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| kanzure | bloop | 06:16 |
|---|---|---|
| JayDugger | bluup | 06:20 |
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| kanzure | "Chemoenzymatic transformations in nucleoside chemistry" http://diyhpl.us/~bryan/papers2/DNA/Chemoenzymatic%20transformations%20in%20nucleoside%20chemistry.pdf | 06:50 |
| kanzure | http://hackteria.org/wiki/index.php/DIY_Micro_Laser_Cutter | 06:51 |
| chris_99 | cool | 06:53 |
| kanzure | "A two-neuron system for adaptive goal-directed decision-making in Lymnaea" http://www.nature.com/ncomms/2016/160603/ncomms11793/full/ncomms11793.html | 07:04 |
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| kanzure | "Scheme 20 is nice it adds an acyl group. Rutgers 2014 igem project used an acyl group to protect dNTPs. They used ammonia to remove it. I believe ammonia does not require protecting groups on nucleotide bases in fact it's sometimes used to remove them. However scheme 20 only works for bases a and t. I wonder if you could modify the enzyme to work on c and g. Scheme 17 only works on a u base." | 08:04 |
| kanzure | "Well I've thought about this at length actually. Two posable strategies for alternative blocking groups have occurred to me. The first it may, just may, be posable to use a disaccharide synthase to add a sugar based compound to the 3 prime position of a dNTP. You can see scheme 31 in that paper shows a way of using a disaccharide synthase to add at the 5 prime position but there are a lot of disaccharides in nature and lots of different ... | 08:04 |
| kanzure | ... enzymes to make them. You'd have to screen a lot of disaccharide synthases till you found one with week activity for 3 prime addition then do directed evolution to get something that could give you dNTPs blocked by joining another monosaccharide to the ribose. To the best of my knowledge all disaccharides break down into monosaccharides in sufficiently hot water. So you could make your own thermal liable blocked dNTP. It won't be ... | 08:04 |
| kanzure | ... cheeper to do this than buy cleanamp." | 08:04 |
| kanzure | "So the question in my mind is how hard would it be to make a dirty dNTP chemically with out an enzyme. Is there a reagent I could add to dNTPs and phosphoric acid that would attach PO4H2 to the 3 prime location with out the base or 5 prime end needing protecting groups. There are 4 OH groups hanging off the phosphors at the 5 prime end so can we expect some PO4H2 groups added here? What if I turned the phosphoric acid into a free ... | 08:04 |
| kanzure | "The other option might be to use dirty ends. When dna breaks it doesn't always leave clean 3 prime ends. Often you get a lot of 3 prime ends with PO4H2 groups on them. You can't polymerise off this. But there is an enzyme PNKP that nips off the PO4H2 group so polymerisation can continue. If you used dirty dNTPs and used PNKP instead of heat to deblock that might be an option. However the only simple way I can think of to get dirty dNTPs ... | 08:04 |
| kanzure | ... is to get a DNA sample, subject it to lots of oxygen, possibly ozone. Use exonucleases to break it down into clean and dirty dNMPs painstakingly purify out the dirty dNMPs turn them into dirty dNTPs using NDP / NMP kinases then separate them by base. This will also not be cheeper or easier than buying cleanamp." | 08:05 |
| kanzure | ... radical before adding it using electrical discharge? All things I've considered. Basically I'm a sucky chemist and it takes a very talented chemist to do serious organic synthesis only using reagents you can purify out of things you can buy at your local supermarket or buy from amazon." | 08:05 |
| kanzure | "And again none of this is going to be cheeper or easier than cleanamp. But as I said a cheep solution is unrealistic this method is aimed at those who a) want a learning experience or b) can't get industry made DNA sequences." | 08:05 |
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| fictor_de_aljabr | I'd be interested in hearing why a group like this would be for or against Hilary Clinton | 10:23 |
| kanzure | well if you pay us, we might suddenly have an opinion | 10:24 |
| kanzure | also: why are you here. get lost. | 10:24 |
| fictor_de_aljabr | What? | 10:44 |
| fictor_de_aljabr | Who the hell..? | 10:47 |
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| Jawmare | kanzure : can you summarize your question? | 11:05 |
| @kanzure | my what | 11:06 |
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| Jawmare | or whatever you said 3 hours ago? | 11:07 |
| @kanzure | i was quoting something from the diybio mailing list | 11:07 |
| @kanzure | Jawmare: it was from the author of http://diyhpl.us/~bryan/papers2/DNA/A%20hypothetical%20protocol%20for%20DIYBIO%20DNA%20synthesis.pdf | 11:07 |
| Jawmare | oh ok | 11:07 |
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| ybit_ | https://www.youtube.com/watch?v=Yth7O6yeZRE | 12:29 |
| ybit_ | .title | 12:29 |
| yoleaux | Decentralized Web Summit - Live From The Internet Archive - YouTube | 12:29 |
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| @kanzure | https://www.hodinkee.com/articles/interview-meet-dan-spitz-anthrax-guitarist-turned-master-watchmaker | 12:51 |
| @kanzure | http://danspitz.com/spitz-bench/ | 12:51 |
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| archels | kanzure: reposting this but, what's good mindmapping software that does different views like timeline and spatial (graph/network?) organisation? | 13:59 |
| archels | slide based presentations should be a subset of mind mapping software too | 14:01 |
| @kanzure | dunno. i hate mindmapping software. i think there was one called "mindmapper" that people liked. | 14:03 |
| @kanzure | .tw https://twitter.com/BoredElonMusk/status/556184760721371136 | 14:03 |
| yoleaux | Move Fast and Break Rockets. (@BoredElonMusk) | 14:03 |
| archels | are you still using textfiles for mind mapping | 14:04 |
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| @kanzure | i'm not sure i am doing any mindmapping at all. what signs would i have to look for to decide whether that's happening ? | 14:06 |
| archels | I'm using a textfile for my todo list/braindump, I thought you were doing similar things | 14:08 |
| @kanzure | oh is that a mindmap? | 14:09 |
| archels | close enough | 14:09 |
| chris_99 | heh i thought mindmaps where graphy things? | 14:09 |
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| maaku | I use mindmaps but never found software useful for it | 14:17 |
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| @kanzure | chris_99: i think they are the things where you have lots of "links" between things. | 14:20 |
| @kanzure | i could spend hours enumerating links between concepts but i'm not sure there's any point... semantic web stuff has never worked out positively for me. | 14:20 |
| chris_99 | hmm it seems they're forming many hierarchies as i understand it from wiki? i guess you could represent that similarly just by using multiple levels of headings in text | 14:25 |
| maaku | chris_99: not sure what you're describing but it's not a mindmap | 14:28 |
| maaku | mindmap is just an arbitrarily structured graph of idea space | 14:28 |
| chris_99 | yeah, where the subgraphs form hierarchies | 14:28 |
| maaku | it's a way of thinking about something larger than your working memory | 14:28 |
| maaku | chris_99: arbitrary graph, not hierarchies | 14:29 |
| @kanzure | i would just sit there all day adding links. not a good use of time. | 14:29 |
| maaku | chris_99: e.g. cycles are ok (and common in fact) | 14:30 |
| chris_99 | ah, the ones i was looking at didn't have cycles | 14:30 |
| maaku | i've only found it to be useful for a specific task, often scoping problems | 14:30 |
| maaku | chris_99: probably because if you're googling 'mindmap' you get a bunch of mindmap software, most of which don't know how to handle cycles (part of why I say mindmap software is junk) | 14:31 |
| @kanzure | why scoping in particular | 14:31 |
| maaku | kanzure: let's take the canonical example of "moving overseas" | 14:32 |
| maaku | if I mindmap that I'll end up with a huge graph of things that need to be done in relation to pulling off sucha move, with clusters related to acquiring visas and updated passports, finding accomodation, schools for kids, setting up forwarding, hiring movers, packing up my belongings, etc. | 14:33 |
| maaku | and all the dependencies between these items, represented as linkages, etc. | 14:34 |
| maaku | it's way too big of a task to keep in memory, and a hierarchical text document will not allow the cyclical or non-hierarchical cross dependencies to be adequately documented | 14:34 |
| maaku | *way to big a project (too many tasks) | 14:35 |
| maaku | mindmapping is just "assisted cognition" -- a way of dumping thoughts so you can focus on specific pieces at a time | 14:35 |
| maaku | I typically only do it at the start of a project to identify all the moving parts and interdependencies however | 14:36 |
| chris_99 | could always have goto's in the text document ;) | 14:36 |
| xentrac_ | yeah, that's what I do | 14:37 |
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| @kanzure | bloop | 18:45 |
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