I had somewhat the same reaction when I first read the article back in February, but you've missed the important point. The puzzle was how morphological changes that require multiple gene changes across chromosome pairs could come about given that they're so incredibly unlikely. The results of the study revealed that a single change to a dominant
Hox gene on a single chromosome can have a dramatic impact on body plan by turning on or off multiple genes on other chromosomes.
You probably believe the example illustrated in the article where six-legged insects evolve from multi-limbed crustacean-like ancestors is a case of loss of information or de-evolution, but it's actually an example of suppression of expression. Insects evidently still have the information for multiple limbs, but information was added to their genome, specifically in
Hox genes, instructing many of the limbs to not be expressed.
The opposite process whereby an organism acquires limbs not previously present is, I think, well understood, but I have no reference I can provide. Perhaps someone else here knows more about this, but a couple possible avenues are obvious. Gene duplication is one where during reproduction two copies are accidentally made of a single gene. Another is a
Hox-like approach where one gene controls how many times another set of genes is expressed. It's a simple change from saying "five limb segments" to saying "six limb segments".
--Percy
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