When Sean Carroll's books came out- "Endless Forms Most Beautiful" and "Making of the Fittest", I was told the answers to my questions were contained within.
That is these books were supposed to tell me how organisms changed- ie evolved- and in the grand fashion I claimed lacked supporting genetic data.
So I read the books and came away very disappointed.
More speculation. But reasoned speculation nontheless.
It is interesting stuff. A few slight changes at the right time in development could cause large effects in the end result- evo-devo.
However it hasn't been until recently that it is come together for me- why evo-devo? And why now?
"Now" could be answered that we have just been able to uncover such secrets.
"Now" could also be answered because there is no way to produce new genes because that also requires all the meta-information- transcription factors etc.- so the faith is now in a change in a few (or even many) switches.
I say there is no way to create the new genes- I know of gene duplication- because recent mathematical studies have demonstrated the daunting task of getting a new binding site- a very small segment of DNA- for already existing genes.
So you could duplicate a gene but without a binding site, promoter, enhancer and whatever else it needs, you don't have anything except more DNA.
Back to Carroll.
He couldn't show that any amount of switch flicking can turn a fruit fly into a butterfly.
He just knows that the ONLY hope left for his position is some magical combination of switches, thrown at the right time, controlling the right chemical reactions, can provide that "holy grail" of evolutionary biology- how do new body plans arise?
No one knows but his faith is in those switches because that is the last hope...