--- Log opened Thu May 11 00:00:57 2023
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04:02 < stipa> https://www.androidpolice.com/youtube-ad-blockers-not-allowed-experiment/
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08:58 < docl> early exposure to creationist notions on abiogenesis immunized me to a large category of overly specific skepticism
08:58 < docl> including smalley (who was a creationist)
09:03 < muurkha> ...smalley was acreationist?
09:04 < docl> that's my understanding, yeah
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09:04 < muurkha> https://creation.com/richard-smalley
09:05 < muurkha> > Smalley at first accepted theistic evolution, but as he studied the issue in detail he became an outspoken anti-Darwinist. In 2004 he delivered an anti-Darwinist address at Tuskegee University’s 79th Annual Scholarship Convocation/Parents’ Recognition Program and received a standing ovation
09:06 < muurkha> https://en.wikipedia.org/wiki/Richard_Smalley#Religion_during_final_years
09:06 < muurkha> wow, that sure puts the drexler debate inn a different light
09:06 < docl> yeah, no kidding
09:11 < docl> low probability of abiogenesis does resolve the fermi paradox relatively cheaply (i.e. no other assumptions needed) though, and given only one reference case of life existing it can afford (i.e. with no surprising coincidence being implied) to be arbitrarily low. discovering life of independent origin anywhere else in the galaxy would actually puzzle me more than a sterile set of earthlike worlds
09:12 < muurkha> though https://hope.edu/news/2005/10/29/remarks-by-richard-smalley-at-alumni-banquet.html doesn't really say anything anti-Darwin
09:12 < muurkha> sterile how?
09:12 < docl> no microbial life
09:13 < hprmbridge> nmz787> "NO MICROBES ALLOWED"
09:14 < docl> no non-microbes either, of course
09:14 < muurkha> isn't that what you would see if there was no life of independent origin?
09:15 < docl> plenty of organic molecules of the simple sort, plenty complex nonfunctional ones, just nothing capable of replicating itself and mutating
09:15 < docl> that's what I'm suggesting. no life of independent origin -> no microbes anywhere besides Earth and nearby places it could reach by meteorite
09:15 < muurkha> oh, sorry
09:16 < muurkha> I had a bit flipped
09:16 < docl> :)
09:16 < docl> I'm making boring points, just chattering a bit
09:16 < muurkha> what do you call the many-worlds anthropic principle?
09:17 < muurkha> that would allow you to set the probability of abiogenesis arbitrarily low
09:17 < hprmbridge> Katylase> What about molecular entities, like us enzymes? :3
09:17 < docl> hmm, there's probably enzymes on some worlds
09:18 < muurkha> haha!  hi Katylase!
09:18 < docl> hi Katylase :)
09:18 < muurkha> is an enzyme just a peptide that has some catalytic activity?
09:19 < muurkha> that's just a matter of degree; you could say a peptide was more enzymatic than another but not that it wasn't an enzyme
09:20 < docl> is that true? hmm
09:21 < docl> one thing I'm given to understand is that organic catalysts tend to have special pockets for metal ions
09:21 < muurkha> yeah, life has evolved some really, really good enzymes
09:22 < muurkha> but any molecule you introduce into an environment will affect the rates of all the other reactions going on there, up or down
09:23 < hprmbridge> Katylase> yea, enzymes are catalytic proteins (except ribozymes, they're RNAs)
09:23 < muurkha> freaky!
09:24 < docl> ah, fair enough
09:26 < muurkha> I've been thinking that for micron-scale synthesis pathways you might want to rely on pressure, pH, and pE
09:26 < muurkha> traditional benchwork leans heavily on temperature changes
09:27 < muurkha> but temperature excursions are infeasibly expensive to maintain at the micron or even millimeter scale
09:28 < muurkha> which is why your stomach doesn't use a heating mantle to make gastric juice and there are no fly-sized hummingbirds
09:30 < hprmbridge> Katylase> TrpAspTyrMet?
09:34 < docl> what's TrpAspTyrMet?
09:35 < docl> muurkha: photolytic maybe? you can also do mechanical pressure changes
09:37 < docl> temperature excursions can't be focused to specific sites, yeah. good old square-cube rule
09:38 < hprmbridge> Katylase> read it as one letter codes! W-D-Y-M it's "what do you mean" converted to protein language🙂
09:38 < docl> ooh
09:38 < kanzure> .gpt4 -c convert TrpAspTyrMet to amino acid acronyms/abbreviations and tell me what famous saying it refers to
09:39 < gptpaste> ​The amino acid acronyms/abbreviations for TrpAspTyrMet are W, D, Y, and M. This refers to the famous saying "WDYM," which stands for "What Do You Mean?"# Thu 11 May 18:39:09 CEST 2023 - convert TrpAspTyrMet to amino acid acronyms/abbreviations and tell me what famous saying it refers to - http://sprunge.us/SPHEOH
09:39 < docl> very cool
09:39 < hprmbridge> Katylase> I sometimes talk like that
09:41 < kanzure> Katylase: can you fathom a way to use amino acid polymers (proteins) to create arbitrary three-dimensional objects
09:42 < docl> Katylase: are you familiar with the square-cube law? it's why polar bears are big, and elephants can't be mouse shaped. bigger objects can't be cooled efficiently. like why crushed ice will cool your drink faster vs a big chunk of ice. for some reason this came as a big revelation to me when I was in my 20's instead of learning it as a child
09:43 < docl> .wik Square-cube_law
09:43 < EmmyNoether> "The square–cube law (or cube–square law) is a mathematical principle, applied in a variety of scientific fields, which describes the relationship between the volume and the surface area as a shape's size increases or decreases." - https://en.wikipedia.org/wiki/Square-cube_law
09:44 < docl> so in micro/nanophysics you end up with some consequences of that like if you heat one enzyme you have to do it as part of the whole batch including all nearby ones. unless you do it very briefly
09:46 < kanzure> muurkha: by any chance do you have calculations or estimations for the theoretical performance of a (~nano) mechanical computer built out of proteins relying on transfer of kinetic energy through motion?
09:46 < kanzure> this calculation is not in "nanosystems"
09:47 < hprmbridge> Katylase> The surface/volume ratio! yea, i read about it in one biochem comic, it's the reason why amoebas can't be big (and why are people/other creature multicellular)
09:48 < kanzure> there is a seaweed lifeform that is 10 meters long and a single cell. don't know the surface area of it though.
09:50 < docl> it has some super interesting applications in astrophysics as well, like stars are not really producing heat very fast by fusion but they get away with it by being so freaking big
09:53 < docl> well worth pondering endlessly until it's your first reaction to everything to think about how this rule impacts it. like part of the logistics of refrigeration and hence fresh fruit in our civilization is that big warehouses are inherently cheaper to keep cold (per unit volume). or how skyscrapers depend on air conditioning to get rid of the heat from so many human bodies
09:54 < hprmbridge> Katylase> as our bio teacher said, biology is one big "but"🙂 there's lots of exceptions...
09:57 < muurkha> kanzure: I don't, no
09:58 < kanzure> hrm well someone should do an estimation of protein mechanical computer performance at some point
09:58 < muurkha> docl: photolytic and photocatalytic are good ideas
09:58 < muurkha> I suspect the mechanical pressure changes are the most underexplored
09:59 < muurkha> Katylase: what did I mean by which thing?  sorry, I just saw the question
10:01 < docl> was that wrt "temperature excursions are infeasibly expensive to maintain"?
10:01 < muurkha> kanzure: I agree that this would be very worthwhile?
10:01 < hprmbridge> Katylase> you said something was freaky, and i don't know what...
10:01 < muurkha> oh, ribozymes!
10:02 < muurkha> I didn't know they existed
10:02 < kanzure> do you know about DNAzymes
10:02 < muurkha> even less
10:02 < kanzure> aptamers?
10:03 < muurkha> no!  I have a lot to learn
10:03 < kanzure> .wik deoxyribozyme
10:03 < EmmyNoether> "Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic.  This is similar to the action of other biological enzymes, such as proteins or [...]" - https://en.wikipedia.org/wiki/Deoxyribozyme
10:03 < docl> I'd heard of rybozymes but not pondered them... same with aptomers. dnazymes are new to me
10:04 < hprmbridge> Katylase> ✨ a ribo**some** is a ribo**zyme**✨  the rRNA is catalytic
10:04 < docl> yeah the etymology makes sense to me :)
10:05 < docl> drmeister is working on spirologozymes, I believe they might be called
10:05 < muurkha> ahh
10:06 < muurkha> don't ribosomes contain peptides too?
10:06 < kanzure> here are some known dnazymes- they seem to perform ligation, cleavage, phosphorylation, amino acid sidechain modification, DNA capping, ester hydrolysis, amide hydrolysis, glycolysation, reductive amination https://www.genesilico.pl/DNAmoreDB/dnazymes
10:08 < hprmbridge> Katylase> yea, they are complexes of RNA and proteins😉
10:10 < docl> ah, and they also seem to work by metal ions. I wonder if that's just a general rule or more like always the case
10:17 < docl> the key selling point for spiroligomers is their folding is more predictable because they form stiff structures. so it's more friendly to designing in a computer simulation first, which makes it cheaper. they also don't degrade as easily. DNA and RNA are more like protein in that they are floppy molecules with heavy amounts of quantum fluid dynamics applying. the nice thing with DNA/RNA/protein though 
10:17 < docl> is their replication capability, so once you have one copy in DNA you can make more
10:22 < kanzure> what is the most interesting spiroligomer that has been designed in computer modeling?
10:22 < hprmbridge> nmz787> I think it's basically electric potentials... using fake/example numbers... if it takes 1 volt to make or break a carbon bond, how would carbon be able to cause such a reaction without risking itself? The answer is to use other atoms with different (stronger?) bond properties
10:29 < hprmbridge> nmz787> (maybe that's too simple of an idea... I was trying to think about it like the halting problem)
10:31 < docl> one thing they actually do use pH for is protection/deprotection
10:38 < docl> drmeister: what's the most interesting spiroligomer that has been designed so far?
10:38 < docl> .wik Spiroligomer
10:38 < EmmyNoether> "Spiroligomer molecules (also known as bis-peptides) are synthetic oligomers made by coupling pairs of bis-amino acids into a fused ring system." - https://en.wikipedia.org/wiki/Spiroligomer
10:40 < docl> there are some chemdraws on the wiki of some examples of enzymes, but all the cites are a few years old
10:40 < docl> .t https://onlinelibrary.wiley.com/doi/abs/10.1002/ange.202302809
10:40 < EmmyNoether> HTTPError: HTTP Error 403: Forbidden (title:75)
10:41 < docl> "Spiroligomer-Based Macrocycles for Atomically Precise Membranes"
10:41 < docl> I thought that was pretty interesting, as it works as a molecular sieve. potentially a cost cutter
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10:46 < docl> https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.202302809
10:48 < docl> weirdly it's paywalled but the 2nd link worked for me
10:58 < kanzure> check under the "science" section http://www.transistorstudio.co.jp/works2016.html
10:58 < kanzure> https://www.youtube.com/watch?v=5JcFgj2gHx8
10:59 < kanzure> they also did this weird one about the central dogma? https://www.youtube.com/watch?v=DB0gnar0Ndw
11:02 < kanzure> oh they have an english version https://www.youtube.com/watch?v=ZNcFTRX9i0Y
11:27 < docl> hmm. aerographite is 1000x lighter than air. so I guess that means if you solve production costs, you can make cloud cities from it. or permashades for climate control, space launcher platforms, stratospheric wind turbines, etc. anything a balloon would be good for. https://onlinelibrary.wiley.com/doi/abs/10.1002/adma.201200491
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11:38 < hprmbridge> Katylase> Oh! That's the one where Poly2's tail changes colors! I know a better version though...
11:38 < hprmbridge> Katylase> https://youtu.be/J3HVVi2k2No
11:38 < hprmbridge> Katylase> This one has a story, and also subtitles✨
11:38 < Muaddib> [J3HVVi2k2No] Animation: The Central Dogma (10:48)
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12:08 < hprmbridge> Katylase> Also, my drawing of Poly2✨ https://cdn.discordapp.com/attachments/1064664282450628710/1106296896760315985/IMG_2166.png
12:09 < hprmbridge> Katylase> (she's holding her tail)
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12:26 < docl> ooh, the supplementary pdf for the aerographene paper is darned interesting. https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fadma.201200491&file=adma_201200491_sm_suppl.pdf
12:41 < docl> after the carbon nanolayer (mostly sp2 hybridized) is deposited on the ZnO crystals they use hydrogen to scrub the oxygen from the zinc, then vaporize the zinc and condense it out. it doesn't describe creating the zinc crystals, but apparently this is also a cvd process (put zinc and oxygen in gaseous form in a chamber and let them react to grow nanocrystals). so mass producing this at large scale 
12:41 < docl> wants big vacuum chambers and a lot of energy and coolant...
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13:04 < docl> muurkha: check out that pdf
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14:04 < muurkha> Katylase: https://en.wikipedia.org/wiki/RNA_polymerase_II? your drawing is super cute!
14:05 < docl> ok the summary I linked to "smaller than μg/cm^3" was wrong (should have had 200 prepended), and it's actually something like 6x lighter than air rather than 1000x. and it's porous so you'd need to pump the air out and seal it (maybe fill with hydrogen or helium)
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14:05 < muurkha> docl: that's great!
14:05 < docl> :)
14:08 < muurkha> you presumably have to pump the air out slowly to avoid rupturing it
14:08 < docl> kind of seems possible to build a self expandable cloud city from this stuff. set up a cool nerd base there...
14:10 < muurkha> :)
14:10 < muurkha> how strong is it?
14:11 < muurkha> I haven't read through the supplemental PDF yet
14:11 < docl> well it's graphene like, as it tends to be sp2
14:12 < muurkha> I mean, at low densities, strength depends very strongly on structure
14:21 < docl> its E/ρ^2 appears to be absurd due to the low density
14:22 < docl> it's also ductile, unlike diamond and so on
14:26 < docl> it's also old enough to be on sci-hub. apparently newer papers aren't getting there now :/
14:35 < muurkha> some are
14:35 < muurkha> but not as reliably as before
14:35 < docl> muurkha: if you are at a place where you can see images, here's a screenshot from the paper https://i.imgur.com/gWd05cI.png
14:36 < muurkha> looks like a Young's modulus of about 10 kPa
14:37 < muurkha> well, it say 15, which is maybe fair
14:37 < muurkha> and ultimate strength of about 1 kPa
14:40 < muurkha> https://www.makeitfrom.com/material-properties/High-Density-Polyethylene-HDPE says HDPE has an ultimate strength of about 24 MPa
14:40 < muurkha> so this is about 24000 times weaker than HDPE
14:41 < docl> ahh. so per unit volume it's not that strong
14:42 < muurkha> dividing that by the density of 6 kg/m³ we get a free breaking length of 17 meters
14:43 < docl> should be 180 milligrams
14:43 < muurkha> that is, if you make a cord out of the stuff and unreel it from the top of a skyscraper, the point at which the weight of the cord hanging below you will break the cord you're unrolling is 17 meters
14:44 < muurkha> except in ther test it doesn't really break, it just stops resisting further deformation
14:45 < docl> well 180 grams more like. micrograms per cubic centimeter should be grams per cubic meter
14:47 < muurkha> oh, sorry, I misremembered "6 times lighter than air" as "6 times heavier than air"
14:47 < docl> ahh
14:47 < muurkha> so we get 570 m, which is a lot more reasonable
14:48 < muurkha> on the order of materials like rubber, concrete, and copper, according to https://en.wikipedia.org/wiki/Specific_strength
14:51 < docl> so definitely not space elevator material. but mostly I'm wondering if it can work as a vacuum balloon, which would be more of a compressive force. it would densify then. but less at bigger volumes since there's less surface area then. you could also trap hot air in it maybe
14:55 < muurkha> yeah, it sounds like you could build self-supporting structures from it
16:02 < hprmbridge> kanzure> recent longevity-related companies https://twitter.com/adanguyenx/status/1656700883399512069
16:02 < hprmbridge> kanzure>  https://cdn.discordapp.com/attachments/1064664282450628710/1106355652252672050/image0.jpg
16:20 < muurkha> I don't think you can build a vacuum balloon in the troposphere
16:21 < muurkha> a vacuum balloon has to withstand the pressure of the atmosphere, which is 100 kPa
16:21 < muurkha> this aerographite collapses at 1 kPa, a hundredth of an atmosphere
16:22 < muurkha> if I'm understanding that diagram right
16:22 < muurkha> if your vacuum balloon is floating in I think the stratosphere you can get down below 1 kPa and then you have a vacuum balloon
16:36 < hprmbridge> kanzure> Alternate funding strategy for rare diseases: give desperate parents of diseased children lots of capital https://twitter.com/eperlste/status/1656486311912415232
16:48 < muurkha> good plan
16:49 < fenn> there is no financial upside to rare diseases, which is why there isn't any investment in finding cures
16:50 < fenn> the only way to make it work is developing methods that are also applicable to rare diseases
17:04 < kanzure> or fund making other people better- maybe life sucks because of some rare disease nobody could have predicted, but at least you can do 50,000 reps a day
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19:46 < fenn> .t https://twitter.com/VivaLaPanda_/status/1523367484929183745
19:46 < EmmyNoether> Incredibly hot take: developed countries have birthrate collapse because old-age social safety nets socialize the costs of not having children
19:53 < hprmbridge> kanzure> another matrix deepfake https://youtu.be/evJkPPf1Dkc
19:53 < Muaddib> [evJkPPf1Dkc] Matrix Monohydrate (1:05)
19:54 < hprmbridge> kanzure> make children cheap enough and people would make a lot more of them. one way to do this is vertical integration.
19:54 < hprmbridge> kanzure> this is why we need the human gigafactory
19:55 < fenn> there has been very little interest in creche technology and as a result the field is a primitive backwater
19:56 < hprmbridge> kanzure> creche?
19:57 < fenn> uh it's a heinlein thing, some sort of mix between https://en.wikipedia.org/wiki/Cr%C3%A8che_(zoology) and https://en.wikipedia.org/wiki/Child_care
19:58 < fenn> unfortunately (and perhaps causatively) all the examples i can think of are politically inflammatory
20:02 < muurkha> kibbutzim?
20:03 < fenn> it's not supposed to be a guessing game
20:03 < fenn> but yes that was one of them
20:04 < muurkha> I mean kibbutzim aren't politically inflammatory, are they?
20:04 < fenn> fuck if i know, can't say anything without stepping on a landmine these days
20:04 < jrayhawk> cyborg midwives are very trustworthy and competent when it comes to the ensuring the little ones grow big and strong
20:04 < muurkha> they aren't West Bank settlements
20:05 < fenn> where can i acquire a cyborg midwife
20:05 < muurkha> they were politically inflammatory 60 years ago
20:05 < fenn> top ten cyborg midwives in my area amazon review
20:06 < jrayhawk> the von braun hydroponics deck, mostly
20:06 < fenn> muurkha: notice the thing where i'm not engaging
20:06 < muurkha> curious
20:07 < fenn> well, other peoples' children is deeply political subject so i suppose the shitstorm can't be avoided
20:07 < fenn> unfortunately we can't get much traction on the live forever meme for some reason
20:08 < fenn> at least there's no shitstorm just talking about living forever, until you make progress anyway
20:10 < fenn> has anyone read the heinlein books talking about group marriage and its advantages? specifically related to economy of scale and economic robustness for the children
20:10 < fenn> i'm just not sure if i'm pointing at a visible moon or one below the horizon
20:11 < muurkha> no, but I'm going to visit some friends later this month whose household consists of four adults in romantic relationships, one child, and I think a dog
20:11 < fenn> do the four adults share responsibility for the child and dog?
20:12 < muurkha> yes
20:12 < fenn> well that's something then
20:12 < fenn> people used to do this thing called godparenting which was like a safety net but not government mediated
20:12 < muurkha> something like thirty children in Argentina have now been born with three parents on the birth certificate
20:13 < muurkha> godparenting was totally government-mediated
20:13 < fenn> church mediated
20:13 < muurkha> except when and where separation of church and state happened
20:13 < fenn> you didn't actually need the church to make it happen
20:14 < fenn> what does it mean to have three parents on a birth certificate?
20:14 < muurkha> r
20:14 < muurkha> they all share responsibility for the child from birth
20:14 < muurkha> -r
20:15 < muurkha> even if they aren't biologically related
21:07 < hprmbridge> nmz787> Children are time-expensive MUCH MUCH more than monetarily
21:09 < fenn> that's why you put them in a box with other children and robots
21:10 < fenn> i mean, um, childcare professionals. yeah, that's it.
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--- Log closed Fri May 12 00:00:58 2023