The Star Trek Deep Space Nine episode “Doctor Bashir, I Presume” was the 16th episode of season 5 and premiered on February 24th, 1997. This was the first appearance of the real life Dr. Zimmerman, who created Voyager’s EMH and the episode we learn about Bashir’s genetic enhancements.
The main plot of this episode was Lewis Zimmerman coming to Deep Space Nine to use Dr. Bashir as a template for a new medical hologram that would be used as the primary medical provider for distant outposts and stations where there was a lack of space. This would be called the Long-Term Medical Hologram or LMH. The first script writer Jimmy Diggs produced had this as the B plot with a different A plot. The producers didn’t like the A plot but liked the Bashir/Zimmerman story. Producer René Echevarria recalled that producer Ronald D. Moore wanted there to be a big secret.“his instinct was that there needed to be some big secret that Zimmerman uncovers, but we couldn’t, for the life of us, think what it would be.”(Star Trek: Deep Space Nine Companion), Ronald Moore was curious as to the dark secret Bashir is hiding and in discussing it with René the idea of genetric engineering came up. “I kept saying ‘What’s the secret of Bashir’s past? What’s the thing that this guy Zimmerman is going to find that’s so interesting?’ I remember that René and I started talking about genetics, and René pointed out that genetic engineering is one of the things that is oddly missing in the Star Trek universe. It’s a concept that’s very much out there in science fiction, and even in the real world of science, but in Star Trek, it’s virtually never discussed, aside from the fact that there was this thing called the Eugenics Wars at some point, and Khan came out of it.”(Star Trek: Deep Space Nine Companion).
According Ira Steven Behr having Bashir be genetically modified was a last minute decision.“at the time we were working on “In Purgatory’s Shadow” and “By Inferno’s Light”, we had no idea that Bashir was going to turn out to be genetically engineered. So even though it was the very next episode...” He was also never comfortable with the idea of genetic modification. “Doctor Bashir I Presume” was a terrific episode, but I was never totally comfortable with Julian’s genetic engineering. It was one of those revelations that did not seem quite authentic to me. We’d had to work backward to get it. So I felt we needed to do something to help the idea along”.(Star Trek: Deep Space Nine Companion). The idea of explored further in a Season 6 episode “Statistical Probabilities” which was written by René Echevarria.
Ronald D. Moore felt it explained some of the previous action that Bashir had made, “It really explained a lot about the character to me. He’d had some strange jigs and jags in his profile over the course of the first four seasons. We have this guy with a lot of arrogance, who almost became a tennis player, who has all these different tales of why and when he went to medical school, and why he didn’t become valedictorian of his class, and who has something about his past on Earth that he doesn’t want to talk about. When Odo was going to Earth in “Homefront”, he asked Bashir ‘Is there anybody you want me to look up?’ and Bashir says ‘I have nobody there I want to talk to.’ There was something in this guy’s back-story that was interesting, And it suddenly all made sense if this was a guy who’d been genetically engineered to be very, very smart but who’d had to hide it all his life.” (Star Trek: Deep Space Nine Companion).
According to the Star Trek Deep Space Nine Companion, the episode that aired ended differently than what was written at first, The original story had O’Brien discover that Dr. Zimmerman had deliberately sabotaged the LMH because he didn’t want it to replace the EMH. Zimmerman had planned to reveal the secet about Bashir’s genetic modifications. O’Brien threatens to reveal the truth about Zimmerman’s modifications to the LMH if he does. In the end a deal was made. Zimmerman would not reveal the truth about Bashir and O’Brien would keep quiet about the modifications made to the LMH. Alexander Siddig was not a fan of this. He didn’t like the long term implications of playing a character with a secret only he O’Brien and the audience knew about. He was concerned that having a secret would affect how the character interacted with others down the road. In the end the secret was revealed to everyone.
Alexander Siddig was not a fan of how the information about this major change to his character was revealed. In 2010 he did an interview with ugo.com but the link on Memory Alpha was dead. I was able to find his comments on a different site.