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I have no idea how synthetic biology works, but have a couple of questions from the applications section in the link.

They talk about designing vats of bacteria that extract gold from water. If this level of customization is possible, is it also possible that you could use this to create new disease strains ? For example, can you take a Tuberculosis and engineer it to make it harder to cure? Or create entirely new diseases with elements from different infections?

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yup that's one of the biggest fears with respect to bioterrorism.

engineering bacteria to produce new strains or even deadlier toxins is well within realm of synthetic biology (although currently extremely nontrivial).

Falling synthesis prices and better assembly techniques however will make the repeat-test cycle fast enough to debug and engineer such organisms.

However, even if one could produce such an organism with diybio technology, not killing oneself in the process would still be non-trivial.

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