As Timothy Lee says in the article, the problem with this type of patent is that it boxes in how you can use the original technology: you can freely tie your shoes with this shoelace, but if you use a double knot, now you infringe a patent.
In some ways, this mirrors the difference between copyleft and permissive copright licenses. By failing to patent the original invention, Duda made ANS useful and widely available, but he now has no leverage against Microsoft.