the genome rambler
@genomerambler
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microbes, genomes, paleovirology, natural history, etc exploring the vast smallness
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Joined November 2022
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gonna take a break, this'll be my last post for the foreseeable future, ciao
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aegean region has such cartoonish geography, like something invented for a bad fantasy novel
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one of the problems with AI discourse is that programmers think of "research" as something you do on a computer
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the europe of europe, geographically speaking
one could argue for italy but while cartoonish it is too simple
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"now famous image" honestly still not famous enough
if biology classes reliably included this image so many misunderstandings about the central dogma would vanish
Francis Crick correctly predicted the basic details of protein synthesis by 1958, years before direct experimental evidence had confirmed the existence of mRNA or tRNA.
His 1958 paper on the subject is among the best in molecular biology's history.
***
After solving the
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i like linguistics because its like evolutionary biology but with more fighting and less data
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so putting quotes around your google search query straight up doesnt work anymore correct?
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near total biomass conversion. remarkable efficiency.
In all the decades of caterpillar rearing, I have never seen a case of parasitoidism as extreme as this. Anyone knows what it is? On tomato today, Gainesville, FL (host - probably once was a cabbage looper). RT if you don't but want to find out.
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"alphafold has solved the protein folding problem"
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my most insane belief: it is not a coincidence that two of the things ai is worst at are robotics and drawing hands
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hate this structure so much
q: "what atom is the iron bound to?"
a: "yes"
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the asparagus family really just follows no rules, huh
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if all microbes magically disappeared from the earth, how soon would we notice? what would be the earliest signs?
(assume all microbiologists and other folks actively looking for microbes are on holiday)
(also organelles dont count for this question)
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the state of biological understanding of AI people is...well,
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@SilverVVulpes
its a non-europoid thing, nobody in europe gets it because you all live in various cartoon countries
iberian peninsula? lol just a square jammed on the end of europe, separated by a mountain range for NO REASON
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what a wonderful coincidence that we share a similar olfactory aesthetic with the planet's dominant pollinator clades
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i can accept that grasses evolved relatively recently, but it still weirds me out that it seemingly took so long for evolution to figure out how to make something grass-like
was the grass niche really empty for 400 million years after the emergence of land plants?
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"no concept in psychology is valid"
yeah sounds about right
"IQ tests are among the most reliable, predictive measures in psychology – one of the field's crowning achievements. If IQ isn't a valid concept, no concept in psychology is valid, and we might as well quit and become plumbers or electricians."
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huh, i did Not know that the flagella has gearing
My grandfather built motors that powered big machines. In a lab not so different from his workshop, my colleagues and I uncovered the assembly of the bacterial motor. Today, this discovery has been published in
@NatureMicrobiol
#MolecularNodes
#Discovery
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oh noos theres dna in my mrna vaccine, the horror
my brother in christ, what do you think is in adenovirus vector vaccines
hell, what do you think is in chickenpox vaccines
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spinning up 10k competent postdocs to run westerns, easy peasy
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"sure that proline might be necessary in all other mammals but im built different"
What gene therapy would be on the top of your wishlist?
One biotech friend's answer: short sleep. It's ONE base pair flip and changes you into the type to only need 4 hours of sleep per night (!!!)
Isn't that basically a 17% "life" extension?
@bryan_johnson
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@tautologer
neat fact i just learned: the larvae are typically clonal descendants of a single brother and sister and some of them are sterile soldiers that try to kill off the other sibling's clones
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to a lesser extent this phenomenon is widespread outside of china as well, eg new england, 1890 vs 2013
The most interesting thing about historic photos of China is finding out that there basically weren’t any trees anywhere
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the lesswrong post about crispr editing adult brains to make geniuses might take the prize for dumbest lesswrong post in history, despite steep competition
at least the basilisk was kind of original
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new generation of HBDers dont even read their gwern, smh
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trying to decide what probability i would ascribe to genuine aliens using straight up bog standard DNA as their genetic material
Dr. Romero and his colleagues compared DNA samples from the aliens to an NCIB database of known DNA sequences on Earth.
70% of the DNA sequences identified were completely unknown.
They had never before been seen in any living organism on Earth.
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i wonder if observing llm chat agents being simultaneously superhuman at a bunch of tasks requiring intelligence but dumber than rock at other tasks is making anyone question the concept of g
probably not
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rux: alphafold can't handle point mutations
liron: ok, but...can it handle point mutations?
at this point its unclear to me if these folks know how to read
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@PicoPaco17
this would be relevant if all "problems of interest" fall under AI research
which, tbf, seems to be the position held by many at the moment
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update your estimates of their understanding of biology accordingly
Very interesting read. I wouldn't have thought that a startup that counted Peter Thiel, Sam Altman and Naval as its investors would be an outright fraud, but the
@yashgaroth
makes a very strong case for it.
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teaching med students means never being able to take med students seriously again
Wait, did ya’ll know this about reheating rice? 😳
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its funny how people are pretending this is an argument about facts when its actually an argument about branding
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tech guys learn to accurately read biology papers challenge level: impossible
(no they did not install a "kill switch" leading to chlorhexidine sensitivity, chlorhexidine is a broad spectrum antiseptic strep mutans is already sensitive to it)
also this paper isnt about lumina
3. It’s genetically stable? Also, any possible kill-switch in case things go wrong?
In one of my posts in the prior thread (), I mentioned “4. It’s genetically stable.”
That was rightly treated with some skepticism, given that I didn’t provide any
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they used crispr to make blander veggies
Our lab as well as students in the class I teach this semester enjoyed tasting the first CRISPR-edited salad greens, in which the myrosinase gene that results in the pungency of raw mustard greens (Brassica juncea) has been disabled, yielding a nutrient-dense, tasty, and
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huh
@briab_briar
somehow we figured out that if you put a chicken's head on the ground and draw a line extending out from its beak, the chicken will just lay there for as much as a half an hour. this is demonstrable on any given chicken. it does not seem that this is a behavioral generalization.
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its funny how folks will be like "science is broken, institutional science is either boring or fraudulent or both" but also when they find a study they like they take its results at face value without a second thought
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openai tweets that theyre scared of their creations: i sleep
some rando figures out how to make midjourney draw realistic hands: RUN FOR THE HILLS
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today i learned that miasma theory saved a lot of lives
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the One Ring was made from a trans-uranic metal change my mind
At what point do you as a scientist start asking “is this stuff ontologically evil”
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hey guys wanna have a rave in my tissue culture hood
oh my fucking god they used UVC germicidal lamps as blacklights. they're just fucking OUT THERE. you should NEVER see this
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i dont believe the moon landings were faked because the moon landing conspiracy theories are inconsistent with a flat earth
Seems like a big story, but I don't see proof that the researchers were the *first* to be ill. After all, the researchers could have been infected by others as they went about daily life in Wuhan.
There's some indication Covid-19 was circulating in Italy in November, which
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so many plagiarized theses out there i started worrying that maybe my thesis was plagiarized too
apparently im not a plagiarist but i do suck at writing
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recently learned about closed vs open mitosis and yet again am feeling like this is something i should have learned in, like, sophomore year of undergrad
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ok covid emerging in an american wet market is objectively the funniest option and thus this is now my opinion
@Sharon_Kuruvila
After the poll of Chinese mainlanders' opinion on origin of covid, I never want to see people claim that mainlanders have unique insights into the world because they're bilingual and intelligent ever again.
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@m_jivetoaster
yeah i decided a while back that at least half of europe's screwed up geography can be traced back to it being the only place in the world at the moment with a convergent plate boundary that hasn't quite finished converging
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i now have a near encyclopedic knowledge of the different ways people have died in yellowstone, courtesy of my wife buying Death in Yellowstone on our honeymoon
This is absolutely insane.
A group of tourists in Yellowstone was spotted exiting their cars and sprinting towards a mama bear and her two cubs.
One of the tourists had a child in his arms.
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pouring one out for all the homies dying of silicon deficiency
Rice and wheat, two of the most crucial food staples worldwide, have experienced a significant decline in nutritional quality over the past 50 years.
The essential mineral concentration in rice has decreased by 36%, while in wheat, it has dropped by 57%.
At the same time,
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seriously considering including a section on cryptography and information theory next time i teach mol bio
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@scareduck
sadly, they dont try to estimate how much faster things would go sideways if you get rid of all microbes, just that it would definitely Be Worse
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your occasional reminder that malaria used to be endemic in the US
“California confirms 2nd local dengue case”
…it sucks when things you wrote in grant significance sections years ago start coming true
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guys i am not an idiot i know there are types of research problems you can do on a computer, the issue is thinking that such problems comprise the entirety of research, please stop being tedious in my replies
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the thing is darwin's finches (and, importantly, the rest of the fauna and flora on the galapagos islands and other islands) provide much, much stronger evidence for evolution than apes
it’s fascinating that evolution by natural selection came out of finches and not hey those apes look and act concerningly like us
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not ideal
This paper is such a good example of capturing the effect of socioeconomic changes to ecological disruption that can lead to potential zoonosis.
And also a thinking about the ongoing H5N1 spread in cattle
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k9 unit pulls up to the crime scene and like 15 dachshunds spill out the back
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honestly to have an entire Project devoted to figuring out how much fraud you committed is such a flex
Today was the launch of the Many Co-Authors Project, which is seeking to ask all of Gino's collaborators to pin down the data for 100+ papers and identify her role in collecting it. You can check it out for yourself here:
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oh shiiiit
This is somewhat alarming given the spread of Chronic Wasting Disease (deer TSE related to BSE or mad cow disease). 2 hunters who ate venison from infected deer population both got CJD.
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thesis: within the heart of every "normal" woman resides a weird little gremlin they will only release if they feel absolutely safe in your presence
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oh dear
Probably my single favorite thing about 2024 is that
@ID_AA_Carmack
is sitting in front of a computer near Dallas working to make an AI unlike any other and that almost no one is paying attention to this.
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tbh there's probably dna in most if not all vaccines, either from the cells used to produce the vaccine and/or from the plasmids used to produce either the virus or the protein
dna is everywhere, if integration of random dna into our cells was a huge problem we'd be so screwed
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in another timeline i am studying the endogenous virus like particles of parasitoid wasps, and thriving
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no they cant!
no they cant!!
aaaaaahhhhhh why do people keep saying this
(i know why its just annoying is all)
@MatthewJBar
Why would you expect a machine superintelligence to not be able to do this? Non-general AIs can solve biological protein folding without even doing intelligent deliberation about it.
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holy shit
We discovered that these noncoding flanks hide a noncoding RNA that directs the IS110 DNA element to integrate into its target site.
A striking computational analysis uncovered that this RNA acts as a "bridge" between target and donor DNA to enable programmable recombination!
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this is kinda true except neuroscience is like 80% bullshit too
Years ago I talked to a fancy school dean who told me: “The thing about Psychology is everyone knows it’s bullshit but we can’t get rid of it because students spend 18 years watching Law & Order SVU and they decide they want to ‘understand the mind’ but neuroscience is too hard.”
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i will know we have actually reached the Future once somebody manages to make a slightly less shitty rubisco than the one evolution has produced over the past billion years
My father-in-law is a gardener.
He is insanely gifted. We were looking at a plant together years ago and I asked him what it would cost to build it today. I will never forget his answer… 'We can’t, we don’t know how to do it.'
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do the lantern bioworks people know what makes their magic bacteria resistant to its own bacteriocin? i can't find anything with a quick literature
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@flawedaxioms
this is why eden was a garden
our calling is to turn the world back into a garden
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as virologist but not one who had paid a huge amount of attention to respiratory viruses pre-covid, it was a bit of a shock to realize how little we understand respiratory transmission when i started looking into it in 2020
@PrasadKasibhat1
@ScientistAndre
@moog77
@ukhadds
@PeacockFlu
@Nucleocapsoid
@CathNoakes
@EvonneTCurran
2) which means we don't a priori understand aerosol infectivity in a physiologically-relevant way (as in, infectiousness per unit ??? for people)
3) We can make different modeling choices within that uncertainty, but then calibrate to epi data with some kind of fudge parameter.
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viral anthropic principle: the viruses we understand best and study most are typically those that infect humans the best
thus the viruses we study most will always be weird in ways that specifically make them better at infecting humans
you're telling me there is no other lentivirus where Vpu counteracts tetherin, and this is the key to allowing HIV to spread widely? and we're just handwaving about how this thing magically evolved an ability never before seen? sounds like a unicorn to me
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not at all surprising
We did 370 experiments to discover that protein language models primarily learn structure and won't scale for protein function prediction.
We need new pretraining tasks!
Work led by
@francescazfl
with
@avapamini
@yisongyue
@alexijielu
See Alex's thread + the paper for more!
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im so mad that biosphere 2 failed so spectacularly that nobody wants to build biosphere 3
For the cost of a tiny, fraught, lethal Moon-base, we could create *hundreds* of experiments in creating efficient, long-term, closed biospheres for human life.
23/
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lol they just photoshopped an image they stole from siemens energy
Announcing: BlueSea Frontier Compute Cluster
The Biden admin's AI Executive Order and the EU’s AI Act aim to centralize control under guise of safety
The solution is at sea.
BSFCC's are not just barge based compute platforms, but sovereign nation states
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frustrating thing about h5n1 is that odds are still good that it will not cause a pandemic in the near future, so i can imagine people freaking out and then concluding that scientists were scaremongering
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here's another story i've avoided telling because it feels unbelievably crass but: did you know eliezer had a little brother who died in 2004? did you know he's written about it publicly?
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i suspect that its almost impossible not to end up a heretic if you delve too deep into theology
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tho perhaps the grass niche was co-created with ungulates? is the evolutionary success of grass somewhat contingent?
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afaict the main practical outcome of behavioral genetics to date is to drive some highly online people insane
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ok but keep in mind that i am easily 10x more intelligent than you, you should Be Very Afraid
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this is one of those things that feels wrong but is actually pretty true to life
lotta short lived empires out there
One of the funnier aspects of Star Wars lore is that something called THE GALACTIC EMPIRE barely lasted 20 years. Shorter run than Family Guy
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funny thing is understanding why this is not a mystery requires nothing more than basic reasoning skills but once youve drunk the koolaid its easier to keep adding conspiracy epicycles rather than turn your brain back on
One of the greatest mysteries of COVID-19: Where did the flu go in 2020 and 2021?
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giving nitrogen mustards to a patient after theyve gotten a bone marrow transplant is wild ngl
My latest story is about how a very old and very cheap drug has been quietly revolutionizing bone-marrow transplants.
(1/3)
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@m_jivetoaster
mediteranean is just an ocean in the process of being squeezed to nothing, filled with continental fragments getting crushed up against each other and making mountains and islands and peninsulas all jumbled together
also explains the random volcanos here and there
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uhhhhhhhhhhhhhhhhhhh
A feeding electric eel can cause transfection of plasmids from the surrounding environment into nearby organisms - natural, eel induced, electroporation.
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generating ideas for new chemical weapons is not hard, i am begging you to do more than cursory research
Here’s an interview with the author of a paper, published in Nature last year, that showed a model was able to generate ideas for 40,000 new chemical weapons, many more lethal than VX, in 6 hours. I am begging you to do even the most cursory research.
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i did not realize bohr had this level of fame in denmark
what other scientists have reached this level of recognition, either nationally or internationally?
Remarkable memory of Niels Bohr from Victor Weisskopf.
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