Captain's Clerk position has probably existed as long as there were vessels with multiple crewmembers. It is a Warrant or Petty Officer position, as Terry stated. One of the jobs this position entailed was communication between the Captain and the Executive Officer of a vessel when the old adage "Familiarity breeds contempt" came into effect. (Whittle and Waddell on the C.S.S. Shenandoah) They were titled "Mister" in every reference I have read.
Mr. Hans Campbell was Lord Admiral Nelson's "secretary", another term I have found for "Captain's Clerk".
Some links to nautical sites that anyone could spend the rest of their lives reading are:
http://www.boat-links.com/linklists/boatlink-19.html