Jeffrey C. Erlich @jerlich@qoto.org

"In line with the guidelines of Transparency and Openness Promotion (TOP), all research materials and analysis code for this study are available by contacting the corresponding author."

Uh...nope, that's not how that works.

C'mon folks, we can do better in 2023.

Each year in December, I donate 10% of my net income to charity.

My picks this year:

- **Women's Earth Alliance** https://womensearthalliance.org/, women's empowerment in climate action & adaptation

- **Coalition of Rainforest Nations** https://www.rainforestcoalition.org/ helps communities protect their rainforests, critical for carbon storage, biodiversity, and the livelihoods of indigenous communities

- **Doctors Without Borders** https://www.doctorswithoutborders.org/, friends who work in humanitarian aid tell me that Doctors without borders still give medical care after all the other charities leave. See also their recent commitment to stop showing so many white doctors treating patients around the world.

- **Milieudefensie** https://milieudefensie.nl/ pushes for major campaigns and legal actions in NL to protect the environment and challenge fossil-fuel interests

- **Fossil-free NL** https://gofossilfree.org/nl/ another major player in NL, coordinating large campaigns for decarbonizing and divestment across sectors

- **Climate emergency fund** https://www.climateemergencyfund.org/ a network who support many grassroots groups such as @ScientistRebellion

- and finally, my local food bank https://voedselbankleiden.nl/; it's shameful that a rich country like NL has these at all.

Happy holidays and new year folks! ✨​

May I present for your delectation The Spike's review of the year in neuroscience!

https://medium.com/the-spike/2022-a-review-of-the-year-in-neuroscience-ae4e0de082e7?sk=85b3166c4824c57e5f8153f91c1e7bdd

A Cell (IF = 67) paper claimed that vasopressin worsened COVID. The editor was notified of inaccuracies in the paper, but they refused to take any action—unless a replication refuted the results.

The critics took this challenge on, and did not find support for the original study's findings. Yet, the editor still has not issued a correction and stopped responding to emails.

The original authors have since had 5 other papers retracted.

https://retractionwatch.com/2022/12/29/researchers-lost-five-papers-soon-after-scientists-critiqued-another-of-their-papers-in-retraction-watch/
@academicchatter @OpenScience

@tsawallis @julialang This blog has a nice outline of nice things about the Julia language. https://viralinstruction.com/posts/goodjulia/

Julia is still evolving, so there are problems that arise from that. So also a useful read: https://viralinstruction.com/posts/badjulia/

As for Bayes modeling projects, I develop Stan models mostly, and then I can deploy them in R/Py/Julia/whatever. So I haven't done as much work with Turing as I'd like

If you know any undergrads who might like to work in my lab next summer, I'm accepting applications here:
https://forms.gle/rVSDzf7s5cPhBYUY9

New rule: Airline execs should be mandated by law to only fly coach of their own airlines.

The 1492 globe (the "Potato"/Erdapfel https://en.wikipedia.org/wiki/Erdapfel) that inspired Columbus to sail westwards to Asia of course has lots of flaws. Like the Americas are missing. But it's notable that this potato botches even Europe. I guess it wasn't until Gauss hundreds of years later that geography stops charting like a drunken sailor?

If you subscribe to the common trope that you should avoid "causal language," I strongly recommend getting all the way to the very final two paragraphs in the discussion of this paper.

There is a big plot twist there, and it might change your mind.

But to understand the potentially counterintuitive conclusion, you really really need to understand the framing and methods.

AJE pub: https://doi.org/10.1093/aje/kwac137
Near identical preprint version: https://doi.org/10.1101/2021.08.25.21262631

Friends:
The men, women and children who perished in extermination camps had *lives*. They were grandparents, musicians, rabbis, schoolgirls, craftsmen, mothers, shopkeepers, toddlers, artists. They played, created, dreamed, wondered, wrote, cooked, studied, taught, cared for others, were imperfect, and were loved.

We must not forget them.
@auschwitzmuseum

Hi all, instead of a re- #introduction after moving instances, I'd like to introduce you to my graduate student Peter Salvino, who passed away under tragic circumstances last week.

Because of his way too early passing, most of you didn't get to know him. So I wanted to make sure my #neuroscience community knows how brilliant and kind a scientist he was. Peter wore many hats in the lab. Being my very first student, he built with me, and knew the ins and outs of every bit of hardware and software. He was also a masterful engineer and inventor, and had a keen scientific mind. He knew what the big questions in the field were and was completely fearless in going after them. We will slowly publish all his great contributions, so you will read his name again.

Most importantly, he was so generous to his lab mates. He helped every single person in the lab, with such selflessness and genuine humbleness. He was really loved by all of us. This is such a huge loss to our field. He was destined to greatness.

Peter's family has set up a GoFundMe campaign to help support research similar to his at Northwestern. They welcome any contributions to honor the memory of this amazing human being.

@IdahoLark @Flash Kathrin Swoboda https://novanaturephotography.com/

@jerlich Re writings: this is a gentle introduction to my view of consciousness https://www.philosophersmag.com/essays/222-the-lure-of-the-cartesian-sideshow
This recent lecture is also fairly accessible:
https://www.youtube.com/watch?v=qfUPucMNvJE

@NicoleCRust @albertcardona @matthewcobb
One of the things I've been struggling with recently is how the vast majority of papers (including most or arguably all of mine) don't propose an idea that could in principle get us closer to understanding how the brain does what it does. I have the feeling that there was this moment in time when people were coming up with tons of crazy theories. They were all wrong (probably) but it was exciting. Now we're just talking about how many dimensions a 'neural manifold' has and I just can't get excited about that (sorry manifold people). In my case, I think I've had a small handful of ideas that went in the direction I'd like neuroscience to be going in of proposing ideas that could scale to part of a full explanation of the brain, but I haven't pursued them because they were hard to define or get funding for. My resolution for 2023 is to focus more on those interesting questions and less on things that I think are easy to get published or get funding. For what it's worth, the biggest challenge to neuroscience I reckon is how it can operate in a stable way based on what seems to be a surprisingly unstable substrate (e.g. synaptic turnover). If I had a good idea about how to solve that problem, that's what I'd be working on.

Wow, this is an amazing shortcut to understanding mixed (aka multilevel, hierarchical ...) models, both conceptually and with applications: https://m-clark.github.io/mixed-models-with-R/ #rstats #statistics #methods

I wrote a tribute to Chuck Stevens, an incredible scientist who passed away recently. I was fortunate to work with, and learn from, him over the years. I will deeply miss him. https://www.cell.com/neuron/fulltext/S0896-6273(22)01074-1

The Hanukkah of Data is going well!
https://hanukkah.bluebird.sh/5783/
#HanukkahOfData #AdventOfCode

A very poignant #hannuka photo from December 1931

https://www.theguardian.com/world/2022/dec/18/photo-taken-by-rabbis-wife-in-1931-symbolising-jewish-defiance-of-the-nazis-comes-home?CMP=Share_AndroidApp_Other

'Why some animals can regenerate while many others cannot remains a fascinating question. Even amongst planarian flatworms, well-known for their ability to regenerate complete animals from small body fragments, species exist that have restricted regeneration abilities or are entirely regeneration incompetent. Towards the goal of probing the evolutionary dynamics of regeneration, we have assembled a diverse live collection of planarian species from around the world.'

#Regeneration #preprint #Planaria

https://www.biorxiv.org/content/10.1101/2022.12.19.520916v1