠🧪
November 6, 2025 at 4:52 PM
Check this out - first image of a new Halococcus species I discovered with collaborators. Still figuring out the scheme to name the darn thing.
Independent research & amateur biology FTW.
🧫🦠🧪
Independent research & amateur biology FTW.
🧫🦠🧪
Huh, there's no dedicated nd2 image viewer/puller package for R? I'm surprised, normally R's more feature rich in these things than python.
November 6, 2025 at 4:41 PM
Huh, there's no dedicated nd2 image viewer/puller package for R? I'm surprised, normally R's more feature rich in these things than python.
Reposted by naturepoker
나는 폐급이다 나는 일 못해 이런 생각 들 때
루브르 박물관의 영상보안시스템 비밀번호가 “루브르”였다는 점을 떠올리십시오
여러분은 잘하고 있습니다
루브르 박물관의 영상보안시스템 비밀번호가 “루브르”였다는 점을 떠올리십시오
여러분은 잘하고 있습니다
진짜 오늘 일때문에 너무 바쁘고 스트레스받고 내가 진짜 잘하고 있나 이런 생각을 했는데 나는 잘하고 있는게 맞았다
November 5, 2025 at 9:35 AM
나는 폐급이다 나는 일 못해 이런 생각 들 때
루브르 박물관의 영상보안시스템 비밀번호가 “루브르”였다는 점을 떠올리십시오
여러분은 잘하고 있습니다
루브르 박물관의 영상보안시스템 비밀번호가 “루브르”였다는 점을 떠올리십시오
여러분은 잘하고 있습니다
Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org.
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
November 5, 2025 at 3:19 PM
Going through @samuelhorsfield.bsky.social presentation on pangenome graphs in comparative genomics, courtesy of @training.ebi.embl.org.
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Fascinating tidbit on history of alignment based sequence graph - it goes all the way back to 1989 (Hein), era of Apple IIs and IBM PS/2s. Great talk!
💻🧬🦠🧫
Reposted by naturepoker
I am on the job market and wanted to advertise myself here! 🤠
Looking for full-time or contracting roles!
Historically, my work spans population dynamics, healthcare informatics, robust adaptive controls, software engineering, and community engagement. 🧪
#STEMjobs #academicsky #publichealth
Looking for full-time or contracting roles!
Historically, my work spans population dynamics, healthcare informatics, robust adaptive controls, software engineering, and community engagement. 🧪
#STEMjobs #academicsky #publichealth
November 4, 2025 at 6:31 PM
I am on the job market and wanted to advertise myself here! 🤠
Looking for full-time or contracting roles!
Historically, my work spans population dynamics, healthcare informatics, robust adaptive controls, software engineering, and community engagement. 🧪
#STEMjobs #academicsky #publichealth
Looking for full-time or contracting roles!
Historically, my work spans population dynamics, healthcare informatics, robust adaptive controls, software engineering, and community engagement. 🧪
#STEMjobs #academicsky #publichealth
Reposted by naturepoker
My paper 'Hegel, Absolute Knowing and Epiphany' published in the International Journal of Philosophical Studies is now freely available from my institutional repository @openuniversity.bsky.social Here's the link: oro.open.ac.uk/97415/ Feel free to download, and do get in touch with your comments!
The Open University
Copy the page URI to the clipboard
oro.open.ac.uk
November 4, 2025 at 6:34 PM
My paper 'Hegel, Absolute Knowing and Epiphany' published in the International Journal of Philosophical Studies is now freely available from my institutional repository @openuniversity.bsky.social Here's the link: oro.open.ac.uk/97415/ Feel free to download, and do get in touch with your comments!
Well well well, it looks like apt is going to be based on rust starting next year. And with it huge part of the Linux ecosystem.
#linux #debian #rustlang
Hard Rust requirements from May onward
lists.debian.org/debian-devel...
#linux #debian #rustlang
Hard Rust requirements from May onward
lists.debian.org/debian-devel...
Hard Rust requirements from May onward
lists.debian.org
November 4, 2025 at 6:44 PM
Well well well, it looks like apt is going to be based on rust starting next year. And with it huge part of the Linux ecosystem.
#linux #debian #rustlang
Hard Rust requirements from May onward
lists.debian.org/debian-devel...
#linux #debian #rustlang
Hard Rust requirements from May onward
lists.debian.org/debian-devel...
Reposted by naturepoker
Would you or your colleague like to improve the performance of your data analysis? Then please join us at our @julialang.org workshop at the 247th @aas.org meeting on Jan 3, 2026 in Phoenix, AZ. The regular registration deadline is Nov 7.
aas.org/meetings/aas...
#aas247 #JuliaLang #astrocode
aas.org/meetings/aas...
#aas247 #JuliaLang #astrocode
AAS 247: Registration | American Astronomical Society
aas.org
October 29, 2025 at 3:55 PM
Would you or your colleague like to improve the performance of your data analysis? Then please join us at our @julialang.org workshop at the 247th @aas.org meeting on Jan 3, 2026 in Phoenix, AZ. The regular registration deadline is Nov 7.
aas.org/meetings/aas...
#aas247 #JuliaLang #astrocode
aas.org/meetings/aas...
#aas247 #JuliaLang #astrocode
Reposted by naturepoker
We have had some amazing abstracts submitted to the free
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
APSPM 2026: Structural Phylogenetics Meeting
A pivotal SMBE regional meeting in Brisbane on the interface of protein structure, function, and evolution.
biosig.lab.uq.edu.au
November 3, 2025 at 4:21 AM
We have had some amazing abstracts submitted to the free
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
@official-smbe.bsky.social APSPM meeting. To help you make up your mind, here is a sneak peek. Join for what will be an amazing meeting. biosig.lab.uq.edu.au/strphy26/sneakpeek/ . #StrPhy26 @strphy.bsky.social #Evolution #Science
Woot! Great to see STC back. Apparently there's still work to be done for fully restoring images on older posts, but I'm just glad STC is back online again. 🧪
Ray: Just a note to say STC is officially back up and running!! You can view our new home via smallthingsconsidered.blog
November 3, 2025 at 2:22 AM
Woot! Great to see STC back. Apparently there's still work to be done for fully restoring images on older posts, but I'm just glad STC is back online again. 🧪
Reposted by naturepoker
OTD in 1977 Carl Woese and George Fox redrew the tree of life. They proposed a third “urkingdom”—the “archaebacteria”—in addition to eukaryotes and bacteria. Woese later called this taxon “Archea.”
AFAIK, he didn’t publish his famous tree diagram until the late 80s.
🐋🌱🧪 #HistSTM 🗃️🧠 #evobio 🐡
AFAIK, he didn’t publish his famous tree diagram until the late 80s.
🐋🌱🧪 #HistSTM 🗃️🧠 #evobio 🐡
November 2, 2025 at 4:04 PM
No more review articles for arXiv due to innundation of LLM generated submissions.
I genuinely don't understand - what's the point of generating random nonsense for preprint submissions?
blog.arxiv.org/2025/10/31/a...
I genuinely don't understand - what's the point of generating random nonsense for preprint submissions?
blog.arxiv.org/2025/10/31/a...
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
blog.arxiv.org
November 2, 2025 at 5:48 PM
No more review articles for arXiv due to innundation of LLM generated submissions.
I genuinely don't understand - what's the point of generating random nonsense for preprint submissions?
blog.arxiv.org/2025/10/31/a...
I genuinely don't understand - what's the point of generating random nonsense for preprint submissions?
blog.arxiv.org/2025/10/31/a...
Reposted by naturepoker
I’ve spent many years explaining/defending biorxiv’s “no reviews” policy.
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
arXiv will no longer accept review articles and position papers unless they have been accepted at a journal or a conference and complete successful peer review.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
This is due to being overwhelmed by a hundreds of AI generated papers a month.
Yet another open submission process killed by LLMs.
Attention Authors: Updated Practice for Review Articles and Position Papers in arXiv CS Category – arXiv blog
blog.arxiv.org
November 2, 2025 at 5:33 PM
I’ve spent many years explaining/defending biorxiv’s “no reviews” policy.
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2
The logic was always that opening Word and opining is a far lower barrier than doing actual research, so noise’d be >> signal and we didn’t want to make subjective quality judgements.
LLMs mean it makes even more sense 1/2