By CARL ZIMMER
JAN. 20, 2014 NY TIMES
Excerpt 1: In the journal Neuron, a team of scientists has unveiled an unprecedented view of X-chromosome inactivation in the body. They found a remarkable complexity to the pattern in which the chromosomes were switched on and off.
My comment: The remarkable complexity of nutrient-dependent pheromone-controlled chromosomal rearrangements that led to difference in sex chromosomes was detailed in our 1996 Hormones and Behavior review article in the section on: Genetic Considerations
“Sexually dimorphic genes (some prefer the term sex-linked genes), and their dimorphic proteins. It is generally understood that most genes code for the synthesis of specific proteins. Another example of biological sex differences which are neither gonadal nor hormonal, however, is provided by the homologous but dimorphic zinc finger proteins ZFX and ZFY encoded on the X and Y chromosomes (North et al.,1991). An early study of human expression of ZFX and ZFY reported different transcript sizes from the two genes and this difference was even apparent in somatic tissues (Page, Disteche, Simpson, De La Chapelle, Andersson, Alitalo, Brown, Green, and Akots, 1990). ZFX and ZFY are described as “DNA-binding proteins” and via their binding of sexually dimorphic proteins, chromatin structure and transcription could be modulated in sexually dimorphic ways as a result of females having only ZFX binding events, whereas males would have a mixture of both ZFX and ZFY binding events (Fiddler, Abdel-Rahman, Rappolee, and Pergament, 1995; Lau and Chan, 1989; Zwingman, Erickson, Boyer, and Ao, 1995).
Similarly, ribosomal proteins S4X and S4Y (rpS4X, rpS4Y) are produced by sexually dimorphic genes whose protein products are sexually dimorphic. This suggests the possibility of subtle nuances in the ribosomal translation of at least some mRNA, in certain cell types (Fisher et al.,1990; Zinn et al., 1994).
The Genome, positioning, timings. There are major structural differences between the X and Y chromosomes; e.g., centromeric aiphoid repeats sequences and distribution of heterochromatin (Graves, 1995; Wolfe et al., 1985). These structural differences correlate with sexually dimorphic chromosomal positioning within the nucleus and with male/female differences in replication timing of the active X, the inactive X, and the Y chromosomes, e.g., Boggs and Chinault (1994), Clemson and Lawrence (1996); Hansen, Canfield, and Gartler (1995). Increasingly the structure and timings within the nucleus are realized as contributing to gene expression regulation (Manders, Stap, Strackee, van Driel, and Aten, 1996; Stein, Stein, Lian, van Wijnen, and Montecino, 1996).”
Excerpt 2: When a cell divides, new copies of the molecules silence the same chromosome in its descendants.
My comment: Chemical ecology determines whether or not a cell divides in the context of “Biology the new light.”  If the two descendants of one cell vary only slightly in their metabolism, subtle changes in the two descendants will lead to their differentiation into different cell types, like the sexually dimorphic cell types of yeasts at the advent of sexual reproduction. That is how nutrient-dependent pheromone-controlled alternative splicings, amino acid substitutions, de novo creation of genes, and silenced chromosomes lead to the diversity of morphological and behavioral phenotypes.
Cause and effect was recently detailed in a report on birds Estrogen receptor α polymorphism in a species with alternative behavioral phenotypes and two reports on bees 1) DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees; 2) Epigenomics and the concept of degeneracy in biological systems 
We can now see X chromosomes and Y chromosomes in mammals in the new light of biological facts about nutrient-dependent RNA-mediated amino acid substitutions and chromosomal rearrangements that have been known since 1996 and we can dispense with the nonsense of  mutation-driven evolution, where differences in the X or the Y chromosome result from accumulated mutations.
Addendum:
Carl Zimmer added: Here’s a picture that didn’t make it into my X chromosome story in today’s New York Times. It’s a heart. Cell’s with Mom’s X active are green, Dad’s red. Photo by Jeremy Nathans and Hao Wu/Neuron (Cell Press) Story: https://scontent-b-iad.xx.fbcdn.net/hphotos-prn2/t1/s403x403/1524754_10151817755047541_2131360145_n.jpg
My comment: This picture may help to focus some attention on the atom to ecosystem “Systems Biology” approach that links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms sans mutations. The conserved molecular mechanisms link nutrient-dependent pheromone-controlled ecological adaptations to genomic imprinting, chromosomal rearrangements, and mosaicism of brain tissue to the mosaicism of other tissues like those of the heart.
Some studies now address the advantages of studying the biology of behavior in the context of multiple levels of structural and functional complexity that begin with atomic-level differences in cell types that link chemical and electrical changes to unconstrained electromechanical disorders that are typically biophysically constrained.