To come to the point, it is arguable that recent events challenge the notion of human perfectibility aided by scientific progress. It is also arguable that some event like a pandemic challenges the notion that decisions will always be better when left to the individual. — graham hackett

If the objective is to find a set of principles that apply in any hypothetical environment, I don't think you'll ever be successful. At some point, I think you have to apply some degree of pragmatism when circumstances change, temporarily or permanently. The point being, in times when an infectious disease does not threaten to wipe out the human race (and I understand that is an exaggeration of the current situation), what sorts of individual liberties ought be afforded and why? I think Mill's responses to that are persuasive, and I'm not terribly concerned and ready to jettison his theories just because we now are facing that sort of crisis. As with all theories (and consider perhaps comparing his ethical theory to Kant's), you can always arrive at some hypothetical that makes it unworkable. Will Kant really allow the world to explode if it means having to sacrifice a single person? Would Mill really allow me to throw innocent children in front of a runaway train in order to save a larger group of people? I mean, maybe, maybe not, but those sorts of things really don't happen enough for me to be concerned (again pragmatism).

These sorts of issues arise in other contexts. The US Constitution affords certain rights (not wholly different from what Mill advocates), and so one day a guy says he doesn't have to be inoculated against smallpox because that's his right. The Supreme Court in Jacobson v. Mass. said:

"The liberty secured by the Constitution of the United States does not import an absolute right in each person to be at all times, and in all circumstances, wholly freed from restraint, nor is it an element in such liberty that one person, or a minority of persons residing in any community and enjoying the benefits of its local government, should have power to dominate the majority when supported in their action by the authority of the State.

It is within the police power of a State to enact a compulsory vaccination law, and it is for the legislature, and not for the courts, to determine."

It's fairly clear the Constitution sounds fairly absolute in its declarations, yet, when it's interpreted, it has to make sense within the context it's being applied. But, as noted, the Court does not say "we hereby discard the principles set forth in the Constitution as unworkable" (as you suggest maybe it's time to swap Mill for Hobbes), but it instead explains how this exception must now apply. Philosophically we might consider this ad hoc because we don't have to live in the real world and apply our principles, which is why I consider pragmatism the proper way to describe how we allow for these exceptions.

There is a statement in the law that says "the Constitution is not a suicide pact" , which more clearly can be stated as "the belief that constitutional restrictions on governmental power must be balanced against the need for survival of the state and its people. It is most often attributed to Abraham Lincoln, as a response to charges that he was violating the United States Constitution by suspending habeas corpus during the American Civil War." https://en.wikipedia.org/wiki/The_Constitution_is_not_a_suicide_pact

I think you can apply this same logic to Mill.

And, no, don't kick yourself for now realizing there might be problems with your thesis or that you should have least considered additional matters before submitting it. The purpose of your thesis was to get your degree, and you did that. But then again, I'm a pragmatist as to all things.

The Mill of On Liberty wasn't the only Mill. Perhaps as part of his efforts to free himself from the teachings of his horrible father, Mill in other works took the position that certain individuals, in fact the majority of them, should have a reduced influence on politics. So, for example, in his Considerations on Representative Government, he favored a system of weighted voting, with the "common man" being given one vote while the votes of others, being better educated, wiser, more thoughtful, more experienced, would be counted as the equivalent of four or five of the votes of a commoner.

He even supported Coleridge's idea of a clerisy, a kind of elite, made up of an awkward combination of theologians, scientists, scholars, experts, ruling the land at public expense. A kind of benevolent oligarchy, as it were.

A complicated fellow. I frankly doubt that he would leave decisions to individuals in a pandemic; at least not to most individuals.

Am I too pessimistic in thinking that I should throw out Mills "On Liberty", and buy a new copy of Hobbes "Leviathan"? — graham hackett

There are two meanings of liberty.

We can mean liberty in the sense of individual freedom of action as you have been considering.

However, there is another meaning of liberty which is "equal political participant"; arguably the original meaning. The concepts naturally go together, as an equal political participant and first class citizen naturally has lots of liberty of action and expression, as much as anyone else (otherwise, by definition, there would be some higher political class with such liberties that actually manages things).

For instance, serfs did not have liberties of a political sense of equally participating in politics compared to aristocrats. They also didn't have liberties of the physical actions sense in terms of where they could go, what they could sell, etc. So although serfs "becoming equal" really only matters in terms of political participation (as there will always be rules) the visceral experience of "not having liberty" is being subject to those rules that apply to second class citizens and not first class citizens and so the two ideas are easily confused one for the other.

Getting rid of rules beyond the ideal of equal participation has no expected bearing on both kinds of liberties. For instance, if getting rid of a rule creates endemic corruption and subjugation by a new aristocratic class that has all the meaningful levers of power, then one has "given up essential Liberty, to purchase a little temporary Grift and deserve neither Liberty nor Grift."

So a situation like a pandemic which obviously requires changes to our general liberty of action, need not change political liberties of being a equal political participant.

Countries that can be said to have genuine political liberty of this sense (Switzerland, Scandinavia, New Zealand and a few others) the pandemic creates no "authoritarian anxiety", as there was none to begin with. Of course, there's lot's of discussion of what's best to do, as with any subject of government policy, but there is no fear that the pandemic will remove this liberty of political expression and participation and that the government can somehow "take advantage" (they will simply be voted out if they don't manage in a way generally approved).

However, countries that don't have much political liberty in this sense (where people objectively aren't equal political participants; either due to electoral design, endemic corruption and disenfranchisement, or simply being a straight up totalitarian state not even pretending to be democratic) then the pandemic amplifies authoritarian anxiety, as well as the real risk of even more of it, as the people don't have a sense of "being in control of a transparent and accountable government" before the crisis, and so the emergency powers and chaos of the pandemic simply bring this fact to the fore with very real reasons things may go even further away from genuine political participation (that the first class citizens that have the real liberties in both senses of the word, don't let a crisis "go to waste").

In other words, those who have liberty shall be given more and those that do not have liberty shall lose even that liberty which they had.

One thing to wonder about is how much "freedom" is happening before the alarm clangs and we are all called to carry buckets of water.
Most of us don't know where the well is. A large number are surprised that there is a well at all, as a concept.
It is not an ideal situation for collective action.

I am very appreciative of the responses to my post.
I suppose what I am clawing my way towards (a journey which I think will never end), is a model of democracy which will cope well in “normal” times, but have enough flexibility in it to deal with the unusual, the cataclysmic, the lifestyle threatening event - and then be able to return to the (almost) status quo ante bellum.

We might recognise that some forms of anarchism are arguably democratic, in holding that personal freedom is so important, that there is no role whatsoever for the state. Nozick is not quite anarchistic, in that he will allow govt a nightwatchman role. However, many would argue that this would allow a pre-eminent role for those who have a large share of resources, and can therefore position themselves favourably when any calamity strikes.

Mill would certainly have argued for an instrumental justification of democracy, in that it produces good results, good solutions, good laws, whereas non democratic states arguably result in the opposite. He seemed happy with the majority based representative democracy that many of us may think is the essence. He would probably have argued for an aristocratic element in the presence of a “selectorate” of participants with a base in science and technology. However, it could be argued that a government based on speeches and majorities is not a true democracy. Am I falteringly arguing for the kind of deliberative democracracy advocated by Fishkin? (Stanford Center for Deliberative Democracy). As I tentatively view it, deliberative democracy argues that purely representative democracy would not be able to cope well with such issues as pandemics. We need to “own” the decisions made by government. It is not good enough just to have these decisions validated by a majority. They must be our decisions. Perhaps if the pandemic, or other calamity is “our” pandemic, democracy will be ably to cope.

Mills version of democracy is suspicious of paternalistic intervention, but paternalistic intervention might have a part to play in unusual times (eg; “good samaritan laws).

I must stop here, because my Rousseau Detector has just set off an alarm.