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| kanzure | fenn: why did http://fennetic.net/irc/cyberfenn/hplus_proposal/ not happen? | 07:29 |
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| kanzure | andrew hessel is doing an AMA on r/futurology today https://www.reddit.com/r/Futurology/duplicates/515il5/andrew_hessel_coding_life_the_future_of_genetic/#AMApromo | 07:34 |
| kanzure | http://a.thumbs.redditmedia.com/y8vOHs0bIIeQMZydcV6VDJsPgfoCypJs6yXs8AWjgr8.png | 07:34 |
| kanzure | other scheduled AMAs: https://www.reddit.com/r/Futurology/wiki/ama#AMApromo | 07:37 |
| kanzure | no wait, that's backwards. | 07:37 |
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| kanzure | https://www.reddit.com/r/Futurology/comments/51ryoy/hi_my_name_is_andrew_hessel_im_a_futurist_and/ | 08:54 |
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| kanzure | virus-mediated positron emission tomography imaging http://diyhpl.us/~bryan/papers2/bio/Molecular%20imaging%20of%20lentiviral%20vector-mediated%20reporter%20gene%20expression%20with%20positron%20emission%20tomography%20and%20bioluminescence%20imaging.pdf | 09:48 |
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| kanzure | "Noninvasive imaging of lentiviral-mediated reporter gene expression in living mice" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155985/ | 09:59 |
| kanzure | "Advanced fluorescence protein-based synaptic detectors" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4927625/ | 10:02 |
| kanzure | "Understanding these capabilities thus requires a precise description of the individual synapses that comprise neural networks. Recent advances in fluorescent protein engineering, along with developments in light-favoring tissue clearing and optical imaging techniques, have rendered light microscopy (LM) a potent candidate for large-scale analyses of synapses, their properties, and their connectivity. Optically imaging newly engineered ... | 10:02 |
| kanzure | ... fluorescent proteins (FPs) tagged to synaptic proteins or microstructures enables the efficient, fine-resolution illumination of synaptic anatomy and function in large neural circuits. Here we review the latest progress in fluorescent protein-based molecular tools for imaging individual synapses and synaptic connectivity. We also identify associated technologies in gene delivery, tissue processing, and computational image analysis ... | 10:02 |
| kanzure | ... that will play a crucial role in bridging the gap between synapse- and system-level neuroscience." | 10:02 |
| kanzure | "A simple and effective in vivo non-viral RNA transfection method for labeling the whole axonal tree of individual adult long-range projection neurons" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4796015/ | 10:04 |
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| ybit | there was a whole album mixing elements of blade runner | 14:45 |
| ybit | it was exactly this: https://youtu.be/2qzEEISZYbI?t=142 | 14:45 |
| ybit | but it was an entire album | 14:45 |
| ybit | if anyone happens to know what i'm talking about, i've been looking for this album for a couple of years now and would love to know the name of it | 14:46 |
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| ybit | aha! http://dawhois.com/site/bl2derunner.com.html | 14:53 |
| ybit | that's the album, bl2derunner.com doesn't exist anymore, but at least i have the name of it | 14:54 |
| kanzure | ybit: https://soundcloud.com/john-hyperion/bl2derunner | 14:57 |
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| ybit | http://www.chartmp3.site/download/c291bmRjbG91ZC0xNzM3NjAyMzY/ | 15:03 |
| ybit | oh nice! there's a download link at soundcloud, thanks kanzure | 15:03 |
| ybit | this is the happiest point of my day right now, never thought i'd hear it again | 15:04 |
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| juri_ | https://dx.doi.org/10.1016%2FS0140-6736%2894%2992353-1 | 17:08 |
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| kanzure | "This article does not have an abstract to display." | 17:08 |
| juri_ | um. no paperbot? | 17:09 |
| kanzure | nope | 17:09 |
| * juri_ sads. | 17:14 | |
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| kanzure | https://en.wikipedia.org/wiki/Protein_design | 18:30 |
| kanzure | strange that "cell surface display" isn't an article but https://en.wikipedia.org/wiki/Bacterial_display is an article. | 18:31 |
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| kanzure | "I'm really late here, but I hope you don't mind me asking: when you say it's "relatively easy" to edit a line of code in a bacteria and compile, what do you mean by relatively easy? Like, possible for anyone who has a basic understanding of programming? Or easy for someone who understands DNA and programming well?" | 19:11 |
| kanzure | from https://www.reddit.com/r/Futurology/comments/51ryoy/hi_my_name_is_andrew_hessel_im_a_futurist_and/ | 19:11 |
| kanzure | not sure what to tell this guy. it's like programming, but it's definitely not like programming. | 19:12 |
| kanzure | and also it's expensive because biology is expensive. so it's easy, except for all the umpteen zillion problems you run into. | 19:12 |
| kanzure | and it's easy except in the sense that nothing works and there's a million variables that go wrong | 19:12 |
| juri_ | tell him it's more like editing a program on disk using magnets directly. | 19:13 |
| kanzure | well, it's not though.... even if you edit using individual bit flips, at least you know which bits to flip, what instructions to write, what the opcodes are, what the APIs are, and you have a lot of documentation available about bit flipping itself, the processor, the motherboard, all of which were designed for human use. | 19:14 |
| kanzure | "... there is no source, the bytecode has multiple reentrent abstractions, is unstable and has a very low signal to noise ratio, the runtime is unbootstrappable, the execution is nondeterministic, it tries to randomly integrate and execute code from other computers... multiple reentrant and self-modifying abstractions. absolutely everything has subtle side effects." | 19:14 |
| kanzure | "Those of you who have not done biology can't realize how primitive things still are. A CS analogy is that we're trying to reverse engineer a non-deterministic alien architecture from the future via a remote debugger over a noisy line that has no error correction and runs at a fraction of a millibaud, where every peek or poke costs hundreds to thousands of dollars. With the advent of high-throughput sequencing we just figured out how to ... | 19:14 |
| kanzure | ... get noisy ROM/RAM dumps (genotype), but still have precious little ability to quickly interact with the biological systems under study (phenotype). Biology is much more like hacking and reverse engineering than it is like physics or mathematics." | 19:14 |
| kanzure | above is from https://news.ycombinator.com/item?id=8832407 | 19:14 |
| kanzure | "So you can't just expect to write useful linear source code unless you're doing the most primitive cut-and-paste style synbio of a handful of unmodified genes. i.e. just screwing around. (which is fun and great - but not really what synbio is ultimately about)" | 19:14 |
| kanzure | "Abstractions work in machine code because we built the machines to make abstractions possible. Natural cells don't work like that. The closest thing to cells in the machine code world are demoscene x86 assembly blobs -- filled with insane hacks to make something awesome work in a small amount of space, with lots of weird code and data reuse and generative magic." | 19:14 |
| kanzure | "It's worse than that though. Never forget that the true "compiler" of DNA is Physics, specifically that of protein folding, conformational dynamics, and catalysis. It won't be simulated anytime soon with anything approaching useful kinetic accuracy. (It's not clear if we'll ever get kT-accurate quantum simulations of correlated electron wavefunctions that scale to protein-sized systems, though there is some hope in the far future ... | 19:14 |
| kanzure | ... with exotic computing architectures.)" | 19:15 |
| kanzure | "So ultimately what software useful for synthetic biology is going to do is help us curate all of our brute-force efforts to build and screen libraries of pseudorational libraries of proteins, pathways, and cells. -Not- provide shitty abstraction layers that rest upon our incredibly shaky understanding of what's going on circa 2012. Think of curating an incredibly complicated genetic-programming run across a hundred-thousand clusters ... | 19:15 |
| kanzure | ... -- that gives a better sense of the flavor of what's needed." | 19:15 |
| kanzure | "We invented the light-build long before we understood QFT. We'll be building amazing cellular machines long before we really understand them quantitatively. Synbio's (and diybio's) biggest sin is repeatedly elevating the convenient metaphors with EE/CS into a slick-looking action plan that doesn't respect the fundamental differences between these machine architectures." | 19:15 |
| kanzure | "Let me reemphasize the point here. Programmers can exist because WE built computers -explicitly- to support those abstraction layers. The Wizards of EE formed a powerful magical convenant that protects all the gentle digital denizens from concerning themselves with the horrors of physical reality that lays sealed beneath the woven lithography. It took them decades and a trillion dollars to build those magical seals." | 19:15 |
| kanzure | "In biology we haven't even begun to form powerful enough magic to seal away the chaos of physical reality. Over the next few decades we'll almost certainly rebuild simple microbial cells (piecemeal, haltingly, not all at once) with an increasingly modularized set of signaling components and metabolic cores whose behavior we'll have -evolved- to be isolated and predictable. It will take bajillions of manhours to do that, and it will ... | 19:15 |
| kanzure | ... almost entirely be done by limited guesswork and brute-force screening (i.e. traditional engineering). Only once we've untangled the gordian knot of the cell will we be able to construct these magical abstraction layers atop it.... and they'll probably be leaky layers at that." | 19:15 |
| kanzure | "Yes, but what -isn't- hackable? Look, my gripe here is that cells are really -nothing- like a von neumann machine. They're both nonlinear dynamical systems that happen to carry lots of "code" that controls their evolution in time. That's the strongest similarity. Cells deserve more than crappy metaphors to other kinds of systems. If y'all really want to improve how we engineer cells, it's worth taking a few years to begin ... | 19:15 |
| kanzure | ... understanding how they really work. As Bryan pointed out, SynBio suffered for a long time under the domination of a naive pack of EE/CS enthusiasts who couldn't pull the blinkers from their eyes to see that they weren't operating in the same kind of world anymore. My recommendation to DiyBio enthusiasts is not to repeat their mistake." | 19:15 |
| kanzure | https://groups.google.com/d/msg/diybio/GxRTESzUWUI/zd5MpKNzBzgJ | 19:15 |
| kanzure | https://groups.google.com/d/msg/diybio/GxRTESzUWUI/IS-zLDlUu_YJ | 19:15 |
| kanzure | on the other hand, i don't want to discourage people from pretending that it is like computer programming, because maybe they will accidentally figure out a way to make biology not suck so much, and maybe they wont do that if they hear lots of discouraging things about how miserable biology can be | 19:17 |
| kanzure | a big chunk of genetic engineering is going to be replacing all this parallel execution distributed system nonsense with more linear-interactable systems, like by inserting barcodes to gate different regulatory networks and features rather than using a thousand different organic molecules in metabolism or whatever.. | 19:19 |
| kanzure | or by directly implanting semiconductor microchips into individual cells (for the cells that are large enough for microchips) | 19:20 |
| kanzure | (which reminds me that we should encourage more people to use microchips in emulsion sorting in vitro selection / directed evolution experiments. but nevermind..) | 19:21 |
| kanzure | *inside emulsion droplets | 19:21 |
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| abetusk | any suggestions on command line svg to gcode converters would be appreciated | 21:29 |
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| kanzure | surprisingly you might have better luck going through a printer driver | 21:32 |
| kanzure | also xentrac has been doing related things recently | 21:32 |
| kanzure | and.. he's not online. weird. | 21:32 |
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| fenn | so... wtf is going on here? "Wayback Machine doesn't have that page archived." but it says 19 captures for this url? http://web.archive.org/web/*/http://dp.jstenback.com/gcode/* | 22:13 |
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| abetusk | maybe I should be investigating another workflow? SVG -> DXF -> GCode? | 22:28 |
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| fenn | yes, i've had good luck with dxf2gcode by christian kohloffel | 22:50 |
| fenn | but i don't know how to automatically convert svg to dxf | 22:50 |
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| kanzure | xentrac would say something about svg -> ps -> gcode or something | 23:09 |
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| --- Log closed Fri Sep 09 00:00:47 2016 | ||
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