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napari 0.6.5 is out! 🚀

Rapid-fire highlights are: colorbar overlay, custom startup script, and better and prettier documentation! Check out the full release notes here: napari.org/dev/release/...

Image depicting the napari viewer in grid mode with scale bars and color bars enabled

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Reposted by Jeffrey Perkel (he/him)

Kendall Powell @kendallsciwrite.bsky.social · 7d

At long last, the 2025 @nature.com global PhD Survey is out! This first article by @lindanordling.bsky.social charts the state of the PhD experience in 2025. Good news: satisfaction is high. Bad news: so is harassment and discrimination.

www.nature.com/articles/d41...

How money, politics and technology are redefining the PhD experience in 2025

Nature’s global survey of 3,785 doctoral students shows satisfaction has recovered from pandemic lows, but harassment and inadequate supervision remain widespread.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 8d

The challenge of staying up to date with the scientific literature has become a burden for everyone from students to senior investigators. New @nature.com, three researchers offer strategies for separating the wheat from the chaff #phdlife #AI 🧪 www.nature.com/articles/d41...

How to find the papers you need to read — and avoid the ones you don’t

With thousands of papers being published everyday, it can be a task working out which matter. Here are some tips to help you decide.

www.nature.com

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Reposted by Jeffrey Perkel (he/him)

Aleksandra Lazić @alelazic.bsky.social · 11d

When's an #RStats movie coming to the silver screen?

Jeffrey Perkel (he/him) @jperkel.bsky.social · 13d

It was a real pleasure to speak with @numpy.bsky.social creator Travis Oliphant about NumPy, SciPy, and #Python: the Documentary! New @nature.com 🧪🐍 www.nature.com/articles/d41...

Python, the movie! The origin story of the programming language comes to the silver screen

The creator of the NumPy and SciPy libraries reflects on their supporting role in the story of Python, now the subject of a documentary.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 12d

"NumPy has been a driving force for my whole life." It was a real pleasure to speak with @numpy.bsky.social developer Travis Oliphant about NumPy, SciPy, and #Python: the Documentary! New @nature.com 🧪🐍 www.nature.com/articles/d41...

Python, the movie! The origin story of the programming language comes to the silver screen

The creator of the NumPy and SciPy libraries reflects on their supporting role in the story of Python, now the subject of a documentary.

www.nature.com

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Reposted by Jeffrey Perkel (he/him)

Olivia Guest · Ολίβια Γκεστ @olivia.science · Sep 6

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia:
doi.org/10.5281/zeno...

We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical
thinking, expertise, academic freedom, & scientific integrity.
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Abstract: Under the banner of progress, products have been uncritically adopted or
even imposed on users — in past centuries with tobacco and combustion engines, and in
the 21st with social media. For these collective blunders, we now regret our involvement or
apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we
are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not
considered a valid position to reject AI technologies in our teaching and research. This
is why in June 2025, we co-authored an Open Letter calling on our employers to reverse
and rethink their stance on uncritically adopting AI technologies. In this position piece,
we expound on why universities must take their role seriously toa) counter the technology
industry’s marketing, hype, and harm; and to b) safeguard higher education, critical
thinking, expertise, academic freedom, and scientific integrity. We include pointers to
relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI
(black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are
in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are
both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and
Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf.
Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al.
2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms
are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

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Reposted by Jeffrey Perkel (he/him)

Max Kozlov @maxkozlov.bsky.social · 13d

NEW: Nature trained AI to predict which NIH grants from 2014 would have been cut if the Trump admin had its way back then — and what science would have been lost to history.

"The results show the damage that cuts in funding can do to research, and the unpredictable nature of the research process."

Nature @nature.com · 13d

We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US NIH grants to reveal the broad-reaching consequences

go.nature.com/4pBArFH

What research might be lost after the NIH’s cuts? Nature trained a bot to find out

We used machine-learning tools in an attempt to recreate the method for cutting funding, and then applied it to past US National Institutes of Health grants to reveal the broad-reaching consequences of such action.

go.nature.com

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Reposted by Jeffrey Perkel (he/him)

Jonathan Eisen @phylogenomics.bsky.social · 12d

We need additional ways to fund science www.nature.com/articles/d41...

Will the public support basic science? A new non-profit aims to find out

The Science Foundation seeks donations to fund ten $10,000 ‘what if’ seed grants.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 13d

It was a real pleasure to speak with @numpy.bsky.social creator Travis Oliphant about NumPy, SciPy, and #Python: the Documentary! New @nature.com 🧪🐍 www.nature.com/articles/d41...

Python, the movie! The origin story of the programming language comes to the silver screen

The creator of the NumPy and SciPy libraries reflects on their supporting role in the story of Python, now the subject of a documentary.

www.nature.com

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Reposted by Jeffrey Perkel (he/him)

Elizabeth Warren @warren.senate.gov · 14d

Let's be clear: no one should be taking medical advice from the man who told Americans to inject bleach.

To moms worried about the Tylenol they took while pregnant: you deserve better than being RFK Jr's scapegoat.

And to the autism community: you are loved exactly as you are.

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 15d

"By outfitting cells with the molecular equivalent of flight recorders, scientists can now log, in real time, the signals that cells receive, the paths they travel and the decisions they make — all inscribed indelibly in genomic ink."

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 15d

For decades, researchers have strained to reconstruct cellular backstories through indirect means. But these are forensic efforts at best, postmortems of a vanished process. A new generation of DNA-recording tools promises to change that. By Elie Dolgin @nature.com 🧪 www.nature.com/articles/d41...

Real-time molecular recorders expose the inner lives of cells

Gene-editing tools transform cells into record-keepers, capturing hidden timelines of health and disease.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 19d

Incredible work: "This is the first time #AI systems are able to write coherent genome-scale sequences.” Researchers at
@arcinstitute.org use AI to design new viruses capable of infecting bacteria. @nature.com 🧪 www.nature.com/articles/d41...

World’s first AI-designed viruses a step towards AI-generated life

Scientists used AI to write coherent viral genomes, using them to synthesize bacteriophages capable of killing resistant strains of bacteria.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 19d

Shameless plug, but for more on genomic AIs, including the Evo models used here, see my recent feature in @nature.com: www.nature.com/articles/d41...

Beyond AlphaFold: how AI is decoding the grammar of the genome

Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 21d

"Amid a backdrop of massive cuts in US federal support for scientific research, a new effort — the Science Foundation — launched last week to raise public funds for transdisciplinary, discovery-based research." @virginiagewin.bsky.social reports for @nature.com 🧪 www.nature.com/articles/d41...

Will the public support basic science? A new non-profit aims to find out

The Science Foundation seeks donations to fund ten $10,000 ‘what if’ seed grants.

www.nature.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 22d

Neat trick! But it requires no blank lines in LIST.txt!

Reposted by Jeffrey Perkel (he/him)

Jessica Valenti @jessicavalenti.bsky.social · 25d

I know everyone is consumed with other news, but this is a big fucking deal: The Trump administration says that IUDs and the Pill are actually abortions.

Here's what USAID told the NYT about the $10m in birth control they plan to destroy.
www.nytimes.com/2025/09/11/h...

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Reposted by Jeffrey Perkel (he/him)

Julia Carrie Wong @joolia.bsky.social · 25d

“Did you consider not complying with this request?”

Judith Butler spoke to @samtlevin.bsky.social about being reported to the feds by UC Berkeley for supposed antisemitism

UC Berkeley shares 160 names with Trump administration in ‘McCarthy era’ move

Prominent professor Judith Butler among students and faculty investigated for ‘alleged antisemitic incidents’

www.theguardian.com

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Jeffrey Perkel (he/him) @jperkel.bsky.social · 26d

Through lawsuits, grant tracking, whistle-blowing and more, resistance to the US war on science is growing. Read this fantastic story by @dangaristo.bsky.social @maxkozlov.bsky.social @heidiledford.bsky.social @nature.com! 🧪 www.nature.com/articles/d41...

Scientists take on Trump: these researchers are fighting back

Through lawsuits, grant tracking, whistle-blowing and more, resistance to the US war on science is growing.

www.nature.com

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Reposted by Jeffrey Perkel (he/him)

Jeffrey Perkel (he/him) @jperkel.bsky.social · 27d

From large national databases to bespoke sample collections, biobanks offer a wealth of avenues for scientific enquiry. New @nature.com, @smjyoti.bsky.social speaks with @ukbiobank.bsky.social & other biobanks and users to learn how best to make use of their services www.nature.com/articles/d41... 🧪

Using biobanks to boost research: a how-to guide

From large national databases to bespoke sample collections, biobanks offer a wealth of avenues for scientific enquiry.

www.nature.com

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