Welcome to PaleoLife.info


IMPORTANT COPYRIGHT NOTICE: Copyright İ 2014 Mark J. Zamoyski. All rights reserved. No part of this website may be reproduced, scanned, stored, introduced into a retrieval system, or distributed in any printed or electronic form.

This website is always under construction and new material is posted on an ongoing basis. The below are excerpts from the book “On the Origin of Life and Biodiversity” which is now available on CreaeSpace.com and Amazon.com

Overview

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

Site Index



Preamble: Paleo Geology of the Site

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

USGS Surface Soil Map of Arizona



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

Permian Extinction / Recovery Pulses


Millions of Years Ago (Ma)

The Permian period is often referred to as "The Great Dying" but could equally well be called "The Great Rebirth". The reasonable inference is that these life forms from Arizona were part of a recovery pulse, and were killed and fossilized by a subsequent extinction event.


Section 1: A Brief History of Life on Earth


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

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



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

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

2) 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 cellıs 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 suspectıs 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?”.

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



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

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

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

That is the question that these Permian fossils finally answer.



The Origin of Multicellular Life: The Great DNA Heist


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

Sectioning reveals the life forms range from unicellular giants to life forms made up of only a few specialized cell types (humans are made up of more than 210 specialized cell types). These early multicellular life forms appear closer to unicellular protists, as they have no bones or circulatory system, and only a few specialized cell types. However, they are morphologically similar to known, more advanced life forms.

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

These observable features include 1) Motility, 2) Skin, 3) Bone, 4) Vision 5) Smell, 6) Reproduction, 7) Pre-Terrestrial and Pre-Triassic/Jurassic features.

1) Motility


Unicellular organisms can use flagella, cilia, or pseudopods for motility.

Flagella and cilia are structurally identical in eukaryotic cells. In humans, the sperm cell uses a flagellum to propel itself. Cilia drive the movement of the mucus blanket that sweeps dirt out of the lungs. Beating of cilia in the fallopian tubes moves the egg from the ovary to the uterus.

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



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



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




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




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




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




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



Pseudopod DNA (e.g. paws, claws) also appears in these transitional specimens and examples are presented in the Pre-Terrestrial and Pre-Triassic/Jurassic features sub-section and in the Life Forms That Never Made it Into Earth’s Playbook of Life section. An example from the Pre-Terrestrial and Pre-Triassic/Jurassic features sub-section is shown below:





2) Skin

Unicellular organisms have cell signaling capability in colony situations that causes the outermost cells to differentiate and form a hardened protective outer layer.

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

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

On an atomic level, physiological life can be defined as a collection of concentration gradients. The presence of concentration gradients means life. The absence of concentration gradients means death.

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

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

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










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




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

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




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




3) Bone

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

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

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

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

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

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

The point being, the integration of bone with soft tissue, is a significant advancement in life forms.

The DNA for bone building cells may have come from a class of unicellular eukaryotes that are collectively known as Calcium Secreting Filter Feeders (CSFFs). Archaeocyathans are the first known CSFF, appeared some 500 million year ago, and were the first unicellular eukaryotes that lived in colonies and secreted calcium carbonate as skeletal material. CSFF structures use moving ocean water to create accelerated, turbulent streams inside a hard skeleton labyrinth. The purpose apparently was to shear membranes of suspended cells to obtain intracellular nutrients. An unintended consequence appears to be their ability to host the genetic reassortment process capable of creating unimaginably biodiverse new life forms. Several Permian CSFF structures are evaluated in Section 3 for their ability to host Hyper-Evolution by this grab bag DNA reassortment process.

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




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




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




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




REMAINDER OF SECTION UNDER CONSTRUCTION. MORE TO COME SOON.


4) Vision (Phototaxis)

UNDER CONSTRUCTION.

5) Smell (Chemotaxis)

UNDER CONSTRUCTION.

6) Reproduction

UNDER CONSTRUCTION.

7) Pre Terrestrial and pre Triassic/Jurassic Features

UNDER CONSTRUCTION.


Section 3: The Perpetrators of the Heist

UNDER CONSTRUCTION.

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.

Cell Walls

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




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




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

DNA and DNA Expression

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




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

DNA Efficiency

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

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

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

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

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

The genomic efficiency of ancient prokaryotic cells (from “On the Origin of Life and Biodiversity”, İ 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.

Review of 4 CSFF Structures - Did they have the means?

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 structure.

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.

Fluid Dynamics

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

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

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

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

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




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

REMAINDER OF SECTION UNDER CONSTRUCTION. MORE TO COME SOON.


Section 4: The Fate of the Perpetrators

UNDER CONSTRUCTION.

Section 5: Life Forms that Never Made it into Earth’s Playbook of Life

UNDER CONSTRUCTION.

Section 6: Summary and Conclusions

UNDER CONSTRUCTION.

The book “On the Origin of Life and Biodiversity” contains the complete collection of the 35 sectioned life forms that document the transition from unicellular to multicellular life and is available from CreaeSpace.com and Amazon.com

IMPORTANT COPYRIGHT NOTICE: Copyright İ 2014 Mark J. Zamoyski. All rights reserved. No part of this website may be reproduced, scanned, stored, introduced into a retrieval system, or distributed in any printed or electronic form.