--- Log opened Sat Jan 17 00:00:26 2015
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01:08 < maaku> JayDugger: SpaceX isn't looking for people with families
01:09 < maaku> insane work ethic got them where they are now
01:10 < maaku> there will be time for more diversity in the workforce later
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05:01 < yoleaux> kanzure: paperbot unit tests
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06:32 < kanzure> "I am pleased to announce the release of the Machine Intelligence from Cortical Networks (MICrONS) program Broad Agency Announcement (BAA).  MICrONS seeks to revolutionize machine learning by reverse-engineering the algorithms of the brain.  The program is expressly designed as a dialogue between data science and neuroscience, in which participants will have the unique opportunity to pose biological questions with the greatest potential ...
06:32 < kanzure> ... to advance theories of neural computation and obtain answers through carefully planned experimentation and data analysis.  Over the course of the program, participants will use their improving understanding of the representations, transformations, and learning rules employed by the brain to create ever more capable neurally-derived machine learning algorithms.  Ultimate computational goals for MICrONS include the ability to perform ...
06:32 < kanzure> ... complex information processing tasks such as one-shot learning, unsupervised clustering, and scene parsing, aiming towards human-like proficiency."
06:32 < kanzure> scene parsing? what a lame climax.
06:33 < kanzure> abetusk: there's a chroot for nanoengineer (see the README) so just put the chroot in a docker container and you're done
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08:05 < kanzure> instead of yielding next steps, paperbot should have a general planner and then something to execute the plan
08:05 < kanzure> then the planner can be tested independently of the execution, and the execution can be decoupled from next step knowledge
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08:06 < AmbulatoryCortex> paperbot?
08:08 < kanzure> a long time ago (like a week or something), paperbot was in here serving up requested papers
08:08 < kanzure> https://github.com/kanzure/paperbot
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08:23 < kanzure> "Analysis of the impact of ploidy on the genotypic effects of directed evolution" http://dowell.colorado.edu/assets/pdf/richmondthesis.pdf
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08:35 < kanzure> yashgaroth: thoughts? http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569010/
08:35 < kanzure> .title
08:35 < yoleaux> A Heritable Recombination System for Synthetic Darwinian Evolution in Yeast
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10:22 < kanzure> .to yashgaroth "A heritable recombination system for synthetic Darwinian evolution" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569010/
10:22 < yoleaux> kanzure: I'll pass your message to yashgaroth.
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11:48 < kanzure> this is the dumbest distinction ever http://en.wikipedia.org/wiki/Neats_vs._scruffies
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12:00 < justanotheruser> neat
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12:08 < pete4242_> lol
12:11 < pete4242_> Anyone from London here? I just spoke to one of these guys: http://biohackspace.org/
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12:15 < kanzure> chris_99 maybe?
12:15 < kanzure> umm, nsh might have visited them at some point
12:15 < nsh> unknown to me sorry
12:16 < kanzure> what
12:16 < nsh> biohackspace
12:16 < nsh> (.org)
12:16 < kanzure> this is just the london hackspace
12:16 < kanzure> pretending to be something else
12:16 < nsh> meh
12:17 < kanzure> yeah, good point
12:17 < pete4242_> haha
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12:18 < pete4242_> I guess most people that know how to do stuff already work in a lab or at uni.
12:18 < pete4242_> *bio stuff
12:19 < kanzure> shared lab space is a lot of trouble because of the consumption rate of a single person multiplied by all the other jerks
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12:19 < pete4242_> heh
12:20 < kanzure> this is fun:
12:20 < kanzure> http://ayronwohletz.com/debugging-with-hypotheses/
12:20 < kanzure> "Many programmers intuitively fix bugs by following a gut feeling of what might be wrong, inserting print statements, stepping through with the debugger, changing things to see what happens, and so on. For trivial bugs that you can fix in 5 minutes, maybe this approach works. However, if we go over that 5-minute time limit, making our debugging more rigorous and explicit saves time and effort."
12:20 < kanzure> "Why does it save time? For one, by clarifying your reasoning in writing, you can often find solutions faster. Second, if you don’t truly understand what you’re doing when fixing a bug, you have a high chance of adding even more bugs by putting in your fix. Your lack of understanding will come back to haunt you; it will very likely cost more than the up-front investment of doing it properly the first time. In essence, never fix a bug ...
12:20 < kanzure> ... unless you’re certain that the fix will totally eliminate the error and won’t introduce any more errors."
12:20 < kanzure> "The core idea is to form hypotheses, write them down, and prove or disprove them. In this way it has strong parallels with the scientific method."
12:20 < pete4242_> future: http://www.humane-assessment.com/
12:21 < kanzure> .title
12:21 < yoleaux> Humane assessment
12:22 < kanzure> this is a bad summary: "Managers decide the strategy. Architects decide the technical direction."
12:23 < kanzure> aaa it is an awful gui why http://www.humane-assessment.com/guide/moose/
12:24 < kanzure> what a waste of my time
12:24 < pete4242_> Awful?
12:24 < kanzure> guis are the number one sign that someone hasn't thought his problem through very well
12:25 < kanzure> this: http://humane-assessment.com/pierfiles/9f/wnmg8v6gqd09s9xkt5palhpjqnm0gl/Meta-Browser-behavioralentity.png
12:25 < kanzure> that is their system
12:25 < pete4242_> kanzure: haha.
12:25 < kanzure> http://humane-assessment.com/pierfiles/42/bhtcj234v2yudtvmkiyr06w7h1ugha/Blueprint-complexity.png
12:25 < kanzure> http://humane-assessment.com/pierfiles/97/r272zn31ppukgc71uwyk9jgvqhr2y9/Moose-Panel03-class-source.png
12:25 < kanzure> http://humane-assessment.com/pierfiles/da/swcopdikpj8by9e5az9nkrgxiutlcv/Moose-Code-Browser.png
12:25 < kanzure> http://humane-assessment.com/pierfiles/0a/3twdky36uvxr590qlq3v6l34rpp1sf/icons-600-400-26.png their "problem description" -_-
12:25 < pete4242_> You leave me speechless. So I won't say anything.
12:26 < kanzure> look at these screenshots. does this really look like an excellent example of thought?
12:26 < pete4242_> hell yes.
12:26 < kanzure> hell it's even uml
12:26 < kanzure> you are arguing for uml man :P
12:27 < pete4242_> No. Read more. Play with it.
12:27 < kanzure> if i was making a tool to assist with probabilities over competing hypotheses and observations, it would primarily deal with text entry of the different observations and competing hypotheses
12:27 < kanzure> probably from a stream (like stdin or a file)
12:28 < kanzure> also, it would track which things once broken need to be re-computed or re-considered (e.g. when certain observations fail, it may trigger the recomputation of probabilities of other hypotheses being valid that were previously ignored)
12:29 < kanzure> pete4242_: most of these links that i have pasted lead me to awful things. can you give me a link that leads to what you consider to be a good thing from them?
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12:32 < nmz787> kanzure: planner sounds good, basically instead of actually sending the requests, just queue them up, then we can print that out/save to file to read during debug
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12:33 < kanzure> the problem with the planner idea is that much of the logic branches depending on the results, so it's hard t indicate that in planner output
12:33 < kanzure> *to indicate
12:33 < nmz787> yeah we'd need date-versioned unit tests
12:33 < kanzure> for example, failure through one gateway should trigger the use of other gateways, while still keeping the previous accumulated information
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12:34 < kanzure> this sort of plan is very hard to make explicit
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12:39 < kanzure> (i suspect that passing in a callback doesn't count as explicit)
12:42 < kanzure> fenn: regarding your unhealthy interest in that cult... http://adam.chlipala.net/itp/tactic-reference.html "general goal management: assumption - proves the goal if it is computationally equal to a hypothesis"
12:46 < kanzure> hehe "The problem [with ai] is: nobody knows. Its a bit like two cavemen banging rocks together until one says "hey, lets use these rocks to kill something" and the other one goes "eh? How?" and the first one says "I don't know, keep bashing until something dies..""
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12:53 < pete4242_> How's the roadmap looking? Best guess for how long it will take us to cure death?
12:56 < kanzure> there are already many ways to not completely die, like gene preservation, but a lot of state is definitely still being lost at the moment
12:58 < kanzure> i wouldn't want to commit to an exact deadline, but i think that with a reaonable amount of effort that whole brain emulation can be working within 100 years
12:58 < kanzure> however, even emulations are capable of experiencing death
12:58 < kanzure> so i'm not sure if that's going to satisfy your question
12:58 < pete4242_> bah. Hurry up.
12:58 < pete4242_> If I can get you more money, do you think you could do it faster?
12:59 < kanzure> yep
13:01 < nmz787> anyone here have compelling evidence against use of antiperspirants? jrayhawk ?
13:01 < nmz787> the aluminum based ones
13:01 < kanzure> you mean harmful effects?
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13:02 < fenn> nmz787: all antiperspirants are bad, don't use them.
13:02 < fenn> they make me die, quickly
13:02 < nmz787> fenn: I haven't, but a med school friend of mine has always and still does
13:07 < pete4242_> Why does localbitcoins.com say people will pay more in cash to buy bitcoins than they will by bank transfer?
13:08 < kanzure> bank transfers are less privacy-preserving
13:08 < kanzure> there is a premium on privacy-preserving transactions
13:08 < pete4242_> They care that much!?
13:08 < pete4242_> Are they laundering? Drug money?
13:08 < kanzure> some people do not want their governments to know that they have any bitcoin
13:09 < kanzure> there are many good reasons to not reveal all information to such an overwhelmingly asymmetrically powerful entity such as a government
13:09 < pete4242_> Do you think they'd agree to do the trade at a bank, so the clerk can count and verify the cash?
13:12 < kanzure> some people have done that, apparently, yeah
13:12 < pete4242_> Cool. I'm gonna try it. Or get someone else to do it
13:13 < pete4242_> I'm too lazy to leave my desk
13:14 < kanzure> uh, do you want some bitcoin?
13:14 < pete4242_> No. I want some cash.
13:14 < kanzure> oh, well i can't help you there
13:15 < pete4242_> I haz bitcoins
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13:17 < pete4242_> Where's Eugen?
13:18 < kanzure> that's an excellent question
13:18 < kanzure> he should definitely show up
13:18 < pete4242_> Why? When?
13:19 < pete4242_> Did he make his 'big guns' bio list?
13:20 < pete4242_> Too bad Amon went into 'mainstream' politics
13:20 < pete4242_> like fuck is transhumanism gonna get popular with the masses in the next 20 years
13:21 < pete4242_> Zoltan for president!
13:21 < kanzure> my assumption has been that my projects will continue regardless of the relative mass popularity of transhumanism
13:21 < kanzure> the exact popularity does not seem to matter too much to me
13:21 < kanzure> and i highly recommend not caring
13:22 < pete4242_> Ya. but he says when he's pres he'll put all the money from the mil into transhuman projects
13:23 < pete4242_> I told them they're wasting their time.
13:24 < pete4242_> LOL: [2015-01-15 16:44:14] <jontyw> pete42: Given you think you are the smartest person in the hackspace I query why you spend any time there, clearly you can’t learn anything more from the members?
13:26 < pete4242_> Does Eugen still use retroshare?
13:27 < kanzure> i'm not sure. cathal might use retroshare.
13:28 < pete4242_> Who?
13:30 < kanzure> cathal garvey
13:30 < nmz787> http://www.diva-portal.se/smash/get/diva2:749485/FULLTEXT02.pdf
13:30 < pete4242_> Here? IRC name?
13:32 < nmz787> "In conclusion the study found that the time and temperature controlled how much BPA migrated from the bottles made of polycarbonate (PC) plastic, whereas the non-PC bottles in comparison only leached traces of BPA."
13:33 < nmz787> "In a related study, Martin Wagner and Jörg Oehlmann (2009), tested 20 types of mineral water in different containers made of PET, glass or coated paperboard in an in vitro system with a human estrogen receptor. They were able to show that 60% of the mineral water samples were contaminated with estrogenic like substances by leakage from the plastic."
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13:34 < nmz787> "The estrogenic activity in the water was determined with the U2OS-luc assay and expressed as bioassay-derived estradiol equivalents (Bio-EEQ). The polypropylene (PP) bottle gave the highest Bio-EEQ of 0.5 pg/ml, whereas High Density Polyethylene (HDPE) gave 0.3 pg/ml and Polyethylene Terephthalate (PET) 0.04 pg/ml. These results indicate that there is a small leakage of estrogenic substances from the plastic bottles. Further study is needed to ...
13:34 < nmz787> ... determine whether or not the estrogenic activity in the water could have any significant biological effect in humans."
13:34 < nmz787> yeah this sucks they don't compare to polycarbonate
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13:35 < nmz787> apparently they BPA-free plastic now just uses BPS (a sulphone group instead of dimethlymethyl) which is just as estrogenic and leachable
13:35 < pete4242_> You so need threaded IRC.
13:38 < pete4242_> jrayhawk: Is it OK to experiment on Kanz?
13:46 < nmz787> what is the acronym for effective glucose impact of a food?
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13:47 < nmz787> glycemic index
13:51 < fenn> glycemic load
13:51 < fenn> index is the load per gram
13:52 < fenn> also it's stupid because it only considers glucose, not all insulinogenic substances
13:52 < fenn> so pure fructose has a glycemic index of 0 and this results in diabetics chugging fructose
13:53 < nmz787> lol
13:53 < nmz787> i actually used it in that context
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13:54 < fenn> what would be mimicking estrogen in polypropylene?
13:55 < kanzure> does it have to? it just has to bind to the things that estrogen might, right?
13:55 < fenn> that's what mimicking estrogen means
13:55 < kanzure> words are hard man
13:57 < nmz787> the plasticizer
13:58 < nmz787> BPA and BPS are the big-name ones
13:58 < nmz787> but they are mainly talked about re: polycarbonate
14:00 < fenn> polypropylene has no plasticizers
14:00 < fenn> BPA is a resin monomer, not a plasticizer, and it's not in PP
14:01 < nmz787> well that PDF says it has estrogen inducers leaching
14:01 < nmz787> idk how it compares to PC
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14:14 < fenn> "Eating MealSquares has freed up lots of my time for working on MealSquares." --John, MealSquares cofounder
14:15 < fenn> wow they are stupidly expensive
14:16 < kanzure> surely john realized that he could just hire someone
14:16 < kanzure> instead of making mealsquares
14:17 < fenn> he did say "working on" not "making" so presumably it means advancing the company itself
14:18 < fenn> they are just packed in a jumble, which is stupid for a square object
14:18 < fenn> the whole point of squares (rectangular parallelepipeds) is that they tile in 3 dimensions
14:19 < kanzure> they mean square as in hipster
14:19 < fenn> this doesn't have a hipster vibe
14:19 < kanzure> hm
14:20 < fenn> i actually clicked on an ad, because it was on slatestarcodex
14:20 < fenn> they look pretty similar to my oat bars, but i'm not going to pay $3 each to have someone else make them
14:21 < fenn> their stupid website is borken too
14:24 < fenn> mealsquares ingredients: Eggs, orange juice, whole grain oats, milk, dark chocolate chips (chocolate, sugar, cocoa butter, milkfat), whey, rice bran, sunflower seeds, dates, vegetable glycerin, chickpeas, carrots, coconut oil, tapioca starch, xylitol, iodized sea salt, potassium citrate, cinnamon, baking powder, Vitamin C (ascorbic acid), Vitamin D3, Vitamin K2, lactase
14:24 < fenn> that is too many ingredients
14:25 < kanzure> has a strange order
14:25 < fenn> not really
14:25 < fenn> i dont get why they added dates AND orange juice AND glycerine AND xylitol
14:25 < fenn> since they all do basically the same thing
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14:35 < kanzure> "Having the entire energy output of 100 billion stars radiate uselessly into infinite space is very thermodynamically inefficient indeed, and yet that is exactly what we observe. If ET had sent just one single Von Neumann Probe to a nearby star at a speed no faster than what our spacecraft can travel at today then a Von Neumann Probe could be sent to every star in the galaxy in just 50 million years, a blink of a eye cosmically speaking. ...
14:36 < kanzure> ... And if that had happened a blind man in a fog bank could detect ET. But we don't see the slightest hint of ET despite having looked for him with our largest telescoped for over half a century. So where is everybody?"
14:36 < kanzure> eh? so we would have to spot a galaxy going dark in a few years? i'm not sure of the exact conditions. it's not like we have precise charts on all the known galaxies (we can barely observe the cosmic background radiation for every point)
14:38 < kanzure> *haven't yet
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14:45 < fenn> what's all that dark matter then
14:46 < kanzure> spores
14:46 < kanzure> oh wait
14:46 < kanzure> uh, not spores
14:46 < kanzure> too bad that dark matter halo thing was too unlikely
14:48 < kanzure> if dark matter is engineered material then i strongly doubt that it's just spores or whatever
14:48 < fenn> it might be spores
14:48 < fenn> that would explain the uniform distribution
14:49 < fenn> bad intergalactic trajectory leads to an orbit outside the star zone
14:49 < kanzure> why would you put so much material into spores like that?
14:49 < fenn> because you are a mindless automaton
14:50  * kanzure looks for his dark matter map
14:51 < fenn> ramachandran and hoyt measured the absorption spectrum of interstellar dust clouds and found that it perfectly matched the spectrum of a bacterial cell wall
14:51 < fenn> robert forward's camelot 30k seems relevant here too
14:52 < kanzure> i don't know this one?
14:52  * fenn shrugs
14:53 < kanzure> http://en.wikipedia.org/wiki/Camelot_30K
14:53 < kanzure> er this does not seem to be a spore nebula story
14:53 < fenn> it was a bad piece of fiction to describe how to build a spore-dispersing nuclear bomb from oort cloud objects using self replicating biological colonies
14:53 < kanzure> "The scientists discover the tragic conclusion of the kerack life cycle almost too late to save Merlene; when a kerack colony accumulated a large enough stockpile the queen would instinctively arrange it in such a way as to trigger a nuclear explosion, blasting kerack spores off of the Kuiper belt object to colonize other objects in the belt."
14:54 < kanzure> that's cute
14:55 < fenn> i'm not sure what the delta V on a microscopic dust grain from a nuclear explosion would be (prepositions..)
14:58 < delinquentme> fenn!
14:58 < kanzure> did you see the other day the set of extropy-chat quotes about dark matter and von neumann probe things? around 19:04 http://gnusha.org/logs/2015-01-15.log
14:58 < delinquentme> just the dude I was looking for.  The grey mill you made @ IPDX .. what is the name of that machine / build ?
14:59 < fenn> another possibility is that aliens have learned how to do warp travel and the space-time distortion is what's creating the illusion of large amounts of invisible mass
14:59 < fenn> dust clouds with that much mass wouldn't be transparent
15:00 < kanzure> i think that nebulas are more likely to be spores than dark matter, i think?
15:00 < kanzure> or i mean, some nebulas. obviously not all nebulas.
15:00 < kanzure> er, more likely to be spores than dark matter is likely to be spores
15:03 < kanzure> also i don't think we have pointed enough telescopes at the same spot for long enough to determine whether or not a certain spot is expected to be dark or not
15:03 < kanzure> in astronomy what do you call a map that shows everything in the sky?
15:04 < fenn> a map of the sky
15:04 < fenn> or "star chart" if you want to be a dork
15:04 < kanzure> all of the maps i have seen have been things like "between radians 1 and 2 of the sky"
15:06 < fenn> yes nebulas reflect and absorb light so they could be spores
15:06 < kanzure> like this http://www.posterpal.com/_images/z110626.jpg
15:06 < kanzure> (most maps of the sky do not look like this... or at least the ones that i find...)
15:07 < fenn> most maps don't cover the entire earth at once either
15:08 < fenn> delinquentme: zenbot
15:09 < fenn> it's running the "braindead" EMC install I think
15:09 < kanzure> is this supposed to represent all observable points http://cdn.thewire.com/img/upload/2011/05/26/Universe%20map.jpg
15:09 < fenn> now known as linuxCNC
15:11 < kanzure> i liked this visualization http://upload.wikimedia.org/wikipedia/commons/e/e7/Observable_universe_logarithmic_illustration.png
15:11 < fenn> kanzure: https://en.wikipedia.org/wiki/Mollweide_projection
15:12 < fenn> kanzure: please add a warning when linking directly to a 28MB png file
15:12 < fenn> better yet just link to the file page
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15:12 < fenn> http://wikimediafoundation.org/wiki/File:Observable_universe_logarithmic_illustration.png
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15:15 < fenn> 4096x4096 isnt too many pixels really
15:15 < kanzure> you mean 4200x4200
15:15 < fenn> er, yes
15:15 < kanzure> "Created specially for Wikipedia.org by Pablo Carlos Budassi any comments or suggestions: www.nuevemillas.com.ar unmismoobjetivo@gmail.com "
15:16 < kanzure> http://nuevemillas.sdf.org/
15:17 < kanzure> "+54 02615 320515 (pablo)"
15:17 < kanzure> uh.. i have no idea what this site is.
15:18 < kanzure> http://en.wikipedia.org/wiki/User:Unmismoobjetivo
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15:23 < fenn> delinquentme: i just learned of smoothieware/smoothieboard which may or may not be of interest
15:23 < nmz787> i've heard a few good things about it
15:24 < nmz787> saw it on hackaday yesterday or the day before
15:24 < nmz787> some best idea wins a free board contest
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15:35 < kanzure> http://armchairastronautics.blogspot.com/2014/06/blank-sky-maps.html
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15:39 < kanzure> very big file, wrong map http://upload.wikimedia.org/wikipedia/commons/f/f0/Claudius_Ptolemy-_The_World.jpg
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16:47 < kanzure> .title http://betterembsw.blogspot.com/2014/09/a-case-study-of-toyota-unintended.html?m=1
16:47 < yoleaux> Better Embedded System SW: A Case Study of Toyota Unintended Acceleration and Software Safety
16:48 < kanzure> "1. The Throttle Angle function in the Toyota code had a McCabe Cyclomatic Complexity of 146 (over 50 is considered untestable according to slides) [slide 38] 2. The main throttle function was 1300 lines long, and had no directed tests. [slide 38] 3. I find the static analysis results quite alarming. [slide 37] 4. 80+% of variables were declared as global. [slide 40] I find this to be a stunning lapse of quality, especially for a ...
16:48 < kanzure> ... safety-critical system."
16:48 < kanzure> https://news.ycombinator.com/item?id=8905718
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16:56 < delinquentme> paperbot http://pubs.acs.org/doi/abs/10.1021/la402244h
16:56 < kanzure> "The infeasibility of quantifying the reliability of life-critical real-time software" http://www3.cs.stonybrook.edu/~tashbook/fall2009/cse308/butler-finelli-infeasibilit.pdf
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17:50 < souljack> /list cisco
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18:28 < AmbulatoryCortex> paperbot http://ntrs.nasa.gov/archive/nasa/casi.ntrs.nasa.gov/19770085619.pdf
18:28 < AmbulatoryCortex> bah, and here I was so hopeful
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19:29 < kanzure> bloop
19:31 < cluckj> bleep
19:32 < kanzure> bleeping engaged please specify corresponding playback mode
19:34 < cluckj> bleep
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19:53 < kanzure> yashgaroth: howdy
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19:56 < yashgaroth> goddamn internet
19:56 < yoleaux> 17 Jan 2015 18:23Z <kanzure> yashgaroth: "A heritable recombination system for synthetic Darwinian evolution" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3569010/
19:58 < yashgaroth> trap sprung eh
19:59 < kanzure> hrm?
19:59 < kanzure> i trapped you in here years ago
19:59 < yashgaroth> oh, goading me into a reply so yolo could give me homework
20:00 < yashgaroth> also yes true
20:00 < kanzure> it's more like happy.... funtime.. biology.. homework. okay, yes, homework.
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20:23 < kanzure> yashgaroth: but you did look at it, right?
20:24 < yashgaroth> I currently am; so far it seems like very early stage work, low efficiency etc...interesting work though
20:25 < kanzure> surely there's other stuff that uses meiosis?
20:25 < kanzure> i was reading their review of earlier stuff and was sort of surprised about the lack of other methods
20:25 < kanzure> not sure what's going on here
20:25 < yashgaroth> seems like you can really only set blocks that get shuffled rather than real mutagenesis, but still better than before
20:26 < kanzure> simultaneous, multiple plasmid injection to do targetted mutagenesis sounds pretty great to me, yes
20:26 < yashgaroth> yeah no one really tries stuff like this
20:26 < kanzure> hmm
20:28 < kanzure> "Homology-directed library cassettes target the mutations to the regions of interest in a vast excess of chromosomal DNA, thus avoiding the undesired genomic instability often observed with mutator strains that prevent continuous rounds of mutation and selection.(26) The recently reported PACE technology uses continuous phage infection of E. coli to surmount the genomic instability problem, but does not enable targeted mutations or ...
20:28 < kanzure> ... addition or deletion of DNA and does not address recombination of beneficial mutations.(7) By using an endonuclease-induced double-strand break in a heritable cassette plasmid inside the cell to initiate mutagenesis, our method is distinct from previous efforts—both long-standing work in yeast (27–30) and the more recent MAGE technology in E. coli (8) and work from our laboratory in yeast (6)—to generate molecular diversity ...
20:28 < kanzure> ... that rely on transformation of linear DNA fragments to achieve recombination. A technique called “gene gorging” uses DSBs generated by SceI to initiate lamda Red-mediated recombination in E. coli, but this process has not been explored for library creation and cannot be iterated over multiple rounds.(31) Several methods using in vivo recombination in E. coli to generate antibody libraries have been reported (32, 33), but these ...
20:28 < kanzure> ... methods are often limited to antibody-derived genes and, unlike Heritable Recombination, have no mechanism for repeated diversification through sexual reproduction."
20:28 < kanzure> "DNA shuffling can mimic sexual reproduction, but it relies on PCR and therefore lacks the other benefits of our entirely in vivo process.(34) Thus, Heritable Recombination uniquely breaks the transformation barrier to library size and, by analogy to computational algorithms like dead-end elimination, enables virtual searches of extremely large libraries.(35) Most important, our strategy allows heritable cassette plasmids to be exchanged ...
20:28 < kanzure> ... among cells via mating and sporulation and so provides a simple and efficient way to track and combine beneficial mutations. In contrast to CAGE, which relies on bacterial conjugation to combine large contiguous regions of E. coli chromosomes, mutations can be crossed organically with Heritable Recombination over many rounds of the mutation and sexual reproduction cycle.(36)"
20:29 < kanzure> like, "and cannot be iterated over multiple rounds" sounds like a pretty huge problem or downside to me
20:29 < kanzure> multiple rounds is like one of those important fundamental parts of the idea of selection over many generations
20:29 < kanzure> or even multiple rounds on the same generation/samples, yeesh
20:30 < yashgaroth> I feel they may be exaggerating its impossibility with other methods
20:30 < yashgaroth> like "DNA shuffling relies on PCR so it's not in vivo so bleh" but in vivo has both benefits and drawbacks
20:31 < kanzure> also, can you help me understand how much mutagenesis is necessary to get a strain to respond to certain changes (like slightly different incubation conditions) ?
20:32 < kanzure> for example, without mutagenesis is it just totally impossible to convince most life to figure out a good solution in 10-20 generations, or does mutagenesis just often kick it up to <10 generations etc
20:32 < yashgaroth> no one can definitively help you there, other than "enough mutagenesis to get results"
20:32 < yashgaroth> e.g. adapting mammalian cells to serum-free media, sometimes it's five passages sometimes 20 sometimes never
20:32 < kanzure> but i mean, there must be some allowable variation that cells can survive in
20:33 < kanzure> so it would seem to be a funtion of initial strain "robustness" or something
20:33 < kanzure> *function
20:33 < kanzure> hm
20:33 < yashgaroth> that too, often it's less mutagenesis than some tiny fraction of the cells growing, just worse/slower
20:34 < kanzure> oh right, i guess you can bound this by the lower limit of the known error rate in polymerases etc
20:35 < kanzure> and various mutation rate estimates regarding stray gamma rays or whatever
20:36 < yashgaroth> I forget how many years it took for e.coli to evolve to digest citrate but that's a shit-ton of generations, albeit for a major metabolic change
20:36 < yashgaroth> ah 31000 generations
20:38 < kanzure> i am thinking of an oil-in-water microfluidic device for these sorts of shenanigans
20:38 < kanzure> where you trap the cell in the water droplet inside of some oil (to separate the drops)
20:38 < kanzure> and then you merge certain bubbles together when you want to forcemate particular phenotypes
20:39 < kanzure> also you could imagine breaking the bubbles and letting the strains replicate in some growth chamber in mass quantities, before trapping them again for further rounds of selection and forcemating
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20:40 < yashgaroth> putting both bubbles into a larger habitable bubble, I don't think even yeast get it on too readily when they're in a bubble the size of two yeast
20:41 < yashgaroth> but then I haven't read much yeast porn
20:41 < kanzure> oh, well, presumably the bubbles are larger than single-cells
20:41 < kanzure> i don't know if anyone has studied the optimal amount of water per cell to keep them alive
20:42 < kanzure> and couldn't you just lie somehow? surely someone has investigated this
20:42 < kanzure> oh right, my terminology is losing track of me there, whatever
20:42 < kanzure> "you put the cells in a supercollideher, obviously"
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20:42 < yashgaroth> oh no the female yeast sporulated, better luck next time
20:44 < yashgaroth> anyway yes I can certainly imagine all of that, practically however it's a lot of work
20:48 < yashgaroth> can't I just manufacture irisin in e.coli and sell it to rich people instead
20:49 < kanzure> oh, probably, why not?
20:49 < yashgaroth> good question
20:49 < kanzure> do you have a list of such things
20:50 < kanzure> because i sure as hell don't :/
20:50 < yashgaroth> that one's fairly high on the list now...I was looking into like NGF and GDF11, but the cystine knot is almost impossible to do in e.coli with any useful yield
20:51 < kanzure> only list i have at the moment is http://diyhpl.us/wiki/dna/projects/#igem-2014
20:51 < kanzure> which is the wrong kind of list
20:51 < kanzure> the chlorophyll one just caught my eye... reminds me, i saw a recent paper about optimizing chlorophyll and photosystem1 efficiency in crops... apparently nobody has done that yet.
20:52 < yashgaroth> tbf plants have been trying to optimize chlorophyll for a few billion years
20:52 < yashgaroth> there was the stuff about using cyanobacteria rubisco or whatever, could be promising
20:52 < kanzure> that doesn't mean they found a local maxima
20:52 < kanzure> hm
20:52 < kanzure> although i dunno if dropping a more efficient photosystem is a good idea?
20:52 < kanzure> does that fuck up other metabolism stuff
20:53 < yashgaroth> I'm sure the metabolism will cope, it's all other plant life on the planet that'll get fucked up
20:53 < kanzure> hm?
20:54 < yashgaroth> like faster photosynthesis in a given plant will be fairly tolerable, but if that plant outcompetes all other plants...
20:54 < kanzure> eh isn't that weeds are supposed to be good at
20:54 < yashgaroth> weeds are a balanced part of your complete ecosystem
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20:55 < kanzure> so if i collect enough cardboard boxes, i can have an entire ecosystem?
20:55 < yashgaroth> it's the prizes inside that count, but yes
20:56 < kanzure> like diabetes
20:57 < kanzure> hmm teamfourstar has new stuff out
21:00 < yashgaroth> oh dear
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22:14 < jrayhawk> nmz787: Nothing aside from the usual concerns about plasticizers and parabens.
22:16 < jrayhawk> Sove of which you seem to have stumbled upon.
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--- Log closed Sun Jan 18 00:00:27 2015