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| -!- Topic for ##hplusroadmap: biohacking, nootropics, transhumanism, open hardware | sponsored by lobsters everywhere, banned by the Federal Death Administration (5 times) | this channel is LOGGED: http://gnusha.org/logs | http://diyhpl.us/wiki | "ray kurzweil is a pessimist" - george church | 00:32 | |
| -!- Topic set by kanzure [~kanzure@unaffiliated/kanzure] [Wed May 20 12:46:25 2015] | 00:32 | |
| [Users ##hplusroadmap] | 00:32 | |
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| superkuh | https://arxiv.org/abs/1610.08425 "Nature does not rely on long-lived electronic quantum coherence for photosynthetic energy transfer" | 05:08 |
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| kanzure | WizJin: hi | 05:55 |
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| kanzure | "For many virus families the naked synthetic DNA or RNA (once enzymatically converted back from the synthetic cDNA) is infectious when introduced into a cell. That is, they contain all the necessary information to produce new viruses." | 06:08 |
| kanzure | cool, virus bootstrapping is easy | 06:08 |
| kanzure | we should be making more ncbi backups | 06:09 |
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| kanzure | "One reason for this is that in 1964, and for about 15 years after, there was almost no understanding of what freezing damage actually consisted of. Indeed, our understanding of cryoinjury is still far from complete and we are only now learning about things like the effect on gene expression, signal transduction, protein and lipid denaturation and so on. The ignorance about exactly what freezi... | 07:04 |
| kanzure | ...ng injury "looked like" was truly astonishing during this period. Probably the best example of this was the decade long attempt at freezing complex organs for transplantation. Several of the leading surgeons in the U.S., including the genius-maverick Richard Lillehei, spent a fair bit of time and money trying to freeze hearts and kidneys. In 1968 Lillehei remarked that he thought he would be s... | 07:04 |
| kanzure | ...uccessfully cryopreserving and reviving dogs by the mid-1970's! And Lillehei was rarely wrong. | 07:04 |
| kanzure | "In hindsight, one of the most straightforward ways to have gotten the lay of the land would have been to LOOK at tissues before and after freezing using the most definitive technologies then available. This would have meant transmission electron microscopy to determine the degree of structural damage and preservation. This work would have needed to be systematic and carefully designed to answ... | 07:04 |
| kanzure | ...er questions that are relevant to the issues raised by cryonics. An example of this is examining post preservation brains for conservation of the connectors. While connectomics is only a few years old, cryonicists back in the early 1970's were acutely aware of the importance of maintaining neural connectivity and Greg Fahy, Jerry Leaf and I were all obsessed with finding evidence that we were... | 07:04 |
| kanzure | ... preserving synapses AND preserving the interneuronal connectivity of the neuropil. We were, for instance, horrified to learn that while synapses were pretty robust in freezing, they were very often simply lying around in debris fields no longer attached to anything." | 07:04 |
| kanzure | "While I was the first to understand the "no feedback" problem in cryonics, it took me quite awhile longer to understand all of the damaging related problems it generates, such as the ability to seamlessly revise the past and to dismiss any failures, errors or misconduct that occurred. Since no patient ever gets demonstrably hurt in any way, no patient ever dies and no patient or their family ... | 07:06 |
| kanzure | ...ever sue the CSO, there are, for all practical purposes, absolutely no consequences to incompetent or otherwise bad behavior. The outcome is always the same; a body or brain in LN2 with an uncertain, but hopeful future. After some ghastly screwup has occurred, one of the most common "mitigating remarks" I hear is, "Well, not to worry too much, he may have to wait a little longer to be revived.... | 07:06 |
| kanzure | ..." More common is the statement that mature Nanotechnology will be able to reverse whatever additional damage the catastrophe at hand has just inflicted." | 07:06 |
| kanzure | "While the situation is much more complicated than what I've briefly outlined here, the effect of these things has been to cause all cryonics organizations to morph into faith-based, rather than science-based, enterprises. Put less delicately, they are religions with a veneer of science and that scientific veneer is often distorted, misrepresented, or used as outright fraud. Tell people you ca... | 07:06 |
| kanzure | ...n get then on cardiopulmonary bypass in 3 minutes if that's what they want or need to hear. Claims about what medicine can currently achieve become reckless and inaccurate and poor to bad research outcomes in cryonics, such as the results of brain vitrification ultrastructural studies are reported as major advances." | 07:06 |
| kanzure | "My first question to Brian Wowk was, "what did these brains look like after they unloaded of cryoprotectant and were thus no longer dehydrated? I never got an answer to that question, but after Robert McIntyre left 21CM, I asked him. It turns out he had the same question and he never got an answer, either. He said that he assumed it was because the brains could not be successfully unloaded of... | 07:07 |
| kanzure | ... CPA by perfusion. However, nothing precludes them from slicing the brains and then unloading the slices by diffusion. This is an absolutely critical element in evaluating the degree of structural integrity. It's the biological equivalent of unpacking an assumption in logic. And if you can't get "acceptable" results after unloading CPA, then this is a very material fact that needs to be discl... | 07:07 |
| kanzure | ...osed, along with the details of what happens when your try. This is substandard science and I believe it is such science informed by a desire to see what you both want and need to see." | 07:07 |
| kanzure | "As it is, virtually no cryonicists understand the magnitude of injury that accompanies the dying process and virtually none understand that in most patients there is extensive ischemia-reperfusion during the period of agonal shock and that some fraction of patients experience failure of flow to the brain for many minutes, or even for hours before cardiopulmonary arrest occurs. And why should ... | 07:08 |
| kanzure | ...they? There are no criteria or standards of any kind and Nanotechnology will make everything right in any event." | 07:08 |
| kanzure | "So, I am not proposing another futile iteration of cryonics, but rather a carefully structured clinical trial complete with an IRB and an iterative program informed by focused research to improve the quality of care given. I am also not proposing any reliance whatsoever on "future medical technology" or on any unknown contingent agents. Such a trial has as a core element within it the obligat... | 07:08 |
| kanzure | ...ion to perform and facilitate, if possible, or to the extent possible, the recovery of its patients. There is no assumption, express or implied that such research will materialize as a result of technological inevitability, chance, the beneficent nature of the universe, or wishful thinking." | 07:08 |
| JayDugger | Source? | 07:08 |
| kanzure | "This is very different than cryonics. The equipment and supplies I am acquiring are to undertake the pre-clinical validation of the preservation technology (or technologies) selected and to be prepared to start human trusting at the successful conclusion of that validation trial. A robust dataset that describes the conditions of preservation will exist prior to the start of human application.... | 07:09 |
| kanzure | ... Once human application begins, there will be extensive sampling, testing and monitoring to provide feedback for further refinement. Participation will be by invitation and referral and only after a pre-specified work-up and screening, followed by approval by the IRB. As to Jordan Sparks, as I've previously noted, he shares a very different view of how to proceed. " | 07:09 |
| kanzure | "In the back of my mind I've been thinking/hoping that Jordan Sparks would eventually get his operation up to par with your standards, as the criticisms you made about OregonCryo seemed fairly easily remedied, and he didn't seem completely opposed to them. As far as I remember he insinuated that things like the board of directors would eventually be created." | 07:09 |
| kanzure | docl: is that you? | 07:09 |
| kanzure | JayDugger: just some email | 07:11 |
| JayDugger | Got it. Thank you. | 07:21 |
| docl | I didn't send the email. | 07:54 |
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| kanzure | docl: no i mean the portland thing | 07:59 |
| kanzure | "oregoncryo" | 08:00 |
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| docl | yeah oregon cryo is us. | 08:34 |
| nmz787_w1 | docl: you're in OR? | 08:36 |
| docl | yep | 08:41 |
| docl | I'm in Salem | 08:41 |
| nmz787_w1 | I'm in Hillsboro :) | 08:42 |
| docl | cool | 08:43 |
| CaptHindsight | kanzure: are you planning on building a lab with new types of sequencing and synthesis equipment or is this just a info gathering project? | 08:43 |
| kanzure | CaptHindsight: equipment, yo. need stuff to actually work. | 08:44 |
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| nmz787_w1 | docl: what are you doing down there? | 08:48 |
| nmz787_w1 | I mean, school, research lab, etc? | 08:48 |
| nmz787_w1 | cabin in the woods... | 08:48 |
| docl | currently I'm holding down an unremarkable job as a support tech for open dental software | 08:49 |
| CaptHindsight | kanzure: you have to make things work, difficult to learn the skills to do so sitting on the sidelines | 08:49 |
| kanzure | CaptHindsight: yes excuse me for making enormous amounts of income at the moment. wat? | 08:50 |
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| kanzure | CaptHindsight: i'm not going to splurge on useless equipment that just sits there looking pretty. i still haven't found a chemist to help debug an inkjet printer. unless you want to become a chemist.... | 08:50 |
| CaptHindsight | not talking about the inkjet | 08:52 |
| CaptHindsight | it's about building anything | 08:53 |
| kanzure | an hour in the library saves a year of building something that wont work | 08:54 |
| CaptHindsight | an hour in a library and many more hours actually building things | 08:55 |
| kanzure | sure. | 08:55 |
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| kanzure | my point is that it is important to minimize the amount of wishful thinking. stuff doesn't just magially work. you have to minimize the number of steps where you handwave and say "and then some magic happens". i'm not going to waste $50k-200k on stuff where i have 20 different steps that are completely impractical..... that's going to bleed me dry. | 08:56 |
| CaptHindsight | do be afraid to build things and learn from mistakes | 08:56 |
| CaptHindsight | keep it low budget | 08:57 |
| kanzure | *magically | 08:57 |
| CaptHindsight | magic depends on perspective | 08:57 |
| kanzure | "gosh let's hope someone else will solve it" is still magic/handwaving | 08:58 |
| CaptHindsight | is the magic the chemistry? | 08:58 |
| kanzure | for the inkjet stuff, yeah there's a lot of aspects of the chemistry that need to be very carefully analyzed and debugged once the machine is constructed :( | 08:58 |
| kanzure | it's not a "push button and it goes" sorta thing. lots and lots of variables that require tweaking and careful characterization on various scientific instruments. | 08:59 |
| CaptHindsight | is the other magic assembling millions of oligos into one? | 09:00 |
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| kanzure | sooo for assembly, yeah.... there is now a brief outline on how to do that, but the method could take 5 or 10 years to get to the point of having a cell able to assemble 10,000 dna fragments correctly. or it might take less time. the magic is designing a directed evolution experiment that will select for cells that are better at the task. | 09:01 |
| kanzure | for dna assembly through directed evolution of specialized cells, there's "magic" but it's much more confined magic.... it's a "spray and pray" approach on an industrial scale. bruteforcing etc. | 09:01 |
| CaptHindsight | thanks for your perspective | 09:03 |
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| kanzure | to put it in perspective, out of the biologists i have mentioned that idea to, they all agree it's possible to do dna assembly using that technique, it will just take a while to evolve a cell that is specialized to do that task | 09:03 |
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| kanzure | and if i had chemists, i'm sure i could talk to them and they would say that yes, chemical dna synnthesis on an inkjet printer, sure here's how you debug those chemical reactions and the different variables you must absolutely control etc etc.... but since i don't have chemists, this is much more difficult---- i could sit around learning chemistry, but this is not the same thing as having actu... | 09:04 |
| kanzure | ...al chemistry experience. | 09:04 |
| CaptHindsight | more hands on | 09:05 |
| kanzure | there's lots of crazy details that i don't even think about-- like humidity, pressure, interactions of the chemicals with their containers, correct procedures for washing different tubes, the composition of the wash cycles, the compatibility of different DNA-bound beads with the wash reagents... etc. | 09:06 |
| kanzure | and "side reactions" | 09:06 |
| kanzure | i would be willing to pay someone, it's worth it. | 09:07 |
| CaptHindsight | thank you for putting together a nice library of papers that are often paywalled in the open | 09:08 |
| kanzure | probably the right thing to do would be to hire a chemist that worked on POSAM or something...... | 09:09 |
| CaptHindsight | that chem is too pricey and finicky | 09:10 |
| CaptHindsight | it works but it's old now | 09:11 |
| CaptHindsight | bbl | 09:12 |
| kanzure | yep... agreed. | 09:35 |
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| kanzure | https://blog.octopart.com/archives/2016/11/common-parts-library-now-github | 11:13 |
| kanzure | https://github.com/octopart/CPL-Data/blob/master/README.md | 11:13 |
| kanzure | https://join-chat.octopart.com/ | 11:14 |
| kanzure | https://github.com/octopart/CPL-Data | 11:14 |
| kanzure | https://github.com/octopart/CPL-Data/blob/master/CPL%20for%20Prototyping/Wearables.yaml | 11:14 |
| nmz787_w1 | I think someone should just make a nice tool that you upload a PDF to, and direct the tool to the correct dimensions (which I guess it could then do OCR on, prompting you to correct it if there are mistakes)... the KiCad footprint tool that already exists online is super dumb and it works pretty well for standard pin-pitch and stuff, standard arragements of pins | 11:19 |
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| nmz787_w1 | and while their reasoning behind part choices seems solid... many times people just want whatever fits the bill and is the cheapest... | 11:23 |
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| chris_99 | you mean create a kicad footpint from a pdf? | 12:03 |
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| nmz787_w | chris_99: yeah KiCad or whatever output format a user would want... kicad seems like the obvious first choice for me | 12:16 |
| chris_99 | there was a paid for service whose name i forget that makes footprints reasonably cheaply | 12:16 |
| chris_99 | https://www.snapeda.com/instapart/ | 12:17 |
| nmz787_w | I guess my point is making footprints isn't hard... but then now that I think about those links kanzure posted, their focus didn't seem to be just footprints, they were also trying to reduce the confusion for newbs | 12:17 |
| nmz787_w | (they can be tedious to make, mostly due to having to ALT-TAB back and forth between some CAD tool and a PDF with dimensions on it | 12:18 |
| nmz787_w | ) | 12:18 |
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| CaptHindsight | tedious and best done by somebody that knows how solder paste, masks and pick-n-place works | 12:49 |
| CaptHindsight | I've seen some pretty retarded footprints | 12:49 |
| chris_99 | in what way where they bad out of interest | 12:49 |
| CaptHindsight | pad size and space, solder mask opening vs pad size or unrealistic mounting holes for connectors | 12:51 |
| CaptHindsight | you or a good board house would have to fix it | 12:52 |
| chris_99 | ah gotcha | 12:52 |
| CaptHindsight | i once had Intel give me a mirror of a bga footprint | 12:53 |
| CaptHindsight | 500 pads, all wrong | 12:53 |
| chris_99 | eek, you'd think with a company like Intel that couldn't happen? | 12:54 |
| nmz787_w | hahaha | 12:54 |
| nmz787_w | CaptHindsight: I figure if you're making your own footprint, you probably know how to solder or have a close friend that will set your straight... unless you're getting paid, then you might be a cog in a big machine that never touches real widgets | 12:56 |
| CaptHindsight | they actually gave us a complete Orcad file that was completely broken when you went to layout | 12:57 |
| CaptHindsight | was for the 440BX | 12:57 |
| CaptHindsight | ends up they designed it in another CAD tool and then translated to Orcad | 12:58 |
| nmz787_w | I was trying to reverse engineer some CAD files like that, for the Intel Edison that they released publicly | 12:58 |
| CaptHindsight | no realizing that it was for appearance only and all the database behind it was broken | 12:58 |
| nmz787_w | didn't get too far, but got lazy too | 12:58 |
| CaptHindsight | no/bot | 12:58 |
| nmz787_w | bot/not? | 12:58 |
| CaptHindsight | heh | 12:58 |
| CaptHindsight | no/not | 12:59 |
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| archels | .wik funny current | 13:36 |
| yoleaux | "Funny current (or If, or IKf, or pacemaker current) is an electric current in the heart that flows through the funny channel (which comprises the HCN channels, that is, pacemaker channels). Such channels are important parts of the electrical conduction system of the heart and help constitute the natural pacemaker." -- https://en.wikipedia.org/wiki/Funny_current | 13:36 |
| archels | "Among the unusual features which justified the name "funny" were a mixed Na+ and K+ permeability, activation on hyperpolarization, and very slow kinetics." | 13:36 |
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| kanzure | .title https://news.ycombinator.com/item?id=13072956 | 14:18 |
| yoleaux | Amazon Rekognition - Image Detection and Recognition Powered by Deep Learning | Hacker News | 14:18 |
| chris_99 | the AWS FPGA thing looks cool too | 14:19 |
| kanzure | https://aws.amazon.com/blogs/aws/developer-preview-ec2-instances-f1-with-programmable-hardware/ | 14:22 |
| kanzure | snowball has been upgraded to snowmobile (now 100 PB/week of upload throughput) https://aws.amazon.com/blogs/aws/aws-snowmobile-move-exabytes-of-data-to-the-cloud-in-weeks/ | 14:28 |
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| kanzure | .title https://news.ycombinator.com/item?id=13072432 | 15:32 |
| yoleaux | Developer Preview - EC2 Instances with Programmable Hardware | Hacker News | 15:33 |
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| kanzure | "elon musk song" https://www.youtube.com/watch?v=EoyFFxCtfXo | 15:54 |
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| streety | I had always connected FPGAs with hardware, interesting to see what they will be used for in the cloud | 16:17 |
| kanzure | weird computation, basically | 16:26 |
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| streety | the best kind | 16:35 |
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| kanzure | "Optimizing complex phenotypes through model-guided multiplex genome engineering" http://biorxiv.org/content/early/2016/11/20/086595 | 18:13 |
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| kanzure | "Logic synthesis of recombinase-based genetic circuits" http://biorxiv.org/content/early/2016/11/21/088930 | 18:14 |
| kanzure | "Millstone: Software for Multiplex Microbial Genome Analysis and Engineering" http://biorxiv.org/content/early/2016/11/10/086868 | 18:18 |
| kanzure | "Engineering genetically-encoded mineralization and magnetism via directed evolution" http://biorxiv.org/content/early/2016/11/02/085233 | 18:21 |
| kanzure | from https://news.ycombinator.com/item?id=13075440 | 18:28 |
| kanzure | "I'm a biologist by training. Eventually my research hit a data wall (my simulations produced too much data for my storage and processing system). I had read a paper on GFS and Mapreduce and Bigtable from Google, and decided to go work there. I got hired onto an SRE (production ops) team and spent my 20% time learning how production data processing works at scale." | 18:29 |
| kanzure | "After a few years I understood stuff better and moved my pipelines to MapReduce. And I built a bigger simulator (Exacycle). It was easy to process 100+T datasets in an hour or so. It wasn't a lot of work, really. We converted external data forms to protobufs and stored them in various container files. Then we ported the code that computed various parameters from the simulation to MapReduce." | 18:29 |
| kanzure | "I took this knowledge, looked at the market, and heard "storing genomic data is hard". After some research, I found that storing genomic data isn't hard at all. People spend all their time complaining about storage and performance, but when you look, they're using tin can telephones and wind up toy cars. This is because most scientists specialize in their science, not in data processing. So, ... | 18:29 |
| kanzure | ...based on this I built a product called 'Google Cloud Genomics' which stores petabytes of data (some public, some private for customers). Our customers love it- they do all their processing in Google Cloud, with fast access to petabytes of data. We've turned something that required them to hire expensive sysadmins and data scientists into something their regular scientists can just use (for exa... | 18:29 |
| kanzure | ...mple, from BigQuery or Python)." | 18:29 |
| kanzure | "One of the things that really irked me about genomic data is that for several years people were predicting exponential growth of sequencing and similar rates of storage needs. They made ludicrous projections and complained that not enough hard drives were made to store their forthcoming volumes. oh, and the storage cost too much, too. Well, the reality is that genomic data doesn't ahve enough... | 18:29 |
| kanzure | ... value to archive it for long times (sorry, folks, for those that believe it: your BAM files don't have value enough for you to pay the incredibly low rates storage providers charge! Also, we can just order more harddrives, Seagate just produces drive to meet demand, so if there is a real demand signal and money behind it, the drives will be made. Actual genomic data is tiny compared to cat vi... | 18:29 |
| kanzure | ...deos." | 18:29 |
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| kanzure | "Automated scalable segmentation of neurons from multispectral images" https://arxiv.org/abs/1611.00388 | 19:38 |
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| kanzure | "Neuromorphic silicon photonics" https://arxiv.org/abs/1611.02272 | 19:39 |
| kanzure | "On the mechanism of homology search by recA protein filaments" https://arxiv.org/abs/1611.04179 | 19:39 |
| kanzure | cc yashgaroth, ^ | 19:40 |
| kanzure | "Proteins analyzed as virtual knots" https://arxiv.org/abs/1611.06185 | 19:41 |
| kanzure | "Hierarchical neural representation of dream contents revealed by brain decoding with deep neural network features" https://arxiv.org/abs/1611.09520 | 19:43 |
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| kanzure | "Probabilistic fluorescence-based synapse detection" https://arxiv.org/abs/1611.05479 | 19:45 |
| kanzure | "approximately 1 billion synapses per cubic millimeter of human cortex" | 19:46 |
| kanzure | "Mapping brain activity with flexible graphene micro-transistors" https://arxiv.org/abs/1611.05693 | 19:46 |
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| kanzure | "The evolution of sleep is inevitable" https://arxiv.org/abs/1610.00293 | 19:54 |
| kanzure | "Analytical modelling of temperature effects on synapses | 19:55 |
| kanzure | "Analytical modelling of temperature effects on synapses" https://arxiv.org/abs/1610.00611 | 19:55 |
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| nmz787 | .title http://qibec.org/q/downloads.html | 22:43 |
| yoleaux | 29 Nov 2016 05:58Z <__mz_o> nmz787: i see that youve torndown a Applied Biosystems pcr-mate, do you know where i can find a manual? | 22:43 |
| yoleaux | 29 Nov 2016 06:03Z <__mz_o> nmz787: and would it be worth buying? | 22:43 |
| yoleaux | Qibec - 1-bit, 1-instruction CPU made from transistors | 22:43 |
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| --- Log closed Thu Dec 01 00:00:15 2016 | ||
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