--- Log opened Thu Nov 19 00:00:29 2015
00:03 < andares> Is there any work on a protocol for reduced-risk DIY gene therapy?
00:05 < andares> I was thinking something along the lines of: try it in vitro on a selection of tissues from biopsy, some sort of quality control to make sure no RNA or DNA targets that aren't intended are in there..
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08:29 < kanzure> bloop
08:34 < heath> bleep
08:36 < kanzure> hm.
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09:09 < Aurelius_Work> plop
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09:10 < kanzure> https://www.reddit.com/r/Bitcoin/comments/3tftas/mike_hearn_now_working_for_r3cv_blockchain/cx5tlis?context=1
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09:25 < kanzure> "And electrical outlets. When we built our new hackerspace, I asked for quad outlet boxes set in the floors and ceilings on a 12'x12' grid. Costs forced us to settle on 15'x15'. Each box had 4 data jacks and 4 110VAC power outlets, except for shop areas, which are 208 VAC 5 wire (3 hots, neutral & ground), from which we can derive anything we need in the shop, mostly 208 3 phase, 208 2 pole, and 110. The electricians thought I was insane ...
09:25 < kanzure> ... until I told them we never knew where anything was going to be and things would be rearranged constantly. They still didn't get it until we compared it to a theater or a museum. "
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09:58 < andares> The hackerspace here seems underwhelming
09:59 < andares> Mostly a vehicle for selling field trips to high school classes it seems
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10:07 < kanzure> gotta pay the bills somehow
10:07 < kanzure> i think a consulting model would work well for hackerspaces
10:07 < kanzure> instead of membership fees
10:10 < andares> I was thinking of trying to organize as a nonprofit medical research company
10:10 < andares> That licenses discoveries to larger firms
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12:23 < justanotheruser> http://www.nature.com/nrd/journal/v11/n3/fig_tab/nrd3681_F1.html
12:25 < kanzure> .title
12:25 < yoleaux> Figure 1 : Diagnosing the decline in pharmaceutical R&D efficiency : Nature Reviews Drug Discovery
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12:45 < justanotheruser> emoor law, moore backwards for obvious reasons
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12:51 < kanzure> meredith will be showing off some neurofeedback stuff at 32c3 this year https://events.ccc.de/congress/2015/wiki/Assembly:Neuro_Hacking
13:04 < Aurelius_Work> Hmmm
13:04 < Aurelius_Work> I'm curious what she's working on, I'll have to poke her
13:06 < kanzure> she says neurofeedback fixed her insomnia
13:07 < Aurelius_Work> she also gets to sleep from 4am to 11am, which I guess is the benefit of not being on a 9-5 schedule
13:07 < chris_99> ooh they've released the talks for ccc
13:07 < chris_99> or..?
13:07 < kanzure> i think this was hacker village dunno
13:07 < chris_99> aha
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13:37 < kanzure> "Today, Wal-Mart runs a centralized economy bigger than Soviet consumer production in the 1970s. It's all run out of Bentonville, Arkansas. Wal-Mart is so centralized that the thermostats in the stores are controlled from Bentonville."
13:37 < kanzure> heh
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13:42 < nmz787_i1> oh snap! I get up to $40k in conception health benefits (ever in my life) from my company's health plan!!!
13:42 < nmz787_i1> including """Diagnostic services to establish the cause or reason for infertility, and to treat an underlying medical condition. Fertility prescriptions Assisted reproductive technology (ART) e.g., in vitro fertilization, artificial insemination, intrafallopian transfer Cryopreservation and storage of egg, embryo, sperm Cord blood retrieval and storage"""
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14:08 < kanzure> nmz787_i1: i wonder if anyone commits insurance fraud regarding fertility just to get cool healthcare around eggs/embryos/stem cells/sperm freezing etc etc.
14:11 < nmz787_i1> https://www.eaglegenomics.com/wp-content/uploads/Periodic%20jpeg.jpg
14:12 < nmz787_i1> kanzure: seems possible
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15:14 < kuudes> ah, kanzure you may like it that finland integrated the maternal blood test for chromosome anomalies into the public healthcare may this year.
15:15 < kuudes> it is only done if there are risk factors from the age, ultrasound and other factors, but it is offered before needle biopsy to rule out most false positives as needle biopsy has some 1% of rate for termination of pregnancy
15:16 < kanzure> fetal needle biopsy has 1% termination rate??
15:19 < kuudes> somewhere around that iirc
15:19 < kuudes> that is why it is not done very often
15:19 < kuudes> and that is why the blood test is really useful
15:19 < kanzure> perhaps plugging the hole you create during biopsy would prevent the 1% termination
15:20 < kanzure> stick in some glue or something
15:20 < kuudes> yeah, maybe.
15:20 < drethelin> hah
15:21 < kuudes> so before it was 1. calculate the risk factors from age and ses questionnaire and the assessment of the ultrasound 2. if there was risk level higher than some level, propose needle biopsy -> 1. 2. offer blood test 3. if blood test not negative, offer needle biopsy
15:22 < kuudes> so it takes some half or more of the needle biopsies away
15:23 < kuudes> I suppose it may be cost effective even in considering the amount of raw work and salaries, though maybe not.
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19:08 < kanzure> https://tree.opentreeoflife.org/opentree/argus/opentree4.0@1
19:14 < kanzure> "Synthesis of phylogeny and taxonomy into a comprehensive tree of life" http://www.pnas.org/content/112/41/12764.abstract
19:16 < kanzure> docl: yes gene therapy for cryonics-adaptation is a possibility, if cryonics-adaptation can be demonstrated somewhere first.
19:17 < kanzure> however, i am a little hesitant to promise people that this would work
19:17 < kanzure> i am willing to claim cryonics-adaptation has high chance of working, but cryonics-adaptation plus gene therapy working for existing adults? seems much more difficult.
19:18 < kanzure> for example, cryonics-adaptations might require biochemistry or physiology that is incompatible with an adult's existing physiology
19:26 < kanzure> i also suspect that there will be low survival rates and for those who do "survive" will initially experience a lot of problems with healing after that sort of extreme trauma
19:28 < kanzure> .. which is okay.
19:38 < kanzure> docl: it occurs to me that you may not have seen the version of that idea that involves selective breeding....
19:38 < kanzure> rational design of cryoprotectant synthesis is a good dea, although i think that selective breeding will be necessary to smooth out the rough spots in an organism like the mouse
19:38 < kanzure> *good idea
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19:50 < docl> Yeah, I saw that. It just seems like selective breeding would be too slow, even in mice, at least for deep cryo. If you could splice in some e. Coli genes that confer dessication resistance, it might be another story though.
19:51 < kanzure> what do you consider too slow vs. too fast? for reference
19:53 < docl> Hmm. more than a few decades is too slow.
19:53 < kanzure> i think that selective breeding can get results in <20 years
19:54 < kanzure> i also think that by increasing the size of the population of mice you are breeding, you decrease the total number of generations required
19:54 < kanzure> also you have to include a mutagenesis mechanism to increase the mutation rate
19:54 < kanzure> you can jack up mutation really really high everywhere
19:54 < kanzure> which also helps things happen in that 20 year window
19:54 < kanzure> i am thinking of throwing a few million mice at this problem
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19:56 < kanzure> furthermore, you don't need whole-animal survival first. select first for higher cell survival rates, then for whichever organ seems most close to survival, then for multiple organs, then finally whole-animal. of course, if there are intermediate promising whole-animal results then go for it.
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19:59 < docl> http://www.researchgate.net/publication/12657942_Trehalose_expression_confers_desiccation_tolerance_on_human_cells
20:02 < kanzure> ""Many organisms that withstand desiccation express the disaccharide trehalose. We have now expressed the otsA and otsB genes of Escherichia coli, which encode trehalose biosynthetic enzymes, in human primary fibroblasts using a recombinant adenovirus vector. Infected cells produced increased amounts of trehalose with increasing multiplicity of infection (MOI). Human primary fibroblasts expressing trehalose could be maintained in the dry ...
20:02 < kanzure> ... state for up to five days. Fourier transform infrared spectroscopy indicated that dry, but viable, human cells contained no detectable water. This study shows that mammalian cells can be engineered to retain viability in the absence of water."
20:02 < kanzure> researchgate has js paste spam :(
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20:05 < docl> Of course, this was 15 years ago. I should check to see if any recent papers are citing it.
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20:27 < docl> https://scholar.google.com/scholar?as_ylo=2014&cites=10037239639279618146
20:28 < docl> Here's a good one: http://www.sciencedirect.com/science/article/pii/S0005273614000753
20:30 < docl> Design of novel cell penetrating peptides for the delivery of trehalose into mammalian cells
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20:40 < docl> Highlights
20:40 < docl> A novel cell penetrating peptide (CPP) was designed based on molecular simulations.
20:40 < docl> The CPP has high efficiency of penetrating into cells with little cytotoxicity.
20:40 < docl> Trehalose can be specifically delivered into cells with high efficiency.
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21:06 < kanzure> a while back someone (maybe fenn?) asked for evidence that larger populations would entail faster results
21:06 < kanzure> at the time for whatever reason i didn't think of the most obvious answer, which is that you can search over the genetic landscape much faster with higher parallelism
21:06 < docl> right
21:07 < kanzure> something something population genetics.....
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21:07 < docl> With e. coli or some other bacteria/microbe, can't you get a much bigger degree of parallelism?
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21:08 < kanzure> yes but you can already freeze those suckers
21:09 < docl> That's true. But you could use them to develop novel kinds of protein if you know what you are looking for, then transplant them into mice.
21:38 < nmz787_i> you're assuming infinite resources and 'landscape' realestate
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22:32 < docl> http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130323
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--- Log closed Fri Nov 20 00:00:30 2015