Ed Hagen

Teen daughter savoring a Trader Joes cornbread muffin: "This tops the invention of the polio vaccine"

Death rates from cardiovascular disease have fallen dramatically 🧪 ourworldindata.org/cardiovascul...

Michael Druker 🇨🇦@mdruker.app

Social media loves talking about how everything is getting worse. But what’s something that you’ve seen get _better_ in your lifetime?

Earthquake, SW Washington

TIL that Auschwitz's emergence as a symbol of the Holocaust is an example of survivorship bias. Operation Reinhard, during which most perished in gas chambers at the death camps Belzec, Sobibor, and Treblinka, was the largest single murder campaign of the Holocaust 🧪 www.science.org/doi/10.1126/...

zbib.orgZoteroBib: Fast, free bibliography generator - MLA, APA, Chicago, Harvard citationsFree, accurate citation and bibliography maker for APA, Chicago, Harvard, MLA, and 10,000 other styles. No ads, no downloads, no account required.

TIL of zbib.org. I've been using Zotero for years, but sometimes I need to generate a quick reference for a misc webpage like a blogpost or news article. Copy-paste the url here and boom, a formatted ref. You can also enter a doi, ISBN, or other identifier 🧪 #AcademicSky

TIL that SRY, the sex-determining Y chromosome gene, is expressed in midbrain dopamine neurons, which are involved in voluntary movement, motivation, learning, & other functions. SRY expression might help explain the male bias in DA-mediated diseases, eg, Parkinson's 🧪 www.pnas.org/doi/full/10....

github.comGitHub - tonyantony300/dashbeam: Share files nearby and beyond.Share files nearby and beyond. . Contribute to tonyantony300/dashbeam development by creating an account on GitHub.

If you need to transfer large files from your laptop/desktop to someone else, I've had good luck with this open source app. It's peer-to-peer (no server involved), end-to-end encrypted, and uses the well-regarded iroh library under the hood: github.com/tonyantony30...

19 Sept

Jesus, too, was an apocalyptic prophet 🙂 en.wikipedia.org/wiki/Histori...

SE Gyges@segyges.bsky.social

Yudkowsky's most viral idea, the one that infects the most people and spreads the farthest, is that AI, if we continue to develop it, will inevitably 1) achieve superintelligence ("RSI"), 2) escape human control 2) kill everyone ("paperclip them", "doom")

icloud.comwordcountShared with iCloud

19 Sept

A macOS shortcut to count lines, words & chars in any selected text (falls back to clipboard) #AcademicSky Keyboard: ctrl-opt-cmd w Review the shell cmd before using this or any shortcut Shell: wc | awk '{printf "Lines: %s\nWords: %s\nCharacters: %s\n", $1, $2, $3}' www.icloud.com/shortcuts/69...

16 Sept

🧪 #BioAnth anthro.vancouver.wsu.edu/media/docume...

pnas.orgConflict, violence, and warfare among early farmers in Northwestern Europe | PNASBioarchaeological evidence of interpersonal violence and early warfare presents important insights into conflict in past societies. This evidence i...

14 Sept

"Violence was endemic in Neolithic Europe, sometimes reaching levels of intergroup hostilities that ended in the utter destruction of entire communities" 🧪 #BioAnth www.pnas.org/doi/abs/10.1...

science.orgBetel nut sucking is the earliest recorded evidence for the habitual use of a neuroactive plant drugThe modern custom of chewing betel nuts is practiced by around 1 in 10 people worldwide, yet the earliest beginnings of this widespread drug use habit are unknown. We report rare skeletal remains of t...

10 Sept

The title of this cool new paper is accurate (dental evidence c. 25-16k BP). However, routine consumption of ethanol is likely ancient: 1) Wild chimpanzees consume perhaps the equivalent of 1.4 drinks/day from naturally fermenting fruit; 2) ADH genes are widespread🧪🧵 www.science.org/doi/10.1126/...

Study confirming ethanol metabolites in wild chimpanzee urine: royalsocietypublishing.org/rsbl/article...

royalsocietypublishing.orgUrinary concentrations of a direct ethanol metabolite indicate substantial ingestion of fermenting fruit by chimpanzeesAbstract. Frugivorous animals routinely ingest fruit sugars and the associated products of microbial fermentation. Yeast-derived ethanol within fruit is a

cell.comThe evolutionary ecology of ethanolThe consumption of ethanol has frequently been seen as largely restricted to humans. Here, we take a broad eco-evolutionary approach to understanding ethanol’s potential impact on the natural world. T...

10 Sept

Recent TREE paper making the case that ethanol has been a component of animal diets since the Cretaceous based on evidence that yeast have been producing ethanol since the rise of angiosperms, and the evolution of ethanol metabolic pathways in animals: www.cell.com/trends/ecolo...

Study finding surprisingly high levels of ethanol consumption by wild chimpanzees: www.science.org/doi/full/10....

science.orgEthanol ingestion via frugivory in wild chimpanzeesNatural daily consumption of dietary alcohol by chimpanzees suggests human attraction to alcohol may come from our ancestral diet.

9 Sept

The #rstats {livelink} package packs your short R script / shiny app into a (long!) URL. No server. No file upload 🧪 webr_repl_link("myscript.R")→url→R console, your script, plot pane, in the users' browser shinylive_r_link("myapp.R")→url→running app in the browser 👇 shinylive.io/r/app/#code=...

shinylive.ioShiny App

r-pkg.thecoatlessprofessor.com/livelink/

9 Sept

r-pkg.thecoatlessprofessor.comlivelink: Create Shareable Links for WebR and ShinyliveGenerate shareable URLs for R code that can be executed in WebR environments and create Shinylive links for R and Python Shiny applications.

Ed Hagen reposted

Chive

@chive.pub

8 Sept

Alongside a bunch of bug fixes, we've got a few new features on chive.pub we're excited about. Most of them involve connecting a paper to other things that relate to it on the Atmosphere and beyond.

chive.pubChive | Decentralized Eprint ServiceDecentralized eprints on ATProto.

sdctools.github.ioStatistical Disclosure Control Methods for Anonymization of Data and Risk EstimationData from statistical agencies and other institutions are mostly confidential. This package, introduced in Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>, can be used for the generation ...

8 Sept

This #rstats package can help you avoid doxxing the participants in your study when you publish your data 🧪 #AcademicSky: sdctools.github.io/sdcMicro/

Institute for Replication@i4replication.bsky.social

1/ What is the prevalence of personally identifiable information (PII) in author-collected data publicly shared in the social sciences? We audited 327 replication packages from 11 leading journals in economics, political science, and psychology Answer: surprisingly high 🧵

3 Sept

Academia in the US 🧪 #AcademicSky My plot of data from: www.nature.com/articles/s41...

Ed Hagen reposted

@evoroseman.bsky.social

25 Aug

RE: freedom of speech, academic freedom, and race science. In this (long) thread, I’m going to 1) establish my bona fides on academic freedom and race science, 2) show why academic freedom and freedom of speech are different and… 1/34

22 Aug

All of us posting on social media (or producing for any media) should be aware of the results of this 2015 meta-analysis 🧪 doi.org/10.1542/peds...

Ed Hagen reposted

blog.edhagen.netA theory of natural selection, 5th century BC – GrasshoppermouseBlog posts and talk slides

19 Aug

Replying to @juemos.bsky.social

To understand the Santa Barbara school of ev psych (SBEP), put aside the brain for a moment, and consider the rest of the body: It's been recognized since the time of Empedocles, if not before, that 1. organisms comprise specialized parts benefitting the organism... blog.edhagen.net/posts/2019-0...

Human Behavior & Evolution Society

17 Aug

Growth and movement of cells in a human hair follicle. From this paper (see ALT for more details). 🧪 Mapping cell dynamics in human ex vivo hair follicles suggests pulling mechanism of hair growth www.nature.com/articles/s41...

Ed Hagen reposted

@humbehevosoc.bsky.social

17 Aug

Membership fees will increase starting September 15 (see below for details). If you are currently on a one-year membership, you can upgrade to a three-year plan at the current prices. You have until September 15 to upgrade your one-year membership. www.hbes.com/hbes-members...

hbes.comHBES membership fees are increasing starting September 15 - HBESMembership fees will increase starting September 15 (see below for details). If you are currently on a one-year membership, you can upgrade to a three-year plan at the current prices. You have until…

1. Much human genetic variation has ~zero impact on phenotypes. Why? Cooperative genes are locked in a forever war w/ selfish genes (red queen dynamics). The cooperative genes have won most battles but now our genomes are littered w/ the dead & decaying bodies of a million selfish genes 🧵 🧪 #BioAnth

16. The profound biological significance of the human genome is almost entirely in the sequences that do NOT vary! bsky.app/profile/edha... \End

Ed Hagen@edhagen.net

7. My solution: we need a new cultural model of the genome based on the highly conserved (universal) interactions *within* the genome, whose biological significance VASTLY outweighs the biological significance of differences between genomes.

Addendum: Here is the genome size plot in tweet #2 that didn't display correctly (note that the x-axis is on a log scale):

2. Genome sizes vary tremendously in ways that do not obviously relate to organism complexity, e.g., many fish and amphibians have huge genomes compared to mammals (note that the number of base pairs on the x-axis is on a log scale): en.wikipedia.org/wiki/Genome_...

science.orgEvolutionary constraint and innovation across hundreds of placental mammalsZoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter di...

Damn alpha channel! Here is the genome size plot:

14. Consistent with much of the human genome comprising inactive and neutrally evolving TEs, studies typically find that less than 15% of the human genome is constrained by purifying selection (i.e., is functional), for example 10.7% in this recent study: www.science.org/doi/full/10....

15. The upshot is that the PCA/STRUCTURE/UMAP plots that seem to indicate profound biological differences between human populations are mostly just displaying degrees of similarities or differences in random genetic noise inherited from more or less recent common ancestors.

12. Of the million+ human TEs, all but a very few are inactive and probably evolving neutrally: link.springer.com/article/10.1...

journals.plos.orgRepetitive Elements May Comprise Over Two-Thirds of the Human GenomeAuthor Summary Our study is concerned with a fundamental question about the human genome sequence: what is it made of? At present, approximately 50% of the genome sequence has unknown function or orig...

13. Thus, much of her 👇 genetic variation is equivalent to the noise on her TV screen:

10. In humans, approximately 1/2 of the genome, and perhaps more than 2/3, comprises TEs and other repetitive elements: journals.plos.org/plosgenetics...

cell.comTransposable elementsTransposable elements are a near ubiquitous feature of eukaryotic genomes, and they are among the most abundant coding sequences in nature. In this Primer, Hayward and Gilbert discuss key aspects of t...

11. TEs inactivated by hosts will accumulate mutations that permanently disable them. Although parts of some inactivated TEs have been co-opted by natural selection into regulatory roles in the human genome, most appear to be decaying under genetic drift: www.cell.com/current-biol...

8. Recent sequencing data confirm that large genomes indeed have large numbers of TE base pairs (human genome = 3 Gbp). "We...found that the substantial differences in...genome sizes can be largely explained by the proportion of transposable elements (TEs) within them." www.pnas.org/doi/full/10....

pnas.orgDNA methylation enables transposable element-driven genome expansion | PNASMulticellular eukaryotic genomes show enormous differences in size. A substantial part of this variation is due to the presence of transposable ele...

annualreviews.orgA Field Guide to Eukaryotic Transposable ElementsTransposable elements (TEs) are mobile DNA sequences that propagate within genomes. Through diverse invasion strategies, TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes...

9. Active and inactive TEs comprise a substantial fraction of almost all eukaryotic genomes: "TEs have come to occupy a substantial fraction of nearly all eukaryotic genomes, and they represent a major source of genetic variation and novelty" www.annualreviews.org/content/jour...

6. Eukaryotic hosts (cooperative genes) have therefore evolved a number of mechanisms to repress & silence TEs, including interference RNA (RNAi) pathways that modify chromatin to suppress transcription or degrade transcripts. www.nature.com/articles/nrg...

nature.comTransposable elements and the epigenetic regulation of the genome - Nature Reviews GeneticsCells use a range of increasingly well understood epigenetic mechanisms to keep transposable elements under control. These silencing mechanisms have been co-opted during the course of evolution to con...

link.springer.comCo-evolution between transposable elements and their hosts: a major factor in genome size evolution? - Chromosome ResearchMost models of genome size evolution emphasize changes in relative rates of and/or the efficacy of selection on insertions and deletions. However, transposable elements (TEs) are a major contributor t...

7. TEs, in turn, evolve mechanisms to escape host silencing and repression, leading to a host-TE co-evolutionary arms race (red queen dynamics). It has long been thought that rampant TE copying is responsible for the puzzlingly large genomes noted above. link.springer.com/article/10.1...

4. Transposable elements (TEs) are selfish "parasitic" genetic elements that "copy-paste" (retrotransposons 👇) or "cut-paste" (DNA transposons) themselves within the germline, increasing their frequency by vertical transmission.

annualreviews.orgOur Conflict with Transposable Elements and Its Implications for Human DiseaseOur genome is a historic record of successive invasions of mobile genetic elements. Like other eukaryotes, we have evolved mechanisms to limit their propagation and minimize the functional impact of n...

5. TE activity, however, is often harmful to the host. TEs can insert into genes or regulatory regions, impairing function and causing disease: www.annualreviews.org/content/jour...

3. Why? The explanation requires the Williams/Dawkins concept of selfish genetic elements that "enhance their own transmission at the expense of other genes in the genome, even if this has no or a negative effect on organismal fitness": journals.plos.org/plosgenetics...

14 Aug

From Tinbergen (1963), where he puts forward his famous four questions 🧪 #BioAnth

12 Aug

Create an (almost) free personal/professional 1-page website in 4 steps using #rstats and R Markdown 🧪: 1. Buy a personal domain name (~ $10/yr): www.cloudflare.com/products/reg... 2. Create your page in R markdown using this R package (this is one of five templates): github.com/seankross/po...

12 Aug

3. Put the rendered index.html file into a folder & drag & drop folder to cloudflare pages (free): developers.cloudflare.com/pages/get-st... 4. Connect your custom domain: developers.cloudflare.com/pages/config... Here's mine: edhagen.net

cos.ioOSF Changes | Center for Open ScienceWe are preparing substantial changes to OSF that will reduce its functionality, focus OSF on its unique strengths, and move toward an integrated model with complementary services. As part of that shif...

11 Aug

Many osf.io features could be built on #atproto: your project repos would be hosted on your PDS (eg your bluesky acct). Institutions could host PDSs, distributing costs. Every record would have a unique id (analogous to a doi). Multiple apps could access the records in multiple ways @atproto.science

Brian Nosek@briannosek.bsky.social

Over the next several months, we will phase out some popular OSF features. These changes do not affect current public content, which remains safe and accessible. We have prepared support material to help users adapt. I am very sorry for the disruption to your work. Please read this post for details.