Final answer:
In paper chromatography, pencils are used to mark the application point to avoid interference with the separation process, as pencil graphite does not dissolve in the solvent unlike pen ink.
Step-by-step explanation:
In paper chromatography, a pencil is used to mark the application point instead of a pen because pencil marks don't interact with the substances being separated. Pens could dissolve in the solvents used in chromatography, possibly interfering with the results by adding extra substances to the mixture.
Pencil graphite does not dissolve in the solvent and therefore does not travel with the substances being separated, which makes it ideal for marking the starting point on the chromatography paper.