The Glacial Pace of Scientific Publishing
fasebj.org
fasebj.org
It's like Mark Zuckerberg telling young programmers, don't start an internet company because society is suffering from all the evils of internet.
What I'm arguing is that she, like you apparently, aren't seeing the situation from the other person's perspective. Telling everyone else they are "wasting time and clogging the system" is just a game of "he said, she said". It's a battle nobody will win.
Papers are subjective. Notice Leslie Vosshall continues to publish frequently in these top 3 journals after her FASEB post (2012). Is she really being honest with herself? It is pretty easy to come up with reasons why anybody's papers should or should not be published in the top 3 journals. Again, its subjective.
What we need is not a pointing fingers solution, but a meritocratic one like the internet itself. We need data-driven decisions and not yes man/woman editors and wink-wink, nudge-nudge 3 crony reviewers behind closed doors.
It continues to baffle me as to how the scientific community can be so scientific about their research and yet so unscientific about how they communicate this research. Technology is making more science possible, and yet we stick with thousand year old practices of evaluating and communicating science?
For example, if a researcher chooses an algorithm with a "fairly recent" publication date of 2 years ago, that paper may have been first written 3 years prior to that, after a 1-year process of developing the algorithm and another 2-year process of generating and analyzing a dataset that showcases the algorithm so they can get it published. So that "2 year old" algorithm is actually 2 + 3 + 1 + 2 = 8 years old. If the algorithm is in a fast-moving field like next-generation sequencing analysis, it is probably obsolete several times over (i.e. the tool that obsoleted it is already itself obsolete), if it isn't completely useless now due to increases in dataset size during the past 8 years (e.g. it can only handle 1 million sequences, but today's datasets are 100 million sequences).
Any bioinformatics programmer knows this, of course, and only relies on the publication record as a last resort for information about bioinformatics algorithms. But a biologist who has a dataset they want to analyze and is looking for an algorithm to use probably won't know this, and will end up selecting a hopelessly outdated algorithm as a result.
https://en.wikipedia.org/wiki/List_of_academic_journals_by_p...
Publishing/broadcasting whether its music, words, video, or code has always been about doing something first. Seems like human nature. Don't see that pyschology changing any time soon.
And really you can shorten those timelines by a couple of months because people make their papers available as soon as they're publicly accepted.
In my opinion this puts an unnecessary burden on conference organizers, because they have in short notice to make a decision about the correctness of the article as well as other more mundane matters such as the formatting and presentation for the proceedings publication.
Funny stuff. In the end most of these papers are not reproducible anyway, so what is taking so long?
Funny stuff. This editorial is about making it so that preclinical publications are only published when they're ready for the clinic. It's not about the same experiments being reproducible. It's not an indictment about the quality of research or the utility of research for advancing knowledge. However, this editorial is often cited by people outside of the field to bolster something that it does not bolster.
Can you find one biomed paper published this month that is reproducible in its current form? I mean no missing/conflicting methodological information.
Ok, so totally forget how you're citing an editorial that doesn't support your pint and move on to new baseless accusations?
>and how the authors make confident claims in the paper ("this shows that", "therefore this is true") then back down and admit it was preliminary data afterwards.
This would be of interest if you had documentation of your extraordinary complaints.
>Can you find one biomed paper published this month that is reproducible in its current form? I mean no missing/conflicting methodological information.
My experience is that methodological descriptions are sufficient for reproduction in the papers that I read. Given the outlandish claims you've made, and your changing the subject when a bad cite is called out, I'd rather see some documentation from you than go on a fishing expedition.
Your reading of the paper did not make sense to me, so lets figure that out first. You wrote: "This editorial is about making it so that preclinical publications are only published when they're ready for the clinic."
To me, the problems identified and suggestions provided by Begley and Ellis sound more like science 101 lessons rather than complaints about premature publication:
"In studies for which findings could be reproduced, authors had paid close attention to controls, reagents, investigator bias and describing the complete data set. For results that could not be reproduced, however, data were not routinely analysed by investigators blinded to the experimental versus control groups. Investigators frequently presented the results of one experiment, such as a single Western-blot analysis. They sometimes said they presented specific experiments that supported their underlying hypothesis, but that were not reflective of the entire data set. There are no guidelines that require all data sets to be reported in a paper; often, original data are removed during the peer review and publication process.
[...]
As with clinical studies, preclinical investigators should be blinded to the control and treatment arms, and use only rigorously validated reagents. All experiments should include and show appropriate positive and negative controls. Critical experiments should be repeated, preferably by different investigators in the same lab, and the entire data set must be represented in the final publication. For example, showing data from tumour models in which a drug is inactive, and may not completely fit an original hypothesis, is just as important as showing models in which the hypothesis was confirmed."
So why have we been able to interpret the meaning of these words so differently?
The reason why we still have journals is that they work as a recording of past research that has been peer reviewed by a well known group of experts (the editorial board). In fact, with the Internet pretty much any journal will have a list of accepted papers so you can access them before they are formally "published". So you can read these papers as soon as they receive the OK from the editorial board.
For better or for worse, biology isn't like computer science. Wet lab experiments take orders of magnitude more time, interpretation of results is often pretty complex, and there are a lot more articles published, which together combine to make this situation a little different.
There have been several moves to establish ArXiv-like compendia for biology, but they haven't really caught on yet. I'm not sure exactly why.
Anyway, you are responding to an argument that I didn't originally make.