9.V: From Amoebas to Amniotes

This armored fish or placoderm, one of the earliest animals with a face, may have been our ancestor about 400 million years ago.

A. Overview

B.  Multicellularity and Animals

C.  Animal Cells, Tissues, and Organs

D.  The Vertebrate Body Plan

E.  Tetrapods:  From Sea to Land

F.  Consciousness, Communication, Cooperation, and Competition

G.  Citations

A. Overview

The oldest and deepest division of life was the diversification into three domains of cell structure:  bacteria, archaea, and eukaryotes.  As we’ve seen, our ancestors were first bacteria and archaea, which then co-evolved into the domain of eukaryotes.  As this book progresses, we will take note of the key evolutionary events that led to our kingdom, then phylum, and so on until we arrive at our species.  In fact, modern biologists have added several sub-layers to the Linnaean scheme.  The table below summarizes the major evolutionary breakthroughs in our heritage over the last few billion years.  Early dates are not known very precisely, so they are rounded roughly.  See the special human ancestor image gallery at the end of the chapter to see an illustration of each phase of evolution.

Linnaean Level Human Form Basal Example Evolutionary Breakthroughs Time
Domain Eukaryote Amoeba Cells with nuclei, organelles, chromosomes 2 BYA
Kingdom Animal Sponge Multicellularity 800 MYA? 1
Subkingdom Metazoa Comb jelly Tissues, mouth 800 MYA?
Superphylum Deuterostome Sea cucumber “Through gut” and body cavities. Respiratory / Circulatory system. 700 MYA? 2
Phylum Chordate Lancelet 3 Bilateral symmetry, three layers of tissue.  Spinal cord. Glands. Pharyngeal arches. 600 MYA 4
Subphylum Vertebrate Lamprey Vertebral column, teeth, eyes, brain, two-chambered heart, viscera. 500 MYA
Infraphylum Gnathostome 5 Fish Jaw, paired appendages, inner ear, internal fertilization. 400 MYA
Superclass Tetrapod Amphibian Bony skeleton with four limbs suitable for walking. Neck.  Lungs, three-chambered heart. 400 MYA
(Unlabeled clade) Amniote Reptile Amniotic sac. Loss of larval stage. Middle ear. Fully land-based. 300 MYA

B. Multicellularity and Animals

The table shows that once again the most fundamental traits took longest to evolve.  After waiting two billion years for eukaryotic cells to appear, it took them another billion years to come together into multicellular plants and animals.  The first step was the formation of cell colonies.  As cells reproduce, they tend to cluster together to form biofilms like algae or slime mold.  It is even common for several different types of cell to live within the same biofilm.  Living in numbers can help a colony survive, especially when the cells reproduce sexually.  Aside from sex, though, each cell within a colony performs its own vital life functions like eating and breathing.  The very gradual transition from cell colony to body involved three related breakthroughs: connectivity, communication, and specialization.

The most obvious breakthrough was cell connectivity.  A body is not just a bunch of cells.  It’s a bunch of cells held together.  Cells can attach to each other with junctions in their cell membranes.  They can also secrete proteins or minerals to form an extracellular matrix, which can be anything from a soft tissue to a shell that holds the cells together in a particular shape.

Cells within a colony evolved techniques for communicating with each other.  Intercellular communication can involve contact or chemicals.  Cells can signal their neighbors to activate or deactivate genes, make proteins, divide, stop dividing, or even to die.  As an embryo grows, the very shape of its body is determined by allowing cells to live in the right places and to die when they are out of place.

To maximize the benefits of colonial life, cells within a colony evolved distinct specialties.  The first and most basic form of cell specialization was between those that reproduce sexually and those that reproduce asexually.  Cells that divided asexually remained the majority and became body cells.  The cells that underwent meiosis became germ cells, and developed in distinct places within the colony / body.

By 600 – 800 million years ago, cell colonies had achieved the requirements for being considered true multicellular organisms:  fungi, animals, and plants.  Our earliest animal ancestor was the lowly sponge.  For the record, there are a suite of traits that define the animal kingdom distinctly from plants or fungi.  Only animal cells lack cell walls and produce a vital protein called collagen in the extracellular matrix. 6  Animals ingest other living things and move during some or all of their life cycle (yes, even sponges swim freely when they are larvae!)

C. Animal Cells, Tissues, and Organs

Sponges are organized at the cellular level.  If you cut out a tiny sample of a sponge, you will find about six or eight types of cell interlaced with each other.  That same pattern is repeated throughout the sponge’s entire body.  Essentially, the tiny sample is a miniaturized version of the whole organism.  You know that is not true of a person.  If someone extracted a sample from your finger, it would not look like a small copy of yourself.  Animals have evolved large-scale structure.  This includes a proliferation of cell types; humans have about 200.  More significantly, those cells are now organized into larger units called tissues.

There are four major classes of animal tissue.  Muscles are made of muscle tissue, and nerves are made of nervous tissue.  Epithelial tissue forms surfaces such as the outer skin and the lining of the gut.  Epithelial tissue can fold or branch to form glands.  Connective tissue includes the collagen extracellular matrix that holds the body together.  It is a framework that supports the epithelial layers.  Muscles and nerves are embedded within the connective tissue. 7

These four classes of tissue all evolved in the next wave of animals, metazoa.  Some basal metazoans were corals, sea anemones, and jellyfish.  Structurally, they had a mouth but an incomplete digestive tract.  Food and oxygen were essentially absorbed directly into the cells, and waste was expelled through the mouth!

The trend of cell specialization continued, allowing for increased complexity and efficiency.  Early deuterostomes (like sea cucumbers) possessed body cavities and a through gut, with a mouth on one end and an anus on the other.  This provided obvious advantages making it easier to eat!  Deuterostomes also developed the first true organs.  An organ is a specialized combination of different tissues, which work together to perform a specific bodily function.  For example, sea cucumbers have a set of tube feet for movement.  Blood and vessels evolved at this stage, providing a much more reliable way to carry food and oxygen to all cells.  Some portions of the blood vessels were lined with muscle tissue to enable circulation of blood; this was a form of proto-heart.  The gut started to form specialized passageways such as the esophagus, stomach, and intestine.

D. The Vertebrate Body Plan

By 500 – 600 MYA, animals had speciated into 20 or 30 body plans, or phyla.  Body plans are defined by symmetry, layers of epithelial tissue, body cavities, and unique body parts.  Chordata is the phylum of most interest to us, because we are chordates.

Our symmetry is bilateral, meaning that chordate bodies are comprised of two mirror images, the left and right halves.  The mouth end is differentiated from the anus end, and the belly is differentiated from the back.  Chordates have three layers of epithelial tissue.  The innermost layer forms the gut, the single tube from mouth to anus.  The outermost layer is the skin.  Between them, the middle epithelial layer forms internal body cavities, which support organs.

Chordates are also distinguished by five particular body parts, which might strike you as random and surprising.  We have a hollow spinal cord down the back.  The spinal cord is accompanied by a notochord made of cartilage, a semi-rigid connective tissue.  Chordates all share an endostyle, effectively the thyroid gland.  Chordates are the only animals with a tail that extends past the anus.  Finally, all chordates have a series of pharyngeal arches, cartilaginous segments around the throat such as a fish’s gills.  “What?!” you protest.  “I don’t have a tail or a segmented throat!”  Not anymore, but you did before you were born!  Even humans have all five chordate features as embryos, certainly proving that we still have the genes for them.  In fact, the pharyngeal arches develop into distinct parts of head anatomy during gestation.

Most chordates are vertebrates, with a notochord that has evolved into segmented vertebrae.  The earliest vertebrates were something like jawless fish.  Their spinal column was not yet properly a “backbone”, because the interior skeleton was still composed of cartilage for another 100 million years.  Vertebrates evolved other crucial body parts such as the teeth, eyes, brain, liver, kidneys, and pancreas.  This phase of evolution was influenced by the Cambrian explosion, which will be discussed below.

E. Tetrapods:  From Sea to Land

Evolution has an important recurring theme that has not yet been discussed.  This is as good a time as any to bring it up.  The theme is repurposing.  It is common for features that already exist to be modified or exploited in new ways, especially in new environments.  The evolution of our ancestors from sea to land involved some very successful repurposing of body parts.

Recall that all chordates have pharyngeal arches around the throat, at least during embryonic development.  Originally, these pharyngeal arches developed into gills.  Some gill arches have become repurposed by evolution as they have assumed useful new shapes.  The “first” gill arch (closest to the head) of jawless fish assumed a boomerang-shaped profile and migrated forward in the head.  It became affixed to the skull and has forevermore served as the jaw.  Arches further back in the body started to bud outward from the side of the animal, becoming paired fins.  Fins provide stability.  They enable fish to get up off the sea floor and become good swimmers.

Our ancestors were jawed fish called placoderms a little over 400 MYA.  An interesting recent discovery shows evidence that placoderms had external sex organs and got pregnant – the earliest fossil evidence of internal fertilization! 8 Prior to intercourse, reproduction was accomplished by spawning.  Sperms and eggs were released into the water, where they were free to meet for fertilization.  Internal fertilization would be vital for subsequent land animals, as spawning does not work on dry land.

In many lines of fish, cartilage evolved into bone.  Fins developed bony support structures separately from the vertebrae.  For certain bottom-dwelling lobe-finned fish, a pair of front limbs and a pair of rear limbs proved useful for scuffling along the bottom of the riverbank. 9 The fin bones evolved to become adjoined to the rest of the skeleton.    The bone structure of lobed fins started to resemble hands and feet, earning these animals the title of tetrapod (four-legged).  Each arm or leg had one upper limb bone, two lower limb bones, a series of small irregular ankle / wrist bones, and then five digits.  Tetrapods had bony pectoral and pelvic girdles.  The skull was separate from the pectoral girdle, giving tetrapods a neck and a head that could turn freely from the body.  These skeletal features are still shared by all members of the tetrapod clade: the amphibians, reptiles, birds, and us mammals.

Meanwhile, air bladders that were originally effective for controlling the depth of swimming were repurposed into lungs.  With lungs and a complete skeleton that could support their weight, tetrapods were able to walk onto land.  The first tetrapods were also still able to breathe water, making them amphibians.  They lived a little less than 400 MYA, and were well-adapted for life in slow, shallow rivers near the sea.

In many ways, the first land tetrapods had it made in the shade.  They had discovered a whole new realm where they could eat without being eaten.  These circumstances created a lot of evolutionary pressure to adapt to the dry-land environment.  There is some evidence that their water was running low on oxygen anyway. 10 But think of the serious challenges.  If you’ve ever seen a mudskipper crawling around, you know that it isn’t very graceful on land.  A riverbed is practically a zero-gravity environment.  On land, skeletons and muscles had to evolve to support the full weight of the body, without the assistance of buoyancy.  Acoustics, too, are completely different in air and water.  Organs that had evolved for hearing underwater were useless in the air.  This problem was eventually solved by the shrinking and migration of an upper jaw bone into the middle ear, where it became the stapes, an auditory bone.  Various land-animal body parts such as the eyelids, diaphragm, and tongue evolved during this Devonian poolside party. 11

The last great breakthrough of the Carboniferous period was the speciation of our clade the amniotes, as first represented by ancestral reptiles about 310 MYA.  An amniotic sac encloses and nourishes the embryo, whether in an egg or the mother’s womb.  Amniotic eggs are hard-shelled, offering protection against predators, parasites, and dehydration.  Reptiles no longer had a larval stage like tadpoles, but were born or hatched as miniature adults.  The perfection of internal fertilization and the appearance of hard-shelled eggs signaled animals’ complete emancipation from the water.  Reptiles were also better suited to dry land than amphibians because of their tough, scaly skin.

F. Consciousness, Communication, Cooperation, and Competition

In Chapter 10, I raised the point that there are three mysteries of nature so unique and profound that they are the doorways between science and religion:  the formation of the universe, the beginning of life, and the mysteries of consciousness.  It is impossible to say exactly when animals first became conscious, but it almost certainly occurred in the Chapter 9 time frame, a good part of a billion years ago.

1. Defining consciousness
2. The early evolution of conscious behavior

F.1. Defining consciousness

A camera and an eye can both “see”.  However, we would never say that a camera is “aware” of what it sees.  A camera could see a hammer swinging directly at it, but would never discern fear that it is about to be destroyed.  By contrast, even a fly will immediately flee from an incoming swatter.  How do people and animals become aware of themselves and their surroundings in a way that is different from cameras or computers?

The traditional religious answer was that we are animated by spirits, something external to our bodies.  This answer is roundabout for the same reason as other religious pseudo-explanations:  it begs the question.  It doesn’t explain how spirits would be self-aware.  Rather than wasting our time wondering how consciousness would work in an invisible spirit that may or may not exist, the modern approach is to see how much we can learn about consciousness in the physical world.

If there’s one thing that seems clear, it is that conscious thought requires a brain.  Since no brain exists by itself, by extension consciousness is always associated with an animal body too. 1 The body has the essential sensors that interact with stimuli both inside and outside the body.  Sensory input all travels through nerves and is somehow processed in the brain.  It is the sensory data and something about how it is processed that lead to self-awareness.

Though the end-goal question of how a brain can create an “inner world” is baffling, there is plenty about consciousness that does make sense.  In this discussion, we are not yet concerned with higher cognitive functions.  We’re just exploring the minds of the earliest self-aware sea creatures.


This likeness of a face is pretty “impressive”, yet it was simply forced into being by the stimulus that caused it. Most sensory perceptions are the same way. When an animal looks at a shape, an impression of that shape is automatically cast in the mind.

That inner world of the mind is not created from scratch.  Most of what the mind processes is sensory information from the outside world.  The inner world represents the outer world like an impression. 12 The senses are “analog”, as we say in the digital age.  Many patterns in the environment are transmitted directly through the body and nerves into analogous patterns in the mind.  Cognitive processing is required to make sense of them, but these patterns pass into the brain with no thought required.

Cambrian animals became equipped to see, hear, feel, and smell many details about their environment.  If a shark swam by, it would exude a great deal of information about itself.  It seems fair to conclude that a nearby ray, inundated with self-corroborating information about the shark, would be “aware” of the shark.  In fact, it is hard to imagine how a ray that saw, heard, felt, and smelled a shark could not be aware of it.  The ray’s brain synthesizes or binds the sights, sounds, water pressures, and smells all into one mental object in space and time:  “There’s a shark to the left.”  This is something that computers can’t do.  The binding process seems to be a key in forming a mental state of awareness – and it remains one of the great unsolved mysteries of the brain. 13

From awareness of the environment, it might not be a huge step to awareness of the self.  Much knowledge about an animal’s own body derives from how it interacts with other things.  Knowing that “The shark is to the left and the cave is to the right” is equivalent to knowing “I am between the shark and the cave”.  The fact that an animal can move its own body must also contribute to awareness of self.

There is good reason to believe that consciousness begins and ends with the material world.  Remember from Chapter 10 that the properties of life derive from the way ordinary matter is organized, not from the use of extraordinary matter.  Consciousness is complex and must have a complex cause.  If you’re looking for complex organization, you can’t do better than a brain!  Even an insect brain consists of a million neurons 14 with a billion connections among them.  Numerous mental processes – including the sense of “self” – are linked to particular kinds of nervous activity in specific parts of the brain. 15 Controlled experiments do not observe brain activity that violates physical law, for example electrical signals doubling as if by spiritual intervention.  Despite our religious predilection to believe in spirits, it seems that the physical brain is doing all that mental processing by itself.

F.2. The early evolution of conscious behavior

If consciousness leads to free will, it could very well have evolutionary advantages.  A creature that is aware of pain, hunger, and the pleasure of a good meal will want to eat or flee at appropriate times.  To the extent that this is heritable and advantageous over reflexive action, evolution will pressure the development of conscious thought.  There is a surprising level of opposition to this idea among biologists, but it sure seems that pleasure and pain are well honed to train survival behavior.

It is natural to speculate about the line between conscious and non-conscious animals.  Consciousness is not necessarily an on / off state of being.  There is a whole spectrum of responses to the environment.  Even without nerves, bacteria and plants can move toward light or food.  Higher on this spectrum, there are reflexes, instincts, needs, involuntary body functions, conditioning, emotions, and subconscious thoughts.  Some of the more complex forms of consciousness can probably be explained in terms of the simpler forms.  It is likely that animals such as octopi, snails, and lobsters have a more semi-conscious outlook on the world than we do.

To be conscious as we know it would seem to require detailed senses (especially vision) and a reasonably developed brain.  Based on this minimal biology, good candidates for our first fully conscious ancestors were the jawless fish.  (I wonder if they knew how ugly they were?!)  Despite their primitivism, today’s eels and lamprey, which are very similar to the first living vertebrates, are known to engage in social behavior that suggests conscious thought. 16

For most animals, social behavior amounts to communication, cooperation, and competition.  Animals may cooperate to hunt, avoid predators, or keep each other clean of parasites.  They may compete for food or mates.  Since these are the very basics of survival, behavior became as crucial to evolution as body parts.

There are obvious ways in which cooperation and competition can help particular genes survive.  Males often fight each other over females.  A male that is larger, stronger, or faster is likely to defeat a less well-endowed challenger.  When the winner goes on to mate, it is his genes for being large, strong, and fast that get passed down to his sons.  Many species develop a sexual dimorphism for this reason, with males being substantially larger than females.

Behaviors get passed down in less obvious ways.  In some animals, females choose their favorite males based on looks or courtship rituals.  Some species of fish swim in large schools.  This helps most of them evade sharks or other predators.  These behaviors make for clear survivors.  But what actually gets passed down to the next generation?  Are there genes that make female peacocks prefer males with the most ostentatious tail fans?  Does DNA control fish predisposition to swim in schools?  Or are these behaviors passed down socially in an endless cycle of observing, imprinting, and mimicking?  Behavioral scientists define a meme as a behavior or preference that is perpetuated socially within a population.  Each species’ brain tends to naturally imprint some behaviors.

It might seem that evolution would quickly wipe out memes of self-sacrifice, yet “altruistic” behavior has survived billions of years and is still prevalent throughout the animal kingdom.  Altruism can provide an indirect route to survival for some alleles, since most animals live in extended families.  A mother might fight to the death to save her children from a predator.  The mother dies, but her genes live on.  A worker bee will sacrifice having children, instead doting on the queen.  But the queen is closely related to the worker, and she perpetuates the family genes.  In the long run, we must remember that evolution is a tournament of genes and alleles, not organisms.

Back to Section 9.IV:  The Sexual Evolution

Continue to Section 9.VI:  The Rest of the World

G. Citations

  1. Prave et al, “The first animals: ca. 760 million year old sponge-like fossils from Namibia,” South African Journal of Science, 1/18/2012, http://www.sajs.co.za/sites/default/files/publications/pdf/658-7276-6-PB.pdf (accessed 4/11/15)
  2. Ayala and Rzhetsky, “Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates,” Proceedings of the National Academy of Science, vol. 95 no. 2, 1/20/1998, http://www.pnas.org/content/95/2/606.long (accessed 4/11/15)
  3. Yu and Holland, “Cephalochordates (amphioxus or lancelets): A model for understanding the evolution of chordate characters,” Cold Spring Harbor Protocols 2009, doi: 10.1101/pdb.emo130, http://cshprotocols.cshlp.org/content/2009/9/pdb.emo130.abstract (accessed 3/29/15)
  4. Ayala and Rzhetsky, “Molecular clocks and the origin of animals”, Evolutionary Theory and Processes: Modern Perspectives, Springer, p. 151.
  5.  Placoderm photo by Chip Clark, National Museum of Natural History, public domain, http://paleobiology.si.edu/geotime/main/evidence/dev_01.html
  6. Maiorana, Virginia, “Animal,” Encyclopedia Britannica, 2014, http://www.britannica.com/EBchecked/topic/25501/animal (accessed 4/17/15)
  7. Thanks to David King for his excellent website on tissues.  King, David, “Connective Tissue Study Guide, ” 2013, http://www.siumed.edu/~dking2/intro/ct.htm#components (accessed 4/18/15)
  8. Long et al, “Copulation in antiarch placoderms and the origin of gnathostome internal fertilization,” Nature, Vol. 514, 10/19/14, doi 10.1038/nature13825, http://www.nature.com/articles/nature13825.epdf?referrer_access_token=G22hTHkTfNIKKOaWD25l4NRgN0jAjWel9jnR3ZoTv0Nu6R31hpOpF814-6btZAxZ7U62tKkLO3io6vvxCr6mSYZKZHCMi8Ypnt3CdSDPC4RNKEuzGevKsDl2x9QxEB9CmeTnoJ5V_aiE-pOnjruW6caSRpIle01Nosn0-SZSf3BbsWOsw4EvSBYVVPoIBs4V7EFZl329_ssCD8-9jCO_hSfe50kjRUSlNSvg_boI67A%3D  (accessed 5/29/15).  Or if you’re feeling brave, you can even view Flinders University’s computer-generated video of this prehistoric copulation.
  9. Radinsky, Leonard B., The Evolution of Vertebrate Design, University of Chicago Press, 1987, ISBN 0-226-70235-9, p. 56.
  10. Algeo, T.J., and S.E. Scheckler. 1998. Terrestrial marine teleconnections in the Devonian: links between the evolution of land plants, weathering processes, and marine anoxic events. Philosophical Transactions of the Royal Society of London, B Series 353: 113-130.
  11. Radinsky (1987) pp. 77 – 85.
  12. Pin art image: © 2013 by Ruslan Gilmanshin, Chaikovsky | Dreamstime.comHuman Face Made From Pin Board Toy Photo, licensed to author.
  13. Velik, Rosemarie (2012), “From Simple Receptors to Complex Multimodal Percepts: A First Global Picture on the Mechanisms Involved in Perceptual Binding”, Front Psychol. 2012; 3: 259, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3402139/#B25 (accessed 6/24/15)
  14. Menzel, R. and Giurfa, M., Cognitive architecture of a mini-brain: the honeybee, Trd. Cog. Sci., 5:62-71, 2001
  15. Modinos et al, “Self-reflection and the psychosis-prone brain: an fMRI study,” Neuropsychology, 2011 May; 25(3):295-305, doi: 10.1037/a0021747, http://www.ncbi.nlm.nih.gov/pubmed/21443341 (accessed 6/27/15)
  16. Bshary, R., Hohner, A., Ait-el-Djoudi, K., and Fricke, H., 2006, Interspecific communicative and coordinated hunting between groupers and giant moray eels in the Red Sea, PloS Biology 4, 2393-2398 ; Diamant, A., and Shpigel, M., 1985, Interspecific feeding associations of groupers (Teleostei: Serranidae) with octopuses and moray eels in the Gulf of Eilat (Aqaba), Environmental Biology of Fishes 13, 153-159; Dubin, R.E., 1982, Behavioral interactions between Caribbean reef fish and eels (Muraenidae and Ophichthidae), Copeia 1982, 229-232.
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