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-- It probably could be clearer, but at the moment the article tries to address this with the line:
Some government departments also have a Chief Scientific Adviser, most notably the Ministry of Defence.
A lot of Goverment departments have their own in-house scientific policy staff, led by somebody internal reporting to the highest level. Or, they may have a nominated external expert they use as the department's most visible external top-level consultant and/or scientific policy front man. Somebody acting in any of these roles might get the title of Chief Scientific Advisor to the deparment. The CSA to the Department of Transport is one example of one of these departmental CSAs.
The most notable of all is probably the MoD Scientific Adviser, as he has much by far the biggest budget to play with, and overall responsibility for the state of UK defence scientific knowledge - about eg possible new weapons systems (as opportunities, and as threats); biological weapons, and how to guard against them (and any risks of so doing), the scientific state and prospects of country's nuclear capability, etc, etc.
But talking about the CSA means the man responsible for briefing at government and cabinet-level, and the public face of the whole government's scientific awareness -- that is the UK Government Chief Scientific Adviser.
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