Ian Holmes
@ianholmes.org
Berkeley professor (Bioeng, Compbio). Visiting Scientist at Calico. JBrowse genome browser / Apollo annotation editor, ML for gene regulation / molecular evolution / synbio. Occasional music, games, jokes
Pinned
Ian Holmes
@ianholmes.org
· Jan 25
Sophie Wilson - Wikipedia
en.m.wikipedia.org
I feel moved to write about one of my technological heroes, possibly the most influential on my youth as an 8-bit hacker: a trans woman named Sophie Wilson. en.m.wikipedia.org/wiki/Sophie_...
I did NOT have a good faith exchange of views between @mcuban.bsky.social & @colincarlson.bsky.social on my Christmas wishlist, but that just goes to show I don’t ask for big enough presents. This is a fun thread. Wish there were more conversations like this on here. (Firmly “team Colin”, of course)
Lol. Why hasn't the best public health school already designed it ?
And why can't a 29 year old design it ?
The last place I would go to design UHC is another university. Or a think tank.
But feel free to have anyone there send me there suggestions, plan,design, anything. I'll read it
And why can't a 29 year old design it ?
The last place I would go to design UHC is another university. Or a think tank.
But feel free to have anyone there send me there suggestions, plan,design, anything. I'll read it
December 26, 2025 at 1:28 AM
I did NOT have a good faith exchange of views between @mcuban.bsky.social & @colincarlson.bsky.social on my Christmas wishlist, but that just goes to show I don’t ask for big enough presents. This is a fun thread. Wish there were more conversations like this on here. (Firmly “team Colin”, of course)
This is such a cool story, we were nerding out about it this morning
Congrats @jeffgroh.bsky.social et al. Some avocado trees open female-phase flowers in the morning & then male in afternoon. Others show complementary pattern (m->f), to synchronize pollination of two types. Jeff show this to be a >45Mya polymorphism at a transcription factor across 100s of species.
Balanced polymorphism in a floral transcription factor underlies an ancient rhythm of daily sex alternation in avocado https://www.biorxiv.org/content/10.64898/2025.12.22.695989v1
December 25, 2025 at 8:41 PM
This is such a cool story, we were nerding out about it this morning
Cries in Sony Walkman
Mp3 players fucking rock we fucked up so bad putting everything on phone
December 25, 2025 at 8:11 PM
Cries in Sony Walkman
Reposted by Ian Holmes
Release the Jack Smith transcript.
Jack Smith is calling for the House Judiciary Committee to release the recording of his full closed-door deposition before the panel.
"Doing so will ensure that the American people can hear the facts directly from Mr. Smith, rather than through second-hand accounts."
"Doing so will ensure that the American people can hear the facts directly from Mr. Smith, rather than through second-hand accounts."
December 25, 2025 at 2:06 PM
Release the Jack Smith transcript.
Looks interesting, I am curious how this compares to Rasmussen & Kellis (2012)… and potentially more recent papers (have not surveyed this space for a while)
A Probabilistic Algorithm for Gene-Species Reconciliation with Segmental Duplications https://pubmed.ncbi.nlm.nih.gov/41433090/
December 25, 2025 at 8:03 AM
Looks interesting, I am curious how this compares to Rasmussen & Kellis (2012)… and potentially more recent papers (have not surveyed this space for a while)
Reposted by Ian Holmes
Deep deep organisms that might live for thousands of years
aeon.co/essays/the-d...
aeon.co/essays/the-d...
The discovery of aeonophiles expands our definition of life | Aeon Essays
The discovery of organisms that have been alive for many thousands of years requires a revolution in how we understand life
aeon.co
December 20, 2025 at 10:50 PM
Deep deep organisms that might live for thousands of years
aeon.co/essays/the-d...
aeon.co/essays/the-d...
I am aware that "the Die Hard Christmas joke is still funny" is a subjective statement. But hey. It is. The MOVIE ITSELF relies heavily on that joke and surely you will not risk offending its many sincere worshippers by denying that it was a force for good in the world, what is wrong with you
The true* meaning of Christmas is peace, love, and the celebration of a virtuous birth. That is why the Die Hard Christmas joke is still funny: it inverts that, to be about violence, marital strife and the celebration of an evil death. Anyway, I made a Christmas carol soundcloud.com/ian-holmes-2...
Nakatomi Christmas (quick-get-it-down cut)
The true* meaning of Christmas
soundcloud.com
December 23, 2025 at 6:36 PM
I am aware that "the Die Hard Christmas joke is still funny" is a subjective statement. But hey. It is. The MOVIE ITSELF relies heavily on that joke and surely you will not risk offending its many sincere worshippers by denying that it was a force for good in the world, what is wrong with you
The true* meaning of Christmas is peace, love, and the celebration of a virtuous birth. That is why the Die Hard Christmas joke is still funny: it inverts that, to be about violence, marital strife and the celebration of an evil death. Anyway, I made a Christmas carol soundcloud.com/ian-holmes-2...
Nakatomi Christmas (quick-get-it-down cut)
The true* meaning of Christmas
soundcloud.com
December 23, 2025 at 6:17 PM
The true* meaning of Christmas is peace, love, and the celebration of a virtuous birth. That is why the Die Hard Christmas joke is still funny: it inverts that, to be about violence, marital strife and the celebration of an evil death. Anyway, I made a Christmas carol soundcloud.com/ian-holmes-2...
Reposted by Ian Holmes
2025 Headline of the Year nominee (April)
December 22, 2025 at 11:49 PM
2025 Headline of the Year nominee (April)
These incompetent fascist idiots have no idea how rapidly samizdat spreads
here's the 60 minutes cecot video part 1 of 5 - recorded/uploaded by and all credit to @jasonparis.bsky.social
I just reduced background noise, chopped the 14 minutes into 3 minute segments each compressed under 100 mb for bsky's limits, cropped and rotated a few degrees for easier viewing on here
I just reduced background noise, chopped the 14 minutes into 3 minute segments each compressed under 100 mb for bsky's limits, cropped and rotated a few degrees for easier viewing on here
December 23, 2025 at 12:25 AM
These incompetent fascist idiots have no idea how rapidly samizdat spreads
Reposted by Ian Holmes
here's the 60 minutes cecot video part 1 of 5 - recorded/uploaded by and all credit to @jasonparis.bsky.social
I just reduced background noise, chopped the 14 minutes into 3 minute segments each compressed under 100 mb for bsky's limits, cropped and rotated a few degrees for easier viewing on here
I just reduced background noise, chopped the 14 minutes into 3 minute segments each compressed under 100 mb for bsky's limits, cropped and rotated a few degrees for easier viewing on here
December 22, 2025 at 10:58 PM
here's the 60 minutes cecot video part 1 of 5 - recorded/uploaded by and all credit to @jasonparis.bsky.social
I just reduced background noise, chopped the 14 minutes into 3 minute segments each compressed under 100 mb for bsky's limits, cropped and rotated a few degrees for easier viewing on here
I just reduced background noise, chopped the 14 minutes into 3 minute segments each compressed under 100 mb for bsky's limits, cropped and rotated a few degrees for easier viewing on here
I am so grateful to live in a town with a sci-fi bookstore like Dark Carnival. Obscure series you half finished in the 80s? Latest dungeon-crawling genre romp? Thought-provoking dystopias, guilty pleasures, experimental crossovers… all to be found in their labyrinth of piles www.darkcarnival.com
Dark Carnival Bookstore
Science Fiction and Fantasy Bookstore in Berkeley, with a huge selection and helpful staff! Rare and out of print books. We do mail order!
www.darkcarnival.com
December 22, 2025 at 11:57 PM
I am so grateful to live in a town with a sci-fi bookstore like Dark Carnival. Obscure series you half finished in the 80s? Latest dungeon-crawling genre romp? Thought-provoking dystopias, guilty pleasures, experimental crossovers… all to be found in their labyrinth of piles www.darkcarnival.com
This whole thread is horrifying and contains MANY new details. This documentary needs to be torrented and played everywhere to the shame, vilification, and electoral destruction of Weiss, Miller, and all the collaborators and enablers
Guards began beating him. Beat him until he bled. Knocked his face into the wall, broke all his teeth. No access to outdoors, no contact with relatives.
Now describing US knowledge of CECOT's torture practices, followed by footage of Trump praising those practices.
Now describing US knowledge of CECOT's torture practices, followed by footage of Trump praising those practices.
December 22, 2025 at 10:48 PM
This whole thread is horrifying and contains MANY new details. This documentary needs to be torrented and played everywhere to the shame, vilification, and electoral destruction of Weiss, Miller, and all the collaborators and enablers
Electronic music production is a hobby I’ve given myself permission to be gloriously bad at. This year, I did (after being encouraged to by my very supportive partner) submit some terrible beginner tracks to @sfpubliclibrary.bsky.social’s Bay Beats platform: baybeats.sfpl.org/albums/wally...
December 22, 2025 at 10:41 PM
Electronic music production is a hobby I’ve given myself permission to be gloriously bad at. This year, I did (after being encouraged to by my very supportive partner) submit some terrible beginner tracks to @sfpubliclibrary.bsky.social’s Bay Beats platform: baybeats.sfpl.org/albums/wally...
Reposted by Ian Holmes
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Reposted by Ian Holmes
CBS didn't run the 60 Minutes segment on CECOT, but over here at @propublica.org we've been working on the story since March, including finding out who each and every man sent to that maximum security prison was.
You can see our reporting here: www.propublica.org/series/depor...
You can see our reporting here: www.propublica.org/series/depor...
Deported and Imprisoned Archives
A case-by-case investigation that examines the Trump administration’s claims that these immigrants are all “sick criminals” and “terrorists” and that shows what they suffered during months in one of t...
www.propublica.org
December 22, 2025 at 4:08 PM
CBS didn't run the 60 Minutes segment on CECOT, but over here at @propublica.org we've been working on the story since March, including finding out who each and every man sent to that maximum security prison was.
You can see our reporting here: www.propublica.org/series/depor...
You can see our reporting here: www.propublica.org/series/depor...
Reposted by Ian Holmes
People are dying inside American concentration camps right now.
www.elpasotimes.com/story/news/i...
www.elpasotimes.com/story/news/i...
Exclusive: 911 calls from migrant detention center highlight dire conditions
About 90 emergency 911 calls have been made from the Camp East Montana immigration detention center in El Paso, Texas, during the 15 weeks since it opened.
www.elpasotimes.com
December 22, 2025 at 7:59 PM
People are dying inside American concentration camps right now.
www.elpasotimes.com/story/news/i...
www.elpasotimes.com/story/news/i...
Reposted by Ian Holmes
Hey, fellow evolutionary biologists:
If you support trans rights, like, comment, or repost this. I want to show that transphobes like Richard Dawkins are a loud minority that does not represent our community
If you support trans rights, like, comment, or repost this. I want to show that transphobes like Richard Dawkins are a loud minority that does not represent our community
And that’s a follow.
Actually I do have a question if you have a sec.
Without exception the most transphobic group of scientists I’ve run into online are evolutionary biologists. Every single one of them has expressed the same opinion: transness cannot be anything other than social contagion. Why?
Actually I do have a question if you have a sec.
Without exception the most transphobic group of scientists I’ve run into online are evolutionary biologists. Every single one of them has expressed the same opinion: transness cannot be anything other than social contagion. Why?
December 22, 2025 at 3:18 PM
Hey, fellow evolutionary biologists:
If you support trans rights, like, comment, or repost this. I want to show that transphobes like Richard Dawkins are a loud minority that does not represent our community
If you support trans rights, like, comment, or repost this. I want to show that transphobes like Richard Dawkins are a loud minority that does not represent our community
Reposted by Ian Holmes
Apparently this was the 'year of the octopus'
2025 is ‘year of the octopus’ as record numbers spotted off England’s south coast
Milder weather led to a bloom in the invertebrates off the coast of Cornwall and south Devon, wildlife charity says
www.theguardian.com
December 22, 2025 at 4:14 PM
Apparently this was the 'year of the octopus'
Reposted by Ian Holmes
once again plugging this amazing resource for anyone in the paediatric cancer space. so much data, so easily accessible
🎉 As we wrap up the year, we’re excited to share new updates to the #SingleCell #PediatricCancer Atlas (ScPCA) Portal! All datasets have been updated with features that improve data quality and usability.
Here’s what’s new! 🧵
Here’s what’s new! 🧵
December 22, 2025 at 4:32 AM
once again plugging this amazing resource for anyone in the paediatric cancer space. so much data, so easily accessible
Reposted by Ian Holmes
Now seems like a swell time to point out that Frontline just released this excellent 11-minute mini-documentary about what happened inside CECOT.
Surviving CECOT (full documentary) | Deported to a Maximum-Security Prison | FRONTLINE + ProPublica
YouTube video by FRONTLINE PBS | Official
m.youtube.com
December 21, 2025 at 10:26 PM
Now seems like a swell time to point out that Frontline just released this excellent 11-minute mini-documentary about what happened inside CECOT.
A lot of people on here angrily mocking someone for saying that academics may not have time to read every paper in their field, when those people would cheerfully acknowledge that truism in more relaxed circumstances, shows the extent to which polarization obliterates nuance in… certain debates.
December 21, 2025 at 10:32 PM
A lot of people on here angrily mocking someone for saying that academics may not have time to read every paper in their field, when those people would cheerfully acknowledge that truism in more relaxed circumstances, shows the extent to which polarization obliterates nuance in… certain debates.
Not sure if anyone has noticed but the honeymoon period of people trying to be kinder and gentler on this site may, possibly, have ended
December 21, 2025 at 8:20 PM
Not sure if anyone has noticed but the honeymoon period of people trying to be kinder and gentler on this site may, possibly, have ended
I saw precursors of this numerous times in SF while I lived there. A Waymo unable to comprehend that a garbage truck was cutting through a one-way street as a shortcut, kept it plugged for half an hour. Another refused to pass a crosswalk while a wailing toddler sat on the curb, stalling the block
Failed Waymo robot blocking emergency services during a widespread emergency:
Grant St at Sacramento, heart of Chinatown, San Francisco
I've been warning about this scenario for ~7 yrs. Safety drivers fix this in seconds. SFPD will prob have to drive this out of the way.
OP:tiktok.joolyana
Grant St at Sacramento, heart of Chinatown, San Francisco
I've been warning about this scenario for ~7 yrs. Safety drivers fix this in seconds. SFPD will prob have to drive this out of the way.
OP:tiktok.joolyana
December 21, 2025 at 5:38 PM
I saw precursors of this numerous times in SF while I lived there. A Waymo unable to comprehend that a garbage truck was cutting through a one-way street as a shortcut, kept it plugged for half an hour. Another refused to pass a crosswalk while a wailing toddler sat on the curb, stalling the block
Reposted by Ian Holmes
The story of Farage and Putin, told by British-Ukrainian soldier Shaun Pinner on a destroyed apartment block in Kyiv.
December 19, 2025 at 4:54 PM
The story of Farage and Putin, told by British-Ukrainian soldier Shaun Pinner on a destroyed apartment block in Kyiv.