Separation of concerns

In protein folding

At least three competing purposes for protein side-chains

• internal cohesion (hydrophobic side-chains in aqueous solution tend to nestle inside; lack of that gives intrinsically disordered proteins or worse)
• inter protein binding (protein quarternary structure; larger interfaces needed for decently controllable and stiff binding angles)
• outer functionality (binding small molecules and possibly catalyzing reactions between them)
• (allosteric long range motion transmission effects – when looking beyond stiff proteins as building blocks)

Related: Orthogonal set of protein binding interfaces

Holistic behavior on single side chain changes

Changing one side-chain on a protein to change a specific function
can often change conformation and function of the protein at a completely different site.
This is either ...

• ... a case of bad separation of concerns (that is tolerable for the host organisms species survival) or
• ... a case of separation of concerns at a higher level of abstraction that we do non yet understand

Both cases can pose interesting research problems but
neither case is useful for fast targeted development.

That is why stiff predictable folding protein motifs are of especial interest.
Protein that are rather insensitive to local changes.
See: De-novo protein engineering

Related: Fat finger problem

In design of artificial advanced productive nanosystems

Separation of concerns is highly desirable for

• better testability that is: easier narrowing down of bugs and
• better system comprehesability

=> Well distributed well debugable systems
rather than (outdated) ultra compact self replication monoliticmolecular assemblers following the biological cell analogy.

Both for bootstrapping (Modular molecular composite nanosystems, early diamondoid nanosystem pixel (direct path))
and for advanced productive nanosystems (gemstone metamaterial on chip factory).

In design of "early" nanosystems

The strong separation into one-task-only units in the cases of:

• 2D rail-frame based distributed modular pick-place assembly system
• Early diamondoid nanosystem pixel (direct path)
• Modular molecular composite nanosystems

In evolution and life

See: Decompression chain#Philosophical

Related

• Decompression chain
• Fat fingers & Floppy fingers – (Finger problems)
• Expanding the kinematic loop
• better system extendability by compsability of smaller predictably behaving sub building-blocks
  Thus there is no need for investing again and again in fom-near-scratch-one-off-research-effort for every new product.

External links

• Wikipedia: Separation of concerns

Generally in research and engineering

In cases where there …
– too many parameters that can be adjusted (for debugging and/or optimization) and
– it takes too much time/effort/money for one single of these many tests/experiments
Clear separation-of-concerns and changing just one parameter at a time is no longer a viable option.
Then there are available statistical methods that can help.

• Youtube video: Test Multiple Variables at Once to Optimize Anything – by NightHawkInLight (Taguchi arrays)
• Wikipedia: Taguchi_methods (German page with other info ~ i.e. more concrete as of 2024-03)
• Wikipedia: Design of experiments (DOE) (German page "statistical experiment-planning")