Biophotons, Microtubules & Brain
Light generated inside brain and the involvement of neuronal microtubules
If the brain is related to mind is, from the point of view of this site, because the more complex and extensive multilayer electromagnetic fields working there, and if we test about possible role of biophotons we found that maybe are very related because microtubules, more present in neurons that in other cells, are one of the very possible guiding mechanisms for those emissions. ...
Biophoton emission have been measured from numerous living systems including bacteria , cells , multicellular organisms , brain slices  etc.. and is speculated about their possible role in information exchange and maybe consciousness generation.
It must be said first that biophoton emissions must have one energetic origin that can be modulated by organism or cell metabolism but this origin is not absolutely clear, or more exactly, various origins can be opearting here. The classical theory propose that the action pathway relates to oxygen-dependent mechanisms operated by oxidation-reduction enzymes of the respiratory chain, particularly cytochrome c oxidase (CcO).
But definitely is not the only source (even if possibly is a source), for example in  they found that
" the initiation and/or maintenance of biophotonic activities can be significantly blocked by oxygen glucose deprivation together with the application of 2DG and cytochrome c oxidase inhibitor, but only partly by cytochrome c oxidase inhibitor, suggesting that the glutamate-induced biophotonic activities were dependent on energy metabolism and that alternative anaerobic metabolic pathways may be a compensatory method to meet energy requirements when the aerobic metabolic pathways are inhibited."
Is very interesting to see the other possible sources, one of them may be water , that has very interesting ordering capacities (see section ) and photon storage capacity 
DNA has also proposed as possible source for biophotons (or Ultraweak Photon Emissions, UPE) , but if you are interested there is a section  in this web dedicated to more specifically discuss about possible physical origins of those electromagnetic emissions.
It is conceivable that evolution might have found a way to utilize these precious high-energy resources for information transfer, even if they are just the byproducts of metabolism (that for the editor of this site is not the winner idea), so is expected to find photon guiding or manipulating mechanisms in biological systems.
Newly discovered cell to cell membrane nanotubes are proposed as photonic waveguides for UPE  but there is more theoretical work developed with a similar proposition but related to axons of the cells/neurons , and in this case also more direct evidence is available :
" we observed the glutamate-induced biophotonic activities in mouse sagittal brain slices and found that the extensive biophotonic activities were located at the area of the corpus callosum and the thalamus, and were significantly decreased by the application of PP2A inhibitor (OA), suggesting that the extensive biophotonic activities in these two areas may mainly originate from axons or axonal terminals in the corpus callosum and thalamus, respectively, which may be at least partly due to the active biophotonic transmission along the axons or axonal terminals of cortical projection neurons."
Sun et al.  discovered some year ago that stimulation with light at one end of the spinal sensory or motor nerve roots resulted in a significant increase in the biophotonic activity at the other end. They propose that light stimulation can generate biophotons that conduct along the neural fibers, probably as neural communication signals. In their paper they propose also that two different proteins may achieve biophotonic conduction if they form a biophotonic interaction couple and that this may be the mechanism of biophotonic conduction along neural fibers.
Rahnama et al.  propose that both the mitochondria and the microtubules could act as optical waveguides and taking in consideration that microtubules transmit electric signals between distant points within a neuron and the theoretical work that suggest that interaction of biophotons and microtubules causes transitions/fluctuations of microtubules between coherent and incoherent states, proposes also that biophotons can influence membrane electrical activity via microtubules.
Moreover, as axons are filled by microtubules, specially in neurons, is timely to note the interesting investigations that propose that biophotons are generated and conducted through microtubules by means of ordered water capacities as proposed in :
" Micro-Tubules are considered as quantum cavities. Their role is to provide a single mode of biophoton field, in such a way that water molecules to be considered not as independent individuals, but rather as whole, in this manner water molecules are embedded in and interacting with a common radiation field.In the model proposed, collective behavior of water molecules is characterized by coherent water states analogous to Bloch states, whose main feature is to trap biophotons in a collective fashion."
Also is interesting to note that is known that the brain response can change dependent of an incident unique photon to the eye, so this is sensitive to the minimum quantum of energy, an unique photon! the brain is also sensitive to photons incident to other parts of the skull, that is, skull is permeable to photons and brain functioning is affected by the characteristics of photon sequences that pass through it . There is a complete overview of the experimental investigation on the effect of low intensity light on living systems, including possible therapeutic application in this section .
There is a well developed hypothesis by Bokkon and others which proposes that biophotons may actually be the information from which dreams and visual images during the waking state are constructed. They have some experimental findings like spontaneous and visible light-induced photon emission from rat eyes, or that the photon-like component of discrete dark noise is not caused by a direct contribution of the thermal activation of rhodopsin, but rather by an indirect thermal induction of biophotonic activity, which then activates the retinal chromophore of rhodopsin. (See this section  to get more info about this theory).
Very curious and interesting may be the theory proposed by Grass :
" The nervous system would have excellent conditions for a cell to cell communication by light. Neurons are large, metabolically very active (lightproducing) cells with wide arborisation, contain little pigment and are protected from ambient light by bone and connective tissue. Signal to noise ratio should be high for photon signals. It has been shown that light can be propagated along the axis tracts. Also the hollow microtubules (neurofibrillae) could act as light guiding structures. According to Jibu et al. their inner diameter of 15 nm is ideal for light guidance free of thermal noise and loss. Other findings that may be of importance in this context, are the strong flurescence properties of the major hallucinogens: LSD, bufetonine, dimethyl-tryptamine, psilocybine, psilocin, iboguanin, harmine, cannabidinol and mescaline. Furthermore it has been shown that hallucinogenic properties of these substances have a direct correlation to their fluorescence properties and their readyness to donate electrons. As hypothesis we propose that the fluorescence interacts physically with the proposed Biophoton mediated cell to cell communication thus producing hallucinations. This would be an easy and plausible explanation for the strong hallucinogenic properties of these fluorescent substances."
And, although away of the scope of this section, may be interesting to note that some investigations on nonlocality of mind take in consideration a possible important role of biophoton emission characteristics  also because biophoton emission and surrounding environmental geomagnetic intensity are inversely related  and manipulation of surrounding magnetic environment is related to these non-local phenomena (see section )
Biophotons generated by living systems can integrate in a more general framework of electromagnetic mind theory, as proposed in section , being a layer of this more general mind. How concrete is this layer or what are the specific qualia to what this layer is equal (or of what level of consciousness is representative) taking also in consideration the possibility that this electromagnetic layer is an upconversion of other coherent phenomena  is difficult to imagine at this moment. Anyway there are some concrete theories that relate biophotons with consciousness in some ways , in  is speculated that:
" the process of radiative relaxation of the electro-solitons allows for the transfer of energy via interactions with deoxyribonucleic acid (DNA) molecules to induce conformational changes in DNA molecules producing an ultra weak non-thermal spontaneous emission of coherent biophotons through a quantum effect. The instantiation of coherent biophotons confined in spaces of DNA molecules guides the biophoton field to be instantaneously conducted along the axonal and neuronal arbors and in-between neurons and throughout the cerebral cortex (cortico-thalamic system) and subcortical areas (e.g., midbrain and hindbrain). Thus providing an informational character of the electric coherence of the brain — referred to as quantum coherence. The biophoton field is realized as a conscious field upon the re-absorption of biophotons by exciplex states of DNA molecules."
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Very related sections:
↑ text updated: 07/08/2016
↓ tables updated: 31/08/2017