> Ingredients in royal jelly can inhibit an enzyme - "cytosine methyltransferase" it methylates cytosine bases in honeybee DNA.  That paper seems to have ignored work that has been well-known for some years now. 

§

newer work by Oldroyd & Yagound

Early work on honeybees suggested that DNA methylation plays a causal
role in the divergent development of queen and worker castes. This view
has now been challenged by studies that did not find consistent associations
between methylation and caste in honeybees and other species. Evidence for
the involvement of methylation in modulating behaviour of adult workers is
also inconsistent. Thus, the functional significance of DNA methylation in
social insects remains equivocal.

This question has been addressed in five studies using
increasingly sophisticated genomic techniques and better
taxon sampling. Overall, we think that the major conclusion
from these studies [47,63,101–103] is that there is no clear
relationship between the level of sociality and the extent of methylation.

§

Comment: Science is constantly in the process of being revised. Because something was accepted as fact in 2001, doesn't mean it's accepted as fact today. 

There may be chemical differences between worker jelly and queen jelly, but these may be incidental and not essential to caste differentiation. 

Jelly is hastily fed to tens of thousands of larvae whereas queens receive far beyond what is needed, as evidenced by the surplus food in the cells when they pupate.

As far as whether the queen or the worker is "the default" obviously you can't have one without the other. Over time, intelligent people have debated: "the colony and their queen" vs. "the queen and her colony." 

Considering that queen bees are known to enter hives, kill the reigning queen, and commandeer the workforce, in my opinion supports the queen and her colony paradigm.

PLB

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