Human Source Code

We were not given any instructions, manuals, or source code to the human body.

this is similar to having purely a compiled ELF or EXE executable file and a hex editor to work with. In fact, it's even worse than that.
we are only hackers and reverse engineers, if we want to make any changes to the human body
- i.e. genetic engineering is actually reverse engineering.
- i.e. performing plastic surgery is just hacking. And so is hair styling.
we have no way of even contacting the company that released the human software that runs in our nervous system and brain. At least at proprietary software companies (i.e. microsoft), you can contact them, and the source code is available if really necessary.
Maybe the source code is available, but we were stubborn or ignorant and didn't find it or listen when we were supposed to
We have no tests, and adding them is costly and slow.

We have all of the source code, it just isn't well documented. Every line of code was written at random, so the author's intention would be meaningless. If we could view the acceptance tests that selected every change we'd see a very long series of reproductive events.

When an animal, plant, or human adapts to nature, is this new source code, or source code already inside the storage device?

There is no source code. Not unless by "source code" you mean machine instructions (not even assembler). And if you do then we really don't need to be wasting our time with you.

It's worse even than all of the above depicts because although we know what all of the instructions are named, we don't know the architecture of the computer that runs the machine instructions so we don't know what the instructions actually do, let alone how it gets done. (The Central Dogma of biology is quite dead.)

Further, we're pretty sure that the computer architectures of different species are sufficiently different that the same machine instructions will code for different things.