Reader Comments
Post a new comment on this article
Post Your Discussion Comment
Please follow our guidelines for comments and review our competing interests policy. Comments that do not conform to our guidelines will be promptly removed and the user account disabled. The following must be avoided:
- Remarks that could be interpreted as allegations of misconduct
- Unsupported assertions or statements
- Inflammatory or insulting language
Thank You!
Thank you for taking the time to flag this posting; we review flagged postings on a regular basis.
closeInteresting paper but a strange claim that doesn't pass muster
Posted by AnimeshRay on 22 Nov 2013 at 18:30 GMT
The author summary claims, "Controls are required in experimental biology, but they are ill-defined in many computational approaches."
Do the authors have quantitative evidence (with significance P values) to support the claim that indeed controls are "ill-defined in many" (what is "many"?) computational approaches? Perhaps they are ill-defined in bad computational approaches, but they are also ill-defined in bad experimental biology reports; the distinction is between bad and good science. I wonder how this statement got through the peer review process.
RE: Interesting paper but a strange claim that doesn't pass muster
carlsonh replied to AnimeshRay on 23 Nov 2013 at 02:21 GMT
First, I'm a theoretician, so please be assured that I am not unduly lauding experiments over calculations.
For many genomics studies (sorry, I don't have a number), the statistics are well established. However, there is a large field of molecular mechanics modeling where it is ill defined. What is the null hypothesis for docking a ligand to a protein or running a molecular dynamics simulation? There is no "control", so people look for whether their results are consistent with existing data on a system. On previous mining studies of protein structures, authors have not addressed statistical significance of their findings, and we are trying to appeal for more complete analysis of such data, now that the PDB has enough structures. I don't think there was anything wrong with the earlier studies because the data was limited and they were reporting what could be known at the time. Janet Thornton did several of those studies, and she is a scientific goddess. (Can you tell I am a fan of her work?)