the post composition process
I think there's actually a lot of opportunities in life for someone who loves to put together teams of specialists with different skills like in a heist movie
raginrayguns reblogged
haven't noticed any patterns in a while it feels like
Maybe you already noticed them all.
raginrayguns reblogged
Malaria cells have plastids homologous to chloroplasts
"We now recognize that this large group of parasites had a photosynthetic ancestry and were converted into parasitism early in the evolution of animals."
What!
so this paper gives more context... ok first of all did you know that coral photosynthesize?? I didn't know that... but the way they do that is intracellular endosymbiotic uh protists or algae or whatever. The branch of parasites that malaria is from, plasmodium, their closest relatives seem to be these endosymbionts in coral. So we can guess that a long time ago the ancestors of plasmodium weren't parasitic, they were an endosymbiont in a photosynthesizing animal like coral
Ooh boy, serial endosymbiosis is really something.
(source: Patrick Keeling, 2004, The Number, Speed, and Impact of Plastid Endosymbioses in Eukaryotic Evolution)
So basically bacteria invented photosynthesis a bunch of times, but oxygenic photosynthesis, the kind that breaks water molecules to make oxygen (which is a lot easier than using e.g. hydrogen sulfide, but also requires a more complex apparatus, it's actually a really interesting adaptation) appeared exactly once, among Cyanobacteria. However, photosynthesis, especially the oxygenic kind, is a really really useful trait. The way most photosynthetic organisms on Earth accomplish it is by swallowing someone else who is already photosynthetic.
Eukaryotes -- i.e. all life on Earth with a nucleus in their cells, or if you will everything living that is not bacteria and such -- got their start in the first place by engulfing smaller oxygen-breathing bacteria that became mitochondria, so they (we) already have some good experience in that. A clade of Eukaryotes called Archaeplastida engulfed Cyanobacteria, turning them into plastids, granting themselves the power of photosynthesis. (This is primary endosymbiosis, as was the earlier origin of mitochondria. Both mitochondria and plastids are surrounded by two membranes -- their own old bacterial membrane, and the internal membrane of the host cell). From the first Archaeplastida grew red algae, green algae, and then the plants with roots and leaves we're familiar with. Some success!
However, the first Archaeplastida made themselves a target, just like Cyanobacteria had done. Not just for grazing, but for endosymbiosis too. At some point, members of several other clades of Eukaryotes -- Haptophyta, Cryptomonadida, and possibly the ancestors of a large and diverse group recorded as SAR -- engulfed unicellular red algae in turn. (This is secondary endosymbiosis. The resulting plastids have four membranes: the original bacterial membrane, the inner & outer membrane of the red alga, and the inner membrane of the new host.)
Other groups -- the flagellate Euglenids and the spiderweb-like Chlorarachniophyta -- did the same by engulfing unicellular green algae instead. (See my Tree of Life series for more info on all these groups.)
The SAR group did well: its photosynthetic lineges include diatoms, giant kelp, and the Dinoflagellates responsible for red tides. Other lineages are not photosynthetic, though, so either they lost their chloroplasts, or those other group did in fact acquire them independently. Ciliates like Paramecium, for example, lost or never had them. (Well, actually some Paramecium incorporate green algae, but not to the point of endosymbiosis.) Inside SAR we also find Apicomplexa like the agents of malaria and toxoplasmosis, which modified their chloroplast into a structure that can't do photosynthesis anymore but helps with other biochemical processes.
it doesn't end here. Dinoflagellates got creative. Some cast aside their red chloroplast and acquired a new one by engulfing a green alga instead. Others, multiple times, independently, engulfed diatoms or haptophytes. Tertiary endosymbiosis! A cyanobacterium inside a red alga inside a diatom inside a dinoflagellate!
... And meanwhile the armored amoeba Paulinella started all over again with primary endosymbiosis by engulfing a different Cyanobacterium, unrelated with all the rest of this story.
And now, just a couple weeks ago, the discovery was announced of the nitroplast, a chloroplast-like organelle that was also the result of endosymbiosis of a Cyanobacterium. This happened in a Haptophyte, and this time the point of the endosymbiosis does not seem to be photosynthesis but nitrogen fixation (i.e., breaking the infamously hardy molecules of nitrogen in the air to incorporate their atoms in a form easier to digest. Legumes can do that too, thanks to symbiont Cyanobacteria in their roots, but not so directly.)
For bonus weirdness points: the Haptophyte carrying the nitroplast has an armored stage of its life cycle that looks like a perfect dodecahedron:
Ah, but of course plenty of animals would find photosynthesis useful as well.
OP kindly mentions corals, many of whom have incorporated red algae in their tissues to provide some extra sugar. Many other low-metabolism animals did the same with green algae or cyaniobacteria. There's even a slug, Elysia chlorotica, that sucks chloroplasts from the algae it grazes, incorporates in its own tissues, and keeps them running long enough to do some photosynthesis on its own -- Elysia's body even looks like a leaf!
Indeed, George McGhee's Convergent Evolution on Earth (which admittedly might err a tad to the side of more convergence) lists 14 events of photosynthetic endosymbiosis among protozoa, and 19 among animals, including sponges, cnidarians such as corals, flatworms, sea squirts, clams, and slugs.
ok i know it's ridiculous that i'm so emphatic about correcting these:
Your periodic reminder that one of humanity's biggest mistakes is not making thousands of clones of John von Neumann. Dolly (sheep) was cloned in 2003. So say in 2005 we made von Neumann clones so they would now be 16, on verge of making massive contributions to science.
In our 2005 we didn't have the ability to clone a human based on DNA alone, so this assume a (rational) multibillion R&D drive to clone humans.
Two years and a few billion dollars to go from real cloning (which begins with living tissue) to "cloning" dead animals? Based on what people have proposed for mammoth de-extinction, I'm gonna say this knowably could not have been done.
It's an inessential objection, of course you could just clone a living genius, but... ok I'll just move on to more stuff.
Octopuses are surprisingly intelligent, and reproduce at 1 year old. If we'd started a breeding program 50 years ago, we probably could've gotten them smarter than dolphins by now. A disappointing failure of the long-term mad science ecosystem.
a dolphin has over a hundred times as many neurons as an octopus. What's the expectation here, that all the morphological innovation required for a 100x scaleup can be done in fifty generations? I mean, do you expect to have a mutant with 10% more brain cells in each generation? This is impossible.
OK those ones are silly, but... ok there's the tweet I posted here
environmental activism added to the cost, but even before the seventies nuclear power had proven expensive to construct, and at least in the united states faced harsh competition from natural gas. I don't think this is obviously false, but it's far from obviously true. Important to "remind" people of anyway?
Or how about the O'Neillite resentment over apollo. From Engines of Creation:
Some of the pioneers had seen what to do: build a space station and a reusable spaceship, then reach out to the Moon or asteroids for resources. But the noise of flustered politicians promptly drowned out their suggestions, and U.S. politicians clamored for a big, easy-to-understand goal. Thus was born Project Apollo, the race to land a U.S. citizen on the nearest place to plant a flag.
So we'd totally be asteroid mining if only politicians had set their priorities straight? This is an old book, but the view is still alive, one of you was messaging me saying stuff like this. Again, this is not obviously false. But it seems to me probably false. Just as a major issue facing nuclear was the surprisingly deep natural gas reserves of the US, a major issue facing this plan would have been the surprisingly deep reserves of natural resources on Earth. I doubt space would have been attractive as an investment. A lot of the nuclear optimists and the space optimists had in mind 70s projections of dwindling resources and overpopulation.
Recently I was told that the reason Drexler's nanotechnology is so behind schedule is because the momentum for it was derailed. This is referring to something real, the term and the political momentum were stolen by material scientists. But if you read Engines of Creation it's clear that the first generation of nanotechnology is supposed to emerge from biotechnology, as it finds uses in industry and manufacturing. Nobody can accuse the people of the 1980s to 2000s of investing too little in futuristic biotech dreams. It didn't happen because it didn't work, there's a whole boulevard of broken dreams if you list all the ideas that consumed money and crashed. Not that it's impossible to make nanotech, but it's not like we would have had it already if only the nerds had been savvier politicians.
OK one more. I should have put this one earlier...
Within this environment, death is the destiny for you and everyone you know, even though living forever is possible with today’s technology, if only this world were not multiply headed towards self-caused extinction.
this is something i've argued on this tumblr before... why think the line between permadeath and preservation is between what alcor does and aldehyde-stabilized cryopreservation? I've never seen the claims made for it backed up. It supposedly maintains information at the molecular level, but when I ask for any evidence, I get electron micrographs at the micron level?
actually, while i'm posting zizians, how about ziz herself?
I expect de Grey silently gave up inside a long time ago. Probably on failing to complete root cause analysis of why people paid money weren’t doing real things.
Is that so? So Aubrey de Grey proposing ways to use gene therapy as a preventative medicine is doing real things. But he doesn't get money, that all goes to the biotech companies that have been working for 20 years to make gene therapy safe enough to be worth it even in cases of debilitating disease. Seems like someone has to do that before we can even think about using it as a preventative, right? People threw hundreds of millions of dollars into each one of these biotech companies for the promise of profiting from treating a disease, and much of that money was lost when it didn't work. But if only they weren't in a pro-aging trance
Put all this together, it's this whole ideology and mythology. It's the same pattern over and over again and the technical case never justifies the level of confidence, and often there's no real technical case. It may seem silly when I argue against the inconsequential expressions like the octopus thing but it's all one thing.
raginrayguns reblogged
(Command for my followers) read this Wikipedia article. Not for its form but for its content; you know, to learn what is in it.
i did this when my friend was playing skyrim and then i told her it didn't seem feasible as a strategy. To invent the gun
Interesting, my main takeaway from this article is that the invention of at least the matchlock musket, and from there perhaps various other improvements, seems a lot more "inevitable" following the discovery of gunpowder than I had thought it was. It seems like once you have "put gunpowder in a tube and make it go boom out one end", it's a series of incremental, individually natural seeming improvements that gets you from to what we would recognize as a true firearm.
The lesson I got was that it was primarily dependent on the quality of steel. Try to make it in Skyrim and it will explode in your hands. Fire lances to hand cannons to pistols is increasing ability to contain the explosion
raginrayguns reblogged
(Command for my followers) read this Wikipedia article. Not for its form but for its content; you know, to learn what is in it.
i did this when my friend was playing skyrim and then i told her it didn't seem feasible as a strategy. To invent the gun
raginrayguns reblogged
mrsbandicoot-deactivated2021061
Analogy I’ve heard: If you have a drink with the bartender, you’ll be fine. If the bartender has a drink with every patron, the bartender’s going to the hospital.
this is not necessarily true. at the exposures where it’s possible to accurately observe cancer risk from ionizing radiation, the risk is proportional to the exposure; getting twice as much radiation doubles the cancer risk. there’s significant debate over whether that relationship extends down to zero dose, but regulatory agencies like the EPA assume it does.
if that framework is correct, an x-ray has a small chance to give the patient cancer. here’s a simple analysis of the risk from different procedures; based on a few assumptions, a typical dental x-ray might have a 1 in 3 million chance of causing a fatal cancer in the patient. That’s equivalent to the radiation a person would normally receive from environmental sources in 24 hours, just by living a normal life. i wouldn’t worry too much about that if the dentist needed to know something about my teeth.
the reason the dentist hides behind lead shielding is because they get no benefit from the x-ray which would justify the risk.
raginrayguns reblogged
do chemists ever, like. get extremely fixated on this One Weird Molecule That Will Go Great With EVERYTHING
& then they totter around their lab trying to figure out every possible weird way this molecule can react with other stuff
& eventually they run out of all the obvious candidates, so they start working themselves into a tizzy, b/c what the fuck do you MEAN xeon won't react with my cool molecule. fuck YOU noble gases. i'll show YOU who's boss
& then they waste SO much time and energy pioneering bizarre new techniques to make this reaction kinda sorta work, but in circumstances that ONLY exist in a lab but never ever in nature in a million years
...because i feel like this is my general approach to what is known as "shipping" in fandom circles
A. G. Streng, with difluorine dioxide:
FOOF is only stable at low temperatures; you'll never get close to RT with the stuff without it tearing itself to pieces. I've seen one reference to storing it as a solid at 90 Kelvin for later use, but that paper, a 1962 effort from A. G. Streng of Temple University, is deeply alarming in several ways. Not only did Streng prepare multiple batches of dioxygen difluoride and keep it around, he was apparently charged with finding out what it did to things. All sorts of things. One damn thing after another, actually:
"Being a high energy oxidizer, dioxygen difluoride reacted vigorously with organic compounds, even at temperatures close to its melting point. It reacted instantaneously with solid ethyl alcohol, producing a blue flame and an explosion. When a drop of liquid 02F2 was added to liquid methane, cooled at 90°K., a white flame was produced instantaneously, which turned green upon further burning. When 0.2 (mL) of liquid 02F2 was added to 0.5 (mL) of liquid CH4 at 90°K., a violent explosion occurred."
And he's just getting warmed up, if that's the right phrase to use for something that detonates things at -180C (that's -300 Fahrenheit, if you only have a kitchen thermometer). The great majority of Streng's reactions have surely never been run again. The paper goes on to react FOOF with everything else you wouldn't react it with: ammonia ("vigorous", this at 100K), water ice (explosion, natch), chlorine ("violent explosion", so he added it more slowly the second time), red phosphorus (not good), bromine fluoride, chlorine trifluoride (say what?), perchloryl fluoride (!), tetrafluorohydrazine (how on Earth. . .), and on, and on. If the paper weren't laid out in complete grammatical sentences and published in JACS, you'd swear it was the work of a violent lunatic. I ran out of vulgar expletives after the second page. A. G. Streng, folks, absolutely takes the corrosive exploding cake, and I have to tip my asbestos-lined titanium hat to him. Even Streng had to give up on some of the planned experiments, though (bonus dormitat Strengus?). Sulfur compounds defeated him, because the thermodynamics were just too titanic. Hydrogen sulfide, for example, reacts with four molecules of FOOF to give sulfur hexafluoride, 2 molecules of HF and four oxygens. . .and 433 kcal, which is the kind of every-man-for-himself exotherm that you want to avoid at all cost. The sulfur chemistry of FOOF remains unexplored, so if you feel like whipping up a batch of Satan's kimchi, go right ahead.
Do you have ships which are comparably energetic?
raginrayguns reblogged
huh, troll names are six letters... cambridge structure database entry ID's are six letters...
Deposited 2021:
looks like KARKAT is an "additional database identifier" for this molecule, and the main one is "KARJOG02"? I haven't seen that before...
huh, troll names are six letters... cambridge structure database entry ID's are six letters...
They say "there's no cure for the common cold", but it seems like there could at least be an antiviral drug right? Like what we do with covid19, the antigen tests + a drug if positive, there's no reason something similar couldn't be developed for other coronaviruses. Just not a priority I guess
idk why drexler was writing in 1986 like "wow what if we discovered a treatment for schistosomiasis by understanding the parasite's molecular machinery", like at time of publication there was already a schistosomiasis drug that seems to work fine, and it's still used. And it was discovered in the old-fashioned drug-first way, rather than target-first, the protein inhibited by the drug wasn't identified until much later
this seems to be one of two drugs given by Deworm the World btw
raginrayguns reblogged
yeah
So it's kind of a gimmick, but I'm making a git repo for this paper that not only contains the analysis code, but produces the figures, and even has the latex for the paper. Like it's everything from doing the simulations to compiling the pdf. I'm wondering if I can promote the paper by getting featured on some reproducibility related blog. Kind of an annoying thing to do because it's not like I think people should really be making githubs with their tex files including even pre-publication drafts in the commit history but whatever
birds have gizzards so it makes sense but it's so funny to see videos of them just swallowing something. Like gulp
i posted way too much yesterday. I was on a train, it was hard to focus on my work. I really want to post more though. I was thinking about how different it is to "chase" resistance mutations with a drug vs a mRNA vaccine. But I've got to finish my plotting code to show results at lab meeting in 20 min