Coronavirus Tests Science's Need for Speed Limits (nytimes.com) 89
Preprint servers and peer-reviewed journals are seeing surging audiences, with many new readers not well versed in the limitations of the latest research findings. From a report: Early on Feb. 1, John Inglis picked up his phone and checked Twitter, as he does most mornings. He was shocked at what fresh hell awaited. Since 2013, Dr. Inglis, executive director of Cold Spring Harbor Laboratory Press in New York, has been helping manage a website called bioRxiv, pronounced "bio archive." The site's goal: improve communication between scientists by allowing them to share promising findings months before their research has gone through protracted peer review and official publication. But the mess he was seeing on Twitter suggested a downside of the service provided by the site, known as a preprint server, during the emerging coronavirus pandemic. The social media platform was awash with conspiracy theories positing that the new coronavirus had been engineered by the Chinese government for population control. And the theorists' latest evidence was a freshly submitted paper on bioRxiv from a team of Indian researchers that suggested an "uncanny similarity" between proteins in H.I.V. and the new virus.
Traditionally, the Indian researchers would have submitted a paper to a peer-reviewed journal, and their manuscript would be scrutinized by other scientists. But that process takes months, if not more than a year. BioRxiv, medRxiv -- another site co-founded by Dr. Inglis -- and other preprint servers function as temporary homes that freely disseminate new findings. For scientists on the front lines of the coronavirus response, early glimpses at others' research helps with study of the virus. But there is a growing audience for these papers that are not yet fully baked, and those readers may not understand the studies' limitations. Views and downloads on medRxiv, for instance, have increased more than 100-fold since December, Dr. Inglis says. People with little scientific training, or none at all, are desperate for new knowledge to better inform their day-to-day decisions. The news media wants to keep readers and viewers updated with the latest developments. And agents of disinformation seek to fuel conspiratorial narratives.
Traditionally, the Indian researchers would have submitted a paper to a peer-reviewed journal, and their manuscript would be scrutinized by other scientists. But that process takes months, if not more than a year. BioRxiv, medRxiv -- another site co-founded by Dr. Inglis -- and other preprint servers function as temporary homes that freely disseminate new findings. For scientists on the front lines of the coronavirus response, early glimpses at others' research helps with study of the virus. But there is a growing audience for these papers that are not yet fully baked, and those readers may not understand the studies' limitations. Views and downloads on medRxiv, for instance, have increased more than 100-fold since December, Dr. Inglis says. People with little scientific training, or none at all, are desperate for new knowledge to better inform their day-to-day decisions. The news media wants to keep readers and viewers updated with the latest developments. And agents of disinformation seek to fuel conspiratorial narratives.
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Normally I agree, but these "preprint" servers are just absolute garbage. Full of nonsense. It is like submitting Slashdot posts and pretending they are "scientific papers".
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Yeah, you don't start to browse these preprint sites directly unless you want tons of junk. But there are other sites doing an okay job "crowdsourcing" worthwhile papers, by linking to them on arXiv. So they're kinda okay to use as hosting, it's not all junk. You need a good filter.
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You shouldn't. But people do. And that is how these nutty conspiracy theories start because people think it is "scientific". Thus the article. The guy who runs it should just shut them down.
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In severe cases, that goes so far, that *forcing* them to lose that and face reality, becomes a severe act of violence and can lead to a complete shutdown of that person. E.g. a catatonic state, confusable to (higher) brain death at first glance or if the person is really good at it.
It may make life worse for them, but so much better for the rest of us.
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Anyone could always post stories and conspiracies, but the fact that they are posted on site that is related to the scientific community give it more credibility.
Therefore it has made it worse, and ending it should make it less bad.
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Have you ever tried to talk to a conspiracy theorist because it sounds like you haven't. Their beliefs have nothing to do with the alleged scientific validity of the source of their crazy ideas. They believe things for emotional reasons not factual ones. You cannot change their minds through logic or reason. Allowing such people to change how the rest of us do things is not acceptable.
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I have talked to conspiracy theorists a lot. Most of conspiracy thinking is done by perfectly normal people, whether they believe in Russiagate or 9/11 inside job.
Scientific validity is a real problem but how do you deal with cases where you can reasonably assume those involved are doing their best to hide all the evidence? Throw in the towel?
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That's what they have been taught to do. Not trying to absolve the conspiracy nuts, but what do you expect if the way people are taught to learn is rote learning and believing what they're told instead of giving them what's required to tell bullshit from facts?
As long as our schools put more emphasis on regurgitating whatever the teacher tells you, independent of its validity, because the word of the teacher is equated to the word of some deity, as long we won't get people who are actually able to validate
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Yeah, you don't start to browse these preprint sites directly unless you want tons of junk.
That's not true for my field of research.
I'm an astrophysicist and I see very little "junk" in the astro-ph section of arXiv.
The majority of papers there are at least in the process of being reviewed, and most of those will make it through the process.
Having near-to-final versions of papers available on arXiv is great for when I'm not on my work computer and can't get past
the journal paywalls.
If you want real junk you should go to https://vixra.org/ [vixra.org]
(i.e. "arXiv" backwards.)
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Because astrophysics supplies little grist for conspiracy theories.
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You've never heard of the Electric Universe? Really? They're the Flat Earthers of astrophysics, and they made a bunch of noise a while back.
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I have corrected this distorted tale on other social media forums.
First, the researchers did not connect the coronavirus with HIV, which has been reported all over the place (and suggested here by OP). What they described was what they believed to be two separate protein "inserts", which together could mimic (the "uncanny similarity") a cell-binding site on some variants of HIV.
In other words, two different RNA sequences which
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Another researcher did a database scan for the RNA sequences in question, and came up with a list of other organisms which had similar sequences, including 3 coronaviruses. She claimed that this laid waste to the authors' claim that it appeared these sequences were artificially inserted into this virus.
However, those other organisms are of course not viruses at all, much less coronaviruses.
And th
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And those 3 coronaviruses she "found" all turned out to be this same virus, just listed under 3 different names... because it hadn't been given an official name yet.
This part is false.
Identical inserts were found in RaTG13, the suspected precursor family of SARS-CoV-2.
They were also found in 2 strains of betaCoVs found in bats: ZC45 and ZXC21
These are not the same as SARS-CoV2/2019-nCoV.
You seem like an intelligent person. It's a shame that you're always full of shit.
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If it was found in other viruses, do you have a link to the paper(s)?
"Full of shit" is easy to say (and you've said it -- incorrectly -- before).
I'm always happy to admit I'm wrong if I'm shown real evidence that I'm wrong.
But only if you produce that evidence.
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There are other lines of evidence which still point quite strongly to the virus having escaped the Wuhan Institute of Virology lab.
Including a first-hand account of an intern getting accidentally infected and then visiting the nearby wet market.
But escaping the lab is not, of course, in itself evidence that the virus was intentionally modified in any way.
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I did, however, find and article and associated paper published on March 17 suggesting that what you say is not true, and that the furin-cleavage site (which is the feature of the spike protein in question here) does not occur in other coronaviruses:
"SARS and other SARS-like viruses donâ(TM)t have those cutting sites."
Here is the article. [sciencenews.org]
And here is the paper. [nature.com]
It should be noted, though, that the authors conclude in their paper that the virus is likely natural... in part because it differs so much fr
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Because conspiracy nuts in your field of research (read: flat earthers and the like) aim way, way lower than what you consider science. I highly doubt that there are any papers in your field that deal with the shape or the earth or whether it was created by some magical man in the sky.
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Re:What good has peer review done anyway? (Score:5, Insightful)
You have hit the nail on the head. That reason -- to act as a filter of some sort or another -- is exactly why peer-review was established and why journals exist at all, and why both continue to hold value, whether that idea is popular on Slashdot or not.
I say this as a publisher of a scientific periodical. We get submissions from all around the world. We have them peer reviewed. I personally know each of the reviewers, and know how fair and objective they are, otherwise they aren't used. Our completely open-source publication has download numbers that makes the people at Cell jealously pay attention (I've seen it when I casually mentioned our numbers to them before I understood how good they were). Why is our periodical so well-respected? Because we serve as a filter so that our readers don't waste their time reading dren. Is our process perfect? Nope. Do we make mistakes? You bet. Do we learn from our mistakes? Every. Single. Time.
Do we stand as a barrier to publication? Yes, and no. If your work isn't good enough to appear associated with our name, then there are plenty of other places that will accept it. You don't get to stand with us for nothing: you have to do good work.
And there, exactly there, is the value that publishers and journals bring to science -- as a filtering service. Different journals use different filters, and that implies a certain value has been ascribed to papers that appear in each publication. Some journals will publish anything, as long as you're willing to pay their fees ... and it shows, if you read the work that appears there. Some journals will publish anything that is scientifically sound, no matter how mundane the question, or unsurprising the answer. And that shows, too. Some journals will publish something that they perceive has moved the needle in some field. And that shows. And, for each and every journal I've ever read, there have been whacky mistakes ("That is NOT a Science/Nature/PNAS/etc paper -- how the heck did that get published?!?"), but, for good journals, those are relatively infrequent.
But --- and this is to counter the standard argument that attempts to show journals are damnable because they make mistakes --- even if the filter isn't perfect, that does not mean it is not valuable.
These days, you have a choice: you can wade through endless papers on a pre-print server that will mostly be a waste of time, or you can pay a journal to do the work for you, and read their selections. Neither approach is perfect, and anyone who tries to say otherwise is selling something.
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These days, you have a choice: you can wade through endless papers on a pre-print server that will mostly be a waste of time, or you can pay a journal to do the work for you, and read their selections. Neither approach is perfect, and anyone who tries to say otherwise is selling something.
~pz
You're selling access to readership of prestige that serve a margin of profit a "house" might expand when the labor of expert scrutiny is evolving away from traditions of a predominately white-male hierarchy.
Slowly evolving. Kicking and screaming evolving. Sabotagingly evolving.
Re: What good has peer review done anyway? (Score:2)
Well, a larger French study just found no statistical difference in outcomes for patients treated for covid19 with hydroxychloroquine than those who didn't. Shows why peer review and reproducibility is important in research.
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The problem here is that "experts" are coming out of the wood work. I'm seeing guys whose degree is in bioethics making grand declarations about herd immunity and virology. They get lots of play on places like Fox, which, I presume, is desperate to not make the President of the United States look like the biggest snake oil dealer in history.
At any rate, no one pretends peer review, double blind studies, animal trials, limited human trials and the like are perfect. But they are a helluva lot better than havi
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Politicians made the federal government god of all business because of interstate commerce. If you love every manner of intrusive regulation because you can tie something to interstate commerce with a Rube Goldbergian argument, enjoy Trump's power to open back up all states' business.
This is your world. Enjoy it.
As an aside, I'd welcome the newfound relance on the idea it's too much power for the feds, but we all know this high valuation of it will be abandoned as soon as someone else is elected.
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Note that hasn't always been that way; Representatives and Senators used to jealously guard their own power over the Executive branch. That attitude has been whittled away over the years by putting "practicality" over principle whenever something big came up, but has been completely abandoned by the Re
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Well, a larger French study just found no statistical difference in outcomes for patients treated for covid19 with hydroxychloroquine than those who didn't. Shows why peer review and reproducibility is important in research.
The amazing thing to me is how many people are surprised by that finding, despite the history of hydroxychloroquine being espoused as a miracle cure for both SARS and H1N1 in vitro, but having no effect (SARS) or even making things worse (H1N1) in vivo.
That a malaria drug would have no detectable protective effect on a viral illness was blindingly obvious to most people the moment it was first mentioned. The past two months have mostly been about damage control and trying to find a way to convince all the
Re: What good has peer review done anyway? (Score:3)
Peer reviewers are human too, and have their individual quirks. Some bend over backwards to be encouraging and wrap their criticisms in way too much qualification. Others will bloviate endlessly about how they would have done the research, without bothering to understand what the research is about. Quite a few skim the paper for the first thing that catches their eye and dash off a quick and superficial note.
Then there are what I call "the mean girls". They will year into your work mercilessly and supercil
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Nothing about the hydroxychloroquine claims even made any sense. Hydroxychloroquine and the other quinines are used to treat a plasmodium; a single-celled eukaryotic organism. It's in an entirely different order of life from an RNA virus (if you count viruses themselves as even living organisms at all). The rubbish spread around, even on here, about red blood cells, just reeked off pseudoscientific word salads. The only thing missing was the word "quantum" to make the quackery truly complete.
Re: What good has peer review done anyway? (Score:4, Insightful)
All you need to know about that "study" is that (a) it wasn't blind and (b) it used people who refused treatment as the controls.
But it's not out of the question for that compound to have therapeutic effect against viruses. It works by altering the chemistry of eukaryote organelles; in an anti-viral scenario it supposedly inhibits the release of replicated virus by the host cell.
That's been shown to work in vitro, but that's not proof it works therapeutically. For one thing the therapeutic dose is not necessarily lower than the toxic dose.
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My understanding is that pneumonia kills most people
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We do know that the cytokine storm happens, but it's not clear that it causes the pneumonia and death. It may be coincidental.
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It's pretty certain that the cytokine storm causes the damage to organs that leads to death in at least some of the cases.
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"Moreover, ammonia and methylamine, which react as weak bases like chloroquine, reduced synthesis and secretion of proinflammatory cytokines."
So, why not test ammonia and methylamine like we're testing Chloroquine? Based on the studies, they would have just as much of a chance of decreasing the cytokine storm in sick people (not much), and just as likely to have adverse side effects (very likely).
Re: What good has peer review done anyway? (Score:2)
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Incorrect. We a
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The problem isn't as simple as finding out if it work
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Also, some people die when wearing car seatbelts. So logically seatbelts have no value in terms of safety. In fact, you are clearly safer not wearing a seatbelt.
There are valid arguments against peer reviewed journals. You should try making one sometime.
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That's an utterly false analogy. The problem with the hydroxychloroquine claims, as shown by early studies, is that it does not appear to make a difference. If seatbelts saved no more lives than not wearing them, then you would have a point.
I get it. The Moron in Chief made some absurd public claims, so the problem clearly must lie with peer review, and not with a senile demented halfwit with the intellectual of a five year old and the actual intellect of a brain damaged ten year old.
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If no study has shown effectiveness, then no study can show ineffectiveness since all these studies are too small, too poorly controlled, and in many cases influenced by those conducting the study.
Getting the, "Proof" you insist on, for any possible therapy, will take years.
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Not really. "Showing" effectiveness or ineffectiveness can be done by a study of almost any size. "Proof" is what's hard and takes years.
If small studies show effectiveness, we usually continue to larger studies. If small studies show ineffectiveness, we usually don't. We are in this case we are doing larger studies, partly because some early (albeit low-quality) studies do show effectiveness, and partly because this is a huge pandemic, many people are dying, and we don't have that many treatments which
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Anyone who claims hydroxychloroquine is not effective based on the existing studies seem to have an agenda.
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From https://www.cebm.net/covid-19/... [cebm.net]
Current data do not support the use of hydroxychloroquine for prophylaxis or treatment of COVID-19. Two trials of hydroxychloroquine treatment that are in the public domain, one non-peer reviewed, are premature analyses of trials whose conduct in both cases diverged from the published skeleton protocols registered on clinical trial sites. Neither they, nor three other negative trials that have since appeared, support the view that hydroxychloroquine is effective in the management of even mild COVID-19 disease.
Two studies who changed conduct partway through (thus very low-quality). Three negative studies. To which studies are you referring?
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I... don't think you read my comment at all. Care to try again?
Peer review is not (and has never claimed to be) perfect and flawless, but it is one of the best tools we have. I don't know how to balance the need for faster access to (poorer) results against the fact that idiots will use the worst-quality results for idiocy. My guess is that scammers gonna scam, gullible fools gonna believe conspiracy theories, and conspiracy theorists gonna vote for morons; the fact that the scams come from misreading "s
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Too many people would gladly watch patients die, prehaps even themselves, [babylonbee.com] as long as it meant Orange Man Bad. Including you, apparently.
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and not with a senile demented halfwit with the intellectual of a five year old and the actual intellect of a brain damaged ten year old.
I can't imagine the detailed accuracy of a study that can discern the difference between a 5 year old and a brain-damaged 10 year old!
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Maybe the good scientists are not reviewing, but actually sciencing.
We're actually generally doing both.
Those of us who are active researchers also realize that it's important to participate in the review process, even though
it is time consuming.
Reviewers in my field are generally selected from people who have published papers in the same area.
(Including doing proposal reviews as well.)
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Just like how all the big name software houses who have tons of code reviews still end up shipping bugs, clearly we should abandon code reviews and just ship as soon as the product compiles!
Sure, get rid of peer reviews, but not until you come up with a superior solution.
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Most criticism on peer review is simply assuming it does something which it does not. It's got an error matrix. You use it to filter out a large mass of true negatives and accept there are false positives and false negatives. Specificity is not perfect and sensitivity is modest.
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"Someone"? Just...anybody? I'm pretty sure the 'mistakes' you refer to are only mistakes depending on the training of the person finding the mistakes. No scientific training IN THE SPECIFIC FIELD IN QUESTION?
Then no one cares about the 'mistakes' you find, because you do not know what you are talking about. Peer-review is INDISPENSABLE to scientific progress. Period.
If you disagree, that is because you are not in the sciences and do not understand it. If you think journals like Nature and the journals I reg
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There is simply no need for the lock-away-from-the-public journals for peer review to happen. The old school paywall journals are incidental to the peer review process. Peer review is indispensable, sure, but Boomer journals can go.
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I suppose someone's gotta make my fries.
speed limit for dcience (Score:2)
the only speed limit in science is c
I can't peer review 55! (Score:1)
I can't peer review 55!
Journals do not make it better either. (Score:3)
They are staffed by people with personal triggers, natural biases and resulting "agendas" just as well.
As are peer reviewers.
It is a nice delusion though. It gives life a calming order.
But in the end, you will still only have "anecdotal evidence" of that study and its peer-reviews, and only YOU will have to be the final judge. Like the final watchmen watcher.
And therein lies the core problem, that David Dunning noted: If you are very stupid, how can you possibly tell if you are stupid or smart? If you lack competence in something, you also lack competence in determining if you lack competence.
If you are not competent in the field of the study, and in the scientific method, and in the philosophical basis behind it, you will not be competent to be that judge!
And as far as I can tell, there is really no way out of this. (I could say I am smarter because I am more successful in my predictions, but that is based on me being able to tell that I succeeded, bringing me back to square one.)
So you cannot know if you can actually judge a paper, or even judge if it was peer-reviewed well.
All you have, is the experience of you succeeding in getting closer to your goals because your predictions were successful. You cannot tell however, if you are actually an epic failure at it, who is merely deluding himself.
There are people who argue that it does not matter. If you think you lived a great life, it was great. If you think the journal is reputable, the study is good.
But then, why not just attach yourself to a "happy wish machine" that gives you a perfect illusion?
What I'm saying is, ... This is all useless low-brow bickering that can only emerge in gross ignorance of the higher fallacies that I mentioned above, which make this whole discussion moot.
Like fighting about which is the best oil lamp for your horse carriage while sitting in a car with quantum dot LED headlights, to give an analogy that is mirrored in two aspects.
TL;DR: People will hold their views regardless of open pre-publishing, journals and peer-reviews. And from this direction, there is nothing you can ever do about it. They will look only for what they need to be true right now. Like you may have done with my comment at this very moment. :)
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Never abandon principles (Score:2)
Utter bullshit (Score:1)
Peer review doesn't ensure better science. It enshrines politics in science.
Competition for academic positions is intensely political. A single tenured professor can mentor many dozens of PhD candidates during their career. About half are looking for careers in academics. Those going the academic route will usually have the goal to secure a tenured position. A single-digit percentage of those earning PhDs will achieve such positions. Everyone attempting to gain acceptance must be in the good graces of
See also: Dr. David Goodstein from 1994 etc. (Score:2)
http://www.its.caltech.edu/~dg... [caltech.edu]
"Peer review is usually quite a good way to identify valid science. Of course, a referee will occasionally fail to appreciate a truly visionary or revolutionary idea, but by and large, peer review works pretty well so long as scientific validity is the only issue at stake. However, it is not at all suited to arbitrate an intense competition for research funds or for editorial space in prestigious journals. There are many reasons for this, not the least being the fact that th
Re: See also: Dr. David Goodstein from 1994 etc. (Score:2)
Mod up
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I raised the possibility of a lab breach with them. I said the lab was collecting sick animals it's possible for something to happen there. A counter argument for that is that the body of research shows it comes from animals not a lab.
When I talk to a normal person about the topic it's like there are two brains in the room.
Re: Utter bullshit (Score:2)
Nobody's perfect. PhDs often get a kick out of knowing stuff. Not knowing is uncomfortable for them.
Of course, if you're trying to convince them 5G is responsible, they should slap you down like the gullible paranoiac you are.
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A very good example of that is that they keep referencing "experts" and authorities because they "know a lot". None of that is very relevant. Some mysteries to ev
The real problem (Score:2)
Can we just ban the times? (Score:2)
What the times wants is for all papers to first go through them before being approved for publication.
Just like what China is doing.
Blameless freedom. (Score:2)
"Information wants to be free"...of responsibility.
That's how conspiracies work (Score:2)
You take what you want to be true, then you hunt for anything that supports your pet hypothesis. If you find something that sounds like authority (preferably someone who can tack "Doctor" to his name, even if the diploma is from a diploma mill housed in a trailer), attach it and claim it gives your bullshit validity. Such peer review boards are a godsend for those bullshit peddlers because "it's scientific!".