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Comment Re: 6 fold reduction in antibodies (Score 1) 94

Handwashing does both. Soap's mechanism of action is twofold: first, it is made of fatty acids which causes bacterial cell lysis by chemically reacting with the cell membrane (which is a lipid bilayer), bursting it open. Second, it has excellent ability to emulsify oils in water--in other words, it removes dirt and grease by attaching itself to both and allowing grime to be washed away by mechanical action. It's why, if you get oil on your hands, just rinsing with water is not going to do much. Our skin has a tough layer of dead cells that protects us from the cytotoxic effects of soap.

The reason why bacteria cannot (for the most part) evolve resistance to soap is because there is no real effective defense against it. One way would be to make an endo- or exospore in response to hostile environments. But this doesn't happen fast enough upon contact with soap, and even if it did, the mechanical/emulsifying action will simply wash the bacteria away.

So now that we know why soap works, it becomes apparent why putting antimicrobial agents like triclosan into soap as a marketing gimmick is unnecessary.

Soap really is a fantastic invention.

Comment Re:6 fold reduction in antibodies (Score 1) 94

The (imperfect) analogy I had used earlier is about thinking of the global human population like one giant host, and each individual human is like a cell of that host. When I speak of "diligent" mask use and social distancing practices, I am not talking about the individual risk of infection despite adherence. Rather, I am talking about the proportion of the population with proper and consistent compliance that is required to substantially reduce transmission in that population. "Partial protection" therefore does not refer to the individual degree of effectiveness against becoming infected if one adheres to social distancing and mask wearing. It refers to the fact that some people are not doing it, or doing it correctly, or have gotten tired of doing it, thereby sustaining transmission in the population.

It is an understandable consequence of human nature to think of this pandemic in terms of individual actions and the consequences to oneself, but this is one of the reasons why the pandemic remains uncontrolled, because most individuals are unwilling or unable to conceptualize the risk in terms of the collective actions of everyone in their community.

Comment Re:6 fold reduction in antibodies (Score 5, Insightful) 94

It's a combination of two things: high prevalence in a population, and selection pressure favoring mutations that are able to infect others even when social distancing and mask wearing is observed.

Think about it like bacterial resistance to antibiotics. The total number of mutations per unit of time is proportional to the bacterial load. The more bacteria, the higher the probability that there will be a random mutation that improves fitness. Now, consider what happens when antibiotics are introduced: if the antibacterial effect is not complete, then the antibiotic is merely selecting for those mutations that result in the bacteria being able to better evade it, until that strain becomes dominant, at which point a second- or third-line therapy is needed. This is sometimes why combination therapies are used--you're hitting the bacteria with multiple agents, achieving the reduction of bacterial load to the point where mutation rate is not high enough to develop resistance, and at the same time, making it more improbable for mutations to be able to evade those agents.

So when we think about how the novel coronavirus is mutating, it is obvious that it is not simply that more people are getting infected; it is that they are getting infected despite circumstances that are intended to limit transmission. That is not to say we should stop social distancing or wearing masks or practicing hygiene; rather it is a reminder that these practices are not the end-all and be-all to stopping the virus. Distancing is not a magic bullet. It is a temporary change in our behavior that, if not adhered to diligently, only confers partial protection, just like improper antibiotic use. And the solution to ending this pandemic is the same: combination therapies, or in this case, combination tactics. Highly effective vaccines, new formulations of vaccines to address mutations, social distancing, mask wearing, proper hygiene, economic relief, restrictions on travel, contact tracing, isolation/quarantine measures, increased testing, viral genome sequencing--all of these need to be done, and done well, in order for the pandemic to stop. Half-assed approaches at best only buy a little more time and at worst are ineffective, create resentment, and cause further noncompliance.

Comment Re:This is undoubtedly low. (Score 1) 263

The model that I've been following most closely is https://covid19-projections.com/path-to-herd-immunity/ by Youyang Gu.

His models proved to be highly accurate back in the spring of 2020, when there was relatively little information about the epidemiology of COVID-19. In particular, he criticized what he felt was low-quality and inappropriate assumptions made by other, more authoritative outlets like IHME.

Around the middle of last year, I was estimating that the prevalence ratio was somewhere around 3 to 5. I think the current estimate of 3 is a reasonably close figure, which would put the total proportion of Americans who have been infected at roughly 25% as of this writing. The prevalence ratio in the initial stages of the outbreak was substantially higher because of lack of testing; however, this has changed.

To comment on a child post reasoning that the actual number of infected people is not that much higher than the confirmed cases because otherwise the rate of new infections would not be as high as it is now, I would like to point out that the confirmed cases have are delayed in time, thus reflect infection rates that might be lagged by as much as a week or so. But more importantly, there are multiple factors contributing to the effective reproduction rate R_t, not just the number of previously infected/recovered individuals. Even at a proportion of 25%, that leaves 75% of the population on average who remain susceptible, and combined with lower public health order compliance (i.e. people getting tired or lax with wearing masks and distancing), as well as selection pressure favoring more highly contagious strains of the virus, it is entirely reasonable to see a continued high rate of confirmed cases even with a quarter of the population already infected. Note that estimates of the herd immunity threshold are around 65% and may actually need to be revised even higher due to the more contagious British and South African strains.

My projection is that about 40 to 45% of Americans will have been infected by the time we reach herd immunity. This is higher than what is predicted by Youyang Gu. I also predict that the number of confirmed US deaths due to COVID-19 by that time will be around 600-700k, and that total excess deaths will be around 800-900k, with an eventual total excess deaths exceeding 1M. The long-term public health impact will not be known for several more years, by which time we will have a better understanding of how symptomatic and to a lesser extent asymptomatic infection with nCov-2 influences long-term clinical outcomes.

Comment Re:Side Effects (Score 1) 243

I am very glad to hear that you caught this serious side effect early and took immediate action to address it. Not everyone who takes medications is as self-aware about such things.

You are absolutely correct that FDA approval of a drug or biologic does not ensure safety. In many cases, it doesn't even ensure efficacy! The thing to understand is that it's impossible to develop a treatment that works for everyone and is safe for everyone in the indicated population. While drug companies and the FDA generally strive to meet this goal, the realities of biological variation is such that almost universally, drugs are approved on the basis of evidence that, on average, they are safe and effective. But that's on average--there will be patients who do not benefit, or worse yet, are harmed. Where that risk-benefit profile lies is something that we can study and estimate for a large cohort of patients, but it is by no means a guarantee for the individual patient response. This is something patients need to understand, and is why it is not only the drug manufacturer's responsibility to convey this information through labeling, but also the physician's duty to help educate the patient, rather than simply being a diagnosis and prescribing machine. After all, a computer could do those things. What is needed--and is often lacking in the American health care system--is a physician that takes the time to explain and educate. Patients also have a responsibility for their own health too: they need to be invested in their own care, to monitor their health, as you clearly do, to ask questions, and to not merely take medications blindly.

In regard to a potential vaccine against COVID-19, I understand and to a fair extent agree with your hesitation. One should be skeptical about any novel treatment or medicine. That said, there are a few things we should note about the differences between vaccine trials and drug trials. A typical drug for a serious condition may be approved on the basis of data from maybe a few thousand patients across the entire development program. Generally speaking, the more serious or rare the condition, the fewer the total patient-years of exposure data are needed. So a cancer drug might be approved with only a few hundred patients' worth of data, but a cosmetic drug like Botox would need tens of thousands or more patients.

Where does a COVID-19 vaccine fall on this spectrum? Well, on the one hand, there is a clearly urgent unmet need, and many people worldwide are currently infected, with substantial impact socioeconomically. This argues in favor of fewer data. On the other hand, such a vaccine would be administered to otherwise perfectly healthy people, including special populations such as children and the elderly. Most importantly, the indicated population is immensely broad--essentially almost anyone who is not immunocompromised. Therefore, it is necessary to accrue a large amount of exposure data in order to detect extremely rare but serious adverse events. This argues in favor of more data. If such a vaccine had a 0.001% chance of causing serious injury, that's somewhere around the order of 50000 people who would be injured by this vaccine globally that would not have been otherwise. You may say this is acceptable since the risk of COVID-19 mortality is substantially greater, but that is little comfort to those unlucky individuals who are maimed by a vaccine. This kind of reasoning is what is used in a rather distorted way by anti-vaxxers to justify not vaccinating, which is why vaccines in practice must have even lower risks of serious harm. But to even detect one case of such injury at an incidence of 0.001%, you would need to expose on average 100000 people; and to gather enough clinical data to suggest a causal relationship, you'd need to expose millions. That's simply impractical in a controlled trial. In the meantime, it may take a very long time to more accurately assess the risk profile for such rare events.

Although it is generally true that later generations of a treatment tend to be safer, it is not always the case, especially when compounds with different mechanisms of action are developed in parallel. In closing, I would personally suggest (this is not medical advice) that depending on your own risk/benefit evaluation, you make a decision on how long you would be willing to wait to be vaccinated once a vaccine is approved. The biggest argument in favor of early vaccination is that the ones currently in development are not capable of causing COVID-19, and depending on their technology, are mechanistically unlikely to cause lasting side effects. This is in contrast to early polio vaccines that used attenuated poliovirus that carried a nonzero risk of active polio infection, for instance.

Comment I work in drug development (Score 5, Informative) 243

And here's my take based on what I've seen so far. Bear in mind that as the science progresses, the situation may change and the opinions I present may need updating.

Having years of expertise in applying biostatistical principles to clinical trial data in support of approval of novel therapeutics, I have been paying close attention to the recent early phase studies of the nCoV-2 vaccines currently being investigated. The first thing to understand is that to date, no confirmatory trials have been completed. All data that have been presented thus far have been from preliminary, hypothesis-generating/dose-finding studies.

Under the current accelerated approval pathway for these vaccines, it is entirely possible that a suboptimal dose may be approved for use, given our ongoing lack of understanding of how strong an immune response is needed to confer protective benefit. In other words, the earliest vaccines approved to prevent COVID-19 infection may be stronger than what is required to protect the individual while minimizing adverse events.

Second, only through large-scale confirmatory studies will we have a better understanding of the safety profile as well as the efficacy. Currently, I would say that the adverse events reported so far are generally a tolerability concern, not a safety issue. Having a fever or injection site pain, as long as these do not require hospitalization and do not generate long-term adverse health effects, would most likely be considered acceptable. The main safety concerns for any compound would be things like toxicity or organ injury. In this case, we would want to pay special attention to hypersensitivity reactions leading to injury. This is because there is evidence of a correlation between COVID-19 mortality and immune system hyperstimulation--the so-called "cytokine storm" that is treated with immunosuppressants to avoid damage to healthy tissues. And the high fevers that are reported as a result of vaccination is a possible sign of such a reaction, as well as potential evidence of efficacy.

Third, we have yet to determine the posology of these vaccines in relation to risk of infection, duration of response, and safety/tolerability. For example, some vaccines need "boosters," such as the HPV vaccine. Some are reformulated for each strain that becomes prevalent in a given season, such as for influenza. Some are administered once and that's enough to confer lifelong or nearly lifelong protection. Then the dosing of each injection is not finalized. Given that natural immunity arising from actual infection and recovery is likely to wane over a time scale that is measured in months and not years or decades, it is more likely that any successful vaccine will need to be administered multiple times in order to have sustained benefit.

I personally believe--and this is without any hard evidence--that an effective vaccine will not only cause adverse events such as fever, pain, and fatigue, but will need to do so, because these are signs of elicitation of an adequate immune response. Thus, the correct dosing and administration will only be determined with time. My main concern is that vaccine efficacy could be compromised as a result of incomplete adherence, noncompliance, and/or incomplete protection resulting in selection pressure for the virus to mutate. We have evidence that nCoV-2 is more easily transmissible than other respiratory diseases such as influenza; moreover, the existence of asymptomatic infection is another reason for concern for long-term control of COVID-19 through vaccination.

The bottom line is that it is still too early to be worried about the reported safety profiles from these small trials, because too much is still unknown, there isn't enough subject-years of exposure, and there isn't yet conclusive evidence of clinical benefit in the form of reduced risk of infection. We don't even have an estimate of the reduction in risk. The only efficacy data we have is antibody levels, and that is a surrogate for the real efficacy endpoint, which is the reduction in risk of infection as measured by a time-to-event analysis.

Comment Re:Stop using Facebook, problem solved (Score 1) 207

I block all Facebook-owned properties at the hosts file level and/or at the VPN level (for devices I cannot modify hosts). The only thing I haven't done is use a Pi-hole. Before COVID-19 I didn't see much point, but now that nearly all of my internet traffic is going through my home network, I am revisiting the idea. On all my devices, I can't load anything from their websites even if I wanted to, which I don't. So I don't see any ads. I'm not complaining about their ads because I block that shit from even being served. If the tradeoff is that I can't see someone else's instagram post or read their facebook feed or see a calendar invitation, I gladly accept that and have accepted it for at least the past 5 years. When my friends use this method of communication, I tell them flat out that I won't see it and they're going to have to use another way to loop me in. If that makes me a jerk in their eyes, I don't need their friendship.

So, what I am complaining about is the fact that I can't block everyone else--my employer, my friends, my family--from voluntarily uploading my personal information to their servers. Your viewpoint is a bit like the proverbial ostrich with its head in the sand--just because I don't see it doesn't mean I'm unaffected by it. It can't be helped, so why worry? Well, the way I make my stand on the issue is to do everything I can to block their sites and tell everyone I know to do the same.

Comment Re:Stop using Facebook, problem solved (Score 4, Insightful) 207

The problem is that the information they give to Facebook includes non-users' personal information, such as their names, contact information, address, dates of birth, etc. The only way to protect my information from being used to connect the different people I know in my life is to not give them my personal information at all. That's not feasible unless I want to have zero friends. They blindly upload their address books.

And then let's talk about their trackers. Every fucking website has a Facebook tracker on it these days. Yes, there are ways of blocking these, but this whole "just don't use Facebook" attitude is simplistic. I can't go into my work computer and prevent those trackers from loading on work-related websites. It's maddening how deep their reach is. Not having an account is just the bare minimum of what one must do to avoid having them track you, and most of what they get comes from your idiot friends who don't care. I've tried patiently and calmly educating, explaining...it all falls on deaf ears because they are addicted. It's like trying to explain to a meth or heroin user why their addiction is bad. They know, but they can't stop themselves from enriching bowl-cut Zuck's pockets so he can buy another Hawaiian island with all the dirty money he gets.

Comment Smaller class sizes (Score 1) 252

It's all too predictable that most comments are focusing on the "rich" versus "poor" debate, which completely sidesteps the real issue of the lack of quality education in American K-12 schools.

This is why smaller class sizes are important, not because smaller classes are easier to manage in the classroom, but because they enable instructors to actually devise and grade homework and tests that aren't easy to cheat. I see the comments that call for such tests, but fail to appreciate that in a high school environment, a single teacher could have well over 200 students, with no TAs. Imagine having to grade 200 exams on top of a full classroom schedule. Each assignment is a mountain of work to grade, especially if carefully designed to test understanding. And then to craft them so that they are different for each class, and sometimes different forms within a class.... A university professor has the benefit of graders, TAs, a teaching schedule that is more relaxed, and more mature students with fewer behavioral problems that require parent-teacher interaction.

I don't fucking care about whether Apple Watches are a sign of social class, or the political subtext such a statement might imply for the reader. The fact that we have cheating facilitated by technology is nothing new. The point is that teachers in America are expected to impart valuable critical thinking and reasoning skills to the next generation while being paid paltry salaries compared to far less stressful and time-consuming jobs in the private sector, while getting blamed by everyone from politicians and parents--and the students themselves. Meanwhile, class sizes continue to grow because of fiscal mismanagement and corruption, and lack of investment in education. Americans like to talk about how important education is, but when it comes down to spending taxpayer money, they'd rather build missiles and walls because fear sells shit to an uneducated and easily deceived public. So is it any wonder that we are in this situation? Who the fuck cares about whether a kid having an Apple Watch means they're rich. I care that a cheating student is in all likelihood going to grow up to be yet another irresponsible, uneducated, entitled, egocentric American whose corporate overlords can manipulate at will. Downvote me all you want. Call me a troll. I don't fucking care anymore.

Comment My objection (Score 0) 511

After seeing how the test was carried out, I find that the issue I have with the alerts is that they are causing phones to screech quite loudly in a staggered fashion. I was in the middle of a conference call at work, and some of the attendees are outside of the US, so they had NO idea what this sound was that kept interrupting the meeting. One person's phone would start going nuts, then another's, and another's. The total interruption to the meeting was over a period of about 10 minutes.

Since I had heard about the test in advance, I turned off my phone (something I rarely do) shortly before the scheduled time, and kept it off for about 30 minutes to be sure. And I just kept hearing everyone's phones in the office going off at different times.

Yes, I understand that the carriers can't ensure that these alerts are received at exactly the same time. Yes, I understand that there may be a legitimate need for them, and in an emergency, it can be critical. But the implementation leaves much to be desired. It doesn't need to be as disruptive as it is; it doesn't need to be as obnoxious as they are. People are already addicted enough to their phones; in an age where everyone has them glued to their hand, where we scarcely pass a few minutes without checking them, it is not necessary nor desirable to have a mandatory alert wailing at full volume, because people already devote a lot of attention to their phones. The hearing or visually impaired have ways of using their devices. The way these alerts are designed is a relic of a bygone era, without consideration for the way we use technology now.

Comment Re:Pedestrians (Score 1) 136

They can afford a smartphone--that's how one reserves the scooter. So don't tell me that they can't afford a bike. That's not to say it should be a $5000 fine, but it should be high enough that even the rich and entitled Bay Area brats that are commonly seen recklessly tooling around on these scooters would think twice about zipping around on a sidewalk. For a lot of these riders, even $5k is not that much money. Ideally, traffic fines should be a percentage of your income, like they do in certain Scandinavian countries.

Comment Pedestrians (Score 1) 136

Where I live, scooter riders almost always ride on the sidewalks, which are already very narrow. They almost never wear helmets. I have seen several instances of two people squeezing onto a single scooter. I have seen falls and accidents. I've seen pedestrians get hit. Almost every day I walk around in my neighborhood, some scooter rider whizzes by me, unannounced--I can't hear them coming, and they get within inches of me.

Whether or not a law is passed to regulate the use of these motor vehicles--and they ARE, by construction, motor vehicles--is irrelevant, because the users have already become accustomed to riding them on sidewalks, leaving them wherever they want--often obstructing doorways and walkways, wearing them without helmets, and so forth. The only way this will change is if the police start handing out $5000 tickets and court appearances for violations. Just having a law isn't enough--it is the enforcement of existing laws, with penalties steep enough to make users painfully aware to change their behavior, that will have an effect.

On the flip side, requiring that these scooters be on the roadway is also problematic because now the drivers have to watch out for what amounts to a 15 mph pedestrian sized object weaving in and out of traffic, making illegal turns, not having signals or mirrors, and so forth. They're smaller than a bike rider, and because scooter riders are casual users who do not have to expend energy to power themselves, they are less likely to obey traffic laws. But at least if someone gets injured, it'll be the idiot on the scooter.

I don't want to become a statistic. These things are so quiet and move so fast, that I can't possibly react in time to avoid them while walking around my neighborhood. Moreover, my neighborhood is filled with bars, so consider the combination of public intoxication with electric scooters. The bottom line is that sidewalks are for pedestrians ONLY. You are a pedestrian if you are walking, or you are in a wheelchair. It is only a matter of time before a child gets mowed down by one of these.

Comment I teach both (Score 1) 180

Each has its advantages. A calculator obviously can get you very precise numbers for critical values, probabilities, and the like. For those learning statistics though, teaching how to use a table helps to slow students down, reinforce their understanding of what they are actually doing, and facilitates a conceptual connection to the underlying probability distribution. It is very easy to mistype the wrong number into a calculator, or use the wrong function, or fail to calculate the probability of the appropriate tail(s). So by forcing a student to use a table, it helps them to think about what they're actually looking up. It's not quite the same as using a table of trig functions or logarithms, because those are single-argument functions, whereas a statistical distribution can have a density, cumulative probability, quantile, and/or degrees of freedom. And that ties into another reason to teach tables: unless everyone agrees to use the same calculator syntax, teaching the computation with a specific calculator will make students dependent on that particular syntax. R, SAS, SPSS, Excel, Mathematica--each one uses different syntax for the same computation. Now, tables are laid out differently too, but for the most part, they are consistent and not difficult to understand. Once you've seen one, you know how to use others.

So, I teach both, and I show how you get the same (or similar) results either way.

Comment Re:I generally side with the woman in these cases (Score 3, Interesting) 290

And if you think that I'm just some feminist SJW snowflake, the same thing applies to bullying, something I imagine a lot of Slashdot readers have had experience with. How many of you remember being bullied in school? Having someone more popular, more athletic, more socially adept, treat you like shit just because they thought it would be "fun?" That your day-to-day existence was turned into a living hell for no other reason than the amusement of others?

What was the first thing you thought of doing? You thought you could go to your teachers or parents or principal and tell them everything and that would somehow suddenly make all your problems disappear? How laughably naive does that idea sound to you?

So, why would you think that just because this is about men harassing women that such behavior is any different? That you might think that she did something to deserve this kind of treatment, or that now you expect the victim to write everything down and tell HR right away, when we all know that HR is not there to protect the rights of the employees, but of the company? Now how realistic does that sound, to say that you have to tell HR right away when some asshole spikes your drink with whiskey at work?

Comment Re:I generally side with the woman in these cases (Score 4, Insightful) 290

Why should anyone be SOL for not immediately reporting a problem? Is there some kind of statute of limitations that absolves the perpetrators from liability simply because those who are targeted do not complain right away?

That kind of thinking is exactly why workplace harassment is so pervasive, because what happens is that a culture is created in which prompt reporting is discouraged. You claim to understand why someone "might be uncomfortable reporting these problems." But it's clear that you don't because you immediately follow that with this absurd notion that the victim is not entitled to redress precisely because of those reasons you claim to understand.

These reasons for not immediately reporting are well-known and researched, for example, in cases of rape. While vastly different in severity--by no means do I claim that rape is the same as workplace harassment--the underlying psychology of not wanting to report such offenses is similar. The emotional trauma of being targeted and victimized, compounded by the additional trauma of not being believed, having to immediately retell your story, being expected to remain level headed about your experience, then being isolated from your peers, the focus of gossip and suspicion and talk about whether you did anything that caused you to "have it coming" or "deserve it"--these are just the beginning of a litany of reasons why people do not always do what you seem to blithely suggest one must do in order to be deserving of justice.

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