--- Log opened Tue Jun 27 00:00:06 2023
--- Day changed Tue Jun 27 2023
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00:27 < hprmbridge> Eli> Life is a heat engine. Your body breaks down macros to release energy to do work. Waste heat is generated. This happens at the body level. So it has to happen at the cellular level, somewhere, no?
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03:58 < nsh> .t https://www.khanacademy.org/science/ap-biology/cellular-energetics/cellular-energy/a/atp-and-reaction-coupling
03:58 < EmmyNoether> ATP cycle and reaction coupling | Energy (article) | Khan Academy
04:51 < hprmbridge> kanzure> "king of clones" netflix documentary https://twitter.com/antonioregalado/status/1673384259141382147
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09:56 < fenn> @eli the ATP synthesis reaction is driven by a proton gradient across the cell membrane. the protons are pumped out with chemical energy against an osmotic pressure and also an electric field gradient, and then flowed back in through a turbine later to synthesize a different kind of chemical energy, ATP. is a capacitor a heat engine? is a battery? a balloon? biology is somewhere in between. you
09:56 < fenn> could think of the electron transport chain as a staged combustion/decompression to reduce the energy/pressure per reaction step to a manageable level: https://www.news-medical.net/image.axd?picture=2018%2F7%2Fshutterstock_277344065.jpg
09:57 < fenn> there are other chemical reaction networks that don't fit so neatly into the heat engine paradigm
10:01 < fenn> we can tell if a cell is "alive" or "dead" by whether its cell membrane is polarized, with polarization-sensitive dyes. basically, once you lose that pressure it's very difficult to restart the engine
10:03 < fenn> maybe "on" or "off" is a better terminology, since a depolarized cell is not anywhere near information theoretically dead
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11:54 < kanzure> do we have an actual mechanical self-replication plan yet or do we still only have naturally evolved replicators
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12:01 < fenn> nobili and pesavento described a cellular automaton that reproduced from tape
12:02 < fenn> reality is a lot noisier and more complicated
12:06 < fenn> https://www.youtube.com/watch?v=CMt8vspQRa4&t=2m30s
12:06 < fenn> i remember this being more interesting to watch it run
12:09 < hprmbridge> kanzure> an industrial self-replicator is the only way for america to get back all the machine shop capability and make up for loss ground.
12:10 < fenn> the machines still exist, they have just been made economically unviable
12:12 < fenn> USA could annex canada, that would be one way to get more automated manufacturing capability
12:12 < fenn> and there is a lot of, uh.. less automated manufacturing capability in mexico
12:24 < fenn> ah i figured out why chinese and indian factories always have dark green floors. it's to hide the blood stains
12:52 < docl> I wonder if those 2D replicators could be placed in slightly noisy models and evolved to be more noise tolerant over time. maybe repeat the process several times and look for commonalities in the results
12:56 < fenn> first you'd have to have simulators that are efficient and performant enough to be capable of running large numbers of models
12:56 < fenn> is hashlife capable of running millions of large systems like that thing i just showed?
12:58 < fenn> i guess kanzure was talking about seed factories, not nanotech?
12:59 < fenn> ugh everything's broken
13:04 < fenn> i guess this is all that's left of the project: https://en.wikibooks.org/wiki/Seed_Factories
13:10 < fenn> he really should have hired an artist
13:22 < hprmbridge> nmz787> Is there any reason, besides no google results, that it couldn't be done with an rtlsdr or some other existing opensource radio workbench (maybe the phased array stuff, but that sounds pricey)
13:23 < hprmbridge> nmz787> https://www.rtl-sdr.com/ksdr/
13:24 < hprmbridge> nmz787> https://www.reddit.com/r/RTLSDR/comments/6ueuq9/anyone_tried_making_a_phased_array/
13:25 < hprmbridge> nmz787> https://www.crowdsupply.com/krakenrf/krakensdr#products
13:25 < hprmbridge> nmz787> $400 buy it now
13:38 < muurkha> fenn: what was there before of the project other than the wikibook?
13:40 < muurkha> Eli: it sounds like you're unclear on the concept of "heat engine".  I recommend reading https://en.wikipedia.org/wiki/Heat_engine and, say, https://en.wikipedia.org/wiki/Phosphoric_acid_fuel_cell#Advantages_and_disadvantages to understand th issues a little bit better
13:42 < muurkha> nmz787: what are you trying to do with an rtlsdr?  presumably not seed factories
13:55 < hprmbridge> nmz787> Just find stuff around the house, lab, workshop
13:56 < hprmbridge> nmz787> My workshop is about 2000sqft and about 1/4 or 1/3 is shelving at this point, full of various parts or tools
13:56 < hprmbridge> nmz787> If I wanted to invite people in to help out, it'd be good for locating things, asset tracking (getting and putting things away properly, theft/forgetfulness prevention)
14:03 < muurkha> oh, RFID?
14:04 < muurkha> Eli: in particular "heat engine" does not mean "engine which produces heat" :)
14:08 < hprmbridge> nmz787> https://skyrfid.com/Mid-Range_RFID.php#:~:text=EPC%20Class%201%20Gen%202%20Tags
14:08 < hprmbridge> nmz787> Iso 18000-6c==EPC C1G2==EPC class 1 gen2
14:09 < hprmbridge> nmz787> """Generic longevity specifications for Gen 2 IC's are 40 - 50 year data retention and 100,000 write cycles
14:09 < hprmbridge> nmz787>
14:09 < hprmbridge> nmz787> A pallet tag can have a read distance of over 10 meters when attached to the cardboard or wooden case, but when attached to a metal shelving support the pallet tag has a read distance of zero to 0.5 meters.
14:09 < hprmbridge> nmz787>
14:09 < hprmbridge> nmz787> For attaching to metal objects a metal mount tag should be used and depending on the type of metal and the type of metal mount tag you can achieve a read range of 10 meters or more when attached to metal. Each metal object does provide a different metal mount tag requirement and depending on the overall environment the reader frequency may need to be changed in order to achieve the best read rate
14:09 < hprmbridge> nmz787> and distance.
14:09 < hprmbridge> nmz787>
14:09 < hprmbridge> nmz787> Tags can also be orientation sensitive due to the inlays used in making the final tag.  Some tags can only be read in a vertical or horizontal position, some tags will only read on the edge, and then some tags can be read regardless of the orientation.  Just because your friend uses XYZ tag does not mean that this is the best tag for your application."""
14:39 < fenn> you'd have to reimplement the entire RFID protocol stack
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14:41 < fenn> the metal mount "tag" is just a piece of plastic to stand off from the metal slightly
14:43 < fenn> about 1 cm standoff distance. it's not something you want to put on an excavator bucket
14:44 < fenn> when dealing with hackerspaces i always wanted a system where every exit doorway was lined with RFID readers and you had to tag in and tag out, so whoever took the widget last was recorded as having done so, and at least there's an answer as to where the thing went rather than just mysteriously disappearing
14:46 < fenn> often things get lost and misplaced outside the space, people don't realize they forgot a tool at a worksite or event, and then it's just there any nobody at the other place knows where it came from. it's not really theft
14:46 < fenn> but it you say "hey bill, where's the widget" it's likely to stir some memories
14:47 < fenn> if the door is lined in RFID readers, tagging in and out consists of just walking through the door
14:48 < fenn> the problem is those stupid short range readers
14:48 < fenn> hopefully we have moved past that as a society by now
14:49 < muurkha> hopefully we have moved past stupid short range readers as a society by now?
14:49 < fenn> yes
14:49 < fenn> it was always a bad idea
14:49 < fenn> it's inconvenient, and if you're relying on obscurity of your data for security you're doing it wrong
14:50 < muurkha> sometimes it's convenient
14:50 < fenn> you have to take the tag out of your pocket and hold it up to a reader, or if you're lucky you can hump the doorway and try not to spill your coffee while doing so
14:50 < muurkha> I mean it's nice to know that the RFID tag you're reading is the one on the object you're holding in your hand and not one on the shelf across the room
14:51 < fenn> signal strength is a thing
14:51 < muurkha> yes, for stupid short-range readers
14:51 < fenn> even better would be to use beamforming or trilateration to limit the activation zone
14:52 < fenn> signal strength is a thing for long range readers too
14:52 < fenn> i mean you can put the reader at the doorway and say "signal strength must be greater than 1 dB" or whatever
14:53 < fenn> (i can never figure out how radio signal strength is measured tbh)
14:55 < muurkha> typically we use dBm
14:55 < muurkha> -20 dBm, -40 dBm, -80 dBm
14:55 < muurkha> 0 dBm is a milliwatt, which is a hell of a lot of signal to receive
14:56 < muurkha> -30 dBm is a microwatt, -60 dBm is a nanowatt, -90 dBm is a picowatt
14:56 < muurkha> beamforming works really well for reading short-range RFID tags at long range
14:56 < fenn> dubious - discuss
14:59 < muurkha> [bluesniper]
15:02 < fenn> proof of concept hack is not the same as "works really well"
15:02 < fenn> also a yagi is not beamforming
15:07 < muurkha> the reason people use directional antennas such as yagis is because they form a beam by running multiple antenna elements in a fixed phase relationship to one another.  it's true that in a yagi, or in a parabolic mirror, the signal reaches the various elements through the air rather than through wires
15:08 < muurkha> but the principle is exactly the same as in actively driven phased arrays
15:08 < muurkha> I didn't appreciate this until I read the Feynman Lectures on Physics, but it's true
15:12 < hprmbridge> Eli> So, I’m seeing very different answers on the internet regarding whether or not humans and respiration are actually a heat engine. Specifically, respiration is exothermic, and heat generated is used by the body to help maintain homeostasis. So, that argument says humans are heat engines
15:14 < muurkha>   21:04 < muurkha> Eli: in particular "heat engine" does not mean "engine which produces heat" :)
15:15 < muurkha> it's not surprising that you've found people being wrong on the internet; that's kind of what it's for
15:16 < muurkha> respiration is exothermic in ectotherms too
15:19 < muurkha> reptiles are ectotherms that use exactly the same respiration reactions the humans do, being quite closely related
15:21 < fenn> "Since fuel cells and batteries can generate useful power when all components of the system are at the same temperature, they are clearly not limited by Carnot's theorem, which states that no power can be generated when T_H = T_C ... Carnot's theorem applies to engines converting thermal energy to work, whereas fuel cells and batteries instead convert chemical energy to work."
15:22 < fenn> cells are so small you're never going to get a large temperature gradient
15:25 < fenn> you don't have to throw out all of thermodynamics just because it's not a heat engine
15:27 < muurkha> indeed, the Gibbs free energy that actually drives life is a wholly thermodynamic concept
15:27 < muurkha> what I said above is that some cells are large enough to hypothetically have a large enough temperature difference to do work, but such large cells evolve very slowly
15:29 < fenn> i must have missed that
15:30 < muurkha> 06:03 < muurkha> cellular metabolism mostly isn't literally a heat engine because very few cells 
15:30 < muurkha>                  are big enough to maintain a useful temperature difference
15:30 < muurkha> 06:03 < muurkha> (and those that do can't evolve very fast)
15:30 < muurkha> 06:05 < muurkha> but cellular metabolism is dissipative chemical reactions, and those happen 
15:30 < muurkha>                  when they reduce the non-thermal energy of the system, in this case the Gibbs 
15:30 < muurkha>                  free energy
15:32 < fenn> ty
15:34 < hprmbridge> Eli> I’m not sure this is a simple question to answer. Check out this response here: https://physics.stackexchange.com/a/59367
15:35 < hprmbridge> Eli> Also, mitochondria apparently operate at 50 C: https://pubmed.ncbi.nlm.nih.gov/29370167/
15:39 < muurkha> that answer says "Peter Shor's answer that humans aren't heat engines, but are instead powered by chemical energy, is entirely correct." which seems like a simple answer to me
15:40 < muurkha> mitochondria can operate successfully over a wide range of temperatures
15:40 < muurkha> well.  wide to humans
15:40 < fenn> eli, it's a very well written answer and you should keep reading it until you understand it all
15:46 < fenn> there's a similar conceptual problem of estimating the "temperature" of an accelerated ion
15:48 < fenn> 50C is nothing, we can calculate the expected thermodynamic efficiency that delta-T at a couple percent
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15:49 < hprmbridge> Eli> Is heat energy released via the Krebs cycle used to keep the body at homeostasis not useful work? We are going from a sink to a source and it keeps us alive and at homeostasis
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15:49 < fenn> i mean it's surprising mitochondria are that hot, but it's not evidence that they're generating work by extracting energy from a temperature difference
15:50 < fenn> whether something keeps you alive or not is not how you define "work"
15:51 < fenn> work is a kind of energy defined as force through a distance
15:52 < hprmbridge> Eli> Right, but would the ability of the body to apply force be the same at a different temperature?
15:52 < fenn> yes
15:53 < fenn> you can melt a gasoline engine, or freeze all the oil in it so it won't turn over. this is not relevant
15:54 < hprmbridge> Eli> But there’s an energy cost
15:54 < fenn> what energy cost?
15:55 < hprmbridge> Eli> Takes more energy to start up the cold engine
15:56 < fenn> material temperature limits are usually what put working fluid limits on heat engines in practice, which limits the attainable efficiency
15:58 < fenn> the heat sink of a gasoline engine is the atmosphere
15:59 < fenn> the fact that it has coolant is an engineering choice
15:59 < fenn> same thing with an animal
16:00 < fenn> the fact that something has a heat sink doesn't mean it's a heat engine
16:01 < hprmbridge> Eli> Right, because it also needs to perform work
16:04 < muurkha> no, heat energy released used to keep the body at homeostasis is not "useful work" in the thermodynamic sense, which is, as fenn said, the line integral of force over distance
16:06 < muurkha> it seems like you are taking divulgations of scientific terms from the science-popularizer literature and interpreting them as if they were normal phrases rather than jargon (improper nouns)
16:06 < muurkha> having a heat sink and performing work also does not make something a "heat engine"
16:06 < hprmbridge> Eli> I have taken physics
16:07 < muurkha> and forgotten it :)
16:07 < muurkha> a "heat engine" is specifically an engine that converts a temperature difference into "useful work" in the above sense
16:08 < fenn> don't badger the student
16:09 < fenn> no offense to badgers
16:09 < muurkha> that is not what respiration does, except in the sense that Jaynes explains in his excellent paper in which a molecule containing chemical energy can be at several thousand degrees
16:10 < muurkha> sorry
16:13 < hprmbridge> Eli> I guess I don’t know enough about the intersection of physics, biology, and chemistry at the quantum level to say what I want to say
16:17 < fenn> ok this is a cool protein synthesis animation (4x realtime) https://www.youtube.com/watch?v=2dV5s6v2v8Q&t=9s
16:23 < fenn> wah. all these other molecular biology animations use crystallography states for the animation rather than molecular dynamics simulations
16:25 < fenn> i guess this is the best you're going to get https://www.youtube.com/watch?v=kXpzp4RDGJI
16:25 < muurkha> that's pretty cool
16:25 < fenn> .t
16:25 < EmmyNoether> ATP synthase in action - YouTube
16:30 < fenn> the rotating subunit of ATP synthase has a lot of similarities to a heat engine, as it's driven by a proton gradient, which is very similar to the pressure gradient in some heat engine cycles
16:37 < muurkha> yeah, you could almost say it's an osmotic pressure gradient, except that what's diffusing through the membrane is protons and not water molecules
16:39 < fenn> it is literally an osmotic pressure gradient
16:39 < fenn> it's also an electrical charge similar to a capacitor
16:39 < muurkha> is it?  I mean it doesn't care about other solutes, just hydroniums, right?
16:40 < fenn> uh.. like everything else?
16:40 < muurkha> I've heard that before, but the video seems to disagree; it says it's a proton concentration gradient, not a charge gradient, that drives the proton flow
16:41 < fenn> the protons stick to the outer surface and anions stick to the inner surface of the membrane
16:42 < fenn> they're attracted by the small electric force which is still transmitted through the membrane, which is an insulator
16:42 < muurkha> oh, well, I guess that would produce quite a proton concentration gradient, wouldn't it?
16:43 < fenn> "proton concentration gradient" is trying to communicate the fact that there are more protons on one side than the other
16:43 < muurkha> right
16:43 < muurkha> which is a result of the charge separation you're describing
16:43 < muurkha> rather than, for example, because a bunch of acetic acid is dissolved on the other side of the membrane
16:44 < fenn> the difference is because protons were pumped out earlier by the electron transport chain proton pumps
16:44 < muurkha> right
16:44 < muurkha> the charge separation also would result on a force on the protons that drive them into the pump
16:45 < muurkha> which is another force above and beyond the concentration gradient which drives simple diffusion
16:45 < muurkha> (and then, perhaps, sucks them out of the pump on the other side)
16:45 < fenn> yes, you get it
16:45 < muurkha> the ATP synthase pump, I mean, not the proton pump that created the charge separation in the first place
16:46 < fenn> i call it a turbine
16:46 < muurkha> that's probably a better term
16:48 < fenn> perhaps superkuh can educate us about voltage sensitive dyes
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21:22 < hprmbridge> ml3> Met with Elena Sergeeva, thanks so much for the recommendation!
21:25 < hprmbridge> ml3> She mentioned that some of you might be interested in investing in a wetware computing project I‘m working on
21:25 < hprmbridge> ml3>
21:25 < hprmbridge> ml3> If any of you are or just want to learn more just dm me
21:28 < fenn> i think we'd all generally be interested if you want to talk about it in the channel
21:28 < fenn> no pressure
--- Log closed Wed Jun 28 00:00:43 2023