In Star Trek episode Space Seed, around the time 39:05, someone radios the bridge to inform the captain that Kahn had escaped. Moments after Kirk tries to sound security alert but then is unable to because communication channels had been jammed. Strangely, he could radio engineering, however he couldn't contact starbase 12. How is this explained?
I haven't seen the episode, but in old Naval ships there was a direct communication pipe between the bridge and engineering. Speaking Tube:
Voice pipes have generally been replaced by sound powered telephones. Even on modern ships, however, they may still be found linking wheelhouse and binnacle for communication of magnetic compass heading to the helmsman in the event of a blackout
So perhaps the Enterprise had a similar system, with some way of the bridge contacting engineering in the event of a communications failure.
According to the excellent (and semi-canon) "TNG Technical Manual", Federation Starships have long been fitted with multiple layers of communication between the bridge and sensitive locations such as Engineering.
"The hardware configuration for dedicated intraship communications involved a minimum of 12,000 allocated data line sets and terminal node devices distributed throughout the ship, in parallel with the pure hardware telemetry links of the Optical Data Network (ODN). This is the primary route for voice and data signals. An equal number of radio frequency (RF) based terminal node devices are distributed throughout the ship as a first backup layer. A second backup layer runs parallel to the Electro-Plasma System (EPS) and consists of 7500 kilometres of copper-yttrium-barium superconductive strands. This layer utilizes the same terminal node devices."
While it's a pretty common trope for the Bridge to be isolated from other parts of the ship, the writers seem to have gone to reasonable lengths to ensure that there are hard-lines between the most obvious places. While the ODN + RF systems may be down in "Space Seed" (as a result of electro-magnetic interference?), there's no reason to assume that the last backup layer had also been blocked.
Presumably (I do not remember this episode) what was being jammed was wireless communication (radio and the like), that is the only type that can be jammed, remotely at least and AFAIK. So, they were unable to use remote communications equipment.
The internal communications of a ship, especially a military vessel, are bound to be hard wired (again, no references, just my assumption) and would therefore be immune to jamming.
So, if there was, as would probably have been the case, a physical wire connecting Engineering to the Bridge, communications between them would not be affected by any kind of jamming.
A couple of possible reasons:
- It was on a different system, like how a house has different electrical circuits and all internal communications worked. Only off-ship communications (and process that used them) were jammed.
- Khan allowed him to communicate with engineering as that's where Khan was. If he couldn't communicate his demands, then holding the ship hostage (by tweeking life support) would have been pointless.