| --- Day changed Fri Apr 04 2008 | ||
| 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? | 00:09 |
| kanzure | fenn: http://heybryan.org/chats/2008-04-03_self-replication_with_Tony.html | 00:30 |
| -!- kanzure [n=bryan@70.113.54.112] has quit ["Leaving."] | 00:42 | |
| epitron | hmmm | 04:48 |
| epitron | eugenics is dangerous :) | 04:48 |
| 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 | 04:49 |
| 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? | 04:50 |
| 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 :) | 04:51 |
| epitron | or not | 04:53 |
| epitron | it's up to you | 04:53 |
| 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 | 04:54 |
| 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 | 04:55 |
| * epitron furrows his brow | 04:56 | |
| epitron | anyhow | 04:56 |
| 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 | 04:57 |
| 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 | 04:58 |
| epitron | how so? | 04:59 |
| 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 :) | 05:00 |
| 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 :) | 05:01 |
| 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 | 05:02 |
| 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 | 05:04 |
| fenn | epitron: here's a bit of cognitive dissonance for you: which is more preferable, inbreeding (result of racism) or homogeneity | 05:05 |
| fenn | homogeneity = everyone is a hybrid | 05:07 |
| epitron | huh | 05:07 |
| 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 | 05:08 |
| 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 | 05:09 |
| 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 | 05:10 |
| 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 | 05:11 |
| 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 | 05:12 |
| 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 | 05:13 |
| 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 | 05:14 |
| 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 | 05:15 |
| fenn | complain to the UN? | 05:16 |
| fenn | start a zoo? | 05:16 |
| 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 | 05:17 |
| 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 | 05:18 |
| 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 | 05:19 |
| 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" :) | 05:20 |
| 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 | 05:21 |
| epitron | latah | 05:22 |
| fenn | epitron: the difference between a 'smart' person and a 'stupid' person is negligible in the context of intelligence augmentation | 05:25 |
| fenn | i.e. the genetic component doesn't matter nearly as much as the cultural component | 05:26 |
| 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 | 05:27 |
| fenn | does that make me more intelligent? | 05:28 |
| fenn | they seem to think so | 05:28 |
| epitron | i was actually saying you're an asshole, not that i'm stupid | 05:49 |
| fenn | yeah i know | 05:50 |
| fenn | i'm such an obvious counterexample to zimbardo, how could you have not known? :) | 05:51 |
| fenn | although, much of 'innate' is not necessarily 'genetic' but rather the diet and health of your mother when she was pregnant with you | 05:52 |
| 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 | 05:53 |
| 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 | 05:54 |
| epitron | and this one http://en.wikipedia.org/wiki/Asshole | 05:55 |
| fenn | http://en.wikipedia.org/wiki/Resentment | 05:56 |
| fenn | you know, i think the anti-eugenics movement is somewhat fascist | 05:59 |
| fenn | laws telling me how i must BE, how my children must be, a restriction on your very life and existence | 06:03 |
| fenn | isnt that the definition of fascism? | 06:04 |
| fenn | ok, i guess there is no accepted definition of fascism. too bad, because i liked my definition | 06:08 |
| fenn | individual rights and goals are subjugated to group goals, expectations and conformities | 06:11 |
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| fenn | good morning | 07:34 |
| kanzure | g'morning | 07:36 |
| 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 | 07:40 |
| kanzure | I don't have that | 07:41 |
| 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" | 07:45 |
| 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 | 07:47 |
| 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 | 07:48 |
| kanzure | what happens if somebody else does it? | 07:49 |
| fenn | then we see selection for people who are resistant to the virus | 07:49 |
| fenn | and probably a lot of new in-vitro reproductive technology | 07:50 |
| kanzure | yep | 07:50 |
| 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? | 07:51 |
| 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" | 07:52 |
| 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?" | 07:53 |
| 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 | 07:54 |
| 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 | 07:55 |
| 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 | 07:56 |
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| fenn | you got kicked at (eye-sight & glasses) which btw is not due to genetics | 07:56 |
| 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? | 07:57 |
| 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 | 07:58 |
| 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 | 07:59 |
| 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? | 08:00 |
| 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? | 08:01 |
| 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? | 08:02 |
| 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 | 08:03 |
| kanzure | child abuse stuff? | 08:04 |
| 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 | 08:05 |
| 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 | 08:06 |
| 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 | 08:07 |
| 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 | 08:08 |
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| 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 | 08:08 |
| 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 | 08:09 |
| 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 | 08:10 |
| 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 | 08:11 |
| 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 | 08:12 |
| 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 | 08:13 |
| 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 | 08:14 |
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| kanzure | so this guy is sending me mixed signals | 08:14 |
| 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? | 08:15 |
| 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 | 08:16 |
| 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 | 08:17 |
| 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 | 08:18 |
| 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 | 08:21 |
| 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 | 08:22 |
| 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 | 08:23 |
| 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 | 08:24 |
| 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 | 08:25 |
| kanzure | hm | 08:26 |
| fenn | university bio labs are amazingly primitive | 08:26 |
| fenn | did you see this? http://www.nanoengineer-1.net/mediawiki/index.php?title=DNA_Origami_-_Creating_the_Nanorex_logo | 08:28 |
| kanzure | neat | 08:32 |
| 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 | 08:33 |
| fenn | DNA is interesting because of massively parallel recombination, so think about that | 08:35 |
| fenn | "we're not going to beat electronic algorithmic execution" not serial algorithms, but you can definitely beat it in parallel algorithms | 08:37 |
| fenn | if it were me, i'd jump on the winfree bandwagon | 08:40 |
| kanzure | http://heybryan.org/mediawiki/index.php/Ellingtonia | 08:42 |
| kanzure | haha | 08:42 |
| 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 | 08:43 |
| fenn | like, if (lactose and lacZ): die | 08:44 |
| 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 | 08:45 |
| kanzure | you get to avoid physics libraries/packages because you're implementing directly on physical matter in the first place | 08:46 |
| 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? | 08:47 |
| fenn | nucleic acid physics :) | 08:48 |
| fenn | what's "computational physics"? | 08:48 |
| 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 | 08:49 |
| 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 | 08:50 |
| 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? | 08:51 |
| 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 | 08:52 |
| fenn | probably comes from 'matter compiler' in the diamond age | 08:53 |
| fenn | ah i've got it | 08:53 |
| 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 | 08:54 |
| 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 | 08:55 |
| kanzure | is that good enough? | 08:56 |
| fenn | i dunno | 08:56 |
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| kanzure | Hey fenn, epitron. | 17:56 |
| kanzure | fenn: quantum dot on a DNA molecule? | 18:35 |
| 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 | 18:39 |
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| epitron | yo kanz | 19:46 |
| epitron | what's happenin | 19:46 |
| kanzure | hehe | 19:46 |
| 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? | 19:47 |
| 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? | 19:48 |
| epitron | oh interesting, i haven't read this | 19:49 |
| 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. | 19:50 |
| 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? | 19:52 |
| epitron | err, i meant his edge interview. :) | 19:53 |
| epitron | him talking, as opposed to text. | 19:53 |
| kanzure | ok | 19:54 |
| epitron | this is good stuff, thanks for the link :) | 19:56 |
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| kanzure | Hey Enki-2. | 22:15 |
| kanzure | http://freelancingscience.com/2008/04/03/biobrick-as-a-functional-role/#comment-356 <-- yarr, I am intense | 22:15 |
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| kanzure | Hey mechie. | 23:40 |
| mechie | hi | 23:40 |
| kanzure | elhaym? | 23:40 |
| 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 | 23:41 |
| kanzure | Meh. Have fun. Hang around a bit. | 23:42 |
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| mechie | he promised me world domination | 23:43 |
| 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 | 23:44 |
| kanzure | Tonight I've been working in computational DNA physics and synthetic biology | 23:45 |
| kanzure | http://heybryan.org/mediawiki/index.php/Ellingtonia | 23:45 |
| mechie | when did you start studing all this | 23:46 |
| kanzure | Not sure. February? | 23:47 |
| mechie | -_-' | 23:48 |
| kanzure | Hm? | 23:48 |
| mechie | were you always into the sciences | 23:50 |
| 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 | 23:53 |
| mechie | o | 23:54 |
| kanzure | Banjo Kazooie/Tooie especially | 23:54 |
| kanzure | Donkey Kong, Super Mario 64, | 23:54 |
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| 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 | 23:54 |
| kanzure | Heh. | 23:55 |
| mechie | i didn't get beyond pokemon red and blue | 23:55 |
| 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. | 23:56 |
| 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? | 23:57 |
| 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/ | 23:58 |
| 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 | 23:59 |
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