Neither Congress nor the Federal judiciary is wholly separate and independent of each other.
Separation of powers is intertwined with checks and balances.
Courts, on the one hand, may check Congress through judicial review, by ascertaining whether congressional enactments exceed delegated constitutional powers or transgress a constitutional prohibition. Congress, on the other hand, is the preeminent branch, at least in theory. The constitutional design of the Federal judicial system is notably sketchy. For example, the number of associate justices, the Court's jurisdiction, and when it is to meet are not specifically stated in the Constitution. Whether there will be lower federal courts is a matter of judicial discretion.