DEEP SCRATCH

Tag: genetics

  • Pangolin Didn’t Kill Itself: For World Pangolin Day 2020

    Pangolin Didn’t Kill Itself.

    Since news of the novel coronavirus spread late last year, I was struck by claims that the virus originated in snakes and/or bats. In my minds eye I quickly saw the image of a brew in a cauldron, “The eye of a newt and the toe of a frog etc..” This gut reaction led me to consider chemistry and microbiology based upon some folkloric themes.

    Snakes and bats have a wide and long history in folklore, and associated in popular culture with poison. Recent studies rebuked claims that Coronavirus was transferred to humans by snakes and/or bats, and instead proposed the missing link is a creature called the Pangolin, in Greek it roughly translates to Horny Scale, in Malay, “something that rolls up”. 

    Until this latest theory for the critter responsible for spreading the novel coronavirus to humans, I knew nothing of the Pangolin, and so discovered all manner research papers and physiological attributes that I would like to share (SEE BELOW) I’ve been disappointed with how news channels and organizations cover the outbreak and hope to share at least one fact that will inspire your own research, perhaps write of what you discovered. 

    My goal is to get to imagine you have a team of researchers in a laboratory. I don’t think it’s too far off the mark to look at the Pangolin and it’s place in genomic studies and its use in studying the immune system of mammals.  Plus it’s mention in folkloric traditions. Consider that Pangolin scales are in high demand around the world for their flesh and scales, for both eating and for medicine.

    The Pangolin is the ONLY scaled mammal in the animal Kingdom, it is noteworthy that it’s scales evolved due to high susceptibility to infection. The armour is a layer of protection when under attack or sleeping. The scales are made of keratin, which human nails and hair are also made, some have said that you can get health benefits by eating toe-nails. The religious-like, toxic belief that certain exotic animal parts will bring good luck, virility and other narcissistic benefits, is a big problem. Pangolin meat is very expensive, and not for the poor working cass.  

    Pangolin were not registered as being sold at the Wuhan market, yet witnesses have said that they were bought and sold there, and kept in unhygienic conditions, they are susceptible to infection.
    Do a quick search Pangolin + Scholar and browsethe articles. The Pangolin is the number ONE most trafficked critter in the global trade of illegal critters. A quick news search will turn up multiple stories of Pangolin busts on par with drug busts, in their estimated value. Who knew that the critter suspected of being the missing link between spreading the virus between animals and humans was also one of the most sought after critters on the black “exotic pet” market?

    To add insult to injury for the innocent anteater, their natural habitat is being destroyed, resulting in species of Pangolin classified critically endangered. This threat of extinction makes the black market thrive.
    In Zimbabwe, folk legend says that anybody who kills Pangolin will have bad luck, if only we would have enforced the laws protecting these critters from poaching earlier and kept in step with tribal wisdom.

    Although the breakout is sourced to Wuhan, and a specific market place, the bigger picture reveals a global network of players, traffickers, customers and middle-men who make up the supply and demand for Pangolin and other exotic animals. This paper reveals that Germany plays a large role in Pangolin smuggling operations. It seems the Germans have a taste for exotic pets and animals, and a worldwide customer base.

    This trafficking must stop immediately for the sake of all critter-kind and for the endangered species. Like trafficking in arms, drugs and sex, the traffick of Pangolin are responsible for a large part of the trouble around the planet today. The greedy don’t care if it’s guns, heroin, teenage-girls or lizards, deregulation helps them thrive.

    Studies show the mistreatment of the Pangolin leads to a higher probability of infection, which brings us back to black markets, illegal trafficking and inhumane treatment. The mucous of the Pangolin, and it’s very long tongue, and unique mouth muscles are worthy of study. Their insectivore diet of ants, termites and small worms are processed by the Pangolin, which lead to a deeper understanding of chemical symbiosis.

    I sincerely hope a cheap and easy to manufacture vaccine is discovered soon. If indeed, the Pangolin is the culprit, may they be treated with respect and may consideration be given to the link between pandemics and animal trafficking for profit.

    THE ROLE OF GERMANY IN THE ILLEGAL GLOBAL PANGOLIN TRADE
    https://www.sciencedirect.com/science/article/pii/S2351989419303233

    DID PANGOLINS SPREAD THE CHINESE CORONAVIRUS TO PEOPLE?
    https://www.nature.com/articles/d41586-020-00364-2

    PANGOLIN GENOMES AND THE EVOLUTION OF MAMMALIAN SCALES AND IMMUNITY.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052048/

    “As an evolutionary consequence of being covered by scales, it is plausible that the pangolin immune system evolved differently than in other mammals. For example, genes such as IFNE, a unique interferon exclusively expressed in skin epithelial cells and inner mucosa-protected tisssues (e.g., lung, intestines, and reproductive tissues), establish a first line of defense against pathogens in other placental mammals (Day et al. 2008; Ponten et al. 2008; Xi et al. 2012; Fung et al. 2013; Demers et al. 2014; Uhlen et al. 2015). Interferons (IFNs) are a cluster of highly conserved gene families that encode for cytokines expressed by host cells for communication between cells, leading to the activation of the immune system in the presence of pathogens (De Andrea et al. 2002; Fensterl and Sen 2009). Strikingly, the single copy intronless IFNE gene is pseudogenized in both pangolin species (confirmed by Sanger sequencing; sample size = 8) but is intact in 71 other mammalian species”

    TRADITIONAL-MEDICAL KNOWLEDGE AND PERCEPTION OF PANGOLINS (MANIS SPS) AMONG THE AWORI PEOPLE, SOUTHWESTERN NIGERIA.
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3179697/

    Here’s a useful guide on how to help, by way of deep learning.

    –Steve Fly

  • A.I AND JAMES JOYCE. Venter and Earwicker Bachwords

    “TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.” – from James Joyce’s A Portrait of the Artist as a Young Man.

    “We report the design, synthesis, and assembly of the 1.08-Mbp Mycoplasma mycoides JCVI-syn1.0 genome starting from digitized genome sequence information and its transplantation into a Mycoplasma capricolum recipient cell to create new Mycoplasma mycoides cells that are controlled only by the synthetic chromosome.
    http://www.sciencemag.org/cgi/content/abstract/science.1190719

    “The genome contains blueprints, in which are encoded the names of the researchers, a website address, contact email and quotes from James Joyce, Richard Feynman and a biography of Robert Oppenheimer. —http://www.guardian.co.uk/science/blog/audio/2010/may/21/craig-venter-synthetic-life-form

    “a rude breathing on the void of to be, a venter hearing his
    own bauchspeech in backwords, or, more strictly, but tristurned
    initials, the cluekey to a worldroom beyond the roomwhorld, for
    scarce one —James Joyce, Finnegans Wake, pg. 100

     

    Synthetic biology is a new area of biological research that combines science and engineering. Synthetic biology encompasses a variety of different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature. –http://en.wikipedia.org/wiki/Synthetic_biology

    http://video.ted.com/assets/player/swf/EmbedPlayer.swf

    http://www.ted.com/talks/craig_venter_unveils_synthetic_life.html

    Synthetic Genomics is a company dedicated to using modified or synthetically produced microorganisms to produce the alternative fuels ethanol and hydrogen. Synthetic Genomics was founded in part by J. Craig Venter. Venter’s previous company, Celera Genomics, was a driving force in the race to sequence the Human Genome.[1]

    The firm takes its name from the phrase synthetic genomics which is a scientific discipline of synthetic biology related to the generation of organisms artificially using genetic material.[2] Currently, Synthetic Genomics is working to produce biofuels on an industrial-scale using recombinant algae and other microorganisms. They are receiving funding from companies like Exxon for this venture. –http://en.wikipedia.org/wiki/Synthetic_Genomics

     

    As a development of that ongoing effort, last week Venter announced in the pages of Science magazine that his research team had – by putting together a living and replicating bacterium from synthetic components, inserting a computer-generated genome into a cell – “created life” in the laboratory for the first time. The experiment suggested the possibility of creating bacteria to perform specific functions: as producers of fossil fuels or medicines.

    Venter, now 63, is nothing if not a showman and the publication of this revelation and the subsequent press conferences, have polarised opinion in ways with which he has long been familiar. Some authorities, and several newspaper leader writers, have claimed him as our Galileo or our Einstein; others have been notably underwhelmed.

    Freeman Dyson, the physicist, captured the full range of academic sentiment in this dry appraisal: “This experiment is clumsy, tedious, unoriginal. From the point of view of aesthetic and intellectual elegance, it is a bad experiment. But it is nevertheless a big discovery… the ability to design and create new forms of life marks a turning point in the history of our species and our planet.”

    Venter’s ego and his preference to turn to corporations rather than research foundations as funding partners (Exxon Mobil is a $600m sponsor of his energy experiments) do not tend to endear him to the academic establishment. Steve Jones, professor of genetics at University College London, and a perennial voice of reason, offered me this verdict on the biologist’s latest headlines.

    “It’s very easy to mock Venter,” Jones suggests. “When he first appeared, people just kind of sneered at him. But they stopped sneering when they saw his brilliance in realising that the genome was not a problem of chemistry but a problem of computer power. I don’t think anybody can deny that that was a monumental achievement and he has been doing fantastically interesting things subsequently with marine life. Having said that, though, the man is clearly a bit of a prick and one with a serial addiction to publicity.” —http://www.guardian.co.uk/theobserver/2010/may/23/observer-profile-craig-venter

    HIGH RESOLUTION PDF OF NEW SELF-REPLICATING LIFE FORM.

    lastly but mostly, in
    her genesic field it is all game and no gammon; she is ladylike in
    everything she does and plays the gentleman’s part every time.
    Let us auspice it! –James Joyce, FW, pg. 112

    * “TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.” – from James Joyce’s A Portrait of the Artist as a Young Man.
    * “SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.”- a quote from the book, American Prometheus which discusses J. Robert Oppenheimer and the first atomic bomb.
    * *“WHAT I CANNOT BUILD, I CANNOT UNDERSTAND.” – attributed to Richard Feynman (physicist, philosopher, badass) as the last words on his blackboard at the time of his death as described in The Universe in a Nutshell by Stephen Hawking (physicist, philosopher, badass).