Ignasi @ignasi@safareig.calbasi.net

Dear Mastodon friends, it's my pleasure to share this new manuscript on distinguishing gene flow from incomplete lineage sorting (ILS)

https://www.biorxiv.org/content/10.1101/2023.07.06.547897v1

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Starting around 1000 CE, the English began building lots of mill dams, and this blocked the migration pathways of lots of fish! Oh no!

They began eating far fewer freshwater fish like salmon, & evidence shows a marked shift to eating marine fish. It's a big of enough thing to get an awesome name:

The Fish Even Horizon

But eels can live out of water for a while, & travel overland if need be. So they could migrate around or over medieval dams.

And so the English kept eating eels. 'Cause eels!

There is no such thing as a “gene for language”. A short thread to help explain why.
In one branch of human genetics, scientists search for correlations between particular gene variants that people carry and variations in an observed trait (e.g. variability in the general population, or presence/absence of a particular clinical diagnosis – basically, anything that can be characterized or measured in an individual human being). “A gene for X” has become a convenient shorthand when talking about the associations that are detected between variation at these distant levels of genes and traits.
Unfortunately, all that “gene for X” talk fuels popular pervasive misconceptions of genes as mysteriously powerful abstract entities that can somehow directly specify traits, including key aspects of human behaviour. The biological reality is very far from this...1/3
#genetics #language #science

Another review for @PeerCommunityIn done -- if there is a right direction for the publishing system to move into, this is it. Let the means of intellectual production remain with the researchers.

Today's must-read by @johanrooryck et al.:

"Diamond is for everyone"
https://www.researchprofessionalnews.com/rr-news-europe-views-of-europe-2023-6-diamond-is-for-everyone/

Delightfully straight talk, showing the path away from parasitic publishers to a modern scholarly information infrastructure.

#openscience #openaccess #diamondoa #oa

Map of night trains in Europe. In combination with high-speed trains and regional trains, a lot of destinations are one evening plus overnight away. Now if only oil subsidies would end, flight tickets wouldn’t be competitive, particularly with Interrail ticket schemes.

Higher resolution version at the website: https://back-on-track.eu/night-train-map/

#Europe #Train #TrainTravel #Travel

The temporal and genomic scale of selection following hybridization http://biorxiv.org/cgi/content/short/2023.05.25.542345v1?rss=1 #biorxiv #EvoBio #preprint

Ultra-realistic simulations of 1.4 million human genomes generated by using a detailed pedigree of French Canadians as input to #msprime! These simulations are hugely useful for large-scale genomics methods development, because they are freely available, easy to download (2.8G for chr1), and efficient to process using #tskit. I hope they will become a standard benchmark across all sorts of methods.

https://www.science.org/doi/10.1126/science.add5300

A large-scale study of mutations in mitochondrial DNA has revealed a subset that does not accumulate with age. https://elifesciences.org/articles/87194?utm_source=mastodon&utm_medium=social&utm_campaign=organic_insights

How treating science as a business is detrimental to quality:

"[In 1999] it was made clear that if, for example, I produced one high-quality paper in two years, then that would not hurt my career; quality would stand above quantity.

In 2022 my department [...] called out some faculty for falling behind in productivity. The lowest average number of publications per year [...] was four [...] One of my colleagues had > 20 per year. That was not seen as problematic"

via https://futureu.education/higher-ed/raging-against-the-mythical-figure-who-keeps-us-down/

Is there any evidence that creating prizes and awards is a good way to encourage good behaviours? It's done a lot in science and universities but I've never seen any evidence about it one way or the other.

If you want to do something to help publishing serve authors instead of publishers, sign up for @PeerCommunityIn - add your name to the reviewers database, signup to be a recommender, and become part of a preprint-based, open, researcher-operated community of publishing. If you want to take it one step forward, there's also @PeerCommunityJournal!

I've written before about why the current system of peer review is failing science. Now I'd like to set out a few ideas about what I think could replace it. This is an opinionated list. It's what I'd like to happen. However, different people and fields will want different things and it's vital to come up with a flexible system that allows for this diversity.

It must be ongoing, open, post-publication peer review, for the reasons set out in the previous article: pre-publication peer review systematically fails as a check on technical correctness and creates perverse incentives and problematic biases in the system as a whole. Making it an ongoing and open process allows us to discover problems that may be missed in a closed process with a small number of opaquely selected reviewers. It lets us concentrate more review effort on influential work that ought to be more closely scrutinised than it is at the moment. And of course, instant publication speeds up science allowing people to immediately start making use of new work rather than waiting months or years for it to be available.

Reviews should be broken down into separate components: technical correctness, relevance for different audiences, opinions of likely importance, etc. Reviewers do not need to contribute all of these, and readers or other evaluators should feel free to weight these components in whatever way suits them.

We need better user interface / experience to navigate and contribute reviews. Every time you look at a paper, just the abstract or the full text, you should be presented with an up to date set of indicators like 3✅ 2❌ 1⚠ for three positive reviews, 2 reviews with unresolved major issues and 1 with minor issues. Clicking on these would pop up the relevant reviews and allow the reader to quickly drill down to more detailed information. Similarly, contributing reviews or commentary should be frictionless. While reading a paper you should be able to highlight text and add a review or commentary with virtually no effort. A huge amount of evaluation of papers is done now by individual readers and journal clubs, but all that work is lost because there's no easy way to contribute it. Realising all this requires shifting away from the PDF to a more dynamic format, and abandoning the outmoded notion of the version of record.

There needs to be a way to integrate all the different sources of feedback so you don't have to visit a bunch of different websites to find out what people are thinking about a paper, but instead it just pops up automatically when you open it. That will require standardised ways of sharing information between different organisations doing this sort of feedback.

None of these are particularly new ideas. The new model of eLife is about creating structured post-publication reviews with standardised vocabulary, and their nascent sciety platform is an attempt to integrate all the different sources of feedback. hypothes.is is a great first step towards improving the interface for review (although their recent move to for-profit status is worrying). The key will be to organise a way to put them all together and make it frictionless and pleasant to engage with it. It will require a revolutionary change because to make all these things work together it all has to be open and free, and legacy publishers will fight that.

Finally, with Neuromatch Open Publishing, we are working towards building a non-profit infrastructure to enable us to collectively do all these experiments and more.

I wanted to write something like, "oh you don't say" but this is *actually* a brutal read

#science #metrics #evaluation

https://journals.sagepub.com/doi/full/10.1177/05390184221142218

#Scientists & #artists are both motivated by creativity & curiosity, and science & art can be mutually reinforcing. Here, @eco_genome & @LouisMuglia provide resources for individuals, groups & institutions to advance science–art collaborations #PLOSBiology https://plos.io/3DXzzVy

When scholars without expertise in infrastructure reform encounter the goals of the reform movement, such as e.g., replacing academic journals,

https://doi.org/10.5281/zenodo.5526634

they sometimes reflexively defend the status quo that served them well, e.g.:

“You ‘open’ wackaloons are forcing your revolution on us, against our academic freedom!”

I was asked to write a *one-page* cheat sheet with the evidence to counter such a reflex:

https://docs.google.com/document/d/1vjbohSsf-qy8ZkCvQ9FRlF9k1N12oSLu8qwXoKxjD2o/edit?usp=sharing

Can you/we improve on that?
#openscience

Extrachromosomal #Borg elements in methane-consuming #archaea are scattered with rapidly evolving nucleotide #TandemRepeats; those within genes encode amino acid repeats that create intrinsically disordered regions @MScholmerich @BanfieldLab #PLOSBiology https://plos.io/3Y0cw3R

Is academia facing a massive burnout crisis?

Academics are increasingly "reevaluating whether their jobs are worth the high cost to their personal well-being. They are less willing to continue in positions with oversized workloads, salaries that do not keep up with inflation, and inflexible policies."

48% of universities report that faculty turnover increased in 2022 and >70% of academics reported mental health difficulties in 2021

via https://www.apa.org/monitor/2023/01/trends-faculty-exiting-academia
@academicchatter #AcademicChatter

This is fascinating - Tapeworms eaten by Acorn #ants secrete more insulin that seems to aid in the ants #longevity. They want the ants to live as long as possible, to increase their chances of being eaten by a #woodpecker 😳.
https://www.quantamagazine.org/ants-live-10-times-longer-by-altering-their-insulin-responses-20230110/