Circadian Biology I: The Beginnings

“If you want to find the secrets of the universe, think in terms of energy, frequency, and vibration.” -Nikola Tesla

When NASA surveys the observable universe in search of life, a criteria has been developed to asses the likelihood that a planet can support the physics of organisms.[R] There must be light, there must be water, and there must be a magnetic field. Without all three factors life cannot exist. The subject of this blog series is the first: how light shapes and controls our biology as humans.

The Beginnings

A Definition of “Light”

Not much is known about the first moments of our universe, but the prevailing theory is of the Big Bang: a moment in which from nothing a primordial soup erupted with abundant and vibrant energy, expanding out into the infinite.[R] Something like 3,000 years after this event matter and radiation separated from each other, and matter (proven by Einstein’s famous equation E=mc2) is a condensed form of light. Since these times matter has communicated via photons.[R]

Light is radiant energy in the form of photons: subatomic particles that carry electromagnetic force. [R]

These photons take the form of a wave, and the frequency of the waves determine the intensity and where the light falls on the spectrum:

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Light is energy and information. The information comes from the rhythm or vibration of the energy, in the same way the vibration of vocal cords relay information in the form of language.

In the visible spectrum, blue is on the higher intensity (shorter wavelength) end and red is on the lower intensity (longer wavelength) end. This has major implications for their biological effects.

A novel way to interpret Albert Einstein’s theory of special relativity (E=mc2) is that energy and matter are exactly the same, the only difference is the environment that each side of the equation is in. This proves that me, you, and everything we can observe is light slowed down to different degrees. We are beings of light, composed of matter and animated by the energy of radiant photons. [R]

Another important fundamental law of light is described by Einstein’s Photoelectric Effect: Light  can only interact with the electrons on a surface. These electrons get “excited” by the photonic energy and become what are known as “excitons.” [R]

Light’s Interaction with Matter on Earth

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The earth is approximately 4.543 billion years old. During all this time of development, sunlight has been the photonic constant and directly manipulated the environment it which the solar system evolved biochemically. In it’s infancy, earth had an especially weak atmosphere that allowed for a larger volume of high intensity (UV range and above) light to penetrate to the surface and interact with the elements. [R]

The interaction of high energy photons (UV light) atmospheric gases, and water created the organic compounds that were necessary for life in the beginning. The UV radiation acted upon the simple molecules in the atmosphere and stimulated chemical bonding and modification. These organic compounds, such as the amino acids that exist in the human eye, make up the fabric that ties our biochemistry back to the solar flux that forged it billions of years ago.

Scientists Miller and Urey performed a famous experiment in 1952 that simulated the effect of solar radiation on earth’s primitive atmosphere: [R]

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Basic gases H2O, CH4, NH3, and H2 combined with an electrical spark simulating UV radiation produce the organic compounds essential for life gathering in the trap seen above. On earth this reaction produced mono-saccharides, fatty acids, amino acids, pyrrols, and nucleotides that were utilized by early life for storage, structure, function, metabolism, and information.

Because these organic compounds are a direct product of the reaction between sunlight and atmospheric gas, they exhibit a structural blueprint that allows them to be receptive to radiant energy. Amino acids like tryptophan, tyrosine, phenyl-alanine, and histidine have a so called “Benzine Ring” as part of their molecular structure that act as a photon trap:

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Molecules that exhibit the benzine structure shown above act as a net for photonic energy in specific frequency ranges. These antenna-like molecules are referred to as “aromatic chromophores.” [R]

Note the structure of these aromatic amino acids, they all include benzine rings:

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Tyrosine, tryptophan, histidine, and other amino acids provide the foundation for the building blocks of complex life. They also have the structural ability to absorb and store UV light. This has major implications for the physics of organisms and their relationship to sunlight, including humans.

Light & Early Life

Adaptation to the day and night cycle was the pre-condition for survival, even for the earliest life forms on earth. Sunlight provides constant but reliable changes in energy flow, this regularity provides the prerequisite for adaptation. Life not only evolved to respond to the stimulus of sunlight, but learned to manipulate its energy and information for biologic processes.

The perfect organism to use as an example of the integration of light in biology is one that is incorporated in all of our human cells today: the mitochondria. The so called “power plants” of the cell, mitochondria are conventionally known to use oxygen to burn food products for energy. However, If you look at these organelles from a biophysics perspective you see that mitochondria are fundamentally using electromagnetism to harness the energy of the sun. These ancient prokaryotes were incorporated into more complex eukaryotic cells in an endosymbiotic process that created a surplus of energy that allowed for increasingly complex evolution: [R]

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What can these ancient prokaryotes do for a eukaryotic organism? Mitochondria allow a cell to utilize photonically-excited electrons “excitons” to create a hydrogen (H+) gradient on the inner mitochondria matrix to build up a magnetic force to spin the ATPase and create ATP. The fundamental laws of physics are at play on the electron transport chain. Oxygen acts as a magnetic dipole that pulls excitons through cytochromes 1-4 to establish the H+ gradient that has the electromagnetic force to spin the ATPase. These steps are well known in biology. The only problem is that principles of biology and physics aren’t often married. People neglect the fact that photosynthesis is the basis of the entire food web and that when organisms consume fuel, what they’re really doing is utilizing the photonic energy of excitons in a stepwise fashion in electron chain transport on the inner mitochondrial membrane:

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This information proves that light is vital to the fundamental processes of energy and function in biology, but do photonics also have a role in the structure and information transfer of organisms?

Photonics at the Cellular Level

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We already discussed how the amino acids and fatty acids that make up the structure of living cells act as antennas for specific frequencies of light using the benzine ring of their molecular structure as a photon trap. But how do cells utilize the photonic capabilities of these organic compounds to grow, function, and communicate?

A German biophysicist named Fritz-Albert Popp was the first to show that cells have very specific and highly regulated emissions of biophotons, which are the smallest physical units of light. It is well known in biology that a single cell has over 100,000 biochemical reactions per second, all of which must be carefully timed and sequenced with each other. For a long time the prevailing view was that these processes were mechanical, and that molecules that fit together like a lock and key would react. It’s clear that the sheer volume of reactions that take place in a cell in a given moment are too precise to be mechanically random, and biophoton emissions moving at the speed of light appear to be a more elegant solution. [R]

Dan Eden wrote in a review of the paper “The Real Bioinformatics Revolution: Proteins and Nucleic Acids Singing to One Another?” writes:

“Veljkovic and Cosic proposed that molecular interactions are electrical in nature, and they take place over distances that are large compared with the size of molecules. Cosic later introduced the idea of dynamic electromagnetic field interactions, that molecules recognize their particular targets and vice versa by electromagnetic resonance.

In other words, the molecules send out specific frequencies of electromagnetic waves which not only enable them to ‘see’ and ‘hear’ each other, as both photon and phonon modes exist for electromagnetic waves, but also to influence each other at a distance and become ineluctably drawn to each other if vibrating out of phase (in a complementary way).

There are about 100,000 chemical reactions happening in every cell each second. The chemical reaction can only happen if the molecule which is reacting is excited by a photon … Once the photon has excited a reaction it returns to the field and is available for more reactions… We are swimming in an ocean of light.”

Dr. Popp proved that light in the cell is stored and emitted from DNA. The DNA strands inside each cell vibrates at a frequency of several billion hertz. The vibration is created through the coil-like contraction and extension of the DNA, which occurs several billion times per second – and overtime it contracts it squeezes out one single biophoton; a light particle. [R]

These biophotons from DNA strands in the nucleus are in the shorter wavelength ranges. This suggest that frequencies towards the UV range have to do with information transfer. The organelles on the peripheral of the cell, such as the mitochondria, are where we find red and infrared light in the longer frequency ranges. Structure and information are found in the center while metabolism and movement are found in the periphery. These correlate with very specific frequencies.


Einstein’s theory of special relativity proves that energy and matter are fundamentally interchangeable, the only variable being the environment in which they exist. In this blog I’ve attempted to lay the foundation for how light and the matter on earth, living and non living, exist in synergy. In examining the biophysics of organisms it becomes clear that life is matter animated by light through an aromatic structure that communicates via biophotons. The beginnings of prehistoric microscopic life (mitochondria) are deeply rooted in biophysics. In future blogs in this series I want to examine how modern humans interact with light on more of a macroscopic level in tissues.



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