Were the SAM units in standby mode until arrival in Andromeda?

Sams without organic puppets are still functional to a degree. Just remember turian pathfinder mission, turian Sam was navigating Ark on it's own.
Which also answers your second question - they control the ship while everyone is asleep.
Also AIs don't rely on chemical processes to stimulate acquiring new experience, so they can't get bored.

Yes, all Arks come equipped with a SAM. 
A quarian being okay with being connected to a SAM wouldn't be that strange. Remember, a decent percentage of the quarians in the Migrant Fleet don't hate AI, seeing the Geth as the victims in the Morning War. And these are quarians who have left the Migrant Fleet so they may be even more accepting of AI. 
The Pathfinder for their Ark is a Quarian. That much is confirmed.

I can't exactly disagree, since I believe that writers themselves didn't think it through completely, but I don't see much of indication for what you are saying.
It wasn't said that they require organic sensory input to function, Sam could use any recording devices on his own just fine. My headcanon is that Sams need organics to develop themselves - reasoning, decision making, priorities - all that jazz programs are weak at.
As you said yourself turian Sam was damaged by failed transfer, so it's functionality would be even worse than without puppet. If it could eject cryopods in "standby mod", then let's call it that, but I wouldn't call it non-functional.


As far as I remember Sam was recalibrating Hyperion's sensors after being hit by the Scourge, so it does have access to ship systems. It might be manually limited for safety reasons, but controlling a ship wouldn't be a problem for any proper AI.

Clarification: Natanus SAM is the Turian AI, Pachero SAM is the Salarian AI.
When NSAM is encountered, this one seems fairly stable as the transfer process had been initiated, but not completed until the replacement Pathfinder was actually in the room.
The only dialogue I remember is that the replacement Turian Pathfinder was getting a series of spatial co-ordinates via their SAM implant, but not direct communication.
PSAM on the other hand, was babbling gibberish until HSAM blocked out the "trauma" of having a connection improperly severed.
In my version, the replacement Salarian Pathfinder was also lost, so the position was transferred to the third candidate, the captain of Ark Pachero.

It makes sense that HSAM is the most advanced one, since he started first, being active for several years and connected to two individuals prior to being installed on Ark Hyperion.
I assume they just copied his design and replicated it for each successive Ark that needed a SAM node.

From the dialogue when HSAM is given a math problem to solve, it appears the data has to be transferred into his matrix directly and the solution downloaded again via omnitool data drives.
I'm assuming this is required because the ones with the problem didn't have direct access to his data transfer channels.
Probably a good thing, since the math problem was loaded with a SAMkiller virus.
So I assumed all modifications he performs are done similarly, he's sent the problem as a data packet, rewrites the code and sends it back to be uploaded to the system he was modifying.

Also, a key difference is that EDI is actually in the Normandy and a portion of her mind is present in every computer storage node on the Normandy SR2, giving her direct access/control when necessary.
SAM by comparison is physically located in the Arks, so perhaps that distance is too far to have realtime contact with the Tempest's computer systems.
Since the SAM nodes operate by quantum entanglement and this communication technology isn't exactly easy to fabricate, it would stand to reason that there is a limited number of quantum connections the SAM nodes can have.
Short version, a quantum entanglement communicator requires the isolation of two synchronised particles, which are then separated and placed at either end of the comm channel.
For each new channel that is required, a new pair has to be created.
I assume the QECs are installed in the Pathfinder implants, thus limiting SAM to conventional transmission channels when contacting non-Pathfinders or accessing ship control systems.


I do read most of the novels, but I chose not to read Mass Effect: Initiation because it appears to be about Cora's personal story and she's my least favourite squadmate.
Given that I didn't enjoy the one mission where I was required to bring her along manditorily, I thought it would best to avoid a novel where she is playing the central lead role.

Tilarta, I believe you're misremembering the game. It was the turian SAM aboard Ark Natanus that was "babbling", though that's not the right word. It was more like stuttering, because it sustained trauma during the failed transfer to Avitus. It was not speaking gibberish or nonsense. It was simply struggling to articulate. It was clear-thinking enough to bring Avitus to it.

I've completed the game 10 times (100% completion) and have never interacted with the salarians' SAM. When and where does this happen? Paarchero's SAM had been dismantled by Zevin Raeka in order to protect herself and it from the kett. When did you speak with it and hear it "babbling"? You're confusing the scene aboard Natanus with Paarchero.

Also, you're wrong in believing that our SAM's code was copied and pasted to the other arks. Those SAMs were based off of early versions of SAM's code, but not his advanced form. SAM was well aware of the other SAMs, as well as his own superiority, in 2184. Those SAMs were already completed by then, whereas Alec continued refining our SAM in secret long after.

I'd recommend replaying the game, watching some YouTube videos and/or hitting the wiki. You seem to have some intricate suppositions concerning SAM, but they don't really match the lore we have.

I don't remember EDI saying she was at any disadvantage controlling the normandy.  Only that it was better to have Joker and her both flying the ship, as he is an organic that is unpredictable, or something along those lines. 

The novel goes into even more details. SAM in ME Andromeda is more restricted than SAM in the novel due to safety reasons. Still, as you say, it assumes a dangerous level of integration with Ryder in order to augment his or her capabilities. Our SAM is what Alex had in mind from the start. The others are a measured concession to the Ai. Alec rightly feared that the true version of SAM wouldn’t have been immediately accepted by the Ai leadership.