The Himalayan butterfly
The problem with intelligent design is: how can the intelligent designer control high level phenomena by monkeying with atoms and electrons?
If the intelligent designer is designing structures and machines within the cell (which is what is claimed), then these are constructed of molecules having interactions via the electrostatic force. These constructions are what evolutionists call "mutations".
But "mutations" are stored within the DNA, and so, ultimately; the intelligent designer designs new species by modifying the genes of the DNA resulting in new configurations of atoms and molecules. This is a very low-level activity involving thousands of changes.
It's like a butterfly flapping its wings in one part of the world causing a hurricane somewhere else.
But how can a butterfly in the Himalayas know in advance, that if it flaps its wings at such and such a time and such and such a place, that a hurricane will form in the Atlantic? Or perhaps this butterfly is benevolent and doesn't want there to be anymore life damaging hurricanes, so it skips a flap of its wings at just the right time and prevents one.
This highlights the problem of any of the intelligent design scenarios. The intelligent designer can only interact with the universe at the very small atomic scale, probably at the level of quantum mechanics by triggering wave function collapse of choosing where the electron (for example) will appear.
Looking at the specific details of intelligent design, we don't see any large scale, high-level, architectural design occurring. Yet we should expect the intelligent designer to be operating at this high-level, rather than being tangled up in molecular concerns.
It's as if a contractor working from a blueprint of an architect has to construct every tiny particle of every nail and screw, thereby loosing the sense of the overall performing arts theater (for example) that they are constructing.
And thus, this kind of intelligent design fails miserably.