--- Log opened Tue May 22 00:00:17 2012
00:00 < LionClan> Patient DL 589.2 has an exon 51-55 deletion
00:01 < yashgaroth> oh it's exons 51-55, not codons
00:01 < yashgaroth> now I have some papers to work with
00:02 < LionClan> http://hmg.oxfordjournals.org/content/12/8/907/F2.expansion.html
00:03 < LionClan> the makers of the original trial were wrong in their hypothesis, so accidentally showed the cure for the 51-55 skip because it was a positive result, their expecting a negative result was irrelevant because their proposed mechanism was not corroberated by observation
00:04 < LionClan> Dystrophin Creation Sequence Interupted By the 51-55 Deletion Is Resumed After Skipping The Missing Sequence
00:06 < yashgaroth> let me see if I can find how they make the drug
00:06 < LionClan> the exact sequence is known
00:06 < yashgaroth> is it just an unmodified oligo, or do they do any wacky shit to it?
00:07 < LionClan> they use a sequencer that is no longer made; I assume there are better ones now
00:07 < yashgaroth> I assume you mean synthesizer, and no one apparently makes synthesizers any more
00:08 < yashgaroth> you can still buy ones used, I might add, or make your own
00:10 < yashgaroth> "They contain a 5
00:10 < yashgaroth> 0
00:10 < yashgaroth> fluorescein group (6-FAM), a full-length
00:10 < yashgaroth> phosphorothioate backbone and 2
00:10 < yashgaroth> 0
00:10 < yashgaroth> -O-methyl modified ribose
00:10 < yashgaroth> molecules"
00:10 < yashgaroth> whoops
00:10 < yashgaroth> well, those modifications make it a little more difficult anyway
00:11 < yashgaroth> ah 1 sec I found the paper where they describe it better
00:12 < LionClan> the exact sequence is known, it was created with the intent of curing the 51 deletion and failed, and as far as I can see they never follwed up on the positive result for patients with the 51-55 deletion, for which the process was successful
00:14 < LionClan> so they are pursuing a cure they failed at, and ignoring the cure that worked
00:14 < LionClan> because their target was the much larger 51 deletion population
00:15 < yashgaroth> that wouldn't surprise me, but if it gets approved for d51 they might come back and try it for d51-55
00:15 < yashgaroth> minimizing the risk for another billion-dollar clinical trial etc.
00:15 < LionClan> it doesn't work for the 51 deltion, it lands in an unreadble frame
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00:17 < LionClan> we'd like to bypass the waiting for a 51 deletion cure, and more directly to a 51-55 deletion cure
00:17 < NonFish[> since when are synths not made anyway?
00:17 < NonFish[> it looks like they exist. just googling dna synthesizer
00:17 < yashgaroth> no, I mean companies are not manufacturing new ones
00:17 < yashgaroth> synthesis companies that use them just buy old ones or make their own
00:19 < LionClan> someone could end up famous over this, there is a path here to a successful muscular dystrophy cure
00:20 < LionClan> if only for the few where the cause in the 51-55 deletion
00:20 < yashgaroth> I must admit, my own research into MD is only where it overlaps with myostatin
00:22 < yashgaroth> so I can't speak to how effective it may be, but even with the backbone modifications, it wouldn't be too hard to synthesize the oligos
00:24 < LionClan> it's been done, but not on a scale large enough to do more than test it on a toe
00:25 < LionClan> there is proof of concept, and no one is doing a larger systemic test
00:26 < yashgaroth> have you written to any of the researchers and asked why they're not pursuing it for d51-55?
00:27 < LionClan> it is as you said, they wish to find the 51 deletion cure so badly they are ignoring the success shown in curing the 52-55 deletion
00:27 < LionClan> 51-55
00:28 < yashgaroth> okay, well generating the sheer amounts of the drug they seem to need would require rather a large setup
00:29 < yashgaroth> the clinical trials for the d51 seem to be up to like a gram a week
00:30 < LionClan> they have a successful 51 skip? that would be news
00:30 < LionClan> to me
00:30 < yashgaroth> trials, not necessarily success
00:31 < yashgaroth> I'm referring to http://clinicaltrials.gov/ct2/show/NCT00844597
00:31 < joshcryer> 15 mins: http://www.spacex.com/webcast/
00:32 < yashgaroth> oh shit I forgot all about the launch, knew there was a reason I stayed up
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00:32 < joshcryer> yashgaroth :)
00:32 < LionClan> here's a reference to the successful 51-55 skip, though not necessarily the primary article
00:32 < LionClan> http://hmg.oxfordjournals.org/content/12/8/907/F2.expansion.html
00:32 < LionClan> http://hmg.oxfordjournals.org/content/12/8/907.full
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00:32 < yashgaroth> the last one was so disappointing, moreso because I was up til 3
00:33 < joshcryer> Same here. Hopefully they'll go tonight.
00:34 < yashgaroth> lionclan: did they do any studies in live animals?
00:34 < LionClan> human beings
00:35 < LionClan> in the successful cases, there is restored dystrophin synthesis
00:35 < LionClan> failure of dystrophin synthesis is the cause of muscular dystrophy
00:36 < yashgaroth> indeed
00:36 < LionClan> so it's a cure, if less than perfect
00:36 < NonFish[> I wrote one of these researchers iirc, to ask if I qualified for an exon skipping trial, giving my deletion location, but nope.
00:37 < LionClan> I assume this is because no one is working on the 51-55 skip
00:37 < yashgaroth> is it super-rare or just rare?
00:37 < LionClan> NonFish[ here has that deletion
00:37 < yashgaroth> I gathered that
00:38 < NonFish[> there is a deletion database if I rem right
00:41 < yashgaroth> I'd need more time to see how effective the drug could be in this case, but assuming it does work, you'd be looking at well over 100 grand for the equipment and reagents
00:41 < yashgaroth> naturally the more people you can treat, the cheaper per patient it becomes
00:41 < LionClan> the idea is to force a jump over the deletion, and land in a readable frame
00:41 < LionClan> if you can force a jump, there is a one in three chance the rest of the sequence is readable
00:42 < yashgaroth> well it's either a 0 or 100 percent chance, depending on the person's gene sequence
00:42 < LionClan> yes
00:43 < yashgaroth> so in nonfish['s case, have you sequenced his dystrophin gene to make sure it'd work first?
00:43 < LionClan> the result is a truncated dystrophin, which is normal dystrophin minus the part coded by 51-55, and minus whatever is skipped
00:43 < LionClan> he has the 51-55 deletion
00:44 < yashgaroth> no I mean the specific bases
00:45 < yashgaroth> (yay rocket launched)
00:45 < LionClan> perhaps my assumption his 51-55 deletion is the same as patient dl 589.2's 52-55 deletion is a hasty generalisation
00:45 < LionClan> perhaps my assumption his 51-55 deletion is the same as patient dl 589.2's 51-55 deletion is a hasty generalisation
00:45 < yashgaroth> it's proooobably close enough
00:46 < yashgaroth> either way, when I say "effective" I mean whether the drug will actually produce a functional improvement in the clinic, regardless of how awesome it should work
00:46 < LionClan> right
00:47 < yashgaroth> and assuming you'd need like 10 grams of it, purified, to have enough to test on one person, you would need many things
00:47 < NonFish[> http://www.umd.be/DMD/W_DMD/search.shtml is one of the mutation databases
00:48 < yashgaroth> holy damn there's a lot of variants
00:49 < NonFish[> leiden in .nl has one too, if i refind it
00:51 < LionClan> a lot of variants yes, and the skip over each deletion requires different sequence, if one exists at all
00:52 < LionClan> in the case of the 51-55 deletion, the sequence that forces the skip is known
00:54 < LionClan> 78 exon gene
00:54 < yashgaroth> yeah
00:54 < LionClan> the skip is readable if it jumps some multiple of three
00:55 < yashgaroth> mm, only if the number of nucleotides in the skipped exons is divisible by 3
00:55 < yashgaroth> but yes
00:56 < yashgaroth> so let's assume your main problem is synthesizing a large amount of this drug
00:57 < yashgaroth> most of the synthesis machines are set up to make tiny amounts of oligos
00:58 < LionClan> the dystrophy caused by the 51-55 deletion is the 12th most common dystrophy caused by a deletion
00:59 < NonFish[> aha the other db http://www.dmd.nl/nmdb/home.php
01:00 < LionClan> they will get around to that after they find the nonexistent cure for 1-11
01:00 < LionClan> it's very frustrating
01:01 < LionClan> the funding is going for this hunt, which they have no idea if it will even work
01:01 < LionClan> but they have this accidental proof of theory for a cure for the very few with this exact condition, a 51-55 deletion, his exact condition
01:01 < yashgaroth> could just break into AVI and steal a bunch, but you'd still have to make your own eventually...hmm
01:02 < LionClan> I've made doctors do things they had never imagined before, by doing all the research and preparing copies for everyone and insisting on a case management meeting and presenting everyone with copies
01:03 < LionClan> but this is far beyond the scope of anything I've done before
01:03 < yashgaroth> doctors are terrible at keeping up on research, sadly
01:04 < LionClan> this is more difficult, in that the research is not actually done; what I want to do is outline an experimental treatment plan
01:05 < LionClan> so I need to quantify it; how much money will this take
01:06 < yashgaroth> oh so you want to convince AVI and a doctor and the government to let you try it out?
01:06 < yashgaroth> that's probably actually easier than making it yourself, I'll admit
01:07 < LionClan> this is the only theoretical cure with proof of concept already demonstrated, for any form of muscular dystrophy
01:08 < LionClan> there's a successful human trial, even though it was not the one they were looking for
01:08 < yashgaroth> it does seem odd they aren't pursuing it, even considering how rare this particular variant is
01:09 < LionClan> it was not their target, they seem fixiated on the idea of curing the 51 deletion first
01:10 < LionClan> even though they have had no success at all
01:12 < yashgaroth> well it's not surprising they didn't let him in to the trial if he didn't meet all the conditions, since they can't change the requirements
01:12 < yashgaroth> maybe email everyone involved and ask them personally whether you could work out some sort of one-off experiment
01:13 < yashgaroth> and/or some people with clout in the MDA
01:13 < yashgaroth> must admit I'm not super familiar with how these things work in clinical trials
01:13 < LionClan> I want a doctor with knowledge of state of the art genetic sequencers to propose making a pile of an exact gggtacatggc... strand of rna, and injecting it into each muscle
01:14 < yashgaroth> heh you won't find a doctor with that knowledge; you mean asking him to propose the company makes some, or that he does it himself?
01:15 < yashgaroth> you won't need a doctor to do the injection, and any that cherishes his medical license won't do it anyway
01:15 < LionClan> I want to quantify the process, determine what it would cost, in estimate
01:16 < yashgaroth> ah so you do want to synthesize it yourself
01:16 < LionClan> I have the actual sequence around here somewhere
01:16 < yashgaroth> that's not the hard part
01:18 < yashgaroth> you'll probably have to synthesize the nucleotides yourself, since AVI will have them patented no doubt
01:19 < yashgaroth> and making a gram of an oligo out of it would require either a lot of expertise or a lot of money, and even with expertise you'll need money
01:21 < yashgaroth> we're working in this channel on making DIY synthesizers, but even then I don't think we've considering making custom precursors like that
01:21 < yashgaroth> ...not that it's impossible, mind you
01:22 < LionClan> it could be one of the first genetic cures, a precident for many to follow
01:22 < yashgaroth> for diseases curable by that type of exon skipping
01:23 < LionClan> accidentally created a functional truncated dystrophin in patient dl589.2
01:23 < LionClan> it was still functional at the end of the trial, 6 months later
01:23 < LionClan> maybe still functional now
01:24 < yashgaroth> depends how fast the molecule gets excreted, but maybe
01:25 < yashgaroth> I don't suppose either of you have a background in organic chemistry?
01:27 < LionClan> I have some knowledge of chemistry
01:27 < LionClan> I used to be a genius, now I'm just old
01:27 < yashgaroth> plenty of those in this channel
01:29 < yashgaroth> I can dig through AVI's patents and see if they outline how they make these modified nucleotides, once I've had some sleep/coffee
01:30 < LionClan> there is an abstract explaining the procedure they used to make the sequrence, and the sequence itself
01:31 < yashgaroth> you're referring to the one where they decide which sequence to use, or how to make the precursor subunits?
01:31 < yashgaroth> because that first part is easy
01:32 < LionClan> they had a programmable sequencer
01:33 < yashgaroth> yes but it's loaded with morpholino monomers, which I imagine are not sold, and so you'd have to make them
01:35 < yashgaroth> i.e. http://www.faqs.org/patents/app/20090131624
01:36 < yashgaroth> so once you can do/find someone to do that process, then it's no problem
01:40 < LionClan> you're the first person I've spoken to that understands what I'm talking about
01:41 < yashgaroth> there's only a half dozen worthwhile biologists in the biohacking community, in my totally unbiased opinion
01:42 < yashgaroth> sadly I'm worthless at organic chemistry, but they seem to lay out the process pretty well, and none of the chemicals needed seem super hard to obtain
01:43 < LionClan> there is a clean bill on toxicity, not toxic
01:44 < LionClan> I believe Mercury and Lead are most often responsible for the deletions, and are widespread and pernicious
01:44 < yashgaroth> you mean the deletions that cause MD?
01:45 < LionClan> the prevailing theory that cosmic rays cause the deletions I consider naive, the energy's would destroy the dna, not nick it
01:45 < LionClan> yes
01:46 < LionClan> I'm not a doctor, I have no credentials
01:46 < yashgaroth> ehh deletions in DNA are caused by any number of factors
01:48 < yashgaroth> regardless...if you had a good organic chemist with lab and a good supply of the precursor chemicals, that's most of your problem solved
01:52 < LionClan> a good organic chemist that is also a grant writer, that would be a plus; I'd like to put together and outline of what I'm proposing
01:52 < LionClan> -d
01:53 < yashgaroth> ha, if you're going for the legitimate approach that's a different story
01:54 < yashgaroth> that'd mean you need to respect patents and such, in which case you should stick with getting a sympathetic doctor to buy some of the drug from AVI
01:54 < yashgaroth> and look into how the FDA regulates such experiments
01:55 < yashgaroth> the stuff about hiring an organic chemist is more of a...black clinic approach
01:56 < LionClan> I'd like to put together a proposed treatment plan and give MDA the opportunity to do their stated mission before someone else does it
01:57 < LionClan> that's one scenario
01:57 < yashgaroth> why does it matter if someone does it before you? unless you're doing lab research yourself, you wouldn't be missing out on some huge amount of credit
01:58 < LionClan> I don't expect credit, I have no credentials
01:59 < LionClan> it's something we'd like to see happen for our own situation
02:00 < yashgaroth> well, find some qualified biologist in the MDA who knows more about the disease specifics than I, and have them validate it, then put that into the plan
02:00 < yashgaroth> that's about the best legal approach I can think of
02:03 < LionClan> we've looked into this for years, since we heard of the research; no one else has progressed in that time
02:04 < LionClan> not on that specific skip
02:05 < LionClan> How did you arrive at the 10 gram esitmate?
02:05 < yashgaroth> dosing regimen for the d51 phase 2 study was something like 50 mg/kg
02:05 < yashgaroth> per week
02:06 < LionClan> let me see that link
02:06 < LionClan> please
02:06 < yashgaroth> http://clinicaltrials.gov/ct2/show/NCT01396239
02:07 < LionClan> right, I see
02:07 < yashgaroth> naturally you might be okay with a lower dose than that, but 10 grams is still a lowball estimate
02:09 < LionClan> researching AVI-4658
02:10 < LionClan> it's applicable for specific deletions; which ones I wonder
02:11 < LionClan> ah
02:11 < LionClan> it is for deletions of exons 45-50, 47-50, 48-50, 49-50, 50, 52 or 52-63.
02:11 < LionClan> not 51-55
02:12 < LionClan> so it won't work, though the doasges may be similar
02:14 < yashgaroth> indeed, but it still operates on the same principles
02:15 < yashgaroth> presumably they could tailor any combination of morpholinos to fix many of the exon deletions, but they only get to test one in a clinical trial
02:16 < LionClan> AVI-5038, perhaps
02:17 < yashgaroth> there you go, it's in preclinical
02:19 < LionClan> it doesn't have to be a complete cure to make a profound improvement
02:20 < yashgaroth> indeed
02:20 < LionClan> MD only becomse serious when nearly all of the dystrophin is gone
02:22 < LionClan> if the treatment expresses dystrophin at all, weak muscles are profoundly better than no muscles
02:23 < yashgaroth> try emailing AVI to see if they have any updates on -5038
02:28 < LionClan> their research confirms my conclusion the treatment is not dangerous and does restore muscle function
02:28 < yashgaroth> ah, good
02:29 < yashgaroth> anyway I'm afraid I need sleep, but I'll be around tomorrow afternoon
02:29 < LionClan> I will likely be around for a very long time
02:29 < LionClan> I'll sleep too
02:29  * LionClan is LionClan
02:30 < LionClan> I always use this nick
02:30 < yashgaroth> there's usually a fair number of people in here at normal hours too
02:30 < LionClan> NonFish is always NonFish
02:31 < yashgaroth> good to know; g'night
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02:32 < LionClan> I'll idle here if you don't mind; thanks to whoever has made this room possible
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03:27 < fenn>  hmm something got lost in translation. i said "16 microstep" == 0.19 micron step size.. nmz wants to do 256 microsteps for 12nm resolution :
03:28 < fenn> though it's still pretty slow at that resolution, 0.15 in/s
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03:41 < fenn> vs an unusable .009 in/s
03:44 < fenn> 16x microstepping might even be too much. with the screws we are using, 4x microstep is still sub micron (0.79um) and top speed is a reasonable 0.6 in/s
03:46 < fenn> sorry 16 mm/s
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06:09 < kanzure> beeeep
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06:57 < kanzure> how embarrassing: https://wwws.whitehouse.gov/petitions/!/petition/require-free-access-over-internet-scientific-journal-articles-arising-taxpayer-funded-research/wDX82FLQ
06:57 < kanzure> only able to get 6k on that?
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07:45 -!- NonFish[ is now known as NonFish_
07:51 < kanzure> 8th International Meeting on Substrate-Integrated Microelectrode Arrays (MEA Meeting 2012)
07:51 < kanzure> Location: Reutlingen, Germany
07:51 < kanzure> Date: July 10 - July 13, 2012
07:51 < kanzure> http://www.nmi.de/meameeting2012
07:55 < delinquentme> http://taketheflourback.org/
07:56 < delinquentme> protesters destroying GM crops on the 27ths
07:56 < delinquentme> ( its on the to-address list )
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11:42 < kanzure> https://groups.google.com/group/brain-training
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13:56  * NonFish_ looks around
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14:45 < kanzure> NonFish_: i was hoping my inactivity would spur others to be active instead of me, but it turns out this strategy is flawed
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15:12 < mensch> kanzure: it always is
15:18 < NonFish_> hello
15:21 < LionClan> hello
15:21 < kanzure> hello
15:27 < NonFish_> last night there was talk about oligonucleotides for exon skipping.. someone mentioned you kanzure I recall
15:27 < NonFish_> was that because you're interested/involved in that kind of thing particularly?
15:27 < NonFish_> or that you're the channel manager?
15:28 < NonFish_> I was pretty much halfasleep, might be mixed up
15:30 < yashgaroth> I mentioned since he's working on a DIY synthesizer, though it'd be nowhere near the size necessary to make therapeutic amounts of oligos
15:30 < NonFish_> ah
15:33 < kanzure> yashgaroth: i don't understand. why not just pcr it?
15:34 < yashgaroth> it has a synthetic backbone, normal enzymes won't work
15:34 < kanzure> why would a phosphoramidite machine be able to synthesize that backbone?
15:35 < yashgaroth> you still need to run the reaction, even if you use their precursors and whatever chemicals they use instead
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15:35 < yashgaroth> I'm not sure how different their multimerization reaction is from normal pamidite chemistry
15:35 < kanzure> right, okay. was just curious how you made that leap.
15:36 < kanzure> because right now it technically doesn't synthesize anything at all :)
15:36 < kanzure> much less oligos, much less modified oligos
15:36 < yashgaroth> heh
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15:42 < Burninate> I want a combination of this: http://www.leapmotion.com/ this: http://www.kickstarter.com/projects/1104350651/tiktok-lunatik-multi-touch-watch-kits this: http://www.brothershopping.com/products/Galactus---Cellphone-Watch-With-Video-Camera-and-Media-Player.html , a solar band, and a waterproofing twist-bezel in front to hide the uUSB/SIM/uSD
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15:45 < Burninate> that would give you life logging, minimal PDA/MP3/ipod functionality, and cell service
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16:54 < kanzure> "If the only way to get to Disneyworld was to spend $20,000,000 and ride a thirty-year-old over-sized Russian vibrator, Disneyworld wouldn't exist either."
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17:00 < yashgaroth> I really hope that's a metaphor for space travel
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17:06 < kanzure> yashgaroth: yes
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18:04 < kanzure> i am somewhat disappointed that the venter institute transfers genomes by email.
18:04 < kanzure> http://xkcd.com/1058/
18:05 < kanzure> apparently they just have mountains and mountains of unmaintained perl cruft.
18:05 < nmz787> thats not truth
18:05 < nmz787> i mean, you're not basing that statement on that comic are you?
18:05 < joshcryer> can you really synthesize a genome yet?
18:05 < nmz787> didn't you read the venter paper?
18:05 < kanzure> joshcryer: yes, it just takes forever and costs a buncch
18:06 < nmz787> http://en.wikipedia.org/wiki/Mycoplasma_laboratorium
18:06 < kanzure> more like mycoplasma laborious :(
18:09 < joshcryer> I'm impressed
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18:14 < kanzure> nmz787: the perl statement is based on talking with jcvi programmers
18:15 < nmz787> what about genomes being emaile
18:15 < nmz787> dd
18:15 < kanzure> just from the comic.
18:15 < kanzure> i don't know though.
18:15 < yashgaroth> nah they use zip disks for some reason
18:16 < kanzure> "WE TOTALLY FTP IT TO DROPBOX"
18:16 < audy> ginko bioworks synthesizes genomes in 6 months (says their website)
18:17 < audy> I hope they MD5'd that human genome after emailing it
18:17 < audy> just to make sure
18:19 < ParahSailin> someone needs to write a better global sequence aligner
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18:20 < audy> ParahSailin what's wrong with needleman wunsch?
18:20 < nmz787> ParahSailin: next-gen sequencing people are probably doing that now
18:20  * ParahSailin is a next-gen sequencing peopleguy now
18:20 < nmz787> i know there is a need for new methods with the pac-bio systems
18:21 < kanzure> ParahSailin: and what's wrong with all the open source alignment software?
18:21 -!- Netsplit over, joins: splicer
18:21 < ParahSailin> bwa doesnt catch everything
18:21 < ParahSailin> i dont have much experience with bfast, bowtie and the others
18:22 < kanzure> ah. bowtie/crossbow is where i'd start looking.
18:22 < ParahSailin> im probably not allowed to be more specific until they publish a paper
18:23 < ParahSailin> novoalign might be a good one to try out
18:24 < kanzure> what's your fragment size?
18:24 < ParahSailin> read length? we go as cheap as possible on gaIIx, typically 36 or 50
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18:25 < kanzure> erm wait, was your company the one that takes in data from others and provides alignment as a service, or are you doing in-house sequencing too?
18:26 < ParahSailin> eureka has a bay area wet lab with next gen sequencers
18:26 < superkuh> It's weird that only one person in this channel split.
18:27 < superkuh> Oh. Geez. Nevermind.
18:27 < kanzure> bay area doesn't sound like the best area to host a wetlab
18:27 < kanzure> in terms of cost efficiency? i mean you don't need your superbrains working in it do you?
18:28 < audy> ParahSailin you work for Eureka Genomics?
18:28 < ParahSailin> yes
18:29 < ParahSailin> bay area is where you get vc for wetlabs
18:29 < audy> Neato. Hire me :)
18:29 < ParahSailin> what can you do?
18:29 < nmz787> heh, hire me
18:29 < ParahSailin> i've been here less than a month
18:29 < audy> I do mostly metagenomics, 16S rRNA, bacterial genomes
18:30 < ParahSailin> when i've been here longer, i can probably push through resumes
18:30 < ParahSailin> audy, wet or silico guy?
18:30 < audy> I used to be wet
18:30 < nmz787> sounds good, I think I'm full til september
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18:30 < audy> but now it's all silico
18:30 < audy> I like doing both
18:30 < ParahSailin> where are you located?
18:30 < audy> Florida
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18:31 < kanzure> ParahSailin: haha all the bio guys are about to ask you for a job
18:31 < audy> haha
18:31 < ParahSailin> ok lets linkedin
18:31 < ParahSailin> send me names in pm
18:31 < roksprok_> is bio employment always kind of sucky? or is it just now?
18:31 < kanzure> from what i can tell it's always sucky
18:32 < kanzure> unless you start your own company
18:32 < roksprok_> well it seems like the suckiness for employers is the inverse of the suckiness for employees
18:32 < roksprok_> the problem of course is you need money to start a company
18:32 < roksprok_> and a job to get money
18:33 < kanzure> you don't need much money to start a company. depends on what you're doing.
18:33 < roksprok_> speaking of money what would be a good estimate for bay area living costs?
18:33 < nmz787> roksprok_: it depends
18:33 < kanzure> at least 1500/mo in rent, or possibly 1100/mo in rent if you want roommates
18:33 < ParahSailin> cool
18:33 < kanzure> if you move further out from SF, it gets a bit cheaper- maybe 800/mo with roommates
18:34 < roksprok_> would you be able to get to public transport?
18:34 < nmz787> i think mainly on size of company... smaller companies can give you more responsibility more quickly... larger companies i would think forget having fun unless you have a phd and 5-10 years of industry experience
18:34 < ParahSailin> wetlab employment is a carefully guarded cartel
18:34 < ParahSailin> computer stuff is more meritocratic
18:34 < kanzure> roksprok_: public transport is all over the place in SF, so yes
18:34 < nmz787> you can find berkeley housing for <$800 in efficieny studios, or cheaper if you rent a room
18:35 < nmz787> publiuc transport from outside the SF peninsula is expensive tho
18:35 < kanzure> ParahSailin: yeah, so i don't see any /reasonable/ job involving wetlab work
18:35 < roksprok_> its mostly buses right?
18:35  * ParahSailin escaped from PhD program doing wetwork to code
18:35 < nmz787> no monthly passes and bulk ticket purchases only dicount you 6.25%
18:35 < kanzure> halcyon molecular had some interesting machining+wetlab work, but they paid very low
18:35 < ParahSailin> wetlab work is very easy relative to the extreme cost of the capital
18:35 < kanzure> the "capital" is mostly madeup costs
18:35 < ParahSailin> such an industry lends itself well to monopolies
18:36 < kanzure> "$500,000 thermocycler!"
18:36 < ParahSailin> oh of course
18:36 < ParahSailin> but the barriers are real
18:36 < ParahSailin> time for 3d printers to make patents unenforceable
18:36 < kanzure> patents are already "unenforcable" in that sense
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18:37 < kanzure> roksprok_: also, california has a state tax
18:37 < ParahSailin> it just isnt that widespread yet, kanzure
18:37 < roksprok_> kanzure: you mean income tax?
18:37 < kanzure> yes
18:37 < kanzure> state income tax.
18:37 < ParahSailin> once it becomes trivial to get your $1000 next gen sequencer, its over for those bio cartels
18:38 < roksprok_> don't most states?
18:38 < kanzure> roksprok_: not texas (where i live)
18:38 < nmz787> only other state i've heard of with no income tax is New hampshire
18:38 < yashgaroth> washington
18:38 < nmz787> man i need to add crap to my linkedin page
18:39 < kanzure> i think my linkedin profile says "director of pixie dust at fuck you inc"
18:39 < nmz787> i've worked about 3X more jobs/research positions than i have listed
18:39 < kanzure> nobody looks at linkedin anyway
18:39 < nmz787> we just did
18:39 < nmz787> its 'cool'
18:39 < nmz787> :P
18:39 < kanzure> http://www.linkedin.com/pub/bryan-bishop/8/397/3a6
18:39 < roksprok_> Parahsailin does :-)
18:40 < ParahSailin> i got into linkedin because i was job-hunting for about 6 months
18:40 < yashgaroth> oh kanz I'm gonna add you on there real quick
18:40 < roksprok_> did it help much?
18:40 < roksprok_> ParahSailin
18:40 < ParahSailin> nope, i found this job on craigslist
18:40 < kanzure> yashgaroth: go right ahead
18:41 < kanzure> yashgaroth: http://heybryan.org/ lists my other accounts
18:41 < yashgaroth> I mainly want to find out how you're a 3rd degree with someone I have added already
18:41 < kanzure> pfft, i'm only a 3rd degree with you? how lame is that
18:42 < kanzure> you don't even know anyone else in here?
18:42 < yashgaroth> I've only added coworkers so far
18:42 < yashgaroth> (ex) coworkers
18:42 < yashgaroth> aight I'll find the rest of you then
18:42 < kanzure> my google+ profile seems to be more popular (5000 followers)
18:42 < yashgaroth> that's because you have a lot of nerd friends
18:42 < kanzure> https://plus.google.com/102967708777429109844/posts
18:43 < nmz787> i never started google +
18:43 < nmz787> i got enough socializing
18:44 < ParahSailin> heh i heard of pico money the other day, and i just realized i had the founder linkedin
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18:45 < yashgaroth> only 3 of the 20 people that got laid off with me have new jobs
18:46 < kanzure> awesome.
18:46 < kanzure> audy: i heart your profile pic, great beard going on there.
18:46 < kanzure> the bike's a bit too hipster though :p
18:47 < roksprok_> yashgaroth: do you think a master's degree improves things at all?
18:47 < yashgaroth> nope
18:47 < yashgaroth> every single person I've talked to says they're useless
18:48 < yashgaroth> several have had violently negative opinions
18:48 < kanzure> yashgaroth: our shared (distant) connection is ratha grimes. she used to live in austin. she and i met when we were setting up the austin hackerspace.
18:48 < roksprok_> and my understanding of a phd is you either have to be lucky or network hard....is that correct?
18:49 < yashgaroth> that's true even without a phd, but yeah
18:49 < yashgaroth> not to mention enduring 8 years of bitch work to get it + a postdoc
18:49 < audy> kanzure it's not a fixie
18:49 < audy> kanzure nothing hipster about bike commuting :)
18:49 < audy> maybe bike + beard
18:49 < audy> + thick rims
18:50 < kanzure> well, if you were wearing flannel in that pic, then i'd totally identify you as hipster
18:50 < audy> kanzure you just can't see it
18:50 < kanzure> yashgaroth: your contacts look very uh, clean
18:50 < yashgaroth> heh
18:51 < yashgaroth> it's all ex-work people
18:51 < kanzure> i know all these lame journalists that keep trying to get a story
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18:52 < roksprok_> kanzure: is that how you met the biopunk guy?
18:52 < audy> kanzure why don't you have your own wikipedia article yet?
18:52 < kanzure> roksprok_: no, i met marcus at harvard
18:52 < kanzure> audy: because i haven't written it, or other people haven't written it
18:53 < kanzure> audy: also, most of the diybio thunder hasn't been directly referencing me, so i'm a wee bit scarce on news resources
18:53 < kanzure> roksprok_: he knew me from the diybio group over the interwebs, and plus people involved in diybio know me, so they probably mentioned me to him
18:54 < kanzure> hahah
18:55 < kanzure> yashgaroth: so.. joseph replied. http://www.youtube.com/watch?v=kmTNtSs1UQY
18:56 < kanzure> oh wow he has it on his youtube account
18:56 < kanzure> damn, i feel so lame now
18:56 < yashgaroth> dude says 'lol' a lot for someone that went to harvard
18:56 < kanzure> http://www.youtube.com/watch?v=TsbaBv9rmeY&feature=plcp
18:56 < kanzure> yeah, but you should read his journal articles
18:56 < kanzure> "Thanks the "secret" is it usually takes about 10 years to build a foundation of muscle and 10 weeks of hard dieting to show it off with very low fat. This was really the first time in 13 years that i got "ripped.""
18:57 < kanzure> "I put on a lot of size fast, like age 12-16 but only after a decade of training did I figure out how to bring out the details, diet properly, etc. You can build a decent physique during the teenage years but it also takes time to fill out."
18:57 < kanzure> "A lot of military presses, bench press. Heavy shrugs for traps."
18:58 < kanzure> his account is http://www.youtube.com/user/philosopherbody apparently
18:59 < yashgaroth> well then
18:59 < kanzure> it seems he didn't associate it with his /name/ though
18:59 < kanzure> so, it's still legit to keep it hosted there
19:00 < yashgaroth> you don't need a name with bilateroids that ripped
19:01 < kanzure> i hosted the video on my youtube account as a sort of public shaming for ever putting a 'muscle montage' on his facebook account (who does that??)
19:01 < kanzure> i mean, he took it down, so then i put it back up
19:02 < kanzure> i'm a little disappointed that he wasn't on steroids
19:02 < kanzure> what sorta transhumanist is this
19:05 < roksprok_> kanzure: I was looking through the logs and saw you helped delinquentme with an email to send out to get work on life extension stuff....did that work well?
19:06 < kanzure> no
19:06 < kanzure> the email was about 10x more ridiculous than yours :P
19:06 < kanzure> but i helped him touch it up a bit
19:07 < kanzure> the problem is that there's really no *good* outlet for transhumanist progress at the moment, it's just *us*
19:07 < kanzure> he wanted to get into a lab where he could be paid to make lab automation tools to advance longevity research
19:07 < kanzure> but there's really no lab that wants that.
19:07 < roksprok_> what about stuff like SENS?
19:08 < kanzure> ParahSailin: that's your expertise
19:08 < kanzure> roksprok_: ParahSailin worked at SENS for quite a while. until they fired all their biologists.
19:08 < roksprok_> i guess that would explain that
19:08 < kanzure> like, they axed rob, lorenzo, wtf :(
19:09 < roksprok_> is the email asking for a job just not a very good way to get one?
19:09 < kanzure> for a job that doesn't exist? email is probably not the best way to make that happen
19:09 < kanzure> especially not a ranty, 10-paragraph email
19:10 < roksprok_> hah and you said mine was long at like 4
19:11 < kanzure> yeah, you also berrated yourself and made it sound like you were a runt, but you're awesome dude
19:11 < roksprok_> yea i took your advice and took out all of that
19:11 < roksprok_> but ironically people still don't want to pay me
19:11 < kanzure> i'm really really cynical about biology-related jobs, sorry
19:12 < roksprok_> actually its funny you say that because the more bio-focused places i emailed i got 1 response and it was 'thanks but no thanks' while software places all emailed me back
19:12 < kanzure> yeah, software is hiring like crazy
19:13 < kanzure> fresh grads out of college are being offered (on average) at least $90k from google, facebook, apple or possibly microsoft (not so sure about ms' pay scales at the moment)
19:13 < roksprok_> which is good, but i enjoy the 'tedious' parts of bio more
19:13 < ParahSailin> yeah i never got paid to do computer shit before this
19:14 < kanzure> roksprok_: the tedious parts.. that should be automated?
19:14 < roksprok_> and i figure you need a bit of leverage before you get to say 'no i only do interesting stuff'
19:14 < kanzure> i mean.. the tedious stuff is being done by people getting paid $8/hour for life
19:14 < kanzure> doing 5 years of tedious work is not leverage
19:14 < ParahSailin> SENS did not fire all their biologists
19:14 < kanzure> ParahSailin: tell us the story
19:14 < kanzure> what's the deal with letting lorenzo go?
19:14 < ParahSailin> just at least two that i know of, myself included
19:14 < kanzure> and you?
19:15 < kanzure> i know they just got that extra $500k from last summer
19:15 < kanzure> so they aren't strapped for cash entirely
19:15 < ParahSailin> lorenzo and gouri did not get along
19:15 < kanzure> gouri was his manager?
19:15 < roksprok_> didn't they spend like 1.x million last year?
19:15 < kanzure> and at some point i think john schloendorn was doing things, but i can't recall the specifics
19:15 < ParahSailin> gouri was hired on about last august as the lead sciencer
19:16 < kanzure> how many other biologists or who's still there?
19:17 < kanzure> i know there's a lot of people that seem to come out of arizona state university.. not sure why
19:25 < roksprok_> is SENS pretty good at bootstrapping? I recall seeing a vid from BIL talking about how they got a lab up for lysoSENS really cheaply
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19:31 < audy> to bed I go
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19:39 < kanzure> damn. only 51 vim shortcuts/min
19:39 < kanzure> https://www.shortcutfoo.com/app/drills/4fa9868ee1fbd4001b00000f/quick
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19:47 < kanzure> 58 shortcuts per minute. this is hard.
19:48 < ParahSailin> my coworkers use the arrow keys with vim
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19:55 -!- Netsplit over, joins: splicer
19:55 < jrayhawk> the shame can be generalized to "my coworkers use navigation keys to navigate with vim"
19:57 < kanzure> gah why can't i get above 58 :(
20:09 -!- n_bentha [~lolicon@70-140-184-45.lightspeed.hstntx.sbcglobal.net] has joined ##hplusroadmap
20:11 < kanzure> maybe it's a limit to their javascript or something
20:11 < kanzure> or my ability to recognize the line of text they are showing me
20:12 < kanzure> it's too bad that my 180+ wpm doesn't apply to vim shortcutting
20:12 -!- docl [~luke@unaffiliated/docl] has joined ##hplusroadmap
20:12 < joshcryer> 180wpm? wow
20:13 < kanzure> joshcryer: http://www.seanwrona.com/typeracer/profile.php?username=kanzure
20:14 < nmz787> i prob suck at typing
20:14 < nmz787> lots of typos
20:14 < joshcryer> Woot, I just won a race.
20:14 < joshcryer> 80 wpm :P
20:15 < nmz787> i will have to play this
20:15 < nmz787> even sounds decent on the evo (phone)
20:15 < kanzure> joshcryer: http://play.typeracer.com/?rt=12i3080y8q7pz
20:15 < kanzure> nmz787: click that too
20:16 < kanzure> blah it wants me to prove i'm not a bot
20:16 < nmz787> i have no idea what just happened
20:16 < yashgaroth> 82 damn
20:17 < kanzure> 156.. but i aced the "prove you're not a bot" with 184
20:17 < kanzure> you can edit your nick by going to "sign in" and clicking "guest nickname"
20:18 < kanzure> 161 :(
20:19 < kanzure> what's up with me and 160 tonight :/
20:20  * n_bentha is a bot
20:20 < ParahSailin> your name sounds like a robot name
20:22 < kanzure> 169.. that's slightly better?
20:28 < nmz787> man i suck
20:29 < kanzure> the important thing is that you know you have a typing problem :P
20:29 < kanzure> typists anonymous
20:29 < ParahSailin> the bottleneck for me in coding or writing is not the manual part
20:30 < kanzure> it is for me :(
20:30 < kanzure> it's all manual labor
20:30 < kanzure> otherwise the compooter would be doing it
20:31 < ParahSailin> i mean manual as in mano = hand
20:32 < joshcryer> I BEAT KANZURE (OK I think he got d/c'd... heh).
20:33 < kanzure> no, i failed pretty hard on that one
20:33 < kanzure> she tied WHAT to a chair??
20:33 -!- lichen|2 is now known as lichen
20:34 < joshcryer> it said you were averaging 129 wpm tho
20:34 < kanzure> maybe i should sit up straight.
20:43 < joshcryer> I have no real ability to sit up straight
20:43 < joshcryer> I mean, I don't have a desk to put stuff
20:43 < joshcryer> so my lap is my desk kinda
21:02 -!- calango [~dnm@201-51-215-215.user.veloxzone.com.br] has quit [Quit: Leaving]
21:24 < nmz787> http://nopr.niscair.res.in/bitstream/123456789/4384/1/IJFTR%2034%282%29%20149-154.pdf  http://nopr.niscair.res.in/bitstream/123456789/4384/1/IJFTR%2034%282%29%20149-154.pdf
21:24 < nmz787>  Electromagnetic shielding effectiveness of copper core yarn knitted fabrics
21:24 < nmz787> sorry those links are the same
21:37 -!- n_bentha [~lolicon@70-140-184-45.lightspeed.hstntx.sbcglobal.net] has left ##hplusroadmap []
21:56 < nmz787> kanzure: http://www.dovermotion.com/Downloads/KnowledgeCenter/Accuracy.pdf -- ACCURACY IN POSITIONING SYSTEMS
21:56 < nmz787> can you bookmark that in the laser projcet
21:57 < kanzure> alright
22:07 < nmz787> any ppl in here can get me papers? http://jcer.com/index.php/jcj/article/view/194
22:08 < nmz787> "Hypothesis on the Central Role of Serotonin in Biological and Anthropological Creation"
22:08 < nmz787> http://journals.lww.com/health-physics/Abstract/2008/10000/Quantitative_Evaluations_of_Mechanisms_of.1.aspx
22:08 < nmz787> "Quantitative Evaluations of Mechanisms of Radiofrequency Interactions With Biological Molecules and Processes"
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23:00 -!- joshcryer [~g@unaffiliated/joshcryer] has quit [Quit: bll]
23:02 -!- Steel__ [43f624a5@gateway/web/freenode/ip.67.246.36.165] has joined ##hplusroadmap
23:02 < Steel__> kanzure
23:03 < kanzure> what.
23:03 < Steel__> who should I talk to in DC besides HacDC
23:04 < kanzure> ask yashgaroth
23:04 < yashgaroth> why me
23:04 < kanzure> is jigsaw in dc?
23:04 < kanzure> no, i guess not
23:04 < yashgaroth> for the last time washington state is not DC
23:04 < kanzure> yes i know
23:04 < kanzure> just not sure which things are at which place:)
23:05 < yashgaroth> ah well anyway I don't know any h+ etc types in DC
23:06 < Steel__> found one
23:06 < Steel__> looks sing heavy tho
23:06 < kanzure> are you in dc now?
23:07 < Steel__> I will be moving down a week from sat
23:08 < Steel__> Starting work June 4th
23:38 -!- skorket [~skorket@cpe-24-58-232-122.twcny.res.rr.com] has joined ##hplusroadmap
--- Log closed Wed May 23 00:00:18 2012