Thanks for your reply nonsequitur.
Not at all, it's something that I complain about at length in my blog lol. I've also thought a lot about this, given the ethics of the people around me.
A few points, the prestige of those journals was considered high, long before the impact factor was invented. I see it as sort of a self fulfilling prophecy, due to the age of those institutions.
I guess published protocols are less common in primary research, but I expect the move towards published protocols to become more common in medical trials. It is meant to keep the authors more honest. Well it would, if they actually stuck to it.
The impact factor was invented for convenience but is used in consideration for grant applications. It has become almost the be-all-end-all in publishing, and in my field it's commonly said that "3/5 JBC papers is the equivalent of 1 PNAS/Nature paper". Of course, what would make more sense would be direct references to that paper... But with that also comes drawbacks because even if other papers refute the original paper, it would still have to reference it, artificially boosting (in an extreme case) the reference count (and supposed importance) of that paper. There's a common joke that goes that "a retraction is also a reference!"
There's something deeply rotten in the core of (at least biomedical) academia and this publishing culture/system, but obviously to revamp the entire thing would not be possible in the short-term.
I've never published in medical trials before, but I would assume that because of commercial interests and patent restrictions, the full details of such studies will never be made public. There's another joke that goes that if you want to get something published without having to disclose the details of your protocols, you just apply for a patent.
You bring up a few interesting points that relate to the incentives involved and I think there are a variety of incentives involved.
Eg.
You have spent lots of time on a particular study, but the results were not as you expected. It is demoralising to put a lot of work into something but get no returns. Your career and livelihood is at stake, you must publish or perish.
Others do it, it is considered standard practise in many labs, so why not do it yourself?
That is some people's attitudes, but not mine. I feel strongly that in academia, it is important not to be TOO ambitious, and that the main goal should always be to serve science and its progression, not the individual. But then, I am highly idealistic and firmly believed this even before those ethics classes became compulsory. I would have problems sleeping at night if this was not the case.
The incentives of faking data are more complex. I think the individuals in question often believe that their science is genuine. Perhaps they feel they do not have the resources to "prove" the data that they'd like, so they fake it. Rational people can participate in such behaviour if they calculate their odds of getting away with it to be high. Kind of like copyright infringement on the internet...
It makes you wonder how many have gotten away with it? Due to cherry picking of data shown to the referees, or even a lack of knowledge and understanding by the referees themselves (common).
The incentives of faking data are obvious. More money, more prestige, tenure, getting paid by conference organisers to fly first class to give a talk (on your fake data) on a nice tropical island...
I have wondered this, but there's no way of knowing, of course. As my INTJ mentor said (when I asked him this), the amount of stuff out there is almost infinite, as is the number of people participating. The only thing that you can do is make sure that you're not one of them.
The media has a strange idea that once research is published by a peer reviewed journal, then it can be considered "fact". This is wrong, the true peer review occurs after publication. Unfortunately, there are lots of limitations on things like letters to the editor etc (and who reads them anyway?).
The media is stupid. I'm sorry, but it's true. So is anyone that takes something published in a newspaper with the headlines "Science/Scientists say..." as fact. Even a lay person who goes back to the original paper will not be able to make head or tail of it. No matter how "well-read" they are. The vocabulary and technical terms used are very specific, and so are the methods. Interpretation of data is often based on experience with equipment/data and spotting if something is "wrong" is dependent on this. That's why I get upset when people try to tell me about "science" in general, or that a lay person's opinion of science actually matters in the big picture. And yet it's precisely lay people who are making policies about it and based on it! (with the aid of "scientific expert opinion", of course, who are mostly more interested in advancing personal interest)
How can the field of science be reformed to become more honest?
People are dishonest, including scientists.
The good thing about science is peer review, and scientists have an incentive to call bullshit on other scientists, in order to advance their own scientific careers. Especially when a scientist sees someone else in their own niche of which they are very familiar coming up with wacky numbers and theories.
My opinion is only partially in line with ajblaise's. People are people, and people are dishonest. There will always be people cheating. It is impossible to uncover all cases of fraud, and the rewards for this kind of behavior is high. The peer review process is very flawed (I could go into A LOT more detail but I think I've said a lot already). However, ideas for reform are sparse. It's partially that the system is already so entrenched - not only in academia, but also in the grant proposal bodies, the entire bureaucracy of it all. There are also a lot of people with vested interests in keeping the status quo. In fact, there are many scientists who believe that the current system works. I don't know if it's because they're deluded, or if they only choose to see the "good". More likely, as the people whom I've spoken to have said, it's impossible to change the entire system. That's the way it works, so the only thing that we can do is go along with it and try not to exploit it or be exploited.