[DocSavage87]

Executive branch agencies aren't independent. They report to the POTUS. You don't just say no, unless it is illegal. Just like in you day job, you boss may sometimes tell you to do things that you think are stupid. You point that out to your boss, and if he says do it anyway, you either do it or you quit. In all organizations, there is a balance between the leaders and the led. Organizations like the FDA are given lots of latitude to police themselves, and no president would like to get "caught" meddling in the FDA's decision making process. However, the fact is the POTUS does have influence. Always has. Other organizations, like HHS, are more command driven. There is an agenda and you follow it.
Good presidents, like all good managers, try to hire good people whose judgement they trust. If a lab head reports back that an idea is absurd, the POTUS will say, OK, thanks for looking and move on. You give your subordinates parameters and trust them to execute within them. It has never been true that the departments in the executive branch just did what they thought was best for the country and who cares what our superiors think.
The problem isn't that the POTUS is the boss. The problem is that the boss is an idiot and tells people to do too many stupid things. Lots of them have quit. Most won't take the job from Trump. However, that isn't because the structure is broken. It is because the leader is broken.

The structure is broken and it's because we had assumed "norms" would be sufficient safeguards and if norms were broken, checks and balances like congressional impeachment powers would be sufficient.  This has proven not to be sufficient.  If the president and the Senate are together on doing whatever they want, POTUS can fire Inspector Generals, which really should be similar to independent counsels.  The IGs have been decimated under Trump and most were monitoring clear violations (e.g., asking UK to move British Open to Trump's golf course, firing employees despite whistleblower protections, etc).  I've edited out examples in a number of departments for the sake of Terry's Rule. In the case of both the FDA and the CDC, norms are also being violated.  CDC has been effectively muzzled.  Compare H1N1 and SARS-CoV-2 in terms of CDC press conferences and autonomy.  Unlike some other institutions, I'm not sure anyone anticipates an attack on medical or science policy.  It's interesting that there are IGs for both the CDC and FDA as well. I didn't know that before I googled it.

[DocSavage87]

Executive branch agencies aren't independent. They report to the POTUS. You don't just say no, unless it is illegal. Just like in you day job, you boss may sometimes tell you to do things that you think are stupid. You point that out to your boss, and if he says do it anyway, you either do it or you quit. In all organizations, there is a balance between the leaders and the led. Organizations like the FDA are given lots of latitude to police themselves, and no president would like to get "caught" meddling in the FDA's decision making process. However, the fact is the POTUS does have influence. Always has. Other organizations, like HHS, are more command driven. There is an agenda and you follow it.
Good presidents, like all good managers, try to hire good people whose judgement they trust. If a lab head reports back that an idea is absurd, the POTUS will say, OK, thanks for looking and move on. You give your subordinates parameters and trust them to execute within them. It has never been true that the departments in the executive branch just did what they thought was best for the country and who cares what our superiors think.
The problem isn't that the POTUS is the boss. The problem is that the boss is an idiot and tells people to do too many stupid things. Lots of them have quit. Most won't take the job from Trump. However, that isn't because the structure is broken. It is because the leader is broken.

The structure is broken and it's because we had assumed "norms" would be sufficient safeguards and if norms were broken, checks and balances like congressional impeachment powers would be sufficient.  This has proven not to be sufficient.  If the president and the Senate are together on doing whatever they want, POTUS can fire Inspector Generals, which really should be similar to independent counsels.  The IGs have been decimated under Trump and most were monitoring clear violations (e.g., asking UK to move British Open to Trump's golf course, firing employees despite whistleblower protections, etc).  I've edited out examples in a number of departments for the sake of Terry's Rule. In the case of both the FDA and the CDC, norms are also being violated.  CDC has been effectively muzzled.  Compare H1N1 and SARS-CoV-2 in terms of CDC press conferences and autonomy.  Unlike some other institutions, I'm not sure anyone anticipates an attack on medical or science policy.  It's interesting that there are IGs for both the CDC and FDA as well. I didn't know that before I googled it.