https://pinboard.in/u:jm/public/ recent bookmarks from jm 2021-12-14T09:48:23+00:00 https://www.sciencedirect.com/science/article/pii/S0960982221007946 jm Our analyses find a strong enrichment in sweep signals at CoV-VIPs across multiple East Asian populations, which is absent from other populations. This suggests that an ancient coronavirus epidemic (or another virus using similar VIPs) drove an adaptive response in the ancestors of East Asians. Further, by leveraging ancestral recombination graph approaches,20,21 we find that 42 CoV-VIPs may have come under selection around 900 generations (∼25,000 years) ago and exhibit a coordinated adaptive response. We further show that the CoV-VIP genes are enriched for anti- and proviral effects and variants that affect COVID-19 etiology in the modern British population (https://grasp.nhlbi.nih.gov/Covid19GWASResults.aspx).22,23 We further show that the inferred underlying causal mutations are situated near to regulatory variants active in lungs and other tissues impacted by COVID-19. These independent lines of evidence support an ancient coronavirus (or a similarly interacting virus) epidemic that emerged in the ancestors of contemporary East Asian populations. ]]> pandemics disease history asia covid-19 coronavirus genes genetics https://pinboard.in/ https://pinboard.in/u:jm/b:4c8833dfd5cd/ 2020-10-05T09:56:24+00:00 https://www.thejournal.ie/selling-our-genes-5219781-Oct2020/ jmGenuity Science, the main company involved in DNA sequencing in Ireland, has at least 25 links to facilities around Ireland. These include funding and collaborations with major hospitals, universities, research facilities and charities. A collaboration agreement signed between Genuity Science and UCD is “restrictive”, according to an academic expert, though Genuity Science Ireland disagree with this assessment. We have the full details in this breakout article. Hospital clinicians have become “agents of a company” due to the nature of agreements in place, according to experts. Researchers are making “the best of the situation” in Ireland by working with the private sector but most would prefer a public system due to data access concerns. Lack of Government policy and adequate regulation means that private companies have no limit on how long they have exclusive access to the data they collect from Irish patients. Researchers and patient representatives are concerned about a potential erosion of trust in genetics research in Ireland. ]]> genomics genuity genetics ucd gmi ireland data-privacy data-protection research https://pinboard.in/ https://pinboard.in/u:jm/b:ec2dde2c0218/ 2020-03-09T11:55:04+00:00 https://nextstrain.org/narratives/ncov/sit-rep/2020-03-05 jm genetics phylogenetics nextstrain covid-19 diseases epidemics viruses https://pinboard.in/ https://pinboard.in/u:jm/b:53d503bf8a50/ 2019-07-15T17:03:53+00:00 https://twitter.com/rossamcmahon/status/1145436655756689409 jmGMI is a big, expensive company. It announced planned investment injection of $400m last year. It is engaged in a hot industry - hot because of investor interest and hot because of regulatory/ethics concerns. GDPR is not new. It has been known since 2016. Data protection law is not new. It has been known since 1988. The impact of these laws on genetic data collection & use is not a surprise. So if you have a $400m+ business and this is a key business issue, you have taken advice. And you have, no doubt, been in a position to take that advice from some of the best and/or most expensive advisors available. Assumptions are dangerous, but I think it is fair to assume this has happened. So read the story again. Would you be looking for repeated meetings with [Department of Health], answers to questions on regulatory matters and assurances from the State, if you had legal advice of your own to the effect that you are operating or can operate as your currently are? ]]> gmi genomics genetics data-privacy privacy gdpr ireland https://pinboard.in/ https://pinboard.in/u:jm/b:aa19ff9e3bf1/ 2018-10-10T11:21:25+00:00 https://www.theatlantic.com/science/archive/2018/10/horsepox-smallpox-virus-science-ethics-debate/572200/ jmAbsent clearer guidelines, the burden falls on the scientific enterprise to self-regulate—and it isn’t set up to do that well. Academia is intensely competitive, and “the drivers are about getting grants and publications, and not necessarily about being responsible citizens,” says Filippa Lentzos from King’s College London, who studies biological threats. This means that scientists often keep their work to themselves for fear of getting scooped by their peers. Their plans only become widely known once they’ve already been enacted, and the results are ready to be presented or published. This lack of transparency creates an environment where people can almost unilaterally make decisions that could affect the entire world. Take the horsepox study [the main topic of this article]. Evans was a member of a World Health Organization committee that oversees smallpox research, but he only told his colleagues about the experiment after it was completed. He sought approval from biosafety officers at his university, and had discussions with Canadian federal agencies, but it’s unclear if they had enough ethical expertise to fully appreciate the significance of the experiment. “It’s hard not to feel like he opted for agencies that would follow the letter of the law without necessarily understanding what they were approving,” says Kelly Hills, a bioethicist at Rogue Bioethics. She also sees a sense of impulsive recklessness in the interviews that Evans gave earlier this year. Science reported that he did the experiment “in part to end the debate about whether recreating a poxvirus was feasible.” And he told NPR that “someone had to bite the bullet and do this.” To Hills, that sounds like I did it because I could do it. “We don’t accept those arguments from anyone above age 6,” she says. ]]> the-atlantic science news smallpox horsepox diseases danger risk academia papers publish-or-perish bioethics ethics biology genetics https://pinboard.in/ https://pinboard.in/u:jm/b:7848b9738f56/ 2018-08-22T22:24:45+00:00 https://www.sciencemag.org/news/2016/08/one-five-genetics-papers-contains-errors-thanks-microsoft-excel jm science microsoft excel spreadsheets autoformatting clippy fail papers genetics https://pinboard.in/ https://pinboard.in/u:jm/b:143492bf59ec/ 2018-06-27T10:57:41+00:00 https://twitter.com/antonioregalado/status/1011675054709661696 jmI used to know some technicians in the NYC Medical Examiner's lab. They had all been DNA typed (to detect accidental contamination). So, their little society was a picture of what is to come, of total DNA transparency. They would do stuff like find out who stuck gum under the table. Also, who was peeing on the toilet seat in the bathroom. So There’s a second technology at play: environmental DNA sampling. Once police get a name they tail the suspect and try to get some DNA he leaves behind. To make the match to crime scene sample. Police have gotten DNA from: - a car door handle - a straw - a paper napkin Imagine storm troopers of a repressive regime descending on a meeting place of the resistance. Just swab the whole place and find out who was there from DNA left behind. Technically, total DNA de-anonymity is possible. Far as I know there’s no law, no protection, against identifying you from your DNA. In crime cases, [this is] being done by “amateur” using a database (GEDmatch) that itself is highly informal. ]]> privacy dna genetics genetic-genealogy gedmatch law transparency https://pinboard.in/ https://pinboard.in/u:jm/b:c533ab41ac49/ 2018-02-07T13:41:11+00:00 https://twitter.com/drg1985/status/961217607838896128 jm europe history prehistory skin-colour cheddar-man race skin slc24a5 genetics david-grimes https://pinboard.in/ https://pinboard.in/u:jm/b:faca50d2d956/ 2016-03-20T22:02:59+00:00 https://www.washingtonpost.com/news/wonk/wp/2016/03/17/a-mans-discovery-of-bones-under-his-pub-could-forever-change-what-we-know-about-the-irish/ jmRadiocarbon dating shows that the bones discovered at McCuaig's go back to about 2000 B.C. That makes them hundreds of years older than the oldest artifacts generally considered to be Celtic — relics unearthed from Celt homelands of continental Europe, most notably around Switzerland, Austria and Germany. For a group of scholars who in recent years have alleged that the Celts, beginning from the middle of Europe, may never have reached Ireland, the arrival of the DNA evidence provides the biological certitude that the science has sometimes brought to criminal trials. “With the genetic evidence, the old model [of Celtic colonisation of Ireland] is completely shot,” John Koch, a linguist at the Center for Advanced Welsh and Celtic Studies at the University of Wales. ]]> celts ireland history dna genetics genome carbon-dating bronze-age europe colonisation https://pinboard.in/ https://pinboard.in/u:jm/b:555711ff236d/ 2016-03-16T21:22:17+00:00 http://www.instituteofcaninebiology.org/blog/health-of-purebred-vs-mixed-breed-dogs-the-data jm This study found that purebred dogs have a significantly greater risk of developing many of the hereditary disorders examined in this study. No, mixed breed dogs are not ALWAYS healthier than purebreds; and also, purebreds are not "as healthy" as mixed breed dogs. The results of this study will surprise nobody who understands the basics of Mendelian inheritance. Breeding related animals increases the expression of genetic disorders caused by recessive mutations, and it also increases the probability of producing offspring that will inherit the assortment of genes responsible for a polygenic disorder.  In conclusion, go mutts.]]> dogs breeding genetics hereditary-disorders science inheritance recessive-mutation data https://pinboard.in/ https://pinboard.in/u:jm/b:aa7d3937bf61/ 2016-01-12T09:55:38+00:00 http://www.technologyreview.com/featuredstory/532796/who-owns-the-biggest-biotech-discovery-of-the-century/ jm crispr algorithms gene-editing genetics genomics genes patents https://pinboard.in/ https://pinboard.in/u:jm/b:fd50896c8bd9/ 2015-10-09T12:39:09+00:00 http://arstechnica.com/tech-policy/2015/10/gene-patents-probably-dead-worldwide-following-australian-court-decision/ jmThe court based its reasoning on the fact that, although an isolated gene such as BRCA1 was "a product of human action, it was the existence of the information stored in the relevant sequences that was an essential element of the invention as claimed." Since the information stored in the DNA as a sequence of nucleotides was a product of nature, it did not require human action to bring it into existence, and therefore could not be patented. Via Tony Finch.]]> via:fanf australia genetics law ipr medicine ip patents https://pinboard.in/ https://pinboard.in/u:jm/b:46c25adbed67/ 2013-12-04T15:51:04+00:00 http://dogbehaviorscience.wordpress.com/2012/09/29/100-years-of-breed-improvement/ jmThe English bulldog has come to symbolize all that is wrong with the dog fancy and not without good reason; they suffer from almost every possible disease. A 2004 survey by the Kennel Club found that they die at the median age of 6.25 years (n=180). There really is no such thing as a healthy bulldog. The bulldog’s monstrous proportions makes them virtually incapable of mating or birthing without medical intervention. (via Bryan)]]> dogs eugenics breeding horror science genetics traits animals pets bulldog pedigree https://pinboard.in/ https://pinboard.in/u:jm/b:b7af1a957a63/ 2012-02-04T20:59:13+00:00 http://www.law.yale.edu/documents/pdf/LEO/LEO_Williams.pdf jm via:fanf genetics ip copyright open-source celera patents papers pdf https://pinboard.in/ https://pinboard.in/u:jm/b:15a4006a8c83/ 2010-05-06T10:00:34+00:00 http://www.pnas.org/content/early/2010/04/28/0914771107 jm via:adulau papers toread genetics genome call-graph linux kernel e-coli operating-systems transcriptional-regulatory-network https://pinboard.in/u:jm/b:eae2a1ce682d/ 2009-09-02T09:28:21+00:00 http://www.irishtimes.com/newspaper/frontpage/2009/0902/1224253666155.html jm science genetics research biology evolution tcd sfi genome junk-dna https://pinboard.in/u:jm/b:86812cc4e864/