Sarah Bagby

Fellow Clevelanders will have seen @neorsd.org's update on the end of their Shaker Dam engineering work. I have some technical-detail thoughts about this, as an engineering-adjacent STEM person and a fan of the lake and brook. Keep reading for a summary (incl. links to slides and video): 1/8

Logo for the Sandpiper website

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

NEBRASKA CROWD: “TAX THE RICH! TAX THE RICH!”

@USRepMikeFlood: “So your proposal to solve (the debt) is tax the rich?”

NEBRASKA CROWD: *CHEERS WILDLY*

(not sure this went quite as he planned 😬)

No PhD students or severely reduced # of admits -> *undergraduates* looking now to start the next phase of their career in support of research & discovery will be stuck without an option.

This is far from the only place in a similar situation, whether announced publicly yet or not.

Medicaid is not for sale.
NASA is not for sale.
The Post Office is not for sale.
America is not for sale.

We have an obligation to resist kings. We outnumber them. And they can be overwhelmed.

NIH indirects case update:

Hearing ongoing now, and I'll try to live tweet some notable exchanges.

Prior to more detailed arguments, Judge Kelley starts off with a few point questions to both sides:

(I'm paraphrasing here)

The Internet Archive has to date downloaded 500 terabytes of US government websites, which it crawls at the end of every presidential term. The whole archive is fully searchable. This effort's housed by a donation-funded nonprofit, not a branch of the US government. blog.archive.org/2024/05/08/e...

I know that all these institutions know how to push back because when Obama directed them to enforce pre-existing Title IX law, universities said no.

They flat out refused until there was a working group and specific guidelines. And even then, they *still* refused.

Everyone, plz share with your stellar undergrads! The UDE program (Undergraduate Diversity at Evolution) pairs students from diverse backgrounds with mentors to attend the Evolution meeting each year. Encourage your undergrads to apply!

Friends, please help spread the word about our microbiology REU program at Montana State University.
www.montana.edu/mbi/reu/

Each student receives a stipend ($7000 for 10 wks). Travel compensation, room, and board are also provided.

Details in the attached pic--Feb 13 deadline
🧫🧪🦠#microsky

For myself, Emacs org-mode, always. For my group, the goal is GitHub task lists in private repos; right now it's a mix of that and Slack. For wider collaborations, Basecamp and a whole lot more Google docs than I would like. The best tool is the one people are willing to use to get the job done.

(1/6) Our new short paper on incidental bacterial domestication between patient isolation and creation of frozen stock. Geno/phenotype changes are obscured by rich media and more prevalent than we previously thought.

#MicroSky

Tapping the treasure trove of atypical phages With advancements in genomics technologies, a vast diversity of ‘atypical’ phages, that is, with single-stranded DNA or RNA genomes, are being uncover…

#phagesky

Some partnerships are always fun!! Excited to share one such 🎉 product w Simon Roux, perspectives on our favorite “atypical” phages, for special issue to celebrate my former mentor Carol Gross @ UCSF

Tapping the treasure trove of atypical phages

www.sciencedirect.com/science/arti...

look at this absolute grob

Microbial people! Especially postdocs and maybe some assistant professors who are feeling antsy ... the University of Montana is doing a search for a microbiologist! This is a great department, in a great place. (I worked there for 10 years, loved it, ping me with Qs)

apply.interfolio.com/159494

Ohio friends: consider contacting Gov Dewine to urge him not to sign the "bathroom bill" (SB 104). Educators are in a particularly good position to made the case against this on practical grounds, though I also brought up the specter of conference/business boycotts, as in NC.

On AI-assisted writing in graduate school What is the proper role of AI ‘assistance’ in graduate student writing? It depends on what you mean by ‘graduate’.

Shameless plug: a post on 'writing as thinking' that I wrote for my own students
hackingsemantics.xyz/2024/writing/

FWIW, we've switched over to CheckM2 (reduces bias against small genomes), and our are-these-bugs-the-same step is usually dereplication with dRep or galah. But I'd agree with the above---"good enough" depends on what you need it for; there's lots to learn even from fragmented assemblies.

Our first B. subtilis paper, published at NatureComms.
Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation. #subtiwiki #bacillus www.nature.com/articles/s41...
Funded by FNP_org_pl and EMBO_YIP

Governor Andy Beshear, in a Trump +30 state, gives advice to Democrats: Do not throw LGBTQ+ people under the bus, it will not work.

His advice to dems: Lead on your values.

This man ran on a fully inclusive campaign in 2023 and won. He received the same kind of ads Harris did.

A few days left to apply! #ProtistsOnSky

We are looking for a dynamic, motivated, interdisciplinary researcher to join our new project RESPECT: Rapid Engagement with Stressed Peatland Environments and Communities in Transformation. Field & lab components working in a cross-disciplinary group. 1/2

...and a miss

Two weeks left to apply. Please reach out if you have questions!

My department is looking for an assistant professor in fisheries and conservation: careers.udel.edu/cw/en-us/job...

Please repost! #marinesky #oceanography #STEM #fisheries

Excited to share: The inaugural Alma Dal Co School on Collective Behavior is coming to Venice (Sep 29-Oct 4, 2025). This unique school honors Alma (1989-2022), whose brilliant work bridging physics and microbiology revealed how metabolic interactions structure microbial communities. 1/12

A couple of weeks ago I posted a preprint and almost immediately got an email from an AI company that (a) incorrectly summarized our abstract and (b) pitched me on testing its two crap hypotheses. Sure, who WOULDN'T pay to have an AI incompetently do a job they'd spent decades training for?!

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