| --- Day changed Sat Sep 19 2009 | ||
| kanzure | plot 10 * (exp(-((((x-.1)/(1/(.01 * sqrt(2 * pi))))**2)/2))) | 00:14 |
|---|---|---|
| kanzure | the two parameters are actually a,b where a and b are the two positional coords of the user's mouse | 00:14 |
| kanzure | and, er, 10 and .01 were supposed t obe the same, and .1 was the other variable | 00:15 |
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| genehacker | kanzure you seen the taq-purification thread? | 10:02 |
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| genehacker | kanzure you seen the taq-purification thread in diybio? | 10:05 |
| drazak | genehacker: the one from like 3 months ago? or the restriction enzyme one currently? | 10:14 |
| * katsmeow-afk wants to slap someone across the face with flowers, whoever it was that mentioned "actionary" caused me to dl gigabytes of data last nite | 10:17 | |
| katsmeow-afk | luckily, i avoided dl'ing it in 28 difefrent languages! | 10:18 |
| genehacker | the one currently | 10:20 |
| drazak | making your own taq or restriction enzymes isn't hard | 10:24 |
| drazak | purifying them is | 10:24 |
| genehacker | CORRECT | 10:25 |
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| kanzure | just so that it doesn't happen again: | 10:54 |
| kanzure | http://adl.serveftp.org/lab/researchers-to-keep-track-of | 10:54 |
| kanzure | i'm missing a lot | 10:54 |
| fenn | richard feynman is dead.. | 10:56 |
| kanzure | :( | 10:57 |
| kanzure | fine. i'll relabel. | 10:57 |
| fenn | also you shouldn't post peoples' email in plain text, it's not nice | 10:58 |
| kanzure | it's on their website | 10:58 |
| kanzure | but ok | 10:58 |
| fenn | there's a war on, man | 10:58 |
| genehacker | drexler? | 11:01 |
| genehacker | hmmm... | 11:01 |
| genehacker | I don't know about this one | 11:01 |
| fenn | perhaps you'd prefer to delete drexler and add bolonkin | 11:01 |
| kanzure | i saw the most awesome name today. 'mackinaw' | 11:02 |
| fenn | yea bro | 11:02 |
| genehacker | I think there was a bridge named that | 11:02 |
| genehacker | it collapsed horribly | 11:02 |
| fenn | gallopin girdie | 11:02 |
| fenn | no i guess that was something else | 11:03 |
| genehacker | yeah I guess so | 11:04 |
| genehacker | it's talk like a pirate day | 11:13 |
| fenn | as per recent discussion on desktop chemical synthesizers: http://fennetic.net/irc/Peter%20F.%20Hamilton%20-%20Misspent%20youth.pdf | 12:08 |
| strages | ybit is at the makers local 256 hackerspace! | 12:38 |
| fenn | has he made a fool of himself yet? | 12:39 |
| genehacker | what page fenn | 12:40 |
| genehacker | that's HUGE | 12:40 |
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| fenn | genehacker: hmm? | 12:40 |
| fenn | it's a novel that quantumg mentioned | 12:41 |
| genehacker | huh? | 12:41 |
| fenn | nevermind | 12:41 |
| genehacker | does it have a desktop chemical synthesizer in it? | 12:41 |
| fenn | praps | 12:42 |
| genehacker | ok | 12:43 |
| genehacker | dang | 12:48 |
| genehacker | I WANT ONE | 12:48 |
| swabbie_strages | fenn: nah he's cool | 12:48 |
| genehacker | 256 hacker meetings? | 12:49 |
| swabbie_strages | Hackerspaces Meetup happening this weekend at our space. 5 hackerspaces represented so far | 12:50 |
| swabbie_strages | more on the way | 12:50 |
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| genehacker | oops | 12:53 |
| genehacker | thought you were talking about 2600 meetings | 12:53 |
| genehacker | now if we only had programmable molecular seives | 13:07 |
| fenn | like a membrane transport protein? | 13:09 |
| fenn | i know it's not diamondoid cogs and wheels but it does the job | 13:09 |
| genehacker | yeah | 13:14 |
| genehacker | if you had a programmable molecular seive it'd work | 13:14 |
| genehacker | thanks to the equilibrium principle | 13:14 |
| genehacker | heck viagra can spontaneously form and unform in solution, but if you remove it you can get more | 13:15 |
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| bct | hello all. | 18:55 |
| bct | i think skdb has a lot of potential and is a very interesting idea so don't take this questtion the wrong way: | 18:55 |
| bct | is it useful for anything right now? | 18:55 |
| fenn | no. go away. | 19:11 |
| fenn | :) | 19:11 |
| kanzure | he's being mean | 19:11 |
| kanzure | the a/c is out again | 19:11 |
| fenn | rawr | 19:11 |
| * kanzure feeds fenn some chocolate | 19:12 | |
| fenn | i think i've had enough candy already | 19:12 |
| kanzure | bct: it can plug stuff together | 19:12 |
| fenn | really we just need people to start putting data into computer parseable formats.. once that's done we can massage the data however we want | 19:13 |
| kanzure | but it has to be data | 19:13 |
| kanzure | not a picture of a datum | 19:13 |
| fenn | that first step is incredibly time consuming if you're trying to do everything in the universe | 19:13 |
| bct | assuming there's data though, what can be done with it? | 19:13 |
| fenn | then you can draw conclusions about what can be done with various sets of tools and materials | 19:14 |
| fenn | or conversely build up a list of things needed to do some task | 19:14 |
| fenn | like build an electric car or something | 19:14 |
| bct | right, but that's not actually useful unless everything needed to build an electric car is readily available | 19:15 |
| kanzure | no it tells you what you need to get | 19:15 |
| fenn | everything needed to build a car is readily available | 19:15 |
| bct | is there a more immediate goal than "can specify the parts for an electric car"? | 19:15 |
| kanzure | bct: have you read the wiki page? | 19:15 |
| fenn | yes | 19:15 |
| fenn | specifically i want to do inventory management for fab lab activities | 19:16 |
| bct | i think so, but let me take another look | 19:16 |
| fenn | http://adl.serveftp.org/dokuwiki/skdb | 19:16 |
| kanzure | i'm not really interested in making an electric car right now, fyi | 19:16 |
| kanzure | but that should be obvious | 19:16 |
| bct | yeah, that's why i'm asking about a more immediate goal. an car isn't realistic right now. | 19:17 |
| fenn | i'm just tired of having to reinvent the wheel every time i try to replicate someone's results | 19:17 |
| fenn | why isn't specifying how to build a car a realistic goal? | 19:18 |
| fenn | ok how about a DIY CNC machine | 19:18 |
| fenn | is that realistic/immediate enough for you? | 19:18 |
| bct | because the current bottlenecks in diy cars aren't something that can be solved by skdb (i suspect) | 19:19 |
| fenn | you'd be surprised | 19:19 |
| fenn | a lot of building an electric car is sourcing components and materials | 19:19 |
| bct | aah, does skdb handle sourcing? | 19:20 |
| bct | because that would be pretty immediately useful. | 19:20 |
| fenn | well, it's supposed to | 19:20 |
| fenn | but so far we only have like two packages | 19:20 |
| fenn | basically whatever you need to know to build something | 19:21 |
| bct | ok, thanks. i think that helps :) | 19:21 |
| kanzure | how about you help us out? | 19:21 |
| bct | do you have anything in mind? | 19:22 |
| kanzure | data | 19:22 |
| fenn | well there's supposed to be this wishlist page | 19:22 |
| fenn | but right now it's a bunch of crap | 19:22 |
| bct | i'm not sure i have any useful data atm. | 19:22 |
| kanzure | http://adl.serveftp.org/dokuwiki/skdb/wishlist | 19:23 |
| bct | i'll take a look though, and maybe i can contribute a simple electronics project or two. | 19:23 |
| kanzure | that would be nice | 19:24 |
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| kanzure | "Probability minimizes the system failure probability whereas possibility maximizes the normalized deviation of the uncertain variables from their nominal values that the system can tolerate without failure." | 20:25 |
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| jonathan__ | no one should synthesize their own oligos. oligos are a commodity item. price is rapidly dropping while quality is rapidly improving. | 20:40 |
| jonathan__ | diy dna synthesis is a ridiculous idea | 20:41 |
| jonathan__ | better to work on the bigger issues, like making re-usable dna parts | 20:41 |
| jonathan__ | leave the synthesis to the commodity vendors. | 20:41 |
| jonathan__ | so there :-P | 20:41 |
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| bct | i guess what i meant to ask is: how close is skdb to being able to describe something like an arduino or a ronja? | 20:46 |
| kanzure | bct: arduinos have .sch files so you should be able to just drop them into an skdb package | 20:50 |
| kanzure | jonathan__: maybe you should stop your body from synthesizing dna while you're not looking | 20:50 |
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| jonathan__ | in that context, my body is a commodity vendor | 20:51 |
| kanzure | jonathan__: hey, do you know of any good papers on transfer functions and interface compatibility and probability of (catastrophic) failure between two connecting components? | 20:51 |
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| jonathan__ | tho only for world class dna. arbitrary dna it refuses to make | 20:52 |
| kanzure | making microliters of the premium every day | 20:52 |
| jonathan__ | good papers on what kinds of transfer functions | 20:52 |
| * kanzure drums his chest | 20:52 | |
| jonathan__ | H(s) = X(s) / Y(s) | 20:52 |
| kanzure | jonathan__: well there seems to be a transfer function that can be used to represent the component. then, there's some probability that the output of the component will exceed the acceptable "range" for the next connected component | 20:53 |
| jonathan__ | probability of failure would depend on the type of system | 20:53 |
| kanzure | but it's not really a "range" | 20:53 |
| kanzure | i wanted to originally specify it as a range between two magnitudes of some unit in skdb | 20:53 |
| kanzure | so a pipe could take 50..100 psi or something | 20:53 |
| kanzure | but that's not really how it works | 20:53 |
| jonathan__ | transfer functions are very complex polynomials, often dozens of vars. so range of any 1 of those vars will affect the output correspoding to the transfer function itself | 20:54 |
| kanzure | sure. let's assume the polynomial is or has been computed for some range of inputs. | 20:54 |
| kanzure | given some output of the system, is it "probably going to make this interface/connection fail" ? | 20:54 |
| jonathan__ | yes, transfer functions are modelled | 20:54 |
| kanzure | i have this whole list of search terms but i'm getting absolutely nowhere | 20:55 |
| jonathan__ | that is a very very tough q and likely there is no real answer. because, transfer functions have very complex behavior. | 20:55 |
| kanzure | http://adl.serveftp.org/~bryan/2009-09-18.txt to see my notes | 20:55 |
| jonathan__ | systems are designed to have self-normalizing parts. | 20:55 |
| jonathan__ | i.e. a stereo amplifier for example | 20:56 |
| jonathan__ | let's say a resistor in the sytem, of the dozens of resistors and transistors, has a crazy range | 20:56 |
| kanzure | sure | 20:56 |
| jonathan__ | the resistor results in change in current, which will pump more current thru the transistors | 20:57 |
| jonathan__ | so in an amateur system, perhaps the system could go into overload (results in loud noise) or damping (no output) | 20:57 |
| kanzure | hm | 20:57 |
| kanzure | well i guess i just mean for "holy shit it will catch on fire" scenarios | 20:57 |
| jonathan__ | however.... a lot of work is done so that, i.e. transistors are self-biasing based on temperature | 20:57 |
| kanzure | not for "everything works but the overall output is wrong" | 20:58 |
| jonathan__ | the point is that the transistor will automatically change beta (amplification) because the current is too high and the temperature changes too hot. so the system re-normalizes | 20:58 |
| jonathan__ | it is fail safe | 20:58 |
| jonathan__ | that's the whole point of engineering | 20:58 |
| kanzure | huh i may need to design some shitty noise generator circuits | 20:58 |
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| jonathan__ | amplifers physically mount transistors to the same heat sink, so all transistors will act in unison, etc. for this purpose (among other purposes) | 20:59 |
| jonathan__ | if one transistor goes into overload, the others will damp. etc. | 20:59 |
| kanzure | this seems to be something you design into the system? | 21:00 |
| jonathan__ | the same goes for bridge construction.... alternating cables damp the others, etc | 21:00 |
| jonathan__ | yes and it takes a lot of work | 21:00 |
| jonathan__ | now look at a s/w algorithm, lets say a feedback control loop, motor control PID, etc, those have big crazy H(s) | 21:00 |
| jonathan__ | and likewise they have self-compensating behavior | 21:01 |
| jonathan__ | for example a jolt to the system which makes it start oscillating crazy, will re-normalize to expected behavior.. auto-damping | 21:01 |
| kanzure | sure | 21:01 |
| kanzure | but this is before that's designed into the system | 21:01 |
| jonathan__ | negative & positive feedback | 21:01 |
| kanzure | at the component selection stage | 21:01 |
| jonathan__ | no it's part of the algorithm | 21:01 |
| jonathan__ | it's in the math | 21:01 |
| drazak | jonathan__: aka jonathon cline/ | 21:02 |
| kanzure | hm | 21:02 |
| jonathan__ | when systems are connected together, they use buffers in electronics | 21:02 |
| jonathan__ | so one system fails, it does not affect the next | 21:02 |
| jonathan__ | of course the input may be bad... but the crazy oscillation or whatever, does not carry thru | 21:03 |
| jonathan__ | in IC design there is some ridiculous % of buffers compared to the actual blocks | 21:03 |
| kanzure | "blocks"? | 21:03 |
| kanzure | ok | 21:04 |
| jonathan__ | consider that 50% of all s/w is error checking, sometimes more.. (or user arg checking).. the actual code that does the "algorithm" is quite small usually | 21:04 |
| jonathan__ | compare to a pentium.. some ridiculous % of the chip in terms of the transistors, is all just for connecting one small system to another small system | 21:04 |
| jonathan__ | buffering | 21:04 |
| jonathan__ | so if one system gets a funny clock impulse, the entire pentium clock doesn't go crazy | 21:05 |
| jonathan__ | clock lines are horrible sources for noise | 21:05 |
| drazak | IC's still have oscillation problems | 21:05 |
| drazak | if you're making something with opamps, oscillation could cause the whole thing to fail | 21:05 |
| jonathan__ | if it is designed well, then it should never happen | 21:06 |
| jonathan__ | opamps are negative feedback | 21:06 |
| drazak | if the system or the opamps? | 21:06 |
| drazak | certain opamps are more susceptive than others | 21:06 |
| jonathan__ | for ex. the op amp will have a temperature compensating element or voltage ref. | 21:06 |
| jonathan__ | that's because the gain is so high | 21:07 |
| drazak | right, it needs to be unity gain stabilized | 21:07 |
| jonathan__ | designers know not to use certain components for that reason, or if they are used, then they have to be biased for run-away | 21:08 |
| jonathan__ | electronics is ridiculous in the amount of fool-proofing included | 21:08 |
| jonathan__ | amazing actually | 21:08 |
| jonathan__ | of course a lot of regulation forces that as well | 21:09 |
| jonathan__ | fault tolerance is the last thing to add on to a system | 21:11 |
| drazak | yes, but certain opamps, such as the lm617x often oscilates for a variety of reasons, but it's a very distortion free opamp and one of the best out there | 21:11 |
| jonathan__ | thats different than suggesting a component tolerance problem willl create that behavior | 21:11 |
| jonathan__ | I assume you mean will oscillate due to external fields or such | 21:12 |
| jonathan__ | electircal noise | 21:12 |
| jonathan__ | whereas bryan is saying, what happens if the 1% resistor is actually substituted for a 20% | 21:12 |
| jonathan__ | mostly though, transfer functions are for academics | 21:13 |
| drazak | you might have issues | 21:13 |
| drazak | that's why you should test your resistors with a watergate circuit | 21:13 |
| jonathan__ | uh, I havent heard of manufacturers testing their resistors | 21:14 |
| drazak | er, watergate bridge, that is | 21:14 |
| jonathan__ | they build the system, then test the major input & output, that's it. | 21:14 |
| jonathan__ | the system works or it's thrown into the recycle bin. | 21:15 |
| jonathan__ | even bridge builders, for final test, drive really really heavy trucks across the bridge.l. that's the "test" | 21:15 |
| drazak | well if you buy 100 resistors, you can safley assume they're from the same batch so their differences in resistance are spread out over a gaussian distribution, so if you check 10 of them and they are all within 1% of your target value then you can fairly safley assume all your resistors are right | 21:16 |
| drazak | that's what good electronics people do | 21:16 |
| fenn | i hear modern EDA systems actually alternate through all the high and low end of the error range for every component | 21:16 |
| jonathan__ | if it were really possible to do such analysis like "what happens to this system, if X subsystem fails" etc... that is likely impossible, because if it were solvable, then NASA would have solved it already, rather than ditching $100 million satellites into the ocean | 21:16 |
| drazak | they test their caps with the capacitor version of a watergate bridge | 21:16 |
| fenn | and do a simulation to see if it still works | 21:16 |
| fenn | "if it were possible NASA would have done it" | 21:17 |
| fenn | i want to smack you for that | 21:17 |
| jonathan__ | instead what teams focus on, is unit test the hell out of each component | 21:17 |
| jonathan__ | then ensure the buffering systems are also good, then hook everything together. | 21:18 |
| jonathan__ | it's true | 21:18 |
| jonathan__ | they probably spend the most effort on such stuff. who else has a system that must work otherwise all $$$ is lost? | 21:18 |
| fenn | one of the profs working on VOICED was actually doing failure analysis for NASA | 21:18 |
| jonathan__ | without any chance of fixing it later? | 21:18 |
| fenn | what happens to X if Y fails (and some info about how X and Y are connected and what their functions are) | 21:19 |
| jonathan__ | so, did he find a generalizable solution? | 21:19 |
| fenn | they were just doing data mining | 21:19 |
| jonathan__ | or was it case-by-case basis | 21:19 |
| fenn | i don't think there was really enough data though | 21:20 |
| fenn | NASA still uses inches and foot pounds ffs | 21:20 |
| jonathan__ | you kow, the couple japanese companies I have worked for, have been the best at testing. they test every single little tiny thing. and if it doesn't work, they want it fixed, and want to know why it was broken. they focus a lot, a lot, a lot, on unit tests | 21:21 |
| fenn | anyway i don't see why it should be impossible or even hard to model failure propagation | 21:21 |
| jonathan__ | I have heard this is part of their engineer culture | 21:21 |
| jonathan__ | uh, because you assume there is a model that resembles the real system well enough to even matter? | 21:22 |
| fenn | yes because the "units" are manufactured by different entities in the zaibatsu organism | 21:22 |
| jonathan__ | again, the transfer functions are for academics | 21:22 |
| jonathan__ | at a certain point, it has to be built, and big trucks drive across it | 21:23 |
| fenn | jonathan__: what's so hard about "if i give this 5 watt resistor 20V*A it will explode" | 21:23 |
| fenn | i'm not disagreeing that you have to actually do a physical test | 21:23 |
| fenn | but most things are just braindead simple | 21:23 |
| jonathan__ | nothing is hard about that, it's not a transfer function either | 21:24 |
| fenn | please explain what you think a transfer function is | 21:24 |
| jonathan__ | dont talk in circles | 21:24 |
| fenn | well, the way i understand it, a transfer function is a model of what happens to the output, based on the input | 21:25 |
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| jonathan__ | ok, i'm talking about systems, and you're talking about components | 21:25 |
| fenn | every system is a component | 21:25 |
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| fenn | ok so whether a resistor will explode is not a transfer function | 21:26 |
| fenn | but you can calculate the power dissipation and see if it exceeds the ratings | 21:26 |
| jonathan__ | when someone says transfer function, usually I envision an equation with about 20 polynomial factors, as the simplest case | 21:26 |
| fenn | why? | 21:26 |
| fenn | you can model things to whatever level of detail you want | 21:27 |
| jonathan__ | you're talking about a component that has a simple linear response | 21:27 |
| fenn | oh i suppose i can add in some temperature variation | 21:27 |
| jonathan__ | sure, but the model wont be correct, and many times won't even be worth the time spent modeling it | 21:27 |
| fenn | or some terms to represent arcing across the leads at high voltage | 21:27 |
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| fenn | but it won't be worth the time spent modeling those details so i'll just use V=IR | 21:28 |
| jonathan__ | ok simplest case. the manufacturer can not tell you anything about whether a resistor will short, or will open, if tolerance is exceeded | 21:28 |
| jonathan__ | already at the component level, the model fails | 21:28 |
| fenn | huh? | 21:29 |
| fenn | they always give you a power rating at some temperature | 21:29 |
| jonathan__ | "if i give this 5 watt resistor 20V*A it will explode" => there are 2 choices; it might explode, or it may short | 21:29 |
| jonathan__ | R goes to infinity or R goes to zero | 21:29 |
| fenn | it will fail, either way | 21:29 |
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| jonathan__ | these are very different failure modes | 21:29 |
| jonathan__ | and - the manufacturer can not provide any math that tells which will happen | 21:30 |
| fenn | "can not" or "will not" | 21:30 |
| jonathan__ | so what happens to "2 components connected together" already gets more complex, just with 1 resistor | 21:30 |
| jonathan__ | they can not | 21:30 |
| jonathan__ | there is no such physics | 21:31 |
| fenn | bah | 21:31 |
| fenn | anyway i'm not after comprehensive failure analysis | 21:31 |
| jonathan__ | you can buy special "will always explode" resistors at extra cost, that are manufactured in a way that exceeding current will guarantee "open" at some probability like 99.91% of the time or something | 21:31 |
| fenn | i just want to know if the thing should work correctly if put together | 21:32 |
| jonathan__ | then? just use PSPICE | 21:32 |
| fenn | sure, spice works fine for EE | 21:32 |
| jonathan__ | however some circuits are not modellable in PSPICE | 21:32 |
| fenn | nobody has bothered to write spice for legos or biobricks or whatever | 21:32 |
| jonathan__ | the simple voltage doubler I posted on my blog, "can't be modelled" | 21:32 |
| fenn | why not? | 21:32 |
| jonathan__ | because it depends on inherent inductance in the leads of the diodes and such | 21:33 |
| fenn | i can do it in falstad.com circuit simulator java applet.. | 21:33 |
| fenn | oh pff | 21:33 |
| jonathan__ | it depends on "real world factors" not the transfer function | 21:33 |
| fenn | you're ignoring reality now | 21:33 |
| jonathan__ | try it in spice and see for yourself | 21:34 |
| fenn | i'll take your word for it | 21:34 |
| jonathan__ | how about some ME stuff.. like fermentors | 21:34 |
| fenn | um, a big steel tank? | 21:34 |
| jonathan__ | why cant bio guys grow biodiesel in bulk enough to feed all the worlds cars | 21:34 |
| jonathan__ | because they can't model the fermentors | 21:35 |
| kanzure | no | 21:35 |
| fenn | what fermentors? | 21:35 |
| jonathan__ | yeast in big steel tank | 21:35 |
| kanzure | (the real problem is that they don't model anything. i've dropped off my local biofuel team.)( | 21:35 |
| jonathan__ | their "simple transfer functions" dont scale | 21:35 |
| fenn | you have to feed the yeast something, that's the real problem | 21:35 |
| jonathan__ | no, its not that simple "you just need to feed them more" | 21:35 |
| fenn | growing corn to turn to alcohol to burn in a petrol engine is what won't scale | 21:35 |
| jonathan__ | even if it did, they wouldnt be able to, today | 21:36 |
| jonathan__ | however they dont frequently admit this because they want $$ | 21:36 |
| fenn | forgive me but i find it hard to believe | 21:36 |
| jonathan__ | and, they want to further the modeling research | 21:36 |
| fenn | people have been fermenting mash for thousands of years | 21:37 |
| fenn | scientifically for hundreds of years | 21:37 |
| jonathan__ | sure, and at what scale? | 21:37 |
| fenn | you're telling me there are no good models of fermentation? | 21:37 |
| jonathan__ | i'm saying it doesn't scale to the size needed | 21:37 |
| jonathan__ | also known as "it works great in the lab but not in real world" | 21:37 |
| fenn | fermentation doesn't scale? have you been to milwaukee? | 21:38 |
| jonathan__ | i'm talking about a different defiition of scaling. | 21:39 |
| jonathan__ | "scaling" does not mean: it works for 1 tank so use 1,000,000 tanks | 21:39 |
| jonathan__ | "scaling" means: it works for 1 tank so use a tank 1,000,000 bigger | 21:39 |
| jonathan__ | which is what is required to be cost competitive | 21:39 |
| jonathan__ | anyway the point is: they have a transfer function that works for a tiny lab beaker "model". then they go to a bigger tank and suddenly the model is different. etc. | 21:40 |
| jonathan__ | classic ME problem | 21:40 |
| jonathan__ | "(the real problem is that they don't model anything. i've dropped off my local biofuel team.)(" ==> they would model things if they could, most likely, if it was worth the time | 21:41 |
| jonathan__ | laziness aside, likely they choose not to model, because it's a waste of time, and easier to build it & measure directly | 21:42 |
| kanzure | i'd rather not go into the horror stories of yet-another-biology-lab | 21:42 |
| kanzure | measurement doesn't mean it will be the same measurement in the future .. | 21:42 |
| kanzure | if you have no model how do you know what is a local effect and what is going to probably happen again? | 21:42 |
| fenn | so why is it we can model combustion with CFD but not fermentation? | 21:42 |
| jonathan__ | physical size | 21:43 |
| jonathan__ | what's the size of the combustion chamber? | 21:43 |
| fenn | a gazillion teracubits cubed | 21:43 |
| fenn | seriously what does it matter? | 21:44 |
| jonathan__ | thermodynamics people will be the first to admit they have a very hard time modeling | 21:44 |
| jonathan__ | because they can't model it! thats why | 21:44 |
| jonathan__ | tiny = sometimes much easier to model | 21:44 |
| fenn | the nuclear bomb simulations looked pretty convincing | 21:44 |
| jonathan__ | bigger = too many variables to model, system behaves other than expected | 21:44 |
| jonathan__ | it depends on the system and the reaction obvioulsy | 21:45 |
| jonathan__ | microfluidics = tough to model apparently | 21:45 |
| fenn | fluids tend to behave differently at different scales | 21:45 |
| fenn | but why would a fermenter? | 21:45 |
| jonathan__ | something about the coefficients and volume vs. size | 21:45 |
| jonathan__ | the most recent talk on biofermenters by the top guys on bio fuels, the guy basically said: "we don't know what we don't know yet" | 21:46 |
| fenn | btw i don't get why this is mechanical engineering | 21:46 |
| jonathan__ | a lot of it has to do with mixing | 21:46 |
| jonathan__ | the stuff in the fermentor mixes easily at small scale, but not at big | 21:46 |
| kanzure | they certainly don't teach me about this in the ME classes | 21:47 |
| fenn | well how are they mixing it? one big propeller blade? | 21:47 |
| jonathan__ | that's as much as I know though... same thing about volume vs size | 21:47 |
| fenn | i mean obviously you have to pay attention to the reynold's number | 21:47 |
| jonathan__ | there are a lot of different types and shapes etc of blades, that in itself is apparentlyquite a science | 21:48 |
| fenn | not much of a science if they don't have a model of it | 21:48 |
| jonathan__ | they have "a" model... just not a 'very good' model | 21:48 |
| jonathan__ | combustion engine is a good example too, there are not good models as far as I know | 21:48 |
| fenn | ok so how does this relate to transfer functions and whether stuff will nominally work or not? | 21:49 |
| jonathan__ | "good" meaning, something > 2nd order effects | 21:49 |
| jonathan__ | it's all over drew endy's talks, ha, he loves saying "to a first order approximation" | 21:50 |
| jonathan__ | sure, it works, to a first order approximation | 21:50 |
| jonathan__ | oh yea, I can turn myself into a tomato, to a first order approximation | 21:50 |
| jonathan__ | it relates because, how can a modeling system work, if you cant even model if the resistor will short, or will open, when it fails? | 21:52 |
| jonathan__ | how can it work when the system is scaled up or down? | 21:52 |
| fenn | because i don't care what happens after it fails | 21:52 |
| fenn | i just want to know if it will fail or not | 21:52 |
| fenn | "failure is not an option" | 21:52 |
| jonathan__ | "the answer is probably yes but no one really knows" | 21:52 |
| jonathan__ | "the system is designed to withstand simple component failure" | 21:53 |
| fenn | i'm fine with that answer | 21:53 |
| fenn | because it's better than no answer | 21:53 |
| jonathan__ | also the exampe you said about voltage arcing? well no one knows about voltage arcs | 21:53 |
| fenn | bullshit | 21:53 |
| fenn | put 200kV through a standard 1/4 watt resistor and it'll arc | 21:53 |
| jonathan__ | maybe if you factor in humidity, then you can get some "first order approximation" | 21:53 |
| jonathan__ | the examples you are giving are way outside 6 sigma | 21:54 |
| jonathan__ | they are not normal falure | 21:54 |
| fenn | how precise is precise enough? | 21:54 |
| jonathan__ | and I'm quite sure 200kV can be put thru a 1/4 watt resistor as long as the 200kV is only carried on 1pA current | 21:54 |
| jonathan__ | I thought you guys were being realistic | 21:54 |
| fenn | well sure but what is "realistic" | 21:55 |
| jonathan__ | i mean, real world | 21:55 |
| jonathan__ | suppose a component is within 1 sigma tolerance | 21:55 |
| jonathan__ | then the general failure would be to put that component at 3 sigma | 21:55 |
| jonathan__ | not way out at 6 | 21:56 |
| fenn | er. what does failure have to do with the component's manufacturing error? | 21:56 |
| fenn | i mean you don't manufacture a resistor with a built-in voltage | 21:56 |
| fenn | it has a resistance | 21:56 |
| fenn | that resistance is +- 5% usually | 21:57 |
| fenn | so sigma = 5% right? | 21:57 |
| fenn | ok let's pretend it's a 1 watt 1 ohm resistor | 21:57 |
| fenn | i'm putting 1V through it so i should get 1W, right on the borderline | 21:58 |
| jonathan__ | sigma refers to the probability that it will be within the stated value | 21:58 |
| fenn | if resistance is too high, it works, too low and it fails | 21:58 |
| fenn | so if i say "valid voltage range is 0 .. 0.95V" is that "realistic"? | 21:59 |
| jonathan__ | depending on temperature too | 22:00 |
| jonathan__ | and also depending on the thermal conductivity of surrounding environment, including the board it is resting on | 22:00 |
| fenn | or does it have to be 0 .. 0.7V (six * 5%) | 22:00 |
| jonathan__ | and also, resistors will fail more often if they are mounted vertically due to heat, which is why they are mounted horizontally | 22:01 |
| jonathan__ | if you are making design rules, then you want "head room" | 22:02 |
| jonathan__ | the head room depends on the kind of engineering. in power systems they want more head room since failure can be dangerous. NASA or DOD also likes a lot of head room | 22:02 |
| fenn | yeah safety factor | 22:03 |
| jonathan__ | so you might say "30% head room" | 22:03 |
| jonathan__ | that is on top of the component variance | 22:03 |
| fenn | safety factor for missiles is only 2 | 22:03 |
| jonathan__ | safety factor for freeway overpass is only 30% | 22:04 |
| fenn | really? | 22:04 |
| jonathan__ | I dont care about missles beause I dont deal with them every day... freeway overpass however... | 22:04 |
| fenn | i thought civil engineering was all about overkill | 22:04 |
| jonathan__ | I dunno if it's 30%. standard ME factor is usually 30% | 22:04 |
| fenn | no way | 22:04 |
| fenn | it's like 7x | 22:04 |
| fenn | 10x if catastrophic failure is possible | 22:05 |
| jonathan__ | 7x of what, of my car? etc | 22:05 |
| fenn | 7x the design load | 22:05 |
| fenn | vs breaking strength of materials | 22:05 |
| fenn | nominal strength, whatever that means | 22:05 |
| fenn | i don't know that much about how statistics is used in these guide books | 22:05 |
| fenn | obviously not all batches of steel are the same | 22:06 |
| jonathan__ | hmmmmmm | 22:07 |
| jonathan__ | so if the speed limit is 65mph then I can go 7x right? | 22:08 |
| jonathan__ | i'll tell the hiway patrol man next time | 22:08 |
| fenn | you can't always do 7x safety factor | 22:09 |
| fenn | like speed limit is usually 40 .. 65 mph on freeways | 22:09 |
| fenn | anyway it's a rule of thumb, probably based on the statistical variation in loads and material quality | 22:10 |
| fenn | sometimes you just don't have a model though | 22:10 |
| jonathan__ | back to the original point, "well there seems to be a transfer function that can be used to represent the component. then, there's some probability that the output of the component will exceed the acceptable "range" for the next connected component" ==> the mode of failure is often unknown, so there is no way to know | 22:39 |
| jonathan__ | that's assuiming there is some given probability curve by the manufacturer | 22:40 |
| fenn | you're saying we don't know the failure modes for a resistor? | 22:40 |
| jonathan__ | or that's assuming some given safety margin is acceptable or will have some desired effect | 22:40 |
| jonathan__ | uh, I already explained that | 22:40 |
| jonathan__ | 1) short, 2) open, maybe 3) some other value | 22:41 |
| jonathan__ | you do not know the probabilities of these events | 22:41 |
| jonathan__ | you could run the model for all 3 of course... for all components in the system.... and then somehow group all the N answers together somehow.. | 22:42 |
| jonathan__ | assuming that the system even fails (i.e. could not compensate for failure) | 22:43 |
| genehacker | PROBABILISTIC FAILURE | 22:43 |
| jonathan__ | also, each component would have to be labelled as: "required for operation, or just included for safety purposes" | 22:44 |
| fenn | if you have a resistor inline with a signal that fails open, that will probably screw up the system | 22:44 |
| fenn | guh.. this is all about failure modes and i don't care | 22:44 |
| fenn | i just want to know if things are compatible | 22:45 |
| jonathan__ | sometimes you can pull parts out of circuits on purpose and they still work fine, ha | 22:45 |
| fenn | sure the chinese do it all the time | 22:45 |
| fenn | you can also run a GA and totally change the circuit to something else | 22:45 |
| fenn | is that failure analysis? i don't think so | 22:45 |
| genehacker | oh I know | 22:46 |
| genehacker | why don't we say not intended for life-support or critical systems | 22:46 |
| jonathan__ | pfff | 22:46 |
| jonathan__ | that's all over every open source license ever | 22:46 |
| jonathan__ | no warranteee express or implied etc etc etc | 22:46 |
| fenn | NO WARRANTY OR SUITABILITY FOR ANY PARTICULAR PURPOSE | 22:46 |
| jonathan__ | it was berkeley's #1 requirement for open source licensing way back when | 22:47 |
| jonathan__ | and mit's | 22:47 |
| jonathan__ | the lawyers insisted apparently | 22:47 |
| jonathan__ | suspiciously missing from biobrick legal discussions, too | 22:48 |
| jonathan__ | well not "suspicious" just "odd" | 22:48 |
| fenn | i don't really understand the purpose in the first place | 22:49 |
| jonathan__ | I would like to know all the sizes & shapes of pcr tubes that people do pcr in. | 22:49 |
| fenn | me too | 22:49 |
| fenn | then i'd package it up in skdb | 22:49 |
| fenn | then anyone else who wanted to know could look it up | 22:50 |
| fenn | i'm doing that for nuts and bolts but after a week fighting with the geometry kernel i've put it aside in disgust | 22:50 |
| fenn | apparently modeling a helix is difficult | 22:51 |
| jonathan__ | uh? why isn't standard size sufficient? | 22:52 |
| fenn | because it doesn't tell you anything about the actual geometry | 22:52 |
| fenn | just a bunch of numbers, searle chinese room argument, etc | 22:53 |
| jonathan__ | isnt that all standardized though? | 22:53 |
| fenn | yes, that's why it's interesting data | 22:53 |
| fenn | if it were some random part that nobody uses, nobody would care would they? | 22:53 |
| jonathan__ | http://www.biocompare.com/ProductListings/2254/PCR-Tubes-%2802ml.html | 22:53 |
| genehacker | now where do we get zinc nanoparticles? | 22:54 |
| genehacker | besides kook medical products? | 22:55 |
| jonathan__ | I dunno what manufacturer is preferred in MBB | 22:55 |
| fenn | what's MBB? | 22:55 |
| jonathan__ | building name | 22:55 |
| kanzure | molecular biology building | 22:55 |
| fenn | you should start saving samples of actual tubes | 22:55 |
| fenn | then we can measure them | 22:55 |
| jonathan__ | compatibility chart http://www.nuncbrand.com/us/frame.aspx?ID=602 | 22:56 |
| jonathan__ | b.s. measure them | 22:56 |
| jonathan__ | get the manufacturer data sheet | 22:56 |
| jonathan__ | mechanical drawing | 22:56 |
| fenn | why does it say 96 well plate if it's talking about tubes? | 22:57 |
| genehacker | current topic? | 22:57 |
| jonathan__ | it says at the top, "all tubes are compatible with all...." | 22:58 |
| jonathan__ | plates however, seem to vary +/- several mm's | 22:58 |
| fenn | jonathan__: didn't you mention that needles were something like +-50% the stated diameter? | 22:58 |
| jonathan__ | according to some lab's paper, yes for needles | 22:59 |
| jonathan__ | but those are metal | 22:59 |
| jonathan__ | I am sure the plastic parts do not have such variance | 22:59 |
| fenn | well i'm not so certain | 22:59 |
| jonathan__ | who knows how the metal is made.. | 22:59 |
| fenn | and without actual samples i'll never know | 22:59 |
| jonathan__ | I am pretty sure the plates have low variance | 23:00 |
| jonathan__ | the robot arm has resolution steps of 0.5mm | 23:00 |
| fenn | actually i was intrigued by how to make hypodermic needle tubing so i searched and finally found it | 23:00 |
| jonathan__ | and between plates it is consistently correct | 23:00 |
| fenn | they use this little double conical piece that floats inside the tubing as they draw it down like wire | 23:00 |
| fenn | the angles are very important and it wears out after a while so it's made of carbide | 23:01 |
| fenn | it's called a floating mandrel | 23:01 |
| genehacker | I think the needles are made by some cold or hot work process | 23:01 |
| genehacker | if you could send me a sample I might be able to do some analysis on them in the metal lab | 23:02 |
| fenn | yeah, right | 23:02 |
| jonathan__ | ha, I am not going to mail needles thru USPS | 23:02 |
| fenn | he's on campus | 23:02 |
| genehacker | yup | 23:02 |
| fenn | i'm just a cynical bastard, that's all | 23:02 |
| genehacker | not far from the mol bio building | 23:02 |
| genehacker | I might be able too | 23:03 |
| jonathan__ | well if you want to, I will round some up | 23:03 |
| genehacker | I'd probably have to schedule time on the sem | 23:03 |
| genehacker | and I don't know what etches whatever the needles are made of so... | 23:03 |
| jonathan__ | just make sure that you dispose them in some biohazard waste | 23:03 |
| genehacker | I'd have to cut the needle | 23:04 |
| jonathan__ | or I suppose cut them up into bits | 23:04 |
| genehacker | polish it | 23:04 |
| fenn | BURN THEM | 23:04 |
| jonathan__ | at what temp? | 23:04 |
| fenn | is "hell" a temperature? | 23:04 |
| genehacker | put it phenolic resin | 23:04 |
| genehacker | put it in phenolic then polishit | 23:04 |
| jonathan__ | I thik it would melt prior to burn lol | 23:04 |
| genehacker | room temperature | 23:04 |
| genehacker | needles are pretty small that'd be hard | 23:05 |
| jonathan__ | hm, you could tr different temps if you want, see how much it expands | 23:05 |
| fenn | weird, this wikipedia page on tube drawing references the book i've been using | 23:05 |
| jonathan__ | "hell" is actually cold, so the temp is low anyway | 23:05 |
| genehacker | give me the metal and it's thermal expansion coefficient and it's easy to figure out | 23:05 |
| fenn | is there a unit conversion for the different levels of cold? | 23:06 |
| fenn | erm. s/cold/hell/ | 23:06 |
| jonathan__ | only for solid metals tho right? | 23:06 |
| fenn | units tempH(7) tempC | 23:06 |
| genehacker | what did hell freeze over or something? | 23:06 |
| jonathan__ | the units for hell are something like... "hell", "damn hell", "f*ing hell", "m*f*ing hell", "god damn m*f*ing hell", ..... | 23:07 |
| jonathan__ | read dante | 23:07 |
| fenn | no those are prefixes | 23:07 |
| genehacker | ok | 23:07 |
| jonathan__ | there are levels of hell | 23:07 |
| jonathan__ | circles actually | 23:07 |
| kanzure | then where's the pi? | 23:07 |
| fenn | abbreviated H, dH, fH, mfH, GdmfH | 23:07 |
| drazak | man it's a bitch to add a bunch of parts to mouser | 23:08 |
| genehacker | ok back to topic | 23:08 |
| drazak | (you guys reminded me about a headphone amp project I started thinking about like 2 years ago) | 23:08 |
| fenn | you and your topices | 23:08 |
| jonathan__ | ummm I think the radius of hell can't exceed the earth's radius, because the inner levels of hell are explicitly at the center of the earth | 23:08 |
| fenn | but the earth is flat so its radius is essentially infinite | 23:09 |
| drazak | I need to figure out all these resistor values too | 23:09 |
| fenn | (essentially because only God is infinite, of course) | 23:09 |
| jonathan__ | ummmmm i dont think earth is flat in dante | 23:09 |
| fenn | no? | 23:09 |
| fenn | does the bible say anything about this? | 23:10 |
| genehacker | no hell is underground and had nuclear fusion reactors | 23:10 |
| genehacker | but got invaded and moved to somewhere else | 23:10 |
| jonathan__ | well, to get to hell, you need to pass the undead boat man, and everyone knows that boat men are sailors, and sailors all know the earth is round | 23:10 |
| jonathan__ | anyway, how could it be a circle of hell on a flat plane, hmm | 23:11 |
| fenn | i think you're thinking of pellucidar | 23:12 |
| genehacker | hey don't you mean go down a well and fight demons and stuff? | 23:13 |
| jonathan__ | this isnt lord of the rings | 23:13 |
| fenn | a well? that only goes down a couple hundred feet at most | 23:13 |
| genehacker | a well that is incredibly deep | 23:13 |
| fenn | like mel's hole | 23:13 |
| fenn | or that borehole in russia | 23:14 |
| fenn | that turned out to be a hoax | 23:14 |
| * fenn returns to his book | 23:15 | |
| jonathan__ | well according to journey to the center of the earth..... | 23:15 |
| jonathan__ | oh here's wikipedia to the rescue. "The Purgatorio is notable for demonstrating the medieval knowledge of a spherical Earth." | 23:16 |
| genehacker | no this is a different reference it's a joke | 23:17 |
| jonathan__ | $self->sleep( 60*60*8) | 23:17 |
| genehacker | sleep is for slackers | 23:17 |
| genehacker | what are the needles made of? | 23:18 |
| genehacker | or do I need to put it in the sem and have it analyzed? | 23:19 |
| fenn | sounds like something you should know how to look up | 23:20 |
| fenn | (i actually know the answer, i'm just not telling) | 23:20 |
| genehacker | stainless steel | 23:27 |
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