Molecular Systems Biology | The Seven Stones

Lack of protocols in cell & molecular biology

by George M Church, Senior Editor

thumb070312.jpgImage manipulation and selective reporting of images have been recently in the focus of a healthy debate on the issue of scientific data manipulation. Of course, as editors tell us how they detect fakes (“What’s in a picture? The temptation of image manipulation”, Rossner and Yamada, JCB 2004 166:11), there is a danger that authors will be tempted to upgrade their ploys. More importantly, I think that these issues are symptomatic of a much larger problem in Cell & Molecular Biology which is the lack of protocols for getting from raw data to conclusions. Contrast this with genomics and 3D-structural biology where raw data are available in databases, not just a few typical photos, but every scrap of data (e.g. sequence trace data, diffraction intensities, raw RNA array data). The algorithms for getting to the conclusions are public and other labs are encouraged to redo the trajectories from data to conclusions using the original or new algorithms. This is mostly missing from Cell & Molecular Biology papers, with some excuse like “too expensive”. Maybe it’s too expensive NOT to do it – not just because of data faking, but because it sends the message that we’re too lazy (or too busy) to describe in detail how we do our science and how to systematically improve it.

Molecular Systems Biology would like to encourage anyone who has creative and concrete ideas how to get Molecular and Cell Biology up to the standards of genomics and structural biology.


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    Eric Deutsch said:

    There are several papers which have passed review but are currently “in community consultation”. Everyone is highly encouraged to go there, pick an article or several, and write a constructive comment. These standards won’t solve the problem, of course, but when journals start requiring adherence to standards like these, the situation will start to improve.

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    Jose G. Castaño said:

    The main problem with “post-modern” molecular and cell biology is to become really quantitative, something that editors, reviewers, and in general, scientist in those fields have “forgotten” from their origins (chemistry, physics, and mathematics). I remember a Nature paper where the authors claimed that the differences in amount of a certain protein do change, because, x secs of exposure (ECL) were needed to see the protein band in the controls and y seconds (longer or shorter, it does not matter) are needed to see with the “same intensity” (by eye-CAMERA digital record) the protein band under the experimental conditions. How many ECLs loading controls are overexposed in published papers?. This applies also to the “omic” world. Apart from journal editors, reviewers, and all of us that certainly can do better, I have a question: Has any grant “authority” (local or global) thought to give enough financial support to actually determine, at least semiquantitatively, within a factor of 2 (or better when possible)

    THE AMOUNT OF EACH PROTEIN AND RNA MOLECULE (or any cell constituent) within A CELL AND IN EACH CELL COMPARTMENT” in a molecular system biology approach?. As a new generation of biological data will be produced, we should give this quantitative approach a new name, my proposal is “posogenome“ posoproteome” “posotranscriptome” “posointeractome” “posoenzymome” , etc and their “omics” derivatives; just by adding poso (from Greek word meaning quantity, ποσότης, ποσό) to the constituent and any real quantitative molecular system biology approach. Few papers try to get to the level of PosoBiology and that should be our “post-modern” molecular and cellular biology goal for the XXI century. Then someday in the future we may come to the full spatial and temporal description of a cell function

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    Willy Valdivia-Granda said:

    I agree with George Church comments on the lack of standards and data to validate these experiments. It is necessary to keep in mind that many of these publications presenting nice figures in Cell and Mol Biology and other publications are derived from a painstakingly process of trial and error. Where hundreds of pictures are taken and only the best are selected. Only the best of the many experiments and pictures are presented as part of the paper and to support a claim about a particular biological process. What is behind these images and would be possible to annotate these images so people can see the metadata and determine if the image really make sense.

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    Dinesh said:

    I completely agree with Dr.Church on the lack of standards and data for validating our experiments which are published.I think this issue can be solved by encouraging scientists/researchers to use e-notebooks and submitting those with the papers as hyper-links in Materials and Methods Section.This would not only help to compare “eventually” the different protocols used by different labs across the globe for generating the data but also highlight the mistakes/novelty/simple great ideas etc in originality.The biggest advantage of this would be to have an intrinsic check on fraudulent data which is becoming common these days in the age of high competitiveness and stress.If maintenance cost for this is the problem, the journals can put the burden of maintaining the e-notebook at authors’ institutional web archive as a part of their scientific data sharing policy. People experts in this field might have much more to suggest.