Can Chromosome Counts Change?

Sure they count as mutations.Check out this linkhttp://www.iephb.nw.ru/labs/lab38/spirov/hox_pro/hoxmap.htmlNote, amphioxus has a single Hox cluster used in segment determination..look at Drosphila, then pufferfish, and mammals. There are more and more novel Hox genes and clusters that have arisen by duplication from an ancestral Hox gene. Each Hox gene specifies a different portion of the development process and therefore, each duplication is not just more of the same thing..they have diverged since duplication and acquired novel function. This is a gain in information...and it correlates with a gain in morphological complexity.Another example of a novel protein that has arisen recently is syncytin. It is a retroviral envelope protein that is crucial to syncytiotrophoblast fusion in hominids and Old world Monkeys but not in other mammals. Thus, a key step in the development of higher primate placental development appeared only recently.

quote:

---

But... but... that begs the question-how did the first hox gene arrive?

---

In both cases, I have off the top of my head provided examples where novel gene families arise from a precursor...precisely what you claimed does not happen. Your answer? Typical, you switch to claiming that because it does not demonstrate how the first gene arose it is a non-answer. Ironic that you bring up Tranquility Base...he had the same problem with logic. However, we can trace back original protein development as Taz suggested by searching for both sequence and functional homologs in single cell organisms which do not for example in the case of hox genes, need segment polarity determination, or in the case of endogenous retroviruses, by their relationships with other retroelements particularly exogenous retroviruses for exampleKim HS, Lee WH.
Human endogenous retrovirus HERV-W family: chromosomal localization, identification, and phylogeny.
AIDS Res Hum Retroviruses. 2001 May 1;17(7):643-8.in the case of homeotic gene regulation (not directly Hox gene origins but origins of their regulation) one can find homologs in yeastTamkun JW, Deuring R, Scott MP, Kissinger M, Pattatucci AM, Kaufman TC, Kennison JA.
brahma: a regulator of Drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2/SWI2.
Cell. 1992 Feb 7;68(3):561-72.and wrt hemoglobinHardison R. Related Articles, Links
Hemoglobins from bacteria to man: evolution of different patterns of gene expression.
J Exp Biol. 1998 Apr;201 ( Pt 8):1099-117. Review.Particularly the last paper focuses on origin and evolution of hemoglobin from an ancient precursor into the mutlifunctional family present in bacteria to humans.So your first point that novel proteins or protein familes cannot evolve is patently wrong. And your second point about where specific proteins come from originally is also possible to address using methodological naturalism as opposed to undefined terms like "kinds" or appeals to god/god's/pink unicorns and other mythological constructs.