Arete

Most empirical examples of adaptive evolution in viruses do not involve vaccines. As stated previously, viruses are not solely RNA based. There are DNA viruses, and some (e.g. lysogenic bacteriophages) switch between RNA and DNA. As previously stated, viruses do not necessarily share a common ancestor with prokaryotes/eukaryotes/archaea. There is no prediction under evolutionary theory that a virus could or would evolve into another kingdom of life. Given we're discussing virus evolution, I imagine not.

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1) Virus genomes can be dsDNA, ssDNA, dsRNA or ssRNA. They can also be linear, circular, segmented or continuous. 2) Directional selection of mutations in viruses can be measured by directly rate of replication. If a mutation increases replication rate, its effect on fitness is positive, if the effect is reduced replication, the effect is deleterious. No change to replication, neutral. 3) Of course selection is environmentally dependent. Mutations can result in life history trade offs where they are beneficial in one environment, but detrimental in another. E.g. increased host range at the expense of thermotolerance in Vesicular Stomatitis Virus. 4) The main mechanism, at least for SARS-COV-2 for the evolution vaccine escape mutants is mutations to the S protein which reduce the binding efficiency of vaccine derived antibodies. If the S protein changes shape, the antibodies selected for by the vaccine don't adhere as well to the novel variant, and the immune response of the host not as effective. Commonly referred to as antigenic variation. 5) The evolutionary origin of viruses is not well elucidated and likely resultant from several independent sources. Standard evolutionary theory would not predict a virus to evolve into a different kingdom of organism, nor necessarily infer common ancestry with prokaryotes/eukaryotes/archaea. We do regularly observe the evolution of novel viruses, especially via interviral recombination (e.g. the recombination of John Cunningham Virus and Epstein-Barr Virus to produce novel variants).

While I don't think one can generalize about everyone's reason for refusing the COVID vaccine, there certainly are a number of widely circulated, obviously false conspiracy theories about the COVID vaccines, many of which involve mind control.

So, my son went through a phase where he would refuse to brush his teeth. He'd claim it "hurt" or it "tasted yucky", but the reality was he just vying for independence and didn't like being told what to do and when to do it. Fortunately he outgrew the phase at age 4. If you're not getting vaccinated, despite the clear and unequivocal evidence that it's beneficial to you and those around you simply because you don't want to be told what to do, you're being childish. A less childish approach would be to separate the two issues - It is possible to oppose government mandates without refusing an obviously beneficial prophylactic vaccine to the detriment of self and community.

I guess as a general statement - infectious diseases fundamentally operate at population scales. Individual co-operation with public health measures have unavoidable implications for the population as a whole. The individual choice to get vaccinated, wear a mask, social distance, etc or not has a probabilistic impact on a pathogen's transmission and virulence properties. Those properties dictate how the disease spreads and how sick it makes people. This of course generates an intrinsic conflict between individual rights, and public health priorities. On the other hand, there's stop signs, red lights, hazardous waste disposal laws, fire regulations, etc. so it's not exactly unprecedented that you may be expected to suffer minor inconvenience for the wellbeing of others, and people don't seem to get all righteous about their FrEeDuM to be a selfish, childish prick that endangers other people when it comes to those other circumstances.

Being an Australian but living abroad I've been loosely following and enjoying the bureaucratic bungling of the whole issue by Scotty from Marketing and his administration. It has been a very publicly embarrassing debacle, which given my general sentiments towards the Liberals, is quite the popcorn feast. I do keep reading about Djokovic sticking by his principles/being principled, and thus being of strong moral fiber... but if you undergo some kind of action to publicly take a stand on a given issue, then attempt to subvert or otherwise avoid the consequences, you're just a garden variety hypocrite. If this really was the hill he wanted to die on, he should have boycotted the Australian Open in the first place. I also have to admit I have a particularly malevolent attitude towards public figures who use their position of privilege to flout and undermine public health efforts in the midst of a pandemic. You may as well be supplying arms to terrorists or dumping oil in the arctic and bragging about it.

You're way nicer than me. I stop grading the paper/exam, fail it, fill out the online academic misconduct report form for the dean, then send the student the boilerplate "You have been formally sanctioned for breach of the academic integrity policy" email. I just don't see any point wasting my time grading work when a student has cheated. I almost have to grudgingly respect the audacity when on the rare occasion a student I caught cheating requests to join my research group.

The students I teach are predominately pre-med, and the stakes are high. They are all paying a lot to be there, need straight A's to get into competitive medical programs. and not all of them are straight A students. Some students will go to extraordinary lengths to try and get that A, including harassing/stalking their professors, cheating, trying to find loopholes in university policies, etc and so on. My take is this: a) I'm there to teach the course, not police the academic misconduct policy. Some students will cheat in my course and get away with it - but I'm not going to run sting operations and deliberately try and catch cheaters, because ultimately it's a waste of my energy which could be spent on better quality teaching and pedagogy. b) If I do catch a cheater (which happens at least once a semester), I don't screw around. You fail and get formally reported for a academic misconduct. I block your email/phone number. You appeal to the dean if you don't like it. I don't give warnings (aside from in the syllabus) "just this one time" or other half measures. If I catch you it's extraordinarily likely this ain't your first rodeo. I trusted you, and you treated me like an idiot - you wrecked your GPA/lost your scholarship/ruined your graduation plans, not me. c) I don't take it personally or get upset about it. I get that this is a deeply flawed system, and the motivations to cheat. I also get that my upper division elective is just not that important in the long run, and I won't get worked up being the integrity gatekeeper of the academic world. I give my students the benefit of the doubt, and try to get on with being the best instructor I can.

The irony of your use of the word "evolve" is quite amusing.

And you have preferred, unbiased collective term for these, or you're expecting them all to be listed each time they are referred to?

Alright, what's you preferred, non- "PC filtered" term for all possible trait states that may result in an ambiguous determination of sex?

And here I was thinking I was using an collective term, frequently used in the scientific literature to describe the diversity of intersex conditions when I should have been writing them all out as an exhaustive list to avoid being the social justice warrior PC police. Apologies, won't happen again. Btw, anyone have a list of every possible color between green and blue? RIP the word count on this lizard manuscript.

There are two, binary GAMETES in an XY mating system. Gametes are distinct from sex - many diploid organisms have two gametes and zygotic states that are generally hermaphroditic. Sex is not defined by gametes and includes both physiological and chromosomal properties, in which there is clearly diversity beyond two binary categories. You can argue semantics about where to draw lines on a spectrum forever. Some critics of the Fausto-Sterling paper state that X0 individuals are female - others disagree, which I imagine depends on your perspective and the scientific utility of categorization to your particular field of study (e.g. a geneticist vs an endocrinologist vs a sociologist etc.) , and has analogous discussions across the sciences - e.g. taxonomic nomenclature.

Some X0 individuals can successfully fall pregnant. A proportion of XXY individuals produce viable sperm. Plenty of XX and XY individuals are sterile. So sex isn't well defined by successful reproduction/production of viable gametes either. Generally those studies only consider true gonadal intersex (i.e. XY karyotype with ovaries and vice versa) to be defined as intersex. It's not my field of study and there appears to be plenty of contention, but it does appear to be the most widely accepted figure, if you go by say, the UN office of Human Rights, or the Intersex Society of North America, for example. The ISNA page has a breakdown of specific intersex conditions included, and I cited the actual peer reviewed paper in my previous post. I would say it appears credible, but doesn't account for population variation - for e.g. It does not test if the rate of intersex births differs between say, North America and East Asia.

Ok, So a person born with a single X chromosome is not karyotypically male (XY) or female (XX). They have female gonads, and can typically reproduce with fertility treatments, but often display masculine secondary features. Typically, they have a female gender identity, but not always. Ergo, such a person exists in a genotypic/phenotypic state between the general definitions of male and female. The medical diagnosis they would generally be given is that of Turner's Syndrome. Yes, they are medical diagnoses of intermediate states. As an analogy most humans have 46 chromosomes. Some have 47. They are typically diagnosed with Downs, Edwards, Patau etc Syndrome - just because there are medical diagnoses for trisomies doesn't mean that ALL humans have 46 chromosomes - because people with 47 chromosomes do exist. Yes I am, and no, it's not about inclusiveness necessarily - it's simply factual accuracy. Intersex people exist, which means that sex is non-binary for a proportion of humans. Stating that they somehow don't count because of the associated diagnoses for these states doesn't make people with Turner's, Klinefelter's AIS etc disappear. As I alluded to previously, you wouldn't throw all the cyan lizard specimens out the window just so you could put the lizards into jars labelled blue and green, so why would you do it with human sexes?

I mean my first post in the thread contained citations with examples, the infographic contains dozens of examples of intermediate trait states, other threads have included numerous examples... If I am to be somewhat presumptive, and I apologize if I'm wrong, if your argument is that these individuals should be excluded based on them being "abnormalities" or "disorders", then yes, I agree that sex becomes binary and fixed if you choose to ignore all of the circumstances in which it doesn't. If you were sorting green and blue lizard specimens in the museum and you threw the one in fifty that was cyan out the window, the lizards would all indeed be blue or green. The arrows indicate potential changes in trait state that may occur with changes in life history or therapeutic intervention. E.g. at conception, an XO indivdual is Karyotypically 50/50 between male and female, at birth they have female gonads, but take on masculine secondary sexual characteristics during puberty. I think regardless of how you define it, at the end of the day it's rather difficult to define sex as binary in any biologically accurate context. The most widely cited proportion for intersex births is 1.7%, although depending on how you define intersex, estimates can range from 0.001% to 4%. At the end of the day, biological classification is messy. I mean even if you go to the gametes - I have a friend who studies selection in sperm morphology - there isn't even a typological definition of sperm that holds universally true. Trying to put virtually anything about nature into binary categories is going to be an oversimplification of existent diversity.

Every one of the boxes that describes a phenotype/genotype that lies between genotypically/phenotypically male phenotypically/genotypically female at either end of the chart. The temporal axis, along with the arrows demonstrates how an individual can transition between states at different life history stages. Ergo. while there are two sexes, they are neither binary nor temporally fixed - so there are a minority individuals to which the question "Are you male or female?" would be "Neither." The biology reality of that is unequivocal.

No. Conception, birth and puberty are the temporal axis to the chart.

When you make up arbitrary criteria to state that the intermediate states don't count, you have two binary categories. Yep. Spot on.

As general rule, yes - with a significant number of caveats. Again, as a general rule virulence (i.e. how sick you make your host) is correlated with replication rate, but negatively correlated with transmission (i.e. the sicker you make your host, the fewer other susceptible hosts they will encounter). As a result, a pathogen will generally evolve to favor high transmission and low virulence over time, unless - 1. Multiple infection: if an individual is infected with multiple strains, the fastest replicating strain will generally outcompete those that replicate slower, thus the predominant strain of the pathogen will generally end up being the most virulent. 2. Multiple hosts: if a pathogen infects multiple hosts, its virulence in an individual host plays a lesser role in governing transmission, thus there is less downward selection pressure on virulence. 3. Partially vaccinated population, non-sterilizing vaccine: If a pathogen's virulence is lowered in a part of the host population via vaccine acquired immunity, there is less downward selection on virulence, as vaccinated individuals can contract and transmit the virus effectively, even if the virulence is high in unvaccinated hosts.

Fungi have tens of thousands of sexes - theoretically up to 36,000. Humans have an XY chromosomal mating system - meaning there are two sexes. However, these sexes are not binary, nor fixed in a small but significant number of cases. "This article began by asking how frequently members of the human population deviate from a Platonic ideal of sexual di-morphism. A summary of the frequencies of known causes of sexual ambiguity based on Tables 1–7 appears in Table 8. The grand total is 1.728% of live births." There are also both biochemical and genetic causes of sex plasticity in humans - i.e. physiological changes that occur post birth that alter sexually dimorphic hormonal and physical traits. E.g. there are a known suite of loss-of-function mutations that can result in male to female sex reversal in humans, and studies of endocrinological plasticity have shown that the "hardwired" neurological difference between males and females are not as well defined or temporally stable as once thought.

Hopefully you never have to interact with a member of the trans community, because they wouldn't deserve to be subject to your outbursts.

Well there's this: Several pages back you were arguing against the prevalence of intersex individuals. Now you're excluding "real" transgender people for your argument to try and give it some form of credibility, which is problematic; 1. You're missing the point that the grey area between sexes is well, grey and not easily classifiable. 2. Why do YOU get to decide who's a "real" transgender person and who is not? 3. How are you going to determine who is "legitimately" non-binary, and who isn't? Does a hormonal imbalance count? What about if one is XX/XY, but gonadally intersex? What about if their external appearance is gender conforming? What if the underlying genetic basis of someone's gender mismatch is not karyotypic variation? What if the determinant is developmentally triggered epigenetics? Even if it was down to environmental response, why would/wouldn't that be legitimate? 4. So, if there are "legitimate" and "fake" non-binary people how are you going to tell? Ask them to drop their pants for inspection? Provide you blood tests in triplicate? A print out of genetic test results? My position is not determined by my institutional conditioning as your appeal to motive fallacy would suggest (incidentally, the same argument is used by climate change deniers and antivaxxers), but by my understanding of biology. Biology is messy. Exceptions to human derived, arbitrary categories universally exist. The existence of transgender and non-binary humans is entirely unsurprising to me and entirely uncontroversial. If people can be legally protected from discrimination because they believe in magic underpants, then gender identity should be protected too.