This is an interesting and well-written exposition of the concept of contextual emergence by one of its prime investigators. It concerns an appealing idea beyond the limitations of simple reductionism. I have the following comments:
1. Ontological emergence. This seems to be a rather speculative remark. From the examples given it is hard to see how emergence could be anything else but related to description or observation. This also holds, e.g., for chirality as discussed by Bishop and Atmanspacher (2007): Having "real" consequences with respect to experiments can hardly be taken as a proof for its ontological nature. In fact, contextuality precludes any ontological (absolute) status. If there is not more to it, I suggest to remove this remark.
2. From mechanics to thermodynamics. This is, of course, an interesting example with a long history. Debates about its foundation are still ongoing. For the laymen the most impressive feature of thermodynamics is the tremendous reduction of relevant parameters, from almost infinitely many microvariables to just a few macrovariables like temperature and pressure. Temperature does not only require the existence of equilibrium states but also weak coupling between separate parts in contact; the zeroth law does typically no longer hold for non-extensive thermodynamics. The reader should be reminded, though, that thermodynamics is much more than just the existence of temperature. Irreversibility despite reversible microdynamics is a pertinent example.
It is impossible to do justice here to this rather broad and complex field of research. For the non-expert the reference to the algebraic quantum mechanics school of thought (Haag, Takesaki etc.) will hardly clarify the underlying problems. A modern account of what has been achieved and what is still missing may be found in N. Linden et al (arXiv:0812.2385) and references therein. In the present context the author would be well adviced to reduce those discussions to the absolutely essential. The saved space might be used for a brief reference to chirality as another important example.
Are there no much simplier examples in physics? How about going from many-particle theory to hydrodynamic variables like particle density or drift velocity?
3. Contextual emergence is a descriptive concept by itself, not necessarily a recipe. In fact, the examples from physics show, how difficult it was (and sometimes still is) to find and justify the proper language on the Level M. It is by hindsight that we recognize the common features as outlined by the author. Physics is a rather mature field by now. The situation is different, e.g., for neurosciences. Here the present concept may show its practical usefulness in active construction. In that sense, I think, the last discussion on mental states and EEG does not only expose another example, but points to a different quality.
4. The final remarks have apparently been written with the applications outside physics in mind. The reader may wonder whether the author wants to indicate that it is here, where contextual emergence may function as a guiding principle -- not so much in natural sciences.