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Arete last won the day on June 9

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About Arete

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    Ecological speciation, functional genomics, phylogenetics, population genetics and evolution.
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    Evolutionary Biology
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    Assistant Professor


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Primate (9/13)



  1. Not to mention breakthrough cases are reported to display significantly milder symptoms and lower rates of hospitalization/mortality than infections in unvaccinated individuals. If ADE were a significant concern, the opposite would be observed. Basically, reiterating what CharonY has already said, there's no evidence for ADE caused by a COVID19 vaccine, and the available evidence suggests it is not an issue. You'll notice this follows a standard antivax/conspiracy format, in that each new claim is unrelated to the prior (e.g. PCR tests don't work, the vaccine alters your DNA, etc) and is an increasing stretch/absurd misinterpretation than the prior. I already checked "Harvard medical School is trying to create a socialist new world order, so you can't trust their publications" on my nutjob bingo card answering questions on COVID.
  2. Apologies - I think the complication stems from the fact that in reality organisms are self replicating and there's nothing analogous to the "monkeys". The point is simply that in the analogy, the typing monkeys are searching the parameter space in a blind, random fashion. In an evolving population, be it genes, organisms, genomes, the probability of fixation or extinction of a mutation is governed by its selection coefficient in the prior generation. Ergo, the parameter space is searched in a directed manner, rather than a random one. Ultimately the big numbers game is not really a compelling argument. It would only take me a short time to roll a six sided dice 100 times. The possibility of getting a particular sequence is 1.53-78. However, just by performing the action you will get a sequence. Saying you couldn't get the specific sequence you did because of the low probability is negated by the fact that if you roll a dice 100 times, there is a 100% chance you will get an improbable result.
  3. The point *should* be a pretty simple statistical point. In English, each set is comprised of a combination of 26 characters, of any length until a monkey pushes the space key -effectively meaning there are infinite sets. There are approximately 470,000 words in the English language, so that many sets are translatable, the rest are not. In DNA, sets are a combination of 4 characters in lengths of three, meaning there are 64 possible sets. All are translatable to a suite of 21 meanings. These two probability landscapes are incredibly different. One is like searching for a needle in a haystack, the other is like searching for a needle somewhere in the universe. This point has to do with redundancy. The phrase "Call me Ishmael" has no redundancy - either all the letters are correct or the phrase is wrong. The genetic code has lots of redundancy. All amino acids have at least two of the 64 codons that encode them. Seven have completely redundant third positions - if the first two letters encode the correct amino acid, the third base pair doesn't matter - theoretically a full third of the nucleotides in the gene/genome could be entirely different from the "right" sequence, but the encoded protein translation identical. All of a sudden, there are a thousand needles in the haystack and you only need to find one. Not quite - selection quickly fixes beneficial or "correct" sequences in the gene pool of a population. So, once a monkey gets a genetic "word" correct, it will tell all the other monkeys about it. In all subsequent iterations of the gene/genome the monkeys uniformly get that word right, iteratively shrinking the parameter space left to search. The monkeys are burning the straw as the search and the haystack iteratively shrinks. Not so for a random smashing of literary keys in search of a phrase in English.
  4. A point I haven't seen made yet is that DNA encodes four nucleotides. Codons are groups of three nucleotides - so there are 64 possible "words". All words translate to either an amino acid, or stop, with multiple codons encoding each amino acid. This means that: 1) All possible sequences can be expressed into proteins. There are no gibberish sequences, unlike the English language. 2) Multiple sequences encode the same string of amino acids. There is a considerable level of redundancy. Several monkeys could type different DNA strings which encode the same protein. 3) All proteins are subject to environmental selection. The process of eliminating or retaining DNA strings is non-random, as opposed to monkeys banging typewriters. So the analogy fails on multiple levels.
  5. Three points: 1) An integral part of higher education and research is critical examination and questioning of the status quo - be it in the context of physics, biology, sociology, history, art etc. This means that the central mindset within higher learning and research institutions is fundamentally progressive, but not necessarily in the political sense. We have seen universities at the forefront of socio-political change, especially during the Bolshevik revolution, the civil rights movement, Arab spring, etc. They tend to be agents of change rather than conservatism, by nature of what they fundamentally do. 2) The Trump administration was an anomalous, unprecedentedly unscientific administration that aggressively attacked both science and education. Being anti-Trump is not the same as being anti-conservative. 3) In context to the US, the division between the major political parties is a kind of bizarre mish mash of political ideologies that don't necessarily align with quintessential conservative/liberal positions. The GOP is not fiscally conservative. Libertarians vote for right wing authoritarians because of gun rights. The democrats support an exploitative, corporate labor structure and military industrial complex. The GOP has painted itself into a corner with regards to science through climate change and environmental policy. Being anti-GOP isn't necessarily the same as being ideologically anti-conservative.
  6. So from Shi Zhengli's wiki page I dug up the gain of function paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4524054/ And searched the the grants cited on NIH Reporter: R01AI089728 - Li Fang, University of Minnesota. No subawards listed. R01AI110700 - Li Fang University of Minnesota, Robert S Baric University of North Carolina Chapel Hill. No subawards listed. Color me shocked that this five minute search shows no NIAID money went to the Wuhan Virology Institute, and Rand Paul is full of shit.
  7. The entire NIH grants database is searchable. Here's the results for Wuhan University. Two R01's awarded to the same PI for AIDS related immunology research. Here's the Chinese Academy of Sciences results. None awarded by the NIAID. That took all of two minutes to disprove. Unless, another institution gave the a subaward from their NIAID grant, but the fact the author's name is not given, the paper not cited and the grant number isn't stated, it's rather impossible to verify that situation.
  8. https://www.medrxiv.org/content/10.1101/2021.02.25.21252415v1 "Applying this approach to published data from the RCT of the Moderna vaccine, we estimate that one dose of vaccine reduces the potential for transmission by at least 61%, possibly considerably more." It would appear that the assumption that at least the Moderna/Pfizer vaccines are likely to provide some level of sterilizing immunity, although data on whether these vaccines are indeed "leaky" and to what extent they prevent transmission is an open question. Furthermore, the heterogeneity of vaccines, and the mechanisms of these vaccines being concurrently distributed has significant implications for the likelihood of the evolution of widespread escape and virulence mutants - insofar as the likelihood is drastically reduced by the implementation of a diversity of vaccines. https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(21)00202-4/fulltext It would seem that an assumption that COVID vaccines do not prevent transmission and therefore are only indicated for high risk individuals would be, at best, premature.
  9. A prima facie critique that stood out to me was the application of a "universal" p-value to every scientific study would seem ignorant to the fact that the multitude of data types, statistical methods etc. have a mind boggling array of sensitivities, assumptions, nuances, etc. A p-value of 0.01 could be meaningless (looking at you, GWAS) or impossible to achieve dependent on your particular hypothesis, data and analysis method. The whole advent of p hacking demonstrates how a one-dimensional approach to hypothesis testing is problematic.
  10. Not to mention the insane level of HIPAA/IRB violation publicly posting your research subject's names on a public forum, then suggesting people dox them to verify the research. OP - Delete the file. Learn to anonymize data. Get an IRB approval for human subjects research. Posting first and last names with morphometric data is probably illegal where you live, and no one in their right mind will publish it, let alone give you a prize. Edit: I quarantined the post. This is a textbook example of why human subjects research requires ethics approval.
  11. 1) The current model of academic publishing is a #%&ing scam. Nowhere else would the creators of a product not only be expected to sign over their copy rights for free, but also perform the review and editing of others work for free, and have our institutions get financially reamed for access to the #$^ing work we created there in the first place. THEN, with the advent of open access publishing, they get to tack on fees to the tune of $USD 11,320 upfront to the %^(&ing authors. It's really no wonder that the profit margin in academic publishing is ~40%. 2) While the idea of open science is generally admirable and beneficial, oftentimes the implementation has been exclusionary, elitist and rife with gatekeeping. See "bropen science". 3) While I see the benefits of preprint servers, and I really do like the fact that money isn't changing hands when you publish an article on one, I don't believe they replace the peer review process. The explosion of really crap COVID19 studies being submitted to preprint servers highlights the problems with omitting peer review to speed up the publication process. 4) I'm a big fan of double blind review. If there was a journal in my field that a) didn't charge an open access fee b)didn't charge a viewing fee and c) implemented a rigorous double blind review process, I'd probably publish there exclusively even if they had a barrage of loud, popup ads for penis pills on every page. 5) Whoever is behind sci-hub is a gift to humanity.
  12. I'm a tenure track professor. I usually get somewhere between 50 and 100 emails a day. I allocate about 45 mins twice a day to responding to them. I sort them by importance, then I answer in order until the time is up. Then I delete the rest. Emails go unanswered every day because I could literally spend the entirety of every single day responding to them, and I have teaching, research and administration to do. I tell my students that if it's important, send it again and tag it as important, or if it's important AND urgent, bang on my office door or call my phone.
  13. You've posted zero evidence to support your speculation that CBD consumption reduces the risk of COVID19, or any other infection. No one claimed that. The risk of anaphylaxis due to the Pfizer and Moderna vaccines is approximately 100,000 to 1, as previously cited. You also have the option of non-mRNA vaccines like the AstraZeneca, Johnson & Johnson and Sputnik vaccines. It's a blatant strawman argument.
  14. Instead of word salad, logical fallacy and articles about the well established anti-inflammatory properties of CBD, please provide a single piece of evidence that CBD reduces the incidence of any infectious disease. If not, we're kind of done here.
  15. 1) I accept that CBD has anti-inflammatory properties to the point where we give CBD to our arthritic dog every day. It's also great at treating the side effects of chemotherapy, and there's some preliminary mouse model evidence is can slow tumor growth. CBD has some very promising medicinal properties but none of them are preventing or treating COVID. The suggestion is just false. 2) You have presented zero evidence to support CBD having antiviral properties. The onus is on you to back up your claim. 3) You haven't articulated any specific risks associated with mRNA vaccines. The fact you seem to be suggesting that "mRNA editing" is a risk insinuates that you fundamentally misunderstand how genetic transcription/translation works. 4) The suggestion that mRNA vaccine associated mortality outweighs COVID mortality makes me wonder how humans that bad at math function. Do you pull a dollar out of your pocket and yell "Wow I'm a millionaire!"? 5) LMAO at drinking pot leaf smoothies as an alternative to vaccination. At least use some bud and make canabutter with it to put in your edibles.
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