For the second time in its history, Steve Jobs will move away from running the company.

If history is any judge, this won’t go well for Apple. But there are lots of reasons to think why history will be a poor judge of Apple’s future performance.

Let’s start with some similarities. First, Steve Jobs led the company for a decade and a half in both cases.

Second, in each case, the previous five years saw a revolutionary and innovative transformation of the company.

In 1984, it had a cycle of innovation in personal computers culminating in the Macintosh which set the dominant design for user interactions on computers. This time around, it appears to have done the same for touch mobile devices.

But what is the difference? A couple of months ago, a Fortune article — sadly, only available behind a paywall — described the cultural transformation inside Apple (It will be the best 99 cent purchase ever on your Kindle).

The last 15 years have been about establishing an internal culture for innovation and a set of norms of behaviour and expectations. While the culture came from the drive of Steve Jobs, it is a reasonable expectation that it is infused in the organisation itself.

Second, if Apple lost out last time following its drastic innovation, it was because it failed to meet low cost competition. I know that many believe it was an open versus closed issue but that was the side effect rather than the ultimate problem. This time around, Apple appears to have pushed hard on the cost envelope.

The reason the iPad is so dominant, with others just giving up, is all about cost. No one has produced a cheaper device. So even aside from the obvious quality differential, Apple is leading on the dimension that failed it last time.

What is more, it is doing the same in light weight laptops. Netbooks are being squeezed on both sides. And who is probably the person most responsible for that? Tim Cook as COO. The signal to competitors is very very clear.

For these reasons — Apple sans Jobs — is still a good bet. The question is how much the Jobs factor will contribute. I suspect that there will be a modest drop in Apple’s share price tomorrow.

Of course, as his resignation was the likely bet, one would expect that it is already built into price.

But markets being what they are, excess volatility accompanies big news. That also means that Apple’s share price will likely bounce back with strong earnings plus new product releases. Jobs will never be a distant memory but his hand is imprinted on the company’s future.

This also appeared on the Core Economics blog and has been reproduced with permission from the author.