Welcome to the Permian Museum

The Permian period ( ~ 250 million years ago) is known as the great dying, however it could equally well be called the great rebirth. The Permian mass extinction was followed by a “quantum speciation” or rebirth of life event, which introduced a new cast of characters that went on to spawn the age of the dinosaurs. The fossils presented on this website appear to be part of this quantum speciation or rebirth of life event. Their scientific significance is that they provide a new narrative on how life transitions from single celled organisms (which first appeared 3.8 billion years ago) to multicellular life, or life as we know it today.

IMPORTANT COPYRIGHT NOTICE: Copyright © 2012 - 2014 Mark J. Zamoyski. All rights reserved. No part of this website may be reproduced, scanned, stored, introduced into a retrieval system, or distributed in any printed or electronic form. The below are excerpts from the book “On the Origin of Life and Biodiversity” © 2014 Mark J. Zamoyski, which is available on Amazon, and an earlier full science manuscript titled “Quantum Speciation and the Origins of Life” © 2012 Mark J. Zamoyski.

This website is always under construction and new material is posted on an ongoing basis. Website Last Updated: January 8, 2018.


Newly discovered fossils from a quarter billion years ago provide a new narrative on the origin of life and biodiversity. They tell the story of how the transition from unicellular to multicellular life occurred.

Site Index

Preamble 1: Soft Tissue Fossilization

Perhaps the greatest advance in understanding how soft tissue preservation / fossilization occurs came in 2005 ( Jozef Kazmierczak and Barbara Kremer, "Early post-mortem calcified Devonian acritrarchs as a source of calcispheric structures", Facies (2005) 51: 554-565.)

The article studied single celled organisms and the authors describe a post-mortem calcium carbonate permineralization that occurs around the organic cell walls. Simplistically, post-mortem bacterial degradation of the calcium rich mucilaginous envelope results in precipitation of fine grains of calcium carbonate, which under pressure of subsequent burial are transformed into crystalline calcium carbonate. The resulting shapes closely match the shape of their organic forerunners.

Our focus is on the paleobiology story told by this rare soft tissue preservation, as contained in a collection of Permian fossils. While it is impossible to obtain DNA from this type of fossil, the underlying DNA can be inferred from the visible physiological features resulting from the expression of the underlying DNA, and as preserved by this calcium carbonate permineralization.

The life forms presented in this book are much larger than those described by Kazmierczak and Kremer. Author’s observations: 1) The full crystallization of these larger life forms is extremely rare and external features are rarely preserved well, while internal features are more commonly preserved. 2) Sometimes external features are preserved in the density of the surrounding matrix, and as such progressively harsher removal methods can destroy these features. 3) When external preservation does occur, it is almost always much better on one side and not the other (possibly due to which side was on the bottom and which was on the top during the postmortem fossilization process). 4) The internal preservation visible by sectioning a specimen (i.e. cutting it in half) is so good that it reveals anatomical features such as neurons, undigested stomach contents, and even gestating progeny. The internal preservation can also reveal the general external morphological shape of the life form much better than removing the external matrix. 5) The key to seeing many of the internal structures in photos depends heavily on the light source used. Light sources that penetrate the crystal, with minimal surface reflectivity, provide the best photos.

Preamble 2: Paleo Geology of the Site

Arizona was a shallow ocean during the Permian period, and shallow oceans were the birthplace of life. Tectonic activity eventually lifted the state, and erosion left the ancient ocean floor at the surface in many parts of Arizona. The USGS surface soil map, combined with a current Arizona road map, is shown below. Permian fossils can be found at the surface in large parts of Northern Arizona (in blue).

USGS Surface Soil Map of Arizona

Several extinction pulses rocked the Permian period, and each was followed by a sharp recovery pulse, similar in respects to a mini Cambrian explosion of life. The below graphic depicts these pulses, based on data published by Sahney and Benton (Sahney, S and Benton M. J., “Recovery from the most profound mass extinction of all time”, Proceedings of the Royal Society B, 275, 759 - 765 , 2008)

Permian Extinction / Recovery Pulses

Millions of Years Ago (Ma)

The Permian period is often referred to as "The Great Dying" but could equally well be called "The Great Rebirth".

The 35 whole body fossils covered in "On the Origin of Life and Biodiversity" provide a new narrative on how life transitions from unicellular to multicellular life. Illustrations of these life forms, based on the photos presented in the book, are shown below to give an idea of the biodiversity that results from such a transition event.

The reasonable inference is that these life forms were part of a recovery pulse. Their preservation leaves a record of not only how the process of quantum speciation by genetic reassortment works, but also provides a sample of the new life forms this process is capable of generating. Unlike the modest improvements over an antecedent lineage achieved by evolution, the genetic reassortment process is capable of generating completely new life forms, without any antecedent lineage. These new life forms would effectively be the starting point for evolution.

A Brief History of Life on Earth

The universe is estimated to have originated from the big bang some 13.7 billion years ago (Ba) and the earth formed 4.6 Ba. Three explosions of life occurred in earth’s history.

The Prokaryotic Explosion of Life

Unicellular Prokaryotic Cells (aka bacteria): Prokaryotes first appeared 3.5 - 3.8 Ba. Chemical traces of prokaryotic cells date back to 3.8 Ba, or 0.1 Ba after the end of the asteroid impacts on earth. Fossil evidence dates back to 3.5 Ba.

They have a tough triple layer cell wall, and can thrive near volcanic vents 3,500 feet below the ocean surface and live two miles deep in soil at pressures of 5,000 PSI. They have circular DNA. They may have a flagella or whip like tail for propulsion, and can aggregate in colonies that function as a unit.

The prokaryotic explosion of life was so successful that today bacterial biomass on earth exceeds that of all plants and animals combined. One gram of soil contains 100 million to 1 billion bacterial cells. Coastal oceans contain 1,000,000 cells per ml.

The Unicellular Eukaryotic Explosion of Life

Unicellular Eukaryotic: Eukaryotes first appeared 1.5 Ba. Evidence indicates they hail, in whole or in part, from prokaryotic cells.

They have a soft single layer cell wall, which is basically one of the three layers of a bacterial cell wall. They have linear DNA that is contained in a membrane bound compartment called the nucleus.

Mitochondria is a cell’s power plant that stores energy from aerobic respiration (metabolism of glucose). Eukaryotic mitochondria is of prokaryotic origin: its DNA is separate from that of the nucleus, is circular (bacterial), and its nucleotide sequence analysis points back to early bacterial origins (rickettsia, rhizobacteria, and agrobacteria per Alberts et. al., Molecular biology of the Cell, Third Edition 1994).

When your favorite detective show talks about matching a suspect¹s mitochondrial DNA to mitochondrial DNA found at the crime scene, what they are really saying is “Which combination of bacteria does our suspect hail from, and does that combination match the one found at the crime scene?”.

The Multicellular Eukaryotic Explosion of Life

Multicellular Eukaryotic (or life as we know it): Multicellular life first appeared 0.5 Ba in the “Cambrian Explosion of Life”. Another explosion of multicellular life occurred 0.25 Ba after the Permian mass extinction event, and introduced a new cast of characters which spawned the reign of the dinosaurs.

A multicellular life form is a collection of eukaryotic cell types that live and function as a unit. In a multicellular life forms, each cell contains the complete DNA to code for all of the cell types, but expresses only its subset of that DNA that makes it a specialized cell type. This simple fact indicates a completely new multicellular life form can only arise at a unicellular level. Multicellular life as we know it starts from a single cell with the complete DNA code, and that cell then goes on to grow and divide into the trillions of cells and hundreds of specialized cell types coded for by the DNA contained in that first single cell.

A mature multicellular organism would require the replacement of its existing genome, with a completely new genome, simultaneously and precisely, in every cell and cell type, in order for it to become a new life form. That is a mechanistic and mathematical impossibility. Evolution can guide the direction of mature multicellular organism by selective advantage, however it can not create a completely new life form that has no antecedent lineage.

So how does a new life form get created at a unicellular level?

That is the question that these Permian fossils finally answer.

The Fossil Record of the Permian DNA Gene Pool

A whole body fossil, that includes internal soft tissue preservation, can be autopsied (sectioned) to provide a snapshot of the internal molecular biology of the time. Although the underlying DNA is not visible, the underlying DNA can be inferred from the observable features resulting from the expression of that underlying DNA.

Sectioning reveals the life forms range from unicellular giants to life forms made up of only a few specialized cell types (humans are made up of more than 200 specialized cell types).

Features seen in unicellular life forms can be seen in these primitive multicellular life forms, implying the multicellular DNA hails from unicellular origins.


Unicellular organisms can use flagella, cilia, or pseudopods for motility. Flagella and cilia are structurally identical in eukaryotic cells.

This ancient DNA, present since around 3.8 billion years ago, made it’s way to present day humans. In humans, the sperm cell uses a flagellum to propel itself. Cilia drive the movement of the mucus blanket that sweeps dirt out of the lungs. Beating of cilia in the fallopian tubes moves the egg from the ovary to the uterus.

Prokaryotic cells can only use a rear mount flagellum for propulsion because of their rigid, triple layer cell wall.

Eukaryotic cells have a flexible lipid bilayer cell wall, allowing them to use either a rear mount flagellum or side mount flagellum. An example of a side mount flagellum is in the unicellular trypanosoma, which causes sleeping sickness, and is only about 25 µm long.

One example of an early transitional life form is a unicellular giant shown below, which has a rear mount flagellum. At 2 inches long, it is 2,000 times larger than the unicellular trypanosoma. The observable flagellum appears to be the same as that coded for by DNA of pre-exiting unicellular life forms, either prokaryotic or eukaryotic.

A slightly more advanced, multicellular life form, Flagella Fish shown below, has a side mount flagellum. At 5 inches long, it is 5,000 times larger than the unicellular trypanosoma. The observable flagellum appears to be typical of the unicellular eukaryotic DNA that codes for a side mount flagellum on a flexible bodied life form.

Another example of an early propulsion system is a contractile sack that can pump fluid. “Blue Jelly” below is an example of this. Jellyfish are not truly fish, but are one of the simplest multicellular life forms. They are a pulsating gelatinous bell with long trailing tentacles.

The actual specimen is 3 inches long and a photo of the actual sectioned specimen in matrix is shown below. The mushroom like central structure appears to be a contractile sack that is in the contracted phase of propulsion.

An isolated, annotated photo of the central “contractile sack” propulsion system is provided below.

Pseudopod DNA (e.g. paws, claws) also appear in these transitional specimens. The Flagella fish above has arm like paws at the front, in addition to its flagellate tail. Another example is a pseudopod, or foot like appendage that appears on Claw-Paw Dragon, shown below:

Later in this section we will also see four legged DNA in a specimen called the “Arizona Lung Fish”. Lung fish can use these legs to walk on land. Lung fish have been around since about 400 Ma., so this DNA was around long before the Permian period.

Skin DNA

Unicellular organisms have cell signaling capability in colony situations that causes the outermost cells to differentiate and form a hardened protective outer layer. Skin may hail in part from this DNA.

Skin is an extremely important feature for multicellular life, primarily because of it’s ability to contain an aqueous environment where concentration gradients can be maintained (aka physiological life).

A 70 kg human (~ 70 liters volume) is made up of ~ 10 liters of cells (~ 10 trillion cells) bathed in 40 liters of extracellular fluid, with the balance made up of bone, fat, muscle fibers and connective tissue. Everything is contained within a skin sack. The resident extracellular saline solution is our gulp of the ocean we needed to take before we could step onto land.

An aqueous environment allows atoms to exist as ions (Na+, Cl-, K+, Ca++) which in turn allows for maintenance of concentration gradients including electrochemical gradients. On dry land, atoms such as Na and Cl combine to form electrically neutral NaCl, or table salt.

At its simplest level, physiological life can be defined as a collection of concentration gradients. The presence of concentration gradients means life. The absence of concentration gradients means death.

Skin also revolutionized cell signaling. Cell signaling is the production of chemicals (e.g. testosterone, estrogen) by a cell that alters DNA expression of distant cells. In a closed environment, the chemical signals are not washed away by the ocean, but can more effectively reach their intended target cells.

In humans, the epidermis is a columnar stack of cells, with roughly one cell a day shedding off the top of the column, and a specialized pluripotent cell at the base dividing daily to maintain the stack depth. Below the epidermis is the dermis, which is mostly connective tissue, produced by a cell type known as a fibroblast.

A harder skin allows for survival in harsher or more abrasive environments, such as mud or land. It allows a life form to encapsulate its gulp of the ocean and take itself onto dry land. An example of a hardened protective reptile like skin and barbs can be seen in the Zamoyski Dragon, which is 7 inches (18 cm) long.

Sectioning reveals the life form was closer to a unicellular protist, as it has no bones or circulatory system yet. The stomach contents reveal a fairly intact undigested fish, implying Zamoyski Dragon used a typical protist approach of swallow whole and digest. The undigested fish has been named “Goby Shark” because it has has features of both a goby fish and a shark.

Specialized cell types would have been responsible for the hardened segmented skin around the head of the Zamoyski Dragon as well as for the backward facing barbs at the top rear, inside of the tail, making this a multicellular life form. The backward facing barbs at the rear would likely lodge in a pursuer¹s throat, preventing swallowing and facilitating forward escape. They would be effective until a kill and chew world arose.

A more advanced version of skin can be found in insects, where the skin also functions as an exoskeleton. One such example is Mud Worm (~ 6" or 15 cm long) shown below. If the position was accurately preserved in death, it may have lived in mud, with only its mouth protruding. The mouth is missing, indicating it was likely made of softer tissue.

A zoom of the tail better reveals the segmented exoskeleton, including preservation of the likely chitin exoskeleton (i.e. cockroach like color).

Phototaxis / Optic Neuron DNA

An optic neuron is a specialized cell type. The appearance of an optic neuron in a life form makes the life form a multicellular organism by definition.

A typical sensory neuron has a sensing part at the front ( e.g. eye, olfactory bulb), followed by a long axon which electrically conducts the signal from the sensory part to a network of branched synapses. When the electrical signal reaches the synapses, voltage gated channels in the cell wall transiently open allowing an inrush of calcium ions, which in turn cause the release of neurotransmitter by the synapses.

The action of the released neurotransmitter depends on what the synapses are connected to (e.g. other neurons, muscle tissue, secretory cells, etc...) and what the released neurotransmitter is. As an example, if the neurotransmitter released is acetylcholine and the synapses integrate into muscle tissue, a muscle contraction could be expected.

The example above is relevant as the first multicellular life forms appear to have no brain, just a sensory neuron connected to muscle ( e.g. a tail or flipper).

An optic neuron without a brain would likely result in mindless, relentless movement toward light, similar to how a moth repeatedly hits a porch light.

In the ocean, moving toward light means moving toward food, as that is where photosynthesis based organisms (algae) thrive, as well as the related food chain that thrives on them. It apparently does not take a brain to go where the food is, just an optic neuron. Even single celled organism (without an optic neuron) have the ability to orient themselves toward light, so this is a primordial trait.

Such an optic neuron is visible in a sectioned specimen called Whaleen. Whaleen resembles a truncated Baleen Whale, and an artist rendering is provided below:

A photo of the external view (Side A) of Whaleen is shown below. The specimen is ~ 5 inches or 12 cm long.

A photo of the sectioned specimen ( Side B) reveals the vestiges of the optic neuron in the upper left of the sectioned specimen. A cutout of the optic neuron is included above the actual neuron for clarity.

The primary importance of the specimen is that it establishes optic neuron DNA existed ~ 250 million year ago. It also means optic neuron DNA was thus available for the DNA grab bag reassortment process hosted by Calcium Secreting Filter Feeders (CSFF) at the time, which is discussed later in this narrative.

A second interesting feature of Whaleen is there appear to be gestating progeny inside the central food lumen (i.e. the encapsulated bluish life forms amidst the white powderish contents of the food lumen in the center of Whaleen). This may indicate the first "womb" may have simply been a sack that allowed digested nutrients from the food lumen to pass across to the gestating progeny, said sack also preventing the progeny from being digested.

Chemotaxis / Olfactory Neuron DNA

Chemotaxis is the initiation of motility (activation of flagella, cilia, or pseudopods) in response to chemicals in the environment. This is used by both prokaryotic and eukaryotic cells to find and move toward food and to flee from poisons (negative chemotaxis). As an example, amoeba feed on other protists, algae, and bacteria and exhibit chemotactic responses to glucose and cAMP.

In humans, cells such as neutrophils, the body’s first line of defense against bacteria, recognize chemicals produced by bacteria and move directly toward them. Additionally, tissue resident mast cells are activated by antigens and in response release chemotactic factors such as Eosinophil Chemotactic Factor A, Chemotactic Factor (NCF IL8) and Leukotriene B4, which in turn result in chemotaxis of a broader set of immune system cells toward the site.

On a macro level, the analog of chemotaxis (smell) is performed by an olfactory neuron, which converts smell into an electrical impulse that provides a signal the brain. In the absence of a brain, as is observed in these transitional life forms, the neuron appears to be connected directly to a muscle group, which in the case of Dino-Seal below is the flipper.

An olfactory neuron without a brain would likely result in mindless, relentless movement toward smell, similar to how the single optic neuron in Whaleen would result in mindless, relentless movement toward light.

Dino-Seal appears to have such an olfactory (chemotaxis) neuron, in addition to a phototactic neuron, as well an unidentified neuron. If is not clear how these 3 neurons interact. An artist rendering of Dino-Seal is provided below:

The actual specimen is ~ 4 inches or 10 cm long, and the vertical undulation orientation of the tail is characteristic of all marine mammals (e.g. sea lions, seals, dolphins, whales), suggesting Dino-Seal is a mammal forerunner.

The exterior photo above of the actual specimen is with partial removal of the encasing matrix. It is an example of what was previously discussed about external features sometimes being preserved in the density of the encasing calcium matrix, without crystallization, which was not known at the time. In this specific case, progressively harder removal methods to get to the fossilized crystal removed these features. This is why author documents features at each step of matrix removal, and no longer pursues further matrix removal if features are preserved in the density of the matrix. The best information is almost always in the sectioned specimen, as shown below.

The sectioned specimen not only provides a much more accurate view of the morphological shape of Dino-Seal, but also reveals a chemotactic neuron that runs from the nose to the flipper. A cutout of the chemotactic neuron itself is shown below the actual neuron for clarity. A further zoom of the head reveals there are actually more than one neuron present, as shown in the photo below:

A zoom of the head shows the sensing part of the chemotactic neuron in the nose area. It appears the eye part of the optic neuron is at the top of the head, behind what appears to be an unidentified neuron. The unidentified neuron’s axon appears to run to the dorsal fin. The front, or sensing part of the unidentified neuron appears to sit on top of a spherical structure, which may be providing sensory information to this neuron. This unidentified neuron cannot be interpreted with certainty, but it is possible that the sensory part may be picking up vibrations from the structure on which it sits. That would make it an early auditory neuron, however this is purely speculative and cannot be presented as a fact.

How the life form would react in situations where there was a conflict among the three neuronal signals is anybody’s guess. However, the presence of a nose and nasal passages, with the olfactory bulb positioned at a gap in the nasal passages, strongly suggest Dino-Seal was an air breather. Accordingly, the olfactory neuron would likely only be active when the animal was above the surface of the water and breathing, which would preclude any potential for underwater conflicts with the other two neurons.

In context of a mammal, the optic neuron would likely function to drive the air breather to the surface, as moving toward light would mean moving toward air.

If the unidentified neuron is an auditory sensor, it would more likely have been specific to vibrations in the ocean, as there is no orifice for air to enter (i.e. no ear canal). In an underwater context, move toward vibrations would mean move toward food.

Accordingly, the only conflict underwater would be 1) move toward food, or 2) move toward air. It is not clear how this would be resolved without a brain. It may have simply been on which of the two signals was stronger. Numerous possibilities exist for how this could work, but all would be highly speculative and not definitive.

An observation of note is that the mammal forerunner appears to have a higher nerve to tissue ratio than other life forms.

The primary importance of the specimen is that it establishes olfactory neuron DNA existed at least 250 million year ago, which means optic neuron DNA was thus available for the DNA grab bag reassortment process hosted by Calcium Secreting Filter Feeders (CSFF) at the time, which is discussed later in this narrative.

Lung DNA


Womb / Birth Lumen DNA



Bone is the most significant development after skin. Bone is a repository for Calcium, Phosphorous, and Mitogens (growth factors). These compounds are routinely moved from extracellular fluid into bone and back from bone into extracellular fluid.

Calcium (Ca++) movement alters nerve function, muscle function, consciousness, and memory. Movement of all three (mitogens, Ca++, phosphorous) enhances activation of the population density management / cell cycle control system. Phosphorous is used in storage of energy (ADP to ATP) and phosphorylation (addition of a phosphorus atom) alters the functions of many proteins.

Movement of these compounds into bone is controlled by a specialized cell called an osteoblast. Osteoblasts also control the population density and activity levels of osteoclasts, a specialized cell type that dissolves bone releasing these compounds back into the extracellular fluid.

Osteoblasts in turn are controlled by numerous endocrines. The result is that many endocrines mediate their effects, in whole or in part, by movement of these compounds into or out of the “bone pantry”.

Vitamin D, parathyroid hormone, prostaglandins, and Vitamin A enhance movement from bone into the extracellular fluid. Estrogen, Testosterone, growth hormones (GH, IGF, BMP), and calcitonin enhance movement of these compounds into bone.

As an example, sunlight (UVB) on skin results in synthesis of the active form of Vitamin D, which then binds to vitamin D receptors (VDR) in the osteoblasts increasing their production of RANKL (receptor activator of NF-kB ligand) that induces macrophage differentiation into osteoclasts (the bone dissolvers), which in turn results in the release of Ca++, phosphorous, and mitogens from bone into the extracellular fluid. The increased Ca++ in the extracellular fluid enhances nerve function by depolarization of nerve membranes (per the Nernst equation), which lowers the threshold required for their firing and enhances neurotransmitter release via the voltage gated Ca++ channels because of both the higher extracellular concentrations of Ca++ and the higher Ca++ concentration gradient differential on the outside of the neuron versus the inside of the neuron. The increased Ca++ enhances muscle function by both the enhanced release of neurotransmitter at the neuromuscular junction and by enhanced inrush of Ca++ through the sarcoplasmic reticulum calcium release channels, enhancing Ca++ release into the fluid around the myofibrils, enhancing muscle contractility by removal of the tropomyosin block between actin and myosin, triggering cross-bridge formation and enabling myosin to bind to actin. Increased extracellular Ca++ enhances brain function by brain neuron depolarization, enhanced neurotransmitter release, and depolarization of NMDA / glutamate channels to release the Mg++ block, allowing a glutamate mediated influx of Ca++ into the nerve cells and astrocyte mediated amplification of the neuronal transmission that creates the Ca++ wave that underlies consciousness (Periera et. al., 2009) and memory formation (Gibbs et. al. 2009). The release of mitogens and phosphorous into the extracellular fluid enhances activation of the population density management / cell cycle control system, with the mitogens binding directly to transmembrane growth factor receptors to initiate the intracellular cascades that transmit the grow and divide signal to alter DNA expression to produce the proteins required for cell division and the phosphorus enhances the many phosphorylations required to transmit the grow and divide signal to the nucleus.

The point being, the introduction of bone into the contained aqueous environment, is an extremely significant advancement in life.

The DNA for bone building cells may have come from a class of unicellular eukaryotes that are collectively known as Calcium Secreting Filter Feeders (CSFFs). Archaeocyathans are the first known CSFF, appeared some 500 million year ago, and were the first unicellular eukaryotes that lived in colonies and secreted calcium carbonate as skeletal material. CSFF structures use moving ocean water to create accelerated, turbulent streams inside a hard skeleton labyrinth. The purpose apparently was to shear membranes of suspended cells to obtain intracellular nutrients. An unintended consequence appears to be their ability to host the genetic reassortment process capable of creating unimaginably biodiverse new life forms. Several Permian CSFF structures are evaluated later in this narrative, for their ability to host Hyper-Evolution by this grab bag DNA reassortment process.

Integration of calcium secreting filter feeder DNA may have happened in Bird-Squito, which appears to have a hard skeleton beak or proboscis. The DNA of early CSFF cells may have eventually gone on to become the osteoblast cell. A head shot of Bird-Squito is shown below:

A close up of the beak from both sides is shown below and reveals one side has serrations in the beak (Side B, lower photo) or possibly a filter feeding beak. Bird-Squito appears to have a single cycloptic eye.

The specimen was cut off-center so one half (Part A) is shorter (and the tail part had to be glued back on). The full half (Side B) shows a fish like tail at the end (with the lowermost part chipped off) and a body resembling something between that of a bird and a mosquito.

The artist’s rendering of what Bird-Squito may have looked like is shown below:

The Fossil Record of the DNA Reassortment Machines

In this section, we will evaluate hard skeleton structures built by a class of single celled organisms collectively called Calcium Secreting Filter Feeders (CSFFs). In particular we will be looking for the ability of these structures to host a DNA reassortment process capable of generating new life forms. A brief synopsis of the relevant related molecular biology and fluid dynamics is presented first, to lay the groundwork for an understanding of the rest of this section.

Relevant Molecular Biology

Cell Walls

Prokaryotic cells have a rigid, triple layer cell wall structure. Eukaryotic cells have a flexible, single lipid bilayer membrane that is a subset of a prokaryotic cell wall, shown diagrammatically below:

Lipid bilayers are made up of molecules that have a water loving head (hydrophilic) and lipid loving tail (lipophilic). When placed in water, they self assemble to form compartments. Likewise, if a lipid bilayer of the prokaryotic wall shown above was scraped off in water, it would self assemble into a lipid bilayer compartment.

Prokaryotes lack internal membrane bound compartments. Eukaryotes use internal membrane bound compartments (nucleus, mitochondria, Golgi apparatus). The membranes are also made of these lipid bilayers.

DNA and DNA Expression

DNA is the blueprint for proteins. DNA expression means synthesis of proteins from that blueprint. Synthesis of proteins in eukaryotic cells is achieved by a process that involves 1) Transcription of DNA into mRNA in the nucleus, 2) Transport of the mRNA strand to the ribosome (made up mostly of rRNA ), and 3) complimentary base pair binding of tRNA with an attached amino acid, whereby the mRNA strand is translated into a protein. Proteins make up 60% of a cells dry mass and determine what a cell does.

DNA expression is regulated by numerous pathways, including endocrines produced by distant cells (cell signaling).

DNA Efficiency

A simple measure of genomic efficiency can be made by comparing how many proteins are synthesized per million base pairs of DNA.

The cells with the best genomic efficiency could be argued to be the most advanced.

Prokaryotic cells have a single circular DNA chromosome. Some have two.

Eukaryotic cells have linear DNA. Humans have 46 such chromosomes. The human linear fragments look like a debris field when compared to a simple circular DNA chromosome.

So how does today’s linear eukaryotic DNA compare to the 3.8 billion year old circular prokaryotic DNA?

The genomic efficiency of ancient prokaryotic cells (from “On the Origin of Life and Biodiversity”, © 2014 Mark J. Zamoyski, Appendix A) versus a human eukaryotic cell (DOE, Human Genome Project, Oct. 2004 findings) is summarized below.

Well isn’t that interesting. The supposedly superior human eukaryotic cell cranks out only 7 proteins per million DNA base pairs versus bacteria that crank out around 900 proteins per million base pairs. The 3.8 billion year old cyanobacteria’s circular DNA is some 130 times more efficient than the linear human DNA. Archaea, the oldest known prokaryotic cell, is 156 times more efficient.

The human genome project also revealed that 98% of human DNA is non-coding (i.e. not used). We are basically a genetic wasteland, with a few good sequences. The eukaryotic DNA not only looks like a debris field, it is one.

DNA Reassortment

If one desired to create new eukaryotic cells with enormous potential biodiversity, it would require only three conditions.

1) Cells aggregated in close proximity to each other in water:

2) Shear forces or structures capable of rupturing cell membranes:

3) A confined space where the spontaneously reassembling lipid bilayers could effectively encapsulate a batch of the ambient genetic slurry.

The “grab bag” or random DNA reassortment process could be expected to generate cells with much lower genomic efficiency than the cells one started out with, as well as having much unused DNA.

Although both prokaryotic and eukaryotic cells could be used as input into the process, only eukaryotic cells would emerge as output of the process, because of the ability of their cell membranes to self assemble.

The resulting eukaryotic cells could also be expected to have membrane bound compartments inside the main cell wall membrane compartment.

Relevant Fluid Dynamics

Coastal oceans have around 1,000,000 suspended cells per ml of water. To obtain the intracellular nutrients, such as proteins and nucleotides, the cell wall would need to be sheared open. This is the presumed motive for channeling water through the hard skeleton labyrinth structures built by the CSFFs.

But are these structures also capable of creating cells with reassorted DNA?

Understanding a couple of fluid dynamics concepts is necessary to complete the picture.

Water Velocity Amplification: For a given flow (e.g. in cubic mm / sec) coming in from a source (pipe, ocean etc...), water velocity increases exponentially as the water passes through a confined space. The reason is that flow (Q) equals the velocity (V) times the cross sectional area (A) or Q= VA. The area (A) of a circle is A= 3.14 X R2 where R is the radius. For a given Q, a reduction in radius results in an exponential reduction in area (i.e. R2), which in turn requires an exponential increase in velocity to maintain equality.

A simple example of this is a fire hose nozzle attached to a fire hose. The velocity acceleration in the nozzle results in a high velocity stream that is used to fight fires from a distance.

Turbulence: Turbulence occurs when a high velocity stream of water enters low or no velocity water. Vortexes form at the border region of the two bodies of water. The vortexes spin water backwards and perpendicular relative to the direction of the high velocity stream. This can be thought of as “nature’s mixer”.

A simple example of this is shooting a sharp stream of water into a bucket filled with standing water. Large amounts of turbulence are generated between the fast and no velocity water.

An example of both velocity acceleration and turbulence is an occluded blood vessel, as shown below. As blood, with its suspended cells, is squeezed through the occlusion, it undergoes velocity acceleration (from the equation above). As it enters the lower velocity blood past the occlusion, turbulence results. Even though blood vessels are soft and blood velocity is low, damage to cells from this process results in a higher risk of stroke.

By boosting velocity and replacing the soft blood vessel with a hard skeleton labyrinth, we can begin to understand what happens in a CSFF. With the requisite fluid dynamics and molecular biology background we can now review the 4 selected CSFF structures to determine if they are capable of hosting the proposed grab bag DNA reassortment process.

Meet the CSFFs (Calcium Secreting Filter Feeders)

The hard skeleton structures built by these single celled organisms come in various shapes and sizes. Sometimes part of the matrix is broken open revealing the preserved hard skeleton labyrinth inside:

A zoom better shows the hard skeleton structure embedded in the matrix:

However, most of the time the structure is not visible, and appears as an odd shaped rock below:

It is almost impossible to remove the structure from the matrix, and a more practical approach is to cut the specimen in half (section) to reveal the hard skeleton structure preserved inside:

The lighter parts are the encasing calcium matrix. The darker parts are the hard skeleton structure.

An artist’s illustration of what the specimen above, called the Permian Porotopharetra, likely looked like, is shown below:

This specimen is morphologically identical to the Cambrian Protopharetra, an irregular archaeocyathan, (Boardman et. al., Fossil Invertebrates, 1987, p. 114 Fig. A and B), with the notable exception that the Permian specimen is about 5 times larger than its Cambrian counterpart. Archaeocyathans were the first unicellular eukaryotes that lived in colonies and secreted calcium carbonate as skeletal material. They were filter feeders, channeling moving ocean water through the hard skeleton labyrinth.

The Cambrian Protopharetra first appeared at the onset of the Cambrian explosion of multicellular life and then disappeared as the new multicellular ecosystem emerged. We have named the above specimen the Permian Protopharetra, which once again appears at the onset of the Permian multicellular explosion of life, and will once again disappear as the new multicellular ecosystem emerges.

Another example of a CSFF is the Spherical CSFF. The artist rendering is shown below:

The sectioned specimen photo is shown below:

Examine the DNA Reassortment Structures

The sectioned specimens reveal internal structures that can be reviewed in context of fluid dynamics and molecular biology to see if they have the potential for host a DNA reassortment process that would account for both the transition from unicellular to multicellular life and also be capable of creating enormous biodiversity in the resulting life forms.

DNA Reassortment Structure 1: Nozzle and Slurry Chamber Structure

Starting with the spherical CSFF above, we can zoom in on one of the structures visible in the sectioned specimen on the left hand side. It is identified in the blue square:

The structure in the blue square above is further enlarged in two side by side pictures below:

The dark parts in the photo on the left outline the hard skeleton structure and the lumen is filled with the lighter colored calcium matrix . The photo (right) has the lumen / water channel in blue for clarity and depicts where the ocean water would have been when the CSFF was alive.

A tracing of the structure is shown below. Two noteworthy attributes are: 1) a nozzle structure that amplifies water velocity and 2) a post nozzle structure (slurry chamber) that enhances turbulence.

Water Velocity Amplification (~16X ): The opening on the ocean side of the nozzle orifice is more than 4 times larger than the nozzle tip that feeds the slurry chamber. For a given flow (e.g. in cubic mm / sec) coming in from the ocean, water velocity increases exponentially as the water passes through a confined space. The reason is that flow (Q) equals the velocity (V) times the cross sectional area (A) or Q= VA. The area (A) of a circle is A= ΠR2 where R is the radius and Π= 3.14. For a given Q, a reduction in radius results in an exponential reduction in area (i.e. R2), which in turn requires an exponential increase in velocity to maintain equality.

For a circular pipe: Q = ΠR2V or V = Q / ΠR2

For a given Q, velocity at the opening is V1 = Q / ΠR12 and velocity at the nozzle tip is V2 = Q / ΠR22

Accordingly, for a given Q, the velocity will increase exponentially with a reduction in radius. If the radius is reduced 4 fold, the velocity will increase 16 fold (i.e. 42).

The 16 fold velocity amplification shooting out of the nozzle tip into the perpendicular wall is analogous to accelerating a car from 10 mph to 160 mph by the time it hits the brick wall.

Turbulence. As previously discussed, turbulence occurs when a high velocity stream of water enters low or no velocity water. Vortexes form at the border region of the two bodies of water. The vortexes spin water backwards and perpendicular relative to the direction of the high velocity stream. This effectively functions as “nature’s mixer”.

Turbulence or Vortexes (shown in red) could be expected to form in several places as this high velocity stream enters and travels through the no or low velocity water in the slurry chamber. Some of these anticipated turbulence zones are shown below in red:

Combining fluid dynamics with molecular biology we can now review the structure¹s mechanism of action to see if it has the means to achieve the proposed genetic reassortment.

An inbound wave with its 1,000,000 suspended cells per ml is accelerated 16 fold and smashed into a perpendicular hard skeleton wall (back of the slurry chamber).

The ruptured cells in the slurry chamber are subjected to turbulence as the high velocity stream enters and travels through the low (or no) velocity water in the slurry chamber.

As the lighter lipid membranes spontaneously assemble, they take a gulp of the genetic slurry and can escape through the top vent. Heavier proteins and DNA fragments settle downwards, presumably toward the feeding colony.

The structure fulfills the requirements for hosting a grab bag DNA reassortment process.

While the intended purpose of the structure was apparently to shear open cell membranes to release the intracellular nutrients for the feeding colony, the unintended consequence appears to be a process capable of creating enormously biodiverse life forms from single celled organisms suspended in water.

This attribute is not unique to the spherical CSFF. The Permian Protoharetra specimens have numerous structures capable of hosting this type of DNA reassortment process. They contain at least 4 identified structures that can do this, with cyclonic based structures used extensively in their hard skeleton designs.

DNA Reassortment Structure 2: Cyclone Structure


DNA Reassortment Structure 3: Nozzle / Cyclone Structure


DNA Reassortment Structure 4: Nozzle / Cyclone / Nozzle / Slurry Chamber Structure


DNA Reassortment Structure 5: Dual Port Perpendicular Injection/ Cyclone Supercharging Structure


Life Science Implications of the Specimens

Copyright © 2012 Mark J. Zamoyski. All rights reserved.

Physiological Life

At its most basic level, physiological life can be described as a collection of concentration gradients. The presence of concentration gradients means life. The absence of concentration gradients means death.

A feature common to all motile multi cellular specimens is that they have a “Skin” that surrounds the collection of eukaryotic cells and allows the cells to be bathed in extracellular fluid. A skin may have originated from the cell signaling DNA used for colony specialization that coded for creation of a protective outer layer around the colony.

In context of multi cellular eukaryotic life, skin is the most significant development for several reasons:

Evolution onto Land: The ability to encapsulate and control a microenvironment set the stage for migration from the oceans onto land. A 70 kg human has ~ 40 liters of extracellular fluid bathing the cells. Humans effectively needed to take their gulp of the ocean with them before they could step onto land.

Protection of Eukaryotic Cells: Eukaryotic cell walls are more fragile than prokaryotic cell walls and the encasing fluid distributes various external traumas over large areas, preventing rupture of the eukaryotic cells walls.

Cell Signaling:
A skin encased aqueous microenvironment took cell signaling to a whole new level. Autocrine, paracrine, and endocrine molecules are not washed away by the ocean but are now contained in a microenvironment where they can much more effectively reach their intended target cells.

Ion and Concentration Gradient Maintenance: In this new microenvironment, concentration gradients could be controlled to support multi cellular life. Physiological life as we know it is basically a collection of concentration gradients. Presence of concentration gradients means life. Absence of concentration gradients means death.

The aqueous microenvironment allows atoms to be maintained as free ions. As an example, sodium (Na) loses the single electron in its outermost valence shell and acquires a positive charge, becoming a positive ion designated as Na+. Calcium loses two electrons becoming Ca++ . Chlorine (Cl) has 7 electrons in the valence shell and gains an electron becoming a negative ion designated as Cl-. Without water, sodium and chlorine combine into the neutral molecule NaCl (table salt).

Ions are electrically conductive. Concentration gradients of ions are called electrochemical gradients. Traveling perturbations in electrochemical gradients carry signals along the axon (long body) of a nerve cell to the synapse, where they are then converted into a chemical signal.

Nerve Function:
Electrochemical gradients allow for function of a cell called a neuron. The most rudimentary function of nerves is perception of the environment and initiation of a coordinated response to the environmental stimuli. In more advanced organisms, neurons play a part in consciousness and memory formation.

A neuron is a single cell. The specialized task of a neuron is to receive, conduct, and transmit signals. Sensory neurons, motor neurons, and interneurons all have the same overall structure: a spherical central cell body (soma) that contains the typical organelles found in all cells, branching dendrites on one side to receive signals, and a long axon on the other side for transmitting signals. The axon commonly divides into many branches at its far end so it may pass the message to many target cells simultaneously.

Neurons contain ion channels that maintain an electrochemical concentration gradient balance between ions (primarily potassium, sodium, and chloride) so that the resting membrane potential inside of the neuron is around -85 mV relative the outside of the cell (ranges from -30 mV to -100 mV depending on cell type). Changes to the membrane potential are called “depolarizing” if they make the inside of the cell less negative. Depolarizing a nerve makes it much easier for the nerve to fire (i.e. lowers the input voltage required for the nerve to fire).

Above a threshold level, a depolarizing event initiates a traveling perturbation in the electrochemical gradient, which travels until it reaches the end of the axon which terminates in structures called synapses.

Propagation of initiated perturbation toward synapses at the end of the axon is shown below:

Each synapse contains transmembrane voltage gated calcium channels and intracellular vesicles containing neurotransmitter.

When the electrochemical signal reaches the synapse, the voltage gated calcium channels open transiently, allowing an inrush of calcium ions (Ca++).

In inrush of calcium ions causes the vesicles containing the neurotransmitter to fuse with the synaptic cell membrane and release the neurotransmitter into the post synaptic gap (aka cleft).

The intended target of the neurotransmitter depends on the type of the nerve and what it is connected to.

As an example, if the neuron is connected to muscle (neuromuscular junction), the release of the neurotransmitter acetylcholine causes the muscle to depolarize via neurotransmitter gated channels. The depolarization spreads along the muscle surface and the T-tubules that run along the surface of the muscle fibers. The depolarization opens voltage gated Ca++ channels in the T-tubule surface that allows Ca++ from the extracellular fluid in the T-tubule to enter the the sarcoplasmic reticulum. The inrush of Ca++ into the sarcoplasmic reticulum activates the “sarcoplasmic reticulum calcium release channels” (SRCaRCs), which in turn release Ca++ into the fluid around the myofibrils. The released Ca++ allows the muscle to contract by removing the tropomyosin block between actin and myosin, triggering cross-bridge formation by enabling myosin to bind to actin.

The Bone Pantry:

In addition to providing structural support and organ protection, bone serves as a repository of calcium, phosphorus, and mitogens (growth factors). Movement of these compounds into and out of bone is mediated by two cell types, osteoclasts which dissolve bone (resorption), and osteoblasts which are the bone builders. Both cell types come together in three to four million sites scattered throughout the skeleton.

Osteoblasts (the bone building cells) secrete collagen and other bone proteins creating a matrix onto which calcium and phosphorus crystallize (~ 90% of bone mass). The calcium to phosphorus ratio in bone is 2.5 to 1. In addition to calcium and phosphorus , various growth factors (mitogens) are also stored in the bone. Osteoblasts arise from osteoprogenitor cells located in the bone marrow and periosteum. Osteoprogenitors are induced to differentiate under the influence of growth factors, including the bone morphogenic proteins, fibroblast growth factor, platelet-derived growth factor.

Osteoclasts (the bone dissolving cells) secrete both proteolytic and hydrolytic enzymes and hydrochloric acid that result in destruction of the bone’s protein matrix, which results in mobilization of calcium, phosphorus, and bone resident growth factors into the extracellular fluid. Osteoclasts arise through the differentiation of macrophages. Osteoclasts are regulated by several hormones including PTH from the parathyroid gland, calcitonin from the thyroid gland, estrogen, vitamin D, and growth factor interleukin 6 (IL-6). Osteoclast population density is modulated by three molecules produced by osteoblasts - two that promote osteoclast development and one that suppresses osteoclast development. The two osteoclast promoter molecules are 1) macrophage colony-stimulating factor that binds to a receptor on macrophages inducing them to multiply and 2) RANKL (receptor activator of NF-kB ligand) that binds to a different receptor (RANK receptor) inducing the macrophage to differentiate into an osteoclast. The molecule that inhibits osteoclast formation is osteoprotegerin (OPG), which blocks osteoclast formation by latching on to RANKL and blocking its function.

The population density levels and activity levels of Osteoclasts and Osteoblasts are mediated by numerous endocrines. Osteoclast / Osteoblast mediated release of Ca++ (calcium ions), phosphorus, and mitogens from bone into the extracellular fluid has a profound impact on many physiological processes.

A summary of some of the more important endocrine interactions with the bone microenvironment that result in systemically increased extracellular calcium levels are listed below:

Increasing Vitamin D (1,25D) increases extracellular Ca++
Decreasing estrogen increases extracellular Ca++
Decreasing testosterone increases extracellular Ca++
Increasing prostaglandins increases extracellular Ca++
Decreasing growth hormones (GH, IGF, BMP) increases extracellular Ca++
Increasing parathyroid hormone (PTH) increases extracellular Ca++
Decreasing calcitonin increases extracellular Ca++
Increasing Vitamin A / Retinoids increases extracellular Ca++
Increasing Lithium increases extracellular Ca++

Calcium: Calcium is the fifth most abundant element by mass in the earth’s crust and fifth most abundant dissolved ion in sea water. It is especially important at a sub cellular level where movement of the calcium ion Ca++ into and out of the cytoplasm functions as a signal for many cellular processes. The average adult human body contains 1.3 kg of calcium of which 99% is contained in bones and teeth, 1% in cells of soft tissue, and 0.15% in the extracellular fluid. Intracellular cytosolic concentrations of Ca++ are kept low relative to extracellular concentrations. This concentration gradient drives Ca++ into the cell when Ca++ channels transiently open, which in turn activates Ca++ responsive proteins. Ca++ is required for function of nerves, muscles, secretions by cells, and cell growth and division pathways (population density management pathways).

Phosphorus is involved in numerous physiological processes including transport of cellular energy via addition of a phosphorus atom to adenosine diphosphate (ADP) to make the energy rich molecule adenosine triphosphate (ATP). Phosphorus is important for key regulatory events such as phosphorylation (addition of a phosphorus atom to a molecule) and phospholipids are the main structural components of cellular membranes. Phosphorus is also used in maintenance of extracellular / intracellular ion concentration gradients via transmembrane ATPase pumps.

Mitogens (growth factors) that are stored in bone and liberated by osteoclast activity include platelet-derived growth factors (PDGF), fibroblast growth factors (FGF), insulin like growth factors (IGFs) I and II, transforming growth factor-beta (TGF-beta), endothelin 1 (ET-1), urokinase type plasminogen activators, and others. The growth factors released from bone are potent mitogens. PDGF and FGF are mitogens that stimulate progression of many cell types through the early part of the G-1 Phase and IGF-1 and IGF-2 are potent growth factors that promote cell progression through the later part of the G-1 Phase.

Deposits to / Withdrawals from the Bone Pantry:

Parathyroid Hormone (PTH): The primary regulatory hormone responsible for increasing serum concentrations, by release of calcium from bone (bone resorption), is parathyroid hormone (PTH). When calcium sensors in the parathyroid gland detect low serum calcium concentrations, production of PTH is upregulated. PTH interacts with its receptor on osteoblasts to upregulate production of RANKL, which upregulates macrophage differentiation into osteoclasts. Additionally, PTH increases calcium reabsorption by the renal tubules (kidney) and stimulates conversion of vitamin D to its active form (calcitriol).

Calcitonin: The primary regulatory hormone responsible for decreasing serum concentrations of calcium by inhibiting release of calcium from bone is calcitonin, which is produced by the parafollicular cells of the thyroid. High serum calcium concentrations result in upregulated production of calcitonin. Calcitonin receptors have been found in osteoclasts and osteoblasts and calcitonin result in the loss of the ruffled osteoclast border responsible for resorption of bone. Calcitonin also increases renal excretion of calcium by decreasing reabsorption by the kidneys and evidence exists that it reduces absorption of calcium in the gastrointestinal tract.

Estrogen has a “triple whammy” ( Rosen C J, “Restoring Aging Bones”, Scientific American, March 2003) effect in inhibiting osteoclast activity by binding to osteoblasts and 1) increasing their output of OPG and 2) suppressing their RANKL production. In addition, estrogen appears to prolong lives of osteoblasts while simultaneously 3) promoting osteoclast apoptosis. As estrogen levels drop after menopause, these “brakes” on osteoclast inhibition are removed, tipping the balance in favor of osteoclast dominated bone destruction which results in osteoporosis.

Androgens such as Testosterone also have an inhibitory effect on bone resorption, and studies suggest that this occurs through local aromatization of androgens into estrogen, however direct androgen interactions with androgen receptors related to bone remodeling have been observed in animal models.

Prostaglandins are autocrine and paracrine hormones produced in many places throughout the body. Prostaglandins have a wide array of effects, including involvement in the inflammatory part of an immune response to injury / cell death and antigens / allergens. Prostaglandins exhibit PTH-like (parathyroid hormone) effects that result in calcium mobilization from the bone and prostaglandin synthetase inhibitors are a textbook method for reducing calcium levels in management of hypercalcemia (Therapy of Renal Diseases and Related Disorders,1991, page 98).

Vitamin D is a steroid-like chemical that promotes osteoclast activity by binding to vitamin D receptors (VDR) in osteoblasts and upregulating expression of RANKL. Vitamin D also enhances intestinal absorption of calcium and enhances renal retention of calcium. Its particular significance is discussed further below.

Skin - Bone - Ca++ Mediated Life

In context of the photosynthetic cyanobacterial DNA origins of life on earth, it is not surprising that vestiges of photo activated pathways that alter life functions can be found in humans today.

Skin exposure to sunlight (UVB) alters vitamin D levels, which in turn escalates extracellular calcium, phosphorus and mitogen levels, which in turn synchronizes a broad spectrum of day / night processes.

The active form of Vitamin D (1,25[OH]2D), also known as calcitriol or DHCC or 1,25 OHD or 1,25D, promotes osteoclast activity by binding to vitamin D receptors (VDR) in osteoblasts and upregulating expression of RANKL. Vitamin D also activates absorption of calcium in the intestine and reabsorption of calcium by the kidney. Accordingly, the active form of vitamin D has a “triple whammy” effect on elevating extracellular calcium levels.

Normally, around 90% of the human requirement for vitamin D comes from exposure to sun. Skin is unique in that it is capable of manufacturing biologically active 1,25 D in the presence of UVB light from start to finish (unlike the “need regulated” conversion by the kidney). Full body exposure to UVB for 20 minutes in midday summer sun, in fair skinned people, can result in 10,000 IU of vitamin D being synthesized by the skin ( 25 times the recommended daily allowance of 400 IU). The effectively unregulated production of active 1,25 D by the skin would boost Ca++ levels by the three pathways previously discussed (i.e. increased release of calcium from bone, increased reabsorption of calcium by the kidneys, and increased absorption of calcium from the intestines) and the biological effect would last for a period of time commensurate with the amount of 1,25D synthesized and its half life ( 3 - 6 hours).

The other source of vitamin D synthesis is inside the body. The conversion of the inactive form of Vitamin D to the active form 1,25 D (calcitriol) involves two hydroxylations (addition of OH groups). The first hydroxylation is at the C-25 position and occurs in the liver through a cytochrome P-450 dependent enzyme and the second hydroxylation is at the C-1 position and occurs in the kidney. Parathyroid hormone (PTH) stimulates 1-hydroxylase and inhibits 25-hydroxylase. Calcitriol represses synthesis of 1-hydroxylase and enhances synthesis of 25-hydroxylase. Under normal conditions, low serum Ca++ levels increase PTH synthesis, which in turn increase conversion of vitamin D to its active form, which in turn elevates extracellular calcium levels by the three pathways disclosed above (i.e. increased release of calcium from bone, increased reabsorption of calcium by the kidneys, and increased absorption of calcium from the intestines). Elevated levels of the active form of vitamin D function to repress synthesis of 1-hydroxylase, which in turn functions to repress further conversion of vitamin D to its active form.

Vitamin D levels can vary widely. The reference range for plasma levels of 25 D is from 8 - 80 ng/ml (20 - 200 nmol/ L) and plasma levels of 1,25 D range from 16 - 65 pg/ml (40 - 160 pmol/L).

The Skin -Vitamin D mediated increase in daytime extracellular Ca++ levels result in enhanced nerve function, muscle function, and brain function, including consciousness and memory formation.

It should be noted that the concurrent decrease of another light mediated endocrine, melatonin (the sleep hormone), which drops with exposure to light and rises with exposure to darkness, likely creates a double whammy effect on daytime alertness. However, the focus of our discussion below is only on the Ca++ mediated enhancement of daytime functions.

The effects of increased daytime calcium levels on nerves is as follows:

a) nerve membrane depolarization

Increased extracellular Ca++ levels enhance nerve function. Since the active form of Vitamin D is synthesized during daytime, resulting in release of Ca++ from bone into extracellular fluid, nerve function is effectively heightened during daylight and reduced at night.

The basic science underlying neuron function were covered previously. This section covers more advanced neuron science.

Neurons contain ion channels that maintain an electrochemical concentration gradient between the outside of the cell and the inside of the cell. The resting membrane potential inside of a typical neuron is around -85 mV relative the outside of the cell (-30 mV to -100 mV depending on neuron type). The cell membrane acts as a capacitor, storing charge separated by the thickness of the membrane, and has a typical capacitance of about 1µ Farad per square centimeter. Changes in ion concentrations outside the cell versus inside the cell change the strength of the electric field across the cell membrane. Changes to the membrane potential are called “depolarizing” if they make the inside of the cell less negative or “hyperpolarizing” if they make the inside of the cell more negative. The term negative is relative, as it refers to an electrical potential differential between two points. If the inside is less positive than the outside, it is negative, relative to the outside of the nerve.

Electrical impulses that travel along the neuron are called action potentials and are transient perturbations in the membrane potential. Action potentials are conducted in a all-or-none manner and for an action potential to be generated the input signal must depolarize the neuron by more than its “threshold” membrane potential. As an example, for the -85 mV resting membrane potential neuron above, the threshold voltage is around -70 mV, meaning that the input signal must depolarize the membrane by at least 15 mV to generate a nerve impulse (i.e. action potential).

Changing the extracellular or intracellular concentrations of ions changes the resting membrane potential. Depolarizing concentrations (i.e. that make the inside of the cell less negative) bring the resting membrane potential closer to the threshold potential, and consequently the neuron requires a smaller input voltage to trigger an action potential. Polarizing concentrations (those that make the inside more negative) move the resting membrane potential farther away from the threshold potential and result in a larger input signal being required to trigger an action potential.

A traveling nerve impulse opens voltage gated Na+ (sodium) channels and K+ (potassium) channels, which allow Na+ to flow into the cell and K+ to flow out of the cell, passively along their respective electrochemical concentration gradients. Both the Na+ channels and K+ channels are rapidly inactivated by a “ball and chain” amino acid complex that rapidly plugs the respective channels. Potassium (K) is the most significant ion in impulse transmission because of the large disparity between the extracellular and intracellular concentrations. Typical extracellular concentrations potassium and sodium are about 3 mM of K+ and 117 mM of Na+ and the typical intracellular concentrations are about 90 mM of K+ and 30 mM of Na+ . The 30 fold concentration gradient disparity of K+ ( i.e. 90 / 3) overwhelms the 4 fold gradient disparity of Na+ (i.e. 117 / 30).

The resting (equilibrium or E) membrane potential for a given ion concentration can be calculated using the Nernst equation:

Ek = (RT/zF)(ln(Co / Ci))

Ek is the equilibrium (or resting) membrane potential for the ion
R is the gas constant (8.31 joules/mole/ oK)
T is the absolute temperature (Kelvin = 273 +oC)
z is the valence of the ion (e.g. + 1 for potassium, + 2 for calcium)
F is the Faraday constant (amount of charge on a mole of ions, 96,500 coulombs/mole)
Co is the outside (extracellular) concentration of the ion (in mM)
Ci is the inside (intracellular) concentration of the ion (in mM), and
ln is logarithm to the base e

As an example, at room temperature (20oC = 293 oK) and for potassium (K):

RT/zF = (8.31)(293) / (+1)(96,500) = .02523 V = 25 mV

and for concentrations of 3 mM outside the cell and 90 mM inside the cell:

Ek = (25 mV)(ln (Ko / Ki)) = (25 mV)(ln 3/90) = (25 mV)(-3.4) = -85 mV

The effect of elevating extracellular concentrations of positive ions can be seen from the Nernst equation. Increasing extracellular concentration of the positive ion K+ results in a more positive resting membrane potential, which is by definition depolarizing, and brings the resting membrane potential closer to the threshold potential. This means a smaller input signal voltage is required to trigger the “all-or-none” action potential.

As an example, as extracellular concentrations of K+ are raised to 4 mM, the resting membrane potential becomes more positive (less negative):

Ek = (25 mV)(ln (4 / 90)) = (25 mV)(-3.11) = -78 mV

Using the -70 mV threshold voltage, the input voltage required to initiate an action potential is now only 8 mV versus 15 mV.

The actual resting membrane potential is a summation of all ions that are permeable. Calcium ions are permeable through the sodium - calcium exchanger (NCX).

From the Nernst equation, we can see that increasing extracellular concentrations of positive ions, relative to intracellular concentrations of positive ions, is a depolarizing change. Accordingly, elevating extracellular Ca++ levels relative to intracellular Ca++ levels is a depolarizing event that would lead to neuronal membrane depolarization (i.e. reducing the magnitude of the input signal required to initiate an action potential).

Neuronal intracellular Ca++ levels are kept low as calcium is a signaling molecule within a neuron (used for neurotransmitter release at the synapse). NCX in the plasma membrane and Calcium ATPase (PMCA) pumps in the synapse pump calcium out of the cytoplasm. Extracellular concentrations of Ca++ can range from 1 to 2 mM (Alberts B., et. al., 1994 p. 508). However, intracellular concentrations are kept very low and do not increase proportionately relative to extracellular increases. Studies of mammalian brain nerve cells showed that as extracellular concentration of Ca++ were raised from 1 mM to 2 mM, the intracellular concentrations only rose from 130 nM to 160 nM, respectively (Nachshen D. A., 1985) Accordingly, for a 100% increase in extracellular concentrations of Ca++, the intracellular concentrations only rise 25%.

From the above information we can approximate the amount of depolarization that would occur across the range of 1 mM to 2 mM of extracellular Ca++. Using the Nernst equation and the change in the ECa between the 2 nM and 1 nM levels would provide the amount of depolarization in mV that could be expected (per 1 mM) over this range (i.e. ECa @ 2 mM - ECa @ 1 mM = net change in resting membrane potential from a 1 mM change in extracellular Ca++ concentrations), or:

 ECa per 1 mM increase in [Ca]o = ECa @ 2 mM - ECa @ 1 mM

For calcium, RT/zF = (8.31)(293) / (+2)(96,500) = 12.6 mV

and the  ECa when extracellular Ca rises from 1 mM to 2 mM and the corresponding intracellular Ca levels rise from 130 nM to 160 nM:

= (12.6 mV )(ln (2 / .000160)) - (12.6 mV)(ln (1 / .000130))
= (12.6 mV) (9.43) - (12.6 mV)(8.948)
= + 6.12 mV

Accordingly, the increase in extracellular Ca2+ concentrations from 1 mM to 2 mM would make the resting membrane potential more positive by around 6 mV. In our previous example, this would reduce the resting membrane potential from -85 mV to -79 mV, which in turn would reduce the amount of input stimulus required to trigger a nerve impulse from 15 mV to 9 mV.

This nerve hypersensitization via neuronal membrane depolarization disclosed above is the first mechanism by which rising extracellular calcium ion concentrations affect the nervous system.

b) calcium mediated neurotransmitter release

The second mechanism is calcium mediated neurotransmitter release, via the voltage gated calcium channels.

As a nerve impulse reaches the synapses at the end of the nerve cell, it results in the release of chemicals called neurotransmitters, which in turn trigger a nerve impulse in the next cell in the transmission path. The electrical impulse causes voltage gated Ca++ channels to open which allows an inrush of Ca++ to enter the pre synaptic cell, along its electrochemical concentration gradient. Neurotransmitter is stored in vesicles at the synapse and Ca++ causes the vesicles to fuse with the cell membrane, releasing the neurotransmitter by exocytosis into the synaptic cleft. The neurotransmitter binds to and opens transmitter-gated ion channels on the post synaptic cell, which triggers a depolarization in the post synaptic cell, triggering an action potential if sufficient depolarization occurs. The extent of the depolarization of the post synaptic cell is graded according to how much neurotransmitter is released at the synapse and how long it persists there (Alberts B., et. al., 1994, p. 536).

For a 100% increase in extracellular concentrations of Ca++, the intracellular concentrations only rise 25%. As extracellular Ca++ levels increase from 1 mM to 2 mM, not only does the absolute amount of molecules available to rush in through the voltage gated channels double, but the concentration gradient (i.e. the driving force for the inrush) increases 63% from being 7,672 times greater on the outside at 1 mM ( i.e. 1 mM / 130 nM) to being 12,500 times greater on the outside at 2 mM ( i.e. 2 mM / 160 nM). Accordingly, the much larger amount of Ca++ entering the pre synaptic cell during the transient period when the voltage gated channels are open would result in much greater release of neurotransmitter.

Since depolarization of the post synaptic cell is graded and related to the amount of neurotransmitter released, as previously discussed, the effect of rising extracellular Ca++ levels would also be “ hypersensitization of synaptic gap transmission” via greatly upregulated neurotransmitter release from the pre synaptic cell combined with the neuronal membrane hypersensitization in the post synaptic cell (i.e. via the depolarization per the Nernst equation). Accordingly, rising extracellular calcium concentrations would have a direct “double whammy” effect on enhancing nerve function.

Extracellular Ca++ levels also have a direct effect on muscle tissue. Elevated extracellular calcium levels would increase muscle contraction by two pathways.

a) neuromuscular neurotransmitter release

The first relates to nerves and the neuromuscular junction. Muscle contraction is triggered by a nerve impulse traveling down a neuron which is then converted to a release of the neurotransmitter acetylcholine at the synapses where the neuron meets the muscle. Enhanced neurotransmitter release results when extracellular Ca++ levels are high, by the voltage gated Ca++ channel pathways previously disclosed above. Accordingly, more acetylcholine is released at the neuromuscular junction, causing a greater post synaptic depolarization.

b) sarcoplasmic reticulum calcium release channels

The second pathway relates to extracellular Ca++ concentration’s direct effect on muscle contraction. The release of the neurotransmitter acetylcholine described above causes the muscle to depolarize via neurotransmitter gated channels. The depolarization spreads along the muscle surface and the T-tubules that run along the surface of the muscle fibers. The depolarization opens voltage gated Ca++ channels in the T-tubule surface that allows Ca++ from the extracellular fluid in the T-tubule to enter the the sarcoplasmic reticulum. The inrush of Ca++ into the sarcoplasmic reticulum activates the “sarcoplasmic reticulum calcium release channels” (SRCaRCs), which in turn release Ca++ into the fluid around the myofibrils. The released Ca++ allows the muscle to contract by removing the tropomyosin block between actin and myosin, triggering cross-bridge formation by enabling myosin to bind to actin.

With an increase in the extracellular calcium concentration, there will be a larger release of Ca++ from the T-tubules, which in turn will activate more SRCaRCs and the release of more Ca++ onto the myofibrils, which in turn will cause greater cross-bridge formation and muscle contraction.

The skin - bone - Ca++ mediated daytime elevations in Ca++ levels enhance sensory and motor neuron function throughout the body.

The Calcium (Ca++) Wave, Consciousness and Memory

The daytime enhancement in basic brain neuron activity would be in part attributable to the a) neuronal membrane depolarization and b) enhanced neurotransmitter release mediated by elevated Ca++ as previously discussed.

However, a very powerful effect on consciousness and memory formation would come from the elevated Ca++ levels affect on enhancing the propagation of the calcium wave in the brain. Propagation of the calcium wave in the brain has been associated with consciousness and memory formation.

The calcium wave is driven by a propagating chain reaction between a certain type of neuron ( glutamate activated, NMDA channel gated) and a certain type of glial cell (astrocyte).

Memory consolidation depends on astrocyte metabolism (Gibbs et. al., 2008). Astrocyte release of glutamate coupled with post synaptic depolarization leads to long term potentiation (Perea et. al., 2007). There is also evidence that “the informational content of perceptual conscious processes is embodied in astrocytic calcium waves” (Periera et. al. 2009).

Neurons make up only 10% of the brain and glial cells make up 90% of the brain. Astrocytes are the most numerous glial cells. Astrocytes are star shaped cells that make up one half of brain tissue volume. Astrocytes contact neuronal soma (cell body), dendrites, and presynaptic terminals of nerves. The dendritic tree of a neuron requires numerous astrocytes for complete coverage and conversely 300 - 600 dendrites are located within an astrocyte (Halassa et. al., 2007). The average cortical astrocyte also enwraps 4 neuronal cell bodies.

The contribution of Glial cells to intelligence and brain function is known, but has yet to be fully characterized. Empirical evidence strongly supports the correlation between higher glial to nerve cell ratios and intelligence. Moving up the evolutionary ladder (Koob, 2009): Leech -one glial cell per 30 neurons or 3% glial content, fruit fly: 20% glial, mice and rats 60%, Chimpanzee 80%, human 90%.

Ca++ Mediated NMDA ion channel activation

Glutamate is the main excitory neurotransmitter in the mammalian central nervous system. In the hippocampus, which is involved in the consolidation of short term to long term memory, there is a subclass of glutamate gated ion channels, known as NMDA receptors.

The NMDA channels are doubly gated, requiring that both glutamate to be bound to the receptor and the nerve membrane to be strongly depolarized (Alberts B., et. al., 1994, p 545). The second condition is required to release Mg++ that normally blocks the resting channel. Mg++ block removal combined with glutamate bound to the receptor allows Ca++ to enter the post synaptic cell. The increased Ca++ in the post synaptic cell produces a retrograde signal that produces a lasting change in the presynaptic cell that allows the presynaptic cell to release a greater amount of glutamate when subsequently activated.

Escalation in extracellular Ca++ functions to depolarize nerves by the Nernst equation as previously discussed. The depolarization in turn enhances removal of the Mg++ block, allowing glutamate mediated influx of Ca++ into the nerve cells.

Nerves, astrocytes, and the calcium wave

In an activated astrocyte cell, inositol trisphosphate (IP3) pathways are activated inducing the release of calcium ions from internal stores (mitochondria and endoplasmic reticulum) which in turn result in the astrocyte releasing Glutamate (Glu) extracellularly, which in turn binds to and activates receptors on post synaptic neurons that allow Ca++ inflow into the neuron.

A mechanistic explanation for the propagation of the calcium wave is not well elucidated in literature. Accordingly, author presents a mechanistic outline below of what has not been elucidated, but should be inferred from available studies.

Author would like to note a significant implication from the elucidation is that these specialized brain neurons can conduct signals in two ways instead of just one: one by the traditional Na+ / K+ driven membrane depolarization route and the second by Ca++ intra neuron propagation. Although each of the two transmission modes is antagonistic to the other, the combination of both being activated would effectively provide a third state that appears may be responsible for long term memory formation.

Starting with the above glutamate activated inrush of Ca++ into a neuron, the inrush of calcium would be expected to propagate along the concentration gradient differential toward the synapse.

From the Nernst equation, we know the intracellular Ca++ inrush is a hyperpolarizing event. As an example, if the inrush transiently doubled intracellular Ca++ levels to 320 nM from 160 nM:

 ECa = (12.6 mV )(ln (2 / .000320)) - (12.6 mV)(ln (2 / .000160))
= (12.6 mV) (8.74) - (12.6 mV)(9.43) = (110.1 mV) - (118.8 mV) = - 8.7 mV

Accordingly, the transient increase in intracellular Ca++ concentration would make the resting membrane potential more negative (i.e. less positive) by around 9 mV (from -85 mV to - 94 mV), boosting the amount of input stimulus required to trigger a nerve impulse from 15 mV to 24 mV for the traditional Na+ / K+ driven depolarization.

Because the two transmission modes are antagonistic, it would require a much higher input voltage for a double mode firing to occur simultaneously. While not normal, a double firing, or this“third state, is not impossible, and could be expected in heightened excitory situations. It is possible this third state may involved in enhanced memory formation in heightened excitory situations.

In the normal Ca++ only firing mode, the inrush of calcium would propagate along the concentration gradient differential toward the synapse. Once the Ca++ reached the synapse it would fuse the vesicles containing neurotransmitter to the membrane, releasing the neurotransmitter (glutamate). The end result is effectively the same as that of a Na+ / K+ driven action potential opening voltage gated Ca++ channels at the synapse, fusing vesicles, and releasing neurotransmitter. The Ca++ would then pumped out of the cell by PMCA pumps at the synapse. A double firing could be expected to release a much larger amount of neurotransmitter and Ca++ into the synaptic cleft.

Released glutamate in turn triggers the next astrocyte in line, as well as directly activates any nearby post synaptic NMDA gated neurons, propagating the calcium wave in a process that is repeated until the end of the propagation path.

While the above physiological elucidation deals with how the propagating calcium wave is created, it does not deal with the observable electromagnetic phenomena associated with consciousness and memory formation. An elucidation of that is next.

The Calcium Wave Driven Electromagnetics of Consciousness and Memory

There is a clear electric / electromagnetic connection to consciousness and memory formation that has not been elucidated in literature, and author will attempt to elucidate it below:

Simplistically, the propagation of the calcium wave is likely what hosts the electromagnetic phenomenon responsible for consciousness and memory formation. Mechanistically, a traveling ion wave could act as an “electron broom”, unidirectionally moving ambient unbound electrons, which is what an electrical current is, and what is measured in most brain studies.

An electric current is defined as a flow of electrons. A traveling perturbation in ion concentration gradients is not a true electrical current per se. However, true electrical currents were measured by Dr. Becker ( Robert O. Becker MD and Gary Selden, “The Body Electric - Electromagnetism and the Foundation of Life“, © 1985, First Quill Edition.)

Dr. Becker found a negative electrical potential at the front of the head versus a positive potential at the back of the head, which suggested a direct current flow from the back of the head to the front of the head. Negative potentials in the brain’s frontal area and at the periphery of the nervous system were associated with wakefulness, sensory stimuli, and muscle movements. The more activity the greater the negative potentials were. A shift toward the positive occurred during rest and even more so during sleep.

An Electroencephalogram (EEG) records the underlying voltage fluctuations over various parts of the head. The frequency of these brain waves are correlated with states of consciousness. Beta waves (~ 15 - 30 cycles per second) are observed during daytime consciousness, in contrast to Delta waves ( ~ 1 - 3 cycles per second) which are observed during deep sleep.

The source of the electric current has never been elucidated. However, from physics we know that an electric field extends outward from electrically charged particles such as ions, which can in turn interact with other nearby electrically charged particles such as electrons (i.e. attract or repel them). A traveling ion perturbation wave could attract or repel electrons directionally along the path of travel, which would in turn create the electrical current measured by Dr. Becker.

The traveling electric current is required for consciousness and memory formation. The most compelling data comes from inhibiting this flow of electrons, which result in loss of consciousness and memory formation.

A strong magnetic field oriented at right angles to an electric current magnetically “clamps” or stops its flow. Dr. Becker (Becker et. al., 1985, p. 238) found he could anesthetize animals using this process, just as well as with chemicals, and found EEG recordings of magnetic and chemical anesthesia were identical. The absence of consciousness and memory formation during anesthesia induced by magnetic clamping of the electrical current flow confirms the required involvement of the moving electrical current in both consciousness and memory formation.

Alternatively, an opposing current source can be used to stop the flow of current. When Dr. Becker (Becker et. al. 1985, p111) passed a minute current from front to back through the head to cancel out the internal current, the animal fell unconscious.

Electrons have a magnetic field associated with them (because of their spin).

A traveling direct electric current is accompanied by a traveling magnetic field, which is perpendicular to the direction of the electron flow, and proportional to the strength of the current. A traveling magnetic field can interact with its surroundings in one of 3 ways: 1) induce a current flow in a conductor that is perpendicular to the direction of motion of the magnetic field, 2) deflect electrons flowing in a conductor so as to flow perpendicular to the direction of current flow (Hall effect), and 3) magnetize, or alter the magnetic orientation of, magnetic material in its path.

The human brain produces steady DC magnetic fields one billionth the strength of earth’s field of about one-half gauss (Becker et. al. 1985, p240). The mineral magnetite (Fe3O4) is known to be precipitated biochemically by bacteria, mollusks, arthropods, chordates, fish, animals, and humans and appears in the fossil record extending back to the Precambrian time (Kirschvink et. al., 1992). Kirschvink et. al. used high resolution transmission electron microscopy to estimate the presence of a minimum of 5 million single-domain crystals per gram of human brain tissue, with 100 million+ crystals per gram for pia and dura. The crystals are in clumps of 50 - 100 particles. The crystal alignment was interpreted as a biological mechanism for maximizing the magnetic moment per particle, as the direction yields 3% higher saturation magnetization than do other directions.

Magnetite is known to be used in geomagnetic orientation, indicating it interacts with brain tissue, possibly through the tissue’s associated electric field.

Whether the brain’s electric currents, associated magnetic fields, and magnetite play a role in memory or brain functions other than geomagnetic orientation has yet to be studied. In electronics, electric currents, magnetic fields, and magnetizable materials are used to store and recall memory. As an example, in a video camera, light entering the camera is converted to a set of electrical pulses that are converted at the recording head into magnetic fields that in turn magnetize the magnetic material on the tape below. This creates a record of the electrical pulse pattern. In playback mode, the play head is passed over the tape an reconverts the magnetic pattern back into the electrical pulse pattern as originally seen.

In summary, the effect of skin-bone mediated daytime escalation of extracellular Ca++ on the calcium wave would be to: 1) elevate intracellular astrocyte Ca++ levels, hence enhancing the astrocyte intracellular Ca++ mediated glutamate release, 2) elevate extracellular Ca++ levels to depolarize neurons and remove the Mg++ block from NMDA receptors, allowing glutamate to open Ca++ channels. The elevated extracellular calcium would also 3) provide a greater influx of calcium into neurons when the glutamate mediated Ca++ channels were open, which in turn would 4) result in a greater release of neurotransmitter when the higher levels of Ca++ reached the synapse. The combinational effect would be enhancement of the calcium wave. The calcium wave in turn may be what drives the observed directional flow of electrical currents (and their associated magnetic fields) in the brain, which in turn are associated with consciousness and memory formation by pathways which have yet to be elucidated.

The abundance of magnetite crystals in the brain, combined with the presence of magnetic fields in the brain, the strength of which is proportional to the underlying electric currents, which in turn would be expected to be proportional to the strength of the underlying calcium wave, indicate a possible novel mechanism for memory formation via magnetization of the magnetite crystals.

Copyright © 2012 Mark J. Zamoyski. All rights reserved.

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