APDU SELECT communication on T=0, 1, CL

Outside of the software simulation realm, I am trying to figure out what data communications look like on the low level serial channel when APDU SELECT is sent via T=0, T=1 or T=CL.
I have reference material showing me the APDU (SELECT) packet format. Let's say a javacard is placed in the reader, and the terminal generates SELECT with a certain bytes sequence.
Before being sent over the channel, is the byte sequence (packet) for SELECT encrypted?
I had been skimming Global Platform and saw mention of the "secure channel" but don't understand where that comes into play. Is APDU SELECT wrapped within the secure channel and therefore encrypted?
Before SELECT arrives, there is no active applet so I am trying to figure out who would do the encryption, and with what keys. Or am I missing a layer -- is in fact everything that goes over the physical serial channel encrypted, so no APDUs are ever in the clear?

Outside of the software simulation realm, I am trying
to figure out what data communications look like on
the low level serial channel when APDU SELECT is sent
via T=0, T=1 or T=CL.SELECT command itself for a Java Card / Global Platform card is described on the application layer in the corresponding specifications. On the low level only the protocol (T=0/1: ISO7816-3, T=CL: ISO14443) is described . The APDU structure is described in ISO7816-4. The commands described are not supported with the exception of the GET RESPONSE command (commands are defined in JC/GP).
>
I have reference material showing me the APDU
(SELECT) packet format. Let's say a javacard is
placed in the reader, and the terminal generates
SELECT with a certain bytes sequence.
Before being sent over the channel, is the byte
sequence (packet) for SELECT encrypted?No. For a JC/GP card the SELECT command is never encrypted. It has a well defined structure.
>
I had been skimming Global Platform and saw mention
of the "secure channel" but don't understand where
that comes into play. Is APDU SELECT wrapped within
the secure channel and therefore encrypted?
Secure channel is used to establish a secured connection between the terminal and the card (Security Domain on-card). There are three levels of security (SCP01/02). First one is plain authentication, second is that a MAC is always added to every command (except SELECT, it closes a secure channel) after authentication, third one is that every command (exc. SELECT) is encrypted and MAC added after authentication.
Before SELECT arrives, there is no active applet so I
am trying to figure out who would do the encryption,
and with what keys. Or am I missing a layer -- is in
fact everything that goes over the physical serial
channel encrypted, so no APDUs are ever in the clear?By default the so called CardManager is selected. It is possible to have a default selected Applet or a Supplementary Security Domain as well. The CardManager (on-card representative of the issuer, also called Issuer Security Domain) or a Supplementary SD is handling the secure channel, this would include encryption.

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