--- Log opened Thu Oct 20 00:00:52 2022
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04:25 < faceface> hi friends
04:26 < faceface> What is the fastest PCR machine you know?
04:33 < faceface> e.g. time to 30 rounds...
04:34 < faceface> I believe it's not enzyme limited, but rather heat cycle limited... not sure though
04:34 < faceface> (assuming your amplifying a small region of DNA for identification purposes that is)
04:45 < maaku> L29Ah: did they move from darcs to git because darcs itself sucked or because github/gitlab/etc. were better?
04:46 < maaku> to be clear I think everyone should use git, just like everyone should learn english
04:47 < maaku> it's a terrible fucking inconsistent bastard of a language, but it is the universal language we're stuck with
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05:55 < docl> I'm thinking one could make some overlay scripts so that fossil acts just like git
05:56 < docl> how many git commands does the typical developer use anyway? like 5?
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06:04 < kanzure> faceface: use a sso fast kit?
06:05 < kanzure> https://www.youtube.com/watch?v=Bkv8c978DWU
06:05 < Muaddib> [Bkv8c978DWU] Bio-Rad GTCA Song (2:20)
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06:29 < kanzure> .wik invention secrecy act
06:29 < saxo> Article not found: https://en.wikipedia.org/wiki/Invention_secrecy_act gave 404 | Searched en for 'invention secrecy act' | https://en.wikipedia.org/wiki/No_result_found gave 404 | Searched en for 'No result found'
06:30 < kanzure> .wik Invention Secrecy Act
06:30 < saxo> "The Invention Secrecy Act of 1951 (Pub.L. 82–256, 66 Stat. 3, enacted February 1, 1952, codified at 35 U.S.C. ch. 17) is a body of United States federal law designed to prevent disclosure of new inventions and technologies that, in the opinion of selected federal [...]" - https://en.wikipedia.org/wiki/Invention_Secrecy_Act
07:02 < faceface> kanzure: err...
07:06 < kanzure> faceface: how's it going?
07:06 < faceface> hehe
07:06 < faceface> Good thanks
07:06 < faceface> Talking to some guys doing 'ultrafast' pcr with a propietary heating system... Just researching their competition
07:07 < faceface> https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/926410/Understanding_Cycle_Threshold__Ct__in_SARS-CoV-2_RT-PCR_.pdf <- figure 1 shows 'cycles', but how long is each cycle?
07:13 < faceface> https://www.thermofisher.com/uk/en/home/life-science/cloning/cloning-learning-center/invitrogen-school-of-molecular-biology/pcr-education/pcr-reagents-enzymes/pcr-cycling-considerations.html <- looks promising, reading now
07:15 < faceface> The initial denaturation step is commonly performed at 94–98°C for 1–3 minutes. ... that's slower than 30 cycles according to the guys I'm talking to!
07:24 < faceface>  typical extension time for Taq DNA Polymerase is 1 min/kb
07:25 < kanzure> is that true? google tells me taq polymerase is 2-4 kilobases/minute
07:26 < faceface> out of date I guess... 
07:26 < kanzure> well it's not like Taq pol has changed
07:26 < faceface> Seems the thermal cycle itself is a bottleneck (which is what the guys I'm talking to claim (indirectly))
07:26 < faceface> it's advertising, so the next paragraph is probably, "however, our kits..."
07:27 < kanzure> i think the lava amp PCR people were working on a fast thermocycler of some kind. obsolete by now.
07:28 < faceface> I've forgotten already... The figure 1 in the above PDF shows 'relative Flurescence' as the readout... how does the flourescence develop?
07:28 < faceface> what changes as the product accumulates?
07:28 < faceface> Yeah, these guys are using gold nanoparticles and lazers to rapidly heat a few uL
07:29 < faceface> Their initial data looks sound, just a question of sensitivity
07:39 < faceface> https://www.nature.com/articles/s41565-022-01175-4 I wonder where the IP is supposed to be
07:39 < kanzure> smaller volumes are easier to rapidly heat and cool
08:01 < faceface> anybody got this:     https://doi.org/10.1039/D0AN02496A
08:01 < faceface> no in s hub
08:04 < faceface> found on gugu
08:15 < kanzure> gugu?
08:18 < kanzure> .title https://www.meetup.com/vitadao/events/287981908/
08:18 < saxo> [online] 2nd VitaDAO Crypto meets Longevity Symposium, Thu, Oct 20, 2022, 3:00 PM   | Meetup
08:18 < kanzure> (running now)
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14:19 < fenn> faceface: idaho systems thermocycler heats thin glass tubing with a light bulb and flows air over them with a fan to cool, it's faster than peltier block systems but you have to heat seal the tubing with a flame, which is actually quite easy
14:20 < muurkha> jesus fuck, why has nobody thought of that before?
14:20 < fenn> "30 Cycles in 10 Minutes"
14:20 < fenn> i guess they went out of business
14:20 < muurkha> HOW?
14:21 < fenn> it's not THAT fast
14:23 < fenn> i've used it, and it does finish in 10 minutes, but i mean that's not a mind blowingly fast PCR reaction in my opinion
14:27 < fenn> faceface: from your paper, "The average run time, including all the steps of RT-PCR thermocycling, was 17.9 ± 0.1 min."
14:30 < docl> https://wikimapia.org/15675552/Idaho-Technology-Inc
14:31 < docl> apparently they moved to salt lake. their website points to a differently named company now
14:31 < fenn> "Unless otherwise noted, for the plasmonic instrument, thermocycling conditions were as follows: reverse transcription for 2–5 min at 45–50 °C, followed by initial denaturation for 10–20 s at 95 °C. Next, the reaction cycled 40–45 times between a low temperature (58–60 °C) held for 0–8 s and a high temperature (91–97 °C) held for 0–1 s."
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15:45 < kanzure> oh weird, a light bulb is faster than a peltier block heater?
15:53 < fenn> and for unknown reasons this technology has disappeared
15:54 < fenn> the machine also has a temperature sensor that's calibrated to match the thermal properties of the glass tubes
15:55 < fenn> i suppose light bulb technology has also disappeared...
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15:57 < fenn> "Unlike the typical Hollywood CGI depictions of asteroid impacts, where an extraterrestrial charcoal briquette gently smolders across the sky, in the Yucatan it would have been a pleasant day one second and the world was already over by the next."
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16:21 < muurkha> hmm, how much damage would an asteroid going 20 km per second do?  that would give you like five seconds of brilliant light before impact, right?
16:23 < muurkha> kanzure: what's faster than the peltier block heater is the air
16:28 < L29Ah> muurkha: thin film resistor in aerogel
16:30 < fenn> the light bulb (and radiative heating) is faster too
16:30 < fenn> it could use hot air to the same effect, but that would use more energy
16:31 < muurkha> oh, thanks, fenn 
16:31 < muurkha> I assumed it was using convection to get the heat from the bulb to the tube
16:32 < fenn> originally PCR was done by dunking tubes into hot and cold water baths. i wonder why that isn't still used more often
16:32 < muurkha> L29Ah: thin film resistors in aerogel can heat up fast, but they can't cool down fast
16:32 < L29Ah> remove aerogel, blow air
16:32 < fenn> a bucket of ice water has phenomenal cooling rates
16:33 < L29Ah> yes
16:34 < fenn> probably you want a bead bath instead of a hot water bath, to eliminate all the steam condensation
16:34 < fenn> or maybe some combo of lazers and ice water would work better
16:35 < fenn> glass capillary tubes also eliminates the problem of water evaporation changing the reaction mix concentration
16:35 < L29Ah> laser sound like a good way to heat a laser
16:36 < fenn> (block heater style machines use a heated lid to prevent condensation)
16:37 < fenn> yeah one of those 500W halogen cylindrical tube light bulbs closely surrounded by glass capillary tubing seems pretty efficient
16:37 < fenn> not that anyone really cares about the energy efficiency of PCR reactions
16:37 < fenn> a microwave oven would be even beter
16:39 < fenn> microwave ovens tend to have hot spots, vs a light bulb which is a point or line source and thus easier to think about
16:40 < fenn> i think most of the magic built into the idaho technologies thermocyclers was the temperature calibration
16:41 < muurkha> fenn: metglas is made by a non-ice-water process
16:41 < fenn> maybe there is some way to do closed loop temperature feedback with thermal IR sensors
16:41 < fenn> organic crystals with known melting points
16:42 < muurkha> hm
16:42 < fenn> just for calibration anyway
16:42 < muurkha> or sal mirabilis
16:42 < fenn> the thing is you want it suspended in water to match the thermal conduction from the glass tubing walls
16:43 < docl> just thought of an interesting way to use orbital mirrors: make them only reflect UVC, and create high pressure zones to steer hurricanes by heating the upper atmosphere to make high pressure zones
16:49 < fenn> cool i didnt know about this trick: "If two substances melt at the same temperature, a mixed melting point determination can reveal if they are one and the same substance. The fusion temperature of a mixture of two components is usually lower than that of either pure component. This behavior is known as melting point depression."
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17:05 < muurkha> can *usually* reveal
17:05 < muurkha> melting point depression doesn't always happen
17:06 < fenn> sure
17:07 < fenn> if you're just confirming that a thing is what it says it is, this is a quick and easy way to double check
17:14 < docl> well it's how they vitrify people in cryonics. mix something else with the water so the melting/freezing point is low enough that you can reach the glass transition temperature
17:15 < docl> .wik Colligative_properties
17:15 < saxo> "In chemistry, colligative properties are those properties of solutions that depend on the ratio of the number of solute particles to the number of solvent particles in a solution, and not on the nature of the particles present." - https://en.wikipedia.org/wiki/Colligative_properties
17:17 < docl> my understanding is the rabbit kidney experiment used freezing point depression to a point above the glass transition point, so it was more complicated. this is where ice blocking polymers come in useful, as a small concentration of that has an outsized effect
17:18 < docl> that is, the state temperature could then be lowered below the freezing point without ice formation, which is known as supercooling
17:18 < docl> .yt _9N-Y2CyYhM
17:18 < docl> .t https://www.youtube.com/watch?v=_9N-Y2CyYhM
17:18 < saxo> Watch supercooled water freeze - YouTube
17:18 < Muaddib> [_9N-Y2CyYhM] Watch supercooled water freeze (0:35)
17:19 < docl> as the video shows, you can supercool water if you are careful and it's very pure
17:23 < docl> the colligative property of lowering the point at which freezing happens is important/complementary to the ice blockers though. problem is of course that mixing stuff with water to make it more concentrated than cytosol tends to make a lot of osmotic pressure which tries to pull water out of the cells. (the main reason ice formation is so bad is that crystallization purifies the water and causes this 
17:23 < docl> to happen suddenly)
17:47 < muurkha> hm
17:52 < docl> so then the process involves ramping up the concentration at a rate where the bulk solutes (EG, glycerol, etc) can enter cells fast enough that it won't damage the cytostructure. alcor has this worked out, but CI uses a simpler to implement method of stepped perfusion (well, last I checked). some kind of nanopore pretreatment could really help this a lot
18:49 <+gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=bbb1ec3a Bryan Bishop: transcript: austin bitcoin developers seminar 33 >> http://diyhpl.us/diyhpluswiki/transcripts/austin-bitcoin-developers/2022-10-20-socratic-seminar-33/
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--- Log closed Fri Oct 21 00:00:55 2022