--- Day changed Thu Jun 05 2008
00:00 < kanzure> a projection fallacy?
00:00 < Phreedom> wishful thinking/cognitive dissonance
00:01 < joshcryer> 1.0 was met, so hah!
00:05 < joshcryer> Just FYI I doubt a RepRap developer, even if he lurked on IRC, would address some of these comments.
00:07 < Phreedom> joshcryer: why?
00:08 < joshcryer> Phreedom, why waste time arguing with someone on IRC? :)
00:08 < fenn> because academics never respond to direct, reasonable questions from the general public
00:08 < fenn> especially not on irc
00:08 < Phreedom> fenn: you hate academics ;)
00:09 < fenn> it's true, those fuckers never answer my email
00:09 < fenn> no polite "i'm too busy to talk to the unwashed masses"
00:09 < joshcryer> They always answer mine.
00:10 < joshcryer> I recently emailed Robert Sheldon with regards to the Dusty-M2P2 concept he had going.
00:10 < joshcryer> Maybe you fill your emails with useless jargon.
00:10 < fenn> maybe a lot of things, i dont know what the problem is
00:12 < Phreedom> fenn: quit emailing, do something ;)
00:13 < fenn> Phreedom: i made some shelves today, they're very pretty (no pics sry)
00:14 < Phreedom> lol
00:14 < Phreedom> that's gonna help replication :)
00:14 < fenn> then i stacked my prototyping supplies on them
00:14 < fenn> Phreedom: hey at least i have a design for a less expensive motor driver
00:14 < Phreedom> like?
00:15 < fenn> uh, this is the overview i guess http://fennetic.net/machines/index.php?motherchip
00:15 < Phreedom> fenn: microstepping driver?
00:15 < fenn> no, steppers suck
00:16 < Phreedom> :)
00:16 < Phreedom> so what are you going to use for position feedback?
00:27 < fenn> encoder on the motor
00:31 < Phreedom> as usual
00:31 < Phreedom> oh well
00:31 < Phreedom> fenn: do you have any completion timeframes
00:37 < fenn> nope
00:37 < Phreedom> fenn: so you aren't actively developing it
00:37 < Phreedom> ok
00:38 < Phreedom> anyhow it would be hard for us to cooperate at this particular moment :(
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02:30 < kanzure> fenn: uh
02:30 < kanzure> by the way
02:30 < kanzure> so, as you know, I mentioned that Andy's lab has DOD funding
02:31 < kanzure> as it turns out, the synthetic biology group that I am in, is specifically funded by a grant from DOD
02:31 < fenn> whee
02:31 < kanzure> so
02:31 < kanzure> basically I have evidence with you and on the site that I've done all of htis already
02:31 < kanzure> therefore there's no way they can claim it
02:31 < kanzure> and do weird things to me.
02:32 < fenn> hmm, guys with guns can take whatever they want
02:32 < fenn> 'national interest' and all that
02:32 < kanzure> oh right
02:32 < fenn> eminent domain, they'll plow your house over
02:32 < kanzure> fun stuff.
02:32 < fenn> to make a toll booth
02:32 < fenn> yah, anyway, i think DOD is too clueless to recognize the significance
02:33 < kanzure> but they are funding it
02:33 < kanzure> oh
02:33 < kanzure> point.
02:33 < kanzure> who knew that a humanitarian project would ultimately be funded by DOD.
02:34 < fenn> lots of good stuff has come out of it.. polywell was not DOE but Navy
02:34 < fenn> they're just focused on killing machines, that's all
02:34 < kanzure> humanitarian killing machines?
02:34 < fenn> works both ways
02:34 < fenn> technology can do good or bad
02:35 < fenn> ICBM's gave us the space program (for what its worth)
02:35 < kanzure> eh, what about the original rocketgangbangers ?
02:35 < fenn> who?
02:35 < kanzure> don't know their names :)
02:35 < kanzure> the russian, the American, those guys
02:35 < kanzure> pioneers of rocketry stuff
02:36 < fenn> von braun was making toys in his yard until WWII
02:36 < fenn> then he made thousands of V2's
02:36 < fenn> supersonic rockets fifty feet tall
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02:36 < kanzure> ooh.
02:37 < fenn> btw the russian, were you thinking tsiolkovsky?
02:37 < kanzure> don't know :(
02:38 < fenn> its sad, funny, and relevant that nobody believed in rockets until they were demonstrated
02:38 < kanzure> is that so?
02:39 < fenn> "theres nothing to push against" was the general consensus
02:39 < kanzure> birds are like rockets
02:39 < kanzure> except possibly more intelligent?
02:39 < fenn> the objection was against flight in a vacuum
02:39 < fenn> er, powered flight
02:40 < fenn> blah
02:40 < kanzure> what happened to newton
02:40 < fenn> what happened to freitas
02:40 < fenn> or von neumann
02:40 < kanzure> drexler happened to freitas
02:40 < kanzure> death happened to von Neumann.
02:41 < fenn> i mean, von neumann had a theory of replicators
02:41 < fenn> and now we're stuck with "someone will think of a way"
02:41 < kanzure> I don't know why von Neumann wasn't more ... mechanical. He had his abstract theory, and his von Neumann machine theories, he was even a chemical engineer so I *know* he knew about manufacturing engineering
02:42 < fenn> it was too complex to build at the time
02:42 < kanzure> dunno, it's worth a footnote
02:42 < fenn> i guess he didnt want to pull a babbage
02:42 < kanzure> heh
02:42 < kanzure> I've been impressed by the old fashion mechanical calculators, the ones that were as large as rooms
02:43 < kanzure> just to do multiplication :)
02:43 < fenn> the zuse 1 was actually desktop sized
02:43 < kanzure> like Leibniz's machine, Pascal's, Babbage's logic engine, etc.
02:43 < kanzure> oh?
02:43 < kanzure> I heard it was tin pans in Konrad Zuse's parent's kitchen
02:43 < fenn> http://www.visionfutur.com/img/histoire/zuse1-2.jpg
02:44 < fenn> cost something like a million dollars (2008 dollars)
02:44 < kanzure> impressive
02:44 < fenn> i think it could be scaled down easily
02:44 < fenn> the question is how far
02:44 < fenn> er, how far do you want to scale it down
02:45 < fenn> i'm skeptical of drexler MNT
02:45 < fenn> it's just too far from working everyday experience to say anything about
02:45 < fenn> like people talking about colonizing mars back when they thought there were plants and stuff
02:46 < kanzure> yes
02:46 < kanzure> right now Drexler and Freitas are working on comp chem tools to do simulations and so on
02:46 < kanzure> they even have nanomanipulators for like, well, hydrogen
02:46 < kanzure> and are slowly building an atomic toolkit of sorst
02:46 < kanzure> *sorts
02:46 < kanzure> but I haven't seen evidence that they have their heads on straight
02:47 < kanzure> the fact that they know about comp chem tools is suggestive that they might
02:47 < kanzure> especialyl re: their molecular assembler desktop machine ideas
02:47 < kanzure> Freitas has good visualization skills, but...
02:51 < fenn>  you know the reprap conversation reminds me of that AI researcher talking about building a good theoretical framework first
02:52 < fenn> roles reversed
02:52 < kanzure> hm?
02:52 < kanzure> to me it seems like the reprap guys are like the ai guys
02:52 < kanzure> but the weird thing is that the reprap guys are calling us the ai guys
02:52 < fenn> oh the top down bottom up thing?
02:53 < kanzure> not so much that, but that they think we're just sitting here waiting for ai to come about to solve the problem for us
02:53 < kanzure> whereas that's what *they* are doing (waiting for somebody to come along to do it)
02:54 < kanzure> when you jump the spectrum from linear to parallel, from non-replication to replication, from computational stuff to fabricational stuff, roles and jobs get reversed in weird ways
02:54 < kanzure> so the communication issue is more apparent
02:54 < kanzure> ultimately we're both taking what seems to be a more computational approach to it all
02:54 < kanzure> it's obvious too, it's processes
02:54 < kanzure> hrm, anyway, I need to sleep, dream about some protein engineering tactics or something, and then figure out what I'm doing tomorrow
02:54 < kanzure> 'night
02:54 < fenn> night
02:55  * kanzure wonders if anybody has done any serious protein engineering before
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06:45 < nsh> what's this jibbajabba now?
06:45 < nsh> it seems i've been slandering some machine
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10:43 < kanzure> Hi all.
10:59 < shogunx> kanzure  re previous thread with you and fenn... check freegeek.org
11:00 < fenn> portland is the only place in the world that can support something like that
11:01 < kanzure> why portland?
11:01 < kanzure> shogunx: looks like a charity?
11:01 < kanzure> http://freegeek.org/mission.php
11:01 < kanzure> 'REE GEEK is a 501(c)(3) not for profit community organization that recycles used technology to provide computers, education, internet access and job skills training to those in need in exchange for community service.'
11:02 < shogunx> its a recycling lab started in portland
11:02 < fenn> kanzure: because people are too jaded/apathetic everywhere else
11:02 < shogunx> organizing as a non-profit can be very handy.
11:03 < shogunx> fenn, actually, there are other chapters springing up all over the place.
11:03 < fenn> how are they doing?
11:03 < kanzure> shogunx: re: freegek.org, http://freedomofscience.org
11:03 < shogunx> its turning into a very popular idea.
11:03 < kanzure> I'm starting to hate chapter organizations
11:03 < kanzure> diversity sucks, we need unification
11:03 < shogunx> i hear you on that, but this is a good one.
11:03 < kanzure> no, I don't care whether it's good or bad
11:04 < kanzure> even if it's bad I would still try to show up and help out -- i.e., subtle approach
11:04 < kanzure> however
11:04 < kanzure> there's too many of these chapters
11:04 < shogunx> they are essentially replicating a known functional model.
11:04 < kanzure> hplusclub, meetup, metalworking, makerfairegroup, dorkbot, geekaustin, indieaustin, atxfutureclub, lab, 
11:04 < kanzure> nono, hold on, let me suggest my alternative
11:05 < kanzure> my suggestion is to have the /community/ integrate the chapters together
11:05 < kanzure> to serve their needs, so that they can get the same people, who would otherwise be unable to attend all of the chapters, still doing good work
11:05 < shogunx> freedomofscience looks pretty good... i made the solarnet development pretty open along those lines.
11:05 < kanzure> oh, add NSS and other rocket society chapters to that list
11:05 < kanzure> shogunx: I've been talking with the freedomofscience guys, I want to see what comes of it
11:05 < kanzure> have you heard of them before ?
11:05 < kanzure> are these guys respectable etc. ?
11:05 < fenn> kanzure: most people dont see the connection between i.e. metalworking and computers
11:05 < shogunx> freedomofscience?  have not heard of them
11:06 < kanzure> the connection /is/ hard to see
11:06 < kanzure> how many people know about silicon itself
11:06 < shogunx> fenn  that is the role of genius... to put together the disparate building blocks scattered around society for the greater good.
11:06 < kanzure> more to the point, how many people know about the fabrication setups that go behind the computers
11:07 < kanzure> greater good? shogunx, just to make it clear, this all /just so happens/ to have a byproduct that might look like 'greater good'
11:07 < kanzure> I'm completely, totally selfish
11:07 < kanzure> many people are worried that exponential growth will *not* be for The Greater Good
11:07 < fenn> good thing you are not a nanobot
11:08 < shogunx> look...  i know you are a very smart lad, so I will say this once and drop it:  99.9 percent of the world are total sheep.  those of us who are not have a choice:  be a wolf, or a shepherd.
11:08 < kanzure> hm?
11:08 < kanzure> a wolf in sheep's clothing comes to mind
11:09 < nsh> {{{{ }X }X }}}}}
11:09 < shogunx> you don't have to be toally selfless, but we are the modern shamen.  it is our role to guide the masses.  if we do it solely for personal gain, that gain comes at the expense of society as a whole.
11:09 < shogunx> current president is a perfect example.
11:11 < kanzure> expense?
11:12 < shogunx> yes, expense.
11:12 < kanzure> you're assuming scarcity
11:12 < fenn> he means oppression
11:13 < fenn> killing, slavery, mind control
11:13 < kanzure> I don't see how you can get from 'what we are doing' here to --> opression (killing, slavery, mind control)
11:13 < shogunx> don't get me on the tangent of artificial scarcity of commodities...  i'm talking about the guy who gives you $10/hour then bills $100/.hour for your work product.
11:14 < fenn> uh, ok i guess he does mean expense
11:14 < shogunx> both examples are right.
11:14 < shogunx> mine is simply in microcosm.
11:14 < fenn> shogunx: do you understand what 'post scarcity society' means?
11:14 < shogunx> of course.
11:15 < fenn> so, how does trying to build a post scarcity industrial base turn into giving people less money than you earn?
11:15 < shogunx> kanzure, i was not saying that you were indulging in these odious behaviours, but you will have the opportunity to in your lifetime.
11:16 < fenn> shogunx: which is worse, giving the guy $10/hr or building a robot that does his job automatically?
11:16  * fenn thinks giving him $10/hr
11:16 < shogunx> $/10 hour, for sure.  with the robot, you are not stealing the guys life.
11:17 < fenn> so, i think that's what we're doing, systematically
11:18 < fenn> human-free factory
11:18 < fenn> well, that's the end goal at least
11:20 < fenn> this site really pisses me off http://techref.massmind.org/
11:20 < fenn> "look at all the cool info we've aggregated, but YOU CANT HAVE IT"
11:31 < shogunx> yeah, thats absurd
11:33 < shogunx> i'm sure you guys saw this one this morning:
11:33 < shogunx> http://hardware.slashdot.org/article.pl?sid=08/06/04/2312227&from=rss
11:33 < fenn> nah i dont read news :)
11:34 < fenn> lies, LIES!
11:34 < shogunx> heh heh
11:35 < fenn> well at least the commenters have some sense
11:37 < shogunx> that is usually the case.  technocrat.net is a reasonable source... belongs to bruce perens
11:54 < kanzure> kl;fjl;kdfjkljfklasdfja
11:55 < kanzure> I did NOT need to click that Slashdot link
11:55 < kanzure> oh my god I love Slashdot :)
11:55 < kanzure> first few comments call out the bullshit
11:57 < shogunx> as always... :)
11:58  * kanzure feels better.
12:38 < kanzure> haha
12:38  * kanzure grins
12:38 < kanzure> http://heybryan.org/mediawiki/index.php/2008-06-05
12:39 < kanzure> fenn: polymerase "pause" problem solved (more or less). Now on to the nucleotide typing problem. Your mechanical/chemical belt (of tips) idea seems like the only thing so far, but I'm still looking.
12:57 < kanzure> fenn: I don't understand how you expect polA to be able to make a new strand without a template to read from.
12:57 < kanzure> I'm looking at some papers that describe the physical sites of action in the polymerase molecule and how this works
12:58 < kanzure> and it's looking like the requirement of an input template strand to copy from is highly required
12:58 < kanzure> I mean, to hack up polymerase to just have a matching nucleotide-tip activated or whatever, would be a tremendous feat of engineering
13:03 < kanzure> http://pubs.acs.org/cgi-bin/abstract.cgi/bichaw/1996/35/i07/abs/bi951682j.html
13:05 < kanzure> hm, they have to be bound to a strand in the first place /me checks the logs
13:06 < Phreedom> kanzure: I don't see anyone on slashdot addressing actual shortcomings except for "self-replication", like degradation of parts over several generations
13:07 < kanzure> there were a few people pointing out that the design is flawed
13:07 < kanzure> i.e., it doesn't self-replicate
13:07 < kanzure> there must be an easier way to say that
13:07 < kanzure> from the outside it looks degrading
13:07 < kanzure> like saying "well, your book isn't complete, so you suck"
13:07 < kanzure> but that's not the point at all
13:07 < kanzure> how do I express this?
13:08 < kanzure> a book can be written, typed out; the design of a self-replicating machine isn't quite like that ... it's something totally new that nobody knows how to do, and they claim /they/ do, and they are lying
13:11 < kanzure> (2008-06-03 21:28:52) fenn: you wouldnt be copying the template strand, just using it to crawl along
13:11 < kanzure> (2008-06-03 21:29:01) fenn: the information comes from elsewhere
13:11 < kanzure> aha
13:11 < kanzure> (2008-06-03 21:29:16) fenn: so its not actualy a template, more like a scaffold
13:11 < kanzure> (2008-06-03 21:29:53) fenn: so, when you add some arbitrary sequence opposite the scaffold strand, the bases dont really fit
13:11 < kanzure> (2008-06-03 21:31:09) fenn: normally the "doesnt really fit" would activate the proofreading domain
13:11 < kanzure> hrm
13:11 < kanzure> the template is specifically used to figure out what dNTP to bind with 
13:12 < kanzure> however, if we can "lock" it somehow ..
13:12 < kanzure> for example, making it so that the first nucleotide that polymerase reads is locked in place, or that the polymerase structure is pre-set and doesn't actually care about input molecules
13:15 < kanzure> (oh, plus inhibition of DNA repair / checking mechanisms)
13:15 < fenn> the way i see it, the template strand presses against some levers which activate the various nucleotide types
13:16 < fenn> so just hack those levers off and replace them with some kind of photonic signalling mechanism
13:16 < fenn> and you need a 'feed' switch too of course
13:16 < fenn> 'next'
13:17 < fenn> one problem with the scaffold strand idea is.. where does the scaffold come from? if its just some random dna then the strand being written won't stick, and it'll pull the enzyme off
13:32 < kanzure> hrm, the strand won't stick? 
13:33 < kanzure> I thought that it's attached to the DNA backbone
13:33 < fenn> no, sequence specific hybridization, remember
13:33 < kanzure> well, I'm ok with it not sticking really; the polymerase still does the input feeding thing
13:33 < kanzure> so it's still attached
13:33 < fenn> i guess
13:33 < kanzure> kind fo like by a hair thread ... :/
13:34 < fenn> would be annoying to only be able to print 50 bp before it falls off
13:34 < kanzure> 'Expanding the Substrate Repertoire of a DNA Polymerase by Directed Evolution' <-- I've emailed the authors and asked about /reducing/ the substrate repertoire
13:34 < fenn> what does 'substrate repertoire' mean?
13:34 < kanzure> the number of nucleotide types that polymerase can use
13:35 < kanzure> "Residues 614 and 615 are located in the C-terminus of the third strand of the four-stranded antiparallel  sheet of the "palm" region of the polymerase, at the junction with an -helix.30 The residues are part of the DYSQIELR motif A sequence, highly conserved in the DNA polymerase I enzyme from prokaryotes and eubacteria.45 This strand is of obvious functional relevance as it contains Glu610, which chelates one of the two catalytic
13:36 < kanzure> 'The problem with simply creating space in the active site for the OMeNTP by mutation of Glu615 to Gly or Ala is that the other functions of the Glu615 side chain will be lost. Thus, secondary mutations are required to restore these functions, possibly including binding a Mg2+ ion or a minor groove water molecule. This may explain why each of the isolated mutants also possesses mutation of Ile614 to Glu or Tyr, either of which shou
13:36 < kanzure> '. In fact, two of the three unique protein sequences isolated (SFM19 and SFM30) contain the Ile614Glu mutation, including the most active SFM19 clone, possibly to most efficiently compensate for the loss of other Glu615 side-chain functions. Thus, it appears that the directed evolution process succeeded by first creating space for the 2'-substitutent and then retailoring the binding site as required for function.'
13:39 < kanzure> '. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. ' 
13:39 < kanzure> '' By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin
13:41 < fenn> nice
13:41 < fenn> 11-fold, so it should be good up to 1000C right? :)
13:42 < kanzure> heh
13:43 < kanzure> http://nar.oxfordjournals.org/cgi/content/abstract/25/6/1307 'In addition, the mutagenesis rate can be controlled over a wide range by the inclusion of Mn2+or Mg2+during DNase I digestion, by choice of DNA polymerase used during gene reassembly as well as how the genes are prepared for shuffling (PCR amplification versus restriction enzyme digestion of plasmid DNA). These protocols should be useful for in vitro protein evolution, f
14:48  * kanzure cries a little bit inside
14:49 < kanzure> the grad student I am assigned to mentioned RepRap and that it replicates
15:26 < wrldpc> Anyone here in Boston know if the DIYBio meeting is actually happening tonight?
15:26 < wrldpc> There's been little to know communication.
15:26 < wrldpc> *no
16:50 < kanzure> check the mailing list
16:50 < kanzure> although that might have been your email
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20:16 < kanzure> Hey.
20:16 < Phreedom> kanzure: FUD seems to do wonders for RepRap ;)
20:16 < kanzure> How's that?
20:17 < Phreedom> (21:48:59)  kanzure:  the grad student I am assigned to mentioned RepRap and that it replicates 
20:17 < kanzure> so, I talked with him about it
20:18 < kanzure> and it turns out that what the problem might be, re: the definitions and so on, is more about issues related to the sigmodal levelling off of the exponential ideal of self-replication, i.e. exponentially goes up, then exponentially levels off (since parts to RepRap /cost/ money)
20:19 < kanzure> whereas I want to maximize the exponential up via 'philanthropic bootstrapping' (which I've recently decided isn't the best thing to hope for -- but he thinks it's ok, I could possibly be persuaded)
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