| --- Day changed Thu May 07 2009 | ||
| kanzure- | this is weird. | 00:19 |
|---|---|---|
| kanzure- | (destruct (fp (:constructor create-fp | 00:19 |
| kanzure- | so constructors for a struct/object has a name like 'create-fp' ? | 00:19 |
| kanzure- | I mean, variable names for constructors for data structs? seems a bit unusual | 00:19 |
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| fenn | heh http://www.shiftinsert.com/ | 13:26 |
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| kanzure | hello cis-action | 13:43 |
| kanzure | nothing quite like receiving a file named "unknown.zip" from your professor | 14:16 |
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| kanzure | does anybody have references to AFM instances of stacking of boxes or giant molecules? | 14:43 |
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| genehacker | woohoo I got some more reprap parts | 15:00 |
| kanzure | http://www.cdna.dk/origami | 15:02 |
| kanzure | SARSE - DNA designer package is a sequence editor with a toolbox for designing DNA origami structures in 2D and 3D: | 15:02 |
| kanzure | http://sarse.org/ | 15:02 |
| kanzure | A yoctoliter-scale DNA reactor for small molecule evolution. | 15:03 |
| kanzure | http://www.cdna.dk/index.php/software/26-a-yoctoliter-scale-dna-reactor-for-small-molecule-evolution-j-am-chem-soc-2009.html | 15:03 |
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| kanzure | http://wikileaks.org/wiki/To_the_moon_and_beyond:_NASA's_Exploration_Systems_Architecture_Study%2C_630_pages%2C_2006 | 15:28 |
| kanzure | 15:48 | |
| fenn | thanks for nothing patrick! | 15:55 |
| fenn | rawr | 15:55 |
| fenn | i need a copyright lawyer to come in and swing his balls around | 15:56 |
| kardan_ | fenn i received your mail and will adept the model accordingly | 15:58 |
| kardan_ | are there any reliable info sites about chemtrails? | 15:59 |
| kanzure | hm. my eyeball has a pulse. | 16:04 |
| fenn | kardan_: as soon as you start delving into conspiracy theories and disinformation, no source of information but your own observations is reliable | 16:12 |
| fenn | but that's true in any case | 16:12 |
| kanzure | fenn: what's wrong with being an outlaw. | 16:13 |
| fenn | it's hard to get funding.. oh wait | 16:13 |
| fenn | kanzure: you can put a lot of work into something and then have it all taken away because you based it on something illegal | 16:14 |
| kanzure | you can have it taken away anyway because you don't have any money | 16:15 |
| fenn | not really | 16:15 |
| kanzure | if people with money want it, they can go and get it. | 16:15 |
| fenn | i'm talking about software here | 16:15 |
| wrldpc | http://www.ballerride.com/2008/03/24/buy-640-ft-cruise-ship-bring-1279-friends/ | 16:17 |
| wrldpc | only $31M, guys! | 16:17 |
| fenn | hmm. bio-electricity, is that like Mako energy? | 16:21 |
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| kanzure | fenn: I can't seem to find the function 'eb-oper' by grepping. what do I do? it's used in codeGeneral/ and codeEM/ frequently. | 16:41 |
| fenn | eb-* doesnt seem to be defined anywhere | 16:45 |
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| kanzure | maybe there's an update.lisp (or one of the older versions) that has a functional update-across or update-through method that does not rely on eb-opers. | 16:51 |
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| kanzure | update.2001.08.24.lisp, for instance, does not contain a reference to eb-opers | 16:53 |
| kanzure | hm. the parameter list is a bit different though than the one in update.lisp. will take some fudging. | 16:54 |
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| fenn | i admire your tenacity | 17:03 |
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| kanzure | :( I just spent 20 minutes playing with a god damned syringe | 17:17 |
| genehacker | why? | 17:18 |
| kanzure | was just pondering about the maximum size hole to generate a certain pressure at the oriface | 17:23 |
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| fenn | where is one supposed to learn how to make a gantt chart? | 19:01 |
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| kardan_ | fenn sounds interesting | 19:06 |
| kardan_ | there are plenty of open implementations yet | 19:07 |
| kardan_ | what do you need? | 19:07 |
| fenn | well i'm really just trying to lay out a set of tasks for completing a project so i know what is possible to work on | 19:08 |
| fenn | a dependency tree, if you will | 19:08 |
| fenn | but gantt chart looks like it is a similar concept that already exists | 19:09 |
| fenn | i'm playing around with kplato and it has a lot of built in assumptions that are getting in the way | 19:09 |
| kanzure | fenn: there's a gantt chart GNU thingy. | 19:17 |
| kanzure | not sure if a gantt chart is good for dependency management though | 19:17 |
| kanzure | what about graphviz? | 19:18 |
| fenn | i'm sick of graphviz | 19:18 |
| fenn | http://imagebin.org/48224 | 19:20 |
| fenn | seems like those color bars should add up, not all occur at the same time | 19:20 |
| kanzure | I didn't have a good experience with the gnu gantt chart thingy. the GUI was all out of alignment. | 19:22 |
| fenn | "A Gantt chart showing three kinds of schedule dependencies" | 19:22 |
| kanzure | (was not kplato) | 19:22 |
| fenn | so they do theoretically include dependencies | 19:22 |
| fenn | maybe kplato just sucks | 19:22 |
| fenn | (likely) | 19:22 |
| fenn | ah i figured out how to do it | 19:29 |
| fenn | you drag one bar to the other and a dialog pops up | 19:29 |
| fenn | then you have to press 'calculate' | 19:30 |
| fenn | of course since the dependencies are invisible there's no way to change them if you screw up.. | 19:31 |
| drazak | I have a research project that will require approximately 22500 experiments | 19:31 |
| drazak | :S | 19:31 |
| kanzure | drazak: what is it? | 19:32 |
| fenn | time to get a robot | 19:32 |
| kanzure | quick! kidnap fenn! | 19:32 |
| fenn | very funny, considering the source | 19:34 |
| kanzure | meh, I'm just the ai | 19:34 |
| kanzure | drazak: are you going to explain or not? | 19:35 |
| drazak | kanzure: uh, I'm writing a paper comparing how different developer components affect the final film product | 19:35 |
| drazak | sorry, I was reading something else | 19:35 |
| kanzure | you've effectively said nothing | 19:35 |
| fenn | you're doing experiments for a paper? science! | 19:36 |
| drazak | I know | 19:36 |
| drazak | right? | 19:36 |
| fenn | i thought it was extinct | 19:36 |
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| kanzure | fenn: did you see the yoctoliter DNA (un)lockable boxes? | 19:36 |
| fenn | yes | 19:36 |
| genehacker | why were you playing with syringes? | 19:36 |
| fenn | the simulations looked a lot prettier than the micrographs | 19:36 |
| kanzure- | I'm still trying to think of how to make use of those boxes | 19:36 |
| genehacker | pribnow box? | 19:37 |
| kanzure- | genehacker: I was just playing with a syringe because I found one laying around. | 19:37 |
| genehacker | a metal one? | 19:37 |
| kanzure- | plastic. | 19:37 |
| genehacker | where? | 19:37 |
| drazak | kanzure: I'm varying the amounts of metol, hydroquinone, NaBr, and NaSO3 in black and white film developers, to determine an optimal combination, also at pH's ranging from 5-14, and 3 temperatures | 19:37 |
| kanzure- | by my sink. | 19:37 |
| genehacker | ok | 19:37 |
| kanzure- | drazak: for photographic film? | 19:37 |
| fenn | genehacker: http://heybryan.org/books/papers/Self-assembly%20of%20a%20nanoscale%20DNA%20box%20with%20a%20cont | 19:37 |
| fenn | rollable%20lid.pdf | 19:37 |
| fenn | blah | 19:37 |
| kanzure- | haha | 19:38 |
| genehacker | at least it wasn't metal and not the ground | 19:38 |
| genehacker | you can boil water with a syringe like that | 19:38 |
| fenn | drazak: you can simplify things several orders of magnitude by assuming the components affect the result linearly | 19:39 |
| drazak | kanzure-: yes | 19:39 |
| drazak | fenn: but they don't | 19:39 |
| kanzure- | genehacker: boil water how? | 19:39 |
| drazak | fenn: :S | 19:39 |
| fenn | then you just vary each parameter until it's at its optimum | 19:39 |
| genehacker | put water in it close it and pull | 19:39 |
| kanzure- | genehacker: the water that comes out is cool. | 19:39 |
| genehacker | no | 19:39 |
| genehacker | it doesn't come out | 19:39 |
| fenn | well you dont have to do an exhaustive survey just to show that they interact in odd ways | 19:39 |
| kanzure- | oh, you mean put water in it and pull | 19:39 |
| kanzure- | I see. | 19:39 |
| fenn | a better use would be to verify the results with many repetitions of the same experiment | 19:40 |
| genehacker | if no heat transfer occurs then it doesn't change temperature | 19:40 |
| drazak | fenn: metol and hydroquinone are superaditive, and not linearly, NaSO3 creates a condition called sulfite scavenging, which is where SO3's pick up free electrons instead of allowing a redox reaction | 19:40 |
| genehacker | so what could tiny dna boxes be used for | 19:40 |
| kanzure- | genehacker: in vitro compartmentalization and directed evolution. | 19:41 |
| drazak | fenn: I'm doing atleast 3 reps of each experiment | 19:41 |
| kanzure- | genehacker: did you read the email I sent to diybio? | 19:41 |
| genehacker | drazak what are you doing? | 19:41 |
| genehacker | hey I got an idea | 19:41 |
| kanzure- | genehacker: the one about using light-controlled oligonucleotides for different keys for the boxes | 19:41 |
| drazak | genehacker: writing a paper on photographic black and white film developers | 19:41 |
| kanzure- | (azobenzene stuff) | 19:41 |
| genehacker | make fractals | 19:41 |
| kanzure- | why | 19:41 |
| genehacker | really really detailed fractals | 19:41 |
| genehacker | make an approximation of a menger sponge | 19:42 |
| kanzure- | I want to see if you can stack the boxes | 19:42 |
| kanzure- | with an AFM tip. | 19:42 |
| fenn | i bet they are really floppy | 19:42 |
| genehacker | nanocrates? | 19:42 |
| fenn | more like baskets woven out of snot | 19:42 |
| kanzure- | there was something about how they deform due to force from AFM tips. | 19:42 |
| kanzure- | yes | 19:43 |
| genehacker | nanocrates for nanobots to carry around nanowarehouses | 19:43 |
| * kanzure- shoots genehacker | 19:43 | |
| fenn | let's not get carried away | 19:43 |
| genehacker | ok not | 19:43 |
| genehacker | but we could | 19:43 |
| genehacker | with some sort of transport protein | 19:44 |
| kanzure- | like a DNA motor? | 19:44 |
| kanzure- | but let's not. | 19:44 |
| drazak | fenn: all of the stats and experiment experts that I've spoken with agree that I'll have to do all of the tests | 19:44 |
| kanzure- | http://heybryan.org/books/papers/rothemund/ | 19:44 |
| genehacker | put a specific header on the boxes and you can sort them... | 19:46 |
| kanzure- | well you use oligonucleotides to target the boxes | 19:46 |
| kanzure- | with different IDs. | 19:46 |
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| genehacker | what could we use it for? | 19:47 |
| genehacker | storing atoms? | 19:47 |
| kanzure- | directed evolution | 19:47 |
| genehacker | RNA creature wars? | 19:47 |
| kanzure- | coupling genotypes to phenotypes. | 19:48 |
| kanzure- | for small molecules, at least | 19:48 |
| genehacker | perhaps we could make some weird dna absorbant sponge... | 19:49 |
| kanzure- | anyway, you should check out the DNA origami software | 19:49 |
| kanzure- | it's GPL'd and such. it does stuff other than boxes. | 19:49 |
| fenn | learn how to make a DNA dolphin! :P | 19:49 |
| fenn | swarms of killer nano dolphins | 19:50 |
| kanzure- | they'll just fly off and thank us for all the fish | 19:50 |
| genehacker | ans with a DNA synthesizer we can make one | 19:50 |
| fenn | vicious little dolphins with nano-knife teeth | 19:51 |
| kanzure- | yeah! with nanoeyes! | 19:51 |
| kanzure- | and nanofins! | 19:51 |
| genehacker | we need a flow cell reaction chamber | 19:51 |
| genehacker | and lasers! | 19:51 |
| genehacker | oops meant nanolasers | 19:52 |
| kanzure- | if a DNA box can hold water without leaking, | 19:57 |
| kanzure- | and if you can fold a microfluidic circuit (out of anything foldable), | 19:58 |
| kanzure- | then it should be feasible to design that into CAD, and then get that target structure in DNA. don't know what the input format is to the DNA origami program though | 19:58 |
| kanzure- | it would be fun to see if you could send enzymes through that circuit and selectively modify the circuit based off of the DNA | 20:00 |
| kanzure- | or to turn it into a DNA synthesizer or something. | 20:00 |
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| genehacker | so how do we make a reaction flow plate | 20:03 |
| kanzure- | what is a reaction flow plate | 20:03 |
| kanzure- | have you put any thought into making some graph grammars for organic chemistry, genehacker ? | 20:03 |
| genehacker | the thing that goes on a microscope slide for maskless lithography dna synthesis | 20:03 |
| genehacker | I don't know what a graph grammar is | 20:04 |
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| kanzure- | it's the thing that would let you manipulate an organic molecule to build it into something complex from carbon and chemistry | 20:04 |
| kanzure- | *and other chemical elements | 20:04 |
| genehacker | what is a graph grammar | 20:04 |
| fenn | kanzure-: there is a limit to the complexity achievable with DNA origami | 20:04 |
| kanzure- | it's a substitution rule that works on graphs, basically | 20:04 |
| fenn | related to the oligo length | 20:05 |
| kanzure- | is it less than the complexity of origami in general? | 20:05 |
| kanzure- | oh | 20:05 |
| genehacker | ok | 20:05 |
| genehacker | what do you mean oligolength | 20:05 |
| fenn | beyond a certain length you will start to get non-specific matches | 20:05 |
| genehacker | oh | 20:05 |
| kanzure- | genehacker: I think campbell would be interested in paying you if you were to make an organic chemistry graph grammar. | 20:05 |
| fenn | like in PCR with slow temperature ramping | 20:05 |
| genehacker | I don't know organic chemistry | 20:05 |
| kanzure- | there are lists of organic chemistry reactions | 20:06 |
| genehacker | and I don't know graph grammars | 20:06 |
| kanzure- | like on wikipedia | 20:06 |
| kanzure- | well he can teach you that | 20:06 |
| genehacker | but I am willing to help you | 20:06 |
| fenn | i'd be floored if genehacker managed to write a graph grammar for chemistry | 20:06 |
| fenn | i mean that's like a master's thesis, and most people would screw it up even then | 20:06 |
| kanzure- | wtf, really? | 20:07 |
| kanzure- | to me it seems like something that I could do in a night | 20:07 |
| kanzure- | if I cared. | 20:07 |
| fenn | doesn't everything? | 20:07 |
| kanzure- | so wait, what is supposed to be so complicated about this? | 20:07 |
| genehacker | well I might be able to use one of my friends who knows organic chemistry as a translater | 20:07 |
| kanzure- | there are about 25~ rules for typical reactions | 20:07 |
| kanzure- | so I just need to encode those rules into the GXML format | 20:07 |
| genehacker | have you written graph grammars? | 20:07 |
| fenn | kanzure-: the difference between theory and practice is in practice | 20:07 |
| kanzure- | er, sort of :) | 20:07 |
| fenn | also there's hofstadter's law | 20:08 |
| kanzure- | oh right. there are certain cases where certain reactions don't work. | 20:08 |
| genehacker | hofstader's law is a self-referential | 20:09 |
| genehacker | FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF- | 20:09 |
| kanzure- | fenn: how terrible would it be if I didn't include the "in practice" parts | 20:09 |
| fenn | this gantt chart stuff is fun, it almost makes me want to go work at boeing and pretend i'm doing something useful | 20:09 |
| kanzure- | I mean, those could be appended with experience, right? | 20:09 |
| fenn | no | 20:10 |
| kanzure- | no? | 20:10 |
| fenn | what it means is you neglect to consider all of the steps while planning | 20:10 |
| kanzure- | what? | 20:10 |
| kanzure- | blah. why are my organic chem books packed up when I need them for once .. | 20:10 |
| fenn | it's a common bias, i think there's even a name "planning bias" or something | 20:10 |
| fenn | nothing to do with organic chemistry | 20:11 |
| kanzure- | I don't know what you are talking about | 20:11 |
| fenn | oh look its your favorite author http://www.overcomingbias.com/2007/09/planning-fallac.html | 20:11 |
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| kanzure- | er, does anyone know the name of the method that won the nobel prize in chemistry for something named like "retroactive synthesis"? (that's not it) | 20:17 |
| kanzure- | aha. "retrosynthetic analysis" | 20:17 |
| kanzure- | "This is achieved by transforming a target molecule into simpler precursor structures without assumptions regarding starting materials." | 20:18 |
| genehacker | speaking of chemistry | 20:18 |
| genehacker | did you hear what the guys upstairs did? | 20:18 |
| kanzure- | http://en.wikipedia.org/wiki/Retrosynthesis | 20:18 |
| kanzure- | no? | 20:18 |
| fenn | they made a box inside a box? | 20:19 |
| fenn | matroishkane? | 20:19 |
| genehacker | http://www.physorg.com/news160924908.html | 20:19 |
| genehacker | centimeter squares of graphene | 20:19 |
| genehacker | wonder if it's one sheet | 20:19 |
| genehacker | if it is | 20:20 |
| genehacker | I'd like to stack a bunch on top of each other | 20:20 |
| fenn | you mean single crystal? | 20:20 |
| genehacker | and see if I can support an elephant standing on a pinhead | 20:20 |
| genehacker | single sheet | 20:20 |
| genehacker | single crystal yeah | 20:20 |
| kanzure- | wouldn't that drive the pinhead through the elephant? | 20:21 |
| genehacker | not if the elephant stands on plate with a pin on it | 20:21 |
| genehacker | or some sort of cone | 20:22 |
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| kanzure- | The potential of a chemical graph transformation system | 20:28 |
| kanzure- | http://heybryan.org/books/papers/The%20potential%20of%20a%20chemical%20graph%20transformation%20system.pdf | 20:29 |
| fenn | kanzure-: how is a graph grammar for chemistry different from a reaction simulator? | 20:30 |
| fenn | hey wait a minute | 20:31 |
| fenn | that paper is about something completely different | 20:31 |
| kanzure- | there's a reaction simulator? | 20:31 |
| genehacker | hey is there a format for storing information on DNA? | 20:31 |
| kanzure- | FASTA? | 20:31 |
| kanzure- | fenn: how is this wrong? | 20:32 |
| fenn | you researched it before. there were lots of them, unfortunately i didnt care so i dont remember any | 20:32 |
| genehacker | for storing information like text on DNA | 20:32 |
| kanzure- | it's about graph rewriting. that's what you want. | 20:32 |
| kanzure- | wtf, I don't remember. can you spout out some terms? | 20:32 |
| fenn | uh gee.. they all have stupid quirky names | 20:33 |
| kanzure- | engineers are terrible at naming things. | 20:33 |
| fenn | chemical engineers are worse | 20:33 |
| kanzure- | case-and-point: "A-DESIGN" | 20:33 |
| kanzure- | EWOD | 20:33 |
| fenn | nah, chemistry stuff is always like 'SNARF' or 'PUTT-PUTT' | 20:33 |
| kanzure- | EWOD MEMS A-DESIGN in LISP. blah. /me shoots someone | 20:33 |
| genehacker | I'd like to store text encoded on DNA | 20:34 |
| kanzure- | then use a base-four system | 20:34 |
| fenn | yeah, how about THE CODE OF LIFE | 20:34 |
| kanzure- | or | 20:34 |
| kanzure- | you could look at Watson-Crick pairing | 20:34 |
| kanzure- | and choose two nucleotides that do not pair commonly | 20:35 |
| genehacker | maybe binary would be better | 20:36 |
| kanzure- | "your friendly local organic chemistry" bah. | 20:36 |
| fenn | http://heybryan.org/mediawiki/index.php/Comp_chem_linkdump | 20:36 |
| fenn | "FROWNS is a free implementation of the SMILES system by one of the authors[10]. The FROWNS implementation of SMIRKS, while incomplete, was started mainly because of a disconnection between how SMILES and SMARTS handle hydrogen atoms." | 20:39 |
| fenn | http://www.phdcomics.com/comics/archive/phd111908s.gif | 20:40 |
| fenn | COSY, NOESY, ROESY, DAISY, RELAY, DICE, ICE, and INADEQUATE. | 20:41 |
| fenn | it must be from all the fumes | 20:43 |
| kanzure- | " The SMILES framework provides canonicalization, a convenient | 20:45 |
| kanzure- | query-specification language (SMARTS) and representations for chemical reac- | 20:45 |
| kanzure- | tions (SMIRKS). | 20:45 |
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| fenn | http://imagebin.org/48235 | 21:28 |
| fenn | i wonder if that was even worth doing | 21:28 |
| kanzure- | great, now serialize it. | 21:28 |
| kanzure- | "acquire oxyacetylene welder" heh | 21:29 |
| fenn | serialize? | 21:29 |
| fenn | it's some random XML if you want it | 21:29 |
| kanzure- | make it into a more readable form with ordered steps | 21:29 |
| kanzure- | well, ok, but I'm not going to touch it | 21:29 |
| kanzure- | or maybe I will. don't know. | 21:30 |
| kanzure- | rabid archiving instincts tell me to take the XML. | 21:30 |
| fenn | well the point is there's no inherent order to it except for disassembling/reassembling the rails and painting | 21:30 |
| kanzure- | so anyway, I'm reading about retrosynthesis of chemical compounds where you work from a final product and go backwards until you get stuff that you can actually use. so, naturally, there are many dull candidates that you can pick at a certain point in the tree | 21:31 |
| kanzure- | while other candidates would lead to shorter construction paths | 21:31 |
| kanzure- | too bad I can't see any immediate application of that style of thinking to instruction generation | 21:32 |
| kanzure- | it's not like instructions can be broken up like that.. it's not chemistry. | 21:32 |
| fenn | usually you dont have a specific end-product artifact in mind until you know how you're going to make it | 21:33 |
| fenn | i mean, say i have the plans for starship enterprise; i still dont know how to make the damn thing | 21:34 |
| kanzure- | argh | 21:39 |
| kanzure- | this should be a fucking crime | 21:39 |
| kanzure- | Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation | 21:39 |
| katsmeow | bid out the subsystems, and sue them if they don't deliver | 21:39 |
| kanzure- | "we have made a web interface for retrosynthesis strategies" | 21:40 |
| kanzure- | "but we don't give the link, haha!" | 21:40 |
| fenn | for your rabidity http://adl.serveftp.org/papers/cnc.tgz | 21:44 |
| kanzure- | I tried looking for proxies but couldn't find anything with sufficient documentation or tutorialeage on the net. | 21:45 |
| kanzure- | er, for a proxy for apache or something | 21:45 |
| kanzure- | hm. tar --list chokes while reading that file, fenn. | 21:49 |
| fenn | tar -zxvf cnc.tgz | 21:50 |
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| kanzure- | I need an index of names of facebook users. | 22:38 |
| kanzure- | and then I want to cross-correlate that to a list of authors who have written papers together where two of the names are the same last name | 22:39 |
| kanzure- | and one of the last names is generally a male name, the other is a woman's name | 22:39 |
| kanzure- | this would be an interesting way of finding people who are genetically likely to be very fucked up | 22:39 |
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| kanzure- | (port-maxes (mapcar #'(lambda (x) (1- (length (eb-oper (eval x))))) | 23:39 |
| kanzure- | hrm. this only makes eb-oper more mysterious. | 23:39 |
| kanzure- | (eval x) might as well be '5' | 23:39 |
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| kanzure- | but another one says (eb-opers (nth eb-num ebs)) | 23:48 |
| kanzure- | "nth" is a reserved word/function-thingy | 23:48 |
| kanzure- | so why would eb-opers take an 'eb' as input? whereas eb-oper takes a number? | 23:48 |
| kanzure- | isn't it supposed t obe that any function name ending in a 's' is supposed to be related to a list? in lisp only, I mean, not petty standard naming conventions | 23:56 |
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