Godel's incompleteness and the Halting problem preclude an unbreakable system. Any certificate that code is bug free, secure, has no back doors, halts, etc. is doomed to fail, in general, for systems that are complex enough.
The situation is, theoretically, much worse, where one can even embed backdoors into the compilers themselves and then have the backdoor propagate undetected in perpetuity . This has been known for a long time and Ken Thompson had a famous article "Reflections on Trusting Trust" (1984) [0] that talks about this issue.
In practice, this tends to be very difficult. Extra functionality introduces bloat and complexity. Obfuscation needs to be de-obfuscated by some method, usually known methods. Open source, many eyes, re-implementation and observation and mitigation tend to catch these issues.
Vulnerabilities (in my opinion) tend to get introduced from unintended behavior (bugs) and, very rarely, through directed premeditated malicious action (supply chain attacks, say). Unintended behavior can be exploited by attackers but wasn't introduced with the intent of obfuscation, whereas malice action tends to try and hide themselves.
There's no silver bullet. The best we can do is try to create systems that have certificates of security where we can (for, say restricted computation models) and create empirical tests and responses for the rest. For example, SQL is Turning machine equivalent, so the way around running into the halting problem is to have a timeout that will fail when triggered and leave it up to the user to create a query that runs under time constraints.
You come from biology, so you should know better than most that our body is under constant assault from foreign invaders. Some viruses come in and rewrite code that can then sneak past the immune response, replicate themselves, etc. Our body has evolved a bunch of empirical responses to such malicious action. "Cell not communicating properly?" kill it. "We're under attack?" chop up the invader to get identifying signatures for a counterattack. I'm sure you know better than me all the intricate and complicated ways our immune system handles attacks. It's not perfect, but it does pretty well, considering.
I think there is a contingent of computer scientists and software developers that we should only be using restricted computation models for critical software, so that we can reason about what the software does. This effectively sidesteps Godel's incompleteness/Halting problem because it's not general computing. My feeling is those are, as well, doomed to failure as Turing machine completeness is the norm and very hard to avoid and any system that's so crippled as to not be Turing machine equivalent has limited use.
[0] https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref...