Not much is known about what silica pathways are, but Commander Adama compares them to a brain of sorts for Cylons when he confronts Leoben Conoy within the bowels of Ragnar Anchorage in the Mini-Series.
Apparently, they are affected by the radiation generated by cosmic storms, such as the one surrounding Ragnar Anchorage. Although these affects are not immediate, they do usually occur within the space of hours after initial exposure (Humans appear to experience no symptoms; only Cylons are affected). While the Colonial military picked this location for the depot based on the mechanical Cylon Centurion Model 0005 and similiar models from the Cylon War, it was fortuitous that the Humano-Cylon models were also affected by the storm radiation as well. It is unknown whether the mechanical Cylon models would be affected in a faster fashion.
Through observations of what happened to the Leoben and Aaron Doral copies after their extended stays within the station, symptoms seem to include elements of headache, nausea, and some level of fever or other heat-producing symptom (Humano-Cylons do sweat ("Flesh and Bone")).
Whatever silica pathways may be, medical scanning technology cannot destinguish between them and human brain tissue. Otherwise, a brain scan ("Home, Part II") would visually show the differences between Cylon and human brains, foregoing the need for Gaius Baltar's Cylon detector.
Note
Since humans are based on carbon compounds, viewers may think that synthetic Cylons would be easily detectable since human bodies should have far fewer silicate compounds than that of a Humano-Cylon. But, given Gaius Baltar's duplicity in serving himself versus the good of the surviving Colonials, it is possible that this detection option is one he has chosen to ignore. Or, the use of silicates may still be key to Cylon "brain" design, but could use the same proportions of silicate traces found in the human body, with neglible differences.