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The Glacial Pace of Scientific Publishing

fasebj.org

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Re: The Glacial Pace of Scientific Publishing

#31

Post by epistasis »

nonbel wrote: post #30
epistasis wrote: post #29

Earlier quoted context omitted.

>The term 'non-reproduced' was assigned on the basis of findings not being sufficiently robust to drive a drug-development programme. 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 kn…

Forget whether independent replication worked out 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. Can you find one biomed paper published this month that is reproducible in its current form? I mean no missing/conflicting methodological information.

>Forget whether independent replication worked out

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.

Re: The Glacial Pace of Scientific Publishing

#32

Post by nonbel »

epistasis wrote: post #31
nonbel wrote: post #30

Earlier quoted context omitted.

Forget whether independent replication worked out 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. Can you find one biomed paper published this month that is reproducible in its current form? I mean no missing/conflicting methodological information.

>Forget whether independent replication worked out 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 complain…

Sorry for the miscommunication. I was trying to give biomed an easier hurdle to surmount (reproducible at least in principle), not change the subject.

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?

Re: The Glacial Pace of Scientific Publishing

#33

Post by rgejman »

coliveira wrote: post #21
rgejman wrote: post #15

Earlier quoted context omitted.

In the biomedical sciences most publications DO NOT end up on preprint servers before being peer-reviewed and accepted. Therefore most stories are "done" a year or more before they are published anywhere. Sometimes they are presented at conferences, but often only once the paper is in submission.

Each technical field decides the best way to handle new research. If what you said is true, this is a matter particular to this and similar fields. However, many articles such as the one linked above make it believe that Science as a whole has a big problem because of peer reviewing standards, which is NOT true. In fact, most fields already have procedures to disseminate and archive results in a way that does not con…

That's fair, but she's writing an editorial in FASEB, which is the Federation of American Societies for Experimental Biology journal :).

Re: The Glacial Pace of Scientific Publishing

#34

Post by et2o »

coliveira wrote: post #22
et2o wrote: post #18

Earlier quoted context omitted.

Do you really think this reviewer for FASEB, an HHMI Investigator and a tenured professor at Rockefeller University, doesn't "understand the academic process?" 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…

This only proves that this person is working in a particular dysfunctional field, among thousands of other scientific fields that have no problem with the process. There is probably no research area more competitive than astrophysics. The guys working there, however, decided to use arxiv.org to make available research that costs them millions of dollars and several years of work to produce. I don't see why the biolog…

Idk how you could quantify that astrophysics is more competitive than biology. There is a lot more money and also many more investigators in biomedicine. NIH grant funding is insanely competitive.

Anyway, you are responding to an argument that I didn't originally make.

Re: The Glacial Pace of Scientific Publishing

#35

Post by a_bonobo »

toufka wrote: post #28
rcthompson wrote: post #14

Earlier quoted context omitted.

Most journals require that any research submitted to them must not have been published elsewhere. On the surface, this makes sense, especially in the pre-internet world in which scientific publishing developed. You wouldn't want to allow someone to submit the same paper to multiple journals to inflate their publication count. However, things like preprint servers and blog posts have become a gray area with respect to…

Submit to Biorxiv [1]. Most journals have actually recently changed their terms to explicitly allow pre-print publication. [1] http://www.biorxiv.org/about-biorxiv

Here's a useful list of the bigger journals and their stance on pre-publications:

https://en.wikipedia.org/wiki/List_of_academic_journals_by_p...

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