After testing virtually all reasonable permutations of sample prep, spectra acquisition, database selection, data processing... This team (convincingly, I think) demonstrates that ~85% of the small, *annotated* bacterial proteins are undetectable by mass spec—much less non-annotated ones. (1/4) 🧵

The findings at the recent trial and today's Columbia chaos is pushing me to the edge. I just sent the following email...

I heard this morning that my informatics colleague Dr. Atul Butte passed after a battle with cancer. He was a giant in the field & inspired many of us over his distinguished career. He was a passionate champion of the power of big data & his impact on our field is immeasurable. RIP Atul & thanks.

Very smart, high ROI initiative from the Spencer Foundation. Providing bridge funding for canceled NSF grants: 1) directs funds to projects already screened by a top-noch review process. 2) avoids imposing proposal prep costs on researchers. 3) ameliorates the disruption from GOP sabotage.

Interview with a Harvard graduate student from Harvard about some of the consequences of the administration's current policies.

Senator Durbin noted that some (I believe Republican Senators) had indicated the US had been doing more than its share of biomedical research and it was time for other countries take a turn. I felt I had to interrupt to respond...

I appreciate the offers from other scientists to help Harvard (students, labs, etc) through this attack, but what would be most helpful is for you to use your position to contact your elected representatives and make it clear this fight isn't just Harvard, it will affect you, and their districts too

I'm so excited to share a new preprint on exploring sequence, structure, and function relationships and how we can use evolutionary information to help us design new proteins that work in the native context of a cell www.biorxiv.org/content/10.1...

An NSF PO on its upcoming 75th anniversary: "In nature, systems evolve towards minimum of energy, following the laws of physics. In the US today things evolve to a location of maximum pain, violating the laws of the land." www.linkedin.com/posts/tomasz...

As a follow-up to the Kaiser interview, here is my exchange with Dr. Bhattacharya starting Sunday evening... 1/n

I wrote about how we must stand and fight against the threat of eugenics. Fueled by white nationalism and scientific racism, these beliefs are factually wrong and ethically abhorrent. This fight includes supporting efforts to diversify our workforce & science. To stop now would be a deep betrayal.

Join our lab to study transcriptional regulation in mouse germ cells and embryonic stem cells at @haskoliislands.bsky.social in beautiful Reykjavík! Apply here: tinyurl.com/34y6jcrd #epigenetics #TranscriptionFactors #transcriptomics #stemCells #pluripotency

ATTENTION I am hearing from several sources that "NIH" sent out termination notices for most or all "diversity" awards yesterday to coincide with the new Notice. If you were affected by this and are willing to share, please DM me or reach me on Signal (jeremymberg.78) 1/2

April is #Autism Awareness Month. This is a month to accept, understand and love those in the Autism Spectrum. Above all accepting that someone is different and respecting their differences is the most important thing we can do. Here are some facts to help understand (a thread):

Another moment of WTF... The evolution of the www.covid.gov site... Warning: May be jarring! 1/4

After 21 years at my dream job, I’m very sad to announce my early retirement from the National Institutes of Health. My life’s work has been to scientifically study how our food environment affects what we eat, and how what we eat affects our physiology.

All snails have tentacles. Some have 1 pair, other 2 pair. In some (but not all) snails, the eyes are placed at the end of one of these pairs of tentacles, called an 'ommatophore' or eyestalk. And, as you can see, they can fully RETRACT (evert) them at will.

💐 To NIH and NSF program officers, and anyone else trying to keep those institutions alive: Thank you for trying to do an impossible job in an impossible time. I’m sorry for all of us that this is the world we’re living in. 1/n

New story about grant terminations in Pittsburgh www.post-gazette.com/business/hea... 1/2

🧵 From Medscape (widely read by health professionals): "What Not to Say to People With Complex Chronic Illness" www.medscape.com/viewarticle/... (may require free registration) #MEcfs #LongCovid 1/

I know that the mRNA is larger than the protein it codes for but I don't believe it

If you are wondering why universities and academic medical centers seem so stressed, one major reason is these imposed cash flow challenges. These funds were expected in good faith (and based on past practices), but have not been forthcoming. 12/n

Why wouldn't you want to understand vaccine hesitancy?(Gift link) wapo.st/3Dw7WG0

Bluetorial: Women, courage, and leadership What follows will include some generalizations based on population averages of what I have experienced over the course of my career. There are, of course, exceptions in every group who are substantially more to one extreme or the other.

New post with the WTAE Pittsburgh news story www.wtae.com/article/pitt...

#Microproteins may be the next frontier in #proteomics. But figuring out the publications can be tough. If you are looking for some advice about microprotein evidence, check out the latest from our consortium. Lead by @carvunis.bsky.social and Aaron Wacholder! 🧬 💻 #genomics #RNASky bit.ly/4bgJSDm

Ever see dark grey slime on your faucet? Its from bacteria munching on manganese! watch on YouTube to support us 👇 youtube.com/shorts/7AULY...

Bluetorial: The path to a new pain medication with little potential for addiction Perhaps a good story to share with folks who want to learn about how biomedical research works and where advances come from.

It’s probably a good day to explain to your non-scientist socials that graduate students are not merely the next generation of academic science, they are an important component of the current scientific labor force. Feel free to mention that this is cut rate labor as well.

The press has a big role to play in shining light of what is going on...

The City of Boston is leading 40+ mayors, cities, and counties in an amicus brief against the Trump Administration's drastic and illegal cuts to federal research funding—cuts that will lead to immediate job losses nationwide.

I find it interesting that the response seems to first question my expertise/experience. That is called gaslighting. YES I have been on a variety of situations in which merit is assessed, including committees and study sections. I have many anecdotes as well. But anecdotes are not data

CZI has officially bailed. I have to say one of the most disappointing aspects of all of this has been seeing how many were only doing performative DEI and never really cared about diversity equity or inclusion

I am actively looking for a research scientist position or research administration role within the Raleigh-Durham (RDU) area! Please reach out if my background and skillset might fit your labs needs :-) Lots of experience with preclinical models, translational neuroscience, and behavioral analyses!

So a former postdoc from our department had just started as a PO at NIH and was terminated in the wave of terminations last week. He is in the research triangle and a phenomenal scientist with expertise in stress and glia. If anyone in the RTI is hiring asap please let me know! #neuroskyence

Thanks to all of the NIHers and their friends who reached out to me. I am still here (DM me or Signal jeremymberg.78) I still have a very incomplete picture but based on what I have been told, the damage to NIH and to many wonderful people who work(ed) there is/was impossible for me to imagine 1/n

Rumors are that “it” is likely to happen Tuesday, but no one is sure was “it” is. Prepare and push back any way you can. Senators and reps, especially in red states, need to know how much we think is at stake, not for us but for everybody in the US and the world. cont..

To bee or not to bee?

ATTENTION (PLEASE SHARE) If anyone has or knows of any positions that might be appropriate for the NIH staff members who were terminated, please post the information in this thread. There are lots of talented and accomplished people who may be looking for new opportunities.

OK Yinzers- it's time to stand up for science!!! I will be at Schenley Plaza TODAY AT 5PM. 🙏 please join me there! We need to let people know what's happening!🙏 And yes, I know it's Valentine's Day #StandupForScienceWithYourSweetie 💗💕🧑‍🔬👨‍🔬👩‍🔬💕 💗 Please repost and do something similar at your campus!🧪

It’s Evolution as We Know It (And We Feel Fine)! (With apologies to REM) Registration for Evolution 2025 is now open! Join us virtually May 29-30, in-person June 20-24. www.evolutionmeetings.org/registration... @sse-evolution.bsky.social @systbiol.bsky.social @asn-amnat.bsky.social #Evol2025

March 7. Stand Up For Science. Rallies in DC and nationwide. 🧪 Please visit the website and spread the word. www.standupforscience2025.org

🔎microproteins special issue!

HEADS UP: ALL INDIVIDUALS WITH ACTIVE DIVERSITY-RELATED AWARDS (ANY MECHANISM) It occurred to me while out walking that it might be worth asking your PO about an extension to allow you time to apply to a non-diversity award. I don't know what the answer will be, but it is worth the ask.

Thank you Keystone, Thomas Martinez, Lena Ho, and every single attendee. It was a magical few days of world-class 🧪 microprotein science in the spirit of curiosity, rigor, respect and daring to dream big. I'm grateful for the warmth and inclusiveness of this community, especially in "these times".

Assembling information about individuals affected by this may be an important first step in moving forward to try to address this injustice. THANK YOU AND PLEASE SHARE THIS THREAD

ATTENTION If you are someone who had an F31-Diversity (or similar) application submitted this cycle, please DM me here, contact me on signal (jeremymberg.78), or email me at [email protected]. I will keep all information confidential. 2/n

I have learned from several sources that NIH staff tried to find out how to transfer F31-diversity applications to other program announcements for funding but were not able to do this. I don't know whether this was technical (regulations) or ideological. 1/n

THIS IS NOT FIRM INFORMATION I have heard from several sources what the plan for processing NIH grants may be. All grants (competing, non-competing, no cost extensions) will be subject to certification that they are compliant with the Executive Orders. 1/n

Bluetorial: Metal regulation, an unexpected connection, and a deep evolutionary insight