Bird account

Fig. 1. Genome assemblies, annotations, and transcriptomes. (A) Species representing the four sugar-consuming groups. [Bird photos (top to bottom): Steven L. Hunter (ML426078561), David J. Southall (ML431374521), Gerald R. Allen (ML633429605), and Charles Davies (ML205719751); photos accessioned into the Cornell Lab of Ornithology | Macaulay Library] (B) Cladogram and diet of the birds included in the study. On the basis of the percentage of dietary nectar and fruit intake, we delineated four groups of core sugar-consuming birds (red font) and core non-sugar controls (blue). Core non-sugar control sets were defined as groups phylogenetically close to sugar-consuming clades and comprising a similar number of species but not taking any nectar in the diet. These were used as direct controls in the downstream analyses. (C) Comparison of genome assembly contiguity. The contig N50 value indicates that 50% of the assembly consists of contigs of at least that size. The nine newly sequenced birds are indicated with a blue circle. (D) Status of 15,133 ancestral bird genes, classified by TOGA as those with an intact reading frame (blue), with gene-inactivating mutations (premature stop codons, frameshifts, splice site disruptions, or deletions of exons or entire genes; orange), or with missing or incomplete coding sequences owing to assembly gaps or fragmentation (gray). (E) Status of 8338 near-universally conserved Aves genes (BUSCO, odb10) in annotations generated in this study (green circles) or NCBI RefSeq annotations. (F) Tissue-specific transcriptomes generated for pairs of sugar-consuming and non-sugar control species. Black arrows specify the direction of DESeq2 analysis (for details, see methods and table S11).

Rainbow lorikeets got published in Science. Big congrats to all rainbow lorikeets and bird lovers in general www.science.org/doi/10.1126/...

I like that idea. Linking to a Github or Figshare repo to for scripts and data is pretty much standard practice now, so I don't think it hurts to just dump ChimeraX sessions in there too as a fun optional extra

#27 www.science.org/doi/10.1126/...

Great example of how less is more. The sparing use of colours and black outlines pops against the shades of grey, drawing the eye to exactly where it should go.

The billionaires' eugenics project: how Epstein infiltrated Harvard, muzzled the humanities and preached master-race science Edge - Jeffrey Epstein's favourite intellectual salon - was sold to me as a gathering of the world's finest minds, writes Virginia Heffernan. The files reveal it was something far darker: a decades-lo...

"[Edge's] male members were preaching master-race ideology. Citing their work, Brockman predicted in 2005 that the “dangerous idea of the next decade” would be that “groups of people differ genetically in their average talents”."
www.thenerve.news/p/epstein-bi...

EPA reverses long-standing climate change finding, stripping its own ability to regulate emissions The agency announced it is repealing its 2009 conclusion that greenhouse gases warm the Earth and endanger human health and well-being.

There are so many fucked up things with the current administration that it's hard to focus on one but this recent move is basically a death sentence for the planet. I've been involved with more boots on the ground actions over the years than I can count and this really bums me out.

A story of how science should work: an issue with methodology is picked up in this paper, authors agree they made a mistake and retract: www.science.org/doi/10.1126/...

Meanwhile, many papers using Richard Lynn's fraudulent National IQ data are still unretracted www.statnews.com/2024/06/20/r...

More Invisible Cities (my comfort book)

Pinker said that over the years he has regularly offered his linguistic opinions to Dershowitz for use in various cases. “I don’t recall his telling me that the question pertained to the Epstein defense,” Pinker said. “I was not aware of the charges against Epstein at the time. And no, I was not paid for the letter — it’s something that Alan and I do regularly, as colleagues.”

"Alan [Dershowitz] had us give Dteven Pinker $10,000 for a letter"

Steven Pinker in 2019: “I was not aware of the charges against Epstein at the time. And no, I was not paid for the letter" www.buzzfeednews.com/article/pete...

Epstein files: [shows Pinker was paid $10,000 for the letter] www.justice.gov/epstein/file...

Still processing how so many of the worst happenings of the past 15+ years -- the resurgence of Nazism + race pseudoscience, the anti-feminist culture war bullshit, crypto, the Uber-fication of the economy, etc. -- can all be traced back to Epstein and his rapist pals

I totally get what you mean. It's such an absolute betrayal of principles that makes me feel sick.

I wonder how Nabokov would rate Rowling like he did here: wmjas.wikidot.com/nabokov-s-re...

Probably not well.

It's also one of the world's most famous scientists sending up the balloon to his fellow powerful men that a young woman with no institutional affiliation or financial clout dared to speak out about their raping habits. *She* is organising a conspiracy; *he* is merely giving a friend the heads-up.

I believe this was after Elevatorgate. Pretty sure that's what put Watson on Dawkins' radar and she's been a foul spectre haunting his dreams ever since

Watson really broke these guys' brains. The threat of being rejected by a woman posed an existential threat to Dawkins and men like him. The threat to the ego was too much. Old boys clubs activated and said "we've gotta do something about this" and the solution was ultimately a return to fascism

Begin forwarded message: > From: Richard Dawkins < > Date: July 4, 2011 5:42:43 PM EDT > To: John Brockman .‘Z > > Subject: Lawrence > John • > 1. I hope you recovered well from your operation. > 2. There is a rather nasty young woman called Rebecca Watson, who seems to be running some kind of a witch-hunt against Lawrence Krauss because of his defence of Jeffrey Epstein. > http://skepchick.org/2011/04/lawrence-krauss-defends-a-sex-offender-embarrasses-scientists- everywhere/ > There are people on her blog talking about organising a walkout when Lawrence speaks at TAM in Las Vegas. I remember that you told me something of the circumstances of Jeffrey's arrest, and that his case is not as black as painted. Might you possibly remind of it. > Thanks (and greetings from Jackson Hole, Wyoming) > Richard

From: John Brockman < INIMI> To: Jeffrey Epstein <jeevacation@gmail.com> Cc: Lesley Groff <MIElla> Subject: Fwd: Lawrence Date: Mon, 04 Jul 2011 22:21:56 +0000 Attachments: Jaron.NYorker.pdf Eastover Farm 203-266-5930 JE, Fyi - see Richard Dawkins's email below alerting me to a campaign against our friend LMK re his friendship with you. (I'll deal with Richard). At the farm this week 203-266-5930. JB p.s. Here's a pdf of a the New Yorker profile of Jaron - just out today.

This email from Dawkins in the latest Epstein documents is a kind of perfect glimpse into the psychology of old boys club: Dawkins whinges about the "nasty young woman", but also has an undercurrent of unease, and seeks reassurance from Brockman that the child sex trafficker wasn't all *that* bad

Now the right-wing metabolic response on Alex Pretti's murder is that he retroactively deserved it because he was on camera behaving *unruly* towards ICE a few days prior. Apparently kicking the tail light of the death-squad vehicle warrants an execution. These ghouls...

No surprise, but seems the right-wing has already metabolised the murder of a man by secret police for excercising his constitutional rights. "Well, he shouldn't have been out there with a gun, i-it's dangerous". They act the based tough guys, but their one ultimate value is subservience to The Boot

Can't help but keep thinking that if this is what ICE feels emboldened to do in broad daylight--straight up murder--what the fuck are they getting away with behind closed doors in the concentration camps they have set up? It's going to take years to uncover the full damage they've inflicted

Rapture, but for guys really into ChatGPT

Man, writing is so hard. You're constantly confronted with your own limits, all the papers you have not read, all the terminology and facts you keep forgetting, etc. No wonder people turn to alcohol or worse (generative AI) when writing.

Still crazy to me that the richest man in the world is a straight up white supremacist and constantly trying to incite a "race war". Seems like we really need to do something about that if we want to survive the next decade

A movie that came out in 2025 that deserves way more love is "Mountainhead". Extremely funny satire of tech billionaires and AI zealots.

Bret complains that he "got a lot of crap" for his idea of "explorer modes". Hmmm, care to elabolarte on that part a bit more pal?

Bret does not seem to understand that there's this thing in evolution called variation. Instead, he's come up with his own idea called "explorer modes", which allows organisms to deliberately (not randomly) traverse the fitness landscape. In other words, Lamarckism

Bret reveals that he uses to brush off Intelligent Design people as religious cranks, but now sees that they actually have some pretty good points. He even hangs out with a bunch of them.

Bret seems to be one of those guys that think "junk DNA" must have a purpose/function. Not this again

So Bret's big hypothesis is that "integers" are encoded on the genome, and it is these integers that tell the cell how many times to divide or not, akin to telomere lengths and their shortening putting a limit on the number of cell divisions. And he thinks microsattelites encode these integers

Although Bret mentions Evo-Devo, it seems like he has not bothered reading any papers from the field, because I'm pretty sure they have a good explanatiin for the evolution of the bat wing already...

Bret complains that "his" field of Darwinian evolutionary biology is stagnant (she_doesnt_even_go_here.gif), but that the field of Evo-Devo is on the up. Not sure what he thinks those big differences are exactly

Bret talks to Joe about about protein evolution and how protein evolution has failed to explain the evolution of such large changes in morphology, like the bat wing from a shrew foot. Has this guy never heard of genomic regulation, and how it too can evolve?