I'm not referring to the "human" name or birth certificate name of the scientist, but did the bad guy have a moniker like all of the other bad guys and vigilantes?
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The villain was Curt Connors, played by Rhys Ifans. In the comics, this character is known as the Lizard, as explained here.
From a transcript:
CURT CONNORS: Welcome, my name is Dr. Curtis Connors. And yes, in case you're wondering, I'm a southpaw.
The film's director (Mark Webb) has confirmed in a number of interviews that the character in the film you're referring to is The Lizard. He's also spoken to why he decided to include him as the film's primary antagonist...
SR: Were you the one to select the Lizard as the central villain and what inspired that choice?
MW: “I’d always been a fan of the Lizard. In the world that were creating, I feel like the Lizard embodies, literally, one of the more important themes of the movie which is that we all have a missing piece. Right? Curt Connors is missing his arm, Peter is missing his parents and how you choose to fill that void is how you define yourself. And they make different pathways that become more apparent as the movie progresses but that was one of the things that I thought was particularly symmetrical about that villain. And the other thing is that he’s Peter’s friend in a way. Which gives Peter another set of problems he has to overcome. You can’t just kill the villain without some sort of emotional consequence.”
...and the reason why he selected the 'look' of the Lizard from the older serials, rather than the most recent ("snouted") version.
Question: Can you talk a little about just bringing the Lizard to life and technically how you accomplished it? I imagine it was all motion capture?
Marc Webb: There’s a lot that goes into it. I mean there was… When we shot those sequences we actually shot a human, a rather large… There was a combination of things. There was a guy named “Big John,” who was literally this big guy named John who did a lot of the interactive stuff, because when you are trying to interact with Andrew, with “Peter,” you need someone grabbing him to do those things and then we would replace him with the computer generated Lizard. But then the performance capture was done with Rhys and that was we would shoot Rhys in a similar environment and get his facial components, (Laughs) which we are still working on. I actually just came from SPI trying to incorporate his performance into the Lizard itself. That takes an enormous amount of time and it’s tricky. In the comics there’s different incarnations of the Lizard. There’s the one with the snout, and I was interested more with something that could relate human emotions, because I wanted to keep Rhys’s performance in that creature and I was interested in. You know performance; Pixar does it extremely well like creating the emotional qualities within characters that are essentially computer generated. So Rhys’s performance, getting that nuance and getting those ticks and the looks and creating an armature that can actually speak and lips that make sounds… (Laughs) It’s a very detailed and tedious process, but I really wanted him to have emotion. I wanted him to have a face and have a feeling and that’s the way I chose to do that and then there’s the physical components of it, where I wanted to make him very powerful. I wanted to make him stronger than Spiderman, that’s a really important part of it.