Amos Zeeberg - One Big Question Not Answered by Today’s Nobel Winners

This article is in response to the winners of the 2013 Nobel Prize in Physiology and Medicine [more here], who won for their work in understanding cellular communication.

Via Nautilus, the coolest new magazine on the internets.

One Big Question Not Answered by Today’s Nobel Winners

Posted By Amos Zeeberg on Oct 07, 2013


Synapse via Shutterstock

Earlier today three US-based researchers shared the Nobel Prize in Physiology or Medicine for their research on vesicles, special structures that ferry all kinds of molecules around biological cells, and are fundamental to those cells’ functioning. Their findings provide some key background for our understanding of life—information that will fill textbooks for decades—though they lack the cutting-edge currency of some other Nobel-blessed work, like the discovery that regular cells can be reprogrammed to become stem cells, which won last year. Arguably the most captivating research came from new laureate Thomas Südhof, who showed how vesicles help nerve signals quickly flow through neurons. But what the prize did not include might be just as revealing.

When Südhof started his research 25 years ago, neuroscientists knew that neurons could send signals to each other via molecules called neurotransmitters, which would be rapidly released from one neuron and flood a neighboring one. At the time, though, little was known about the mechanics of how that happened—there was literally not a single involved protein identified. The Nobel Foundation describes the subsequent work like this:

These vesicles are only allowed to release their contents when the nerve cell signals to its neighbours. How is this release controlled in such a precise manner? Calcium ions were known to be involved in this process and in the 1990s, Südhof searched for calcium sensitive proteins in nerve cells. He identified molecular machinery that responds to an influx of calcium ions and directs neighbour proteins rapidly to bind vesicles to the outer membrane of the nerve cell. The zipper [on the edge of the vesicle] opens up and signal substances are released.

The entire process is exquisitely coordinated; it can be completed in less than a thousandth of a second.

While Südhof’s research shows a key neural function on the cellular, mechanistic level, it notably does not include a more holistic description of how the brain works on a bigger scale. There has been a lot of successful work on how bigger neural circuits work, but there is a genuine gap in our understanding of how information about the outside world is encoded and stored in our brains. When President Obama announced the ambitious and costly BRAIN Initiative, neurologist John Donoghue commented on this challenge in particular:

What’s going on in the brain is like a conversation between thousands of neurons all at once. So the tools we need are the ability to pick up many, many cells at the same time. And you have to pick them up so you can hear each conversation very clearly…We know enough to get crude approximations. But if we really understood the brain’s language, the brain’s code, we could potentially recreate everything you do with your own arm.

Thomas Südhof’s effort to analyze a complicated system by breaking it down into parts is a central step in scientific method, and his research succeeding in elucidating a lot about how neurons communicate. But in the case of complicated system that is the brain, the workings of the whole are proving much more difficult to decipher than the workings of the parts.


~ Amos Zeeberg is Nautilus’ digital editor.

The winners of the Nobel Prize in Physiology or Medicine all are working to better understand how cells - especially neurons - communicate. Cool stuff.

Apparently the Nobel folks gave the Physics prize to a couple of guys who (may have) discovered a simple particle at the heart of the universe. Geez.

Nobel Winners Decoded How Neurons And Cells Talk To Each Other

by Michaeleen Doucleff
October 07, 2013

From left: Randy Schekman, Thomas Suedhof and James Rothman 

shared the 2013 Nobel Prize in Physiology or Medicine. Reuters /Landov

The three scientists who shared this year's Nobel Prize in Physiology or Medicine all made discoveries that illuminate how the body's cells communicate.

The research has sweeping implications for our understanding of how nerves in the brain transmit signals, how the immune system attacks pathogens and how hormones, like insulin, get into the bloodstream.

Bioengineers have already harnessed the discoveries to manufacture new vaccines and improve the quality of insulin for diabetics.

How does insulin get into the blood? The hormone (dark blue) is carried to the cell surface in a bubble-like compartment, called a vesicle. When the vesicle binds with the cell membrane, it pops open and releases the insulin. Courtesy of the Nobel Prize

The winners include two Americans — James Rothman of Yale University and Randy Schekman of the University of California, Berkeley — and the German-born Thomas Suedhof of Stanford University. Both Schekman and Suedhof are also investigators at the Howard Hughes Medical Institute.

Their discoveries took place over the course of 30 years. The work got its start with a few simple experiments in cells of yeast – the same organism that leavens bread and brews beer.

In the 1970s, biologists already knew that cells weren't just sacks of fluid. Rather, they contain sophisticated highway systems that shuttle material from one compartment to the next. This cargo moves around cells in bubble-like compartments called vesicles.

In a healthy cell, some of these vesicles make their way to the cell's surface, where the material is released outside the cell. That's one way that cells communicate with each other and with organs in the body.

In 1976, Schekman, a new professor at the University of California, Berkeley, had recently found mutant yeast cells that had faulty transport systems. The cargo just piled up at the cell's surface, like cars stuck in a traffic jam.

By figuring out which genes were defective in these yeasts, Schekman discovered dozens of components that built and controlled the cell's transport system.

But there were still many pieces missing. In particular, it wasn't known how a cargo vesicle knows where to go on the cell's surface and then when to dump out its contents.

"Imagine hundreds of thousands of people who are traveling around hundreds of miles of streets. How are they going to find the right way? Where will the bus stop and open its doors so that people can get out?" Nobel committee secretary Goran Hansson said Monday. "There are similar problems in the cell, to find the right way ... and out to the surface of the cell." 

Take for instance two neurons in your brain. One neuron communicates with another by secreting neurotransmitters, such as dopamine and serotonin. But a neuron must release the neurotransmitter at a particular place — and at the right time. Otherwise the message will never make it to the second neuron, or the signal will get scrambled.

That's where Rothman and Suedhof's research comes in. In the 1980s and 1990s, Rothman, now 62, figured out that a signal on the vesicle's surface that helps it dock at just the right place on the cell's surface. The process works a bit like a zipper: A protein on the vesicle zips up with another one on the cell's membrane to position the cargo in the correct location.

Then a few years later, Suedhof, who is now 57, identified the trigger mechanism that dumps the neurotransmitter outside the cell at just the right time by unzipping the two proteins.

This transport system has served as the foundation of modern cell biology and neuroscience.

And breakdowns of the process is involved in a vast range of diseases, including Alzheimer's, cystic fibrosis, muscular dystrophies and some autoimmune disorders. 
Here is the press release from the Nobel Foundation:

Press Release

2013-10-07

The Nobel Assembly at Karolinska Institutet has today decided to award
The 2013 Nobel Prize in Physiology or Medicine

jointly to

James E. Rothman, Randy W. Schekman, and Thomas C. Südhof

for their discoveries of machinery regulating vesicle traffic,
a major transport system in our cells

Summary

The 2013 Nobel Prize honours three scientists who have solved the mystery of how the cell organizes its transport system. Each cell is a factory that produces and exports molecules. For instance, insulin is manufactured and released into the blood and chemical signals called neurotransmitters are sent from one nerve cell to another. These molecules are transported around the cell in small packages called vesicles. The three Nobel Laureates have discovered the molecular principles that govern how this cargo is delivered to the right place at the right time in the cell.

Randy Schekman discovered a set of genes that were required for vesicle traffic. James Rothman  unravelled protein machinery that allows vesicles to fuse with their targets to permit transfer of cargo. Thomas Südhof revealed how signals instruct vesicles to release their cargo with precision.

Through their discoveries, Rothman, Schekman and Südhof have revealed the exquisitely precise control system for the transport and delivery of cellular cargo. Disturbances in this system have deleterious effects and contribute to conditions such as neurological diseases, diabetes, and immunological disorders.

How cargo is transported in the cell

In a large and busy port, systems are required to ensure that the correct cargo is shipped to the correct destination at the right time. The cell, with its different compartments called organelles, faces a similar problem: cells produce molecules such as hormones, neurotransmitters, cytokines and enzymes that have to be delivered to other places inside the cell, or exported out of the cell, at exactly the right moment. Timing and location are everything. Miniature bubble-like vesicles, surrounded by membranes, shuttle the cargo between organelles or fuse with the outer membrane of the cell and release their cargo to the outside. This is of major importance, as it triggers nerve activation in the case of transmitter substances, or controls metabolism in the case of hormones. How do these vesicles know where and when to deliver their cargo?

Traffic congestion reveals genetic controllers

Randy Schekman was fascinated by how the cell organizes its transport system and in the 1970s decided to study its genetic basis by using yeast as a model system. In a genetic screen, he identified yeast cells with defective transport machinery, giving rise to a situation resembling a poorly planned public transport system. Vesicles piled up in certain parts of the cell. He found that the cause of this congestion was genetic and went on to identify the mutated genes. Schekman identified three classes of genes that control different facets of the cell´s transport system, thereby providing new insights into the tightly regulated machinery that mediates vesicle transport in the cell.

Docking with precision

James Rothman was also intrigued by the nature of the cell´s transport system. When studying vesicle transport in mammalian cells in the 1980s and 1990s, Rothman discovered that a protein complex enables vesicles to dock and fuse with their target membranes. In the fusion process, proteins on the vesicles and target membranes bind to each other like the two sides of a zipper. The fact that there are many such proteins and that they bind only in specific combinations ensures that cargo is delivered to a precise location. The same principle operates inside the cell and when a vesicle binds to the cell´s outer membrane to release its contents. 

It turned out that some of the genes Schekman had discovered in yeast coded for proteins corresponding to those Rothman identified in mammals, revealing an ancient evolutionary origin of the transport system. Collectively, they mapped critical components of the cell´s transport machinery.

Timing is everything

Thomas Südhof was interested in how nerve cells communicate with one another in the brain. The signalling molecules, neurotransmitters, are released from vesicles that fuse with the outer membrane of nerve cells by using the machinery discovered by Rothman and Schekman. But these vesicles are only allowed to release their contents when the nerve cell signals to its neighbours. How is this release controlled in such a precise manner? Calcium ions were known to be involved in this process and in the 1990s, Südhof searched for calcium sensitive proteins in nerve cells. He identified molecular machinery that responds to an influx of calcium ions and directs neighbour proteins rapidly to bind vesicles to the outer membrane of the nerve cell. The zipper opens up and signal substances are released. Südhof´s discovery explained how temporal precision is achieved and how vesicles´ contents can be released on command.

Vesicle transport gives insight into disease processes

The three Nobel Laureates have discovered a fundamental process in cell physiology. These discoveries have had a major impact on our understanding of how cargo is delivered with timing and precision within and outside the cell.  Vesicle transport and fusion operate, with the same general principles, in organisms as different as yeast and man. The system is critical for a variety of physiological processes in which vesicle fusion must be controlled, ranging from signalling in the brain to release of hormones and immune cytokines. Defective vesicle transport occurs in a variety of diseases including a number of neurological and immunological disorders, as well as in diabetes. Without this wonderfully precise organization, the cell would lapse into chaos.

James E. Rothman was born 1950 in Haverhill, Massachusetts, USA. He received his PhD from Harvard Medical School in 1976, was a postdoctoral fellow at Massachusetts Institute of Technology, and moved in 1978 to Stanford University in California, where he started his research on the vesicles of the cell. Rothman has also worked at Princeton University, Memorial Sloan-Kettering Cancer Institute and Columbia University. In 2008, he joined the faculty of Yale University in New Haven, Connecticut, USA, where he is currently Professor and Chairman in the Department of Cell Biology.

Randy W. Schekman was born 1948 in St Paul, Minnesota, USA, studied at the University of California in Los Angeles and at Stanford University, where he obtained his PhD in 1974 under the supervision of Arthur Kornberg (Nobel Prize 1959) and in the same department that Rothman joined a few years later. In 1976, Schekman joined the faculty of the University of California at Berkeley, where he is currently Professor in the Department of Molecular and Cell biology. Schekman is also an investigator of Howard Hughes Medical Institute.

Thomas C. Südhof was born in 1955 in Göttingen, Germany. He studied at the Georg-August-Universität in Göttingen, where he received an MD in 1982 and a Doctorate in neurochemistry the same year. In 1983, he moved to the University of Texas Southwestern Medical Center in Dallas, Texas, USA, as a postdoctoral fellow with Michael Brown and Joseph Goldstein (who shared the 1985 Nobel Prize in Physiology or Medicine). Südhof became an investigator of Howard Hughes Medical Institute in 1991 and was appointed Professor of Molecular and Cellular Physiology at Stanford University in 2008.

Key publications:

Novick P, Schekman R: Secretion and cell-surface growth are blocked in a temperature-sensitive mutant of Saccharomyces cerevisiae. Proc Natl Acad Sci USA 1979; 76:1858-1862.

Balch WE, Dunphy WG, Braell WA, Rothman JE: Reconstitution of the transport of protein between successive compartments of the Golgi measured by the coupled incorporation of N-acetylglucosamine. Cell 1984; 39:405-416.

Kaiser CA, Schekman R: Distinct sets of SEC genes govern transport vesicle formation and fusion early in the secretory pathway. Cell 1990; 61:723-733.

Perin MS, Fried VA, Mignery GA, Jahn R, Südhof TC: Phospholipid binding by a synaptic vesicle protein homologous to the regulatory region of protein kinase C. Nature 1990; 345:260-263.

Sollner T, Whiteheart W, Brunner M, Erdjument-Bromage H, Geromanos S, Tempst P, Rothman JE: SNAP receptor implicated in vesicle targeting and fusion. Nature 1993; 362:318-324.

Hata Y, Slaughter CA, Südhof TC: Synaptic vesicle fusion complex contains unc-18 homologue bound to syntaxin. Nature 1993; 366:347-351.

Scientists Discover Cells Can Communicate Through Physical Barriers

From UCLA and the Charles R. Drew University of Medicine and Science have announced that they have discovered a new, "higher" form of cell communication - what exactly that is they have not said (or do not know).

This actually not a new piece of information - scientists have long known that cells can communicate over a distance, and even through barriers. The mechanism most often cited is biophotons - see here and here for more information.

'Psychic cells': Scientists discover cells can communicate through physical barriers

By Kim Irwin January 31, 2013

Dr. Keith Norris

Scientists at UCLA and Charles R. Drew University of Medicine and Science have discovered a possible method by which cancer cells and dying cells communicate with nearby normal nerve cells without being physically connected to them.

Dr. Keith Norris, senior author of the research and assistant dean for clinical and translational science at the David Geffen School of Medicine at UCLA, said the study contributes to the understanding of cell communication, which until now was known to take place only through direct contact or direct stimulation of receptors in the cells of molecules known as ligands or in hormones, signaling factors, nerves and other pathways.

It now appears, the researchers say, that cells may be able to effectively communicate through physical barriers. Their study appears in the January 2013 issue of the peer-reviewed American Journal of Translational Research.

For the study, Norris and his colleagues reported on how normal nerve cells isolated in an enclosed chamber behave during a function known calcium signal processing. The team found that when these isolated nerve cells were surrounded by other normal nerve cells outside the barrier, they had the same calcium signaling properties.

However, when the normal isolated nerve cells were surrounded by cancer cells or dying cells, they processed the calcium signals differently, suggesting there was communication from the surrounding cells. The physical barrier between the cells prevented hormonal, ligand-receptor and other traditional forms of cell-to-cell communication.

Co-authors Dr. Christopher Reid and Victor Chaban of the Life Sciences Institute at Drew University noted that this novel finding may represent a potentially higher form of cell communication. Discovering that cancer cells and dying cells may have a previously undiscovered communication method with other cells may lead to new treatments for cancer, aging and other diseases, they said. Further studies are needed to uncover how the non-physical communication occurs.

"Understanding the many ways in which cells communicate is an important step toward developing new approaches to treat disease," said Dr. Steven M. Dubinett, executive director of the UCLA Clinical and Translational Science Institute (UCLA CTSI).

The study was funded by the National Center for Advancing Translational Sciences through the UCLA CTSI and the National Institute on Minority Health and Health Disparities at the National Institutes of Health.

The UCLA Clinical and Translational Science Institute is a dynamic partnership of four institutions - Cedars-Sinai Medical Center, Charles Drew University of Medicine and Science, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, and the UCLA-Westwood Health Science campus. Its mission is to bring UCLA innovations to bear on the greatest health needs of Los Angeles and the nation. It is one of 60 such institutes nationwide funded by the National Institutes of Health.

For more news, visit the UCLA Newsroom and follow us on Twitter.

Biophotonic Communications and Information Encoding in Complex Systems - Implications for Consciousness?

How does consciousness emerge from inert matter? This may be the hardest part of the "hard problem" that is consciousness. We have developed pretty solid models for explaining how the various modules and circuits in the brain work together (often in parallel processes) to create awareness and a sense of self.

But how does the brain itself, a three pound lump of fatty acids, produce consciousness? We don't really know, but the research presented below offers the beginning of a possible explanation, but only if the various models are combined (integrated) to generate a coherent theory.

Biological Photonic Communication in Cells

The open access arXiv.org Quantitative Biology platform (a service of the Cornell University Library) recently posted an article on biological photonic communication and information encoding in (otherwise known as biophotons) in loach fish eggs. Before taking a brief look at this article, here is some background on biophotonics.

Wikipedia offers a fairly neutral definition of biophotons, free from the New Age hype about divine light or other such nonsense, and also not as dismissive as some biologists in seeing "ultraweak  bioluminescence" as meaningless.

A biophoton (from the Greek βίος meaning "life" and φῶς meaning "light"), synonymous with ultraweak photon emission, low-level biological chemiluminescence, ultraweak bioluminescence, dark luminescence and other similar terms, is a photon of light emitted from a biological system and detected by biological probes as part of the general weak electromagnetic radiation of living biological cells. Biophotons and their study should not be confused with bioluminescence, a term generally reserved for higher intensity luciferin/luciferase systems.

Biophotonics is the study, research and applications of photons in their interactions within and on biological systems. Topics of research pertain more generally to basic questions of biophysics and related subjects - for example, the regulation of biological functions, cell growth and differentiation, connections to so-called delayed luminescence, and spectral emissions in supermolecular processes in living tissues, etc.

The typical detected magnitude of "biophotons" in the visible and ultraviolet spectrum ranges from a few up to several hundred photons per second per square centimeter of surface area, much weaker than in the openly visible and well-researched phenomenon of normal bioluminescence, but stronger than in the thermal, or black body radiation that so-called perfect black bodies demonstrate. The detection of these photons has been made possible (and easier) by the development of more sensitive photomultiplier tubes and associated electronic equipment.

Biophotons were employed by the Stalin regime to diagnose cancer, and their discoverer, Alexander Gurwitsch was awarded the Stalin Prize.^[1] Various studies have indicated some potential for photon emission to be used as a diagnostic technique.^{[2] [3] [4]}

Much of what we know about biophotons is a result of the work of German biophysicist Fritz-Albert Popp. Here is some additional background on biophotonics, including Popp's contribution, from the same Wikipedia article:

In the 1970s the then assistant professor Fritz-Albert Popp, and his research group, at the University of Marburg (Germany) showed that the spectral distribution of the emission fell over a wide range of wavelengths, from 200 to 800 nm. Popp proposed that the radiation might be both semi-periodic and coherent.

Russian, German, and other biophotonics experts, often adopting the term "biophotons" from Popp, have theorized, like Gurwitsch, that they may be involved in various cell functions, such as mitosis, or even that they may be produced and detected by the DNA in the cell nucleus. In 1974 Dr. V.P.Kaznacheyev announced that his research team in Novosibirsk had detected intercellular communication by means of these rays.^[9] Until 1980s, Kaznacheyev and his team carried out about 12 000 experiments. Details of experiments are described in his book (in Russian).^[10]

Proponents additionally claim that studies have shown that injured cells will emit a higher biophoton rate than normal cells and that organisms with illnesses will likewise emit a brighter light, which has been interpreted as implying a sort of distress signal. These ideas tend to support Gurwitsch's original idea that biophotons may be important for the development of larger structures such as organs and organisms.

However injured cells are under higher levels of oxidative stress, which ultimately is the source of the light, and whether this constitutes a "distress signal" or simply a background chemical process is yet to be demonstrated.^[11] The difficulty of teasing out the effects of any supposed biophotons amid the other numerous chemical interactions between cells makes it difficult to devise a testable hypothesis. Most organisms are bathed in relatively high-intensity light that ought to swamp any signaling effect, although biophoton signaling might manifest through temporal patterns of distinct wavelengths or could mainly be used in deep tissues hidden from daylight (such as the human brain, which contains photoreceptor proteins). Recent review article ^[12] discusses various published theories on this kind of signaling and identifies around 30 experimental scientific articles in English in past 30 years which prove electromagnetic cellular interactions.

In the new article, Photonic Communications and Information Encoding in Biological Systems, by
Sergey Mayburov (2012, May), the observed emission of photons generated by cells in fish eggs reveals a pattern that offers support for the theory that some cells use biophotons to communicate. While there is not, as of now, any definitive proof that cells (and some suspect DNA cells in particular) communicate through biophotonic emission, the evidence is accumulating.

Here is the abstract (and on a personal note, these authors need better translations - so many of these are clunky):

The structure of optical radiation emitted by the samples of loach fish eggs is studied. It was found earlier that such radiation perform the communications between distant samples, which result in the synchronization of their development. The photon radiation in form of short quasi-periodic bursts was observed for fish and frog eggs, hence the communication mechanism can be similar to the exchange of binary encoded data in the computer nets via the noisy channels. The data analysis of fish egg radiation demonstrates that in this case the information encoding is similar to the digit to time analogue algorithm.

In a 2009 paper by the same author, Coherent and Noncoherent Photonic Communications in Biological Systems (based on a talk given at the 2009 Progress In Electromagnetics Research Symposium in Moscow), again examines biophoton emissions in frog and fish eggs. He concludes with the following:

In this paper it was shown that the exciton exchange supposedly constitutes the effective system of signalling and regulation of the bio-system development. It seems that such signalling to the large extent regulates the homogeneity of bio-system growth, preventing from the large fluctuations of its global form, i.e. defines its morphogenesis. In our approach, each cell cluster is the analogue of computer, which reaction is defined by the signals dispatched by the absorbed excitons(13). Basing on it, the simple scheme of information exchange inside the bio-system was proposed, from that the similar scheme of photons communications between the distant bio-systems was derived. It turns out to be analogous to the standard procedure of information exchange between the distant computers by means of photonic signals transferred by the optical fibres. It’s important to notice that the obtained scheme of photon communications is practically independent of particular BP [biophoton production] mechanism. The calculations of BP time spectra in our model are in a reasonable agreement with the experimental results for BP in fish eggs(1). Exploiting the rules of quantum optics, this model explains qualitatively the influence of external nonbiological irradiation on BP rate and ME [mitogenetic effect]. Note that this model doesn’t demand that e-m field of bio-systems will be coherent during the long time periods, it permit to obtain ME and other biophoton effects assuming the produced e-m field to be noncoherent.
 

Yet it's worth to consider also the possibility that this e-m field of bio-system can possess the spacious short-time coherence within the observed photon bursts, similarly to the field coherence within the laser pulse. At least one experiment evidences directly that such coherence really takes place(11).

If cells in eggs communicate via photons as a way to synchronize developmental stages (which is what the research has been attempting to demonstrate), then it seems logical to look for similar evidence in other complex systems of the body - and what system is more complex than the brain?

Biophotons, Microtubules, and Consciousness

Of special interest to me is the research into biophotonic activity in neurons (especially microtubules) and what role it may play in the emergence of consciousness - this is a topic on which there already has been considerable speculation. In 2004, Grassa, Klimab, and Kasper (Medical Hypotheses; 62, 169–172) published an article entitled, Biophotons, microtubules and CNS, is our brain a“Holographic computer”? Here is the abstract:

Several experiments show that there is a cell to cell communication by light in different cell types. This article describes theoretical mechanisms and subcellular structures that could be involved in this phenomenon. Special consideration is given to the nervous system, since it would have excellent conditions for such mechanisms. Neurons are large colourless cells with wide arborisations, have an active metabolism generating photons, contain little pigment, and have a prominent cytoskeleton consisting of hollow microtubules. As brain and spinal cord are protected from environmental light by bone and connective tissue, the signal to noise ratio should be high for photons as signal. Fluorescent and absorbing substances should interfere with such a communication system. Of all biogenic amines nature has chosen the ones with the strongest fluorescence as neurotransmitters for mood reactions: serotonin, dopamine and norepinephrine. If these mechanisms are of relevance our brain would have to be looked upon as a “holographic computer”.

Several years later (2010), Rahnama, et al (J Integrative Neuroscience, 10:1, 65-88), published Emission of Biophotons and Neural Activity of the Brain, for which this is the abstract:

In this paper we argue that, in addition to electrical and chemical signals propagating in the neurons of the brain, signal propagation takes place in the form of biophoton production. This statement is supported by recent experimental confirmation of photon guiding properties of a single neuron. We have investigated the interaction of mitochondrial biophotons with microtubules from a quantum mechanical point of view. Our theoretical analysis indicates that the interaction of biophotons and microtubules causes transitions/fluctuations of microtubules between coherent and incoherent states. A significant relationship between the fluctuation function of microtubules and alpha-EEG diagrams is elaborated on in this paper. We argue that the role of biophotons in the brain merits special attention.

The range of discussion on this topic is wide - from New Age woo to hard-core quantum computing models. On the side of woo, for those who might be interested or amused, this 2005 article by A.U. De and Dhananjay Pal, published in NeuroQuantology, entitled Significance of thought-carrying particles and thought-retaining particles in quantum measurement as well as cognitive problem, begins with this abstract:

The thought force a manifestation of universal consciousness, has been shown to be carried by thought-carrying particle in the inherent presence of thought retaining particle in a previous communication (Pal et al., 2004). The thought force (TF) is the origin of all the existing fields. While TCP is the origin of all the field particles (bosons), TRP is the origin of all the matter particles (fermions). TCP cannot exist without TRP and vice versa. Both TCP and TRP are interchangeable at supersymmetry having the same energy level. In ‘supersymmetry’, these TCP and TRP are inter-convertible to carry and retain a specific "thought" and also for its communication from one person to another. The human nervous system is evolved to provide an appropriate material structure to individualize consciousness, a characteristic of reality, pervading all manifestations. TCP and TRP are assumed here to be the ultimate constituents of matter as well as mind, an infinitesimal part of the universal mind (UM). These conceptual TCP/TRP can address many present day scientific enigmas some of which are detailed below.

"The thought force is the origin of all the existing fields." Okay, sure, you betcha. So that would mean that the universe, which we have determined to be 15 billion years old through a process of quantum measurement, is simply the result of human thoughts (one assumes it must be human) in various forms, even though modern humans have only been here for about 50,000 years. Or maybe it is the universal mind having these thoughts? Whatever. For these folks, biophotons act as TCP and/or TRP.

The researchers looking more specifically at neuronal structures and biophoton emission (BPE) offer much more legitimate explanations for how BPE might contribute to or delineate consciousness.

Returning to Grassa, Klimab, and Kasper (Medical Hypotheses; 62, 169–172) - Biophotons, microtubules and CNS, is our brain a“Holographic computer”? - they suggest that neurons are are perfect environments for biophotonic communication.

Neurons are large colourless cells with wide arborisations, they have a highly active metabolism generating photons, contain little pigment and have a prominent cytoskeleton consisting of hollow microtubules. As brain and spinal cord are protected from environmental light by bone and connective tissue, signal to noise ratio should be high for photons as signal.

Absorbing and fluorescent substances should interfere with such a biophoton communication system. Of all natural aminoacids, nature has chosen the aromatic ones with the strongest fluorescence, tryptophan, phenylalanine and thyrosine as precursors for the neurotransmitters involved in mood reactions: serotonin, dopamine and norepinephrine.

Also many hallucinogens have strong fluorescence properties, e.g., LSD, psylocibine and harmine. The capability of neuronal cells to generate a membrane potential enables them to release a lot of energy in short time by depolarisation. If depolarisation energy can be used to generate light, e.g., within the microtubules, the process of depolarisation could scan the information within the microtubules and MAP-proteins and transmit it to the next neuron. When depolarisation reaches the synapses the fluorescent neurotransmitters are released, the transmission is terminated and retrograde transmission inhibited.

Interestingly, "hallucinogens have strong fluorescence properties, e.g., LSD, psilocybin, and harmine," which may offer some additional explanation for why LSD effects last 8-12 hours while the chemical cannot be detected in the body 30 minutes after ingestion. Anyway . . . .



The presence of light sensitive molecules in the brain suggests it's likely that they might be influenced by biophotons. Because biophotons likely would be absorbed by liquids, membranes, and other materials in the cell, Rhanama, et al (Journal of Integrative Neuroscience, 2010), hypothesize that microtubules act as wave guides, channeling light from one part of a cell to another.

Via Wikipedia, here is a brief overview of what microtubules are and the functions they perform.

Microtubules are a component of the cytoskeleton [in cells]. These rope-like polymers of tubulin can grow as long as 25 micrometers and are highly dynamic. The outer diameter of microtubule is about 25 nm. Microtubules are important for maintaining cell structure, providing platforms for intracellular transport, forming the spindle during mitosis, as well as other cellular processes. There are many proteins that bind to the microtubule, including motor proteins such as kinesin and dynein, severing proteins like katanin, and other proteins important for regulating microtubule dynamics.

Microtubules are the internal scaffolding of cells - they give structural support, but they also create pathways along which the cell's molecular machines move "freight" around the cell.

Rhanama and crew suggest that biophotons channeled by microtubules assist in coordinating activities in different parts of the brain. We already know that electrical activity in the brain is synchronized over inexplicable distances (at least at this point in time), but the electrical signals are too slow to coordinate brain activity, so it's probable that some other mechanism is active.

The teams of Grassa and Rhanama are not the first to point out that microtubules might play an important role in brain function and consciousness - but their inclusion of biophotonics elevates their model (in my opinion) above some competing models, such as the Orch OR model.

Orch OR - Microtubules, But No Biophotons

Stuart Hameroff and Roger Penrose published their Orchestrated Objective Reduction of Quantum Coherence in Brain Microtubules: The "Orch OR" Model for Consciousness in 1996, arguing that
consciousness is a function of quantum mechanics and that microtubules are the location in the brain where the (self-)collapse of the quantum wave occurs. 

Here is the majority of the abstract for that paper:

The particular characteristics of microtubules suitable for quantum effects include their crystal-like lattice structure, hollow inner core, organization of cell function and capacity for information processing. We envisage that conformational states of microtubule subunits (tubulins) are coupled to internal quantum events, and cooperatively interact (compute) with other tubulins. We further assume that macroscopic coherent superposition of quantum-coupled tubulin conformational states occurs throughout significant brain volumes and provides the global binding essential to consciousness. We equate the emergence of the microtubule quantum coherence with pre-conscious processing which grows (for up to 500 milliseconds) until the mass-energy difference among the separated states of tubulins reaches a threshold related to quantum gravity. According to the arguments for OR put forth in Penrose (1994), superpositioned states each have their own space-time geometries. When the degree of coherent mass-energy difference leads to sufficient separation of space-time geometry, the system must choose and decay (reduce, collapse) to a single universe state. In this way, a transient superposition of slightly differing space-time geometries persists until an abrupt quantum classical reduction occurs. Unlike the random, "subjective reduction"(SR, or R) of standard quantum theory caused by observation or environmental entanglement, the OR we propose in microtubules is a self-collapse and it results in particular patterns of microtubule-tubulin conformational states that regulate neuronal activities including synaptic functions. Possibilities and probabilities for post-reduction tubulin states are influenced by factors including attachments of microtubule-associated proteins (MAPs) acting as "nodes"which tune and "orchestrate"the quantum oscillations. We thus term the self-tuning OR process in microtubules "orchestrated objective reduction"("Orch OR", and calculate an estimate for the number of tubulins (and neurons) whose coherence for relevant time periods (e.g. 500 milliseconds) will elicit Orch OR. In providing a connection among 1) pre-conscious to conscious transition, 2) fundamental space-time notions, 3) non-computability, and 4) binding of various (time scale and spatial) reductions into an instantaneous event ("conscious now", we believe Orch OR in brain microtubules is the most specific and plausible model for consciousness yet proposed.

Hameroff has stayed with this model over the years, despite the lack of acceptance it has received among his fellow consciousness researchers. It would be interesting to see Hameroff work with some of the biophoton researchers, especially those who adhere to a microtubule model, to see if they might generate a more complete model.


One final group of researchers - Yan Sun, Chao Wang, and Jiapei Dai - offers a little more evidence for the neuronal communication mediated by biophotons in a paper entitled Biophotons as neural communication signals demonstrated by in situ biophoton autography (Photochemical & Photobiological Sciences, 2010; 9, 315–322).

Their study was essentially focused on developing new methods of detecting biophotons in neurons, but one of the outcomes was increased evidence that biophotons might serve as neural signals. This is from their discussion of the research results:

In the present study, we found that biophotonic signals generated by light stimulation consist of two components: action and background biophotons. A possible explanation for this observation is that external light stimulation might generate action biophotons, being able to conduct along the neural fibers and result in an increase in biophotonic activity. Background biophotons are generated in situ, mostly by mitochondrial oxidative metabolism due to the lipid peroxidation of mitochondrial membranes initiated by the action of the respiratory electron transport system. In addition, the findings that almost no Ag granules could be observed in the spinal nerves after treating with both 1% procaine, and 50 mM 2-deoxy-D-glucose and 0.05% sodium azide, which can block neural conduction and oxidative metabolism, respectively, reinforce our explanation for the mechanism of IBA, as we discussed above, where the formation of visible Ag granules is due to a biophotonic effect, not because of other factors, such as chemical reactions. 

Although we found that biophotons can be generated by external light stimulation and conducted along neural fibers, implying that biophotons might serve as neural signals, there are a few questions that still need to be answered. For example, how do biophotons conduct along neural fibers? What is the relationship between the biophotonic activity and bioelectronic activity in the nervous system? Although we have no direct experimental evidence to provide answers to these questions, a proposed mechanism called protein–protein biophotonic interactions may provide an explanation of the first point based on previous studies showing that certain proteins, such as fluorescent proteins, have unique characteristics of light absorption and emission.

None of the evidence so far is conclusive, but some combination of biophotonics, microtubules, and quantum wave collapse might be the best possible explanation of the emergence of consciousness from matter.


Theories of consciousness tend to be more macro oriented, such as Global Workspace Theory, which explains how the various neural circuits (or modules) work together to generate a sense of self. However, we still need to explain how consciousness itself emerges from inert matter. One possibility is in the material presented above - but the future may bring newer and better models.