Last Saturday night in San Diego, Tim Lincecum, the best pitcher in the National League this season, threw a complete-game shutout against the Padres. It was a magnificent performance — the 24-year-old gave up just four hits, none of them for extra bases, while walking three and striking out 12. Lincecum lowered his league-leading ERA down to 2.43 with this gem, and raised his major league-leading strikeout total to 237.

But was the first career complete game for the second-year righty worth the effort expended to achieve it? In letting his team’s young superstar reach that individual goal, San Francisco manager Bruce Bochy left Lincecum on the mound for 138 pitches. One hundred and thirty-eight is a startling total for a single start in today’s game. The industry has come to feature a hypersensitive awareness of pitch counts and the theoretical warning sign of a 100th pitch. Baseball Prospectus’s Pitcher Abuse Points metric (or PAP) logged Lincecum’s shutout as the first Category Five start (133+ pitches) in the majors this year, and no one had thrown that many in over three years, since Livan Hernandez tossed 145 pitches in late July of 2005.

Bochy has been pushing Lincecum of late in the effort to add a complete game to his already impressive Cy Young résumé. The 138-pitch start followed a game in which Lincecum threw 127 versus Arizona, pitching into the ninth inning but not quite closing it out. It was also three starts after he threw 132 over 7.2 innings in beating Colorado. Lincecum has now made 17 starts of at least 110 pitches this year, and he ranks well ahead of every other pitcher in PAP, with an average of abuse points per game that has not been topped since Livan Hernandez’s 2005 season. (PAP is based on a progressive scale, assigning one point for every pitch thrown from the 101st to the 110th, two from 111 to 120, three from 121 to 130, etc.; it starts at 101 because that is when a pitcher’s peripheral statistics begin to trend downward.)

Hernandez was 30 years old in 2005 and has been the most durable pitcher in the majors, having thrown more innings than anybody since the start of 1998. But he provides an interesting comparison for Lincecum, because both right-handers, despite possessing widely disparate arsenals, are regarded as physical anomalies. Lincecum even recently had a Sports Illustrated cover story (titled “The Freak”) written on the revolutionary biomechanics of his delivery. The 5-foot-11-inch, 160-pound Lincecum’s small frame and violently twisting, maximum-effort windup kept several teams from selecting him on draft day two years ago despite his surreal college statistics, falling all the way to the 10th overall selection. Yet he has not been injured. If looking for proof that Lincecum is simply different, consider that he did not need to ice his arm in college, because it never felt sore, despite the fact that he sometimes came back to pitch in relief on Sunday after starting on Friday. A Category Five start is also nothing new for him; according to college baseball analyst Boyd Nation, Lincecum had 15 such outings in his three seasons at the University of Washington.

Lincecum might well be a uniquely durable, once-in-a-generation specimen, but that is yet to be proven to be the case, and testing the limits of his ability to recover from high-usage outings seems to make little sense at this point in his career and for this Giants team. Lincecum had already thrown 118 pitches through eight innings on Saturday, yet Bochy sent him out for the ninth in defiance of both the smaller picture (San Francisco was up 7-0) and the bigger one (the Giants are well out of playoff contention). The load that San Francisco’s franchise pitcher has carried in the last four starts is beginning to resemble how another righty who dominated in college was worked down the stretch of his second major league season, but Mark Prior was toiling in the midst of a pennant race when he reeled off five starts of at least 124 pitches during his final six outings of 2003.

Prior was also considered to be an anomaly coming off a superb career at USC, thought to have “perfect mechanics,” a notion that was later proven to be false. Even Hernandez, whose right arm is seemingly made out of Flubber, was not immune to the abuse he took in 2005, for, he has not been the same pitcher since — in 2006 his ERA jumped from 3.98 to 4.83, then to 4.93 last year, and 6.21 so far in 2008. That decline could be simply the result of age and the sheer accumulation of innings — or it could have been exacerbated by the six games in which Hernandez hit or exceeded 130 pitches in 2005.

All of this is not to advocate the usage of pitch counts as a strict measure of when to remove a pitcher from a game. The PAP system was designed to create a better framework for managing the risk of fatigue-based injury with the reward of having one’s best pitchers throw the most innings; 100 pitches is simply when to start paying close attention and weighing that risk. Lincecum’s recent work stands out precisely because so few pitchers today have been allowed to go deep into games, as the concept of pitcher abuse and the importance of pitch counts has permeated all of baseball — in part because of Baseball Prospectus’s work developing PAP and explaining the danger of overuse in the late 1990s. In a July article responding to the Mets’ reluctance to extend ace Johan Santana, BP’s Joe Sheehan wrote that pitcher abuse “has all but been eliminated in today’s game,” and that “it’s time for the pendulum to swing back a bit, and let starting pitchers take a greater share of the workload.” The Brewers have done just that with ace CC Sabathia, letting him throw six complete games since he arrived from Cleveland, and the Mets have given Santana a greater amount of slack recently as well.

Sabathia is 28 and Santana 29, both of them already have more than 1,500 major league innings to their name, and both the Brewers and Mets are in the pennant race, making it sensible that those respective aces go deeper than usual into contests. At some point, the Giants will need Lincecum to do the same in their own eventual hunt for a flag. Hopefully, his pitch-intensive outings in the summer of 2008 will not have hurt his ability to deliver on that future promise.

Mr. Peiffer is a writer for Baseball Prospectus. For more state-of-the-art commentary, visit baseballprospectus.com.