--- Log opened Sun Jun 28 00:00:03 2020
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03:50 < L29Ah> https://www.sciencedaily.com/releases/2020/06/200625102540.htm
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07:33 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=f8110f2b Michael Folkson: Add Luke at LA BitDevs on Segwit PSBT vuln >> http://diyhpl.us/diyhpluswiki/transcripts/la-bitdevs/2020-06-18-luke-dashjr-segwit-psbt-vulnerability/
07:33 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=3b2921ec Michael Folkson: Add Sydney June Socratic Seminar >> http://diyhpl.us/diyhpluswiki/transcripts/sydney-bitcoin-meetup/2020-06-23-socratic-seminar/
07:33 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=3a4c491a Bryan Bishop: Merge pull request #122 from michaelfolkson/add-luke-segwit-psbt >> http://diyhpl.us/diyhpluswiki/
07:33 < gnusha> https://secure.diyhpl.us/cgit/diyhpluswiki/commit/?id=efd80667 Bryan Bishop: Merge pull request #123 from michaelfolkson/add-sydney-june-socratic >> http://diyhpl.us/diyhpluswiki/
07:41 < kanzure> .title https://github.com/ihh/dnastore
07:41 < saxo> GitHub - ihh/dnastore: Software for error-tolerant coding of information into DNA sequences using finite-state transducers.
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08:48 < kanzure> "Synthetic ribosomes: Making molecules that make molecules" https://www.tandfonline.com/doi/pdf/10.4161/bioe.23640 (2013)
08:49 < kanzure> was trying to find an entirely protein-based ribosome and found that instead.
08:53 < kanzure> "Their machine comprises a rotaxane—a ring threaded on a rod—in which the ring bears a pendant thiol that can pluck amino acids off the rod; the terminal nitrogen then wraps around to form a peptide bond and liberate the thiol for further reaction. The system was able to link three amino acids in order from the preassembled rod."
08:53 < kanzure> "Sequence-specific peptide synthesis by an artificial small-molecule machine" https://science.sciencemag.org/content/339/6116/189.abstract
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09:49 < kanzure> 3d printing of modular protein backbone components (for physical hand models) https://www.liebertpub.com/doi/pdfplus/10.1089/3dp.2019.0121
09:50 < bsm117532> Diamondoid, atomic precision nanotechnology is not likely to go anywhere outside lab curiosities. Entropy is a bitch and at room temperature your machine is bouncing around in mud like a ping-pong ball. Synthetic ribosomes is a way more practical approach.
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09:52 < kanzure> bsm117532: right, so the assumption should be that these things are moving at ~gigahertz frequencies
09:53 < kanzure> bsm117532: ^
09:53 < bsm117532> Yes basically. Unless you're working in an atom trap or with materials that have extremely high tensile strength (like diamond) at room termperature.
09:54 < bsm117532> Biology is squishy, chemical bond strengths are weak, and the tail of the thermal distribution contains enough rare high-ish energy collisions to break bonds.
09:55 < bsm117532> ~Gigahertz is the rotational and vibrational modes of organic molecules, and corresponds to microwave->infrared radiation.
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09:56 < bsm117532> So on the one hand, you have billions of collisions a second that can break your stuff. On the other hand, you have billions of collisions a second that can bring you into contact with the right bond to incorporate into the protein a la polymerase.
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09:59 < bsm117532> The random mutation rate in both DNA and RNA is alarmingly high. "Errors in DNA, RNA, and protein synthesis occur at rates of, very roughly, 10−9, 10−5, and 10−4 errors per residue, respectively"
09:59 < bsm117532> Which is why DNA organisms have various repair mechanisms. But fundamentally you have to either tolerate this error rate or have error correction.
10:00 < bsm117532> Fun fact: most RNA viruses have multiple transcription errors *per* *copy* of the virus, which is why they mutate so fast...
10:00 < bsm117532> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380820/
10:00 < bsm117532> .title https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380820/
10:00 < saxo> Lost in transcription: transient errors in information transfer
10:06 < kanzure> what about positional accuracy in this context
10:06 < kanzure> of organic molecules
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11:03 < bsm117532> The transcription errors are not "poisitional" they're single replacement of a wrong amino acid generally. (AFAIK, I'm no expert here)
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11:17 < kanzure> bsm117532: i mean our ability to control the position of atoms and molecules in reliable and repeatable ways, not polymerase's function
11:17 < kanzure> in particular, the pick-and-place method
11:48 < bsm117532> Well the only way I know that happens is the way CRISPR does it -- as i understand by having a "start" marker where a splice is made.
11:48 < bsm117532> Does tech exist to synthesize an arbitrary DNA sequence?
11:49 < bsm117532> I mean this is precise control, but only of amino acids, nothing smaller like atoms.
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15:26 < lsneff> .t https://beepb00p.xyz/hpi.html
15:26 < saxo> Human Programming Interface | beepb00p
15:31 < lsneff> Very interesting ideas coming from the guy writing that blog.
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20:45 < fenn> nice stuff lsneff
22:14 < fltrz> is there a reason China doesn't have HDD manufacturing company?
22:15 < fltrz> it seems like theres only 3 HDD manufacturers: SEAGATE (hq US), Western Digital (HQ: US), Toshiba (HQ: JP),... why don't India, China, ... consider it important?
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--- Log closed Mon Jun 29 00:00:04 2020