--- Log opened Mon Jun 26 00:00:41 2023
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16:13 < kanzure> hmph
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20:52 < hprmbridge> Eli> Has anyone read the most recent nick lane book? I’ve kind of been surprised by the idea that cancer is not just about genetics, but a permissive environment from the Krebs cycle running in reverse, causing biosynthesis of carbon building blocks for cancer growth: https://www.quantamagazine.org/a-biochemists-view-of-lifes-origin-reframes-cancer-and-aging-20220808/
20:54 < hprmbridge> Eli> So, he claims the ETC has issues with age, this results in ROS leakage from complex one, epigentic signaling takes place resulting in the Krebs cycle going into reverse, and the Warburg effect kick off.
21:05 < kanzure> eli: did you see https://diyhpl.us/~bryan/papers2/ai/The%20evolution%20of%20self-replicating%20computer%20organisms%20-%20A.%20N.%20Pargellis.pdf
21:12 < hprmbridge> Eli> In general, the world of computational biology, bioinformatics, and nowadays, systems bio is really cool. In a brief glance of this paper, my concern would be “how well does it translate to real life”? Life has to form in a way that is thermodynamically favorable. So, there will be major constraints on how life could possibly form. Ie, Biophysics guides random chance.
21:14 < hprmbridge> Eli> Darwin didn’t understand biophysics. That’s why he would never have been able to understand the Cambrian explosion
21:45 < muurkha> I don't think so
21:47 < muurkha> I mean there's almost a billion years between ocean formation and the oldest fossils
21:52 < muurkha> 1.4 billion cubic kilometers of ocean, which is 1.4e21 liters, which is almost 5e46 molecules
21:52 < muurkha> and conservatively billions of earthlike planets in habitable zones with oceans
21:52 < muurkha> per galaxy, and 200 billion galaxies in the observable universe
21:59 < hprmbridge> nmz787> fenn what's the industrial warehouse very-local RFID tag system that you said was hard to get into because the reader was high cost and you had to buy like 10,000 tags at once?
22:00 < hprmbridge> nmz787> for product locating in a warehouse
22:01 < muurkha> you can get nonliving "cells", micelles sequestering a hydrophobic interior, by stirring mineral oil into soapy water; lipid bilayers aren't far fromm that
22:02 < muurkha> the micelle-forming agent doesn't have to be s
22:02 < muurkha> the micelle-forming agent doesn't have to be as complex as potassium stearate; anything amphiphilic will do
22:12 < fenn> nmz787: it's been a while since i looked at this. 900 MHz UHF tags, wikipedia says EAN which sounds vaguely familiar. they cost $0.05 per tag and have a dozen meter range
22:13 < fenn> the reader was in the $1000 range
22:15 < fenn> also the base stations/readers don't specifically give you 3d coordinates, they report something like signal strength, so you have to get a few of them and do the trilateration math yourself
22:15 < fenn> there was a robot company that offered a mapping service...
22:16 < fenn> 2022-09-08.log: < fenn> precise RFID localization robot from http://fellowai.com https://vimeo.com/480425563
22:17 < fenn> take all this with a grain of salt
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22:30 < fenn> there are now $50 UHF "card readers" available on ebay
22:31 < fenn> it might make sense to try one of those with different antennas
22:32 < fenn> zebra.com sells big rolls of tags but i'm not sure about compatibility
22:33 < muurkha> okay I guess actually sodium laurate is about the simplest amphiphilic molecule
22:37 < hprmbridge> Eli> I’m not sure we are disagreeing. There is a huge probability space. However, it is a constrained space. We don’t have any idea how multicellular life could be successful with oxygen for example. It’s not thermodynamically possible for life to be eukaryotic without oxygens large  electronegativity pulling electrons through the transport chain. In other words, genetic randomization is constrained
22:37 < hprmbridge> Eli> and driven by energy flow. All of our evidence points to this fact.
22:39 < hprmbridge> Eli> We even see this with non-life that forms complex systems. The larger the gradient, the more negentrophy is available to do useful work. Eg, a hurricanes size is due to the size of the gradient it dissipates
22:42 < hprmbridge> Eli> This is also why there are more trophic levels at the equator than at the poles
22:42 < fenn> nmz787: these both claim to support 18000-6C: https://www.ebay.com/itm/391864788048 https://www.ebay.com/itm/224252557401  cheap enough to try and see if it works
22:42 < muurkha> I feel like evolution from LUCA to eukaryotes is not particularly challenging to explain
22:43 < muurkha> the interesting question is how LUCA developed from, like, choline and uracil and benz[a]pyrene and crap like that
22:45 < hprmbridge> Eli> Right, and we can’t explain multicellular life without the Great Oxygenation Event, which killed most of life on earth
22:45 < muurkha> but I feel like in a sense life is almost inevitable.  you'll have some molecules that are autocatalytic, and others that aren't
22:45 < hprmbridge> Eli> So, biophysics is the bottleneck that Mendelian randomization works within
22:45 < muurkha> the ones that are autocatalytic will increase in concentration
22:47 < muurkha> some of those molecules will have some kind of heritable variation, which enables chance to optimize them to be more autocatalytic
22:48 < muurkha> some of those systems will have some kind of membrane, while others don't; the ones with membranes will get optimized better because their heritable variation is more independent
22:48 < hprmbridge> Eli> Or maybe membranes and catalysis came before rna
22:49 < muurkha> yeah, I don't mean RNA
22:49 < hprmbridge> Eli> It’s an open question
22:49 < muurkha> RNA probably happened at a much later stage than what I'm talking about, I think
22:49 < muurkha> but yes, it's certainly an open question
22:50 < muurkha> a modern analogyy might be corporations; they have membranes but only the beginnings of heritable variation
22:51 < muurkha> they're great at increasing external entropy while decreasing internal entropy because they have other optimizers in the loop
22:56 < hprmbridge> Eli> Yeah. I think it’s even simpler than that maybe. Just taking physics you realize how much complex systems are nothing more than a heat engine. Look at the definition of a heat engine and then look at a cell. It’s not a metaphor. It’s the same exact thing
22:57 < hprmbridge> Eli> Just look at that bad boy! https://cdn.discordapp.com/attachments/1064664282450628710/1123130079413800981/IMG_0638.png
22:58 < hprmbridge> Eli> I’m sure people have applied it to the Krebs cycle
23:00 < muurkha> yes, well, close enough anyway
23:01 < muurkha> ultimately nearly all biological energy stems from photosynthesis, which harnesses the temperature difference between Sun and Earth to make sugar
23:03 < muurkha> cellular metabolism mostly isn't literally a heat engine because very few cells are big enough to maintain a useful temperature difference
23:03 < muurkha> (and those that do can't evolve very fast)
23:05 < muurkha> but cellular metabolism is dissipative chemical reactions, and those happen when they reduce the non-thermal energy of the system, in this case the Gibbs free energy
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23:08 < muurkha> but implicitly the question is why so many of the chemical reactions we see are self-reproducing ones with heritable variation even though such a thing seems to have a low a priori probability
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23:08 < fenn> because it only has to happen once
23:09 < muurkha> well, in a strong form
23:09 < muurkha> and we could also retreat into anthropic arguments 
23:09 < fenn> i think you will find life crawling around on many surfaces in the universe
23:10 < muurkha> but I think it's totally plausible for much weaker, more a priori probable forms to develop into the strong form we see
23:11 < muurkha> if it turns out that life is crawling around on many surfaces, it is probably also in places like plasma vortices
23:12 < fenn> brown dwarfs are cold enough for complex organic molecules to form
23:15 < muurkha> neat
23:38 < muurkha> an interesting thing in looking back from our vantage point about 4 billion years later is that LUCA has eliminated virtually every trace of the presumably simpler cells preceding it
23:38 < darsie> WISE 0855−0714 is also the coldest object of its type found in interstellar space, having a temperature in the range 225 to 260 K (−48 to −13 °C; −55 to 8 °F).[1]
23:39 < muurkha> we could imagine GPT-5e9 pondering how implausible it would be for semiconductor fabs could have arisen spontaneously
23:41 < muurkha> much less VLSI place-and-route algorithms and HDL synthesis
23:42 < muurkha> and wondering what sort of processes they might have originally arisen from
23:45 < muurkha> darsie: presumably it's hard to find objects that cold?
23:46 < muurkha> even if there are a lot of them
23:47 < darsie>  the discovery of which was announced in April 2014 by Kevin Luhman using data from the Wide-field Infrared Survey Explorer (WISE).[1]
23:47 < darsie> Wide-field Infrared Survey Explorer (WISE, observatory code C51, Explorer 92 and SMEX-6) is a NASA infrared astronomy space telescope
23:48 < darsie> Making a space IR telescope is hard.
23:51 < darsie> We might find such objects in Webb pics.
23:53 < darsie> Just like we serendipitously find small asteroids in Webb pics.
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--- Log closed Tue Jun 27 00:00:06 2023