John McBride

While journal publishing has always been deeply problematic, hurting both the pace and trajectory of science, something is happening in this moment that is finally causing the system to crumble under its own weight and cost.
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I'm open to that. I find that the semantic distinction between the two is often not useful. Theories (and any logical frameworks), after all, are just boolean models. If you get this, then theories (as I think others think of them) are basically models that are not very specific/detailed.

Aside from the Box quote, I'd like to remind people that "All empirical observations are wrong, but some are useful" (Me)

Outside of physics the distinction seems more clear, since you rarely get a cohesive integrated theoretical framework that is mathematical and predictive. E.g. Darwin's theory of evolution can be boiled down to a few logical statements. Population genetics is a system of models of evolution.

What is the difference between a "model" and a "theory"? In my past questions I have used the terms "model" and "theory" interchangeably. So we have statements along the lines of The Standard Model is our best theory of particle physics but I have also

I've been pondering the difference between models and theories for a while. I haven't heard much consistency in discussions. I certainly get different answers depending on the discipline. The one thing in common is that the word 'theory' seems to be better regarded. - is the standard model a theory?

Can you send it to me also? I'm now curious

Agent-based models by themselves are useful for extended thought experiments. If you want to know, given X, and Y, and some social dynamics, what is Z? But you can't compute it in your head.
Some great work has been done on evolutionary/game theory of cooperation. Sometimes good data is hard to get

Israel’s war on Gaza: Why do legal experts say it’s genocide? Experts, including UN rapporteur Francesca Albanese, are unanimous: the most serious of international crimes is happening in Gaza

Amos Goldberg is an Israeli professor of Holocaust history at the Hebrew University of Jerusalem. He teaches Holocaust and genocide history.

When does Goldberg think the genocide began? In April 2024, Goldberg concluded that Israel was committing genocide …

www.middleeasteye.net/news/israel-...

For some short excerpts of speech, if you listen to them on repeat they start to sound more like music. Not all speech excerpts. But it (repetition) also works with clips of sounds other than speech. @adamtierney.bsky.social has done a lot of work on it (amongst others) if you want to know more.

I'm running a Korean VPN and it works for me

And yes, overleaf has track changes, but I didn't like it last time it was used on a paper. Can't even remember why anymore

Thanks. I have actually used latexdiff before during review. I think the reason I didn't this time was because I was working on overleaf, and wanted to be able to see the changes as I worked.

I'm supposed to upload a new version now that it's been recommended. Something to do this week!

Indeed, it's like track changes. Except done manually in LaTEX, so not everything is colored, just the main changes. Normally this would be done internally during review, but the paper was reviewed at PCI Evolutionary Biology, which requires all manuscripts to be posted to a preprint server.

Any idea of how to differentiate between participants based on how good their memory is vs how good they are at games? Like, could you generate a stockfish-style game engine to assess players?

That was fun! Any chance you can find out how much of an outlier I am? Somehow I got >100% in quite a few. Great activity for me to do while downloading/installing a ubuntu boot disc (after deleting some files that should not be deleted...)

Cool new @PeerCommunityIn.ecoevo.social.ap.brid.gy recommendation by @alexmesoudi.com of an article on melodic evolution by @johnmcbride4lyf.bsky.social et al.
evolbiol.peercommunityin.org/articles/rec...

Which Kind of Science Reform What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.

How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...

I think there's really cool stuff coming - calls for (+ attempts at) building databases for hosting MD simulation data. But for ML to be useful, I think we'll need to see data that captures the statistics of large motions in general, not just for particular motions (e.g. binding to 1 substrate)

Unfortunately ms trajs are probably still too slow. Think big (or even medium) proteins, or how many times do you need to see a change in state before you have equilibrium stats. I'd like to see some standardization of enhanced sampling, but too much there seems to depend on choice of CVs

Who's selling those tall ladders? That's what I want to know

Transparent peer review to be extended to all of Nature’s research papers From today, all new submissions to Nature that are published will be accompanied by referees’ reports and author responses — to illuminate the process of producing rigorous science.

From today, all new submissions to Nature that are published will be accompanied by referees’ reports and author responses — to illuminate the process of producing rigorous science

https://go.nature.com/4kIRR01

Great news! But it would be nice if it were accompanied by some analyses, given that essentially an experimental trial has taken place. How does this affect reviewer uptake? Recommendations? Review content/tone? Biases (age / gender / prestige)? Nature should open its data for such analyses

Great news! But it would be nice if it were accompanied by some analyses, given that essentially an experimental trial has taken place. How does this affect reviewer uptake? Recommendations? Review content/tone? Biases (age / gender / prestige)? Nature should open its data for such analyses

Jury Theorems for Peer Review Marcus Arvan, Liam Kofi Bright, and Remco Heesen Abstract: Peer review is often taken to be the main form of quality control on academic research. Usually journals carry this out. However, parts of maths and physics appear to have a parallel, crowd-sourced model of peer review, where articles are posted on the arXiv to be publicly discussed. In this article we argue that crowd-sourced peer review is likely to do better than journal-solicited peer review at sorting articles by quality. Our argument rests on two key claims. First, crowd-sourced peer review will lead on average to more reviewers per article than journal-solicited peer review. Second, due to the wisdom of the crowds, more reviewers will tend to make better judgements than fewer reviewers will. We make the second claim precise by looking at the Condorcet jury theorem as well as two related jury theorems developed specifically to apply to peer review.

Paper is finally up and open access (www.journals.uchicago.edu/doi/10.1086/...), it's a sequel to an earlier paper where we'd argued that there's not good evidence that pre-publication peer review is a net benefit (www.journals.uchicago.edu/doi/10.1093/...). So in this one we suggest an alternative.

it's good that they clarified what they would do as part of the hunt! from their name I would have expected some sore of blasting

Cover of the textbook used in the workshop

✨We are organising (again) an online workshop on Theoretical Modeling for PhD candidates and Master students in cognitive science and psychology. Check out the website and the schedule: Registration is open! (closes July 1, spaces are limited) 🧵1/n computationalcognitivescience.github.io/workshop/

Or you can make a researchgate account. It allows you to keep private full text pdfs, and people can request them. It streamlines the sharing process. Probably this is quicker to set up, but it means you need to respond to each request.

Most likely you can share a version as a "preprint". I don't know of any journals that don't allow this. You can just upload a basic version (without the journal formatting) on a repository like psyarxiv.

YouTube video by Alonso Gurmendi Is Israel Committing Genocide in Gaza?

I joined bsky as a scientist, not as an activist, but I feel compelled to share this video essay on the genocidal nature of the war in Gaza.

I support the right of Israel to exist, and I commiserate with my Israeli friends on the brutal horrors of Oct 7.

But this brutal war must stop, now.