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RichardKennaway comments on Second-Order Logic: The Controversy - Less Wrong
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First of all, swapped "induction" to "deduction", because I'm a moron.
There's no real semantic distinction between the original contents of the One Tape, or the finite contents of the Input Tape, or an arbitrarily complicated state-machine program, actually. You can build tape data for a Universal Turing Machine to simulate any other Turing machine.
No. You're just making the analogy between Turing machines and real, physical computing devices overly strict. A simple Turing machine takes a finite input, has a finite program, and either processes for finite time before accepting (possibly with something on an output tape or something like that), or runs forever.
Real, physical computing devices, both biological and silicon, run coinductive (infinite-loop-until-it-isn't) programs all the time. Every operating system kernel, or message loop, or game loop is a coinductive program: its chief job is to iterate forever, taking a finite time to process I/O in each step. Each step performs some definite amount of semantic work, but there is an indefinite number of steps (generally: until a special "STOP NOW" input is given). To reiterate: because these programs both loop infinitely and perform I/O (with the I/O data not being computable from anything the program has when it begins running, not being "predictable" in any sense by the program), they are physically-realizable programs that simply don't match the neat analogy of normal Turing machines.
Likewise, human beings loop infinitely and perform I/O. Which more-or-less gives away half my mathematical sketch of how we solve the problem!
They match the neat analogy of Turing machines that start with possibly infinitely many non-blank squares on their tapes. All the obvious things you might like to know are still undecidable. Is this machine guaranteed to eventually read every item of its input? Is there any input that will drive the machine into a certain one of its states? Will the machine ever write a given finite string? Will it eventually have written every finite prefix of a given infinite string? Will it ever halt? These are all straightforwardly reducible to the standard halting problem.
Or perhaps you would add to the model an environment that responds to what the machine does. In that case, represent the environment by an oracle (not necessarily a computable one), and define some turn-taking mechanism for the machine to ask questions and receive answers. All of the interesting questions remain undecidable.