I'm a little perplexed by the direction of the current discussion over Ireland's chief scientific advisor.
The need for scientific advice, as a driver of (and sanity check upon) evidence-based policy formation, has arguably never been greater. Certainly many of the challenges we face living in the 21st century are, directly or indirectly, influenced by a sound understanding of both the science and its limitations. This is why it's attractive for governments to have dedicated, independent scientific advisors.
We need first to be clear what a good chief scientific advisor isn't, and that is an oracle. The chief scientist will presumably be a trained, nationally and internationally respected practitioner who brings to the job an experience in the practice of science but also in its wider analysis and impact. In many respects these are the qualities one looks for in a senior academic -- a full professor -- so it's unsurprising that chief scientists are often current or former (emeritus) professors at leading institutions. They will not be expert on all the areas of science required to address any particular policy question -- indeed, they might never be expert in the details pertaining to any question asked -- but they can act as a gateway to those who are expert, and collate and contrast the possibly conflicting views of different experts who might be consulted in each case. They provide a bridge in this sense between the world of the research and the world of policy, and will need to be able to explain clearly the basis and consequences of what the science is saying.
Ireland has recently abandoned having a chief scientist as an independent role, and has instead elected to combine it with the role of Director of Science Foundation Ireland, the main advanced research funding agency. There are several stated reasons for this, most centring on the current resource constraints facing government spending.
I don't think this structure is really consistent with the role of chief scientist, nor with the principles of good governance.
To avoid any misunderstandings, let's be clear that this has nothing to do with the individuals involved: the current or former directors of SFI would be eminently suited to be a chief scientist in their own right. However, having the SFI director fill this additional role ex officio seems not to be best practice. The concern must be that the combined role cannot be independent by its very nature, in that the scientific direction of SFI may wholly or in part be involved in the policy decisions being made as a consequence of advice received. If this occurs, the chief scientist is then recommending actions for which the director must take responsibility, and the perception of a confusion of interest is inevitable if these roles are filled by the same individual. To repeat, the integrity of the office-holders is not the issue, but rather a governance structure that conflates the two roles of execution and oversight.
If resource constraints are really the issue, one might say that the chief scientist does not need to be independently employed to be independent in the appropriate sense. The chief scientific advisory roles in the UK, for example, are typically filled by academics on part-time release from their host institutions. They collate and offer scientific advice, possibly made better by the fact that they remain active researchers and so remain current on both the science and its practice, rather than being entirely re-located into the public service. (The chief scientific advisor for Scotland, for example, remains a computer science researcher at the University of Glasgow in addition to her advisory role.) The risk of confusion is significantly less in this structure, because a single academic in a single institution does not exert executive control or influence over wider funding decisions. Moreover the individual remains employed by (and in the career and pension structure of) their host university and is bought-out for part of their time, which reduces the costs significantly. It also means that one can adjust the time commitment as required.
I thought when the post was first created that it was unusual that the Irish chief scientist's post was full-time: requiring the (full-time) SFI director to find time in addition for the (presumably also full-time) duties of chief scientific advisor is expecting a lot.
It is of course vital for the government to be getting good science advice, so it's good that the chief scientist role is being kept in some form. But I think it would be preferable to think about the governance structure a little more, to avoid any possible perception of confusion whether or not such confusion exists in practice.