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Most scientists 'can't replicate studies by their peers'

bbc.co.uk

21–30 of 356 posts

Re: Most scientists 'can't replicate studies by their peers'

#21
post #3

Hmmm. Software Engineering has Continuous Integration, since it is so expensive to fix software later in the day. Is there any such thing as Continuous Reproducibility? Constantly checking that the science can be reproduced? How prevalent is this in different branches of Science?

>Constantly checking that the science can be reproduced?

Scientific experiments usually need actual things to be manipulated in the real world. So I think a concept of Continuous Reproducibility may only applicable to a subset of science that can be done by robots given declarative instructions.

Re: Most scientists 'can't replicate studies by their peers'

#22
post #12

Earlier quoted context omitted.

I don't think that analogy is at all accurate and I think the conclusion that you reach from it is completely incorrect.

I think I must have expressed myself poorly, as I think my conclusion is the same as the article suggests i.e. that the science/code shouldn't be considered "done", until it's been peer-reviewed, since it's easy to fool yourself and others if you're not actually reviewing and testing your code. What did you take away from my comment?

Peer review does not imply reproducibility, and it's the latter that is the problem.

I can confirm, as a reviewer, that your methodology and analysis looks sensible, but the flaws may be deeper, and the fact that you didn't publish the 19 other studies that failed, but that this is the "lucky one", or that you simply cherry picked the data, is not something I can see as a reviewer.

This is especially true if the experiment is nontrivial to re-do.

Re: Most scientists 'can't replicate studies by their peers'

#23
This is ego, politics and career ambitions undermining modern science. Unfortunately, the fact that this is occurring so rampantly will bolster anti-intellectuals and give them a very potent argument to point to when presented with facts. This is a systemic failure of basic ethics that will hurt us all. The success-at-all-cost career mindset is toxic in all tracks, but this is one of the most dangerous for it to take hold in.

Re: Most scientists 'can't replicate studies by their peers'

#24

> The problem, it turned out, was not with Marcus Munafo's science, but with the way the scientific literature had been "tidied up" to present a much clearer, more robust outcome. I've seen this time and time again while working in neuroscience and hearing the same from friends that are still in those fields. Data is often thoroughly massaged, outliers left out of reporting and methods tuned to confirm, rather than f…

I wonder if paying grad students to write a more full paper that includes all the steps and the negative results would help. It wouldn't be something that is published right away, and perhaps it wouldn't need to be published. Maybe it would simply be a follow-up to the original paper. It would be a "proof" of sorts, provided by the authors. There are many students out there that would happily do this, I think. I know so many that clamor for even the slightest bit of work in their departments. I think it would also be beneficial to their future, teaching them about reproducibility and impressing upon them to continue this practice down the road. The current climate of publish-or-perish isn't going away anytime soon, and neither are the clean, pretty papers with only positive results. And that's fine. Those are the quick highlights. But the full studies still need to be out there, and I think this could potentially be a way to approach that necessity.

Re: Most scientists 'can't replicate studies by their peers'

#25

>The reproducibility difficulties are not about fraud, according to Dame Ottoline Leyser, director of the Sainsbury Laboratory at the University of Cambridge. That would be relatively easy to stamp out. Instead, she says: "It's about a culture that promotes impact over substance, flashy findings over the dull, confirmatory work that most of science is about." Well, maybe I'm too much of a layman, but that doesn't qui…

A lot of it is people over hyping their results and cherry picking their data to fit a narrative. Can you blame them? You can literally build a career off a paper or two published in Science or Nature.

Meanwhile, no one controlling funding sources or faculty appointments cares that you did amazing, rigorous work if it leads to less interesting conclusions. This is especially true if you generate null results, even though this work may have advanced your field. This puts in place a dangerous incentive system.

Another thing which is not mentioned is that the level of detail provided in many methods sections in papers is not sufficient for adequately reproducing the work. This can be due to word limit constraints or because people forget to include or aren't aware of key steps which are impacting their results. I've been on projects where seemingly irrelevant steps in our assay prep significantly impacted the resulting experiment outcomes.

Re: Most scientists 'can't replicate studies by their peers'

#26

> The problem, it turned out, was not with Marcus Munafo's science, but with the way the scientific literature had been "tidied up" to present a much clearer, more robust outcome. I've seen this time and time again while working in neuroscience and hearing the same from friends that are still in those fields. Data is often thoroughly massaged, outliers left out of reporting and methods tuned to confirm, rather than f…

For what it's worth I see the same thing in enterprise app development.

We've been doing a lot of data visualization and it often happens that someone comes to me with a thinly veiled task that's really to prove this or that person/process is at fault for delaying a project or something.

Sometimes though the numbers either don't support their opinion or even show a result they don't like and so inevitably they have me massage the graphs and filters until they see a result that looks how they want it to and that's what gets presented at various meetings and email chains.

The information at that point isn't wrong per se, just taken out of context and shown in a persuasive (read: propaganda) rather than informative way.

Re: Most scientists 'can't replicate studies by their peers'

#27
post #3

Hmmm. Software Engineering has Continuous Integration, since it is so expensive to fix software later in the day. Is there any such thing as Continuous Reproducibility? Constantly checking that the science can be reproduced? How prevalent is this in different branches of Science?

In the physical sciences experiments can be enormously expensive to run and doing them "continuously" is impractical. Groundbreaking work is usually verified independently, but it varies across fields. E.g. physics is usually quite careful about reproducing new physics before accepting it, while in the biological sciences it seems that work isn't always reproduced.

Re: Most scientists 'can't replicate studies by their peers'

#28
"all you have to do is read the methods section in the paper and follow the instructions."

I wish science was that simple. The methods section only contains variables the authors think worth controlling, and in reality you never know, and the authors never know.

Secondly, I wish people say: "I replicated the methods and got a solid negative result" instead of "I can't replicate this experiment". Because most of the time, when you are doing an experiment you never done, you just fuck it up.

Here is an example: we are studying memory using mice. Mice don't remember that well if they are anxious. Here are variables we have to take care of to keep the mice happy, but they are never going to go to the methods section:

Make sure the animal facility haven't cleaned their cages.

But make sure the cage is otherwise relative clean.

Make sure they don't fight each other.

Make sure the (usually false) fire alarm hasn't sound for 24 hours.

Make sure the guy who was installing microscope upstairs has finished producing noise.

Make sure there is no irrelevant people talking/laughing loudly outside the behaviour space.

Make sure the finicky equipment works.

Make sure the animals love you.

The list can go on.

Because if one of this happens, the animals are anxious, then they don't remember, and you got a negative result which have nothing to do with your experiment (although you may not notice this). That's why if your lab just start to do something you haven't done for years, you fail. And replicating other people's experiment is hard.

A positive control would help to make sure your negative result is real, but for some experiments a good positive control can be a luxury.

Re: Most scientists 'can't replicate studies by their peers'

#29
post #22

Earlier quoted context omitted.

I think I must have expressed myself poorly, as I think my conclusion is the same as the article suggests i.e. that the science/code shouldn't be considered "done", until it's been peer-reviewed, since it's easy to fool yourself and others if you're not actually reviewing and testing your code. What did you take away from my comment?

Peer review does not imply reproducibility, and it's the latter that is the problem. I can confirm, as a reviewer, that your methodology and analysis looks sensible, but the flaws may be deeper, and the fact that you didn't publish the 19 other studies that failed, but that this is the "lucky one", or that you simply cherry picked the data, is not something I can see as a reviewer. This is especially true if the expe…

" Peer review does not imply reproducibility, and it's the latter that is the problem."

I think this is the key to it, I'm suggesting that reproducibility should be part of considering something peer-reviewed, but of course as currently practised, that isn't true.

Of course in a software metaphor, that would probably cover both code review and QA, which is sometimes done by a different job role which further muddies the water.

Re: Most scientists 'can't replicate studies by their peers'

#30

This is ego, politics and career ambitions undermining modern science. Unfortunately, the fact that this is occurring so rampantly will bolster anti-intellectuals and give them a very potent argument to point to when presented with facts. This is a systemic failure of basic ethics that will hurt us all. The success-at-all-cost career mindset is toxic in all tracks, but this is one of the most dangerous for it to take…

> will bolster anti-intellectuals and give them a very potent argument to point to when presented with facts

Case in point: the very first thing I thought of is, does this have any relevance to the field of climate science!

So....does it? Because we're told the reason we have to get on board with the program is because the people telling us the facts are scientists, and scientists are smart and trustworthy. However, we know this is not always true, don't we.

So what is a deliberately skeptical person to think?

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