Network models to evaluate reproducibility in biomedical research
_or, The Future of Science

The traditional way to publish scientific work is to write a narrative describing the performed experiments and related conclusions. Nowadays, the pressures for funding and journal impact factor generate a vicious circle promoting, at the very least, an increase in the minimum number of relevant findings required for publication and the over-stretching of claims. As a consequence, the problem of reproducibility in science has surged to the attention of the media, including The New York Times and The Wall Street Journal.

This situation has already generated several disadvantages for authors, funding bodies and research institutes:

  1. Only a small fraction of the experimental workflow is actually published, creating data loss and underestimation of the labor done by research fellows;

  2. Pressure to publish novel data decreases reproducibility and increases the amount of unconfirmed work;

  3. New technologies, usually developed at the start of a research project, are only published years later, slowing down scientific progress;

  4. Disconnect between funding and publication: research is often funded when most of the work is already done by using grant money from past proposals;

  5. Research papers become increasingly complex and specialized, forcing the peer review process to a black and white decision;

  6. Lack of metrics assessing the quality and reproducibility of research.

Hereby, we envision a solution to break the loop. Consider a platform for storing, peer reviewing and sharing all the scientific work produced within a research institute. We are thinking of a network of science where nodes are single experiments, not entire papers. Each experiment should be meaningful, i.e. must provide a conclusion statement and a short description of the materials and methods (much like it is presented during lab meetings). The envisioned platform provides a key feature: the directional linking of published experiments. This forking feature is critical because it builds the network semantics by establishing where the rationale of an experiment comes from (and where it eventually leads). Network semantics are important because they generate a better proxy index for reproducibility, and thus quality, than the current impact factor. Such a reproducibility index can be calculated from node properties according to network theories or ad hoc metrics like the Fork Factor. Lets call the envisioned platform a Semantic Experiment Network (SEN).

As a complement to the current publishing model, we propose that research centers adopt a local SEN (L-SEN), such that data will only be accessible within each institute. Although pre-print policies of most academic journals allow posting on pre-print servers prior to publication, the intra-institutional boundary may reassure the most skeptical laboratory heads in the transition. A laboratory using L-SEN to store and share data and code can naturally decide to assemble their data in a traditional paper. As such, the envisioned transition from traditional to digital publishing of scientific work will be controlled and gradual. Recent digital publishing projects like Authorea, FigShare, DataVerse and Synapse can provide an excellent starting point, already implementing most of the needed features.

As recently shown, funding is the main driving force for a change in the scientific discovery workflow. Laboratories in research institutes that adopt L-SEN can provide funding agencies with new tools to assess scientific performance and can thus attract more resources. It will not take long for funding agencies to realize the advantages of metrics based on quality of science (see below). At that point, publishing in SEN will be sustainable for authors, and it can go global (G-SEN). This will break the original vicious circle by explicitly adding reproducibility to the equation.

The expected benefits in replacing academic publications with single meaningful experiments for assessing the success of scientists are many and belong to all the stakeholders.

For funding agencies and human resource offices:

  1. Sound and fast assessment of the scientific impact of applicants in a grant application;

  2. Research money associated with the total amount of work performed (and indirectly with the future forking of the research), not just what results in publication;

  3. New options to promote studies addressing reproducibility in the field;

  4. Pre-screening of faculty position candidates based on reliable new metrics.

For laboratory heads, postdocs and graduate students:

  1. Research fellows and graduate students get recognition for all the work performed;

  2. Freedom from “publish or perish” anxiety improves performance;

  3. Increased dissemination of non-confirmatory data and thus faster identification of non-reproducible experiments;

  4. New, more direct proxies for research quality included in grant applications;

  5. Decreased proliferation of academic journal articles (i.e. decreased information noise), thanks to the pruning effect of reproducibility coupled to the buffering effect of pre-publishing platforms.

For academic journals:

  1. Freedom from the indirect responsibility of deciding which laboratories deserve funding;

  2. Decrease the number of retractions, thanks to the reproducibility filter in pre-publishing platforms;

  3. Publish more authoritative and definitive science and less preliminary results;

  4. Better peer revision without any compromise on publishing both good and bad data in a complex article.

For the taxpayers and Science at large:

  1. Increase the pace of scientific discovery since you know what other scientists are developing “on the go”;

  2. Digitization of research data by tagging for equipment, procedures, reagents and other experimental conditions;

  3. Generation of novel metrics for quality of science by reducing the complex entity of an academic journal article into its component figures and experiments.

In conclusion, the need for a sustainable system in which to conduct our scientific endeavours does not require a revolution. A transition is possible and may be already underway.

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