My advice; don't attempt this in a language you're not familiar with. The task you've set yourself is challenging, adding additional obstacles is not wise.
Java is not interpretted, it is compiled to byte code. Well written Java running on a good JIT compiler will be about 80% of the speed of C++ for a typical application. However yours is not a typical application, it is probably more processor heavy and the penalty may be higher. C# is similar in performance to Java.
I strongly suggest you don't use any form of compilation to native code for any of your A-life 'organisms'.