Toby Hodges
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tobyhodges.carpentries.org
Toby Hodges
@tobyhodges.carpentries.org
310 followers 310 following 170 posts
he/him
Director of Curriculum at The Carpentries. Views my own. Sorry I haven't replied to your email.
"I only know that hearts made of stone will rarely sail far and may never reach home" - Chuck Ragan
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Reposted by Toby Hodges
carpentries.carpentries.org
📢 Your contribution matters! Help The Carpentries enhance our Glossary of Terms with real Carpentries community examples of accessibility, diversity, equity, and inclusion. Share your experiences with us today! 🌟

Read more on how you can help: github.com/carpentries/...
DEI and Accessibility in Action: Share with us your examples of actions you have undertaken towards the realisation of accessibility, diversity, equity and inclusion in The Carpentries community · Iss...
Background/Context The Carpentries is committed to diversity, equity, inclusion and accessibility. This is a commitment we have reinforced in recent times, and again, and again. The Equity, Accessi...
github.com
July 22, 2025 at 1:23 PM
Reposted by Toby Hodges
lorencrary.bsky.social
pls enjoy our beautiful new donate.python.org page <3

thank youuuuuu @maureira.dev and @durbin.ee
November 12, 2025 at 8:25 PM
Reposted by Toby Hodges
hansonmark.bsky.social
We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing:

a 🧵 1/n

Drain: arxiv.org/abs/2511.04820
Strain: direct.mit.edu/qss/article/...
Oligopoly: direct.mit.edu/qss/article/...
A table showing profit margins of major publishers. A snippet of text related to this table is below. 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. A figure detailing the drain on researcher time. 1. The four-fold drain 1.2 Time The number of papers published each year is growing faster than the scientific workforce, with the number of papers per researcher almost doubling between 1996 and 2022 (Figure 1A). This reflects the fact that publishers’ commercial desire to publish (sell) more material has aligned well with the competitive prestige culture in which publications help secure jobs, grants, promotions, and awards. To the extent that this growth is driven by a pressure for profit, rather than scholarly imperatives, it distorts the way researchers spend their time. The publishing system depends on unpaid reviewer labour, estimated to be over 130 million unpaid hours annually in 2020 alone (9). Researchers have complained about the demands of peer-review for decades, but the scale of the problem is now worse, with editors reporting widespread difficulties recruiting reviewers. The growth in publications involves not only the authors’ time, but that of academic editors and reviewers who are dealing with so many review demands. Even more seriously, the imperative to produce ever more articles reshapes the nature of scientific inquiry. Evidence across multiple fields shows that more papers result in ‘ossification’, not new ideas (10). It may seem paradoxical that more papers can slow progress until one considers how it affects researchers’ time. While rewards remain tied to volume, prestige, and impact of publications, researchers will be nudged away from riskier, local, interdisciplinary, and long-term work. The result is a treadmill of constant activity with limited progress whereas core scholarly practices – such as reading, reflecting and engaging with others’ contributions – is de-prioritized. What looks like productivity often masks intellectual exhaustion built on a demoralizing, narrowing scientific vision. A table of profit margins across industries. The section of text related to this table is below: 1. The four-fold drain 1.1 Money Currently, academic publishing is dominated by profit-oriented, multinational companies for whom scientific knowledge is a commodity to be sold back to the academic community who created it. The dominant four are Elsevier, Springer Nature, Wiley and Taylor & Francis, which collectively generated over US$7.1 billion in revenue from journal publishing in 2024 alone, and over US$12 billion in profits between 2019 and 2024 (Table 1A). Their profit margins have always been over 30% in the last five years, and for the largest publisher (Elsevier) always over 37%. Against many comparators, across many sectors, scientific publishing is one of the most consistently profitable industries (Table S1). These financial arrangements make a substantial difference to science budgets. In 2024, 46% of Elsevier revenues and 53% of Taylor & Francis revenues were generated in North America, meaning that North American researchers were charged over US$2.27 billion by just two for-profit publishers. The Canadian research councils and the US National Science Foundation were allocated US$9.3 billion in that year. The costs of inaction are plain: wasted public funds, lost researcher time, compromised scientific integrity and eroded public trust. Today, the system rewards commercial publishers first, and science second. Without bold action from the funders we risk continuing to pour resources into a system that prioritizes profit over the advancement of scientific knowledge.
November 11, 2025 at 11:52 AM
Reposted by Toby Hodges
carpentries.carpentries.org
The support the Python community has shown to PSF for its decision has given us hope in the sustainability of open science communities. Please consider extending your generosity to our organisation’s fundraising efforts, and help us to reach others aligned to our mission: carpentries.org/support/
Support The Carpentries
We are grateful to the individuals and organisations who provide financial support to The Carpentries. If you are interested in supporting our work, you can learn more about becoming a Member Organisa...
carpentries.org
November 7, 2025 at 3:52 PM
Reposted by Toby Hodges
carpentries.carpentries.org
We are thrilled with the renewed attention that The Carpentries has received for deciding to withdraw a $1.5 million proposal to the National Science Foundation (NSF), thanks to a recent similar decision made by the @python.org (PSF) and the generous shout-out they gave us when they announced it. 🙏
November 7, 2025 at 3:52 PM
Reposted by Toby Hodges
alastairdunning.bsky.social
"Crucially, students will need to develop sufficient expertise to identify when AI systems produce plausible but incorrect outputs — which poses a dilemma because this requires the very skills that AI is starting to replace."

www.nature.com/articles/d41...
PhD training needs a reboot in an AI world
As machines get better at data analysis and writing tasks, doctoral training must evolve to make the most of artificial-intelligence outputs.
www.nature.com
November 6, 2025 at 9:22 AM
Reposted by Toby Hodges
noamross.net
Between @python.org and @carpentries.carpentries.org, the open-source ecosystem is rejecting the administration's inquisition against DEI. If you can support them with a donation please do. I just did!

Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
python.org Python Software Foundation @python.org · 18d
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 5:47 PM
Reposted by Toby Hodges
lorencrary.bsky.social
I'd also like to shout out @carpentries.carpentries.org for leading the way on this, having made a similar decision earlier this year.
October 27, 2025 at 3:47 PM
Reposted by Toby Hodges
python.org
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 2:47 PM
Reposted by Toby Hodges
esciencecenter.bsky.social
📢 The Netherlands eScience Center is looking for a Programme Officer

• with the drive to help improve research software & impact on sciences
• who is creative and communicative
• enjoys tackling challenges in project management
• has passion in developing funding calls

Apply now! buff.ly/FU2JBVU
October 14, 2025 at 10:15 AM
Reposted by Toby Hodges
infinitescream.bsky.social
AAAAAAAAAAAAAHHHHHHH
October 2, 2025 at 4:31 PM
tobyhodges.carpentries.org
Gym? What's a gym? Oh, a _gym_!
www.youtube.com/watch?v=rFrP...
October 1, 2025 at 7:56 PM
Reposted by Toby Hodges
garethcorn.bsky.social
It was the best of times, it was the BLURST of times?!
rockshrimp.bsky.social Willow @rockshrimp.bsky.social · Oct 1
what's the stupidest/randomest Simpsons quote that lives in your head rent free? Mine is the urge to say "you said go to bread" every time I am about to head to bed.
October 1, 2025 at 7:26 PM
Reposted by Toby Hodges
stephenturner.us
Cory Doctorow (not on Bluesky) published IMHO one of the most compelling pieces about AI being a bubble pluralistic.net/2025/09/27/e...
Pluralistic: The real (economic) AI apocalypse is nigh (27 Sep 2025) – Pluralistic: Daily links from Cory Doctorow
pluralistic.net
September 30, 2025 at 2:10 PM
Reposted by Toby Hodges
jasonwilliamsny.bsky.social
Please share with anyone who cares about NSF support for graduate students and take 30 seconds to sign and leave a comment.

The deadline for the 2025 Graduate Research Fellowship Program is about one month away and literally no one can apply. #NSFGRFP

jasonjwilliamsny.github.io/grfp2025/
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
An Open Letter to U.S. STEM Leadership on the NSF Graduate Research Fellowship Program
jasonjwilliamsny.github.io
September 25, 2025 at 10:09 PM
Reposted by Toby Hodges
zaminiqbal.bsky.social
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
September 25, 2025 at 9:29 PM
Reposted by Toby Hodges
zaminiqbal.bsky.social
Finally, I should cite some related papers
1. From @baym.lol , a beautiful paper looking at genomes going back to the 1880s, showing how chromosomes gained AMR, with a very nice analysis of how AMR genes were mobilised and embedded in MGEs
www.microbiologyresearch.org/content/jour...
19/n
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics
Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...
www.microbiologyresearch.org
September 25, 2025 at 9:41 PM
Reposted by Toby Hodges
betatim.bsky.social
In the age of AI, LLMs and code assistants what does it mean to be an open-source project that is welcoming to newcomers? As a newcomer, is it enough to use AI to solve a good first issue and submit it as a PR? As a maintainer, what should you do with PRs like that?
September 25, 2025 at 9:51 AM
Reposted by Toby Hodges
softwaresaved.bsky.social
📄 A reminder that we are seeking writers (£600) and reviewers (£210) to support the development of new guides on:
- AI in research software
- Green Computing
- EDI in research software

Application deadline: Friday 3 October 2025

Find out more at www.software.ac.uk/news/writers...
September 24, 2025 at 8:10 AM
Reposted by Toby Hodges
ema.europa.eu
Paracetamol remains an important option to treat pain or fever in pregnant women.

Following rigorous assessment of the available scientific data, we find no evidence that taking paracetamol during pregnancy causes autism in children.

Read more 👉 www.ema.europa.eu/en/news/use-...
Use of paracetamol during pregnancy unchanged in the EU | European Medicines Agency (EMA)
Paracetamol medicines can be used in pregnancy, in accordance with official recommendations
www.ema.europa.eu
September 23, 2025 at 10:28 AM
Reposted by Toby Hodges
carpentries.carpentries.org
As our Executive team @drkariljordan.bsky.social @erinstellabecker.bsky.social states, our decision to withdraw was grounded in our commitment to The Carpentries' core values, which explicitly promote diversity, equity and inclusion in programming. "[DEI programming is] baked into everything we do.”
September 23, 2025 at 8:05 AM
Reposted by Toby Hodges
carpentries.carpentries.org
The Carpentries is again in the news, this time in @science.org. Our decision to withdraw from the National Science Foundation's POSE grant funding is discussed in this article criticising how Trump directives are undermining the NSF's 75-year history of independence: www.science.org/content/arti...
Under Trump, NSF faces worst crisis in its 75-year history
Political directives have undermined agency's independence and record of supporting the best basic research
www.science.org
September 23, 2025 at 8:05 AM
Reposted by Toby Hodges
mjdonnay.bsky.social
Come join me on the organising committee for next year's #RSECon. It's a great way to give back and get to know the community, plus we'll cover the cost of your registration at the conference!
society-rse.org Society of RSE @society-rse.org · Sep 22
Have you enjoyed RSECon either this year or in the past?

Would you like to be involved in organising RSECon26 which is taking place 9-11th Sep 2026?

We have a call out for Committee Members, for details and application see

society-rse.org/rsecon26-com...

(Call closes 10th Oct 2025)

#rsecon26
RSECon26 Call for Conference Committee Members - Society of Research Software Engineering
RSECon26 Committee call is now open.
society-rse.org
September 22, 2025 at 1:22 PM
Reposted by Toby Hodges
tommytang.bsky.social
1/ Bioinformatics moves fast.

If you rely only on recipes from books, you’ll soon find they’re obsolete.

Let me show you why. 🧵
September 22, 2025 at 1:45 PM
Reposted by Toby Hodges
philippbayer.bsky.social
Just asked Claude to code me some simple Entrez stuff that pulls down taxonomy IDs for NCBI mitochondrial accessions - the code works and returns a table of taxonomy IDs from the API in a nice table, *but the taxonomy IDs are all wrong*. I hadn't that before: normally AI-written code just crashes
September 22, 2025 at 4:43 AM