Academics do some good work in target discovery and validation, but not anywhere near as much as they think they do. Discovery in big pharma has to repeat everything, because about 80% of the time, the published result doesn’t hold up. I suspect this is the result of no job security among grad students and post docs, because we can almost always reproduce data from Japan, where asst profs generate the data. (And we can always reproduce published data from other big pharmas, always.)
Is anyone here able to corroborate the claim made in OP's linked comment? And does anyone know what kind of experience and oversight the researchers doing discovery in big pharma will have?
Other acquaintances of mine, who are in academia, did not find these results surprising at all. In fact, one added the observation that even when the experimental results can be duplicated, the conclusions of the study are probably still not valid because alternative, more mundane explanations are often overlooked, and the peer review process these days doesn't apply sufficient scrutiny or skepticism toward this.
I don't have any anecdotes on US vs. Japanese research.
I suspect as you say it’s partly down to a lack of expertise, being thrown in at the deep end without much guidance on how to get good measurements, both practically and in terms of avoiding statistical traps like cherry-picking, allied to the pressure to find some exciting results, and journals’ lack of interest in negative results.
There are a LOT of issues with reproducbility in Bio  at the moment, and in US based science in general. From others in 'Big Pharma' that I know, they agree that much of bio-tech based science needs to be re-run. Others in the comments section here point out that Mainland China has a history of suspect research. That may have been true 5 years ago, but they are 'up to par' with US based researchers now. Meaning, that the Chinese have gotten more rigorous and the US has severely slipped in quality.
I mean this next statement with full honestly: I don't believe half the labs out there in the US these since about 2016 onward. From very private conversations with others, many labs are abusive, fraudulent, 'me-too' landmines, and generally lying to grant funders, donors, and potential/enrolled students in a strange game akin to 'Catch Me If You Can' style con-artistry.
Major efforts are being taken to 'fix' the system. Me-Too is a perfect example. The Nature paper that is linked is another perfect example. These efforts are very much needed and those that undertake these efforts should be applauded and emulated. That said, Max Planck's quote is the speed at which this change will occur, namely, one funeral at a time.
 https://www.reuters.com/article/us-science-cancer-idUSBRE82R... A bit old, but should get you started on more up-to-date research.
 https://www.theatlantic.com/health/archive/2018/09/what-is-f... Food Science, but it illustrates the structure that leads to fraud.
I have a friend who worked in a neurology lab a few years ago who described the PI in a similar way. I had assumed that it was not normal and told her to get the hell away from that lab asap... how sad that this kind of shortsighted idiocy is so widespread!
It's hardly a secret. Any grad student in America already knows this - about the blatant/incredulous cheating and plagiarism that goes on between Chinese students. But oh no, can't talk about it. 'Coz it's racist y'know.
If you're saying "The academic culture in China is such that cheating and lying is widespread" -- that's not racist.
I'm pretty sure the post you responded to is making the latter claim.
This statement doesn't "blame the culture". In this sentence, culture means "a set of behaviors". The sentence doesn't speculate about why that (speculated) culture exists, and it certainly isn't saying "Chinese culture promotes cheating". Actually, all it's really saying is, "Cheating and lying is widespread in academia in China". That statement is totally compatible with what you wrote.
When having these discussions, it helps to interpret other people's perspectives charitably. Communication is hard. We don't need to make it harder by assuming that everyone who says something that could be interpreted as racism is actually a racist. Plus, I've found that if I interpret other perspectives charitably, I almost always end up closer to understanding what the other person actually meant.
Two groups can be compared on important values like "honesty" independent of group size. The comparison will look like overlapping normal distributions, usually with substantial overlap. Chinese students were famous for cheating at my school, especially in the pre-med biology track. I witnessed it myself. I also witnessed brilliant, hard-working non-cheating Chinese students in math and physics. Yeah, there's something cultural going on but it's a lot more complicated than "the Chinese are cheaters".
The problem with the parent statement is that it has the typical lack of precision and accuracy of a racist statement.
To choose the maximally flamebaity example, i might not like the current Israeli administration's policy towards Palestinians, but that doesn't make me an antisemite, or even anti-Israeli.
I'm being a bit sarcastic here, but a technology such as git with a platform such as GitHub could maybe make the process of publishing and reviewing research papers easier to control. Maybe you have to tailor it a bit to make it easier to work with this use case. Like open source, peers can start adding and reviewing directly at the source, instead writing a new paper or writing to all of the scientific journals to issue a different statement.
If the content of a paper changes over time, it becomes more difficult to reference that paper. You now have to include both the paper and something which identifies which version of the paper you read. This is possible of course, but is a fairly big inconvenience for mostly stupid reasons, such as various citation styles not allowing hyperlinks of any form. There is also the possibility of the content of a paper changing completely, though we should hope that people would use a tool like this sensibly and it wouldn't be an issue.
This proposed platform puts a burden on the authors of the paper to maintain a paper indefinitely. Of course, any paper you author you are at least partially responsible for, and any legitimate errors should concern you. However, having to keep up with many comments and/or critiques after a paper is published would be very tiring. The metrics by which academics are measured for their employment are heavily biased towards publishing a lot of papers, and having to spend a lot of time curating old work would be detrimental to anybody's career. (These metrics are also a reason that people would rather write a new paper to build on the old, rather than incorporating it into an existing work). Another issues is papers with many authors: do they all need to agree on a change to have it merged? How often do you want to try to contact 10 people in 4 different timezones to debate about minor changes to old research?
I also don't really understand how a system like this would address the problem of fraudulent papers in a better way than is done today, which (as far as I am aware) is academics contacting journals to get the papers retracted.
I don't think it's a bad idea, but it is so far away from how people publish today that many things (journals, metrics, work loads) are against you.
For what it's worth, I think tools like ShareLaTeX and the like are much more usable for tracking changes in documents and enabling collaboration, especially with coauthors with little programming experience.
I think its infeasible for various reasons to have people maintain old work in the way suggested in the original comment. Who is responsible for it, especially if the authors have moved institutions (which happens very regularly, especially for young researchers), or out of research entirely? Perhaps there could just be a shorter window in which the work could be looked at and changed if required, and after that it is frozen forever. But that actually sounds a lot like (a more open version of) the current peer-review-then-publish system.
It sounds like you’re imaging errors propagating through citations. Paper X cites paper Y, which in turn cites paper Z, so if there is an error in Z, X and Y are—-or should be assumed to be--invalid.
It doesn’t work like that. A few citations may be “critical” but a lot of them provide context and credit. Jones et al. first identified this problem. Smith tested several obvious but ultimately unsuccessful approaches. Here, we use the same methods as Wu and Lee. Our results differ from Cantorovich because....
Errors in those papers might make sections of the citing paper superfluous or less interesting but they don’t invalidate it. For ideas and methods, it might not even matter what the ultimate result was....
The ability to inspect, comment, and modify a scientific publication doesn't mean much if the underlying work is unavailable.
And that, in itself, is a problem. How can others identify flaws in the paper if they can't see the data you used?
Open Source software includes all the code you need, not just the final binary executable. Any proposed "Github for Science" needs to do the same.
And any arguments that "the data is expensive to collect and proprietary" can be countered with "code is expensive to write and proprietary, yet open source still works".
In fact, almost all medical trials or epidemiological studies use data that can't be shared outside the study.
e.g. We don't know who this guy is, but we do know that every measurement of him was linked to this same enormous random string.
When doing data linking I can usually identify one person in a dataset of almost 1 million from three innocent seeming pieces of data. Pseudonimisation doesn't really work.
These two are absolutely not equivalent. I'm all for open science, but the comparison with open source code is absurd. With the former you have to invest actual money: infraestructure, materials, suppliers, etc. and of course you have to deal/coordinate those elements. OS is... just time. There is a cost, but it is just an opportunity cost.
There are famous examples of widely-used open-source software having bad bugs (for example, OpenSSL) which no-one found, because although it was so widely used, no-one was performing careful enough analysis of the codebase. And programmers are actually paid to look at code all day. No-one working in a research institution is paid or recognised for trying to verify someone else's data or check that their research makes sense - this was the job of peer review. (Even peer review is unpaid and unrecognised at many institutions.)
The solution to this problem is not iteration and revision.
Any publication should be forked from the main repository, selecting from any relevant data from parent, and in that fork strict procedures of scientific research are recorded, processed, and finally end up with an article.
In this case you can track how an idea was formed, how it was modified to match empirical data. You can track when methods of data processing was chosen (before gathering of data or after), and so on.
Such a repository can give enough information to decide was the research is a fraud or no.
Current situation is bad, because articles do not capture all the information that needed to validate the research findings. p<0.05 is not enough for this. Including more information into the article is one of the ways to deal with that problem. But the other is to leave footprints, to create some historical data, that could be analized. Or not analized if no one needed it. It is like lazy-evaluation: just generate some data to allow your followers to reason about what precisely you've done. If they needed it, they will research your trail. You do not need to go through a difficult task of writing a high-quality texts about every your step.
The only thing you need to change is to make such notes public. It is coupled with some potential ethical issues, like privacy of subjects for example. If I run experiment, I gathered some data, I couldn't just throw this data into public access. It is possible that there are other ethical issues, maybe something about privacy of researcher as a person. These issues can make logging research activities a pain.
The advantage of theoretical papers is that the reasoning is a proof/argument developed in the paper itself. With theory, there's less chance for a fraudulent paper, even though the results may have gaps.
Thats the point. If you published your preliminary silly idea and your colleagues didn't find immediately that it is silly, then your not sillier than they are. :)
> the reasoning is a proof/argument developed in the paper itself
Even when I studied math I found sometimes that just to have proof is not enough to understand. The only way to understand sometimes is to learn how the proof was devised. What the hell author thought to get an idea of some trick in the proof? Some tricks looks as a magic, you see they are true from a logical standpoint, but they make no sense. You cannot understand how they lead to a QED. You can verify proof by logic -- not a problem, but you unable to understand. And if you are unable to understand, then at least you are unable to reproduce this proof at the exam, the only way is to learn it by heart. By I never trained my memory to learn by heart, it is really hard for me and annoying, and moreover I do not believe in learning by heart: to master a subject you need to understand it, not to learn it by heart.
My math experience taught me that if I cannot follow the thoughts of other mathematician by just reading his proof, it means that he is smarter than me, so it doesn't matter then how stupid he behaved while searching for his proof, he outsmarted me already.
But yes, I was talking about experimental research.
I think this stigma against making mistakes is a big problem, as is the ego-investment. We're all stumbling around in the dark, and we shouldn't be afraid to admit that.
At some point, you have to trust other professionals working in your field to do their work well. Or rather, decide who to trust.
It impies trust in good intentions of others. But not the blind trust that anything was done by a scientist was done good.
If logbook can be used to verify that data processing methods was picked before the first experimental subject came to a lab, then it is already a good sign. It could be much harder to do some p-hacking like [this](https://io9.gizmodo.com/i-fooled-millions-into-thinking-choc...).
Everyone would contritube to the same graph without duplicate data, or unaccepted piece of proof/knowledge
In Physics and many other fields Arxiv.org has basically replaced journals as the primary way of getting the latest research results. Unfortunately many high-impact-factor journals like Nature forbid you to publish a preprint of your article there (at least that was the case in 2012) so that they can defend their claim of publishing "cutting-edge" results only (which due to their long review processes are often 12 months old by the time they're actually published).
The most ridiculous thing is that the journals today do little more than act as an intermediary between the authors of a paper and the reviewers, which work for free and are colleagues from the same field. That and maybe styling the papers a bit, which is (IMHO) unnecessary in most cases as the source LaTeX version usually provides very good design already.
I'm not sure that is true, I've studied a fair bit of statistics and I can usually find flaws in most social science studies I read. So I trust an article combined with a few hundred HN comments a lot more than I trust anything published in scientific journals without comments, since usually if something is wrong someone in the comment section will find it. Even on reddit if you wade through it you can usually find some nitpickers adding good discussion on articles with a few hundred comments.
Wikipedia is a perfect example. It has only relatively recently become seen to be trustworthy, after many of years of tweaking and improving their edit process. When Wikipedia first started, few took it seriously. Likewise, when an open journal starts adding more stringent publication requirements, it too will not be immediately trusted.
The point is that quality itself is not sufficient. You need a reliable level of quality over a relatively longer period of time.
Even better, to support this, have an open-source freeware Journal CMS and publishing system for academics to use as a plug and play solution.
It’s laudible these researchers have invested so much in fighting fraud, but this post shows that the offenders will essentially face no negative consequences for fraud. The researchers worked very hard for hardly any return / justice.
Perhaps it’s worth re-inventing science. Open reviews. A network to connect labs that ensures findings are reproduced. We could even re-do much of basic, academic science in the interest of improving exposition and shedding antiquated formulations of theory.
What if, in the face of this fraud, we simply reject tradition wholesale? The only tradition should be an honest, reproducible study of Nature.
Also, independently reproducing studies is super-important, but that going to take HUGE amounts of money, which someone is going to have to pay for. It was have to come from the top, most governments want to see new research, not reproductions, and scientists are guided by that direction.
Edit: You can change the language to English by clicking on the settings cog in the video.
Going forward, should journals, or the peer-reviewers they engage, test new papers with this tool? Sure, it turns up false positives and false negatives, so its results cannot be interpreted mindlessly. It is also possible to game a tool like this. But it seems obvious some authors are already gaming the system.
Undergrad teachers use software tools to check student writing for plagiarism. Shouldn't information-based science use similar tools?
We hackers can contribute to this kind of effort by encouraging and supporting open-source inspectable tools. Maybe there's even a business opportunity around maintaining and using the tools.
Wonder if doing something like establishing "Bounties" (aka Security Bug Bounties in software) would start things in the right direction?
Sounds like there'd be no shortage of targets and low hanging fruit though.
Also, who'd fund it?
Dietary salt promotes neurovascular and cognitive dysfunction through a gut-initiated TH17 response
And it found:
Knockdown of NOB1 expression inhibits the malignant transformation of human prostate cancer cells
Informatician Cyril Labbé at Grenoble Alps University in France and I have developed a tool, Seek & Blastn (go.nature.com/2hsk06q), to identify such papers on the basis of wrongly identified nucleotide sequences.
So far, our work has uncovered dozens of papers and resulted in 17 retractions, with several investigations pending (see Nature 551, 422–423; 2017).
One way to reduce 'fraud' and also increase accountability of the individuals and organizations is to secure raw data at its source which the veracity of the data that will be subsequently used to support downstream conclusions can be easily verified and attributed to its source. I'd say a bottom up approach here is more holistic as it incentivizes people to produce high quality research that future work can then be reliably be built on top of.
I don't think even the author would agree with this if it were about anyone other than them.
Instead of accepting the issues, with the entire process, these professors are now facing disciplinary hearings for submitting false research. In a way I can understand this; they did after all submit papers they knew weren't academic (in bad faith?) in order to prove a greater point. But does that justify what they did?
Yes, it does.
These journals are an absolute joke, make a mockery of any serious attempt to advance knowledge and understanding, and deserve to be pilloried. Their standards of rigour and review are shockingly poor and as such they do not provide a suitable vehicle for the publication of genuine research, or for measured consideration of the content they do publish.
Just this week I ran across this, where a couple of the academics concerned were interviewed by Joe Rogan late last year:
Fascinating, horrifying, and entertaining in equal measure.
For more background, there's also this on wikipedia:
The claim is that they just made up trash and submitted it to high-quality peer-reviewed journals and they accepted them. The reality is much less outragous.
Of the 20 papers, 4 were published and 3 more accepted for publication. They spent a year doing this. The authors note that they submitted the papers to "top journals in the field", leaving out the fact that all of those top journals rejected the 20 papers and they had to revise the papers and send them to shoddier journals instead.
The review quoted by the authors was from an unsure grad student doing their first review of a paper. Said student later said they knew the paper was crap, but still tried to be constructive.
The assertion of the authors is that this stuff getting published means the whole field is worthless. Which is of course ridiculous. Medicine didn't become obsolete when a journal published a paper with an abstract ending in "The fact that these last sentences appear in the published paper tell you, dear reader, exactly how seriously the editorial process has been taken". Computer Science didn't implode when three MIT students made an AI to generate random papers and 120(!) were accepted by the reputable IEEE and Springer. The blame was back then correctly put on the publishers and the general flaws of the current scientific process instread.
So, as people have pointed out, it's ironic that their essay itself is incredibly scientifically unrigorous. No controls, unsourced claims, biased authors and conclusions that aren't supported by the data.
Perhaps, but we're undoubtedly in the midst of a crisis of confidence in the process of scientific publication. From the reproducibility crisis to the Diederik Stapel affair to the paper mills in China, almost every field is being severely undermined by weak or deliberately fraudulent research.
Frankly, I've almost given up on the scientific literature as a source of useful information, because I can't really trust most of it. The tools and processes of scientific publication just aren't fit for purpose. My Google Scholar and PubMed searches are overwhelmed with obviously junk papers from pay-to-play journals. Citation is no longer a credible metric because of citation rings. Established high-impact journals have reasonable quality standards, but they still get bamboozled with junk and a paper doesn't come with the supporting evidence I would need to evaluate its validity in any meaningful way. The signal-to-noise ratio of academic publishing is collapsing, and it's bringing down trust in the scientific method with it.
We need major reform and we need it now, because the credibility of science as a whole is under dire threat. The AllTrials campaign has made significant gains in reducing publication bias in medical research, but we need to go much further. We need a publish-by-default model, where everything associated with a research project is published and failure to do so is treated as academic misconduct. We need gold open access, we need full datasets, we need source code, we need rough drafts and lab notes and reviewer's comments. Equally importantly, we need to fix the cultural pathology of publish-or-perish that's driving the proliferation of poor-quality research.
I don’t get this at all from the authors. My take is that they call out serious flaws in the rigor of how papers are reviewed. I don’t think it’s reasonable to extend that to say the field is worthless. I did read through many papers in the referenced journals and it seems really surprising to me. I’d love to see some of the research reproduced. But I’m not even sure how you could scientifically prove a field worthless.
I think it's rather undeniable that the Authors essay was not a good-faith attempt at criticizing the peer-review process, but an attempt to discredit certain fields that they didn't like, even by their own admission. I mean, the title of the essay alone should make this very clear. Here's some quotes nonetheless:
> We spent that time writing academic papers and publishing them in respected peer-reviewed journals associated with fields of scholarship loosely known as “cultural studies” or “identity studies”
> As a result of this work, we have come to call these fields “grievance studies”
> We undertook this project to study, understand, and expose the reality of grievance studies, which is corrupting academic research
> The biggest difference between us and the scholarship we are studying by emulation is that we know we made things up.
> these fields of study do not continue the important and noble liberal work of the civil rights movements; they corrupt it while trading upon their good names to keep pushing a kind of social snake oil onto a public that keeps getting sicker
[Note also that this essentially an academic way of phrasing the same things you'll hear people like the far-right Stefan Molyneux (on who's show one of the authors has been a guest several times) say.]
Of importance here that it's not the scientific practices that are "corrupting academia" but the fact that these fields exist at all. I'm sure you can find more if you really want to. Compare this to say the "reproducibility in Psychology" study, which unsurprisingly doesn't dedicate half of their text to talking about why the authors think psychology is bad.
Don't be mistaken: The whole thing was an attempt to cash in on the general crisis the scientific process is facing to score some easy political points and not a neutral and constructive attempt at improving the quality of research in the field. Or rather, their proposal at improving the quality would involve getting rid of the fields that they don't personally like.
A thousand times yes. Exposing cargo cults that attempt to co-opt the hard-earned cachet of genuine scientific inquiry for their own ideological ends is exactly what is needed to keep science functional.
If you don't do it, then you let all the pseudo-science out there masquerading as real science, which is bad.
But if you overdo it, you feed into the distrust of proper science too, see Brexit and we're done listening to experts soundbite, or any of the anti-vax crowd.
In other words, their feelings of anti-science came first. Whatever reason provided is ex post facto confabulation.
Meanwhile, the sciences themselves need this kind of scrutiny to stay scientific.
I'm open to being wrong. But I think it is a mistake to put too much weight to the 'we should be careful what the people who never use science anyway' consider.
The humanities, no doubt, deserve criticism, but I honestly don't see the appeal of stunts designed to 'prove' that a certain field is not worth the time of day, by people who don't even understand the field at the most basic level. How would they know? Why would they care? It strikes me as embarrassing for everybody involved- embarrassing, to publish something without properly vetting it, embarrassing, to dismiss something as nonsense without actually having the measure of it, embarrassing, to be so enthusiastic about this kind of 'proof', which so obviously combines ignorance with arrogance.
There is no such thing as grievance studies. Critical theory has nothing to do with identity. The whole thing is about as close to the mark as Pat Buchanan's critique of feminism, and about as clever. In short, depressing.
Amongst the embarrassing amateurishness of it all, and the obvious conclusions, I found it interesting how commonly reviewer comments used the word "exciting" in response to the "Going in Through the Back Door" paper.
You answer your own question. While the methods may claim to be "defending science", the goals are political.
But the problem goes deeper than that. Sokal intentionally included meaningless sentences, self-contradictory sentences, and scientifically false sentences. On none of these was he called out by journal editors or reviewers.
To provide a little explanatory context here, the humanities has always had a great deal more tolerance for bad writing than other fields. Kant introduced the main point of his Critique of Judgment in a footnote. Hegel loved self-contradictory sentences. Somebody like Heraclitus writes a lot of stuff that, if perhaps not meaningless, certainly looks meaningless.
I don't know what that says about the entire history of philosophy, but anyway, it does say something about a small group's willingness to publish something that had some shitty prose.
Seriously, I can't be the only one who sees that?
It pretty much is corruption essentially but you are the 'crazy' one if you point it out because 'things are done that way'.
In this case, the researcher probably should have gotten IRB approval because there were test subjects--the journal editors, peer reviewers, and probably journal readers.
But I'm assuming they just skipped that process and said there were no human subjects.
One of the honeypot papers won an award. That shows you how obvious the publisher bias is, and how obvious it must have been to these people before they decided to do something about it.
Not only did these individuals risk their careers to help save a dying system with this project, they held themselves to a pretty high standard of execution.
We place lots of limits on the amount of heroism individuals are allowed to display, and I think that’s mostly beneficial - but sometimes we need heroes.
1) there are ethics panels for a reason -- many people have run unacceptable experiments on people. Academics don't get to skip the ethics checks because fhey feel like it.
2) their experiment was poorly designed. On their first attempt of their papers got ejected, so they polished and resubmitted them. What is their exact scientific theory?
3) they were clearly trying for contraversy. Maybe some part of Mein Kampf are actually useful valid statements to make. Just because of the terribleness of the Nazis, doesn't mean everything Hitler ever said, or wrote, should automatically be rejected from journals.
4) maybe Grievence Studies actually review better than everyone else. Any good study need a control.
That they found success with this process is damning. That you seem to think otherwise is probably also damning.
That scientific publishing is easily broken by lying is a serious problem which effects all academia.
They've outlined this. There is a specific Grievance Studies nomenclature and orthodoxy which the first papers did not adhere to. When they republished and resubmitted, they followed the Orthodoxy and they got through.
That IS the scientific method. You run an experiment, observe the results. You tweak a few variables and see what happens under those conditions. It’s what distinguishes their work from Grievance Scholarship, where you know the conclusion you want before you start.
> Maybe some part of Mein Kampf are actually useful valid statements to make.
Just in journalistic circles one usually prefers to call the
press a 'great power' of the State. As a matter of fact its
importance is truly enormous. It cannot be overestimated ;
it is indeed actually the continuation of the education of
youth in advanced age.
Thereby one can divide the readers as a whole into three
First, those who believe everything they read;
Secondly, those who no longer believe anything;
Thirdly, those who critically examine what they have
read and judge accordingly.
Monstrous arguments are often assembled from tiny units which may be unobjectionable individually.
The implication that the journal editors failed to notice the evil taint of Nazism from short extracts is nonsense.
But the whole hoax is entirely political. The authors disapprove of what they call "Grievance Studies" and they wanted to call that out.
Which is fine as far as it goes, but as others have pointed out, it's not as if the SNR in other disciplines is perfect.
There's a huge amount of bullshit everywhere in academia - from theoretical physics to medicine to economics to computer science. 
Going Sokal proves nothing at all this point. We already know peer review doesn't work very well, because academia is now driven by financial and economic pressures more than it's driven by a noble quest for knowledge and wisdom.
Ironically the "grievance studies" people have done a better - albeit still slanted and ineffectual - job of pointing this out than the entire peer review system has.