Duke Johnson and Charlie Kaufman, co-directors of “Anomalisa.”

“Apparently I like to have people not understand each other,” mused Charlie Kaufman during our conversation prior to the Chicago International Film Festival’s October 21st screening of his latest masterpiece, “Anomalisa.” Just as “Being John Malkovich” centered on a man bewildered by his failure to connect with fellow Earthlings (when he says, “My name is Schwartz,” to a receptionist, she repeats back, “My name is Warts”), “Anomalisa” follows an author, Michael (David Thewlis), who hears everyone speaking in the same voice (namely that of Tom Noonan, who memorably stalked Philip Seymour Hoffman in Kaufman’s 2008 debut feature, “Synecdoche, New York”). Yet upon hearing the distinctive tones of a voice belonging a young admirer, Lisa (Jennifer Jason Leigh), Michael becomes hopelessly smitten. The stop-motion animation devised by Kaufman and co-director Duke Johnson (“Mary Shelley’s Frankenhole”) is nothing short of astounding, replicating authentic nuances within a surrealistic medium.

Kaufman and Johnson spoke with Indie Outlook about their close collaboration, the endless appeal of Tom Noonan and how they went about meticulously preserving the mundane details of life.

What elements of the original “Anomalisa” sound play did you feel would translate well onto film?

Charlie Kaufman (CK): I didn’t really want it to be my next film project. I had a bunch of things that I was trying to get going, and this one just happened to take. At first, I was reticent because it was a sound play and now we’re making it visual. We’d be giving up a lot of the sort of stuff that I had conceived. We’d be visualizing things that were meant to be heard and imagined rather than seen. Eventually, we learned how it would work on film. For example, during the sex scene onstage—because it just consisted of actors reading scripts—Jennifer and David are standing twenty feet apart and moaning. It played very funny in front of a live audience because of the disconnect. We had to learn an entirely different way of achieving that disconnect onscreen, and make the film it’s own thing. Once the puppets started getting designed and the sets were being built and began to look really beautiful, I got excited about the prospect of what it was going to be.

The stop-motion animation offers a different sort of disconnect. I was blown away by the characters’ naturalistic movements.

Duke Johnson (DJ): The first thing we did was record the actors doing the voices. It was a little different from the play because it was a smaller, more contained, more intimate reading. It was very moving and immediately set the tone for our approach to the rest of the film. We realized that we wanted the film to be real and emotional and soulful, and so we decided to design the puppets based off of real people. We wanted them to have eyes that people could connect to, we wanted them to have eye lights like actors do in live action movies, and we wanted their movements to feel not like the kind of broad gestural archetypal movements that you typically see in animation. We wanted their movements to be kind of, at times, mundane. There are little things Michael does when he’s alone in the room where he scratches himself and adjusts his shirt. He also squeezes his temples a lot.

I loved the detail of Lisa bumping her head on the headboard during the sex scene.

DJ: We got other actors together to film reference videos for the characters’ physicality. The interesting thing with animation is that everything is a choice. Every detail and every subtle movement is a conscious decision that we make. One of the things we’ve noticed is that audiences have a sense of that. They know that every movement was decided upon and therefore, it allows you to pay particular attention to some of the more subtle things—

CK: And the mundane things, things that might not be interesting to people otherwise, like the way in which somebody walks around a hotel room. If it was a real actor walking around the room, it wouldn’t be inherently interesting.

Charlie Kaufman and Duke Johnson’s “Anomalisa.”

What intrigues you about Tom Noonan? His presence pervades both “Anomalisa” and “Synecdoche, New York.”

CK: Everything intrigues me about Tom Noonan. He’s very tall in real life, like 6’ 7’’ or something.

DJ: He’s very imposing but has a soft voice.

CK: I knew who Tom was as an actor, but I first really became aware of him when I saw a movie that he wrote and directed called, “What Happened Was…” I fell in love with that movie and I contacted him. I was working in TV, but wasn’t well-known at the time, and he wrote back to me right away. He was very nice and very appreciative, and we sort of started this correspondence. The quality of Tom that felt right for the radio play was his very specific cadence and his specific sort of intonation. I wanted someone who was recognizably the same voice in all these different places. Someone who had a more standard or generic way of speaking wasn’t going to work in the same way. There’s a sweetness to Tom’s voice, but there’s also a menacing quality to it, which I think is separate from one’s own knowledge of the parts that he’s played. I’m not sure, but I think it is. I just like him.

You’ve spoken about how animating the sex scene was a six-month process to ensure that it would be taken seriously.

DJ: We knew about “Team America,” and we were aware that a sex scene with puppets could fall into the jokey realm, and we didn’t want to do that. We wanted it to feel like a natural progression from the moment the characters enter the hotel room to the moment where they take their clothes off and make love. We spent a lot of time pacing it out, talking about the movements and rehearsing them. There were tons of technical challenges that we had to figure out.

CK: It was a full collaboration between Duke and myself.

What drew you both to working together?

DJ: I was a huge fan of Charlie’s. He’s my favorite writer and a hero of mine. I was so excited to meet him and work on the film with him. I was thrust upon him, he didn’t know me at all. [laughs]

CK: I didn’t know Duke, but when we started working together, I quickly felt like there was a kinship in terms of sensibility, in terms of personality—we’re not the same personality, but we get along really well and had a very harmonious collaboration with very few rough spots. They were minor, considering that this took three years to complete. Our producer, Rosa Tran, was there from day one to day one thousand.

DJ: People are always amazed by how two directors can collaborate. The thing that’s unique about stop-motion versus live action is that I can imagine with live action, you’re in the moment making split-second decisions. With stop-motion, there’s time to go back and forth and talk about a decision and maybe even sleep on it and come to a conclusion the next day.

CK: Yeah, that’s true.

In its animated form, “Anomalisa,” feels like a feature-length marionette show performed by Craig Schwartz in “Being John Malkovich.” Do you sense any parallels between Craig and Michael?

CK: [long pause] It’s hard for me to say yes or no, because obviously I love both of them and they both have elements of me in them, I’m sure. But thinking about them from the outside, Craig seems a lot more frantic and desperate, and Michael seems resigned, though there is a moment of frenzy there. I feel like maybe Michael is Craig in thirty years after the truth sort of becomes apparent to him. I hadn’t thought about that before.

“Anomalisa” opens in limited release on Wednesday, December 30th.