Is the scientific paper outdated ?

There is a provoking paper by Ryan Abernathey (GS) that appeared on  The Chronicle of Higher Education which is entitled: The Scientific paper is outdated. The Author explains why, in his opinion.

I read it and I fully agree with the arguments. I dedicated part of my last 25 year of research in producing good designed software and I know that I sacrificed more than a paper to this task. Fortunately journals like GMD or EM&S built a bridge between paper writing and software building. The Author realizes also that just publishing software should be enough in most of the cases, but he is probably unaware that now this is actually possible with Joos, a new type of "journal" which is also commented here.