Welcome to the Permian Museum

The Permian period ( 300 - 252 million years ago) experienced 4 extinction pulses and 4 recovery pulses. The last extinction pulse was the most severe known on earth and the re-speciation pulse that followed introduced a new cast of characters that spawned the age of the dinosaurs and winged flight. The Permian Museum website tells the story of how that happened.


IMPORTANT COPYRIGHT NOTICE: Copyright © 2012 - 2020 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. New material is copyrighted as added. Any material released for public domain use is clearly marked as such and it is requested that the source be credited as Mark J. Zamoyski / PermianMuseum.com

ABOUT THE AUTHOR Mark J. Zamoyski received his BS in 1977 from Cornell University’s school of Ag. & Life Sciences and his MBA in 1978 from Cornell’s business school. During his career, Mark was awarded various patents, including patents in Oncology (US 7,507,704, 7,309,486 and 6,486,146), Neurology (US 8,197,858), and for Pulmonary Anti-Inflammatories and Antiproliferatives (US 7,102,091 and 7,015,244).

ABOUT THE WEBSITE The Permian Museum web site is dedicated to those with a thirst for science. We make no money from this website. We do not require any "registration" to use this website. We do not track you and target you with ads for having visited the website. So if you enjoy science, please enjoy the website. Just make sure you are coming directly to the website at www.permianmuseum.com and not through some third party service or search engine that is tracking you.

Important Note: The scientific observations, interpretations, and conclusions, based on the fossil evidence presented, are purely those of the author, for the time being. We intend to start gathering alternative interpretations and conclusion for inclusion on this website, once we have finished posting all of the fossil evidence.

Acknowledgments and Special Thanks: Content from the book, “On the Origin of Life and Biodiversity” © 2014 Mark J. Zamoyski, which was originally available on Amazon, and an earlier full science manuscript titled “Quantum Speciation and the Origins of Life” © 2012 Mark J. Zamoyski is now being migrated to this website. Author would like to thank Dr. Justin John Zamoyski for his insights and review of the neurology, molecular biology, and fluid dynamics aspects of the original book, Dr. James T. Sprinkle for his great insight that provided the nexus to the Cambrian Explosion of Life, and Nicholas. J. Lee for his ability to bring unknown life forms to life by his spectacular illustrations. This website is always under construction and new material is posted on an ongoing basis. Website Last Updated: July 22, 2020


PRESS RELEASES - 2020

April 9, 2020 - Permain Museum Announes the Completion of its Spring Fossil Egg Hunt

January 13, 2020 - Dinosaur Forerunner Fossils Discovered

January 2, 2020 - Permian Graboid Fossil Discovered







Website Overview and Index

Newly discovered fossils from a quarter billion years ago provide a new narrative on the origin of life and biodiversity on earth.

Site Index



Chapter 1

Overview of Our Fossils and Their Significance

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 "quantum speciation pulse", or recovery pulse, similar in respects to the quantum speciation pulse known as the Cambrian explosion of life on earth. The below graphic shows 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). The last extinction pulse (~ 252 Ma) was earth¹s most severe known and the quantum re-speciation that followed introduced a new cast of characters that gave rise to the age of the dinosaurs.

Permian Extinction / Recovery Pulses


Millions of Years Ago (Ma)

The 35 whole body fossils covered in "On the Origin of Life and Biodiversity" included fossils of both the structures that hosted this quantum speciation process as well as the resulting life forms that were created by this process. Since then, numerous other fossils have been added to the collection and are being added to this website on an ongoing basis.



Soft Tissue Fossilization and Fossil Photos

Our fossils include preservation of soft tissue as limestone or crystalline forms of limestone. In typical life forms calcium exists as a free ion (Ca++) in solution, or ionically bonded to phosphate in bone, and not as limestone (calcium carbonate or CaCO3).

In many cases, it appears our life forms were instantly turned to stone. To say this type of fossilization is poorly understood is an understatement, however it is not without precedent. It is in respects similar to a case revealed in recently declassified documents where "a source of energy that is still unknown" was able to instantly transform the structure of a living organism "into a substance whose molecular composition is no different from that of limestone." ( source: www.cia.gov/library/readingroom/docs/DOC_0005517761.pdf ). We will refer to this process as "death by limestone fossilization".

A much slower form of soft tissue fossilization as limestone was described 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.

Conversion of amorphous calcium carbonate into its crystalline forms (Calcite, Aragonite, or Vaterite) depends on several variables including temperature, pressure, time, and the ambient chemical environment ( e.g. ambient Ph, the presence or absence of Mg, the activity of certain microorganisms).

Regardless of how our life forms were fossilized, the soft tissue preservation allows one to see a snapshot of the molecular biology of the time and to infer the DNA that was present at the time, as DNA expression is what generates the biological structures.

The simplest limestone fossilization can be found from temperature alone. The below shows a coral colony cooked, cauterized, and immortalized by the temperature of underlying volcanic activity:

Cooked Coral Colony Fossil



The red, avocado shaped bowl at the very bottom is limestone (calcium carbonate) that has been stained by iron that infiltrated it from the lava below.

Rotating the coral colony rock counterclockwise reveals the thermal vent:

Cooked Coral Colony Thermal Vent



A closer look at the vent reveals that it is composed of the crystalline form of calcium carbonate, but the rest of the rock is not. Just to the right of the vent, the calcium carbonate is much denser than in other parts of the rock, and somewhat resembles cement. As will be covered later, external features of some of our fossils are sometimes preserved in the density of the calcium carbonate matrix, and not just the crystal form of the calcium carbonate.

Zoom of Crystallized Thermal Vent



Non mobile life forms, such as coral, would be particularly susceptible to thermal or tectonic death, as they can not run away. Eggs are another example. Eggs that are whole and undamaged would strongly suggest death by thermal activity, or possibly by a high energy event as previously described.

An example of some fairly intact eggs is shown below:

Fossilized Eggs



Cutting one of the eggs open reveals the internal developing infant was crystalizing before either the eggshell or surrounding matrix. Alternatively, the life form may have been instantly turned into the crystal form, with the surrounding calcium carbonate not turned into it’s crystalline form.

Sectioned Fossilized Egg



In some of the egg nest areas there are also fossilized remains of intact bird like life forms, indicating the non destructive form of death happened over a large area. The bird fossils tend to indicate the more instantaneous death and fossilization process. A picture of some of the larger bird forerunners is shown below:

Fossilized Birds



A sectioned specimen of a small bird like life form shows the same crystallization pattern, with the life form entombed in a calcium carbonate matrix. Interestingly, the life form appears to be glancing back a something that caught its attention, just before being turned to stone, which immortalized it’s last glance.

Sectioned Small Coastal Bird



Removing the matrix from the upper part of a longer necked coastal bird shows the crystallization is so good that it reveals external features such as the eye and beak of the life form. The lack of postmortem tissue degradation or distortion also tends to support the instantaneous "death by limestone fossilization" process.

External View of Long Neck Bird Fossil by Matrix Removal



One may question why a bird would not escape a thermal event, but the answer to that may lie in the neurology of the time. Sectioned specimens reveal the life forms of this time period did not have a brain or even neurons for sensing temperature. The basic arrangement was an optic, olfactory, or auditory neuron connected directly to a motility group. As an example, Whaleen had a single optic neuron that connected directly to a motility group (its tail).

Illustration of Specimen Called Whaleen:



Photo of External View of Whaleen with Matrix Removed:



Sectioned View of Whaleen Reveals Single Fossilized Optic Neuron:



Dino-Seal is the most advanced specimen we have to date with 3 neurons ( Olfactory, Optic, and a possible vibration sensing neuron) each connecting to a motility or directional guidance group, but no brain. Dino-Seal is covered in the "Output Specimens" section of Chapter 4.

Accordingly, given the neurology of the time (i.e. absence of pain sensing neurons or a brain), the life forms would have been cooked by the thermal event, without even realizing what was happening, and subsequently fossilized by the thermal event. Alternatively, they could have undergone the observed, but as yet unexplained, high energy "death by limestone fossilization" process.

As for the soft tissue preservation aspect of the discussion, it should be noted that the sectioned specimen of Whaleen above shows what appears to be gestating progeny in an isolated sack in the central food lumen. The progeny have been preserved in crystalline form, versus the rest of Whaleen, which has been preserved as hardened calcium carbonate. This aspect of the soft tissue preservation is not yet understood, as undigested stomach contents in specimens such as Zamoyski dragon are not preserved in crystalline form, but as hardened calcium carbonate, just like the remainder of the life form:



The undigested stomach contents (Goby Shark) found in the central food lumen of the Zamoyski dragon are not preserved in crystalline form, but as hardened calcium carbonate, like the rest of the Zamoyski Dragon. In contrast, the gestating progeny inside Whaleen are preserved in crystalline form, while the remainder of Whaleen is preserved as hardened calcium carbonate.

Further complicating an understanding of the fossilization process is that roughly 15 - 20% of the life forms are whole body fossils that are preserved as a translucent bluish crystal. They are similar to the progeny inside Whaleen, except that the entire life form is preserved as a translucent bluish crystal. Examples:

Examples of Entire Life Form Fossilized as a Translucent Bluish Crystal



And if that was not enough, in early 2020 we discovered a third, very rare, and much more spectacular form of fossilization we call "the resin embeds". We do not understand the geology that created them, but they appear to be life forms embedded in a yellowish crystal matrix. We plan on posting a couple examples in mid 2020.



Observations about the appearance of our fossils:



1) The full crystallization of larger life forms is extremely rare and external features are rarely preserved well, while internal features are more commonly preserved well.

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 often much better on one side and not the other. This is possibly due to which side was on the bottom during the postmortem fossilization process. It may alternatively be related to manner of death, as some more specimens appear to have compression on one side and distention on the opposite side (e.g. eye crushed in on one side and the eye on the other side bulging out of its socket). This would be consistent with the life form being killed by a high pressure event from one side.

4) The internal preservation visible by sectioning a specimen (i.e. cutting it in half) is so good some times that it reveals anatomical features such as neurons, undigested stomach contents, and even gestating progeny. The internal preservation can typically 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.



Calcium Secreting Filter Feeder (CSFF) Photos

The Permian coastal ocean floor was covered with hard skeleton labyrinth structures built by single celled organisms called Calcium Secreting Filter Feeders (CSFFs).

They are the most prevalent, best preserved, and most significant fossils in our collection. Most have been turned into a crystalline form of calcium carbonate and are encased in a calcium carbonate matrix. A photo of the variety of these CSFFs is shown below. The top and bottom rows are sectioned specimens. The middle row shows the external view of exposed specimens.

Calcium Secreting Filter Feeders (CSFFs)



These are the most significant fossils in the collection because they are capable of hosting "Quantum Speciation", or the abrupt and abundant appearance of new life forms without antecedent lineage, through a process that can best be described as "Grab Bag Genetic Reassortment".

An example of a cracked open rock revealing the external features of such a structure shown below:

Permian Protopharetra - Exposed Exterior



Sectioned specimens are even more spectacular and provide an entirely new narrative on the origin of life and biodiversity on earth.

Permian Protopharetra - Sectioned Specimen





Author is extremely grateful to Dr. James T. Sprinkle of the University of Texas at Austin, who took the time to look at the picture and identify a potential Cambrian counterpart. A smaller version of the specimen above first appears in the fossil record around 500 ma at the start the Cambrian Explosion of Life (Boardman, Fossil Invertebrates, 1987, p.114 Figs. A and B ) and was called a Protopharetra. It appears here again during the Permian Explosion of Life, and author has named this larger version the Permian Protopharetra.

Protopharetra structures were built by Archaeocyathans, the first unicellular eukaryotes that lived in colonies and secreted calcium carbonate as a skeletal matrix. These organisms were filter feeders, channeling moving ocean water through the hard skeleton labyrinth, to obtains suspended nutrients.

On earth, new viruses are created by genetic reassortment of existing viruses in co-infected cells.

Similarly, the evidence presented on this website will show that new life forms on earth can be created by DNA reassortment of existing life forms, hosted in CSFF structures.

A cubic inch of coastal water contains more than 15 million suspended cells, from a large variety of life forms. CSFFs channel this water, shearing open cell membranes to release the DNA, proteins, and other intracellular contents to the feeding colony below.

In 2014, we published sectioned CSFF specimens that revealed an unintended consequence of these structures was their ability to host a ³grab bag² DNA reassortment process. This would result in creation of new life forms, such as those that spawned the age of the dinosaurs.

Combining fluid dynamics with molecular biology reveals how these structures are capable of hosting this "grab bag" DNA reassortment process. A detailed presentation of several of the CSFF structures, and a review of how they fulfill the requirements necessary for genetic reassortment, under known principles of fluid dynamics and molecular biology, are included on the website:


Based on the DNA pool available as input into the process, there would be several expected outputs of such a process. They would include new life forms that appear to be quantum leaps backward in evolution, others that appear to be quantum leaps forward in evolution, others that have duplications or redundant features, others that are clear forerunners of the dinosaurs, as well as bizarre, never before seen new life forms. We now have fossil evidence for all of these predicted life forms.

The DNA pool available for input into the process is summarized in "The Input" section of Chapter 4:


The full list of expected new life forms from such a process, given the available input DNA, is listed at the beginning of the "Output Specimens" section of Chapter 4. The actual fossil evidence of all of the new life forms predicted by the process is presented in the balance of Chapter 4.


The other huge empirical evidence that this process actually occurred are the re-speciation timelines observed after an extinction event. They are too short for evolution, but more than adequate for quantum speciation by grab bag DNA reassortment. 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 Extinction / Recovery Pulses are also consistent with two other expectations.

First, the 4 extinction pulses that occurred during the Permian period were not complete extinction events, as a small number or life forms survived the extinction. This means that "survivors" would also be present at the same time "newbies" were being created. The "survivors" were likely spawned 500 million years ago (as newbies at that time) by this grab bag DNA reassortment process and then had 250 million years of evolution under their belt before the Permian period extinction pulses came along. As such, survivor DNA could be expected to be much more complex, and it would also be available for the grab bag DNA reassortment process. This could be expected to give the Permian Explosion of Life a great boost over the Cambrian Explosion of Life, as the deck was stacked with the superior "survivor" DNA for the Permian Explosion of Life.

Second, a well populated, established ecosystem could be expected to be highly detrimental to survival of new life forms. As interesting as a new life form may be, in a well populated ecosystem it would merely be a snack for one of the numerous established predators. Basically, the steeper the extinction pulse, the steeper the recovery pulse. While the chart shows terrestrial tetrapod families, the end permian extinction event wiped out 96% of marine life. The depopulation over 4 extinction pulses, combined with a 96% marine life extinction in the last pulse, created a fairly clean slate for the survival of new life forms spawned during the last re-speciation pulse.

This final recovery pulse introduced a completely new cast of characters, ushering in the age of the dinosaurs, or life forms that had no antecedent lineage. This is what DNA reassortment does. This is something evolution / selective advantage can not do, as selective advantage deals with mature life forms that already have billions to trillions of differentiated cells. To create a new life form from a mature life form would require precise replacement of the exactly same genome in every one of the billion or trillion cells, which is a mechanistic and mathematical impossibility.

Related Note: Evidence of Impacts

We have discussed thermal activity and high energy "death by limestone fossilization" as some of the fossilization methods, however, there is also evidence of high pressure impacts. Since pressure is one of the variables in crystallization and fossilization, it needs to be considered.

Can a short, high pressure, high temperature event instantly turn calcium ions in a life form into calcium carbonate ? If so, that would also explain what appears to be the " instantly turned to limestone" phenomena observed in some of the fossils. Can it turn calcium carbonate structures built by CSFFs into a crystalline form of calcium carbonate? If so, it would explain the exquisite fossilization of the CSFF structures.

Evidence does exists for the presence of numerous impacts and high pressure events during the Permian period, and is presented below for reference. One example is the rock below.

Impact Rock 1: Small Projectile, High Velocity Impact





The major impact site on the rock is shown by the blue arrow. The rock appears to have been hit at such high velocity that it was deformed into to a bagel shape around the impact crater.

Another example is a limestone rock that appears to have been impacted by an iron containing rock. Volcanic activity can be accompanied by explosive events like this.

Rock 2: Iron rock in Limestone



Yet another example is the impactite below that comes from Permian surface soil in Northern California. The site was a deep ocean during the Permian period.

Rock 3: Large Impact or Large Tectonic Activity





The point is, short duration, extremely high pressure pulses existed during the Permian period and may possibly be involved, in whole or in part, or not at all, in the observed killing and/ or fossilization process of the life forms presented.




Chapter 2

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).

The earth formed around 4.6 Ba, with the peak of the meteoroid impacts occurring around 3.9 Ba.

The Oceans formed around 3.8 Ba.

Atmospheric oxygen began appearing around 2.5 Ba, and was close to current levels by 1.5 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.



Cyanobacteria were among the first prokaryotic cells to appear and can live in anaerobic or aerobic environments. They obtain their energy by photosynthesis, taking an electron from water and releasing oxygen as a waste product. They are believed to have created our oxygen atmosphere.

Cyanobacteria also convert carbon dioxide into carbohydrates, providing a food source, and make the enzyme nitrogenase, which fixes nitrogen into a form that can be absorbed by plants and used in the synthesis of proteins and nucleic acids.

Prokaryotic cells 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 fact the mitochondrial DNA is from several different prokaryotic cell types is also proof that DNA reassortment does happen, and the single lipid bilayer cell wall is highly indicative of a "shred and reassort " process.

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 age of the dinosaurs as well as winged air flight .



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.





Chapter 3

Quantum Speciation by Grab Bag DNA Reassortment





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 strands joined as 23 chromosomes. The notable exception is mitochondrial DNA, which is circular and resides outside of the nucleus.

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 5 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)



Photos of the external views of some of the fossilized structures built by the CSFFs are shown below:

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However, sectioned specimens are where the action is, as they provide the roadmap of how the labyrinth like structures channeled moving ocean water. Sectioned specimens of a few such specimens are show below.

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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 Protopharetra, 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.

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

While the above is a highly simplified macro level view, at a micro level, the calcium carbonate "cement like" surface would look more like sandpaper. Cells moved anywhere along the way would be sheared open, like a grape being dragged across sandpaper. The spilled intracellular contents and sheared cell walls would also be moved into the slurry chamber.

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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 Protopharetra specimens have numerous structures capable of hosting this type of DNA reassortment process. They contain at least 5 identified structures that can do this, with cyclonic based structures used extensively in their hard skeleton designs.



DNA Reassortment Structure 2: Cyclone Structure


The preferred structures used by the Permian Protopharetra class of CSFFs are cyclones, as well as advanced versions of supercharged cyclonic structures.

A good example of cyclones is found in "Mega Protopharetra", which appears to be a hybrid between a Permian Protopharetra and a Spherical CSFF. The dual cyclone structure would be able to utilize both inbound and outbound waves for a shred cycle.

A photo of the fossilized Mega Protopharetra specimen, along with an illustration, is provided below. The blue arrow highlights the area of the cyclone structures.




The photo below is a zoom of the fossilized structure, a view showing the isolated structures and water lumens, and a diagrammatic depiction of the functional cyclone structures.



While the cyclone diagram shown is smooth for simplicity, it is important to note that at a cellular level the surface would be more akin to sandpaper. Pressing and dragging a cell across a limestone surface would be akin to dragging a grape over sandpaper. The actual depiction would more like the image below:



That having been said, we will proceed with the simplified macro view in the drawings below.

A simple cyclonic structure operates when a perpendicular stream of gas or fluid (water in this case) is introduced against the walls of a cylinder. This results in a stream that spirals down the wall, centrifuging larger suspended particles against the walls. As the cyclonic structure tapers, the area is reduced and the water velocity exponentially increases (per the velocity and area equations previously discussed). As the stream reaches the bottom of the cyclone, it begins to flow upward through the center of the spiral and exits the cyclonic structure.

While a cyclone is a passive structure, the shallow ocean provides the action in a 4 stroke cycle of 1) Incoming Wave, 2) Calm Water, 3) Outgoing Wave, 4) Calm water. The combination of the 4 stroke cycle of the motion of the water (containing 1 million suspended cells per ml ) with the dual cyclone structure is depicted diagrammatically below:






A cyclone structure also fulfills the requirements for hosting a grab bag DNA reassortment process.





DNA Reassortment Structure 3: Nozzle / Cyclone Structure

UNDER CONSTRUCTION.



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

UNDER CONSTRUCTION.



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

UNDER CONSTRUCTION.





CSFFs have highly specialized structures for shredding and reassorting cells, and their appearance in the fossil record during the Cambrian Explosion of Life and Permian Explosion of Life is not likely a coincidence.

However, It should be noted that the hosting of DNA reassortment was not likely exclusive to CSFFs.

Rocks containing cavitation, when combined with the motion of waves, could also serve as genetic reassortment machines. Internal chambers, as they filled with shredded cell contents, could also serve as incubators for the new, reassorted life forms.

A review of the ability of naturally occurring geological structures, for their ability to host DNA reassortment, is currently beyond the scope of this book. However, a couple of photos of the external view of such cavitation is shown below to give an idea of the potential:

Examples of Cavitation in Rocks



Progressive sectioning reveals the complexity of multiple levels of shred surfaces as well as various internal cavitation chambers.

Progressive Sectioning of Rock with Geological Cavitation



Naturally occurring geological cavitation, combined with moving water, and functioning as shredders / reassorters, likely functioned at a much lower level to create new life forms long before the CSFFs appeared and long after they disappeared once a new ecosystem was established. Cavitation, combined with moving water, still likely functions to this day, and the creation of new life in the ocean is not likely a rarity, but the survival of a new life form to maturity in an established ecosystem would be the rarity.

The explosion of unicellular eukaryotic life 1.5 Ba, with its single lipid bilayer cell wall and mitochondrial DNA that was a reassortment of DNA from several types of bacteria (prokaryotic cells), may have been hosted in naturally occurring geological structures. Among the new life forms created were the single celled eukaryotic organisms (archaeocyathans) that built the CSFF structures, to obtain nutrients from cells suspended in moving water, with the unintended consequence of hosting genetic reassortment and a resulting "Explosion of Life".

It is now time to take a look at the empirical data (i.e. fossil record) of the new life forms spawned by this genetic reassortment process during the "Permian Explosion of Life".







Chapter 4

Fossil Record of Life Forms Spawned by DNA Reassortment





The output of the genetic reassortment reassortment process is dependent on the input available for that process. Therefore, it is essential to understand both the pre-existing unicellular life forms, as well as the multicellular extinction survivors, as both served as input into the reassortment process.

The Input

Unicellular Prokaryotic and Eukaryotic Organisms


The first, and perhaps most important, input into the process are single celled prokaryotes and eukaryotes. Unicellular prokaryotes first appeared some 3.8 Ba and the unicellular eukaryotes appeared some 1.5 Ba. In terms of biomass, they are the most prevalent life form on the planet today.





Mitochondria is a cell’s power plant that stores energy from aerobic respiration (metabolism of glucose). 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 (Alberts et. al., Molecular biology of the Cell, Third Edition 1994). 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. It takes energy to maintain concentration gradients. Without the prokaryotic mitochondrial DNA that arrived on earth some 3.8 Ba there would not be an energy source in cells and life as we know it today would not exist.

Unicellular organisms can use flagella, cilia, or pseudopods for motility. This ancient DNA 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. Pseudopod DNA likely went on to form limbs for mobility.

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 which allows atoms to exist as ions (Na+, Cl-, K+, Ca++) which in turn allows for maintenance of concentration gradients including electrochemical gradients. 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. 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.

Archaeocyathans are the first known unicellular eukaryotes that secreted calcium carbonate as a skeletal matrix ( i.e. the Calcium Secreting Filter Feeders). They first appeared some 500 million years ago and also built the hard skeleton labyrinth structures that hosted the DNA reassortment process during the Permian period. Their DNA may also have found it’s way into an osteoblast cell, which is the bone building cell in boned multicellular life forms.

Chemotaxis is the initiation of motility (activation of flagella, cilia, or pseudopods) in response to chemicals in the environment and is used by unicellular prokaryotic and eukaryotic cells to find and move toward food. 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.

The point is that a significant part of multicellular eukaryotic DNA traces back to ancient unicellular origins.

Extinction Survivors - Multicellular Eukaryotic


While 96% of marine life was wiped out in the last Permian extinction pulse, that means 4% survived and were available as input for the genetic reassortment process. While the Cambrian explosion of life had unicellular life as an input, the presence of multicellular life during the Permian explosion would have stacked the deck for a much more robust explosion of life to occur. The survivors would also stack the deck toward "their form" of life form.

Each cell from a multicellular life form contains the entire genome, or the DNA that codes for all of the cell types made by that multicellular life form. As an example, the human genome codes for more than 200 different cell types, and each cell contains the DNA for all of the different cell types. A cell from a multicellular life form can enter the ambient environment in numerous ways such as skin shedding, injury, death, excretion of body fluids, etc..., much in the same way cells are obtained for DNA evaluation in criminal cases, including contact DNA testing. Any such liberated cell can become input in the genetic reassortment process, with the entire genome being available for reassortment, or parts thereof.

Skin shedding is not a trivial contribution to the input process. An average human has around 18 square feet of skin. At a normal epidermal thickness of 200µm this translates to ~ 0.34 liters of epidermis, or roughly a half trillion cells. The epidermis is a columnar stack with one cell shedding off the top of the stack daily, and one dividing at the bottom of the column daily, to maintain stack depth. Each shed cell contains the entire human genome. In around 30 days, the average human will have shed their entire epidermis, and it is estimated that around 75% of household dust is made up of shed skin cells. If you are single, when you empty your vacuum cleaner, 75% of what you are dumping is you.

As for the fossilized survivors we have found to date, perhaps the most significant is the Lung Fish.

Arizona Permian Lung Fish



Lung fish first appeared some 400 million years ago (during the explosion of fish life) and three genera of lung fish are still alive today, one on each of three continents (Australia, South America, and Africa). Lung fish are extreme survivors. They can use their pseudopods to move on land. They use aestivation (dormancy) burrows when their pools dry up. They breathe air through their swim bladders and drop their metabolic rate. Lung fish aestivation burrows are found in the fossil record during the Devonian (~ 400 Ma), Carboniferous (~ 300 Ma ), and Permian (~ 250 Ma) periods.

Lung fish are believed to be forerunners of terrestrial tetrapods. Their lung is a modified swim bladder that can absorb oxygen and remove waste. Their 4 limbs are in the same relative position as those of terrestrial tetrapods.

Another survivor that made it into the collection is a stingray.

Fossilized Stingray - Upper Matrix Removed



Stingrays first appear in the fossil record some 450 Ma. They are cartilaginous fish with pectoral fins or "water wings" for propulsion. There are more than 200 species of stingrays alive today. Sting rays are also related to sharks, and while trace fossils of sharks date back to some 420 Ma, the majority of modern sharks trace back to around 100 Ma.

Yet another survivor that made it into the collection is the jellyfish. Jellyfish are gelatinous umbrella of bell shaped life forms that pulsate, or use contractile motion, to achieve propulsion for locomotion. Jellyfish have been in existence for at least 500 million years. Jellyfish survived the Permian period and are found worldwide today. Their fossils appear mostly as traces that are part of the limestone. As an example:

Fossilized Jellyfish





As another example, the specimen we call Blue Jelly has a internal contractile sack that is visible:

Blue Jelly





The pre-existing survivors in the collection represent only a small portion of the pre-existing multicellular DNA available for reassortment.

Fish first appeared some 500 Ma , and the Fish Explosion of Life occurred around 400 Ma. There was plenty of fish survivor DNA available for reassortment.

Reptiles first appeared around 312 Ma and their DNA lives on in lizards, crocodilians, snakes, worm lizards, and turtles. There was plenty of reptile DNA for reassortment.

We use a broader definition of "Birds" as life forms using "winged propulsion" , which extends the DNA lineage back to "water wings", such as the Stingray which first appeared around 450 Ma. "Air wings" first appeared 228 Ma in the Pterosaurs ( i.e. "wing lizard") and were formed by a membrane of skin, muscle, and tissue, which is more akin to the respective aquatic forerunner life forms contained in our fossils. This is in contrast to more conventional categorization of "birds" as life forms with feathered wings, which only appeared around 125 Ma. Based on the fossils in our collection, there was lots of "Bird" DNA available, when defined as life forms capable of "winged propulsion".

Output Specimens



The grab bag DNA reassortment process previously disclosed could be expected to generate several types of new life forms:

1) Life forms that appear to be quantum leaps backward in evolution could be expected, as primitive unicellular DNA was reassorted and recombined, in what would be virtually identical to what happened during the Cambrian Explosion of life. While these types of life forms were new 500 Ma, they would appear to be a quantum (250 million year) leap backward in evolution when viewed from a Permian perspective.

2) Biotic Hybrids and DNA Amalgamations would also be expected. Amalgamations is used in context of central DNA in a life form representing features from various life forms. DNA Amalgamation combinations such as fish / reptile life forms, bird / fish life forms, and bird / insects life forms, could be expected, as DNA from very different life forms could combine into new, viable life forms.

Biotic Hybrids is used in context of two life forms, with separate DNA, living biotically as a single organism. The primary life forms found in this category are CSFF / Soft Tissue hybrid fossils. A more contemporary example of a biotic hybrid is lichen, which is a composite organism made up of algae or cyanobacteria living among filaments of various species of fungi. Lichens have different properties from those of their component organisms.

New life forms could also be both DNA Amalgamations and Biotic Hybrids. A contemporary example of such a life form is a human. A human is an amalgamation of 46 strands of DNA, coupled as 23 pairs, contained in the nucleus of every cell. The notable exception is mitochondrial DNA, which is circular, of bacterial origin, and exists outside of the nucleus in the mitochondria, which could arguably be classified as a biotic hybrid. When you then include the thousands of different types of bacteria living in our gut and on our skin, we are unquestionably also biotic hybrids.

3) Duplicate structures, and duplicate life forms living as one, could also be expected. Redundancy is not prohibited but expected, but would only be seen in the fossil record if the resulting life form was viable.

4) Radical Amalgamations Incorporation of extremely unrelated DNA, into multicellular life forms, could also be expected. The results could radically change the direction of life on earth. As an example, the integration of CSFF DNA into soft tissue life forms could spawn the emergence of boned life forms. The integration of CSFF DNA with other life forms would be highly expected because of the proximity of CSFF DNA to the reassortment process, and hence its availability for inclusion in the reassortment process.

5) Future Life Form Forerunners could also be expected. After a mass extinction event, in the absence of established predators, the stage would be set for a new ecosystem to arise. Some of the newly created life forms could be expected to become part of the new ecosystem. Either forerunners, or the new life forms themselves, should be somewhere in the fossil record, starting from the reassortment period(s), through the subsequent re-speciation period, and possibly into the new stable ecosystem period.

6) Unrecognizable or "indeterminate" life forms would also be expected. Only a small percentage of what was generated by DNA reassortment could be expected to be viable, and even a smaller percentage would find it’s way into earth’s play book of life. Some life forms could be so different that we would not have a frame of reference to compare them to.

All of the above are actually observed in our fossils, and are presented in the sections below.



Fish and Fish / Lizard Combinations

Fish first appeared some 500 Ma, and the Fish Explosion of Life occurred around 400 Ma. Reptiles first appeared around 312 Ma. There are many normal looking fish in our collection, however we have not yet had the time or expertise to identify which of them are pre-existing survivors and which are new.

The fish presented below are the ones that are more suggestive of being the product of the genetic reassortment process. Primitive unicellular fish are less likely to be indicative of some process that resulted in a quantum leap backwards in evolution, and more likely indicative of the presence of a genetic reassortment process, likely similar to the one that drove the Cambrian explosion of life. Duplicate life forms living as one, or duplicate structures in a single life form, would also be expected under grab bag genetic reassortment. Some of these duplicate structures, such as double jawed structures, are present in life forms today and are readily expected under principles of genetic reassortment, but not expected under principles of evolution. Evolution can explain adaptive improvements in existing structures, but cannot explain the abrupt appearance of completely new structures or life forms without antecedent lineage. However, this is exactly what DNA reassortment does.

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 life forms generated by the genetic reassortment process appears to be the flagellate 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 unicellular prokaryotes.




Flagellate Unicellular giant was likely similar to something that would have been spawned during the Cambrian explosion of life, when only unicellular organisms were available for input into the genetic reassortment machines. It was motile in water and 2" long so we have included it in the fish section.

The Flagellate Unicellular giant is an example of an expected "Quantum Leap Backward" life form.

Another example of a "Quantum Leap Backward" life form is the Jawless Fish shown below:


Jawless fish first appeared in the Cambrian Period, but were believed to have gone extinct during the Devonian period ( 420 - 360 Ma). It is not surprising that fish like the Jawless Fish (or Flagellate Unicellular Giant) would go extinct, as they are defenseless, small, and instantly relegated to the bottom of the food chain when meaningful predatory fish arise. While their reappearance during the Permian quantum speciation by grab bag DNA reassortment would be expected, their tenure could also be expected to be much shorter because of the established presence of advanced predatory fish at the time.

A possibility is that the inclusion of the DNA that coded for these types of life forms, in the original prokaryotic cells that arrived some 3.8 Ba, was to provide an easy food source for emerging multicellular life forms (i.e. small, defenseless life forms would simply have been "manna of the ocean").

A slightly more advanced, yet still "Quantum Leap Backward" life form is Flagella Fish shown below, which has a side mount flagellum instead of a fish tail. At 5 inches long, it is 5,000 times larger than the unicellular eukaryotic 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. However, the two arm like paws at the front indicate the possibility of more advanced bilateral, pseudopod DNA.




An example of a "Amalgamation / Combinational Life Form" is the specimen below, that appears to have the mouth and body of a stone fish, but a contractile sack propulsion system of a jellyfish. It is not a normal fish as we know it, and as such may be a genetic reassortment product of the 2 different life forms, which resulted in a combination that was still viable.

Stone Fish Hybrid - Sectioned Specimen





Moving to the category of "Future Life Form Forerunners" by genetic reassortment is the specimen called Whaleen, which resembles a truncated Baleen Whale in existence today.




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 a fossilized 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 optic neuron is connected directly to a motility group, and the organism has no brain.


The example above is relevant because a neuron is a separate cell type. A neuron is not the product of an adaptive evolutionary improvement to an existing structure, but the introduction and integration of completely new DNA, as would be expected under genetic reassortment.

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. If the fish that existed prior to the Permian period had a brain, Whaleen would have to be the result of some yet unexplained quantum leap backward in evolution. Alternatively, it is exactly what would be expected under the "starting over after an extinction event" aspect ot genetic reassortment.

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.

The central lumen appears to have gestating progeny (preserved as blue translucent crystals). It is possible that the earliest womb was simply a sack encasing the progeny that allowed nutrients from the food lumen to reach the progeny, as well as protect the progeny from being digested. Internal birth, versus eggs that are subject to predation, is a trait that has survived to this day.

An example in the "Duplicate Structures and Duplicate Life Forms Living as One" category is Double Fish shown below. The genetic reassortment process does not necessarily have to generate a singular, clean life form. Life forms with redundant DNA, which may or may not be synergistic or even compatible, could be expected from the grab bag process. Many would not be viable, but a few could go on to maturity if the additional DNA was beneficial. Double Fish appears to be one such example. It appears to have both a pincer mouth on the exterior and a jawed mouth further back. While most specimens have either a linear central food lumen or a U-shaped lumen, Double Fish has both, indicating the possibility of two entire life forms in one.


Life forms with redundant or duplicate structures would be expected under the grab bag DNA reassortment process. The lack of boned structures likely allowed the more amorphous "body sack" to accommodate other structures, or even two life forms. The presence of both mouths directly in the food intake stream could have made two life forms viable, alternatively, the double mouth structure could also be viable in a single organism.

As an example of the latter, moray eels in existence today have a pharyngeal_jaw , or a second set of jaws, that reside in the throat. The arrangement is basically the same as that observed in Double Fish above.

The evidence of redundant structures are not unique to our fossil. An example of what appears to be a redundant upper jaw and nostril can be seen in the skull photo of Proterosuchidae which is found in the fossil record from 252 - 247 Ma. That double structure appears to add no value, and was likely more of an impediment to capturing prey, which is likely why that life form is no longer with us.

Genetic reassortment could also be expected to combine and integrate DNA from unrelated life forms ( e.g. reptiles and fish, birds and fish, birds and reptiles, etc... ) An example of a Fish / Reptile "Amalgamation / Combinational Life Form" is the Zamoyski Dragon specimen below. It has hard reptilian like skin but the body of a fish.





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.

The mouth of the Zamoyski Dragon was likely akin to the tentacled mouth of a squid, shown below:




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 pursuer’s throat, preventing swallowing and facilitating forward escape. They would be effective until a kill and chew world arose.

That segues us into the next specimen, which is part of the kill and chew world.

Another example of a Fish / Reptile "Amalgamation / Combinational Life Form" is Lizard Fish, which is similar to Zamoyski Dragon in respects, however it has a toothed jaw and head shape more akin to that of a lizard.


In addition to the toothed jaw, Lizard Fish has micro spikes on the outside of it’s skin. The small spikes on Lizard Fish are shown in the photo below, which is a zoom of the top of the head of the sectioned specimen in matrix.




It is not clear if fish got the lizard head DNA from reptiles, or if the reptiles got the lizard head DNA from fish. However, most lizards today are tetrapods which run with a strong side-to-side motion, perhaps a vestige of their combined fish / reptile DNA (i.e. the fishtail motion).

This type of toothed lizard head also appeared terrestrially 250 Ma in a class of reptiles called Pseudosuchia, which includes early lineages such as the Poposaur shown below, and later lineages such as the Crocodiles in existence today.






Another aquatic or fish / lizard "Amalgamation / Combinational Life Form" called Geckosaurus is shown below. It has the head of a dinosaur such as T-Rex and the body of an aquatic life form.






Lizard DNA is extremely important in the origins of Dinosaurs. Dinosaurs first appeared around 243 Ma, or right after the last quantum re-speciation / recovery pulse of the Permian period. The word Dinosaur itself derives from the Greek deinos "terrible" plus sauros "lizard".

Combining lizard like DNA with air breathing tetrapod DNA ushers us into a part of the roadmap leading to the rise of the Dinosaurs.



Birds



Bird like life forms, preserved as whole body limestone fossils, are fairly common in our collection. However, our initial focus will be on combinational life forms because of their significance in corroborating the genetic reassortment process.

Birds may have originated from aquatic life forms that used "water wings" for propulsion. Several of the fossils appear to be aquatic life forms that are morphologically similar to birds, with the major exception that they did not have feathers but skin more suited for the ocean.

One such example is Aqua Duck, which is morphologically similar to a duck, except without the feathers and extensive wing structure necessary for propulsion through air. However, the propulsion structure would be more than adequate for propulsion through water.


Genetic reassortment could also be expected to generate hybrid fish / bird life forms, in a manner similar to the fish / lizard combinations discussed in the previous section.

An example of such a fish / bird "Amalgamation / Combinational Life Form" (or fish / insect combination) is the aquatic life form called Birdsquito, which has the head of a bird and the body of a fish. A close up of the beak from both sides is shown below and reveals one side has serrations in the beak (Side B - Headshot Zoom) or possibly a filter feeding beak.




Another example is an aquatic life form that looks like a mix between a Seahorse and a Bird. The vestiges of a long arm like "water wing" flipper run vertically down the center of the life form. The head and beak are similar to those of aquatic birds.




The bird specimens above were presented because of their significance in corroborating the genetic reassortment process. However, just like with the fish, there are also a larger amount of "normal' bird fossil specimens. We have included some of them below because of their significance in providing insight into the nascent development of an ecosystem.

Out of the chaos of a grab bag genetic reassortment world, ecosystems appear to arise among the new life forms. One example appears to be the biotic relationship between birds and worms.

The photo below shows some of the more normal aquatic birds, still encased in their matrix, and which are pending further processing. Their general morphology can even be seen in the surrounding matrix.

Removing the matrix from the upper part of a longer necked coastal bird specimen shows the crystallization is so good that it reveals external features such as the eye and beak of the life form. The bird appears to be more akin to a "normal" bird, rather than combinational life form.

External View of Long Neck Bird Head and Neck

Sectioning another specimen also reveals a more normal "bird only" life form we call Short Beak Bird. It should be noted that this specimen appears to have the integrated CSFF DNA in both the head area and wing area, similar to the Pteranodon Pelican specimen, which is presented and discussed at the end of this section.

Sectioned Small Coastal Bird



Birds are often found near fossilized eggs. Cutting one of the eggs open reveals an internal developing infant bird. It should be noted that the egg has a cementing layer attaching it to the limestone substrate.

Sectioned Fossilized Egg Cemented to Substrate



The cementing may have been done to keep the egg from being washed away. Flamingos today still use elevated mud nests to protect their young for rising and falling water levels.

However, it may also have been done to protect the egg from being eaten by the mud worms that lived below. Larger eggs in particular appear to have extensive worm burrow activity below. We have recently found a fairly intact specimen of one such egg eater worm, Mud Worm 2, which is shown below.

Mud Worm 2: "Permian Graboid" Below the Eggs



The subterranean worms that lived in those burrows are covered later in the Worms and Insect Section of this chapter.

It appears some birds also ate infant and juvenile worms. The sectioned specimen we call WormEater Bird appears to have linear worm-like life forms and segments in it’s stomach.



Worm-Eating Bird



Birds eventually went on to master flight and moved their eggs to nests in trees and nests on hard stone cliffs, where the "Permian Graboid" type worms could not reach them.

Birds like today’s Robin still seek out and eat earthworms.

The 250 Ma bird forerunners presented above were likely aquatic or coastal, and likely had "water wings" and not "air wings". "Air wings" would require boned structures, which leads us the the next specimen and the rise of the the Pterosaur / Pteranodon lineage.

In the more interesting world of DNA reassortment and creation of new life forms, the specimen below is a double whammy, in that it falls into two predicted categories: the "Radical Amalgamations" and "Future Life Form Forerunners" categories. The result is the rise of the Pterosaurs and winged flight.

"Air wings" did not appear until around 228 Ma with the Pterosaurs . Pterosaur wings were not feathered but formed by a membrane of skin, muscle, and other tissues that stretched from a simple rod like bone structure at the leading edge and were attached at the rear to the ankles. Pterosaurs lived from 228 Ma to 66 Ma and have an extensive lineage that includes the Pteranodon shown below.




While DNA from different types of life forms seems to readily integrate into viable new life forms, the most significant integration was the integration of CSFF DNA with soft tissue, which was likely the beginning of boned life forms. The DNA for bone building cells may have come from of unicellular eukaryotes collectively known as Calcium Secreting Filter Feeders (CSFFs), previously covered for their role in hosting the grab bag genetic reassortment process. Archaeocyathans are the first known CSFFs, appeared some 500 million year ago, and were the first unicellular eukaryotes that lived in colonies and secreted calcium carbonate as skeletal material.

The specimen we call Pteranodon Pelican displays what appears to be two integrations of CSFF DNA, one in the head that likely went on to become a beak and skull, and one in the wing area that likely went on to become the rigid boned wing structure required for airborne flight.




The CSFF structures appear to follow the linear growth pattern observed in many of the stand alone CSFF structures previously presented. In the absence of growth control pathways ( aka. population density management pathways, aka. cell division cycle control pathways) growth of newly integrated cells could be expected to only be limited by available nutrients. Growth control pathways are extremely complex and interconnected and could not reasonably be expected to be established in such early life forms. Accordingly, projecting the growth of the newly integrated CSFF (or bone) structures, in the absence of growth control pathways, is shown below:




The Pteranodon’s exaggerated beak growth forward and head growth backward, and extended wing bone growth outward, are consistent with the projected linear growth pattern of the integrated CSFF DNA in the Pteranodon Pelican specimen.

The Pterosaur wing membrane was likely more akin to the "water wings" that first appeared in aquatic life forms like the Stingray 450 Ma. The simple bone structure of the Pterosaurs could be consistent with ~ 25 million years of integration and progression of CSFF structures outward, first observed in the wing and head structures of the 250 Ma bird forerunner specimen called Pteranodon Pelican. The first version of wing bone could have been a simple un-jointed rod like structure with stretched skin attached, allowing for "glider" like flight on ocean breezes, similar to the Flying Fish in existence today. I our collection, the first appearance of two CSFF structures serving as "jointed bones", is observed in a specimen called Brainiac Worm, which is covered in the Worms and Insects section of this chapter.

The importance of bone in the advancement of life goes well beyond just it’s role in skeletal function or allowing for air flight.

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.

The point being, the introduction of bone into the contained aqueous environment, is an extremely significant advancement in life. The propagation of the calcium wave in the brain is a requisite condition for consciousness and memory formation, as will be discussed extensively later.



Pre-Dinosaur DNA

Dinosaurs are a diverse group of reptiles that first appear in the fossil record right after the last Permian recovery (i.e. quantum speciation) pulse. Their features are consistent with the DNA available for that last Permian recovery pulse, as will be covered in this section. The specimens in this section fall into the DNA reassortment prediction of " Future Life Form Forerunners".

One of the first dinosaurs to appear was a marine reptile called Pistosauroidea, which first appeared between 252 to 247 Ma. Pistosauroidea went on to spawn a long lineage, including the Plesiosaur, which first appeared around 203 Ma. Plesiosaur became common during the Jurassic Period ( 201 Ma to 145 Ma) and eventually went extinct around 66 Ma during the Cretaceous - Tertiary extinction event. Plesiosaurs were air breathers that bore live young. An illustration of a Pistosauroidea is provided for reference below, as our fossil collection includes forerunners of the Pistosauroidea, and hence forerunners of the Plesiosaurs.

Pistosauroidea - Forerunner of Plesiosaurs



Our fossil collection includes 2 specimens that appear to be forerunners of the Pistosauroidea / Plesiosauria dinosaurs.

The first is a sectioned specimen of what appear to be two infants, preserved as the bluish translucent crystals previously discussed. The infant on the right provides a better view of what the life form looked like.

Pistosauroidea / Plesiosauria Forerunners (1 of 2)



The second specimen is the external view (with matrix removed) of a juvenile. The juvenile appears to have died as the result of being chomped by something, as the right front side of the life form (left side of the picture) is flattened and a somewhat circular jaw impression is visible starting at just below the head and extending halfway down the body.

Pistosauroidea / Plesiosauria Forerunners (2 of 2)



As for the forerunners of the Pistosaurs, there are two specimens in our collection that appear as potential candidates. Just as DNA reassortment can result in life forms like Double Fish previously reviewed, the integration of two bi-finned life forms, could result in a tetra-fin life form such as the Pistosaur.

The front end of Pistosaur would be consistent with a specimen we call Dino-Seal.



The nose would suggest Dino-Seal was an air breather like the Pistosaurs.

Dino-Seal appears to have an olfactory (chemotaxis) neuron, in addition to an optic (phototactic) neuron, as well an unidentified neuron. All three appear to be connected to a different motility group. There is no evidence of a brain.

In the absence of a brain, it is unclear how the life form would react in situations where there was a conflict among the three neurons. 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 and the olfactory neuron would likely only be active when the animal was above the surface of the water and breathing. This would preclude any potential for underwater conflicts with the other two neurons.

In context of an air breather, 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.

Dino-Seal only had two fins. If a DNA reassortment resulted in a duplication (akin to double fish), where a second set of fin DNA was appended to the back of Dino-Seal, this could yield a tetra-fin life form variant of Dino-Seal. The DNA for the rear fins would not even have to be related to Dino-Seal, and actually it appears to be morphologically more similar to that of the Stingray. A photograph of the Stingray rear is juxtaposed next to the Pistosaur Forerunner photo to illustrate the point:



A DNA reassortment that creates a life form that has Dino-Seal as it’s front and a Stingray’s rear is just one of the possible reassortments that could result in the Pistosaur Forerunner.

Our collection also includes specimens that document the presence of DNA that codes for several features suited for migration to land. Claw-Paw dragon is a specimen where a claw or paw suited for terrestrial mobility is clearly visible:



Sectioning Claw-Paw dragon also reveals a couple of other pre-terrestrial features. First, the blowhole for air breathing is not behind the top of the head, but is shifted to above the mouth, and is more akin to a nostril than a blowhole. Second, there appears to be an esophagus like tube leading from the mouth to the food lumen.





There are also two specimens found with the Pistosauroidea that appear to be early tetrapod forerunners, possibly DNA reassembled versions of the Pistosauroidea, however also possibly of unrelated origin. The first is once again a sectioned specimen of an infant preserved in the bluish translucent crystal type of fossilization. We have named it Tetrapod Plesi, as it was part of the same stone from which the Pisto / Plesi forerunners were sectioned.

Tetrapod Infant Found with Pistosauroidea



The second Tetrapod Plesi specimen appears to be a juvenile and is still in matrix pending processing (shown below, in matrix):

Tetrapod Juvenile in Matrix (Pending Processing)



UNDER CONSTRUCTION.





Worms and Insects



The fossilized specimens of worms and insects in the collection are typically 6 inches or more in length. However, in the absence of established growth control pathways, the size of adults would only be limited by availability of nutrients.

Worms



Starting with the worms, we previously mentioned how there are numerous eggs in the collection:



And under some of the larger eggs is fossilized evidence of extensive worm burrow activity:



We have finally found a fairly intact specimen of the subterranean worm that lived in those burrows and presumably ate the eggs. We have named the specimen the "Permian Graboid", the term Graboid being coined in the movie "Tremors" which featured a similar prehistoric life form.

Subterranean Egg Eater Worm



The Permian Graboid appears to have a set of lower and upper mandibles.

The lower mandibles appear to be horizontally oriented pincers similar to those one may see on a bull ant, stag beetle, or cheiracanthium punctorium spider. Horizontal insect pincers are typically used to grasp, crush, or cut food.

The upper mandibles of the subterranean worm are vertically oriented with a right angle bend, possibly jointed, and similar to a claw hammer or angled fangs. Spiders have fangs, first appeared 386 Ma, with upgraded versions appearing 318 - 299 Ma, so the DNA for both the lower and upper mandibles was available at the time of reassortment. Some species of mantis shrimp, which first appeared 340 Ma, have similar jointed structures they swing upwards to break shells. The claw hammer of the worm would likely have been pulled down, instead of swung up. An illustration of what the mandibles look like based on the newly discovered Egg Eater Worm:

One possibility is that the Permian Graboid’s lower pincers were used to push through the shell and hold on to the egg, while the upper claw hammers or jointed fangs were used to punch a hole in the egg shell and then pull the contents of the egg into the Graboid’s mouth.

One of the original 35 fossils was a worm that had a chitin like exoskeleton, but was missing the mouth. The illustrator took some artistic license to create a mouth, which we now know is uncannily close to reality. It appears the first "Mud Worm" specimen, or Mud Worm 1, was effectively an armored graboid.



A zoom of the tail show a better view of the exoskeleton.



Worms today are generally soft bodied and insects are characterized by a chitinous exoskeleton. In a DNA reassortment world, traits are readily shared between unrelated life forms via the DNA reassortment process, and categorizing life forms by today's standards is not always possible.

The most significant worm discovered is "Brainiac Worm", which has 3 separate integrations of CSFF DNA, one in the head forming a skull and two in the tail functioning as a "jointed" limb. The life form was effectively a head, pushed along by an attached jointed finger.

An illustration and sectioned specimen photo of Brainiac Worm, with a zoom of the tail is shown below:



The zoom of the sectioned tail shows an "unknown separator" between the two CSFF DNA structures, allowing for jointed motion, or "mobility" versus just "motility". The arch of the tail would not be possible without the ability of the two hard masses to slide past each other, which is what the unknown separator appears to allow.

What generated the separator (e.g. the soft tissue life form, or the CSFF structure(s), or something else) is not known at this time. What is know is that this is the first reassortment specimen in which we have observed "jointed bones" .

Insects



The insects that are part of the fossil collection are not like insects as we know them today. Much like the fish / lizard combinations the winged insects are more akin to insect / bird combinations. They are also much larger than today, typically 6 inches (25 cm) or longer in length. Some have a venom sack in the rear with the injection needle pointed upwards and to the back, indicative of a more defensive mechanism against being eaten, rather than the more offensive / defensive bottom mounted, forward facing stingers in use today.

The first specimen is called Hornet Hawk and appears to have a head closer in appearance to that of a hawk, with a body more closely resembling a hornet, with the notable exception the stinger is pointed upward, rather than downward.

Insect / Bird Combinations - Hornet Hawk



The second specimen appears to be a bee / bird combination because of the CSFF integration in the wing. Bees have membrane wings without bones:



CSFF integration with soft tissue has been observed as a "bone forerunner" in bird wings, such as the Pterosaurs previously examined.



The bee forerunner appears it may have a venom sack and upward stinger (see sectioned specimen photo), similar to that of Hornet Hawk. The mouth of the specimen ( see external view photo) appears to be neither bird nor insect, but more akin to lizard or fish.

UNDER CONSTRUCTION.



CSFF Hybrids



Life on earth starts with a single cell. All that cell needs is a nutrient rich environment (egg, womb, petri dish, etc...) and it will relentlessly grow and divide to become the life form coded for by its DNA. At a point in its maturity, it will be able to leave that nutrient rich environment and actively pursue food in the surrounding environment.

It appears the CSFFs may also have provided a nutrient rich environment, in and around the CSFF, for newly created cells to thrive in, somewhat akin to a petri dish. It also appears some of the newly created cells never left.

While the fossils presented so far are single organisms that posses the DNA and features of multiple organisms, the fossil specimens in this section are "Biotic Hybrids", and more specifically CSFF / Soft Tissue biotic Hybrids. A hybrid is a thing made by combining two elements. In this case, the underlying organism is a CSFF and the other organism resides on or in the CSFF.

Since CSFFs shred suspended cells, they are repositories of readily available nutrients. It is not surprising that soft bodied organisms would establish residence on or in CSFFs, either for structural attachment purposes or because of the proximity to nutrients. These relations can be symbiotic or parasitic.

The first example is a CSFF / Soft Tissue hybrid that appears to be a small carnivorous CSFF. The top part of the CSFF has a pincer like mouth that may have the ability to actively capture multicellular life forms, rather than just filtering feeding of single celled organisms.

CSFF Hybrid 1: Pincered CSFF



The second example is a larger, more pincered CSFF that starts looking more like a Venus flytrap. A Venus flytrap has hinged leaves that spring shut to capture insets that land on them.

CSFF Hybrid 2: More Advanced Pincered CSFF



While the first two CSFF Biotic Hybrids may have been symbiotic, the next ones seem to be more parasitic and detrimental to the survival of the CSFF colony. CSFF Hybrid 3 appears to be a CSFF encased by a surrounding coat of cells, that would prevent water from entering the CSFF and allowing it to filter feed.

CSFF Hybrid 3: Encased CSFF



While all of the above CSFF Hybrids have the soft tissue on the outside, CSFF Hybrid 4 has a soft tissue life form on the inside. While the soft tissue life form benefits from the nutrients on the inside, it also prevent the CSFF from being able to filter feed. The illustration shows the eventual predicted demise of the CSFF, as the soft tissue life form within the CSFF continues to grow.

CSFF Hybrid 4: Internal Parasite







Indeterminate Life Forms


The Indeterminate life forms are the second largest group of fossils found, just behind the CSFF fossil group.

Previous sections have shown life forms that were fish / lizard, or bird/ fish, or insect / bird DNA combinations, as well as integration of CSFF DNA with a variety of life forms. All of these life forms could be categorized in the frame of reference of known or existing life forms.

The fossils presented in this section have no such frame of reference.

However, they are exactly consistent with what a grab bag DNA reassortment process would be expected to create. They represent "one off" creations and other life forms that never made it into earth's play book of life.

UNDER CONSTRUCTION.









Chapter 5

Life Science Implications of the Specimens

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



Physiological Life

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 fluid. Colonies of single celled organisms have the ability of form a protective outer layer of cells around the colony. Skin may have originated from this DNA.

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))

where:
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 Formation

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.



Summary and Conclusions

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UNDER CONSTRUCTION.

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