--- Day changed Thu May 07 2009
00:19 < 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
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13:26 < fenn> heh http://www.shiftinsert.com/
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13:43 < kanzure> hello cis-action 
14:16 < kanzure> nothing quite like receiving a file named "unknown.zip" from your professor
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14:43 < kanzure> does anybody have references to AFM instances of stacking of boxes or giant molecules?
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15:00 < genehacker> woohoo I got some more reprap parts
15:02 < 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/
15:03 < 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
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15:28 < kanzure> http://wikileaks.org/wiki/To_the_moon_and_beyond:_NASA's_Exploration_Systems_Architecture_Study%2C_630_pages%2C_2006
15:48 < kanzure>  
15:55 < fenn> thanks for nothing patrick!
15:55 < fenn> rawr
15:56 < fenn> i need a copyright lawyer to come in and swing his balls around
15:58 < kardan_> fenn i received your mail and will adept the model accordingly
15:59 < kardan_> are there any reliable info sites about chemtrails?
16:04 < kanzure> hm. my eyeball has a pulse.
16:12 < 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
16:13 < kanzure> fenn: what's wrong with being an outlaw.
16:13 < fenn> it's hard to get funding.. oh wait
16:14 < 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
16:15 < 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
16:17 < wrldpc> http://www.ballerride.com/2008/03/24/buy-640-ft-cruise-ship-bring-1279-friends/
16:17 < wrldpc> only $31M, guys!
16:21 < fenn> hmm. bio-electricity, is that like Mako energy?
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16:41 < 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.
16:45 < fenn> eb-* doesnt seem to be defined anywhere
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16:51 < 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.
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16:53 < kanzure> update.2001.08.24.lisp, for instance, does not contain a reference to eb-opers
16:54 < kanzure> hm. the parameter list is a bit different though than the one in update.lisp. will take some fudging.
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17:03 < fenn> i admire your tenacity
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17:17 < kanzure> :( I just spent 20 minutes playing with a god damned syringe
17:18 < genehacker> why?
17:23 < kanzure> was just pondering about the maximum size hole to generate a certain pressure at the oriface
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19:01 < fenn> where is one supposed to learn how to make a gantt chart?
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19:06 < kardan_> fenn sounds interesting
19:07 < kardan_> there are plenty of open implementations yet
19:07 < kardan_> what do you need?
19:08 < 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
19:09 < 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
19:17 < kanzure> fenn: there's a gantt chart GNU thingy.
19:17 < kanzure> not sure if a gantt chart is good for dependency management though
19:18 < kanzure> what about graphviz?
19:18 < fenn> i'm sick of graphviz
19:20 < fenn> http://imagebin.org/48224
19:20 < fenn> seems like those color bars should add up, not all occur at the same time
19:22 < 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)
19:29 < fenn> ah i figured out how to do it
19:29 < fenn> you drag one bar to the other and a dialog pops up
19:30 < fenn> then you have to press 'calculate'
19:31 < 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
19:32 < kanzure> drazak: what is it?
19:32 < fenn> time to get a robot
19:32 < kanzure> quick! kidnap fenn!
19:34 < fenn> very funny, considering the source
19:34 < kanzure> meh, I'm just the ai
19:35 < 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
19:36 < 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
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19:36 < 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
19:37 < 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
19:38 < 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
19:39 < 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.
19:40 < 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
19:41 < 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
19:42 < 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.
19:43 < 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
19:44 < 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/
19:46 < 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.
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19:47 < genehacker> what could we use it for?
19:47 < genehacker> storing atoms?
19:47 < kanzure-> directed evolution
19:47 < genehacker> RNA creature wars?
19:48 < kanzure-> coupling genotypes to phenotypes.
19:48 < kanzure-> for small molecules, at least
19:49 < 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
19:50 < 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
19:51 < 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!
19:52 < genehacker> oops meant nanolasers
19:57 < kanzure-> if a DNA box can hold water without leaking,
19:58 < 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
20:00 < 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.
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20:03 < 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
20:04 < genehacker> I don't know what a graph grammar is
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20:04 < 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
20:05 < 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
20:06 < 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
20:07 < 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 :)
20:08 < fenn> also there's hofstadter's law
20:08 < kanzure-> oh right. there are certain cases where certain reactions don't work.
20:09 < 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?
20:10 < 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
20:11 < 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
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20:17 < 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"
20:18 < 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?
20:19 < 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
20:20 < 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
20:21 < 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
20:22 < genehacker> or some sort of cone
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20:28 < kanzure-> The potential of a chemical graph transformation system
20:29 < kanzure-> http://heybryan.org/books/papers/The%20potential%20of%20a%20chemical%20graph%20transformation%20system.pdf
20:30 < fenn> kanzure-: how is a graph grammar for chemistry different from a reaction simulator?
20:31 < 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?
20:32 < 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?
20:33 < 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
20:34 < 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
20:35 < kanzure-> and choose two nucleotides that do not pair commonly
20:36 < 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
20:39 < 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."
20:40 < fenn> http://www.phdcomics.com/comics/archive/phd111908s.gif
20:41 < fenn> COSY, NOESY, ROESY, DAISY, RELAY, DICE, ICE, and INADEQUATE.
20:43 < fenn> it must be from all the fumes
20:45 < 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).
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21:28 < fenn> http://imagebin.org/48235
21:28 < fenn> i wonder if that was even worth doing
21:28 < kanzure-> great, now serialize it.
21:29 < 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
21:30 < 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
21:31 < 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
21:32 < 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.
21:33 < fenn> usually you dont have a specific end-product artifact in mind until you know how you're going to make it
21:34 < fenn> i mean, say i have the plans for starship enterprise; i still dont know how to make the damn thing
21:39 < 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
21:40 < kanzure-> "we have made a web interface for retrosynthesis strategies"
21:40 < kanzure-> "but we don't give the link, haha!"
21:44 < fenn> for your rabidity http://adl.serveftp.org/papers/cnc.tgz
21:45 < 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
21:49 < kanzure-> hm. tar --list chokes while reading that file, fenn.
21:50 < fenn> tar -zxvf cnc.tgz
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22:38 < kanzure-> I need an index of names of facebook users.
22:39 < 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
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23:39 < 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'
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23:48 < 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?
23:56 < 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