Arlin Stoltzfus

De-novo promoters emerge more readily from random DNA than from genomic DNA Promoters are DNA sequences that help to initiate transcription. Point mutations can create de-novo promoters, which can consequently transcribe inactive genes or create novel transcripts. We know lit...

our next evol-mut-circle seminar (21 Oct, 15:00 UTC) features Timothy Fuqua on

"De novo promoters emerge more readily from random DNA than genomic DNA"

www.biorxiv.org/content/10.1...

DM me to join the email list. Full schedule:

www.molevol.org/evol-mut-cir...

#popgen, #mutation, #evobio

Next Tuesday (20 May), evol-mut-circle hosts a discussion on hypotheses to account for targeted hypomutation

We'll have a panel of experts to help with the discussion, including some with key roles in this issue

Message me to join the email list

www.molevol.org/distinguishi...

The CDC has literally been gutted today.

There’s no need for “April Fools” when reality is a nightmare for every human on this planet.

Thousand of scientists fired.
Entire departments erased.

1/

colleague from CDC: "Taking it day by day. I'm very angry and sad. We lost some really good people."

Yes, thanks! Quiroz, et al (incl. @grey-monroe.bsky.social) is relevant to understanding the proximate causes of non-random patterns of repair and mutation

But this leaves open whether the driver is mutation or damage. That's the issue we are trying to tackle— how to tell these 2 hypotheses apart

...has most of the same implications as gene-targeted hypo-mutation, but is more parsimonious

Later this spring, evol-mut-circle will host an open discussion of competing hypotheses, to include some of the scientists active in this area of research

I'll post more details as the date gets closer

Monroe, et al 2022 argued that mutation in Arabidopsis evolved adaptively to be lower in genes than non-genes

That stimulated a lot of debate over whether the pattern is real

What about the evo model?

A model of gene-targeted hyper-repair (to avoid damage)...

www.molevol.org/distinguishi...

Sorry, I try not to be a jerk but that was rude.

That would have been amazing but it is extremely difficult to get decision-makers to spend large amounts of money or do extremely unpopular things without a guarantee of results. And scientists in early 2020 could not guarantee that air filtration would be a game-changer

We are learning the wrong lessons from lockdown And unless we learn the right ones, we risk making the same mistakes in a new pandemic

It's 5 yrs today since lockdown started in England, but "We must never have lockdown again" is the wrong lesson.

Lockdowns are terrible but so are deadly pandemics.

Our choices 5 years ago were limited - we can & must do better in the future.

Do read my post.

open.substack.com/pub/christin...

dude lost his temper and used force exactly 1 time in his entire recorded life, and this was the context

Great opportunity in a beautiful city

Coming up next Tuesday

@kelleyharris.bsky.social

"What causes mutation rates to vary among populations, species, and cell lineages?"

DM to join the email list

The technofascist coup plan a la Yarvin says the regime must be able to control every institution it does not dismantle. IMHO they picked Columbia bc the admins are so willing to sell out. If they capitulate like NIH, Columbia will voluntarily purge its own people and programs to comply with MAGA

Today is the 100th bday of Margaret Dayhoff! She is the mother of bioinformatics. In her honor, some are celebrating it as Bioinformatics Day or Bioinformaticians' Day.
H/T to Farzana!
www.nature.com/articles/s43...
Happy bioinformatics day to all!

Real chilling effects A extraordinary pattern of government censorship and threats to speech

New, from me: you were told that the threats to free speech came from wokeness. Some compared it to Maoist China.

Now we are witnessing government power being used to silence dissent and censor ideas. Now we know what real society-wide chilling effects look like. 🧵
open.substack.com/pub/donmoyni...

Really wish people would stop talking about the problem with Science under Trump as “budget cuts”.

No. Budgets are set deliberatively by elected members of congress. Budgets haven’t been cut.

What’s happening are *purges* and *censorship*.

Right, it's important to keep stating loudly that this is an illegal seizure of power, an administrative coup. It's a bit like when a cop with no right to search your car or house acts like he has that right. If you let him in, you are the sucker

We all need to be that guy who just keeps arguing

Exploring New Niches With US federal layoffs, we share a Cliffs Notes for some private sector opportunities. And Superorganism is hiring!

Exploring New Niches - Superorganism | a guide to nature jobs in the private sector for anyone who recently lost a government science or nature job

'Reboot' Revealed: Elon Musk's CEO-Dictator Playbook In 2022, one of Peter Thiel's favorite thinkers envisioned a second Trump Administration in which the federal government would be run by a “CEO”

These are some resources I found useful to understand the administrative coup taking place here. The 2-part series by Robert Evans (with guest Ed Helms) is a bit repetitive but worth 2 hrs IMHO

www.thenerdreich.com/reboot-elon-...

medium.com/@alysion42/d...

www.podchaser.com/podcasts/beh...

In the most recent evol-mut-circle seminar, @bryangitschlag.bsky.social (of
@davidmccandlish.bsky.social lab) presented his latest work: Graduated effects of mutation bias in adaptation

The recorded talk plus Q-and-A is free here for 6 months:

umd.zoom.us/rec/share/b-...

Passcode: g3PH=?9v

Same here. Many agencies are doing long-term work for strategic gain. If everyone doing research (into fish, weather, security, COVID, etc) goes on strike— and gets fired— there is no immediate downside. It just makes us stupider, less competitive, and more vulnerable 5 years into the future.

OK, thanks. I don't work on speciation. I have done a lot of reading about "evo theory" writ large, and in that genre, he is a reactionary who can be counted on to bring the same hostile and dismissive tone to intra-scientific disputes as he does to extra-scientific ones

What do you mean by "firings"? By "targeted agencies" do you mean the ones whose employees got the deferred resignation (fork) offer? I am not aware of actual firings at NIST (ideology = 0.01, workforce = 3400)

Which legacy? Gatekeeping and the reactionary mindset are mutually reinforcing.

The fitness advantage of phenotypic switching accrues to the lineage over time as it samples diverse environments. Is that a different "level"? I'm not sure the "levels" concept is apt here.

The Arrival of the Fittest In the early twentieth century, varied audiences took biology out of the hands of specialists and transformed it into mass culture, transforming our understanding of heredity in the process.   In the ...

This new book is going on my reading list. I'm particularly interested in how the development of evolutionary thinking was shaped by highly engaged non-scientist intellectuals who wrote about evolution early in the 20th century

press.uchicago.edu/ucp/books/bo...

Most people will benefit from the intro video that explains some basic concepts, including mutation spectrum and generative bias (a bias in the process of generating variation)

www.youtube.com/watch?v=5xR8...

Also, late last year I gave evol-mut-circle an overview of how the mutation spectrum can shape evo, in 3 modes (each with its own theory and empirical results)

* deleterious mut pressure
* ultimate source of raw materials
* introduction of novelty

www.youtube.com/watch?v=n8Tb...