One time I worked on a power grid simulation that wanted to release its code but it couldn't because it used algorithms from «Numerical Recipes: The Art of Scientific Computing» which has a pretty asinine copyright policy with respect to openness : http://www.nr.com/com/info-permissions.html
Even worse are the researchers who keep their models and data sets secret due to paranoia that some colleague will publish first, which admittedly does happen.
Cultivating a spirit of genuine cooperation and sharing in academia would do wonders for the progress of the sciences, but there are so many hurdles that need to be removed. It's not just a matter of knowing that it's good to release source code or feeling confident in including it as the article suggests.
I've come across the same problem. I was working on some ancient code purportedly released under a BSD license. However, it contained code from Numerical Recipes!
IANAL but as far as I understand copyright law it is impossible to copyright "an algorithm." What one can copyright is source code but as long as you do not copy the source verbatim it is not copyrighted. I would suggest you translate the algorithms from the book into mathematical expressions and then implement your own code from there. This should be legal to publish.
In this case it was a derivative work based upon source code from the book, which is permitted under the terms but precludes open dissemination. Further, the rest of the codebase was very tightly coupled to the algorithms since since the algorithms updated state in-place instead of returning values, so dropping in an open version of these algorithms was very non-trivial.
Even worse are the researchers who keep their models and data sets secret due to paranoia that some colleague will publish first, which admittedly does happen.
Cultivating a spirit of genuine cooperation and sharing in academia would do wonders for the progress of the sciences, but there are so many hurdles that need to be removed. It's not just a matter of knowing that it's good to release source code or feeling confident in including it as the article suggests.