--- Log opened Sun Sep 24 00:00:27 2017
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02:39 < kanzure> .tw https://twitter.com/Nickf4rr/status/911729494226083841
02:39 < yoleaux> Hardware Hackers: We need an open source kit to detect & locate people alive underneath up to 20m of rubble. This is kit only the pros have. (@Nickf4rr)
02:40 < kanzure> "Recent progress in human behavior genetics" (1968) http://libgen.io/book/index.php?md5=e926c2b3e9a5b0d03fb3738b93b39f83
02:45 < kanzure> "Stereodivergent synthesis with a programmable molecular machine" http://www.nature.com/nature/journal/v549/n7672/full/nature23677.html https://twitter.com/NatureNV/status/911680067268472833
02:48 < kanzure> "Artificial molecular machines[8], [9], [10], [11], [12] have been developed for tasks that include sequence-specific oligomer synthesis[13], [14], [15] and the switching of product chirality[16], [17], [18], [19], a photo-responsive host molecule has been described that is able to mechanically twist a bound molecular guest[20], and molecular fragments have been selectively transported in ...
02:48 < kanzure> ...either direction between sites on a molecular platform through a ratchet mechanism[21]. Here we detail an artificial molecular machine that moves a substrate between different activating sites to achieve different product outcomes from chemical synthesis. This molecular robot can be programmed to stereoselectively produce, in a sequential one-pot operation, an excess of any one of four ...
02:48 < kanzure> ...possible diastereoisomers from the addition of a thiol and an alkene to an α,β-unsaturated aldehyde in a tandem reaction process."
02:48 < kanzure> [13] Lewandowski, B. et al. Sequence-specific peptide synthesis by an artificial small-molecule machine. Science 339, 189–193 (2013)
02:48 < kanzure> [14] De Bo, G. et al. Efficient assembly of threaded molecular machines for sequence-specific synthesis. J. Am. Chem. Soc. 136, 5811–5814 (2014)
02:48 < kanzure> [15] Meng, W. et al. An autonomous molecular assembler for programmable chemical synthesis. Nat. Chem. 8, 542–548 (2016)
02:48 < kanzure> [20] Muraoka, T., Kinbara, K. & Aida, T. Mechanical twisting of a guest by a photoresponsive host. Nature 440, 512–515 (2006)
02:49 < kanzure> (stereselection is not particularly helpful to us)
02:50 < kanzure> "Sequence-specific peptide synthesis by an artificial small-molecule machine" http://science.sciencemag.org/content/339/6116/189
02:50 < kanzure> "... The chemical structure is based on a rotaxane, a molecular ring threaded onto a molecular axle. The ring carries a thiolate group that iteratively removes amino acids in order from the strand and transfers them to a peptide-elongation site through native chemical ligation. The synthesis is demonstrated with ~10^18 molecular machines acting in parallel; this process generates milligram ...
02:50 < kanzure> ...quantities of a peptide with a single sequence confirmed by tandem mass spectrometry."
02:51 < kanzure> "Efficient assembly of threaded molecular machines for sequence-specific synthesis" http://pubs.acs.org/doi/abs/10.1021/ja5022415
02:52 < kanzure> "An autonomous molecular assembler for programmable chemical synthesis" https://www.nature.com/nchem/journal/v8/n6/full/nchem.2495.html
02:52 < kanzure> "Mechanical twisting of a guest by a photoresponsive host" https://www.nature.com/nature/journal/v440/n7083/full/nature04635.html
02:54 < kanzure> opentrons protocols tutorial https://gist.github.com/IanLondon/39898c5f57275eb2a4a7918ff87fa4f7
02:57 < kanzure> .tw https://twitter.com/fchollet/status/910998361284546561
02:57 < yoleaux> The belief that stacking layers deeper leads to better models is just a myth pushed by the big DL lobby to sell more tensors (@fchollet)
02:59 < kanzure> here are some hint for working with viruses ordered from addgene i guess http://blog.addgene.org/important-considerations-when-using-aavs
03:00 < kanzure> i wonder if you could recover dinosaur dna from fossilized dinosaur poop
03:00 < fenn> no
03:00 < fenn> now you know :)
03:01 < kanzure> ginkgo spam https://www.wired.com/story/with-designer-bacteria-crops-could-one-day-fertilize-themselves/
03:05 < kanzure> "A single photon induces long-range electron transfer and two PCETs" http://pubs.acs.org/doi/abs/10.1021%2Fjacs.7b08761?hootPostID=0ecfbc65bf3c0bf2dab41111cb8cfbc4 https://twitter.com/J_A_C_S/status/911301641692905472
03:07 < kanzure> alright the internet is boring, back to work
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08:29 < heath> http://james.grimmelmann.net/courses/ip2009F/PatentReview.pdf
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08:30 < heath> "On May 5, 2008, Crichton proudly announced to the world that its scientists, using confidential artificial insemination techniques, had enabled a modern elephant to give birth to a wooly mammoth"
08:30 < heath> "Sadly, Crichton’s wooly mammoth developed a respiratory infection and died on May 7, 2008."
08:30 < heath> "The USPTO issued Crichton a patent, without amendment, on June 9, 2009."
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08:31 < heath> argh. ignore
08:32 < heath> that was a quiz from an IP course
08:32 < kanzure> yes this is asking about intellectual property stuff in a hypothetical situation
08:33 < heath> yeah. pretty much out of hope at this point on finding the wooly mammoth sequence
08:33 < kanzure> you should be mingling
08:33 < kanzure> mammoth genome is not published AFAIK
08:33 < heath> i am mingling, just taking a break
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08:34 < kanzure> heath: http://gizmodo.com/why-bringing-back-a-wooly-mammoth-is-no-longer-science-1797099747
08:35 < heath> reviverestore.org is their site
08:35 < kanzure> "Church isn’t the only one working to clone a mammoth. There’s also Hwang Woo-suk’s Korean dog-cloning lab, Soaam Technologies [...] He was the one who claimed to clone human cells, but it turns out he had been forcing his students to donate their eggs, and secondly that his clone cells are fraudulent, so he’s trying to resurrect his reputation by being the first to clone a mammoth."
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09:04 < kanzure> http://reviverestore.org/projects/woolly-mammoth/
09:04 < kanzure> "The Harvard Woolly Mammoth Revival team headed by George Church (the Church Lab) is working to identify cold climate adapted alleles of the mammoth genome and edit them into living elephant cells. From there, scientists will study the expression of Woolly Mammoth mutations to test predictions about gene function. Specifically, how does evolution shape the same gene to be adapted to tropical ...
09:04 < kanzure> ...habitats in one lineage, while adapting an alternate version of that gene to cold habitats? Not only does this research build the foundations of mammoth de-extinction, it provides potentially valuable insight to evolution for different climate conditions. These insights may demonstrate techniques to apply genetic biotechnologies to facilitate adaptation for wildlife threatened by climate ...
09:04 < kanzure> ...change."
09:04 < kanzure> seems like a pretty slow way to make mammoths
09:05 < kanzure> hm this is a stewart brand thing
09:08 < kanzure> "cautionary vigilance"
09:08 < kanzure> how about "proactionary vigilance" instead. yeesh.
09:15 < heath> "Systems and Synthetic Biology Book" - https://github.com/klavinslab/ssb-book
09:44 < fltrz> and again I discover some software I could use, which used to be in the public domain (from sandia national laboritories, development paid with taxpayer money)
09:44 < fltrz> for which only the executable can now be downloaded and the original is no longer online
09:44 < fltrz> https://web.archive.org/web/20070701012444/http://www.sandia.gov/imrl/XWEB1128/snloftp.htm
09:45 < fltrz> they go off run their own company, and automagically the original public work disappears
09:45 < fltrz> http://www.as-photonics.com/snlo
09:46 < fltrz> https://www.osti.gov/scitech/biblio/752529-how-select-nonlinear-crystals-model-performance-using-snlo-software
09:47 < fltrz> "SNLO is public domain software developed at Sandia National Laboratories. " from the research paper describing the software
09:48 < fltrz> now he's charging scientists 150$ for software which used to be public domain
09:48 < fltrz> and tops it up with 8 satirical snark FAQ's http://www.as-photonics.com/products/matlab-snlo
09:49 < fltrz> the theft is pretty much selfdocumented as in the original paper he himself writes its "public domain software"
09:50 < fltrz> if I accept government work to pave a public domain sidewalk, I can't just put some fences around it afterwards and demand toll fee's even if I made the sidewalk
09:52 < kanzure> research gets 'commercialized' all the time-- in fact, it's mandatory (bayh-dole act etc)
09:53 < fltrz> I don't actually mind him charging money for his improved version afterwards as a spin off, but the sources for his original work should have been kept online at SNL website
09:53 < fltrz> but he probably had the connections to remove the original sources
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09:57 < fltrz> well, no surprise then about the surprising look on my optics and quantum electronics professor as I showed him the cheap SHG laser my brother brought back from his trip to china then
09:57 < fltrz> the west is sabotaging its own progress
09:58 < fltrz> lol from bayh dole act @ wikipedia: ""a Jeffersonian belief that the solution lay with the individual and that the best thing government could do to provide incentives for success was to get out of the way of these individuals""
09:59 < kanzure> basically the trend is to increase transaction costs by hiding knowledge/information-- which is the entire premise of intellectual property.
09:59 < fltrz> well if this individual Smith Arlee V. needed the government to get out of his way, perhaps the government shouldn't have funded his research at all?
10:00 < fltrz> kanzure: I agree
10:00 < kanzure> 'incentives for success'
10:01 < fltrz> lol, perhaps the government should fund random zero to hero pimp rap stars, giving them lamborghinis, and cash to flash, after which they can then commercialize their own labels...
10:02 < fltrz> everybody in favor raise their hands..
10:02 < kanzure> that might be possible actually.  you could start funding rap artists under one of the literature departments or something.
10:03 < kanzure> or er, music i guess.
10:04 < kanzure> fltrz: i had a patent reform proposal, but it needs work: https://groups.google.com/d/msg/openmanufacturing/vS4ju1VqXb0/jD_TZ8U47b4J
10:04 < cluckj> "george church is basically a chiral charles darwin"
10:06 < kanzure> charles darwin had some mad artistry skillz tho
10:08 < fltrz> does the EFF deal with cases like public domain software evaporating and then condensing as proprietary?
10:10 < kanzure> eh maybe. but i think in this context you might be more interested in EFF's work on anti-patent stuff (anti-software patents, defensive patent licensing, etc).
10:11 < fltrz> as far as I understand, its a copyright issue? the software was in the public domain
10:11 < kanzure> so in your particular case it's an *access* problem
10:11 < fltrz> yes
10:12 < fltrz> I wouldn't mind paying a one time amount for the sources, such that I can host them to spite the dude
10:12 < cluckj> yeah but darwin didn't have any genetics skills :P
10:12 < kanzure> the question is: can you find a copy of the software that is distributed in the public domain? and the answer is, so far, no.  but if you find someone with an archive or backup of it... then myabe. you might be able to succeed with a FOIA to the laboratory that you were looking at. perhaps they have it on old backups.
10:12 < kanzure> well FOIA would be how you pay that one time amount heh
10:13 < fltrz> kanzure: I can find the executable, he still has the freeware executable for download, but without sources
10:13 < fltrz> ok FOIA, I guess
10:13 < kanzure> sure-- if you're certain that you need the source code, and you are certain it used to be hosted there, then perhaps they have old backups.
10:13 < kanzure> and perhaps FOIA would be the way to go. it would certainly be an interesting experiment (has anoyne recovered source code using FOIA before?).
10:13 < fltrz> still I think EFF has more experience with this kind of cases?
10:14 < cluckj> if the sources were ever posted online, internet archive may have them
10:14 < kanzure> you could ask EFF but i wouldn't expect them to take this up as their personal battle. i'm still struggling to get anyone to care about MPEG-LA taking over the crispr-cas9 patents.
10:14 < fltrz> I suspect it was public domain, but you had to write to SNL to request  the sources, not sure though
10:15 < fltrz> perhaps I should write a friendly mail to SNL...
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10:15 < kanzure> "Hi, this is a friendly public domain extortion email! Please do the needful and return the source code."
10:15 < cluckj> email the dude and ask :P
10:16 < fltrz> cluckj: you mean ask the dude at his company, instead of SNL where he developed the public domain sw originally?
10:16 < cluckj> the dude at his company
10:16 < fltrz> did you check the 8 snark questions FAQ?
10:17 < kanzure> and make sure you specify the old version btw
10:17 < cluckj> nope
10:17 < fltrz> kanzure: he could just poison the source, or give a really old version instead of the last version at SNL
10:18 < cluckj> if you're nice, and explain your situation, you could probably work something out
10:18 < fltrz> would it be illegal to decompile public domain software lol?
10:19 < fltrz> cluckj: after having read his snark FAQ I'm pretty sure he's dealt with many pleas before
10:19 < cluckj> idk, writing an email sounds a lot less time consuming and frustrating than decompiling
10:20 < kanzure> and it's easier than FOIA
10:20 < kanzure> so do this first, then FOIA, then blog post where you shame the us government or whatever your extortion tactic is, etc.
10:20 < cluckj> ya
10:20 < fltrz> I predict he will just go semantic and claim that freeware executable = public domain software
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10:20 < cluckj> email > public shaming on social media > FOIA
10:20 < cluckj> but all of these things, combined, are likely to cost more in either time or money, than just buying a license
10:21 < kanzure> fltrz: that's fine; you can use his email when you go do the FOIA, and make some stern lawyerly-sounding statements that will freak llnl out or whatever.
10:21 < cluckj> llol
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10:21 < kanzure> blah i need more monitors/screens
10:21 < fltrz> I wish browsers/html had standard user commenting on websites, out of control from the website owner... (i know some such plugins exist)
10:22 < fltrz> if they were standardized or in widespread use, the comments for each such spin-off would be splattered by comments from users in the same boat, and they'd be more inclined to take action as a group
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10:25 < kanzure> heath: you recording any audio today?
10:25 < kanzure> heath: there's a bunch of android apps that can record audio
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10:55 < fltrz> hah, his 'executable' .exe is really just the renamed APL+Win interpreter by APL2000
10:55 < fltrz> so the APL source code is somewhere in the files..
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11:19 < kanzure> nmz787: hey what about storage requirements on the reagents..... didn't we notice that many of them seem to go bad after a few weeks?
11:20 < kanzure> or was that just bluster from the vendors?
11:22 < kanzure> from the standpoint of your hypothetical integrated dna synthesizer hard drive, having to reload the reagents every 2 weeks seems like a pretty big problem.   (not as much of a problem if your device is only operated by warehouses tho)
11:23 < kanzure> it's interesting that desktop printer ink manufacturers don't make their printer inks expire :-)
11:26 < kanzure> perhaps their ink chemists were wise enough to not tell them this is a possibility
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11:34 < kanzure> omg i typoed "in situ"
11:34 < kanzure> as "in C2"
11:35 < heath> kanzure: all of it
11:35 < heath> minus this vr presentation
11:35 < heath> i have a zoom h1
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12:20 < kanzure> nmz787: would you like to write 1-3 pages of summary of your presentation? we could copy-paste it into the overall summary doc.
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12:47 < kanzure> nmz787: if you don't then someone else is going to have to do it, and they will probably not get all of your points across.
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13:24 < kanzure> molecular assemblies reported that they are using TdT with a removable terminator... but to get the terminator to be compatible with the enzyme, they had to pick a terminator that turns out to be difficult to remove from the constructed oligonucleotide.
13:24 < kanzure> i believe we have something in our logs here about an enzymatic terminator method.... we should revisit that and see if it would physically work with TdT.
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14:07 < kanzure> merrifield nobel prize details https://www.nobelprize.org/nobel_prizes/chemistry/laureates/1984/speedread.html
14:08 < kanzure> (1984 nobel prize in chemistry)
14:10 < kanzure> i wonder what the yield was before washing, might have been usable "The elegance of this method is that any by-products and unused starting ingredients that are not attached to the anchored peptide can be easily washed away after each step in the process, increasing yields to staggering levels"
14:10 < kanzure> "Within a few years, Merrifield had automated the peptide construction process, but his method wasn't accepted until he showed it could create fully functioning proteins – from the 9-amino-acid-long peptide hormone bradykinin to his milestone synthesis of an active enzyme, ribonuclease A, created by attaching each of its 124 amino acids individually. His method was later adopted to create ...
14:11 < kanzure> ...designer nucleotides, short fragments of specific sequences of DNA, which meant that Merrifield's breakthroughs in chemistry evolved into an essential tool for molecular biology and biotechnology."
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14:46  * nmz787 reads backlog
14:51 < nmz787> kanzure: re: storage of chems... yeah, that's pretty much why I moved onto thinking about enzymatic methods
14:52 < nmz787> kanzure: I got around inkjet print cartridges going bad by moving to laser printer... I print only once every 2 or 3 months
14:53 < kanzure> molecular assemblies is using chemical reagents with their enzymes. i believe expiration is still a problem.
14:53 < nmz787> kanzure: bill efca didn't seem opposed to single molecule and flowing a single nucleotide in from dilute solution (with detection on when said nucleotide was introduced into the rxn chamber)
14:54 < nmz787> kanzure: he basically sounded like he never had experience with single-molecule... my guess is due to fab limitations and such
14:56 < nmz787> oretty sure expiration in enzymatics is somewhat different though, you can re-charge them with i.e. polynucleotide kinase
14:56 < nmz787> (and ATP)
14:57 < kanzure> not expiration of the enzyme, that is not my concern
14:57 < nmz787> right
14:57 < nmz787> I am talking small molecules
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15:20 < heath> hm..
15:20 < heath> "area of a boeing 747 ~22000ft = 2e21nm^2 = 4e22bp and at 0.001 - 0.1 cents per base, 1 umol scale t50 base $0.013 to $1.33 per airplane
15:20 < heath> "
15:20 < heath> lady thinking about his much it costs to coat an airplane with dna..
15:21 < kanzure> nmz787: you didn't answer my summary quetsion
15:22 < nmz787> uh, umm... I need to find nanofluidic papers today to write to work folks about
15:23 < nmz787> when do you need it by?
15:23 < kanzure> today ish would be really nice.
15:24 < nmz787> hmm, didn't you already type what I said though?
15:24 < nmz787> I can try to clean that up I guess
15:25 < kanzure> right
15:25 < kanzure> that's what i was working for, for the other summaries
15:26 < nmz787> fltrz: that EXE download seems to work to produce some plots on WINE
15:26 < nmz787> fltrz: I click buttons with acronyms and then click "run" and plots show up
15:30 < kanzure> nmz787: on an unrelated note, i think there is a really good argument for going into the asic business on genome assembly and sequence alignment stuff.
15:30 < nmz787> yep
15:30 < kanzure> i don't think anyone is doing that yet.
15:30 < nmz787> I think that is definitely a TBD upgrade that should be pretty straightforward for the existing biz to add into the future generations after proof of concept/gen-1
15:31 < kanzure> hm? i mean outside of data storage context.
15:31 < nmz787> mmm
15:31 < nmz787> yeah it should work
15:31 < kanzure> right now most assembly is done on aws ec2
15:31 < nmz787> pitch-wise
15:31 < nmz787> GPUs I guess?
15:32 < nmz787> I think the assembly is also closely tied to the sequencing tech though, maybe?
15:32 < nmz787> something about the different error patterns
15:33 < kanzure> a first version can be made for GPUs if you want to pitch it as a demo
15:34 < nmz787> I mean aren't they already using them?
15:34 < nmz787> whatever software they're running on amazon?
15:36 < nmz787> fltrz: this tool is pretty interesting, I will definitely have to look into it more... have wanted to do some optical heterodyning to try and analyse chemistry with non-optimal lasers (i.e. the wrong frequency for the known wavelength of best-response)
15:36 < nmz787> (to the chemical of interest, vs other contaminants patterns of wavelength to response)
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15:38 < kanzure> no my understanding is that the public genome alignment/assembly software does not use GPUs
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16:49 < kanzure> Xtal: greetings
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17:21 < fltrz> nmz787: yeah, I also noticed it runs under wine, at first there was something wrong with displayed characters, but after putting the font, into wine font directory it works without problem...
17:21 < kanzure> "Ordered multistep synthesis in a single solution directed by DNA templates" http://evolve.harvard.edu/27-Angew.pdf
17:22 < kanzure> "Genetic encoding of DNA nanostructures and their self-assembly in living bacteria" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838831/
17:22 < kanzure> "Autonomous multistep organic synthesis in a single isothermal solution mediated by a DNA walker" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2974042/
17:22 < fltrz> nmz787: then I tried searching for conversion tools or whatever because apparently most APL software is written in a specific APL implementation in this case APL+WIN and you can't get the code out of the .w3 file...
17:22 < fltrz> unless you have APL+WIN of the correct version...
17:23 < fltrz> imagine gcc being like an IDE and storing your source code into some obfuscated format...
17:24 < kanzure> "Programmable one-pot multistep organic synthesis using DNA junctions" https://www.researchgate.net/profile/Eugen_Stulz/publication/221776918_Programmable_One-Pot_Multistep_Organic_Synthesis_Using_DNA_Junctions/links/00b4951acb95c65577000000.pdf
17:24 < fltrz> I practically spent half a day looking up either file format for .w3 files or tools to convert them...
17:25 < kanzure> "... Synthesis is controlled by the sequential introduction of instruction strands."
17:25 < kanzure> cc yashgaroth_
17:27 < fltrz> I guess tomorrow I will ollydbg the runtime as it loads the .w3 workspace
17:27 < kanzure> "A sequential strand-displacement strategy enables efficient six-step DNA-templated synthesis" http://evolve.harvard.edu/78-DTS%20by%20Sequential%20Strand%20Displacement.pdf
17:29 < kanzure> and also this is manipulable by typical optical/electrical intervention http://pubs.acs.org/doi/abs/10.1021/nl303894h
17:39 < yashgaroth_> interesting, I don't get how they prevent multiples of the same monomer from reacting with the chain
17:39 < yashgaroth_> plus you gotta synthesize these DNA-molecule conjugates
17:45 < yashgaroth_> like okay maybe you don't get much spontaneous strand exchange between two of the same monomer, but even so...
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18:44 < kanzure> nmz787: please clarify if you meant "no" regarding a summary
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19:30 < nmz787> i will look at it now
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19:48 < kanzure> welll?
20:03 < nmz787> I have maybe a paragraphy or two
20:04 < kanzure> need 1-3 pages
20:04 < kanzure> you can include charts/tables to fill up the space
20:04 < kanzure> also you can include the takeitapart dna synthesizer photos if you want
20:04 < nmz787> hrmm
20:04 < kanzure> i think that would be a good contribution
20:05 < nmz787> takeitapart has been offline for a few weeks
20:05 < nmz787> did you make a backup of those pics?
20:06 < kanzure> do you love me? http://diyhpl.us/~bryan/papers2/DNA/abi391/takeitapart/
20:09 < nmz787> haha
20:10 < nmz787> I guess I must have them somewhere on a harddrive or something
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20:58 < nmz787> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000398/     and   http://aip.scitation.org/doi/suppl/10.1063/1.4871595
20:58 < nmz787> .title
20:58 < nmz787> DNA translocation through short nanofluidic channels under asymmetric pulsed electric field
20:58 < nmz787> "applied voltage across a nanochannel with a cross-section of 200 × 400 nm and length of 10 μm"
21:00 < nmz787> I believe the size was chosen for optical monitoring reasons (i.e. not smaller than the wavelength needed for excitation/emission of the fluorophore)
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--- Log closed Mon Sep 25 00:00:28 2017