Beyond side channels I'm even more worried about the ever present issues of poor security design/architecture and of security-critical components being written in unsafe languages. The fact that there is always another buffer overflow waiting in the kernel, in the browser, etc is nonsense. Who knows when someone will find a critical vulnerability in libjpeg and start manipulating images to take over the browser, then call a vulnerable syscall to install a rootkit.
I really want to run a microkernel (so poorly written driver code doesn't compromise the whole system) written in a safe language with arbitrarily nestable security contexts (eg. beyond users having different privileges, I want any program to be able to spawn processes, threads, etc in more restricted contexts, which can also spawn more restricted children, etc).
Also I want a modern Lisp machine...
Yes and no. I would love a usable lisp OS (especially Racket) even without special hardware. But with hardware designed for it I'm sure it would be better. One of the major reasons Lisp Machines died is that Moore's Law was so fast that by the time you finished the longer design of the specialized hardware newer simple chips were already faster. Now that Moore's law (and friends) are largely over that could change.
Just the other day there was an article circulating about recent work on hardware assisted GC. Combined with eg. math instructions that automatically strip and check the type tag, etc, I could see it ameliorating many of the performance concerns of using higher level lamguages.
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