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Reposted by Alex Diaz-Papkovich

Austin Reynolds @awrgenes.bsky.social · 13h

New preprint out with Brenna Henn, led by two fantastic grad students in our labs! www.biorxiv.org/content/10.1...

Recovering the pre-colonial population structure of Khoe-San descendant populations

San populations from Botswana and Namibia retain exceptional linguistic, cultural and genetic diversity, but few Khoisan-speaking groups remain south of the Kalahari Desert. However, historically, far...

www.biorxiv.org

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Reposted by Alex Diaz-Papkovich

Ben Engel @cellarchlab.com · 13d

Time for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on!

#TeamTomo #PlantScience 🧪 🧶🧬 🌾
elifesciences.org/articles/105...
1/🧵

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Reposted by Alex Diaz-Papkovich

Isaac Callan @isaaccallan.bsky.social · 2d

NEW: Vehicles registered to Doug Ford's cabinet ministers have been caught by automated speed cameras more than 20 times.

In one case, they were driving 70 in a 40 zone. On average, they were 17 over the limit. #OnPoli
globalnews.ca/news/1146373...

Vehicles registered to Ford cabinet ministers caught by speed cameras more than 20 times | Globalnews.ca

Documents obtained by Global News reveal that, over three years, vehicles registered to Ford’s cabinet minister received more than $3,300 in fines for speeding.

globalnews.ca

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Reposted by Alex Diaz-Papkovich

Micah McCurdy @hockeyviz.com · 9d

⬡⬢⬡ HockeyViz 2025-2026 Season Preview ⬢⬡⬢

hockeyviz.com/txt/preview2...

Detailed skill and icetime breakdowns for every team, and a million simulations of the upcoming NHL seasons.

There are many, many graphs.

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Reposted by Alex Diaz-Papkovich

Sue AnderBois @sueanderbois.bsky.social · 11d

Adding beautiful and sturdy safety features to North Main this morning w/ friends from the Providence Streets Coalition & Ward 3 neighbors! Inspiring to see folks dedicating their time to improving our community!

Special thanks to Bloom RI who supported this installation!

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Alex Diaz-Papkovich @alexandr.bsky.social · 11d

if you’re ever feeling down I recommend getting a dozen friends and installing planters for traffic calming and beautification

thanks @pvdstreets.bsky.social (and @sueanderbois.bsky.social)!

Katrina Demulling @katrinaspeak.bsky.social · 11d

Helped install planters on N Main St right before Olney St. in Providence, RI. These help keep cars from driving illegally, making it safer for everyone on the street.

Large street planter on North Main St in Providence. Supported by Bloom and Providence Streets Coalition.

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Reposted by Alex Diaz-Papkovich

da share z0ne @dasharez0ne.bsky.social · 20d

IF IT AINT MY COMPUTER IT SHOULDNT HAVE A COMPUTER IN IT - dashare.zone ADMIN

A SKELTON "DESTROY ALL SMART DEVICES" - "I NEED TO USE YOU'RE WIFI NO REASON - PLEASE UPDATE THE SYSTEM SOFTWARE TO CONTINUE MOWING YOUR FUCKIN LAWN , FRIDGE WILL OPEN IN 30 SECOND'S SKIP ADD FOR 0.99 OR SKIP 10 AD'S FOR 7.99 BEST DEAL "DONT WORRY ABOUT IT " LIGHT BULB WILL TURN OFF AFTER 30 MINTUES WATCH THIS BEEF ADVERTISEMENT TO KEEP LIGHT BULB ON FOR UP TO 4 HOURS , TIRES OF WAITING 15 SECOND'S FOR TOILET FLUSH? SAY MCDONALDS FOR 1 FREE INSTANT FLUSH, I NEED TO CONTACT MY MANUFACTURER NO REASON, DO YOU AGREE TO TERMS OF SERCICE FOR CAR? NO REASON DONT WORRY ABOUT IT . NO REASON " - ------
ANY COMPUTER IN A DEVICE WHICH IS NOT A COMPUTER WILL BE USED AGAINST YOU!!! THE COMPUTERS SERVE THE INVESTORS THEY DO NOT SERVE YOU!!! ANY APPLIANCE WHICH HAS A DIGITAL SCREEN FOR NO REASON WILL BE USED TO SELL YOU PRODUCTS OR SHOW YOU ADS - ANY APPLIANCE WHICH NEEDS TO CONNECT TO WIFI WILL COLLECT INFORMATION AND RECORD WHAT YOU ARE DOING IN YOUR HOUSE AND SEND IT BACK TO THE MANUFACTRER - THIS CONSTITUTES A VIOLATION OF HUMAN RIGHT'S AND MUST BE DENIED ENTRY TO YOUR HOUSE AT ALL TIMES!!! NO DEVICE MAY CONNECT TO MY WI FI UNLESS IT IS MY HOLY COMPUTER OR PHONE!!!!!!!!!!!!! I PLEDGE TO DENY THE INVESTOR'S MY DATA AND MY ATTENTION AND ACCESS TO MY LIVING ROOM - DASHARE.ZONE ADMIN

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Reposted by Alex Diaz-Papkovich

Pwnallthethings @pwnallthethings.bsky.social · 22d

Happy Pythagorean triple day (9/16/25) y'all's

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Reposted by Alex Diaz-Papkovich

Thomas Lin Pedersen @thomasp85.com · 27d

I am beyond excited to announce that ggplot2 4.0.0 has just landed on CRAN.

It's not every day we have a new major #ggplot2 release but it is a fitting 18 year birthday present for the package.

Get an overview of the release in this blog post and be on the lookout for more in-depth posts #rstats

ggplot2 4.0.0

A new major version of ggplot2 has been released on CRAN. Find out what is new here.

www.tidyverse.org

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Alex Diaz-Papkovich @alexandr.bsky.social · 28d

thought it looked familiar!

Reposted by Alex Diaz-Papkovich

Madeleine Bonsma-Fisher, PhD @mbonsma.bsky.social · 28d

That drivers are the only serious customers is a common misconception. In Toronto (and elsewhere) studies have found that drivers don't spend more money compared to other modes. The winner in this study of two shopping streets in Toronto was the humble pedestrian!

www.tcat.ca/wp-content/u...

$Figure 6 from the economic impact of bike lanes report by The Centre for Active Transportation. The figure shows the percentage of visitors who spent $100 or more per visit, broken down by travel mode. Bike lanes were added to Bloor Street between the two study years and did not decrease amounts spent, and in all locations and years pedestrians had the highest fraction spending over $100, followed by cyclists for Bloor Street, and for Danforth cyclists are second in 2015 and cars are second in 2016-2017.$

A section from the economic impact of bike lanes report by The Centre for Active Transportation:

"SPENDING
The second data source used to estimate economic impact was monthly spending from the visitor surveys. In 2015, approximately half (44%) of visitors reported spending at least $100, and so this amount was used as a threshold of comparison for the data analysis. Reported spending increased on Bloor Street and Danforth Avenue at a similar rate (see Figure 5). Spending was higher on Danforth Avenue than on Bloor Street, both before and after the bike lane’s installation. Increases in spending were found across all transportation choices except transit (see Figure 6). Both before and after the bike lane’s installation, customers who arrive by foot or on bike reported the highest levels of spending on Bloor Street. On Danforth Avenue, where no bike lane was installed, the top spenders remain people arriving on foot. Spending by people on bikes increased only slightly on the Danforth and was surpassed by people in cars. On both streets, spending was found to increase with proximity and visit frequency. Using a regression model, the research team determined that people who are local (they live or work in the area) were 2.6 times more likely than those who live or work further away to spend at least $100 per month, and for each additional day per month visited, the likelihood of spending $100 or more increased by 7.3%."

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Reposted by Alex Diaz-Papkovich

David Roberts @volts.wtf · Sep 4

Wikipedia's resistance to enshittification is fascinating to me.

Wikipedia is under attack — and how it can survive

The site’s volunteers face threats from Trump, billionaires, and AI.

www.theverge.com

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 29

I had a conversation with a neighbour back home and mentioned studying "genetics and health" and they responded "Genetics? You mean like, Asian or Caucasian...?"

This is a huge challenge in the age of genomics, consumer genetic testing, and the internet.

Ewan Birney @ewanbirney.bsky.social · Aug 29

An evergreen thread: Race/Ethnicity is *not the same* as genetics, and you can't use Race/Ethnicity as a sort of stand-in for genetics. These two concepts are connected via aspects like skin colour, but the connection is alot less profound and categorical than most people think.

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 27

(if you're really curious, we have a full github repo for the paper here: github.com/dkobak/low-d...)

GitHub - dkobak/low-dim-embeddings-review

Contribute to dkobak/low-dim-embeddings-review development by creating an account on GitHub.

github.com

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 27

one of the more fun topics stemmed from a discussion with @hippopedoid.bsky.social over what the oldest 2D PCA visualization we could find was. After some scouring, we settled on a 1960 paper from researchers at the Université de Montréal about turtle carapaces, which we recreated.

Recreated PCA figure from: P. Jolicoeur and J. E. Mosimann. Size and shape variation in the painted turtle. A principal component analysis.
Growth, 24:339–354, 1960.

The figures show PC1 vs PC2 and PC2 vs PC3, with colours and symbols reflecting the sex of the turtle.

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 27

Last year I met a bunch of great researchers who work with high-dimensional data at a Dagstuhl seminar. This week we put out a preprint about the history and philosophy of low-dimensional embedding methods, their applications, their challenges, and their possible future arxiv.org/abs/2508.15929

The participants of Dagstuhl Seminar 24122 standing on steps outside (from https://www.dagstuhl.de/24122)

Multiple types of embeddings (UMAP, t-SNE, Laplacian Eigenmaps, PHATE, PCA, MDS) of Wikipedia text data labelled by a text summaries generated by an LLM. Methods like UMAP and t-SNE show cluster structure that reflect shared subject matter in text, whiel other methods show more continuous structure.

Multiple embedding methods (PCA, Laplacian Eigenmaps, t-SNE, MDS, PHATE, UMAP) of primate brain organoids at different time periods. Different methods highlight different aspects of development, such as clusters of similar cell types or time courses of cell development.

Multiple embedding methods (PCA, Laplacian Eigenmaps, t-SNE, MDS, PHATE, UMAP) of 1000 Genomes Project genotypes. Different methods reflect different aspects of demographic history of populations.

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Reposted by Alex Diaz-Papkovich

Oh The Urbanity! @ohtheurbanity.bsky.social · Aug 24

We fail to respect or enforce traffic laws to the point that people don’t actually perceive ignoring them to be breaking the rules. It’s just normal driving.

www.theglobeandmail.com/opinion/arti...

Photo-radar tickets make you feel like you have been snookered. They provide you a date and a location, and an attached photo, and says you were clocked at an excessive rate of speed – in this case, 54 kilometres an hour in a 40 km/h zone, which isn’t even particularly excessive. You read the letter, try to think back on the day in question, and have no recollection of doing anything out of the ordinary. You were just driving along, at a normal rate of speed. And now, you’re looking at a fine of almost $100.

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 21

More in a thread from @fervillanea.bsky.social

bsky.app/profile/ferv...

Fernando Villanea @fervillanea.bsky.social · Aug 21

Our paper on the evolution of MUC19 in humans, Neanderthals, and Denisovans is finally out today in Science!

This has been a six-year effort by 13 authors to weave together 3 separate but related evolutionary stories around this one gene (more on thread 🧵).

www.science.org/doi/10.1126/...

The MUC19 gene: An evolutionary history of recurrent introgression and natural selection

We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants ...

www.science.org

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 21

(should also specify that the publication is more accurately Villanea and Peede et al, but I hit the character limit!)

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 21

20 years ago we didn't know Denisovans existed, and now we have the first evidence of DNA going from Denisovans to Neanderthals to modern humans via natural selection.

Full publication is out in Science: www.science.org/doi/10.1126/...

The MUC19 gene: An evolutionary history of recurrent introgression and natural selection

We study the gene MUC19, for which some modern humans carry a Denisovan-like haplotype. MUC19 is a mucin, a glycoprotein that forms gels with various biological functions. We find diagnostic variants ...

www.science.org

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 21

@david-peede.bsky.social et al on the convoluted route of a variant of the MUC19 gene: Denisovans (before going extinct) passed the gene to Neanderthals, who (before going extinct) passed it to ancient humans, who then crossed the Bering Strait. Today, 1 in 3 Mexicans carry the genetic variant.

The proposed evolutionary history of the MUC19 haplotype. A tree shows how the gene was likely passed from Denisovans to Neanderthals to modern humans, where it was preserved in Eurasian and American populations through positive natural selection. The Denisovan genomic region is contained within a larger Neanderthal genomic region.

From: https://www.science.org/doi/10.1126/science.adl0882

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Reposted by Alex Diaz-Papkovich

Hannah Shelley, MLIS (Metadata, Lattes & Impostor Syndrome) @hannahshelley.bsky.social · Aug 13

Since search is dead, how soon do you think Google Scholar is headed for the Google Graveyard? I'm betting it's soon, and academia is NOT prepared

Google Scholar Is Doomed

Academia built entire careers on a free Google service with zero guarantees. What could go wrong?

hannahshelley.neocities.org

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Reposted by Alex Diaz-Papkovich

Dominique Potvin @silvereyedom.bsky.social · Aug 13

Newest lab research:
Up to 6% of the wild birds - in all 5 species we looked at - showed a different sex morphology than what their blood tests (read: chromosomes) told us. Sex is not simple!
doi.org/10.1098/rsbl...

Prevalence and implications of sex reversal in free-living birds | Biology Letters

The ability to unequivocally identify the sex and reproductive status of individuals is crucial across many fields of study. Recent evidence indicates that avian sex determination is more flexible tha...

doi.org

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Reposted by Alex Diaz-Papkovich

Michael Hobbes @michaelhobbes.bsky.social · Aug 9

My least popular (and most correct) view is that cars should be automatically limited to the local speed limit. Put the pedal to the floor and you still can't go over 25mph in a residential area.

(15 in Manhattan btw)

Michael Hobbes @michaelhobbes.bsky.social · Aug 9

There is no possible justification for limiting e-bikes to 15mph but not cars.

Charles Ornstein @charlesornstein.bsky.social · Aug 9

New York Has a New E-Bike Speed Limit—and No Way to Enforce It

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Alex Diaz-Papkovich @alexandr.bsky.social · Aug 5

sometimes you can tell when a word gets added to a widely-used Wikipedia template

A google ngram of the word "demonym" shows its frequency from 1950 to 2022. The word was first used in the 1990s and takes off rapidly sometime around 2010, probably from being used frequently on Wikipedia.

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