#urist yells about science again

[urists]

In the notes of this, I said that water bottles are not pressure vessels*, but then I realized that soda bottles technically are. Which lead me to doing some research, and:

god I love chemistry teachers.

Now, from a materials perspective, I don't know if I would honestly trust a soda bottle for use as a process pressure vessel.

This is because soda bottles are made from PET, and this curve doesn't show PET having any sort of endurance limit (the flattening out that you see with PMMA in this graph, or the classic magical material steel here) - so you probably would not want to repeatedly cycle/release a soda bottle pressure vessel. But if you're taking it up to just a couple of bar once or twice, you might be able to get away with it.

(Three hopefully obvious caveats: 1) I am not your engineer. If you do something with a soda bottle pressure vessel and it fails horribly and you go "but Urist said it would work" I am going to be annoyed at you. 2) If you do something with a soda bottle pressure vessel and fail to take adequate safety measures for when-not-if it explodes, you're a dick and you should feel bad. 3) PET has dogshit chemical compatibility. If you pressurize acetone in a soda bottle, you should not be surprised when it fails.)

*water bottles are, technically speaking, pressure vessels, because they don't leak when you turn them upside down; if they're nine inches high, that's a nine inch water column, which is a unit of pressure (more or less). Thing is, nine inches of water is like... a third of a psi. If you need to pressurize something to one third of one psi above atmospheric, then I suppose that will meet your needs; that will not prevent me from wondering what in the fuck those needs are

[urists]

This is a delightful set of posts. However, I do want to take umbrage with "But unlike today’s careful gene editing" - because the vast majority of today's new food crops are still made with the radiation approach! (Or else chemical, but the principle is more or less kind of the same.)

We do this because of exactly one reason, to be clear. And that reason is not that we can't. These tools do exist in plants. And, it's not that these tools have no targets - they do! We know which genes to target! No, the only reason we still do mutagenesis based approaches is because people just will not fucking eat GMOs.

This is, I must say, a bonkers objection. It is MUCH cheaper and easier and faster and safer to perform a genetic edit on a plant than it is to expose a breeding population of plants to a strong mutagen like radiation or ethyl methanesulfonate (EMS, which causes a G:C->A:T change in plants, and also in the people who are administering it if they're not careful), painstakingly genotyping/phenotyping the resulting mutant population, then do the multiple generations of crosses required to integrate the desired trait into at least one of the parental lines. And even with all that work, the end result is either the same or oftentimes BETTER via the editing route - with genetics that are likely closer to wild type to boot.

But the process of intentionally editing the genome makes a plant a GMO. And the process of randomly doing so does not. And so we spend years and years and years introducing random mutations into plants and then removing them, when we could be spending those years addressing actual problems in plant, like TR4 in bananas or malnutrition or citrus greening (jesus please let's address citrus greening).

It's... frustrating.

Get ready kids, because I’m about to tell you all about gamma gardening!

Basically, after WWII, some people were interested in using fission energy for good. One of the uses they came up with was to create useful genetic mutations in plants.

But unlike today’s careful gene editing, gamma gardens took the “just blast them with radiation and pray that the RNG gods give you something good” approach.

According to Wikipedia, the methodology was as follows:

Gamma gardens were typically five acres in size, and were arranged in a circular pattern with a retractable radiation source in the middle. Plants were usually laid out like slices of a pie, stemming from the central radiation source; this pattern produced a range of radiation doses over the radius from the center. Radioactive bombardment would take place for around twenty hours, after which scientists wearing protective equipment would enter the garden and assess the results. The plants nearest the center usually died, while the ones further out often featured "tumors and other growth abnormalities". Beyond these were the plants of interest, with a higher than usual range of mutations, though not to the damaging extent of those closer to the radiation source. These gamma gardens have continued to operate on largely the same designs as those conceived in the 1950s.

They’ve decreased greatly in popularity as the reputation of radiation has gone down the toilet, but one notable product of gamma gardens is the ‘Ruby Red’ grapefruit!

^ this is a proper Fallout-style mutant

[urists]

Now that you mentioned plants in the tags I'm interested about them too - same assumptions as before, handedness is correct, not too many heavy metals or other poisons, etc. (+ we have functional nitrogen/phosphorous/etc cycles too) What would need to be the same about alien soil, codependent microorganisms, etc for it to thrive? How close would each of those things make it in relationship to a common ancestor?

god now this is complicated; I know just enough of plant science to tell you that I don't have a good answer, because plants are stupid complicated. Plants can grow in sterile soil, but the process of even planting them more or less contaminates the soil (for instance, see this) anyways. Beyond that, I don't have a ton of knowledge basis for how a plant would respond to a totally orthogonal life-form - at best they'd probably ignore each other, because I don't think the signaling pathways would transfer. (If they do get along, it might be good evidence for shared origins, but tbh you'd have to have a lot of detail as to exactly what's being exchanged to make that case; ammonia's a lot more fundamental than, idk, a complex hormone.)

[urists]

Just saw the DNA post, how many of those are needed for like, the ability to stick an animal (fox, whale, whatever) into an ecosystem with those changes and have it be able to sustain itself (food mostly)? This assumes correct hands on the molecules + enough local equivalent fauna or flora for it to be able to feed properly if they were compatible. I'm now reeling about how many SF species might be related because they can all coexist with the same food.

Oh, man, this is a deep question. I'm going to vastly simplify a ton of things about digestion, metabolism, etc, but the tl;dr's is that, yeah, things that can eat each other and thrive are probably related, at least to some degree - but it's not quite as surefire an indicator as finding something with total genetic compatibility.

So to start, there's a few important assumptions in your question; to avoid getting tripped up on them, I'm going to state them cleanly. Assumption one is that we're feeding a mammal that does not have a rumen (neither foxes nor whales do; whales are carnivores, while foxes are taxonomically carnivores but technically omnivores). This matters because I don't personally know of many higher animals that can synthesize every animo acid; I don't know which ones are essential for which animals - I'm not a farmer or a vet - but I'm going to assume whatever animal you're feeding has lost the ability to make at least one of them. (Rumen bacteria, on the other hand, likely still have the capability to make all of them, and so their inclusion would make this way more complicated.) Assumption two is that the food source in question is pretty close to whatever the animal normally eats in terms of heavy metal content and other toxic or indigestible substances, because otherwise this is pretty moot; who cares if the feed's viable for muscle growth when the animal dies of cadmium poisoning or thialysine substitution after a week. Assumption three is that the food source in question uses the vague conception of carbohydrates and lipids and proteins at all, because otherwise this animal's doomed from the start.

With those out of the way: if something from another planet can successfully feed a complex mammal for a while without pretreatment or editing, it's... I maybe wouldn't say it's bound to be related, but it's pretty likely, especially the more suitable it is. We have a hard enough time finding compounds of feed that are complete (i.e. provide all essential amino acids) from earth plants; if a xeno-biological feed regiment is complete, that means the alien linage shares those specific amino acids, both in structure and chirality (handedness). There's 20 main amino acids you need to make proteins; all have a specific chirality (handedness) and some are essential, but - as shown in the image below (from here) - those 20 aren't the only choices.

Funnily enough, though, shared amino acids don't mean the DNA's compatible; in theory it's feasible for something with a totally different information storage polymer to use the same amino acids in their proteins. Again, I wouldn't call it anywhere near likely, especially as the number of shared amino acids increases, but it's not entirely impossible.

(You'll note that I've mostly focused on protein this far; that's because imo proteins are probably the limiting issue when it comes to compatibility, thanks to the essentiality of amino acids. The other main concerns would be sugar chirality and structure (essentially, do the sugars of the food source look right enough for enzymes to recognize them) and micronutrients - but those are, at least in my mind, lesser concerns:

Sugars are not as complicated as amino acids (there's only sixteen possible hexoses at all, and enzyme promiscuity might be high enough to degrade even some weird carbohydrate down to pyruvate; once you get to pyruvate you can make both lipids and carbs again), and therefore I care less.

Meanwhile, micronutrients are easily more complicated than amino acids, but are also - by definition - just not needed in the same amounts. Life's surprisingly good at, well, living, and while it might not be pleasant for the animal to have beri-beri or an omega three deficiency, the quantities needed are low enough that perhaps it can find some oblique source of vitamins that works well enough. (i.e. if the animal in question needs 100mg a day of vitamins to survive, and the best source of it still only has 10mg per pound, then the animal needs to eat ten pounds a day. That sucks, but it's feasible. If the only source of viable amino acids exists at the same concentration, that's a problem. It's a concern, yeah, but less of one than protein availability.))

So overall, I'd say you could reasonably assess some degree of relatedness via the suitability of food. If the animal in question is a mammalian carnivore who's thriving off the meat of a random planet's species, I would personally bet those species probably shared a common ancestor somewhere up the line; the number of viable amino acids is too large - and carnivorous mammals are just too complicated and hyper-optimized - for it to be otherwise.

[urists]

(None of this is investing advice, I’m eliding a lot of detail and will occasionally just be outright wrong but in a hopefully useful way, electron orbits aren’t real but we still teach them, please feel to correct or expand, etc.)

Part one: Why banks?

A lot of money is very nice. You can use it to buy things, like comics, or food, or Twitter. But the actual logistics of HAVING a lot of money is often not. You have to carry all those bills around, sometimes you leave them in your other pants, they go through the wash, it’s annoying.

Really, it’d be great if someone else held onto that money for you. Then, when you need to buy your comics, or your food, or your social media website, you’d just say “go talk to that guy who holds onto all my money, he’ll get you what you need”. You still get to buy what you want, the seller still gets paid, and you stop needing to clean wet paper currency out of your washing machine.

Fortunately, that exists! It’s called a bank. Unfortunately, banks have costs associated with them. You have to pay tellers, and engineers, and janitors, and CEOs, and bonuses to the CEOs, etc. So to pay those costs, the bank takes a fraction of the money you put in there and uses it to buy other stuff that earns money. Usually, that stuff that earns money is pretty simple stuff - loans to large organizations, governments, other banks, or the like. Basically, promises that if your bank give that organization money now, they’ll give your bank more money in the future. (The amount of money they’ll give back is called the interest rate. This fact will be important later.)

Critically, the bank does this with your actual money. They don’t invest all of it - if you go back to the bank and ask for some cash to buy some cash-only comics, the bank will say “Here it is” - but if you’re the only person who has put money in the bank and you ask for all of it back, they won’t have it. Because they used some of it to buy a promise that someone else would give them more money in the future.

Now, if there are other people who also put money in the bank, then what they’ll do is pay you back with some of the money that other people have put in the bank, and then recoup that expense whenever those guys they loaned to and who promised to pay them back do. This is fine and well and good.

But if everyone asks for their money at the same time, that won’t work; the bank won’t have enough cash on hand to pay out everyone, and so the people who asked for their money last lose all their money. That’s called a run on the bank, and the critical point is that it’s a spiral: if you think there is about to be a run on your bank, the logical thing to do is to go to your bank and ask for all your money back before the run happens, thereby contributing to said run. (It’s A Wonderful Life, 1946, F. Capra, J. Stewart, D. Reed, et al.)

Now that we’ve got that theory out of the way, on to SVB!

Part two: SVB parties sound insufferable

SVB collapsing is in many ways a textbook bank run - a lot of people asked for their money back all at once - but the reason it collapsed and many other banks didn’t is the fun part.

Unlike other banks, SVB was a very specific bank that almost exclusively took money from startups, and startups are interesting - from a banking perspective - for two reasons.

First, because they’re basically loans. Someone says “Hey I have this great idea that will be worth a lot of money in ten years, but I need cash now to make it happen.” When/if someone gives them that cash, they put it in the bank, and then they pull a little bit of it out every week to light on fire pay their employees, and hopefully after a few years, they give the person who gave them money a lot more money back.

And second, because the ones who banked with SVB are basically herd animals. Those startups are funded by about four people and therefore they end up forming a very tight-knit clique that communicates very quickly. If someone got worried about something, everyone else would know about it instantly.

Having all these people at the same bank meant that if that bank had a problem, everyone would know about it. And because everyone would know about it, everyone would want to get their money out first. And when everyone wants to get their money out first, it’s a bank run. All it needs is a problem.

Part three: a problem.

For reasons I am not getting into here, the US government has recently raised interest rates. This had many effects, but the thing that is germane to our story here is that it meant that the previous loans that were agreed to - loans where someone took your money and promised they would give you more money back in the future - are now worth less. 

(I am using US currency for the below example, but it more or less works with any currency/commodity good: barrels of oil, bushels of grain, nuggets of definitely-not-fake copper.)

Basically: If last week we agreed that I could give you four dollars and in a month you would give me five back, and then this week I could give you four dollars and in a month you would give me six back, the agreement we made last week is worth less than the agreement we made this week. It’s not worth less in the sense of “I will get less than five dollars back” - I won’t! It’s still a valid agreement! - but it is worth less in the sense of “if someone comes to me and asks to buy one of these agreements from me, I can sell her this week’s agreement for more than I can sell her last week’s, despite them both costing me four dollars.”

And this is what happened with SVB. Startups asked for cash from people, promising to give them back more in the future. The startups then gave SVB that cash to handle, and SVB took that cash and used it to buy loans so they could pay for their operations. When interest rates went up, the loans SVB had dropped in price enough that - in theory - if everyone asked for their cash at the same time, SVB would not be able to sell all those loans and cover everyone. And the startups, nervous already because of the rising interest rates, freaked out, and just like that: bank run. Bye, SVB.

(I am also eliding the followup here: technically, bye SVB but not actually SVB’s customers, because the government stepped in to secure the banking system. This is, in my mind, a good thing - yes there are nuances to the expansion of FDIC insurance, and yes there are moral hazards here, and yes there are messes that may need to get cleaned up, but overall: as much as I do not like large banks, they are generally the last to fall in a bank panic; the chaos and problems caused by a large-scale shock to the US financial system would likely outweigh the joy of seeing Wells Fargo plummet into the earth. Unfortunately.)

For anyone wondering what happened to make Silicon Valley Bank here's the TL:DR:

SVB had very few consumer loans. Their investment base was primarily government bonds. A government bond is basically a loan to the gov at a fixed rate for a set period.

Their liability base was primarily consumer and investor savings.

They made money on the difference between what they were paying people in interest for their savings, and what the gov was paying them for the bonds.

They were then investing their profits into startups and tech businesses.

Then the loan rate rose, the interest rate on savings went up in the market, and to stay competative they had to put their rates up. They can't reclaim their investments as startups don't have the money to give back. The rate rises, their profits shrink, and they go boom.

[urists]

Sure, I can talk about selenoproteins! As always, I'm not your professor, any inaccuracies are my own mistakes, etc.

First off: it's important, I think, to keep in mind that generally, a specific enzyme works because one or more specific atoms with specific electron configurations were in just the right spots in order to lower the energy barrier enough for the reaction to proceed. [1]

Often, the cell manages this by using the various residues of the proteogenic amino acids (the bits sticking off the middle carbon in each amino acid). By arranging those just so, the enzyme can create a little pocket where the substrate molecule can slip in and be exposed to the right combination of acid/base/etc. It's worth noting that this pocket is usually defined by just a few amino acids; the bulk of an enzyme is often the structure AROUND the reaction site, not the actual reaction site itself.

Now, because each reaction has different needs, perhaps the catalytic properties of just amine or alcohol or whatever CHON group isn't enough for somewhat exotic or unusual reactions; perhaps a more complicated electronic environment might be needed. That's where sulfur-containing amino acids comes in. Sulfur atoms have a different distribution of electrons, a different electronegativity, etc. - and therefore they can catalyze different reactions. A classic example of sulfur catalysts are the cysteine proteases, which use the thiol (SH) group of a cysteine to faciliate nucleophilic attack on the carbon of a peptide bond, thereby degrading proteins. [2]

Selenoproteins can be thought of as an additional step down this path; selenocysteine is just cysteine with a selenium in the sulfur spot. This swap changes the reaction conditions to make antioxidant activity more feasible. That's good because random oxidation is generally bad for a cell (it causes cancer and also a whole mess of other things), and so selenocysteine tends to show up in antioxidant proteins a whole lot.

Basically, selenoproteins are - like everything in biology - a cool little adaptation that occurred by mistake and then stuck around because it was actually useful. They're also, it must be said, just the tip of the iceberg when it comes to weird protein shit; cofactors, chaperones, and post-translational modifications are all real, very strange things that occasionally make me scratch my head in bemusement. [3]

[1] This is part of why lead poisoning happens; lead ions are uptaken in place of or along with other cofactors, but the lone pair of the lead ion distorts the electronic configuration enough that ligands don't form in the right spots, and so the enzyme basically becomes inactivated.

[2] These proteins were first found in papaya, and are somewhat common in tropical fruits; they're the main component of bromelain, the part of pineapples that actively tries to digest you back, and they're also used as meat tenderizers. I'm honestly unsure WHY tropical fruits have so much of them; wikipedia says they're used in signalling pathways, but tbh everything is used in signalling pathways, so that's not really that useful. You actually have a bunch of them too - there is a calcium activated one that exists specifically in your eyes and brain, but the function is again as far as I'm aware not well understood.

[3] To be entirely fair, I scratch my head in bemusement at biology a lot; proteins aren't really that special here.

Oh does anyone want to know about sericin

Or like

"What Serine Has To Do With Silk"

[urists]

Yeah this is a great question! I would say it’s, uh, extremely unlikely for organisms with totally compatible DNA to evolve independently. Off the top of my head, there’s three main reasons for that. In order of improbability: 

The existence of a separate informational media at all

The existence of DNA as the specific informational storage, and 

The existence of compatible codons.

I’ll expand on each of these, but first:

Tl;dr: If we find something with compatible DNA to us, it’s related to us. Somehow. More detail on why below the cut.

First point of possible divergence is the existence of separate informational media at all. There’s a hypothesis on the origin of life called the RNA world hypothesis, which basically says life started with only RNA. RNA (ribonucleic acid) is a single stranded polymer of ribonucleic bases that can store information (like DNA does), but also catalyze reactions (like proteins do). It’s currently still used by your cells in several key processes, including the extraction of genetic information from DNA (called transcription) and the production of proteins (called translation); the hypothesis states that these roles are more or less left-over functionalities from when life started and RNA handled everything. 

Now given that RNA’s not as stable as DNA, the theory also postulates that the evolution of DNA was a huge step forward in survivability; DNA, with its self-checking double-helix structure, was used to store genetic information, and RNA was demoted to handling just the process of turning said information into enzymes.

That being said, there’s theoretically no reason this had to have happened. It’d be theoretically possible to have a life-form that reads information directly from its genetic storage into enzyme form, without an intermediate. If a xenobiotic life form evolved with an RNA-equivalent that was more stable, perhaps there’d never be a strong enough evolutionary pressure for the DNA equivalent to form at all - and therefore, finding an organism with the same wonky transcription-translation setup as ours would be a decent but not overwhelming point in favor of a common origin.

The next break-point is DNA as a specific choice. @headspace-hotel​ pretty much covered this in the link in their reply, so I’ll be brief: DNA’s just not that incredibly special. It’s a polymeric molecule with a sugar backbone and four bases, and while its structure is specific - i.e. cells have evolved over literal billions of years to be very attuned to and capable of discerning exactly this molecule - the choice of DNA with GTAC bases as the polymer used for storage of genetic information is just as possibly random chance as it is anything else. The exact chemical structure of DNA, and the exact bases we have? That’s not the only option for genetic information storage - it’s just the one that life on earth arrived at. Finding a life-form elsewhere that not only uses the same transcription-translation mechanism, but also stores its genetic information with the exact same chemicals? That’s more than a little unlikely, and another point in favor of a common ancestor.

And finally, we arrive at the last break point: codons! If the bases of DNA are letters, and the protein produced by a gene is a sentence, then the codons are words; they’re groupings of three bases that tell the cell which amino acid will be added to a protein next. It takes three bases to encode for one amino acid because there are only four nucleic bases but 20 genetically encoded amino acids.

If whatever life-form is found uses not only the same transcription translation mechanism, and not only the same genetic information storage molecule (i.e DNA), but also the same bases to encode for the same amino acids, I would not call it xeno-biology. That life-form shares a common ancestor with the rest of life on earth. Full stop.

After all, your cells don’t even have that! The mitochondria inside your cells use a different codon encoding schema than the rest of you! If we found a cell on another planet that had genes our bodies could functionally produce without any changes, that cell is related to us somehow. The chances of that occurring by chance are basically zero.

All of which is to say: life is complicated, and there’s a lot of points at which things could have gone slightly differently. If we ever find life on other planets, it will have a biochemistry that is at least somewhat incompatible with ours; if it doesn’t, I promise you that anyone remotely adjacent to the field of xeno-biology will immediately begin scouring the genome of every organism they can find for any hint of an overlap - and they’ll probably find one too. Independent evolution of the exact same genetics is just too improbable.

why would dna-based lifeforms on other planets imply a common ancestor with earth? could dna not evolve independently?

Okay so it could, but from what I understand it's just as well likely that the "code" for a living thing could be based on a different chemistry or have different types of base pairs or anything really. I'm not sure though, if anyone else knows anything about it I'd love to hear!