Titus Brown
@titus.idyll.org
I am not a deep man, but I have many shallows. [email protected], http://ivory.idyll.org/blog/.
Reposted by Titus Brown
Reposted by Titus Brown
This is the problem with trying to inspire hope using the message "we have the solutions": such a message may inspire the kind of techno-optimism that actually fosters political *dis*engagement.
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⚠️ When “technology will save us” becomes a climate risk!
A new paper from great colleagues takes a careful look at techno-optimism — the belief that technology will largely solve climate change — and what it means for real-world climate action.
(1/4)👇
osf.io/preprints/ps...
A new paper from great colleagues takes a careful look at techno-optimism — the belief that technology will largely solve climate change — and what it means for real-world climate action.
(1/4)👇
osf.io/preprints/ps...
November 19, 2025 at 7:32 PM
This is the problem with trying to inspire hope using the message "we have the solutions": such a message may inspire the kind of techno-optimism that actually fosters political *dis*engagement.
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Reposted by Titus Brown
I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!
November 17, 2025 at 3:52 PM
I recently discovered Conventional Comments (conventionalcomments.org) for providing a pseudo-standard set of labels for feedback and just tried it for an article review and it was really helpful to specify issues vs. thoughts vs. suggestions, etc. Hopefully it's helpful for the authors too!
Reposted by Titus Brown
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.
#WAAW2025 #ActOnAMR
www.ebi.ac.uk/about/news/t...
🧬💻
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
www.ebi.ac.uk
November 19, 2025 at 12:27 PM
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Reposted by Titus Brown
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy
Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...
rdcu.be
November 18, 2025 at 9:01 PM
Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf
Reposted by Titus Brown
“We are in the middle of a scandal of elites palling around with one of the most infamous child sex traffickers in the world, and this is our political press? No wonder Epstein got away with it all so long: many of the men tasked with being the watchdogs were almost as gross as he was with women.”
For my newsletter, I wrote about Olivia Nuzzi and the older men who have taken advantage of her her whole life. www.burnsnotice.com/olivia-nuzzi...
Olivia Nuzzi is an Embarrassment to Journalism
She seamlessly landed a plum role at Vanity Fair and got a sweetheart book deal after breaking a fundamental journalistic ethics rule.
When my co-host Christine Grimaldi and I recorded our October 20...
www.burnsnotice.com
November 18, 2025 at 8:51 PM
“We are in the middle of a scandal of elites palling around with one of the most infamous child sex traffickers in the world, and this is our political press? No wonder Epstein got away with it all so long: many of the men tasked with being the watchdogs were almost as gross as he was with women.”
Reposted by Titus Brown
I’m good in the hood.
November 18, 2025 at 7:35 PM
I’m good in the hood.
Reposted by Titus Brown
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
November 17, 2025 at 6:05 PM
One like = one scene from "AI, Claudius", the epic story of a stammering Markov model who survived corruption, lies, and intrigue to become LLM-peror of Ancient Rome
Reposted by Titus Brown
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?
November 18, 2025 at 5:29 PM
OK, #bioinformatics folk. We have some (many many) reads from a metagenome. They have been binned into a bacterial genome. They have no matches to any known genome in any database. They code for "bacterial" genes. What are good triple-checks to do to argue that they are not, in fact, euk sequence?
Reposted by Titus Brown
Wonderful humanitarian. Her name should be remembered.
What a contrast in humans: she does such good in the world while her ex continues to pillage the planet and the people
November 17, 2025 at 5:35 AM
Wonderful humanitarian. Her name should be remembered.
Reposted by Titus Brown
TRIGGER WARNING
Every woman i know, and every woman i have trained has been sexually assaulted.
Every. Single. One.
It is a very good plan to learn new behaviors that lessen the trauma for women....men can learn how to be less...awful.
Many men need to learn new ways.
So many stuck men
Every woman i know, and every woman i have trained has been sexually assaulted.
Every. Single. One.
It is a very good plan to learn new behaviors that lessen the trauma for women....men can learn how to be less...awful.
Many men need to learn new ways.
So many stuck men
a man in a brown coat says " old man " in white letters
Alt: a man in a brown coat says " old man " in white letters
media.tenor.com
November 17, 2025 at 2:24 PM
TRIGGER WARNING
Every woman i know, and every woman i have trained has been sexually assaulted.
Every. Single. One.
It is a very good plan to learn new behaviors that lessen the trauma for women....men can learn how to be less...awful.
Many men need to learn new ways.
So many stuck men
Every woman i know, and every woman i have trained has been sexually assaulted.
Every. Single. One.
It is a very good plan to learn new behaviors that lessen the trauma for women....men can learn how to be less...awful.
Many men need to learn new ways.
So many stuck men
Reposted by Titus Brown
"it reminded me why open-source communities like Jupyter thrive: curiosity, generosity, and the drive to make knowledge accessible for everyone." ✨
Amazing post by Debsiree Ray on her (first-time) experiences at JupyterCon - Thanks to the team who made it possible!!
medium.com/womenintechn...
Amazing post by Debsiree Ray on her (first-time) experiences at JupyterCon - Thanks to the team who made it possible!!
medium.com/womenintechn...
Reflections from JupyterCon 2025
A Week of Ideas, Code, and Community
medium.com
November 17, 2025 at 9:58 PM
"it reminded me why open-source communities like Jupyter thrive: curiosity, generosity, and the drive to make knowledge accessible for everyone." ✨
Amazing post by Debsiree Ray on her (first-time) experiences at JupyterCon - Thanks to the team who made it possible!!
medium.com/womenintechn...
Amazing post by Debsiree Ray on her (first-time) experiences at JupyterCon - Thanks to the team who made it possible!!
medium.com/womenintechn...
Reposted by Titus Brown
My experience with the academic job market is that there is simply far more luck involved than the vast majority of people are comfortable saying. Which departments are even hiring, what internal politics mean for the research topics they want, what fields the NSF has postdocs for, etc.
All of us from the post-2008 era (and before, no doubt) have traumatic memories of the academic job market, but I don't think the real problem was the hotel rooms (or the ballroom!), & I think it should be noticed that the real problem (no jobs, ridiculous power disparities) is now worse
November 17, 2025 at 8:28 PM
My experience with the academic job market is that there is simply far more luck involved than the vast majority of people are comfortable saying. Which departments are even hiring, what internal politics mean for the research topics they want, what fields the NSF has postdocs for, etc.
Reposted by Titus Brown
Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
ECR connection: Meet Meren when you need to
A means for ECRs to get advice from a senior scientist outside of their support network
merenlab.org
November 16, 2025 at 4:56 PM
Starting this week, I set aside one hour each week to meet ECRs outside my group who want to discuss career development, mentorship, or any non-technical professional questions.
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Here is a blog that explains my motivation for this and how to schedule a meeting:
merenlab.org/2025/11/16/E...
Reposted by Titus Brown
Unreal, the impact this is having on scientists. I spent over 700 hrs writing 4 grants submitted Apr-Sept that *might* have been funded next Apr; 2 abt to be 3 apps missed review bc of shutdown. In normal times takes 9-24 mo to get a grant funded. No hope for labs like mine. Literally no hope.
While the government was shut down, 379 NIH study section meetings (containing 24,380 grant applications) were postponed. NIH is committed to getting these reviewed, but please be patient and understanding with staff, as this is a complex and heavy lift.
November 13, 2025 at 1:58 PM
Unreal, the impact this is having on scientists. I spent over 700 hrs writing 4 grants submitted Apr-Sept that *might* have been funded next Apr; 2 abt to be 3 apps missed review bc of shutdown. In normal times takes 9-24 mo to get a grant funded. No hope for labs like mine. Literally no hope.
Reposted by Titus Brown
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
On Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
November 17, 2025 at 1:32 PM
My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.
Reposted by Titus Brown
Reposted by Titus Brown
“My magic beans can work miracles, they’re different from all of the fake magic beans out there” has been the sales pitch of charlatans since time immemorial.
Anthropic CEO Dario Amodei thinks AI could help find cures for most cancers, prevent Alzheimer’s, and even double the human lifespan. cbsn.ws/4oRZ8Nm
November 17, 2025 at 1:46 AM
“My magic beans can work miracles, they’re different from all of the fake magic beans out there” has been the sales pitch of charlatans since time immemorial.
Reposted by Titus Brown
Sssssooooo... yeah. (Wow!) 😳🤗
✨ Please join SFWA in celebrating the announcement of our latest Damon Knight Memorial Grand Master Award: N. K. Jemisin. ✨
Learn more here about @nkjemisin.bsky.social, the Grand Master Award, and how the work goes on after the accolades for all we've already done:
www.sfwa.org/2025/11/16/p...
Learn more here about @nkjemisin.bsky.social, the Grand Master Award, and how the work goes on after the accolades for all we've already done:
www.sfwa.org/2025/11/16/p...
November 16, 2025 at 11:04 PM
Sssssooooo... yeah. (Wow!) 😳🤗
Reposted by Titus Brown
Whoa whoa whoa
Diving through the purple sulfur bacteria layer of Fayetteville Green Lake with our ROV last month. This is the most intense density of PSB that I've seen in many years!
November 16, 2025 at 11:30 PM
Whoa whoa whoa
Reposted by Titus Brown
very funny to read these emails and then remember summers wondering whether the leaky pipeline in stem was because women are inherently bad at math
The emails have Summers reporting to Epstein about his attempts to date a Harvard economics student & to hit on her during a seminar she was giving.
November 16, 2025 at 1:56 AM
very funny to read these emails and then remember summers wondering whether the leaky pipeline in stem was because women are inherently bad at math
Reposted by Titus Brown
I've long admired @ruha9.bsky.social's work, activism & "life model." When we met & I served as discussant for her last year, I felt a connectedness that has grown. It was a gift beyond measure for her provide comment for "When Trees Testify" (@henryholtbooks.bsky.social / @macmillanusa.bsky.social)
November 15, 2025 at 8:06 PM
I've long admired @ruha9.bsky.social's work, activism & "life model." When we met & I served as discussant for her last year, I felt a connectedness that has grown. It was a gift beyond measure for her provide comment for "When Trees Testify" (@henryholtbooks.bsky.social / @macmillanusa.bsky.social)
Reposted by Titus Brown
Excellent read. My general experience is that AI isn't going to create good, complicated code from scratch...but if you have specific things to do or translation like this, it does indeed save time.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
November 15, 2025 at 3:55 PM
Excellent read. My general experience is that AI isn't going to create good, complicated code from scratch...but if you have specific things to do or translation like this, it does indeed save time.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
I just wish it weren't being marketed as the be-all/end-all...coders no longer needed solution.
Good post.
I just published my weekly newsletter to >10K subscribers: The truth about AI coding for bioinformatics divingintogeneticsandgenomics.kit.com/posts/ai-po...
AI ported 6,000+ lines of Python in 8 hours. Here’s the catch
divingintogeneticsandgenomics.kit.com
November 15, 2025 at 3:50 PM
Good post.