What should a pilot do if ATC issues a clearance that would cause a deviation from regulations or place the aircraft in jeopardy?

4-4-1. Clearance
a. A clearance issued by ATC is predicated on known traffic and known physical airport conditions. An ATC
clearance means an authorization by ATC, for the purpose of preventing collision between known aircraft, for
an aircraft to proceed under specified conditions within controlled airspace. IT IS NOT AUTHORIZATION
FOR A PILOT TO DEVIATE FROM ANY RULE, REGULATION, OR MINIMUM ALTITUDE NOR TO
CONDUCT UNSAFE OPERATION OF THE AIRCRAFT.
b. 14 CFR section 91.3(a) states: "The pilot-in-command of an aircraft is directly responsible for, and is the
final authority as to, the operation of that aircraft." If ATC issues a clearance that would cause a pilot to deviate
from a rule or regulation, or in the pilot's opinion, would place the aircraft in jeopardy, IT IS THE PILOT'S
RESPONSIBILITY TO REQUEST AN AMENDED CLEARANCE. Similarly, if a pilot prefers to follow a
different course of action, such as make a 360 degree turn for spacing to follow traffic when established in a
landing or approach sequence, land on a different runway, takeoff from a different intersection, takeoff from the
threshold instead of an intersection, or delay operation, THE PILOT IS EXPECTED TO INFORM ATC
ACCORDINGLY . When the pilot requests a different course of action, however, the pilot is expected to
cooperate so as to preclude disruption of traffic flow or creation of conflicting patterns. The pilot is also expected
to use the appropriate aircraft call sign to acknowledge all ATC clearances, frequency changes, or advisory
information.
c. Each pilot who deviates from an ATC clearance in response to a Traffic Alert and Collision Avoidance
System resolution advisory must notify ATC of that deviation as soon as possible.
REFERENCE-
Pilot/Controller Glossary Term- Traffic Alert and Collision Avoidance System.
d. When weather conditions permit, during the time an IFR flight is operating, it is the direct responsibility
of the pilot to avoid other aircraft since VFR flights may be operating in the same area without the knowledge
of ATC. Traffic clearances provide standard separation only between IFR flights.