It has been funny for the last four or five days to see NFL traditionalists lashing themselves to the ship mast or clinging to their old verities like they'd cling to life jackets in a squall. Their heads hurt. There's fear in their eyes. They find themselves swept far away from shore, and they do not know what to make of that different sort of cat, Colin Kaepernick, who the San Francisco 49ers are starting at quarterback, and how he has the 49ers needing just two more wins to tsunami their way to a Super Bowl title. But here's what to make of that.

This is what happens when you take an insanely athletic quarterback, cook up an offense that ignores 30 or 40 years of carved-in-stone NFL group think, and then pair him up with a fearless head coach -- Jim Harbaugh. Harbaugh played the position for 14 NFL seasons himself, grew up as the son of a head coach and spent his formative years at Michigan having Bo Schembechler yell in his ear hole, and he has now become the sport's leading guru at developing quarterbacks.

When you throw all that together, what can happen is the heretics can get rewarded. And you get a game like the 444 yards of total offense that Kaepernick personally hung up in lights for the 49ers in last weekend's 45-31 thrashing of Green Bay, a performance that was so breathtakingly good -- and even revolutionary -- that people are still shaking their head in surprise and trying to make sense of it.

Colin Kaepernick has had Jim Harbaugh's attention since before the draft. Stephen Brashear/Getty Images

(Though Bo probably wouldn't if he were still around. The late Schembechler -- a committed three-yards-and-a-cloud-of-dust coach -- knew what an outlier Harbaugh is. Harbaugh now tells a story of how he called Bo after he got his first head coaching job at the University of San Diego. The feisty Schembechler make Harbaugh promise that he'd still use a halfback and fullback before consenting to give him any advice.)

The new discussion now is not just how the Atlanta Falcons can reasonably hope to stop Kaepernick or Harbaugh's offense in Sunday's NFC Championship Game, or what day San Francisco will book for its Super Bowl-winning parade no matter who the AFC sends down to New Orleans. There are a lot of big-picture conceptual debates going on about what this sacrilegeous little traveling show that Kaepernick and Harbaugh are running may mean for the NFL going forward.

The future of the drop-back quarterback is conflicted, to say the least. There may be room at the inn, after all, for a different sort of prototype. Why not judge quarterback prospects by the same rigorous athletic standards as the guys who play wide receiver or safety, and then funnel them into the position with an explicit intent to exploit all of that -- not just their ability to throw a football through a swinging tire nine times out of 10 or some egghead measurable like a Wonderlic score that's off the charts?

Why not demand to have it all, like Harbaugh is?

Nobody at the college or pro football level has had as much success at developing quarterbacks as Harbaugh has lately. Many a coach and NFL general manager will tell you it may be the hardest job in the game. It's also renowned as the sort of gig that can get you fired if you whiff -- something Harbaugh himself heard when he benched former starter Alex Smith, who was leading the NFL with a 70-percent completion rate at the time, because he thought Kaepernick had a "bigger upside." This even though Smith was 20-6-1 for him as a starter.

Yet Harbaugh has now been a winner at developing quarterbacks four times in nine seasons. Before personally targeting Kaepernick as the man he wanted in the 2011 NFL draft, Harbaugh turned Josh Johnson into an NFL prospect at San Diego (an FCS school a step down from the top level of college football), presided over Andrew Luck's development at Stanford, then led Smith's resurrection with the 49ers after everyone termed his 5-year-old career a bust.

Just as remarkably, Harbaugh managed to pull it all off though he had to adjust his offenses to the very disparate skill sets of each man, and Stanford and the Niners had losing programs when he arrived. Luck is a classic drop-back passer. Smith is a deft game manager. And Kaepernick, well, he is Harbaugh's most fascinating project yet.

He's the sort of quarterback who Harbaugh always tried to describe when pressed over the years for what his ideal signal caller would be.

Harbaugh talked at length about the "quarterback DNA" he looks for in this 2011 interview with the Sacramento Bee's Matt Barrows before drafting Kaepernick. He expanded on how he once compared it to how an experienced birdwatcher can identify a bird from some distance away just by the way it flies.

"I feel like I've seen it enough to say, 'OK, that's an NFL quarterback,'" Harbaugh said. "But you want to find better, and also best [Athleticism] has always been really important to me. I call it athletic instincts.

"It could be defined as he could go out and play soccer and make a soccer team or be on the basketball team and at least be the sixth man and be really good on defense and hustle and pass the ball as a point guard. He could go into center field and catch fly balls. We've all known those kind of guys. Someone who's good at everything. In high school, he was probably the best athlete in the school. He's just got those innate quarterback qualities Just being around them -- they've got it. The ability to light up a room and people really want to follow them, a lot of qualities like that."

The technical football term for the offense the 49ers are running is the Pistol, or read-option plays. But that's too bone dry.

Like Seattle with Russell Wilson, like Washington withRobert Griffin III -- and yet in ways that aren't like them at all, because Kaepernick is a unique creature, even compared to them -- what the 49ers are doing with their quarterback is shaking up the idea of what a prototypical NFL quarterback should be going forward.

The conventional wisdom has always been that read-option quarterbacks are not supposed to succeed like this in the pros.

Brian Polian is the new football coach at Nevada, where Kaepernick went to school. He is also the son of NFL general manager Bill Polian, the man who drafted Peyton Manning over Ryan Leaf and presided over the Bills' dynasty that was quarterbacked by Jim Kelly before that. Brian, who also coached two years with Harbaugh at Stanford when Luck was there, says, "Five or seven years ago, I remember having a conversation with my father where I asked, "Do you think can you ever run this offense in the NFL? And he said, 'No. NFL defenders can run fast too. You have to keep your guy upright the whole season. In the long run, we just don't have the body of evidence that it can work or just one guy can do it.'

"But I'll tell you what," Polian laughs, "after what these guys have done this season, I mean --- "

It makes you re-think everything?

"Right," Polian agrees. "It has to."

Why wouldn't you want a hybrid quarterback who can do it all, given the choice?

"I think everybody kinda has to adjust kind of their thinking on what an NFL quarterback is right now," Trent Dilfer, the former NFL quarterback turned ESPN analyst, told ESPN radio's Colin Cowherd this week. "You look at the younger age groups, the quarterbacks coming up a lot of the kids are Colin Kaepernick, a lot of the kids are RG III and Russell Wilson. Smart. Tough. Great passers. But super athletic. And super BIG. And experts in the zone read game. And you know, it is a craft to read this run game out, much like reading defenses in the passing game. They're taking that brain work and applying it to the run game. … And I think we're going to have to adjust our paradigm of what an NFL quarterback is."

For now, the Falcons are, not surprisingly, still clinging to the old orthodoxies. Their safeties made some noise this week by warning how they intend to "blow up" Kaepernick with big hits on Sunday if he keeps the ball and runs against them. The Falcons have hinted they may assign a spy to shadow Kaepernick. The Falcons are insisting they won't be caught by surprise like Green Bay was when San Francisco sprung the Pistol on them a season-high 34 plays.

But look: The most amazing aside about the 181 yards rushing and 263 yards passing Kaerpernick shredded the Packers for is he gained 178 of his rushing yards before contact, according to ESPN Stats & Information.

Repeat: Before contact.

Think about that for a second.

The man ran the ball 16 times and, quite literally, the Packers barely laid a hand on him. You can't hit what you can't catch. It is also the sort of immutable evidence that renders this week's warnings from the Falcons' defense more adorable than menacing. They actually believe they can bottle up Kaepernick, a man who'd already outplayed Tom Brady and Jay Cutler and Aaron Rodgers in a mere half-season of NFL starts? How cute is THAT?

The sight of what Kaepernick did to the Packers sent experienced analysts to the film room to confirm what they just seemed to have seen. They've since remarked again and again how the Packers seemed to underestimate Kaepernick's speed. How the Packers didn't take the right pursuit angles and thought they had a bead on Kaepernick -- only to grab at smoke, only to find he was long gone on TD runs of 56 and 20 yards. It was obvious, too, how his all-around ability creates deadly hesitation and doubt. He also passed for two TDs against Green Bay, and established the threat of the deep pass well enough to open up the underneath game too.

"The thing that surprised me," says Oliver Luck, the father of Andrew Luck, and man who has played quarterback at the college and pro level himself, "was that Green Bay's defense didn't change during the course of the game. For whatever the reason, they thought that was their best chance of shutting them down They played a lot of man coverage. They had linebackers locked on running backs or tight ends and they were only rushing three or four against the 49ers' great offensive line, and so Colin drops back and there's 20 yards of daylight. He's a big, strong, fast athlete. And when a quarterback sees a cornerback or linebacker turn his back to you in man coverage, you know you'll have room to run. You just can just take off -- like a sprinter."

The elder Luck is among those who say "not so fast" when it comes to the demise of the drop-back NFL quarterback. And he's surely right.

But there's still room for Harbaugh's vision of the ideal quarterback too.

Kaepernick looks wildly different, all right. Because he is.

At 6-foot-4, Kaepernick is five inches taller than Seattle's Wilson and two inches taller than Griffin's listed height, yet he's probably faster. Passing from the pocket? Kaepernick throws the ball -- even the deep ball -- as well as either of them or rifle-armed Cam Newton, if not better. Thinking the game? Kaepernick was a 4.0 student in high school and smart enough to be recruited by some Ivy League schools before Nevada became the only FBS school to offer him a scholarship very late. and Harbaugh recently called Kaepernick's ability to pick up the 49ers' game plans early in week, "Savant-like."

Kaepernick isn't "just" a running quarterback. He's a hybrid's hybrid.

He's said his best 40-yard dash time is 4.43 seconds. He's a whippet-like 230 pounds and has the longest, most coltish stride this side of Usain Bolt. He was a three-sport athlete in high school who led his football team to two central California football championships, clinched that Nevada scholarship offer after the coaches saw him play basketball, and -- even then -- had a throwing arm that's now left 49ers receivers like Randy Moss and Kyle Williams saying that they believe the stories that he had a 94-mph fastball as a high school pitcher. The Cubs drafted Kaepernick in 2009, three years after he last threw a baseball in competition.

Kaepernick dares to throw the ball long or into the sort of tight windows that the 49ers' Smith would never try. A few weeks ago, Moss told Bay Area reporters that Kaepernick -- not Brady nor Brett Favre -- was the first quarterback he'd ever played with who dislocated one of his fingers with a pass. "He had to put one them Randy Johnson fastballs on me," Moss said with a smile. "The doctor had to pop it back in I tried not to show any tears. I don't know if they caught me crying or not."

Andrew Luck's success didn't end at Stanford, but he certainly learned from Jim Harbaugh. Streeter Lecka/Getty Images

The Cubs supposedly took their chance on Kaepernick because their scouts had come back saying Kaepernick's somewhat sidearm throwing motion made him an unlikely NFL prospect.

But that wasn't really true by the time Harbaugh went to Reno to work out Kaepernick before the 2011 draft. What was true was other quarterbacks like Jake Locker, Andy Dalton and Ryan Mallett (not just Cam Newton) were rated higher -- this though Kaepernick ended his career as the first college quarterback to ever rush for more than 4,000 yards and pass for 10,000. What hurt him? That old bias about running the read-option again.

Harbaugh came back besotted with Kaepernick anyway. He came back thinking to himself that he wouldn't change much of anything.

The Niners traded up to take Kaepernick with the fourth choice of the second round after sitting tight and taking linebacker Aldon Smith with their No. 7 pick in the first round.

The Kaepernick pick was Harbaugh's call all the way.

Harbaugh just knew he was his guy, all right. But how?

This year's 49ers team was seen as a Super Bowl team with Smith too, after Harbaugh resurrected him last season. So how did Harbaugh know Kaepernick could develop this fast as a starter and not freeze under the NFL's bright lights? Why did he believe that the team could succeed with an offense that changed on the fly when Kaepernick replaced Smith and was disparaged as a novelty act, a fad that wouldn't last? How did he know Kaepernick would be tough enough to endure NFL hits intended to snap his licorice-thin-looking torso in half?

This is the answer: Are these not the calculations a quarterback guru and his quarterback always have to make? Someone is always coming for you. Roadblocks always spring up. There are always tests along the way. The risk/reward equation is always the same: Either it works out. Or you both get fired.

Polian, Harbaugh's former assistant coach, says at least part of the answer is, "All of these quarterbacks have talent. But, also, I have never been around a person who is more comfortable in his own skin that Jim Harbaugh is And Jim Harbaugh may also be the most competitive individual I have ever met -- and remember, this comes from someone who grew up in an NFL household. He just knows exactly who he is. And precisely how he wants his teams to play, practice, compete -- everything. It's always going to be attack. Play downhill. Play physical. Play tough. On top of that, he's played the quarterback position at the highest levels. He knows how to look at players and find ways to take advantage of their talent and what they can do rather than what they can't do well."

Oliver Luck says Harbaugh brings something ineffable to the job, too, that rubs off on his quarterback. "Jim himself probably wasn't the most intrinsically talented guy to play the position," Luck says, "so he learned to get by with the intangibles. And I think there's probably not a better teacher or judge of the intangibles that go with the position too, as far as how to win over a locker room, how to behave, interact with your teammates or make the sort of decisions you have to make during a game."

Harbaugh knows what he sees, all right. Now, the rest of us are getting a look too. He's been the guru who had the drop-back passer, the guru who elevated the game manager, and now the quarterback guru who unleashed the athletic freak. But the basic challenge he and they throw out has always been the same: Stop them if you can.