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I've started watching Voyager, finally, and I've noticed on more than one occasion, we see the Emergency Medical Holographic program (The Doctor) sitting at the desk in sickbay, working on the computer. In "Phage", he even makes a comment about having a lot of paperwork to do. Why? He is the computer, essentially. He could have a direct "mental" link to medical records, as well as medical references.

The only reason that comes to mind is that it's to make him seem more human. But that rationale only would make sense if he were intended to become a part of the crew. This happens on Voyager, but the EMH was intended to be a short-term emergency replacement. Building simulations of writing paperwork seems like a waste of both programmer effort and time that would be better spent during an emergency.

Is there another reason? Is this ever explained?

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    As a programmer I could give you reasons why I would have the doctor use the same interface to the ship's computer as the humans -- modularity, security and logging being some of them -- but I doubt that software engineering is on-topic for this SE. – Kyle Jones Mar 13 '14 at 1:13
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    @KyleJones If well explained, real-life explanations are acceptable to sci-fi questions. What you have in mind is pretty much what I would also answer – Izkata Mar 13 '14 at 1:29
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    As another programmer, this is an excellent question. The doctor is 'an interface' and, assuming security access is sufficiently modularized, there's no reason he can't access through the same security and logging modules that any other interface uses. – Stan Mar 13 '14 at 1:36
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    The security aspect would even work in both directions: By not being connected, he's able to work independently from other systems and other systems won't be able to influence him in a bad way (think of a computer program getting stuck due to a disk failure and the read operation never returning). Also it avoids adding even more complexity to his program and also making it more modular. A standalone system is far easier to integrate as one that has to be integrated with/linked to other systems. Since he already got a physical appearance, he can use that rather than needing a second method too. – Mario Mar 13 '14 at 9:05
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    @Kyle makes a good point but, as a senior software developer I can tell you that it's not good enough. He could be made to interface just behind the console display technology and still enjoy vast efficiency improvements without compromising any of the factors Kyle talks about. It's called re-usable code. There is no need to keep it physical (i.e. what Stan said). Of course in reality the reason is that it would be well boring if we never saw him do anything other than talk to people and perform surgery. – Lightness Races in Orbit Aug 11 '14 at 18:15
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Because The Doctor is performing tasks humans would normally handle

Remember that The Doctor is in a fairly unique position for an EMH:

Most notably The Doctor, a Mark I serving on the USS Voyager, ran almost continuously for years and was forced to expand his programming extensively to keep up. This EMH originally objected to being the replacement for the entire medical staff...

He's not meant to be a virtual medbay, his functions were intended to be an emergency pair of hands in case a human physician is no longer available.

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And let's remember that the Mark I was apparently not even that great at doing that job:

Eventually it was concluded that the EMH Mark I was defective, and they were bounced out of the medical corps. While an ashamed Dr. Zimmerman tried to have them decommissioned, Starfleet reassigned them to scrub plasma conduits on waste transfer barges. Later the Mark I's were also deployed in other menial tasks, like dilithium mining.

Same source, but I think it comes from "Life Line". Although The Doctor obviously beats these expectations. It's probably better to think of The Doctor as a med droid with bedside manner than a holographic interface into the Ship's computer itself.

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    I'd only add that the Doctor may not be designed to interface with the computer that way, not as a conscious design decision, but because it wasn't part of the spec. He's intended to be turned on for a few hours to supplement the medical team, then back off when the emergency is over. Presumably he'd be turned off by the time anyone sat down to do paperwork. He's also a Mark 1. It's possible that later versions of the software have those abilities. – Stephen Collings Mar 14 '14 at 1:17
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    While (regretfully) canon, the idea of holographic simulations being "reassigned" to menial labor is silly almost to the point of ridiculous. It seems that whichever writer came up with that idea forgot the Doctor is software and hardware, not a person. The support systems required for an EMH (computers, holoprojectors, etc) are part of the ship. Its far more likely that they would be refitted in-place (if needed) for a EMH upgrade, rather than removed and somehow installed in the engineering spaces of "waste transfer barges". – T.J.L. Jun 3 '15 at 12:49
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He either uses the computer because it's a 'goof' in the series which the writers' never noticed, or, the doctor's running (he is software) on a different part of the computer system which does not allow him to inter-operate between parts of the system which are not strictly related to projecting his image.

I guess you could say that it would make sense to enable him to interact directly with the computer system - or, if you want to narrow the parameter - allow him to interact completely with the computer's medical related parts, i'e., instead of saying 'computer, do...' he could 'think' it.

The only problem with this - and it's not a tech issue, but, more of a visual, i.e., story issue, is that it wouldn't really require him to do/need anyone else's assistance, input, interaction, as all his (medical) needs would be 'done' for him, and that's not much of a help on a TV series.

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