--- Day changed Fri Jun 06 2008
01:17 < kanzure> http://heybryan.org/pipermail/synth2008/2008-June/thread.html Lab team :)
02:50 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has quit ["Leaving."]
05:22 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has quit [Read error: 104 (Connection reset by peer)]
05:26 -!- Vedestin [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has joined #hplusroadmap
06:02 -!- vircuser [n=Vedestin@d122-109-35-58.sbr3.nsw.optusnet.com.au] has joined #hplusroadmap
06:04 -!- Netsplit card.freenode.net <-> irc.freenode.net quits: Phreedom, faceface, Vedestin
06:05 -!- vircuser is now known as Vedestin
06:34 -!- facefaceface [n=chatzill@bioinformatics.org] has joined #hplusroadmap
06:34 -!- facefaceface is now known as faceface
08:04 -!- Phreedom [n=freedom@www.online.dn.ua] has joined #hplusroadmap
10:33 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has joined #hplusroadmap
10:52 < Vedestin> http://www.newcastle.edu.au/program/undergraduate/2008/10981.html
10:57 -!- nsh [n=nsh@wikipedia/nsh] has quit ["m000p"]
11:14 < kanzure> Vedestin: hm?
11:14 < Vedestin> looking at a few degree programs available to me
11:16 < Vedestin> this looks pretty interesting too http://www.newcastle.edu.au/program/undergraduate/2008/10986.html
11:20 < Vedestin> did you settle on a degree + university yet, kanzure?
11:21 < kanzure> Vedestin: Not quite yet. I have it all narrowed down, of course, but I'm still trying to get them to agree to a double major.
11:21 < Vedestin> your parents? or the university?
11:34 < kanzure> The university.
11:41 < Vedestin> in computer science and neuroscience?
11:43 -!- nsh [n=nsh@87-94-146-186.tampere.customers.dnainternet.fi] has joined #hplusroadmap
11:47 < kanzure> No.
12:00 < Vedestin> still on the engineering path then?
12:02 < kanzure> sort of :)
12:02 < kanzure> I'm trying to do computational/science + manufacturing.
12:06 < Vedestin> ahh ok
12:08 < Vedestin> that sounds pretty interesting
12:08 < Vedestin> doing that hear would be a double degree
12:08 < Vedestin> rather than a double major
12:10 < Vedestin> lol @ hear
12:10 < Vedestin> can you tell it's 2am?
12:57 < kanzure> the terminology doesn't make sense anyway
13:00 < Vedestin> which?
13:17 < kanzure> double degree / double major stuff
13:17 < kanzure> it's probably because the idea of a 'major' (specialization for a piece of paper) is odd
13:17 < kanzure> fenn: So let's just say that I have four polymerase molecules that selectively incorporate a different nucleotide. One does adenosine, the other does thymine, etc. It turns out that the requisite mutations are highly localized to a particular amino acid on a loop in the protein.
13:18 < kanzure> Now what? I'm thinking of trying to have all four of these polymerases 'combined' into one where we can switch the functionality. 
13:18 < kanzure> for example, in pH of xyz, it's in mode #1, in pH of something else it's in mode #2, etc. 
13:18 < kanzure> That sort of thing. But it may turn out that the amino acid substitutions are vastly different. If it's a single atom change or something, what could we do with that?
13:19 < Vedestin> the way it works here is that there's more credit in a double degree than a double major, double major in science would still be 240 credit points, 3 years, while a double degree is 400 points, 5 years
13:20 < Vedestin> and you have BSc and BEng at the end
13:20 < Vedestin> not just one or the other
13:20 < Vedestin> but sorry, go back to your polymerase
13:21 < kanzure> hm
13:22 < kanzure> maybe it would be possible to use four different polymerases, and have them re-attach and scan the length of the already constructed DNA molecules ?
13:24 < fenn> perhaps you could separate the polymerase into two chunks, one chunk that always stays on the strand (placeholder) and another chunk that floats around and can detach/reattach
13:25 < fenn> i dont think its going to be as simple as finding the right amino acid to use
14:29 < ybit> if we can transfer the contents of the brain, we may be able to forgo the current longevity model produced by sens
14:29 < ybit> but how to do this is beyond me right now :
14:29 < ybit> |
14:29 < ybit> ..
14:30 < fenn> kurzweil nanobot 'gradual upload' sounds like a pretty good start
14:30 < ybit> i was thinking of a similiar concept earlier
14:31 < ybit> is this mentioned in his book?
14:31 < fenn> dunno i dont think i've read his books
14:31 < fenn> actually it might have been moravec who came up with the idea
14:33 < fenn> ybit: ever heard of the 'god helmet'?
14:33 < ybit> i have not
14:34 < ybit> wikipedia is telling me all about it though :)
14:34 < ybit> ah, i have heard of this, but not the term
14:37 < ybit> fenn: you wouldn't happen to have a link to lit. on the gradual uploading to nanobots?
14:39 < ybit> after reading it, i haven't heard of the experiment.. i thought it was about to refer to experiments dealing with magnetism and memory
14:39 < fenn> the 'god helmet' is something like rTMS but without all the high power capacitor discharge stuff
14:39 < kanzure> fenn: re: two chunks. check out 'beta clamp'. it's like an anchor on DNA for polymerase. it's a module.
14:40 < fenn> so its something you can actually play with.. there is some site that sells electronics that hook up to your sound card
14:40 < kanzure> then we can have four different types of polymerases swimming around
14:40 < fenn> sweet
14:40 < kanzure> re: mind uploading, check out Joe Stoel or osmething and 'mind uploading action group'
14:40 < kanzure> yeah, so that sounds better
14:40 < kanzure> now I'm thinking about the painful selection experiment
14:41 < fenn> mind uploading research group?
14:42 < kanzure> yep, it was a 'task force' that randomly converged on the internet in the late 90s
14:42 < kanzure> apparently they were working on nematode neuronal uploading
14:42 < kanzure> I don't know what they actually /did/
14:42 < kanzure> but I guess they could have had a slice-and-scan setup
14:44 < fenn> yep, looks pretty fancy: http://minduploading.org/research.html
14:46 < kanzure> woah
14:46  * kanzure regrets not seeing that sooner.
14:47 < kanzure> led by Eugene Leitl
14:47 < kanzure> http://eugen.leitl.org/
14:48 < fenn> yeah. leitl quote that reminds me of the DNA-FPGA idea: " It occured to me that one could create engineered proteins which precipitate nanocircuitry within/around neurons, which could be capable of emulating that particular neuron's function, after the original is defunct."
14:49 < fenn> so you just need to infect all the brain cells with some vector that expresses carbon nanotubes.. hrm :)
14:52 < fenn> " soon, organ banks can actually start banking organs." wow someone's really blowing it
14:53 < kanzure> dunno if you need CNTs
14:53 < fenn> well, some kind of semiconductor
14:53 < kanzure> but Winfree's sierpenski triangles might help
14:53 < fenn> CNT's work better at small scales, so i hear
14:53 < fenn> or graphene, same thing really
14:53 < kanzure> I have a new contact who works in CNTs, he's very eager to help
14:53 < kanzure> he also has ridiculously large machines and free access to
14:54 < fenn> machine = computer?
14:57 < kanzure> machine = make CNTs, has SEMs, all sorts of fun stuff
14:58 < kanzure> now then ... I'm not so sure about the prospects of proteins to replace neurons
14:58 < kanzure> since there's a lot of functionality that you're going to kind of miss, I think
14:58 < kanzure> neuron-by-neuron nanotech replacement therapies have been recommended before, but that requires nanotech
14:58 < fenn> right
14:59 < kanzure> also, on an unrelated note, brain cancer sucks
14:59 < kanzure> that's the one remaining cancer that we can't really do much about, if you have a giant tumor deep inside there you're not going to be able to do much
14:59 < kanzure> (although with the nanoparticle delivery system, something might happen sure, but whatever)
14:59 < kanzure> anyway, my point is that there might be a system to fix this
14:59 < kanzure> if we can harness neurogenesis
14:59 < fenn> to fix what?
15:00 < kanzure> and specifically lesion parts of the brain that develop either (1) tumors or (2) some sort of uber-degenerative issue
15:00 < kanzure> so you lesion it, clean it up, and then have neurogenesis to fill in the gaps again with the same basic circuitry (fit to that part of the brain)
15:00 < kanzure> this doesn't recover the old data
15:00 < kanzure> the old data was degrading and was lost by that point
15:00 < fenn> you'd have to have a way to 'download' the data anyway
15:01 < fenn> as well as a way to upload
15:01 < fenn> might as well grow a neuropod and transplant it :P
15:01 < kanzure> ok, so for preventive measures
15:01 < kanzure> to make sure you don't lose the data
15:01 < kanzure> backups, backups, backups
15:01 < fenn> weekly backups are always a good idea
15:01 < kanzure> nightly
15:01 < fenn> if you are being persecuted, sure
15:02 < kanzure> so
15:02 < fenn> a week of boring nothingness might actually be fun to untangle
15:02 < kanzure> to do backups
15:02 < kanzure> Keith F. Lynch once gave me a good nanotech idea
15:02 < kanzure> the idea was to have nanotech go in and report the connections between each other via encodings into organic molecules
15:02 < kanzure> and then this data is stored and you piss it out
15:03 < kanzure> and then you go read the molecules at some later time
15:03 < kanzure> however, that requires nanotech.
15:03 < kanzure> an interesting alternative might be to make the neurons do self-diagnosis of that sort
15:03 < kanzure> the big issue is getting separate ID schemes going on or something
15:03 < kanzure> there's no way you can coordinate that many ID molecules
15:03 < kanzure> you'd have to be able to generate 64bit ID molecules or something
15:03 < kanzure> and to have them be persistent and so on? yikes
15:03 < fenn> not that many
15:04 < kanzure> many get lost
15:04 < kanzure> perhaps not 64 bit
15:04 < fenn> how many connections in the brain? how many neurons?
15:04 < kanzure> 100 trillion connections, 100 billion neurons,
15:04 < kanzure> you'd need in vivo 'memory' so that you can persistent states
15:04 < kanzure> but not only that, but you need /one/ ID per cell
15:04 < kanzure> having *one* thing per cell is a generally nasty problem IIRC
15:04 < fenn> so 47 bit for 100 trillion
15:04 < kanzure> not each one is going to be necessarily used
15:04 < kanzure> I mean, 
15:05 < kanzure> you need to have significantly more than you need
15:05 < fenn> 23 quads (nucleotides)
15:05 < kanzure> maintaining a persistent ID to a single cell is a very hard task
15:05 < kanzure> apparently there are molecules that there are only 'one' copy of in a cell
15:06 < fenn> not really, b-cells do it all the time
15:06 < kanzure> something to do with whole genome replication
15:06 < kanzure> how so?
15:06 < fenn> dna shuffling and splicing
15:06 < fenn> its how monoclonal antibodies work
15:06 < kanzure> I'll have to look into that
15:07 < kanzure> it would be awesome if we could start with an embryo and have each cell assigned to an 'address space' so that each child is assigned to a subset of that address space and so on
15:07 < kanzure> that way the ID is encoded into the genome of each cell
15:07 < kanzure> but that's not a solution for us
15:08 < kanzure> (viral gene therapy could do it, I guess, but the assignment scheme might be more difficult in that case?)
15:08 < fenn> what's wrong with random assignment?
15:08 < kanzure> how do you know what's already used?
15:08 < fenn> say you have a 64 bit id, and only need 47 bits, well there's a 1/2^(64-17) chance of an ID collision
15:09 < fenn> s/17/47/
15:09 < fenn> around one in a million
15:10 < kanzure> 1/(2^20) eh? with 100 trillion connections, 100 billion neurons, that's only 1E9, which is 2^30 right?
15:10 < kanzure> hrm
15:10 < fenn> is that right? i think there should be a factorial in there somewhere
15:10 < kanzure> you have a million million
15:10 < kanzure> so you'll have a million bad ones
15:10 < fenn> ok, so play with the numbers until it works
15:13 < fenn> summary of immunoglobulin DNA shuffling stuff: http://63.240.200.111/pages/pdfs/data/1998/154-19/15419-22.pdf
15:19 < kanzure> so once you have your ID molecule in a cell, what then
15:19 < kanzure> you still have to encode information somehow
15:19 < kanzure> and the information that we want includes a lot of different variables
15:20 < kanzure> stuff like neighboring connections, in vivo concentrations of various molecules, voltages, and so on
15:20 < kanzure> if we can determine what information we want, and the ranges of the possible values of these variables (Markram is a good place to start looking), then we can do in vivo experimentation to get those values
15:20 < fenn> honestly it sounds like a lot of work
15:21 < kanzure> hrm, remember Markram's patch-clamp robot? we need to do that, except with the cells on their own 
15:21 < kanzure> yes, it sucks
15:21 < fenn> and then you still have to reproduce it somehow
15:21 < kanzure> well, if you want those exact details :/
15:21 < fenn> you could do some kind of transformation "mating" stuff like bacteria do
15:21 < fenn> then splice the two ID's together
15:21 < kanzure> for what?
15:21 < fenn> so you'll get a chain of DNA containing all the neighbors' ID's
15:22 < kanzure> oh, sure
15:22 < kanzure> hrm
15:22 < fenn> how is the 'connection strength' determined in a biological neuron?
15:22 < kanzure> so there has to be a way to distinguish between 'IDs that we are looking to acquire/claim' versus modes where we're just trying to splice them together
15:22 < kanzure> maybe we should move this discussion into ##neuroscience
15:43 < fenn> re: cancer and nanoparticle delivery system, i wonder why nobody's made artifical/recombinant b-cells that target your specific type of cancer
16:32 < kanzure> fenn: why did we need the immediate laser-induced stoppable polymerase system for in vitro DNA synthesis?
16:32 < kanzure> actually, why did we need the laser
16:32 < kanzure> not so much why did we need to stop it
16:32 < kanzure> I know that we can't let it write multiple times, but why not just have it under running water
16:32 < kanzure> a 'stream' or current of water of some sort
16:33 < kanzure> so that upstream DNA molecules get it only once and downstream is protected the longest or something
16:33 < kanzure> hrm, nevermind .downstream would suck.
16:37 < kanzure> just do it biochemically and make it take forever
16:37 < kanzure> 1 bp every 30 minutes, so it just sits there
16:37 < kanzure> while you diffuse the signalers to tell it to dissociate and for another one to become active
16:37 < kanzure> (those two messages can go out at the same time)
17:00 -!- Splicer [n=p@h87n1c1o261.bredband.skanova.com] has joined #hplusroadmap
17:08 < ybit> """[13:52] <fenn> " soon, organ banks can actually start banking organs." wow someone's really blowing it """ :D
17:08 < ybit> way away running some errands
17:08 < ybit> feels good to be off work for a few days
17:13 < kanzure> hurray for eureka moments
17:13 < kanzure> you're not selecting for four different polymerases
17:14 < kanzure> you're selecting for a strand that encodes the four different polymerases
17:15 < kanzure> in fact, you're selecting for the in vitro DNA synthesis system that actually /works/ so it's kind of like starting off assuming that it can work in the end
17:15 < kanzure> and then through building it up, the parts will be selected that actually work
17:41 < fenn> kanzure: the laser is how you get the dna sequence into the cell
17:42 < fenn> using another wavelength as the 'clock signal' just makes the system more reliable, higher data rate since you dont have to wait for some stupid gene product to get synthesized
17:42 < fenn> 30 minutes per bp? gimme a break
17:43 < fenn> the 30 minutes still has to be amazingly precise (unless you have a fluorescence indicator)
17:44 < fenn> considering most bacteria _divide_ in less time than that, i think you'll have some problems
17:45 < fenn> oh, i'm really going for in-vivo btw
17:46 < kanzure> hrm
17:47 < kanzure> well, selection experiment that we could do
17:47 < kanzure> the selection, like I said, is of a normal polymerase
17:47 < kanzure> take an ecoli genome
17:47 < kanzure> insert a new polymerase into the genome, one that has a funky specificity for a binding sequence that does not appear in the ecoli genome
17:47 < fenn> and then punish it severely unless it comes up with a DNA writozyme?
17:47 < fenn> is that vegan?
17:48 < kanzure> now insert that initiator sequence + four hack-polymerases next to each other
17:48 < fenn> bacterial oppressor!
17:48 < kanzure> these hack-polymerases are exactly the same, but they are hacked in the sense that (1) they allow a 'ghost template strand' (engineer the template-acceptor to be a copy of the ddNTP acceptor, except for some molecule that does /not/ appear in the system
17:48 < kanzure> )
17:48 < kanzure> (2) that they are pausable (I have a pausing system with some molecular markers and so on, so it's good)
17:49 < kanzure> now, signal the system to either make something to help it live or something to kill it
17:49 < fenn> it all sounds a bit too magical
17:54 -!- fenn_ [n=pz@adsl-76-251-87-196.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap
17:54 -!- Topic for #hplusroadmap: http://heybryan.org/ http://heybryan.org/mediawiki/ http://heybryan.org/exp.html | krebs is now servicing the channel. try !help
17:54 -!- Topic set by kanzure [] [Tue Apr 29 18:54:31 2008]
17:54 [Users #hplusroadmap]
17:54 [ faceface] [ fenn_  ] [ nsh             ] [ Phreedom] [ Splicer ] [ wrldpc] 
17:54 [ fenn    ] [ kanzure] [ parodyoflanguage] [ shogunx ] [ Vedestin] [ ybit  ] 
17:54 -!- Irssi: #hplusroadmap: Total of 12 nicks [0 ops, 0 halfops, 0 voices, 12 normal]
17:54 -!- [freenode-info] if you need to send private messages, please register: http://freenode.net/faq.shtml#privmsg
17:54 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
17:54 < kanzure> fenn_ what was the list message you received?
17:54 -!- Irssi: Join to #hplusroadmap was synced in 41 secs
17:56 < fenn_> grarg
17:56 < fenn_> 'sounds a bit too magical' was the last
17:56 -!- fenn [n=pz@adsl-76-251-85-42.dsl.bltnin.sbcglobal.net] has quit [Nick collision from services.]
17:56 -!- You're now known as fenn
17:56 < kanzure> uh oh
17:57 < kanzure> that doesn't appear in this log
17:57 < fenn> 'now signal the system to either..'
17:58 < kanzure> bleh, I need to run
17:58 < fenn> you'd think IRC would have a pingback for each message
17:58 -!- kanzure [i=bryan@dhcp-146-6-213-183.icmb.utexas.edu] has quit ["Leaving."]
19:44 -!- fenn_ [n=pz@adsl-76-252-189-224.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap
19:44 -!- Topic for #hplusroadmap: http://heybryan.org/ http://heybryan.org/mediawiki/ http://heybryan.org/exp.html | krebs is now servicing the channel. try !help
19:44 -!- Topic set by kanzure [] [Tue Apr 29 18:54:31 2008]
19:44 [Users #hplusroadmap]
19:44 [ faceface] [ fenn_] [ parodyoflanguage] [ shogunx] [ Vedestin] [ ybit] 
19:44 [ fenn    ] [ nsh  ] [ Phreedom        ] [ Splicer] [ wrldpc  ] 
19:44 -!- Irssi: #hplusroadmap: Total of 11 nicks [0 ops, 0 halfops, 0 voices, 11 normal]
19:44 -!- [freenode-info] if you need to send private messages, please register: http://freenode.net/faq.shtml#privmsg
19:44 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
19:45 -!- Irssi: Join to #hplusroadmap was synced in 42 secs
19:45 -!- fenn [n=pz@adsl-76-251-87-196.dsl.bltnin.sbcglobal.net] has quit [Read error: 104 (Connection reset by peer)]
19:50 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has joined #hplusroadmap
19:51 < kanzure> Hi all.
19:55 < kanzure> fenn_: http://heybryan.org/mediawiki/index.php/Polymerase#Another_way_of_saying_the_same_thing.2C_again
20:29 -!- You're now known as fenn
21:46 -!- fenn_ [n=pz@adsl-76-251-87-17.dsl.bltnin.sbcglobal.net] has joined #hplusroadmap
21:46 -!- Topic for #hplusroadmap: http://heybryan.org/ http://heybryan.org/mediawiki/ http://heybryan.org/exp.html | krebs is now servicing the channel. try !help
21:46 -!- Topic set by kanzure [] [Tue Apr 29 18:54:31 2008]
21:46 [Users #hplusroadmap]
21:46 [ faceface] [ fenn_  ] [ nsh             ] [ Phreedom] [ Splicer ] [ wrldpc] 
21:46 [ fenn    ] [ kanzure] [ parodyoflanguage] [ shogunx ] [ Vedestin] [ ybit  ] 
21:46 -!- Irssi: #hplusroadmap: Total of 12 nicks [0 ops, 0 halfops, 0 voices, 12 normal]
21:46 -!- Channel #hplusroadmap created Sat Mar 22 15:44:12 2008
21:47 -!- Irssi: Join to #hplusroadmap was synced in 43 secs
21:59 -!- fenn [n=pz@adsl-76-252-189-224.dsl.bltnin.sbcglobal.net] has quit [Read error: 110 (Connection timed out)]
22:07 -!- parodyoflanguage [i=pseudony@mmds-216-19-34-118.twm.az.commspeed.net] has quit []