It sounds like a combination of an “classic analog”-sounding drum machine (likely the Roland TR909) and Phil playing actual drums. The drum machine sounds are heard in isolation during the first second of the track, but Phil comes in almost immediately, playing the second “snare” and continuing from there. Phil’s playing becomes especially apparent later in the track when he adds additional sounds and fills, especially after 3:10. However, Phil drops away around 4:32, and the drum machine is again heard in relative isolation until the end of the track.
In terms of the drum machine, I think that the most likely candidate is the Roland TR909, which Colin had on tour in 2003. It just sounds right. However, it is possible that the beat was constructed with Colin’s Akai MPC60, or it may have been made on the Roland MC505. It is also possible that the MPC60 was used to sampled the TR909 along with other sources, such as Jonny’s modular. However, I think that the sound of the beat shows it to be just the TR909.
While the sound of the drum machine is distinctive enough to give us a fair picture of what is, the play/programmer is harder to pin down. While Thom uses drum machines for demos of tracks, it is generally Jonny, Colin, and Phil who program drum sounds and beats, particularly the Greenwood brothers.