Role and function of Benzene rings in microtubules

[Write4U]

Clearing up a few outstanding issues about the importance of benzene rings in microtubules.

Consciousness, Cognition and the Neuronal Cytoskeleton – A New Paradigm Needed in Neuroscience
Stuart Hameroff1,2,3*

• 1Department of Anesthesiology, The University of Arizona, Tucson, AZ, United States
• 2Department of Psychology, The University of Arizona, Tucson, AZ, United States
• 3Center for Consciousness Studies, The University of Arizona, Tucson, AZ, United States

Automata and computer systems generally utilize some type of periodic clocking mechanism to synchronize and update operations. In the microtubule automata simulations done by Rasmussen et al. (1990), collective coherent dipole oscillations among tubulins provided coherent time steps for synchronized updates, for example steps 1–4 in Figure 3 on the right. pThe oscillation updates result in propagating patterns of information, the biological mechanism for this clocking ascribed to “Fröhlich coherence.”

Biophysicist Herbert Fröhlich (1968, 1970, 1975) suggested that dipoles in non-polar intra-protein regions would oscillate due to the most basic structure in organic chemistry—the “pi electron resonance” benzene ring (Figure 4). Each of the hexagonal benzene’s 6 carbons has 4 electron bonds to share with 2 hydrogens and 2 neighbor carbons in a planar ring (Figures 4A,B).

This leaves 3 extra “pi orbital” resonance electrons which are portrayed as double bonds resonating between different carbons. In molecular orbital theory, the pi electrons combine and “delocalize” in a space-filling electron cloud enveloping all 6 carbons (Figure 4C). Such clouds are chemically neutral and non-polar, but polarizable, leading to interesting quantum vibrational properties.

Figure 4

FIGURE 4. (A) chemical structure of benzene, (B) simplified with 3 extra electron bonds, and (C) with a delocalized electron cloud enveloping the ring. (D) individual benzene rings attract by induced dipoles which then (E) oscillate in terahertz.

https://www.frontiersin.org/articles/10.3389/fnmol.2022.869935/full

Does this clear up any confusion about the role played by benzene rings in the MT network?

 

[exchemist]

Clearing up a few outstanding issues about the importance of benzene rings in microtubules.

Consciousness, Cognition and the Neuronal Cytoskeleton – A New Paradigm Needed in Neuroscience
Stuart Hameroff1,2,3*

• 1Department of Anesthesiology, The University of Arizona, Tucson, AZ, United States
• 2Department of Psychology, The University of Arizona, Tucson, AZ, United States
• 3Center for Consciousness Studies, The University of Arizona, Tucson, AZ, United States

Figure 4

FIGURE 4. (A) chemical structure of benzene, (B) simplified with 3 extra electron bonds, and (C) with a delocalized electron cloud enveloping the ring. (D) individual benzene rings attract by induced dipoles which then (E) oscillate in terahertz.

https://www.frontiersin.org/articles/10.3389/fnmol.2022.869935/full

Does this clear up any confusion about the role played by benzene rings in the MT network?

Far from it.

Hameroff seems to have forgotten, or never knew, the quantum chemistry of the benzene ring. It's not 3 electrons in the π-system but 6. They go in pairs into 3 molecular orbitals. The lowest energy one has the same phase across all 6 atoms of the ring, and then there is a pair of degenerate (i.e. equal energy) orbitals, one of which has the same phase across 3 atoms and the opposite phase across the other 3 and one with the same phase across 2. (There are also 3 antibonding orbitals which in the ground state are unoccupied):

The so-called "resonance" structures of benzene are terminology from an earlier bonding model. This tried to explain how the bond lengths are all equal in spite of the Kekulé bonding structure requiring alternate single and double bonds. There is no physical "resonance". It's just an idea that the molecule is an average of 2 bonding structures:

Bond resonance is explained here: https://en.wikipedia.org/wiki/Resonance_(chemistry)
I quote one para:
Due to confusion with the physical meaning of the word resonance, as no entities actually physically "resonate", it has been suggested that the term resonance be abandoned in favor of delocalization[9] and resonance energy abandoned in favor of delocalization energy. A resonance structure becomes a contributing structure and the resonance hybrid becomes the hybrid structure. The double headed arrows would be replaced by commas to illustrate a set of structures, as arrows of any type may suggest to beginning students that a chemical change is taking place.

Hameroff seems to be muddling this bonding "resonance" which, as stated above, is not a physical resonance at all, with the phonon resonance in biological systems that Frölich explored. This is a vibrational excitation, in which the atoms move physically back and forth, at a rate determined by the strength or "elasticity" of the bonds holding them together. Such vibrations arise from normal thermal motion at ambient temperatures but they have nothing to do with any special properties of benzene rings.

He also introduces another notion, that of the polarisability of the benzene ring. This is the ease with which the electron cloud in the π-system can be distorted by an applied electric field. He seems to get this from the 1968 paper by Frölich, which I have tracked down: https://ayuba.fr/pdf/frohlich1968b.pdf This paper is a bit unclear on what the "longitudinal electric modes" discussed really are in terms of molecular or electronic motion but the implication is that they are vibrational, since vibration of cell membranes is referred to. What Frölich is interested in, as a theoretical physicist, is whether a Bose-Einstein condensation of these excitations can occur, concentrating energy in a single long-range mode of vibration. Confusingly, and I suspect wrongly, Frölich suggests that delocalised electrons may participate in such modes. However, this is all a piece of theoretical speculation from 1968, without experimental support.

So I'm afraid it looks to me as if Hameroff has resorted to scratching around, looking up very old stuff that never went anywhere, in order to support his hypothesis. It is notable that Hameroff offers no experimental support either.

Finally, this paper was published by "Frontiers", which is a pay-to-publish outfit that appears on Beall's List of potentially predatory publishers. So it seems highly doubtful that it has been peer-reviewed (in fact any decent reviewer would have picked up the errors on benzene bonding that I spotted immediately.) .

Hameroff seems to be getting flakier and flakier.

 

[Write4U]

Bond resonance is explained here: https://en.wikipedia.org/wiki/Resonance_(chemistry)

I quote one para:
Due to confusion with the physical meaning of the word resonance, as no entities actually physically "resonate", it has been suggested that the term resonance be abandoned in favor of delocalization[9] and resonance energy abandoned in favor of delocalization energy. A resonance structure becomes a contributing structure and the resonance hybrid becomes the hybrid structure. The double headed arrows would be replaced by commas to illustrate a set of structures, as arrows of any type may suggest to beginning students that a chemical change is taking place.

Terminology to describe the same phenomena in a more codified form.

Self-reference, physics
What is meant by self-reference?

Self-reference is a concept that involves referring to oneself or one's own attributes, characteristics, or actions. It can occur in language, logic, mathematics, philosophy, and other fields.
https://en.wikipedia.org/wiki/Self-reference#

I think that's incomplete.
"self-reference" does not refer to self but to identical interactive properties between two identical objects., i.e. data transmission (both ways).

 

[exchemist]

Terminology to describe the same phenomena in a more codified form.

Self-reference, physics
What is meant by self-reference?

I think that's incomplete.
"self-reference" does not refer to self but to identical interactive properties between two identical objects., i.e. data transmission (both ways).

The term "self-reference" does not appear in anything I have written or quoted.

Reported for self-hijacking* (it is your thread that you are hijacking onto a new topic).

* One form of what the Germans don't call Gesellfschaft .

Note for James: I doubt anyone on the forum is likely to pick up the science of this thread, so if you want to close it, now that Write4U has self-hijacked it, that's fine by me.

 

[James R]

Write4U:

For some reason, you have failed to acknowledge the errors exchemist so helpfully pointed out in Hameroff's work.

Claiming that the correct explanation is somehow equivalent to Hameroff's description either shows that you have no clue about what you're talking about, or that you're willing to tell lies for Hameroff.

Either way, there is little point in continuing this discussion. You are, apparently, not equipped to have it, or unwilling to be honest about the topic.

This thread is closed.