Academics have tended to view autonomy as freedom from constraint by the state. We want to be able to go wherever our thoughts lead us, without ‘outside’ interference. This interpretation of autonomy as freedom from constraint is a negative definition, appealing to what is absent. It says, ‘Hands off!’
Politicians have tended to view accountability only in economic terms — that is, accountability has been reduced to accounting and conceived narrowly as something like return on investment (ROI).
Under such ‘old thinking’, autonomy is opposed to accountability, since accountability conceived as demonstrable ROI puts constraints on the autonomy of researchers conceived as freedom from such demands.
Autonomy means self-legislation, rather than freedom from constraint. Under this ‘new thinking’ on autonomy, the point is not for academics to be free from all constraint (the negative definition rooted in old thinking), but rather for academics to give themselves whatever constraints they are subject to.
Accountability means being able to give an account, in the Socratic sense of the term. This is by no means limited to a notion of ROI, though such may be included in the account one is expected to give.
Under this ‘new thinking’ on autonomy and accountability, the accountability demand is expressed as the formal demand that one give an account. There is no reduction of that account to economic concepts. One is free to offer whatever justification one sees fit. In other words, one is able to exercise one’s autonomy to respond to the generic accountability demand: account for yourself! Under this ‘new thinking’, then, accountability and autonomy are compatible.
Someone may be quick to point out that these are not really new definitions of the terms. So much the better!