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6.1- http://mbscientific.org/wiki/Cells_to_Reptiles

ch6.1- Biotic Morphogenesis - single cells to Reptiles, a pictorial family album (fossil record, comparative anatomy and the tree of life)

We covered the genetic structure and discussed how we can quantitatively determine the relationship between species, or individuals for that matter, by comparing their genetic sequence or the protein structures that the genes produce. But that is a relatively recent tool and it can't apply to fossilized, extinct species. There are other tools for studying biotic morphogenesis. The fossil record is the indicator of what species were present in geological time. Comparative anatomy gives us structural relationships between different species and structural nature of evolving morphologies. If you put all of these tools together, you can assemble the tree of life as we know it today.

We are interested in where we came from. So, we are going to follow the tree of life as expressed in the geological record (according to the current body of knowledge) from the single cells until it gets to us pictorially. When you look at a branching of the tree, don't consider it as a single bifurcation point. Rather, consider it as an emergent collective from the progenitor collective. Assembling the tree of life is art as well as science. It is a matter of putting together a giant puzzle piece by piece. And, often a brand new piece is discovered, causing the reshuffling of the puzzle.

We divide the geologic time into Eras, Periods and Epochs. We have Archean (4500 -2500 million years ago), where single cells and single cell colonies are created, Proterozoic (2500-543), where basic shape designs begin to emerge, Paleozoic (543-250), when aquatic life flourishes, Mesozoic (250-65), "the Age of Reptiles", and Cenozoic (65 million years ago to present) The "Age of Mammals".

So let's start at the beginning. The oldest rocks are around 3.8 billion years old. The oldest fossils appear in the same time period. The colonies of single cell archaea used chemo-synthesis to convert chemical energy into biologically useful energy. For more than a billion years they mutated, exchanged DNA and came up with new strains. One such strain was able to successfully integrate chloroplasts into their bodies and started to generate energy from sunlight, producing oxygen as a byproduct. Oxygen turned out to be toxic to many of the anaerobic archaea.

Therefore the chlorophilic bacteria were able to displace the archaea and began to dominate. In turn by 2.5 billion years ago they began to produce an increasingly oxygen rich atmosphere. These bacteria went on to evolve into the plants in the tree of life. In this time frame we see another cellular design. Some cells successfully integrated mitochondria into their bodies, giving them the ability to take organic material and other cells into their bodies, and using oxygen, break them down and process them as food, they could eat. These formed the fungi, proteist and animal branches on the tree of life. We will follow the branching of the animals until it gets to us humans.
Within animal cells we see the familiar types of functions: replication functions, metabolic-energy functions, structural functions, sensory/signaling functions and motion. Evolutionary creation is merely the process of magnification of these functions. In the animal cells motion becomes a particularly important factor in creating morphologies. Cellular motion can be produced by flagellar motion, i.e. by turning of flagellum, and constricting motion performed by constriction of molecules like myelin.

Early cells formed undifferentiated clumps, we see something similar to that in today's bacterial mats and stromatolites. The first cell differentiation becomes evident in the fossil record by 600 million years ago (pre-cambrian, Proterozoic). Sponges are one of the simplest life forms that show cellular differentiation. Cellular differentiation devides the functions of the cells into three specialized functional groups, the structural cells, flagellar cells and amoebacites. The flagelar cells churn the water through the body of the sponge. This motion increases the rate of exposure of the animal to the food supply. So compared to the cellular clump animal, it has a higher intake rate, resulting in a higher growth and reproduction rate. So it can be relatively more abundant and more successful.

As seen above, you basically have 3 types of cells. The structural cells make up the walls that happen to have hollow chambers through which water can circulate. You have the cells with rotating flagellum that churn, forcing water from outside in. And, you have the amoebocytes that are the digestive engines of the sponge. Presumably the digestive cells nourish the other cells in the process. Thus the morphological design achieves a valid state.

Inside the gut there are flagella that circulate the water locally. Incidentally, in these animals, the first nerve cells, eye cells, orientation cells and chemo-receptor cells appear.

Yet another motion based design that we see in this period is that of worm-like creatures such as annelids (segmented worms, giving rise to centipedes, millipedes and earthworks) and flatworms. Cambrian flatworms had a digestive design like the cnydaria, i.e. the mouth and the stomach are in the middle of the body, a design that leads to cephalopods (nautilus, squid, octopus, we won't follow them neither).

The worm design has a directional body (below, nematode annelid) with the mouth on one end, the digestive tract in the middle and the rectum at the other end (remind you of someone?). This is the branch that we'll follow here, since it'll lead to us.

One design variation of the annelid segmented body leads to arthropods (Cambrian era, leading to crustaceans and insects), where segments are few and pronounced and leg and antenna appendages are attached to the segments (we won't follow that branch).

The branch we want to follow are the Cordata.

By the way the same enervation occurs in arthropods as well, except the nerves run along the ventral (bottom) side of the animal. In both cases the sensory and peripheral nerves interconnect at the head of the animal and form ganglia, the beginning of the brain and the central nervous system. Chordates go on to lead to fishes, we'll follow that branch.

The next pronounced modification on the chordate design happens with the introduction of cartilaginous casing of the brain, the beginning of the cranium as seen in hagfishes (right) and others in the animal group craniata, that leads to us. Next design modification leads to the expression of protective sheathing of the nerve chord of the chordates, the beginning of vertebrates. We see this in cartilaginous fishes of the Ordovician period.

Jawles fish- Ordovician (related Hagfish)

By the Devonian era we see the fish design radiating in a variety of directions (below). The next design changes that inches towards us are the expressions of bones instead of cartilage in the fished of that time. The vertebrate branch of the tree becomes entrenched.

Here you see two designs, jawless fish and armored fishes; we won't follow either of those branches.

We'll follow fish design changes that lead to Tetrapods (amphibians, reptiles and on).
The next design change that brings about the amphibians and moves the show of life towards us requires two evolutionary steps. The first was the evolution of ray fins to lobed fins in Sarcopterygians (Lobe-Fin Fishes).

The other is the evolution of fish air sacs to lungs, as in the lungfish as the figures below demonstrate:

Here are two transitional animals:

Dipterus, a Middle Devonian lungfish, and

Ichthyostega, late Devonian, an early tetrapod.

The animals that inherited both of these evolutionary traits were the amphibians and they appeared on land by the Mississippian era.

Through the Pennsylvanian period reptiles evolved from amphibians and established  a niche on land, mainly by the virtue of evolving pronounced limbs (Sarcopterygian lobed-fin fish, amphibian and reptile, below).

In the Pennsylvanian era Cotylosaurs, the stem species of all reptiles appears. During the Permian era, reptiles called Thecondonts appear and lead to establish the dinosaurs and birds.

We won't follow those branches. But in the same Permian era reptiles called Synapsids appears. Synapsids lead to the establishment of  mammals, as we will see in the next section of our big family album.

Chapter Key: Morphological Flows, entities going through functional constructs thereby creating more complex entities with more complex functionalities - See Chapter 6.2, tree of life synopsis.