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Stuart,
Apart from everything else that you wrote, I disagree with you on the above...
Bacteria can't "developed" genes....
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Bojan, I have to agree that I may have worded that better. You are quite correct, bacteria do not set out to "develop" genes.
Perhaps instead of
"Strep pneumoniae developed the genes to allow it to beef up its defences against our immune systems"
I could have written something more like:
"some Strep pneumoniae developed (by chance, not by intention or plan) the ability to produce a more robust external sugar capsule which gave them the ability to withstand human immune defences"
Still, while the bacteria did not set out to develop the genes, the genes must have developed for some reason. The more robust external capsule would not be present without the genetic information to code for it.
Craig, the "blind, unthinking, uncaring process" has no conscious intent. For example, I did not set out to develop immunity to a certain bacterium or virus, my body just did it as part of it's natural immune responses. (Not really a good example because developing an immune response like that is not an example of evolution, but you get the idea)
So at the "whole organism" level, there is no conscious intent. But at a much smaller level, down at the genes level things happen such as random mutations which may by pure chance happen to confer an increased chance of survival on the organism.
Stuart