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Reposted by Richard Sever

Pedro Beltrao @pedrobeltrao.bsky.social · 3d

new preprint: Ubiquitin is a protein modification linked with degradation but known to regulate other functions. Over 100k ubiquitination sites have been discovered and here we (@julianvangerwen.bsky.social + others) try to prioritize those most critical to the cell www.biorxiv.org/content/10.1...

The functional landscape of the human ubiquitinome

Protein ubiquitination regulates cell biology through diverse avenues, from quality control-linked protein degradation to signaling functions such as modulating protein-protein interactions and enzyme...

www.biorxiv.org

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Reposted by Richard Sever

Kristina Šekrst @epiphenomenal.bsky.social · 1d

Accurate.

#academia #academy #philsky #philosophysky #philosophy #science

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Richard Sever @richardsever.bsky.social · 1d

Yeah - response is the more general term I guess. Rebuttal usually specific to a rejection decision.

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Richard Sever @richardsever.bsky.social · 2d

MIT (Kornbluth): The Compact "would restrict freedom of expression...the premise is inconsistent with our core belief that funding should be based on scientific merit alone...we cannot support the proposed approach to addressing the issues facing higher education" orgchart.mit.edu/letters/rega...

Regarding the Compact | MIT Organization Chart

orgchart.mit.edu

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Richard Sever @richardsever.bsky.social · 2d

Question for the hive mind: Is this less or more likely if reviews and rebuttal are public?

Rebuttals currently aim primarily to sway one person (the editor). But if they are increasingly context for readers to judge the merits of criticism (eLife-type process), will they differ?

Elisa Fadda @elisafadda.bsky.social · 2d

What I abhor is the swamp of text in rebuttal (pages and pages on nothing) that does not address my query, but goes endlessly around it, to go to why 'I didn't do this because I can't care less about checking, about making my science accurate as I possibly can' 3/n

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Richard Sever @richardsever.bsky.social · 3d

the comment seemed so apt in that context
bsky.app/profile/rich...

Richard Sever @richardsever.bsky.social · 3d

"Lacking even any particularly useful theory of emergence, and confronted with the obvious wild variety of emergent phenomena, it seems likely that predictive theories of biology are unknowably far off" via @dadrummond.art open.substack.com/pub/clauswil...

D. Allan Drummond on Genes, Minds, Machines

Great piece, Claus. Very much enjoying the rebirth of your blog. "Biology is just physics and chemistry" -- you discuss the "levels of organization" later, but perhaps it's worth saying that "just" i...

open.substack.com

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Richard Sever @richardsever.bsky.social · 3d

"Lacking even any particularly useful theory of emergence, and confronted with the obvious wild variety of emergent phenomena, it seems likely that predictive theories of biology are unknowably far off" via @dadrummond.art open.substack.com/pub/clauswil...

D. Allan Drummond on Genes, Minds, Machines

Great piece, Claus. Very much enjoying the rebirth of your blog. "Biology is just physics and chemistry" -- you discuss the "levels of organization" later, but perhaps it's worth saying that "just" i...

open.substack.com

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Richard Sever @richardsever.bsky.social · 3d

AI in biology: "I read about some new computational method...get excited because it’s exactly what I need...I try the method...Most of the time things don’t work...I have seen this play out so many times my default assumption is nothing is going to work" blog.genesmindsmachines.com/p/we-still-c...

We still can’t predict much of anything in biology

Biology is hard. Yes, even for AI.

blog.genesmindsmachines.com

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Richard Sever @richardsever.bsky.social · 4d

Now on YouTube. This was a fascinating discussion with many open science talking points: pros vs cons, challenges, misrepresentations, cultural change, AI. youtu.be/myYp4nfzK6o?...

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Richard Sever @richardsever.bsky.social · 4d

Very sad to learn of the death of Sir John Gurdon. He made a huge contribution to developmental biology & should be an inspiration to anyone whose potential is dismissed in school. It was a pleasure to work with him when he was Chair of the COB Board. www2.mrc-lmb.cam.ac.uk/john-gurdon-...

John Gurdon (1933 – 2025) - MRC Laboratory of Molecular Biology

Renowned developmental biologist John Gurdon, former Group Leader and Head of the LMB’s Cell Biology Division, has died aged 92.

www2.mrc-lmb.cam.ac.uk

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Richard Sever @richardsever.bsky.social · 6d

New blog post. In which I analyze the new HHMI announcement and what it means for the science publishing ecosystem openrxiv.org/preprint-man...

Preprint mandates gather momentum - openRxiv

By Richard Sever, PhD. Chief Science & Strategy Officer, openRxiv Preprints speed up science by enabling researchers to disseminate reports of new findings immediately. They also represent a simple wa...

openrxiv.org

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Richard Sever @richardsever.bsky.social · 6d

Diana Bianchi out at NICHHD. Hard to see a good reason for letting such a talented individual go www.science.org/content/arti...

After months in limbo, four NIH institute directors fired

Two leaders removed by Trump administration had hoped to stay at agency as in-house investigators

www.science.org

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Reposted by Richard Sever

Life In Wisconsin @lifeinwisconsin.bsky.social · 7d

It should be noted that Google has noticed the backlash enough that they quietly published a code that would removed AI results for their searches.

An enterprising person built a default site to search without AI, and the results are goddamn refreshing as hell.
udm14.org

&udm=14 | the search engine Konami code

A quick way to get an AI-free search without any extra work.

udm14.org

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Richard Sever @richardsever.bsky.social · 7d

Agree 100%. My 2c is that there’s almost always a better term/phrase that more accurately conveys what is being discussed.

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Richard Sever @richardsever.bsky.social · 8d

US "the only major country on Earth not to guarantee healthcare to all people"

James Neal - will know what will happen when it does. @jameswneal.bsky.social · 11d

#bernie and #AOC today

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Reposted by Richard Sever

John Greally @greally.bsky.social · 8d

What an amazing assay.

DAF-seq, the evolution of Fiber-seq from the Andrew Stergachis group, using the @pacbio.bsky.social platform:
www.biorxiv.org/content/10.1...

This will revolutionise our understanding of transcriptional regulation and functional non-coding variants.

Deaminase-assisted single-molecule and single-cell chromatin fiber sequencing

Gene regulation is mediated by the co-occupancy of numerous proteins along individual chromatin fibers. However, our tools for deeply profiling how proteins co-occupy individual fibers, especially at ...

www.biorxiv.org

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Richard Sever @richardsever.bsky.social · 9d

Happening this monday

Gabriel Stein @gabestein.com · 25d

On October 6, join me for a virtual panel with on a vital topic: how can we make sure that open science advances not just science itself, but society’s understanding of, trust in, and willingness to invest in research? Register here: shorensteincenter.org/new-event/ca...

How Can Open Science Practices Increase Trust In Research? | Shorenstein Center

Join representatives from each stage of open science for a frank discussion of how each part of the publishing process must adapt to make sure open science advances not just science itself, but societ...

shorensteincenter.org

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Richard Sever @richardsever.bsky.social · 9d

yep - the irony of the source

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Richard Sever @richardsever.bsky.social · 9d

Lancet editor: "I can’t forgive Bhattacharya and Makary...both know reliable evidence does not exist to restrict paracetamol use during pregnancy...both know evidence linking vaccines to autism simply doesn't exist. What are they doing?"

[politics - that's what]

www.thelancet.com/action/showP...

www.thelancet.com

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Richard Sever @richardsever.bsky.social · 9d

Saying reluctance to revisit questions about vaccine safety is because the research might give "politically incorrect answers" rather because the scientific evidence is utterly convincing is disgraceful www.thelancet.com/action/showP...

www.thelancet.com

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Richard Sever @richardsever.bsky.social · 9d

yeah I couldn't find any info about whether new content processing is affected (it has with shutdowns in the past)

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Richard Sever @richardsever.bsky.social · 9d

As I recall EuroPMC is a mirror. It will not show new content PubMed is unable to process because of the shutdown

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Richard Sever @richardsever.bsky.social · 10d

Can’t believe you copied me!

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Richard Sever @richardsever.bsky.social · 10d

That’s the point of the 3/n post

Reposted by Richard Sever

Lisa Janicke Hinchliffe @lisalibrarian.bsky.social · 10d

It *may* be copyright breach if output is verbatim. There's still fair use for re-use.

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