https://pinboard.in/u:jm/public/ recent bookmarks from jm 2026-03-11T12:00:29+00:00 https://www.rathbiotaclan.com/whole-brain-emulation-achieved-scientists-run-a-fruit-fly-brain-in-simulation/ jm The behavioral repertoire observed in the demonstration included coordinated hexapod locomotion with both tripod and metachronal walking gaits, spontaneous postural correction in response to perturbation, initiation and execution of full antennal grooming sequences with the tripartite synchronization described by Özdil et al., and natural transitions between walking and stationary states. Every behavior arose from the same running brain model - there was no switching between different neural circuits or controllers. This is precisely what happens in a living fly: walking, grooming, and balance are different motor programs that coexist in the same brain and are selected and executed by the same biological circuits depending on the moment-to-moment state of the animal and its environment. Absolutely mind blowing -- a reconstructed, biological brain running in silico.]]> simulation brains uploading drosophila flies emulation science biology neurons https://pinboard.in/ https://pinboard.in/u:jm/b:7b531082c20a/ 2025-04-24T08:15:58+00:00 https://theappendix.net/posts/2014/02/darwins-children-drew-vegetable-battles-on-the-origin-of-species jm evolution biology children history charles-darwin kids drawings https://pinboard.in/ https://pinboard.in/u:jm/b:d0d5be0f393b/ 2022-08-12T14:53:15+00:00 https://www.scientificamerican.com/article/what-the-science-on-gender-affirming-care-for-transgender-kids-really-shows/ jm Data from more than a dozen studies of more than 30,000 transgender and gender-diverse young people consistently show that access to gender-affirming care is associated with better mental health outcomes—and that lack of access to such care is associated with higher rates of suicidality, depression and self-harming behavior. (Gender diversity refers to the extent to which a person’s gendered behaviors, appearance and identities are culturally incongruent with the sex they were assigned at birth. Gender-diverse people can identify along the transgender spectrum, but not all do.) Major medical organizations, including the American Academy of Pediatrics (AAP), the American Academy of Child and Adolescent Psychiatry, the Endocrine Society, the American Medical Association, the American Psychological Association and the American Psychiatric Association, have published policy statements and guidelines on how to provide age-appropriate gender-affirming care. All of those medical societies find such care to be evidence-based and medically necessary. ]]> trans gender science biology transgender https://pinboard.in/ https://pinboard.in/u:jm/b:8f01e282dd0d/ 2021-03-19T16:56:52+00:00 https://blogs.sciencemag.org/pipeline/archives/2021/03/19/ai-and-drug-discovery-attacking-the-right-problems jmseeing the actual problems that the field is wrestling with will very quickly take the shine off a lot of hyped-up headlines and press releases. These include things like “How do we even estimate the uncertainty in our model, and how do we compare it to others?”, “How do we deal with molecules as three-dimensional objects with changing conformations, as opposed to two-dimensional graph-theory objects or one-dimensional text strings?”, “Since no one can actually dock a billion virtual molecules into a protein target, how can we reduce the problem to something theoretically manageable without throwing away the answers we want? And how will we know if we have?” and “What do we do when our model will only start to work if we feed it more data than we’re ever going to have?” The next time you see a proclamation that everything’s been made obsolete by AI-driven modeling, keep those in mind. ]]> ai ml drugs biology bioinformatics drug-discovery simulation derek-lowe https://pinboard.in/ https://pinboard.in/u:jm/b:80c888a5b47d/ 2020-12-26T23:24:02+00:00 https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/ jm biology rna science covid-19 sars-cov-2 vaccines biontech https://pinboard.in/ https://pinboard.in/u:jm/b:15faffa83bf1/ 2020-03-03T14:51:02+00:00 https://www.pnas.org/content/early/2020/02/25/1911359117 jmWhere does knowledge come from? We addressed this classic question using the test cases of the cortical face and scene networks: two well-studied examples of specialized “knowledge” systems in the adult brain. We found that neonates already show domain-specific patterns of functional connectivity between regions that will later develop full-blown face and scene selectivity. Furthermore, the proto face network showed stronger functional connectivity with foveal than with peripheral primary visual cortex, while the proto scene network showed the opposite pattern, revealing that these networks already receive differential visual inputs. Our findings support the hypothesis that innate connectivity precedes the emergence of domain-specific function in cortex, shedding new light on the age-old question of the origins of human knowledge. ]]> brains vision babies knowledge learning science biology https://pinboard.in/ https://pinboard.in/u:jm/b:54e5d8be1755/ 2019-12-20T15:41:59+00:00 https://www.vox.com/identities/2019/12/19/21029874/jk-rowling-transgender-tweet-terf jmTrans-exclusionary radical feminist (TERF) ideology has been helped along in the UK by media under the leadership of Rupert Murdoch and the Times of London for years. Any vague opposition to gender-critical thought in the UK brings accusations of “silencing women” and a splashy feature or op-ed in a British national newspaper. Australian radical feminist Sheila Jeffreys went before the UK Parliament in March 2018 and declared that trans women are “parasites,” language that sounds an awful lot like Donald Trump speaking about immigrants. According to Heron Greenesmith, who studies the modern gender-critical movement as a senior research associate at the social-justice think tank Political Research Associates, gender-critical feminism in the UK grew out of a toxic mix of historical imperialism and the influence of the broader skeptical movement in the early aughts — which was hyperfocused on debunking “junk science” and any idea that considered sociological and historical influence and not just biology. Those who rose to prominence in the movement did so through a lot of “non-tolerant calling-out and attacking people,” Greenesmith said, much like gender-critical feminism. “Anti-trans feminists think they have science on their side. It is bananas how ascientific their rhetoric is, and yet literally they say, ‘Biology isn’t bigotry.’ In fact, biology has been used as bigotry as long as biology has been a thing.” ]]> feminism politics terfs trans-rights gender biology uk jk-rowling transphobia https://pinboard.in/ https://pinboard.in/u:jm/b:92b21900ec46/ 2019-01-02T15:54:24+00:00 https://royalsocietypublishing.org/doi/full/10.1098/rspb.2018.0822 jmUsing a saliva-based assay, we found that students (n = 1495) who tested IgG positive for Toxoplasma gondii exposure were 1.4× more likely to major in business and 1.7× more likely to have an emphasis in ‘management and entrepreneurship' over other business-related emphases. Among professionals attending entrepreneurship events, T. gondii-positive individuals were 1.8× more likely to have started their own business compared with other attendees (n = 197). Finally, after synthesizing and combining country-level databases on T. gondii infection from the past 25 years with the Global Entrepreneurship Monitor of entrepreneurial activity, we found that infection prevalence was a consistent, positive predictor of entrepreneurial activity and intentions at the national scale, regardless of whether previously identified economic covariates were included. Nations with higher infection also had a lower fraction of respondents citing ‘fear of failure' in inhibiting new business ventures. While correlational, these results highlight the linkage between parasitic infection and complex human behaviours, including those relevant to business, entrepreneurship and economic productivity. ]]> science biology infection toxoplasmosis parasites humans behaviour entrepreneurs business brains economics https://pinboard.in/ https://pinboard.in/u:jm/b:d60371f8ab12/ 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/ 2018-04-29T22:18:04+00:00 https://www.dropbox.com/s/deglzs4i2ss282w/repealfacts%20and%20FAQs.pdf?dl=0 jm repeal repealthe8th science biology medicine pregnancy abortion pro-choice ireland miscarriage https://pinboard.in/ https://pinboard.in/u:jm/b:42f341c2db9d/ 2018-01-12T23:07:48+00:00 https://www.theatlantic.com/science/archive/2018/01/brain-cells-can-share-information-using-a-gene-that-came-from-viruses/550403/ jm...a gene called Arc which is active in neurons, and plays a vital role in the brain. A mouse that’s born without Arc can’t learn or form new long-term memories. If it finds some cheese in a maze, it will have completely forgotten the right route the next day. “They can’t seem to respond or adapt to changes in their environment,” says Shepherd, who works at the University of Utah, and has been studying Arc for years. “Arc is really key to transducing the information from those experiences into changes in the brain.” Despite its importance, Arc has been a very difficult gene to study. Scientists often work out what unusual genes do by comparing them to familiar ones with similar features—but Arc is one-of-a-kind. Other mammals have their own versions of Arc, as do birds, reptiles, and amphibians. But in each animal, Arc seems utterly unique—there’s no other gene quite like it. And Shepherd learned why when his team isolated the proteins that are made by Arc, and looked at them under a powerful microscope. He saw that these Arc proteins assemble into hollow, spherical shells that look uncannily like viruses. “When we looked at them, we thought: What are these things?” says Shepherd. They reminded him of textbook pictures of HIV, and when he showed the images to HIV experts, they confirmed his suspicions. That, to put it bluntly, was a huge surprise. “Here was a brain gene that makes something that looks like a virus,” Shepherd says. That’s not a coincidence. The team showed that Arc descends from an ancient group of genes called gypsy retrotransposons, which exist in the genomes of various animals, but can behave like their own independent entities.* They can make new copies of themselves, and paste those duplicates elsewhere in their host genomes. At some point, some of these genes gained the ability to enclose themselves in a shell of proteins and leave their host cells entirely. That was the origin of retroviruses—the virus family that includes HIV. ]]> brain evolution retroviruses viruses genes arc gag proteins memory biology https://pinboard.in/ https://pinboard.in/u:jm/b:96a8d10c1752/ 2017-11-20T16:28:40+00:00 https://www.theatlantic.com/science/archive/2017/11/how-the-zombie-fungus-takes-over-ants-bodies-to-control-their-minds/545864/ jmHughes’s team found that fungal cells infiltrate the ant’s entire body, including its head, but they leave its brain untouched. There are other parasites that manipulate their hosts without destroying their brains, says Kelly Weinersmith from Rice University. For example, one flatworm forms a carpet-like layer over the brain of the California killifish, leaving the brain intact while forcing the fish to behave erratically and draw the attention of birds—the flatworm’s next host. “But manipulation of ants by Ophiocordyceps is so exquisitely precise that it is perhaps surprising that the fungus doesn't invade the brain of its host,” Weinersmith says. [....] So what we have here is a hostile takeover of a uniquely malevolent kind. Enemy forces invading a host’s body and using that body like a walkie-talkie to communicate with each other and influence the brain from afar. Hughes thinks the fungus might also exert more direct control over the ant’s muscles, literally controlling them “as a puppeteer controls as a marionette doll.” Once an infection is underway, he says, the neurons in the ant’s body—the ones that give its brain control over its muscles—start to die. Hughes suspects that the fungus takes over. It effectively cuts the ant’s limbs off from its brain and inserts itself in place, releasing chemicals that force the muscles there to contract. If this is right, then the ant ends its life as a prisoner in its own body. Its brain is still in the driver’s seat, but the fungus has the wheel. ]]> biology gross cordyceps fungi fungus ants zombies infection brain parasites https://pinboard.in/ https://pinboard.in/u:jm/b:de8f315abfd2/ 2017-08-11T08:22:11+00:00 https://www.quora.com/What-do-scientists-think-about-the-biological-claims-made-in-the-anti-diversity-document-written-by-a-Google-employee-in-August-2017/answer/Suzanne-Sadedin?share=1 jm sexism misogyny bias discrimination google biology women gender sex via:klyda https://pinboard.in/ https://pinboard.in/u:jm/b:da02c5193c80/ 2016-10-12T09:59:49+00:00 http://www.davemech.org/news.html jmThe concept of the alpha wolf is well ingrained in the popular wolf literature at least partly because of my book "The Wolf: Ecology and Behavior of an Endangered Species," written in 1968, published in 1970, republished in paperback in 1981, and currently still in print, despite my numerous pleas to the publisher to stop publishing it. Although most of the book's info is still accurate, much is outdated. We have learned more about wolves in the last 40 years then in all of previous history. One of the outdated pieces of information is the concept of the alpha wolf. "Alpha" implies competing with others and becoming top dog by winning a contest or battle. However, most wolves who lead packs achieved their position simply by mating and producing pups, which then became their pack. In other words they are merely breeders, or parents, and that's all we call them today, the "breeding male," "breeding female," or "male parent," "female parent," or the "adult male" or "adult female." In the rare packs that include more than one breeding animal, the "dominant breeder" can be called that, and any breeding daughter can be called a "subordinate breeder." ]]> biology animals wolves alpha alpha-males mra science wolf-packs society competition parenting https://pinboard.in/ https://pinboard.in/u:jm/b:872630cc1167/ 2016-06-03T15:24:53+00:00 http://biorxiv.org/content/biorxiv/early/2016/05/26/055624.full.pdf jm via:bos neuroscience microprocessors 6502 computers hardware wetware brain biology neural-systems https://pinboard.in/ https://pinboard.in/u:jm/b:adbeaa302730/ 2016-05-30T10:04:37+00:00 https://www.quora.com/How-big-an-issue-is-the-nausea-problem-for-Virtual-Reality-products/answer/Steve-Baker-9?share=1 jmSadly (because I want a “holodeck” as much as the next red-blooded geek) - I don’t think it’s possible to make a VR system that both delivers the experience that everyone wants - and doesn’t make a sizeable proportion of the population so sick that they’ll never want to do it again. For the people who can stomach the display - my major concern is that the US Navy studies show that there is some disorientation that might persist long after finishing your game…so driving a car while “under the influence” of post-VR disorientation is probably as dangerous as drunk-driving. If these devices are in pretty much every home - then there are huge problems in store for the industry in terms of product liability. There have been plenty of warnings from the flight simulation industry - there are no excuses for not reading the Wikipedia article on the subject. If people are driving “under the influence” and the VR companies didn’t warn them about that - then they’re in deep trouble. IMHO, these consumer-grade VR devices should be carefully studied and if they do cause possible driving impairment, they should be banned until such time as the problems can be fixed…which may very well be “never”. Sorry to be the bearer of bad news. (via Tony Finch)]]> holodeck vr oculus-rift hmds nausea head-mounted-displays biology brain flight-simulation https://pinboard.in/ https://pinboard.in/u:jm/b:d97c079b9672/ 2016-01-03T10:15:57+00:00 http://boingboing.net/2016/01/01/hangovers-arent-caused-by-de.html jmThe [now-]leading theory implicates a specific gamma aminobutyric acid (GABA) and a complementary brain receptor, "that responds to low concentrations of ethanol, as produced by one glass of wine, in the brain." ]]> hangovers booze brain biology biochemistry gaba ethanol alcohol https://pinboard.in/ https://pinboard.in/u:jm/b:339eaf759787/ 2014-10-21T09:52:34+00:00 http://en.m.wikipedia.org/wiki/BioBrick jmBioBrick parts are DNA sequences which conform to a restriction-enzyme assembly standard.[1][2] These Lego-like building blocks are used to design and assemble synthetic biological circuits, which would then be incorporated into living cells such as Escherichia coli cells to construct new biological systems.[3] Examples of BioBrick parts include promoters, ribosomal binding sites (RBS), coding sequences and terminators. (via Soren)]]> via:sorenrags biobricks fabrication organisms artificial-life biology e-coli genetic-engineering https://pinboard.in/ https://pinboard.in/u:jm/b:091f4fcae82a/ 2014-05-01T20:33:56+00:00 http://catalogue.nli.ie/Record/vtls000538011 jm ireland history science biology t-h-mason photos https://pinboard.in/ https://pinboard.in/u:jm/b:fc03d8ea6f55/ 2014-02-18T23:03:22+00:00 http://www.nytimes.com/2014/02/15/science/disgraced-scientist-granted-us-patent-for-work-found-to-be-fraudulent.html?_r=1 jmKorean researcher Hwang Woo-suk electrified the science world 10 years ago with his claim that he had created the world’s first cloned human embryos and had extracted stem cells from them. But the work was later found to be fraudulent, and Dr. Hwang was fired from his university and convicted of crimes. Despite all that, Dr. Hwang has just been awarded an American patent covering the disputed work, leaving some scientists dumbfounded and providing fodder to critics who say the Patent Office is too lax. “Shocked, that’s all I can say,” said Shoukhrat Mitalipov, a professor at Oregon Health and Science University who appears to have actually accomplished what Dr. Hwang claims to have done. “I thought somebody was kidding, but I guess they were not.” Jeanne F. Loring, a stem cell scientist at the Scripps Research Institute in San Diego, said her first reaction was “You can’t patent something that doesn’t exist.” But, she said, she later realized that “you can.” ]]> patents absurd hwang-woo-suk cloning stem-cells science biology uspto https://pinboard.in/ https://pinboard.in/u:jm/b:f0e6b1ceeaad/ 2014-01-27T17:43:40+00:00 http://arxiv.org/ftp/arxiv/papers/1311/1311.2412.pdf jm plos mozilla code-reviews coding science computational-biology biology studies https://pinboard.in/ https://pinboard.in/u:jm/b:93e2c28d8494/ 2013-10-15T09:01:08+00:00 http://www.wired.com/wiredscience/2013/10/how-to-read-a-research-paper-about-that-scientist-with-a-nematode-in-his-mouth/ jmLet’s rewind to September 2012. It was about then- according to this recently published report (paywall) in The American Journal of Tropical Medicine – that an “otherwise healthy, 36-year-old man” felt a rough patch in his mouth, a scaly little area his right cheek. It didn’t hurt. But then it didn’t stay there either. He started testing for it with his tongue. It traveled. It moved to the back of his mouth, then forward, coiled backwards again. In the language of science: “These rough patches would appear and disappear on a daily basis, giving the patient the indirect sense that there was an organism moving within the oral cavity.” ]]> nematodes parasites biology medicine paper gross funny wired mouth https://pinboard.in/ https://pinboard.in/u:jm/b:370a9d80c693/ 2013-01-26T13:07:47+00:00 http://www.australiangeographic.com.au/journal/all-polar-bears-descended-from-one-grizzly.htm jm animals biology science dna history ireland bears polar-bears grizzly-bears via:ben https://pinboard.in/ https://pinboard.in/u:jm/b:dbf33dcc106c/ 2011-11-02T22:00:44+00:00 http://www.orionmagazine.org/index.php/articles/article/6474/ jm octopus animals biology consciousness neuroscience science https://pinboard.in/ https://pinboard.in/u:jm/b:05f9053e995b/ 2011-09-19T12:30:01+00:00 http://blogs.discovermagazine.com/notrocketscience/2011/09/18/computer-gamers-solve-problem-in-aids-research-that-puzzled-scientists-for-years/ jm foldit gaming games science biology aids viruses protease protein-folding proteins vr https://pinboard.in/ https://pinboard.in/u:jm/b:a50dad86da5a/ 2011-07-02T18:14:43+00:00 http://www.nature.com/news/2011/110628/full/news.2011.388.html jm science anatomy grip evolution water biology https://pinboard.in/u:jm/b:5dded97e9bf2/ 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/