The concept of emergence is misunderstood in this Essay. Emergence doesn't imply that higher level properties aren't derivable from lower-level properties. They are. Emergence states that high level properties aren't reducible to lower-level properties of components alone. This is why P.W. Anderson titled his famous article as "More is different".
As a consequence of this misunderstanding all the following discussion about hierarchy of science and "In this hierarchy physics defines the foundation, chemistry is the physics of the outer atomic orbits, biology deals
with the chemistry of complex organic molecules,..." is wrong. As Anderson demonstrated chemistry isn't applied physic, biology isn't applied chemistry,...
"higher levels of description may actually be more deterministic (a typical example is that macroscopic classical physics appears to be more deterministic than microscopic quantum mechanics)". Maybe if one reduces macroscopic to mean "deterministic Hamiltonian physics" only, because many macroscopic descriptions developed by chemists, biologists, during last centuries aren't deterministic. E.g. kinetic chemists have always considered chemical reactions as stochastic processes.
Zeh is wrong, when he claims there is no particles. Of course, there are particles, they are routinely detected in experiments.
Decoherence doesn't have anything to do with observers and lost of information. Decoherence also happen when there is no observers present and the physical mechanism doesn't have anything to do with ignorance about the environment, but is a dynamical consequence of resonances between the environment and the coupled system. Those resonances generate dissipation and lost of purity on the quantum state of the system.
The idea that decoherence produces "quasi-classical objects such as particles with a definite location emerge" is also incorrect. The phenomenon of decoherence erases the non-diagonal components of the density matrix, but the final result continues being a superposition of states, one per diagonal element of the matrix, not a delta-like f(x).
"In rapport with Zeh's understanding, particles are usually understood as field excitations in quantum field theory". Which is incorrect, because (i) field theory cannot fully describe bound states, so cannot describe fully interacting particles and (ii) those 'excitations' aren't real particles, but unphysical bare particles.
The Unruh effect is based in uncritical mixture of quantum field theory ideas with relativistic ideas and thermodynamic ideas.
"Adopting Occam's razor, one can assume now, that the process of decoherence is entirely responsible for the quantum-to-classical transition which leads to various decohered quasi-classical realities, the so-called Everett branches". But it is well-known that decoherence doesn't explain classical world neither measurements. And Everett ideas have been debunked dozens of times.
"This interpretation of the quantum measurement process is usually known as the Many-Worlds-Interpretation, Many-Minds-Interpretation or Universal Quantum Mechanics." In reality MWI isn't a valid interpretation of QM. Some criticism of early Everett ideas can be found here
http://www.mat.univie.ac.at/~neum/physfaq/topics/manyworlds
"In contrast to dt and dx the spacetime distance ds is, however, not directly observable" because ds is a geometrical construct but the closely related tau is a physical magnitude that can be measured with a proper clock.
Neither it is true that the quantum mechanical wave function is unanimous for any observer.
"the protons and neutrons constituting the atomic nucleus behave so similar that they can be understood as two states of a single particle". They cannot and the reason why we treat them as different particles.
Since when is "direct observability" a requirement for a fundamental description? And what is wrong with an observed-dependent description when the descriptions of the observers can be linked via transformation theory?
"In thermodynamics, states such as gases or liquids are described by parameters or state functions such as temperature, pressure or volume. These state functions are not fundamental in the sense that they do not correspond to a specific configuration of the constituent atoms or molecules (a so-called "microstate"), but to a statistical average of microstates known as "macrostate". This is constraining the concept of thermodynamics to mean XIX century thermodynamics only. Today we can define temperature directly from the microstate, and study fluctuations of temperature around the average; and the same happens with pressure. For instance the pressure in terms of phase space is given by
[math]\mathcal{P}(r,p) = \frac{1}{3V} \sum_{i=1}^N \left[ \frac{p_i^2}{m_i} r_i F_i \right][/math]
So if we don't pretend that the discipline of thermodynamics was frozen in century XIX, we can go beyond the classic concepts and even introduce quantum thermodynamics, which is an extension of quantum mechanics to non-pure (thermal) states.
"The normalized logarithm of the number of microstates corresponding to a given macrostate is known as entropy". This is the statistical concept of entropy, not the thermodynamic one, and this Boltzmanian definition of statistical entropy isn't valid for canonical ensembles for instance. Subsequent discussion is based in such confusions.
"Consequently, the fundamental state of the Universe has zero-entropy (and is arguably timeless). In fact, the Wheeler-DeWitt equation [17] of canonical quantum gravity describes a timeless Universe on the fundamental level". The WdW is a wrong equation, as admitted even by one of his authors.
"Turning back to quantum mechanics, it is well known that in the quantum-to-classical transition the von-Neumann entropy increases as a consequence of the information loss into the environment." Even if we loosy associate entropy with 'information', information isn't lost in the process. In fact quantum mechanics conserves the von-Neumann entropy by virtue of the quantum analog of the Liouville theorem.
"Thus the fundamental state of the Universe can not be a constituent, it has to be the total entangled system of observer, measured system, and environment, also known as the quantum Universe itself." Quantum mechanics isn't a fundamental theory (the field of emergent quantum mechanics is a hot topic of research those days); so a "quantum Universe" is only an approximate conception of Universe.
