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We proceed to motivate why transparent research has superior properties and use ``live mathematics'' as one example of how Authorea enables it.  The core of the transparency problem is that we are still using the original publishing metaphor for documents, dating back to the innovations of 16th century Galileo Galilei, while simultaneously working on 21st century projects which are potentially large-scale, high-dimensional, multi-author and/or internationally distributed. distributed \cite{Pepe}.  The usual scientific document submitted to academic venues today is still oriented towards the printed page, remains opaque to the underlying data, of which it presents static snapshots, and is constrained by page count and margin sizes, often preventing it from providing sufficient detail of methodology and experimental setup. This disconnect between experimental results and publications offers room for unintentional bias and experimental defects to remain unnoticed, making it difficult for reviewers to verify, and for follow-up experiments to continue the work in question. In 2015 we have seen a stream of high-profile retractions from some of the best scored journals that illustrate this problem.