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[ba-ohs-talk] open source + patents = puzzled

This is a follow-on to the recent discussion on open source / free 
software licensing models etc. [there may be more appropriate mailing 
lists for this question but I don't know any I'm afraid so bear with 
me.]    (01)

An Open Source license between Developer and User typically allows 
User to use Developer's covered code without charge. Let's assume 
that Developer implemented XYZ algorithm and that that implementation 
is part of covered (ie open-sourced) code. This means, User can use 
Developer's implementation of XYZ algorithm without charge.    (02)

Let's assume for a second that Developer also patented XYZ algorithm 
(for simplicity, assume Developer patented XYZ algorithm "long 
before" he open-sourced the code). The patent isn't limited to any 
particular "embodiment" (I think that is the term -- this should be 
the normal case if the attorney knows what he is doing).    (03)

It sounds like the Open Source license grants User certain rights ... 
but what are those, exactly, given that there is a patent for XYZ 
algorithm?    (04)

In particular, let's say User re-implements XYZ algorithm in a more 
efficient way, or in a different programming language etc. (e.g. 
assembly code using no dynamic memory allocation for argument's 
sake). User's implementation of XYZ algorithm does not share even a 
single line of code with Developer's implementation of XYZ algorithm 
(which was subject to the Open Source license).    (05)

Am I paranoid, or does it sound like Developer can sue User for 
patent infringement because of User's complete re-implementation of 
XYZ algorithm? My understanding is that the typical Open Source 
license only covers *released code*, not *all* the intellectual 
property used for the code? In other words, Developer's "embodiment" 
of XYZ algorithm, as released in code, would be subject to the open 
source license, but Developer's patent of XYZ algorithm would not be, 
preventing the User from creating a more efficient re-implementation, 
for example?    (06)

Am I off-base here, or is there quite a can of worms hidden here 
somewhere? Anyone ever looked at the patent portfolio of any of the 
(particularly larger) companies that often release some of their own 
code into the public domain?    (07)

Confused ...    (08)

Johannes.    (09)