Doesn't mean there aren't some "gradual changes", but it's the big stuff that counts most ~
As far as evolution goes, it does seem to be "gradual" if you look over the continuum from 4 billion years ago to the present time. However, for the first 3.6+/- billion years NOTHING HAPPENED.
There seems to have been bacterial mats.
Finally, something happened and genetic change started happening ~
That, by itself, is a great mystery. No one has any good idea about why evolution, if it works, didn't bother working for such a long period of time ~ actually, most of the time!
What happened 46 years ago?
As far as evolution goes, it does seem to be "gradual" if you look over the continuum from 4 billion years ago to the present time. However, for the first 3.6+/- billion years NOTHING HAPPENED.
NOTHING HAPPENED is a bit of an embellishment, I think. The Precambrian (particularly the Ediacaran era) is a time of immense biological change - though a lot of it was happening on a molecular level. The first eukaryotic organisms appeared then, and the first macroscopic plants and animals - not a small change at all in the existing biospshere, all prior to the Cambrian explosion. Lateral gene transfer no doubt played a much larger role in that era of evolutionary history. Many of the tools in the genetic toolkit that allow macroscopic change hadn't appeared yet, but to put it in the words of Carl Zimmer, "evolution is and always has been primarily a story about bacteria", if you really want to trace where most of the genetic change in life has taken place. The whole Cambrian explosion is really little more than a 'macro-centric phenomenon', from what I can understand - robust change in living organisms had already been occurring for a long time, only on a cellular level.
What exactly spawned the sudden change is indeed a mystery, but I think it's pretty clear that the reason it didn't occur earlier is because the genetic toolkit of triploblastic organisms wasn't all in place yet (e.g. the HOX genes you referred to earlier).