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(If you missed an upgrade station, it's possible to start new game plus and get it there)
Research PhD also requires Turrets, Cameras and Security Bots (the flying thingies) to be fully researched.
The little sisters can be seen in the menu at every level, whether or not you have them (assuming you know this)
If you did all this, I guess it's bugged? :/
Only the last 3 you list are for the additional content.
http://steamcommunity.com/app/409710/discussions/0/154643249632216242/
In a nutshell, I've upgraded them all. For the Research PhD, as far as I can tell, I've got all the individual research Achievements and have fully researched the turrets, cameras, and security bots (at least that's what the game tells me when I try taking more pictures of them). And for Dealt with Every Little Sister, I've even gone back to each area, hit the ESC key to see the status screen, and confirmed I've saved them all:
Medical Pavilion: 2 Little Sisters saved
Neptune's Bounty: 3 Little Sisters saved
Arcadia: 2 Little Sisters saved
Farmer's Market: 1 Little Sister saved
Fork Frolic: 3 Little Sisters saved
Hephaestus: 3 Little Sisters saved
Apollo Square: 2 Little Sisters saved
Olympus Heights: 2 Little Sisters save
Point Prometheus: 3 Little Sisters saved
Total saved = 21 Little Sisters.
OBE, see below: I see references to one Little Sister in Farmer's Market and I'm positive I saved her. But, I'll have to go back and check (I only used the bathyscaphe to check the areas (assuming Farmers Market would be included in Arcadia's count).
EDIT: Yes. I've also saved the Little Sister in Farmer's Market. I've updated my list, above, to show that. Ditto for Olympus Heights. Thanks Relic62.
There are a total of 21 Little Sisters which can be rescued or harvested, disregarding any extra Little Sisters which may appear as a result of glitches. If the player harvests all 21 of these Little Sisters, he or she will gain a total of 3360 ADAM throughout the game. If the player rescues all of the Little Sisters, and finds all of the gifts from Dr. Tenenbaum, he or she will earn a total of 3080 ADAM and a number of Gene Tonics. Accessing the start menu will reveal the number of Little Sisters in the player's current level, as well as their current status.
https://youtu.be/s26-I9USFLk
EDIT: And this video confirms it. The first two (those in Welcome to Rapture) are inaccessible to us. The first one in the Medical Pavilion is the first we can harvest.
https://youtu.be/vJ15BffoP0o
It's also possible the game didn't give me the Historian Achievement when it should have. I thought I'd missed one in the "Welcome to Rapture" area. But, I've looked over a list of all the audo log transcripts and it sure looks like I picked them all up. I'll see what happens with this New Game Plus thing.
EDIT: For Historian, I finally figured out I could see what recordings I've picked up in the information screen (hit M and select the film icon). It turns out I missed three. Unfortunately, one was in Welcome to Rapture before the hole in the bathroom wall closed behind me. So, I can't go back and get it. I'll have to play an entirely new game to get that. Irritating that the game can close off a way back right at the start.
Medical Pavilion: 2
Neptune's Bounty: 3
Arcadia: 2
Farmer's Market: 1
Fort Frolic: 3
Hephaestus: 3
Olympus Heights: 2
Apollo Square: 2
Point Prometheus: 3
I'm in the midst of a New Game Plus run and will see if I get it there. The game did pop up my Weapon Specialist Achievement when I entered the Medical Pavilion in that NG+ run.
Regarding Research PhD, I've tried taking pictures of everything but a Spider Splicer so far. The game says I've already researched all of them to the max. Since I also have the Achievement for fully researching the Spider Slicer, I don't expect anything different from that when I run across one.
I just don't understand how a game can be fully aware of what I've done, yet not give the Achievements associated with having done those things.
EDIT: I've now tried taking a picture of a Spider Slicer. Again, I've already maxed my research on it. So, unless the game decides to finally decide I've got that Achievment, there's nothing more I can do with that one.
The game still hasn't given me the Research PhD Achievement. And, since there aren't any more events which might jar it loose, I don't expect it to.
At least I don't have to go through the rest of this tedium.
Your BioCherry got popped.
Take care.
This may bode well for me, then! There are a few enemies that didn't have an Achievement pop for me even though the game tells me I have researched them fully. They are Nitro Splicers, Spider Splicers, Bouncers, and Little Sisters.
I could have sworn that there were Achievements attached to researching Turrets, Security Cameras, and Security Bots, but I don't see them anymore. I hadn't played in a few months due to the Achievements not popping correctly (before the latest patch), so I wasn't sure if I just imagined those ones.
Strangely, I was now able to research Spider Splicers again even though the game had previously said it was complete! It happened with the first batch that Cohen sent after me in Fort Frolic! Hopefully the same will happen with the others that didn't work before.