- McFadden sees decoherence as crucial in biological evolution: here TGD view is diametric opposite although decoherence is a basic phenomenon also in TGD.
- McFadden assumes quantum superpositions of different DNAs. To me this looks an unrealistic assumption in the framework of PEO. In ZEO it is quite possible option.
- McFadden emphasizes the importance of Zeno effect (in PEO). In TGD the ZEO variant of Zeno effect is central for TGD inspired theory of consciousness and quantum biology. Mc Fadden suggests that quantum effects and Zeno effect are central in bio-catalysis: the repeated measurement keeping reactants in the same position can lead to an increase of reaction rate by factors of order billion. McFadden describe enzymes as quantum mousetraps catching the reactants and forcing them to stay in same position. The above description for how catalysis catches the reactants using U-shaped flux tube conforms with mousetrap picture.
McFadden discusses the action of enzymes in a nice manner and his view conforms with TGD view. In ZEO the system formed by catalyst plus reactants could be described as a negentropically entangled sub-self, and self indeed corresponds to a generalized Zeno effect. The reactions can proceed in shorter scales although the situation is fixed in longer scales (hierarchy of CDs): this would increase the length of the period of time during which reactions can proceed and lead to catalytic effect. Zeno effect in ZEO plus hierarchies of selves and CDs would be essentially for the local aspects of enzyme action.
- Protons associated with hydrogen bonds and electronic Cooper pairs play a universal role in McFadden's view and the localization of proton in quantum measurement of its position to hydrogen bond is the key step of enzyme catalysis. Also TGD dark protons at magnetic flux tubes giving rise to dark nuclear strings play a key role. For instance, McFadden models enzyme catalysis as injection of proton to a very special hydrogen bond of substrate. In TGD one has dark protons at magnetic flux tubes and their injection to a properly chosen hydrogen bond and transformation to ordinary proton is crucial for the catalysis. Typical places for reactions to occur are C=O type bonds, where the transition to C-OH can occur and would involve transformation of dark proton to ordinary proton. The transformation of dark proton to ordinary one or vice versa in hydrogen bonds would serve as a biological quantum switch allowing magnetic body to control biochemistry very effectively.
What about electronic Cooper pairs assumed also by McFadden? They would flow along the flux tube pairs. Can Cooper pairs of electrons and dark protons reside at same flux tubes? In principle this is possible although I have considered the possibility that particles with different masses (cyclotron frequencies) reside at different flux tubes. For hgr =heff this would make possible both frequency and energy resonance for cyclotron transitions.
The NE between dark codons could also have a useful function: it could determine physically gene as a union of disjoint mutually entangled portions of DNA. Genes are known to be highly dynamical units, and after pre-transcription splicing selects the portions of the transcript translated to protein. The codons in the complement of the real transcript are called introns and are spliced out from mRNA after the pre-transcription (see this).
What could be the physical criterion telling whether a given codon belongs to exonic or intronic portion of DNA? A possible criterion distinguish between exons and introns is that exons have NE between themselves and introns have no entanglement with exons (also exons could have NE between themselves). Introns would not be useless trash since the division into exonic and exonic region would be dynamical. The interpretation in terms of TGD inspired theory of consciousness is that exons correspond to single self.
An updated nuclear string variant is summarized and also its connection with the model of harmony is discussed in chapter Three new physics realizations of the genetic code and the role of dark matter in bio-systems and in the article About physical representations of genetic code in terms of dark nuclear strings.
For a summary of earlier postings see Latest progress in TGD.