--- Day changed Fri Apr 04 2008
00:09 < kanzure> REQUIREMENTS:
00:09 < kanzure> - something other than computation
00:09 < kanzure> - simpler, more robust than the Winfree switch
00:09 < kanzure> - what should we do with transcriptional switches, gates, circuits?
00:09 < kanzure> - what can you do with transcriptional switches that are interesting, computationally?
00:09 < kanzure> - carry out a computation / forment a new emergent property / the whole must be greater than the sum of the parts
00:09 < kanzure> --- ex: ring oscillator
00:09 < kanzure> - Sketch a circuit that can forment the emergence of a new property
00:09 < kanzure> - to go beyond what you can predict (are emergent)
00:09 < kanzure> - we're not going to beat electronic algorithmic execution, ever, so what are we trying to do?
00:09 < kanzure> - Emergent properties are interesting because that is sort of what we are.  A bunch of genes ganged together and coupled with cellular machinery make us.  As Zack might say, we're 'matter computers.' (as opposed to what computers?)
00:09 < kanzure> - amorphous computation, practical implementation of nucleic acid circuits
00:09 < kanzure> - my DNA compiler project
00:09 < kanzure> - tic-tac-toe implemented in DNA logic gates
00:09 < kanzure> I am clueless. fenn, Enki-2?
00:30 < kanzure> fenn: http://heybryan.org/chats/2008-04-03_self-replication_with_Tony.html
00:42 -!- kanzure [n=bryan@70.113.54.112] has quit ["Leaving."]
04:48 < epitron> hmmm
04:48 < epitron> eugenics is dangerous :)
04:49 < fenn> everything is dangerous
04:49 < epitron> it puts too much power in the hands of whoever decides what genes to select. "Cultural diversity is not only humanity?s hallmark of progress, but an insurance policy against extinction as a species."
04:49 < fenn> uh, what? cultural diversity has nothing to do with eugenics
04:50 < epitron> hmmm
04:50 < fenn> *slappity slap slap*
04:50 < epitron> i dunno, there is some intertwingling going on there
04:50 < fenn> let me say it bold and clear: fascism is not eugenics
04:50 < epitron> haha
04:50 < epitron> so i'm conflating the two?
04:51 < fenn> historically they have been promoted by the same people, so it's understandable
04:51 < epitron> ok
04:51 < epitron> well, ignore the 2nd half of my message then
04:51 < epitron> let's address the power aspect :)
04:53 < epitron> or not
04:53 < epitron> it's up to you 
04:54 < fenn> you should say it again it in e-prime
04:54 < epitron> what's eprime?
04:54 < epitron> a channel?
04:54 < fenn> oh, that must have been someone else
04:55 < epitron> explain
04:55 < fenn> e-prime is a way of speaking english without using the verb 'is'
04:55 < epitron> oh yeah, that was me
04:55 < epitron> it's spelt E'
04:55 < epitron> not e-prime :)
04:55 < fenn> whatever
04:55 < fenn> <- math notation hater
04:56  * epitron furrows his brow
04:56 < epitron> anyhow
04:57 < epitron> eugenics means the selection of genes
04:57 < epitron> someone must decide on the selection
04:57 < epitron> whoever decides that has a lot of power
04:58 < fenn> why does that give them power?
04:58 < epitron> they could re-enact Brave New World if they wanted
04:58 < epitron> selecting different classes of people
04:58 < fenn> classes are a cultural phenomenon
04:58 < epitron> and they could turn them into a genetic one
04:58 < epitron> or they could have the power to fuck up our biological diversity
04:58 < fenn> we've already done that
04:58 < epitron> by selecting out genes that could be useful later
04:59 < epitron> how so?
05:00 < fenn> by removing natural selection to the point where it's nearly random noise
05:00 < epitron> how does that reduce diversity?
05:00 < epitron> only when you have a bottlenecking does diversity get reduced
05:00 < epitron> humanity has exploded
05:00 < epitron> i doubt we've lost a single gene :)
05:01 < epitron> there are biases of course
05:01 < epitron> trailer trash out breeding intellectuals :)
05:01 < fenn> if you assume there is a 'right' amount of biological diversity, you must admit that there can be too much diversity, no?
05:01 < epitron> but even the smallest relative fraction of the gene pool is much much larger than it used to be
05:01 < epitron> there's no right
05:01 < epitron> there's just survival :)
05:02 < fenn> then how can we 'fuck up our biological diversity'
05:02 < epitron> by reducing it to the point where it hinders our survival given inopportune future events
05:02 < epitron> reduces our ability to adapt
05:04 < epitron> one scientist is predicting that there will be large worldwide droughts soon
05:04 < epitron> (within 100 years)
05:04 < fenn> good for hir
05:04 < epitron> would you stop being a wang!
05:04 < epitron> geez
05:04 < epitron> must you knock everything?
05:04 < fenn> i dont see what you're trying to get at
05:04 < epitron> nevermind
05:05 < fenn> epitron: here's a bit of cognitive dissonance for you: which is more preferable, inbreeding (result of racism) or homogeneity
05:07 < fenn> homogeneity = everyone is a hybrid
05:07 < epitron> huh
05:08 < epitron> good for homogeneity
05:08 < fenn> but doesnt that reduce the diversity of the system?
05:08 < epitron> i don't see what you're trying to get at
05:09 < fenn> i'm poking at your liberal bias
05:09 < epitron> what the shit are you talking about! :)
05:09 < epitron> i'm talking about gene frequencies
05:09 < epitron> i'm talking about not throwing away useful ones
05:09 < epitron> you could stockpile them on hard drives if you wanted
05:09 < epitron> as long as you could get them back when they are needed
05:10 < fenn> werent you advocating killing people off for population control earlier?
05:10 < epitron> since we're quite capable of reverting to an uncivilized state, however, it's probably good not to store them on hard drives
05:10 < epitron> hahah
05:10 < epitron> no, i don't think so
05:11 < epitron> why do you dislike me so
05:11 < epitron> you're always HARUMPH when i say things
05:11 < fenn> i'm just grumpy i guess
05:12 < epitron> how come?
05:12 < fenn> my life sucks
05:12 < epitron> life not treating you good?
05:12 < epitron> aww
05:12 < fenn> nothing i can complain about in particular
05:12 < epitron> are you powerless to change it?
05:12 < fenn> i'm not sure
05:13 < epitron> well, you could try and find out :)
05:13 < fenn> it's mostly a matter of not being willing to recognize my own limitations
05:13 < epitron> pushing yourself too hard?
05:13 < fenn> just not getting anywhere
05:14 < epitron> hmm... not sure i follow
05:14 < epitron> not getting anywhere in life?
05:14 < fenn> i have ~0 deliverables in the last four years
05:15 < fenn> anyway, when i see stuff like 'eugenics is bad' it's like, so what
05:15 < fenn> what are you going to do about it
05:16 < fenn> complain to the UN?
05:16 < fenn> start a zoo?
05:17 < fenn> try to get google to start a genomics program?
05:17 < epitron> no, i'm going to try to change people's minds :)
05:17 < epitron> good memes must survive
05:17 < epitron> even if they're not prevailing
05:17 < fenn> i think everyone is already against eugenics, buddy
05:17 < epitron> they must exist in at least one mind
05:18 < epitron> so that they may live on
05:18 < epitron> haha
05:18 < epitron> not everyone
05:18 < fenn> except for a few mad scientists
05:18 < epitron> the ruling classes are quite pro-eugenics
05:18 < fenn> what do you base that on?
05:18 < epitron> i believe darwin was pro-eugenics
05:18 < fenn> of course he was
05:18 < epitron> writings, historical events
05:19 < fenn> do you think the modern ruling class has any continuity with historical rulers?
05:19 < epitron> zimbardo did some interesting work on the perceptions of how much of intelligence was innate vs. learned
05:19 < epitron> and how the richer you were, the more you believed that success and intelligence were innate
05:19 < epitron> while the poorer you were, the more you believed that they were the result of hard work
05:20 < epitron> and i believe that mindset leads to the belief in the value of eugenics
05:20 < fenn> pff i have $3k to my name and no job, i believe intelligence is innate and the result of environment as a child
05:20 < epitron> it's a matter of degree
05:20 < epitron> you know you wouldn't seem so angry if you dropped little things like "pff" :)
05:21 < epitron> you could just say it flatly and plainly
05:21 < epitron> then it wouldn't be so enticed to leave
05:21 < fenn> i wanted to come across as angry because that was a stupid thing you said
05:21 < epitron> -it +i
05:21 < epitron> uh
05:21 < epitron> ooookay
05:21 < epitron> then i guess i'll go back to stupidville
05:22 < epitron> latah
05:25 < fenn> epitron: the difference between a 'smart' person and a 'stupid' person is negligible in the context of intelligence augmentation
05:26 < fenn> i.e. the genetic component doesn't matter nearly as much as the cultural component
05:27 < fenn> i grew up with computers, so now i know a lot more than most of my friends, although we are probably about the same, genetically
05:28 < fenn> does that make me more intelligent?
05:28 < fenn> they seem to think so
05:49 < epitron> i was actually saying you're an asshole, not that i'm stupid
05:50 < fenn> yeah i know
05:51 < fenn> i'm such an obvious counterexample to zimbardo, how could you have not known? :)
05:52 < fenn> although, much of 'innate' is not necessarily 'genetic' but rather the diet and health of your mother when she was pregnant with you
05:53 < epitron> you can stop talking whenever you want
05:53 < fenn> so maybe i'm not a counterexample
05:53 < fenn> dammit epi who am i supposed to talk to
05:54 < epitron> i guess yourself!
05:54 < epitron> use /msg
05:54 < fenn> i have this problem http://en.wikipedia.org/wiki/Non-24-hour_sleep-wake_syndrome
05:55 < epitron> and this one http://en.wikipedia.org/wiki/Asshole
05:56 < fenn> http://en.wikipedia.org/wiki/Resentment
05:59 < fenn> you know, i think the anti-eugenics movement is somewhat fascist
06:03 < fenn> laws telling me how i must BE, how my children must be, a restriction on your very life and existence
06:04 < fenn> isnt that the definition of fascism?
06:08 < fenn> ok, i guess there is no accepted definition of fascism. too bad, because i liked my definition
06:11 < fenn> individual rights and goals are subjugated to group goals, expectations and conformities
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07:34 < fenn> good morning
07:36 < kanzure> g'morning
07:40 < kanzure> I still have eugenicists debating with me, and it is annoying
07:40 < fenn> can you read channel logs?
07:40 [Users #hplusroadmap]
07:40 [ andares] [ Enki-2] [ epitron] [ fenn] [ kanzure] [ mech0r] 
07:40 -!- Irssi: #hplusroadmap: Total of 6 nicks [0 ops, 0 halfops, 0 voices, 6 normal]
07:40 < kanzure> "screw you, I refuse to demand all humans receive my 'genetic upgrade v1.2"
07:40 < kanzure> fenn: what do you mean?e
07:40 < fenn> epi and i were just arguing about eugenics
07:40 < kanzure> I log the channels I sit in
07:40 < kanzure> nope
07:41 < kanzure> I don't have that
07:45 < fenn> summary: epi: "eugenics is dangerous" me: "error null statement. eugenics != fascism" epi: "we'll ruin our biodiversity" me: "wah. so what you going to do about it?" epi: "you ass, i'm leaving" me: "anti-eugenicists are fascist"
07:47 < kanzure> heh
07:47 < kanzure> okay, so
07:47 < kanzure> (1) we can change human genomes, yes
07:47 < kanzure> (2) we can, if we had to, do all out eugenics and prevent certain breeding processes
07:47 < fenn> that hasnt been demonstrated has it?
07:47 < kanzure> however, no matter what measures you take to make people sterile, I *will* find a way to get their DNA
07:48 < kanzure> fenn: a friend and I have designed a sterility virus
07:48 < kanzure> it happens to be an STD
07:48 < fenn> uh, why did you do that?
07:48 < kanzure> more of a design experiment
07:48 < kanzure> it was a five-minute thought experiment
07:48 < kanzure> nothing much
07:49 < kanzure> what happens if somebody else does it?
07:49 < fenn> then we see selection for people who are resistant to the virus
07:50 < fenn> and probably a lot of new in-vitro reproductive technology
07:50 < kanzure> yep
07:51 < kanzure> you sound like you're for eugenics
07:51 < kanzure> but I don't know why
07:51 < fenn> this would tend to select for people who could afford the virus
07:51 < fenn> kanzure: i'm generally against laws of any sort, and meddling in other peoples' affairs
07:51 < kanzure> were you just picking on epi?
07:52 < fenn> i'm just cranky, and epi happened to barge in with a holy cause
07:52 < kanzure> unless you mean "personal eugenics" --> which just means "not fucking everything with a slit between her legs"
07:53 < kanzure> hey, speaking of eugenics and invitro fertilization tech
07:53 < kanzure> I announced a challenge to my fellow transhumanists the other day
07:53 < kanzure> and I told them to come up with a way to seriously stop any of us from having a child
07:53 < fenn> maybe i misunderstand the term eugenics. does mild gen-engineering of babies count? removing zygotes that have genetic diseases and such
07:53 < kanzure> and one of the astrophysicist researchers that I admire on the list
07:53 < kanzure> came back and said "Well, us women past 40 can't do shit."
07:53 < kanzure> and I replied with "DNA sequencing."
07:53 < kanzure> "Please be realistic and keep your feet grounded, OK?"
07:54 < kanzure> I think it's completely realistic. You can get DNA sequencers on ebay for under $1k USD.
07:54 < fenn> hard drive -> genome is the hard part
07:54 < kanzure> fenn: not sure if that counts as eugenics. Eugenics is an old sociodarwinist movement.
07:54 < kanzure> gengineering is closely related
07:54 < kanzure> and frankly all of these terms are confabulated
07:54 < kanzure> most people are careless when talking about this stuff
07:54 < fenn> sure, because nobody wants to talk about it
07:54 < kanzure> they make easy mistakes that make them sound like fascists
07:54 < kanzure> for example
07:55 < kanzure> "I'm talking especially about the medical technologies and about the genetic
07:55 < kanzure> improvement of the human species."
07:55 < kanzure> fascist or not?
07:55 < fenn> mu
07:55 < kanzure> Zahray's argument -> The problem with medicine is that it ALREADY strongly influenced our
07:55 < kanzure> evolutionary path. With medicine evolving, the quality of genes that are
07:55 < kanzure> responsible for our well-being is deteriorating. Look at following scenario:
07:55 < kanzure> the people with minor mutations which decrease the overall health level with
07:55 < kanzure> modern medicine are more likely to reproduce and to pass this mutation to
07:55 < kanzure> the descendants . This way the genetic pool of human species is already
07:55 < kanzure> deteriorating. The process won't stop today. It will continue even if the
07:55 < kanzure> overall technology level remains the same, leaving human species open to
07:55 < kanzure> mass suffering (as mutations accumulate). On the other side, as the size of
07:55 < kanzure> human population increases, the probability of new human diseases emerging
07:55 < kanzure> also increases. We have to find better ways to quickly develop ways to
07:55 < kanzure> combat those hazards. The only sustainable way to combat the 1st threat,
07:55 < kanzure> which is not a crime against humanity, is the genetic improvement of humans
07:55 < kanzure> (genetic medicine we have now cannot be considered a permanent solution,
07:55 < kanzure> because it does not remove the source of the problem - and it actually
07:55 < kanzure> becomes a part of the genetic deterioration problem itself). We have to
07:55 < kanzure> develop an ability to fix our own bugs - which is the direct consequence of
07:55 < kanzure> genetic improvement. To combat the second threat we have to develop a good
07:55 < kanzure> understanding of dna-based machines.
07:55 < kanzure> my response
07:56 < kanzure> actually, my response to another similiar argument re: dysgenics or whatever
07:56 < kanzure> On Thursday 03 April 2008, Pieter Bonte wrote:
07:56 < kanzure> > There is often talk of 'dysgenics' and the negative consequences in
07:56 < kanzure> > the long run of compensating for genetic defects through medical
07:56 < kanzure> > technology (popular examples are poor eye-sight & glasses, narrow
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07:56 < fenn> you got kicked at (eye-sight & glasses) which btw is not due to genetics
07:57 < kanzure> Pieter replied with Tay-Sachs syndrome and left it at that, but ..
07:57 < kanzure> uh, I was kicked apparently
07:57 < kanzure> please tell me my last message
07:57 < kanzure> well, screw it, it doesn't matter that much
07:57 < kanzure> it's about 'dysgenics'
07:57 < kanzure> or the idea that medicine is bad because it makes people less dependent on their own genome
07:57 < kanzure> so what the hell are they suggesting? that we stop treating people?
07:57 < kanzure> that we stop doing tech?
07:58 < fenn> 'we have to develop an ability to fix our own bugs - direct consequence of genetic improvement' this is stupid - it's more of a scientific and technological problem. eugenics people need to stop treating genetic improvement as a magic bullet
07:59 < fenn> eugenics is an answer in search of a problem
07:59 < kanzure> yes
07:59 < kanzure> well
07:59 < kanzure> they claim the problem is stuff like stupidity, overpopulation, and other bullshit like that
07:59 < fenn> overpopulation?
07:59 < kanzure> energy crisis too
07:59 < kanzure> eugenics may be a front for master-race ideologies
07:59 < fenn> well duh
08:00 < kanzure> okay, so for the Tay-Sachs syndrome argument -- I'm going to respond with "My genes, my choice."
08:00 < kanzure> if I want to have Tay-Sachs, let me have it
08:00 < fenn> only way to deal with this is to exercise extreme rationality and precise thinking
08:00 < kanzure> yes, 
08:00 < kanzure> I've been elaborating my arguments to extreme detail
08:00 < kanzure> and I've been relying on my type-1 v. type-2 definitions
08:00 < kanzure> techno-humanism != personal genomic improvement
08:00 < fenn> re: tay-sachs how are you supposed to make a choice before you're born?
08:01 < kanzure> well, personally,
08:01 < kanzure> I say let whoever is breeding or whatever choose
08:01 < kanzure> now, it is indeed unfortunate for a suffering being to exist, but so what?
08:01 < fenn> if i want my child to have tay-sachs, let me have it
08:01 < kanzure> right
08:01 < fenn> ok
08:01 < kanzure> but those are your genes basically
08:01 < kanzure> this is self-modification/self-replication
08:01 < kanzure> if you can't design your own child as you want, then what's the freakin' point?
08:01 < kanzure> are we going to have some Child Police running around, examining my children?
08:02 < kanzure> "Hey, this one's too smart! Smart gene 390414!"
08:02 < fenn> ugh you have no idea
08:02 < kanzure> hm?
08:02 < fenn> being a parent is not like being a normal human with rights
08:02 < kanzure> oh?
08:03 < kanzure> (of course, we both agree 'rights' to be bullshit techno-humanism)
08:03 < fenn> i'm not a parent, i've just been examining my roommate and his interactions with the state's child police branch
08:04 < kanzure> child abuse stuff?
08:05 < fenn> more like, you have to express a certain set of views, teach your child certain things, or they claim you are a bad parent and try to take your kids away
08:06 < fenn> basically "bad parent" means "bad person"
08:06 < fenn> regardless what you actually do
08:06 < kanzure> yikes
08:06 < kanzure> now, in all fairness,
08:06 < kanzure> they are fighting a pretty big 'problem' in their own views
08:06 < kanzure> namely there's been this big historical context of rampant child abuse
08:07 < fenn> yes
08:07 < kanzure> but there's also been "people abuse" anyway
08:07 < kanzure> it's a much larger problem than they care to admit
08:07 < kanzure> I think that if we empower those kids to do what they need to do to get out of those situations, give them fabbers or something, they can easily pick up their stuff and leave
08:07 < kanzure> but I'm sure as hell not going to raid homes and steal children
08:08 < fenn> the way i see it, the accepted norms of child rearing are much more hurtful than most alternative value systems
08:08 < kanzure> I'm trapped in a norm, as you know
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08:08 < kanzure> my father flat out refuses to see the lack of benefit of going to high school
08:08 < kanzure> even in the internet age
08:08 < fenn> discipline, expectations, trained to enjoy submission to authority and boredom
08:08 < kanzure> sure
08:09 < kanzure> re: boredom, see reciprocality
08:09 < fenn> i've read some of it
08:09 < kanzure> link in a sec
08:09 < kanzure> ah, good
08:09 < kanzure> yeah, so boredom can be considered with respect to dopamine
08:09 < fenn> the "ghost not" was a bit hard to follow
08:09 < kanzure> yes, I kinda lost interest around there
08:09 < kanzure> but I do agree that there might be some massive chemical networks building up like that across society
08:10 < kanzure> it's "neurochemical kinship"
08:10 < fenn> it's not just occupational behavior, food too
08:10 < kanzure> lots of economics (unfortunately) play into it, then
08:10 < fenn> occupation is the big one though
08:11 < fenn> i dont even know where to begin with that
08:11 < kanzure> I've been seeing a lot of "us v. them" mentality recently, maybe it's just me (even though I don't support it)
08:11 < kanzure> it seems like I can plainly cut the U.S. population into two groups
08:11 < kanzure> those on the autism spectrum and those who are flat out bored
08:12 < kanzure> the boredom-folks seem to treat autism and other interesting brain programs as "diseases" that must be eliminated
08:12 < fenn> 'autism spectrum' does this really mean anything?
08:12 < kanzure> perhaps not
08:12 < kanzure> it just seems as close to type-1 v. type-2 transhumanism topics as ever 
08:13 < kanzure> anyway, I don't want to elaborate because it doesn't matter
08:13 < kanzure> I have a few more minutes this morning to get some work done, so I'm going to drop you with a few links and then go sketch out a few documents
08:13 < fenn> seeya
08:13 < kanzure> particularly I'm planning on (1) an article on eugenics much like my transhumanist-def page, so that we can do that 'extreme analysis' of various definitions
08:14 < kanzure> and then (2) I'm going back to Ellington's challenge for me
08:14 < kanzure> still looking for problem spaces that DNA can work in
08:14 < kanzure> did you get my email last night on this?
08:14 < kanzure> no, apparently not
08:14 < fenn> no
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08:14 < kanzure> so this guy is sending me mixed signals
08:15 < kanzure> he claims that nucleic acids are not good for computation
08:15 < kanzure> which I completely agree with
08:15 < fenn> i wouldnt say that.. thy're just slow
08:15 < kanzure> but then says "Find me a class of algorithms / problems where the inherent abilities of DNA or biomolecules will shine."
08:15 < kanzure> so why do something slow when you can do it otherwise
08:15 < kanzure> it seems to me that he's trying to point me towards 'matter programming'
08:15 < fenn> because it's error-tolerant
08:15 < kanzure> programming with biomolecules is not the same thing as programming with FETs
08:15 < kanzure> _but_ then why just implement logic gates?
08:16 < kanzure> maybe it's more about GRNs, genetic regulation networks
08:16 < fenn> dunno, the logic gates thing always seemed dumb to me
08:16 < kanzure> but even then, these GRNs are mostly just made up of logic stuff
08:16 < fenn> the interesting stuff in my opinion is the self-modifying RNA sequences
08:16 < kanzure> show me a GRN that cannot be modeled as a rate problem or if/then problem with discrete units (you can't - it's all fundamentally discrete since you have enes there)
08:16 < kanzure> sure
08:16 < kanzure> self-modification is awesome
08:16 < kanzure> the DNA-tiling too
08:17 < kanzure> he wants me to come up with an application for my DNA compiler
08:17 < kanzure> but if it's not for computation
08:17 < kanzure> then I don't know why you would even *use* a compiler
08:17 < fenn> 'emergent properties' is a red herring - what you want is orthogonality
08:18 < kanzure> not synergy?
08:18 < fenn> variables that can be combined in many ways
08:18 < fenn> i think orthogonality is more specific than either
08:21 < kanzure> I was thinking of doing a review of all synthetic circuits constructed to date
08:21 < kanzure> and then saying "Hey, we haven't done this yet, how about it?"
08:21 < kanzure> and then a review of computational-DNA physics/thermodynamics/comp-sci to show a class of problems that DNA can do
08:22 < fenn> try to find a way to factor prime numbers
08:22 < kanzure> why
08:22 < kanzure> that's computational, and computers are better at that
08:22 < kanzure> si-computers, I mean
08:22 < fenn> it's a highly parallel problem
08:22 < fenn> and in much demand
08:22 < kanzure> more importantly, I don't want to actually solve this problem right off the bat
08:22 < kanzure> if I can, that'd be great
08:23 < fenn> of course you'll break the world if you succeed
08:23 < fenn> s/world/internet/
08:23 < kanzure> I want to get into the lab over the summer
08:23 < kanzure> I fear that this guy has given me a near impossible task
08:23 < kanzure> but I can't prove this
08:23 < fenn> it's probably just not what you're interested in
08:23 < kanzure> otherwise I'd email him back and prove it to him and say "what gives, buddy, trying to set me up?"
08:23 < kanzure> maybe
08:24 < kanzure> but it looks like a 'hard' problem
08:24 < kanzure> and frankly I need the hard experience
08:24 < kanzure> too many people have been calling bullshit on me and telling me to get into a lab to see how the "real world" works
08:24 < fenn> well, the 'real world' is depressing and takes fucking forever to get anything done
08:25 < fenn> especially when you're sitting there moving drops of liquid around by hand
08:25 < fenn> that's what biotech lab is, basically
08:25 < fenn> but if you feel it will give you some clout/credentials, go for it
08:26 < kanzure> hm
08:26 < fenn> university bio labs are amazingly primitive
08:28 < fenn> did you see this? http://www.nanoengineer-1.net/mediawiki/index.php?title=DNA_Origami_-_Creating_the_Nanorex_logo
08:32 < kanzure> neat
08:33 < fenn> the dna origami algorithm doesnt work the way i thought it did
08:33 < fenn> thought it was all one string, but apparently there are little strands that help it self-assemble in the right order
08:35 < fenn> DNA is interesting because of massively parallel recombination, so think about that
08:37 < fenn> "we're not going to beat electronic algorithmic execution" not serial algorithms, but you can definitely beat it in parallel algorithms
08:40 < fenn> if it were me, i'd jump on the winfree bandwagon
08:42 < kanzure> http://heybryan.org/mediawiki/index.php/Ellingtonia
08:42 < kanzure> haha
08:43 < kanzure> re: DNA and recombination, yes, but that requires evolvability I think
08:43 < kanzure> and that means cells, in generla
08:43 < kanzure> *general
08:43 < kanzure> otherwise you can't do a selection experiment
08:43 < kanzure> I just had an idea -- maybe Ellington is thinking that transcriptional logic could mean something like 'logic in realtime experiments' or something
08:44 < fenn> like, if (lactose and lacZ): die
08:45 < fenn> or was it lacI
08:45 < fenn> bah
08:45 < kanzure> nope, think about this
08:45 < kanzure> suppose that he means computational physics in a sense
08:45 < kanzure> to run simulated experiments in silico we need lots of library overhead
08:45 < kanzure> with DNA we have the advantage of DNA being right there
08:45 < kanzure> as the substrate
08:45 < kanzure> and interesting/novel properties can be investigated as a matter of course of programming with the biomolecules themselves
08:46 < kanzure> you get to avoid physics libraries/packages because you're implementing directly on physical matter in the first place
08:47 < fenn> cant see how that's worth the trouble
08:47 < fenn> simulations are supposed to make your life easier
08:47 < kanzure> But how large is the class of computational physics that can be investigated via in vitro nucleic acid logic, in a way that is more useful than simulations on supercomputers?
08:48 < fenn> nucleic acid physics :)
08:48 < fenn> what's "computational physics"?
08:49 < kanzure> molecular dynamics, for example
08:49 < kanzure> computational chem
08:49 < kanzure> etc.
08:49 < fenn> well, DNA is DNA
08:49 < fenn> you arent going to investigate the properties of, say, cobalt
08:50 < fenn> it can be useful for bringing together materials, as a catalyst
08:50 < fenn> because of binding specificity
08:50 < kanzure> how is that computational?
08:50 < kanzure> hehe
08:51 < kanzure> I'm pretty sure this is a smart guy, why the hell would he box himself in to nucleic acids
08:51 < kanzure> obviously he wants his minions to do the hard work here
08:51 < kanzure> but why would he do that
08:51 < fenn> well, if beaker A combines cobalt and samarium, and beaker B combines cobalt and yttrium, you've done an experiment?
08:52 < kanzure> computational separation of materials?
08:52 < fenn> computers just move bits around, and so a matter computer just moves molecules around?
08:52 < fenn> whatever 'matter computer' is
08:53 < fenn> probably comes from 'matter compiler' in the diamond age
08:53 < fenn> ah i've got it
08:54 < kanzure> hm
08:54 < fenn> because in nanosynthesis you need to do complex sequences
08:54 < kanzure> yeah?
08:54 < fenn> and since DNA makes a handy nano-scale computer, you can do that
08:54 < fenn> blah
08:54 < fenn> good luck
08:55 < kanzure> yeah, not good
08:55 < kanzure> oh
08:55 < kanzure> DNA compiler (mine) -> in vitro implementation of my program -> as a matter compiler
08:55 < kanzure> the program that will be running will compile matter
08:55 < kanzure> okay, so I just need to do patterned synthesis in vitro or something
08:55 < kanzure> from logic control
08:56 < kanzure> is that good enough?
08:56 < fenn> i dunno
08:56 -!- kanzure [n=bryan@70.113.54.112] has quit ["Leaving."]
17:55 -!- kanzure [n=bryan@cpe-70-113-54-112.austin.res.rr.com] has joined #hplusroadmap
17:56 < kanzure> Hey fenn, epitron.
18:35 < kanzure> fenn: quantum dot on a DNA molecule?
18:39 < kanzure> Quantum-dot aptamer beacons for the detection of proteins - Get this article - all 4 versions »
18:39 < kanzure> M Levy, SF Cater, AD Ellington - ChemBioChem, 2005 - doi.wiley.com
18:39 < kanzure> Quantum dots (QDs) offer a number of advantages over stan- dard fluorescent dyes 
18:39 < kanzure> for monitoring biological systems in real time, including greater 
18:39 < kanzure> photostability, larger effective Stokes shifts, longer fluorescent ... 
18:39 < kanzure> Cited by 26 - Related Articles - Web Search
18:39 < kanzure> huh
18:39 < kanzure> that's Ellington
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19:46 < epitron> yo kanz
19:46 < epitron> what's happenin
19:46 < kanzure> hehe
19:47 < kanzure> epitron: was it you or fenn who was mentioning edge.org with me the other day?
19:47 < kanzure> I think it was you, re: Smolin
19:47 < kanzure> and then Hillis.
19:47 < kanzure> epitron: So, if you know about edge.org and Smolin, then you surely know about Kauffman, yes?
19:48 < epitron> hmmm...
19:48 < epitron> it's been a while since i've explored the breadth of edge.org
19:48 < epitron> i might've read something by him, is he a physicist?
19:49 < epitron> oh interesting, i haven't read this
19:50 < kanzure> theoretical/mathematical biologist
19:50 < kanzure> he's hardcore
19:50 < kanzure> I just found a paper written by him and Ellington
19:50 < kanzure> Ellington is the professor that I've been working with at UT.
19:52 < epitron> ohh i have seen this guy's talk before
19:52 < epitron> i never looked more into his work though
19:52 < kanzure> I never saw his talk, linkage?
19:53 < epitron> err, i meant his edge interview. :)
19:53 < epitron> him talking, as opposed to text.
19:54 < kanzure> ok
19:56 < epitron> this is good stuff, thanks for the link :)
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22:15 < kanzure> Hey Enki-2.
22:15 < kanzure> http://freelancingscience.com/2008/04/03/biobrick-as-a-functional-role/#comment-356 <-- yarr, I am intense
23:38 -!- mechie [n=DION102@cpe-74-73-121-30.nyc.res.rr.com] has joined #hplusroadmap
23:40 < kanzure> Hey mechie.
23:40 < mechie> hi
23:40 < kanzure> elhaym?
23:41 < mechie> yes that's me
23:41 < mechie> i play videogames :(
23:41 < mechie> Elhaym is a char from Xenogears
23:41 < kanzure> What brings you around these parts?
23:41 < mechie> epi made me
23:42 < kanzure> Meh. Have fun. Hang around a bit.
23:42 -!- kanzure changed the topic of #hplusroadmap to: http://heybryan.org/ http://heybryan.org/mediawiki/ http://heybryan.org/mediawiki/index.php/Self-replication
23:43 < mechie> he promised me world domination
23:44 < kanzure> Type one or type two world domination?
23:44 < mechie> i don't know
23:44 < mechie> he didn't specify
23:44 < mechie> he told me to hang around
23:45 < kanzure> Tonight I've been working in computational DNA physics and synthetic biology
23:45 < kanzure> http://heybryan.org/mediawiki/index.php/Ellingtonia
23:46 < mechie> when did you start studing all this
23:47 < kanzure> Not sure. February?
23:48 < mechie> -_-'
23:48 < kanzure> Hm?
23:50 < mechie> were you always into the sciences
23:53 < kanzure> nope
23:53 < kanzure> I am a gamer at heart :)
23:53 < mechie> nice
23:53 < kanzure> Nintendo64 is kind of lodged into my brain forever
23:53 < mechie> zelda ocarina of time?
23:53 < kanzure> yes, and most anything Rareware
23:54 < mechie> o
23:54 < kanzure> Banjo Kazooie/Tooie especially
23:54 < kanzure> Donkey Kong, Super Mario 64, 
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23:54 < kanzure> I was a sharker, obviously.
23:54 < mechie> i mostly played Zelda + mario stuff
23:54 < kanzure> Yep. Good times.
23:54 < mechie> i was big into rpgs at the time
23:54 < kanzure> Same here. I was a pokemon addict.
23:54 < mechie> lull.... my channel is called team rocket
23:54 < mechie> hahahahah
23:55 < kanzure> Heh.
23:55 < mechie> i didn't get beyond pokemon red and blue
23:56 < kanzure> I learned to read on those games, and to hack, and so essentially I kind of learned to read + program at the same time, in an odd "reverse" sort of way.
23:57 < mechie> dont they also have a free guide to programming nintendo gameboy games
23:57 < mechie> my bro had it
23:57 < mechie> my bro also turned a ninentdo ds into an oscillisope
23:57 < kanzure> Sure, I was writing ROM files of my own for a while, until I realized that I could just do normal computer programming anyway.
23:57 < kanzure> into an oscilloscope? interesting
23:57 < kanzure> what were the inputs?
23:58 < mechie> i dunno 
23:58 < mechie> hahahaha
23:58 < kanzure> I guess it could be anything, they have onboard signal processors, right?
23:58 < mechie> yes i guess
23:58 < mechie> he didn't show me
23:58 < mechie> it's @ his work place
23:58 < mechie> he's trying to make a tiny affordable oscilliscope for college students
23:58 < kanzure> neat
23:58 < kanzure> yes, I'm big into DIY hardware
23:58 < mechie> he works @ http://www.linkinstruments.com
23:58 < kanzure> hell, I made a kit on how to do your own genetic engineering
23:58 < kanzure> http://biohack.sf.net/
23:59 < mechie> i was mostly just the solder person there
23:59 < kanzure> neat device
23:59 < kanzure> haha
23:59 < kanzure> solder person == eye damage? :)
23:59 < mechie> so i made like
23:59 < mechie> $100k worth of oscilliscopes and logic analyzers in 10 days
23:59 < kanzure> ah, they aren't free?
23:59 < kanzure> then it's useless
23:59 < mechie> i was pretty high
23:59 < mechie> and my eyes pretty much died