--- Log opened Wed Jan 01 00:00:55 2020
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00:49 < fenn> "the concentration of NGF in the blood plasma is significantly higher in individuals who have been in a romantic relationship with another person for less than 12 months"
00:49 < fenn> .title https://doi.org/10.1016%2Fj.psyneuen.2005.09.002
00:50 < EmmyNoether> Redirecting
00:50 < fenn>  "Raised plasma nerve growth factor levels associated with early-stage romantic love". Psychoneuroendocrinology.
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09:49 < kanzure> "What is immoral about eugenics?" https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1129063/
09:49 < kanzure> https://www.lesswrong.com/posts/aFtWRL3QihoF5uQd5/guardians-of-the-gene-pool
09:49 < kanzure> http://intelligenceexplosion.com/
09:50 < kanzure> https://www.lesswrong.com/posts/Aud7CL7uhz55KL8jG/transhumanism-as-simplified-humanism
09:52 < kanzure> https://intelligence.org/files/IEM.pdf
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09:53 < kanzure> https://www.rintrah.nl/the-case-for-genetic-augmentation-of-humans/
09:54 < kanzure> https://diyhpl.us/~bryan/papers2/futurism/On%20the%20overwhelming%20importance%20of%20shaping%20the%20far%20future.pdf
09:57 < kanzure> "How hard is artificial intelligence? Evolutionary arguments and selection effects" https://www.nickbostrom.com/aievolution.pdf
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11:14 < archels> didn't we have a new term for eugenics
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11:37 < kanzure> probably. people like making new words, so that sounds about right.
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12:11 < kanzure> e56ce8c34134b1fcccb648ca44f9293a97596983b6ffd23f745d58b21986de2b http://gnusha.org/logs/archives/hplusroadmap-logs-2020-01-01.tar.gz
12:12 < kanzure> http://gnusha.org/logs/archives/hplusroadmap-logs-2020-01-01.tar.gz.ots
12:34 < kanzure> "To underline this point: we shot a red tesla into space about 2 years ago [1]. We cannot detect it any more. We'd need a telescope with a mirror of 15km to see it. Due to uncertainties accumulating, even if we'd had a scope like that, we'd probably not be able to point it exactly enough."
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12:36 < kanzure> https://www.whereisroadster.com/
12:42 < kanzure> https://www.capitalismmagazine.com/2019/07/the-federal-death-agency-fda/
12:42 < kanzure> "(Re fraud: we must be constantly on guard against preventive law: government cannot demand that anyone prove that he is not engaged in fraud. The government cannot interfere with private activity unless there's "probable cause" of a rights violation-which, in the case of fraud, means evidence of a specific fraud involving specific representations made in specific media on a specific ...
12:42 < kanzure> ...date(s).  The government cannot treat doctors or medical firms as guilty until proven innocent.)"
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12:57 < kanzure> apparently capitalismmagazine.com is not in the internet archive, so here's some fun things https://diyhpl.us/~bryan/papers2/capitalism-magazine/
13:15 < kanzure> .wik opentimestamps
13:16 < EmmyNoether> HTTPError: HTTP Error 404: Not Found (wik:99)
13:18 < kanzure> "Bitcoin for the biological literature" https://www.nature.com/articles/d41586-019-00447-9
13:18 < kanzure> .wik OpenTimestamps
13:18 < EmmyNoether> "OpenTimestamps (OTS) is an open-source project that aims to provide a standard format for blockchain timestamping. / With the advent of systems like Bitcoin, it is possible to create and verify proofs of existence of documents (timestamps) without relying on a trusted third [...]" - https://en.wikipedia.org/wiki/OpenTimestamps
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15:38 < user235> hi, has anyone retrieved SNP's from ancient DNA? i'm trying to retrieve SNP's from https://www.nature.com/articles/s41467-019-13549-9
15:39 < user235> the .fastq file can be downloaded from here: https://www.ebi.ac.uk/ena/data/view/ERX3277049
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16:48 < kanzure> .title
16:48 < EmmyNoether> No title found
16:48 < kanzure> .title https://www.nature.com/articles/s41467-019-13549-9
16:48 < EmmyNoether> A 5700 year-old human genome and oral microbiome from chewed birch pitch | Nature Communications
16:49 < kanzure> user235: yes.
16:50 < user235> kanzure: do you know how to retrieve it?
16:50 < user235> i have been using usegalaxy.org
16:51 < kanzure> .wik neanderthal genome project
16:51 < EmmyNoether> "The Neanderthal genome project is an effort of a group of scientists to sequence the Neanderthal genome, founded in July 2006. /  It was initiated by 454 Life Sciences, a biotechnology company based in Branford, Connecticut in the United States and is coordinated by the Max [...]" - https://en.wikipedia.org/wiki/Neanderthal_genome_project
16:51 < kanzure> i saw a recent comparison article. not sure where i put it. hrm.
16:51 < darsie> Could we resurrect Neanderthals?
16:51 < kanzure> anyway, use this:
16:51 < kanzure> https://bioinf.eva.mpg.de/jbrowse
16:52 < kanzure> and https://www.eva.mpg.de/genetics/genome-projects/neandertal/draft-neandertal-genome/data.html?Fsize=0%2CGrawunder
16:52 < user235> darsie: you could clone a neanderthal with ancient DNA
16:52 < darsie> It would be fucking unethical.
16:52 < user235> or mammoths etc
16:52 < kanzure> darsie: see https://www.theverge.com/2013/1/20/3896854/wanted-an-adventurous-mother-for-a-neanderthal-baby
16:53 < darsie> Ok, but they're probably less smart than us.
16:53 < user235> kanzure: do you know about personal genomics testing?
16:54 < user235> like sending DNA sample to 23andme, then download the raw data to test the data at for instance codegen.eu
16:54 < darsie> Human rights might not apply to them, so maybe they could be used like animal testing.
16:54 < kanzure> user235: yesterday was the last day of free service offered by promethease ever since their acquisition
16:55 < user235> what i was interested in is to convert WGS (whole genom sequence) to what 23andme typically gives customers
16:55 < user235> and in this case, a 5700 year old sample
16:55 < kanzure> that's just a vcf file
16:56 < user235> yeah after a bunch of tools, one starts .fastq
16:56 < user235> with*
16:59 < user235> here's the fastq file. that is the standard file directly from sequencing. https://www.ebi.ac.uk/ena/data/view/ERX3277049
16:59 < user235> ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR325/004/ERR3250144/ERR3250144.fastq.gz (zipped)
17:02 < user235> "Anyway, if you have somehow obtained DNA sequencing, you willneed to have that analysed as well. The most raw output of DNA sequencingcomes in something called a .fastq file. An extremely large file just withrows and rows of sequential A, C, T, and Gs. Any serious provider, however,would have pre-processed these somewhat for you. Subsequent
17:02 < user235> formatsare typically called .bam (the A, C, T, and Gs in their right genomic position)and .vcf (the highlight of just the things where your genome is differentthan the genome reference)."
17:02 < user235> "From the .vcf file onwards, the analysis and interpretation methodologiestend to merge with those of microarray -- although with more opportunitiesin the realm of rare mutations. Therefore, the remaining chapters are equallyrelevant, just with this twist on price and initial pre-processing."
17:03 < kanzure> acquire knowledge of bioinformatics pipelines, there's a lot of books and tutorials about this
17:03 < user235> from Understand Your DNA (2019) L Folkersen
17:05 < user235> kanzure: do you know how to convert vcf to 23andme? I've tried using plink but it gives me an error i can't find on google
17:07 < user235> here's a vcf file of the 5700yr old WGS https://usegalaxy.org/datasets/bbd44e69cb8906b56650b81458f74c74/display?to_ext=vcf
17:08 < user235> this tool also returns nothing https://github.com/2sh/vcf-to-23andme
17:32 < galambo> hi. is it not possible to just import directly from 23andme?
17:33 < user235> galambo: this data isn't from 23andme.
17:34 < user235> it's a Whole Genome Sequence of an individual who lived 5700 years ago
17:35 < galambo> ah my bad. is it the same one they are trying to find a surrogate mother for?
17:35 < user235> nope, that's neanderthals, a "different" human species
17:36 < galambo> I dont see why they cant find a surrogate mother for that one either while they're at it
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17:39 < user235> it was a meme article probably
17:40 < galambo> lets go full jurassic park
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18:28 < fenn> ooops
18:28 < fenn> did anyone get a copy of the promethease wiki, or is that backed up somewhere?
18:29 < fenn> SNPedia
18:37 < fenn> supposedly it will remain free to use, but i don't trust companies that buy out open projects like this
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19:34 < kanzure> oh snpedia is operated by them? feck
19:39 < kanzure> fenn: https://diyhpl.us/~bryan/irc/snpedia.partial-backup.2020-01-01.xml
19:43 < kanzure> hmm this didn't get everything, like https://www.snpedia.com/index.php/MTHFR_comments since it has no category
19:44 < kanzure> anyway see https://www.snpedia.com/index.php/Special:SpecialPages
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21:08 < fenn> does mediawiki just have a built in XML dumper?
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22:25 < fenn> 268271 page titles loaded from SNPedia
22:26 < fenn> downloading XML...
22:28 < fenn> should be done in about a day
22:29 < fenn> assuming i don't get blocked
22:44 < nmz787> https://wiki.debian.org/WhyTheName
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22:59 < fenn> wish that etymology data was in apt-cache somewhere
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--- Log closed Thu Jan 02 00:00:54 2020