Evolution & Genetics

Sapolsky:

• Sexual selection and reproductive fitness
• Kinship and degree of relatedness
• Reciprocal altruism. Must be smart enough to remember each other and their interactions. Must be long lived. Cooperation, cheating, detecting cheating. Caveat: bacteria still do tit for tat and reciprocal interaction. 
• Game theory. Prisoner’s dilemma
• Optimizing genetics for the given environment. Minimum effective dose. 
• Tit for tat strategies is vulnerable to signal error. Resulting in a forever fluctuating pattern. Forgiving tit for tat is a way out of this loop. If retaliation occurs 5x, forgive and move on. 1 round of forgiveness before retaliation again. This is vulnerable to exploitation by those that don’t have forgiveness in them. Next is to only forgive those who have behaved altruistically in the past. Must prove themselves.
• Sexual dimorphism
  • Tournament species: male and female physical difference/size, female caregiver, strong and healthy attract mates.
  • Pair bonding: look similar, female cuckoldry, looking for evidence of competency, more twins, greater lifespan 
• Genetics
  • DNA is not doing much
  • Transcription factors activate different expressions of the genes
  • Promoters allow access to the DNA by getting chromatin to unfold
  • Splicing enzymes remove introns and join together introns
  • Mutations in any of these may cause issues
• Epigenetics is the change in the expression via these pathways. Sometimes it can change access to the DNA permanently.
• Fertilization is all about genetics and development is about epigenetics.

Deep History Notes

Common Ancestry

Nick Lane (The Vital Question): the ancestor of life on earth is a cell that arose between 4-3.8 billion years ago, about half a billion years after earth was formed. LUCA – Last universal common ancestor. Not likely to be the first instance of life. RNA, DNA, and proteins likely formed primitive forms called protocells.

Natural selection drives organisms toward a better fit for their environment. If resources change, the organisms that are better adapted to suit the new environment will survive. A group that has done really well in the past may become vulnerable with the introduction of a predator they aren’t adapted to avoid. Besides selection and migration, genetic mutation is also a key source of variability. Genetic drift: random changes in the frequency of certain genes in a population. Like a hurricane wiping out a certain trait in a population with no regard to the actual trait itself. Less numbers, less likely to reproduce.

Differences based on common ancestry are said to be homologous, while those that are not based on common ancestry are merely analogous.

What is an Organism?

An organism is a living thing, an entity that functions as a physiological unit, the component parts of which operate with a high degree of cooperation and a low degree of conflict to help ensure well-being and sustain the life of the overall entity and to reproduce itself so that its kind can continue.

Its objective is to acquire nutrients and energy so that growth can occur and life can be sustained to at least the point of reproduction. Viability (the ability to grow and persist) and fecundity (the ability to reproduce) are key characteristics of organisms. They both require metabolism. Living things make and use energy in the process of living, while nonliving things are acted on by energy.

Behavior

While an organism’s traits are useful in the quest to survive, their behavior is a decisive factor in natural selection. Behavior is a feature of all organisms, not just those that have nervous systems or muscles. BF Skinner defined it as “that part of the functioning of an organism which is engaged in acting upon or having commerce with the outside world.”

A reflex is the simplest form. An innate stimulus-response reaction that occurs by way of nerves, that directly connect sensory input systems with muscles. Automatically elicited by certain stimuli and are not dependent on volitional control.

Fixed reaction patterns are complex hardwired responses that are similar to reflexes as they may be inborn. Complex sequences of behavior like a mother goose extending the neck when an egg is out of the nest to retrieve it. Universal survival activities like eating and drinking too. Although, species specific. They can be influenced by environmental factors, so not necessarily innate.

Our everyday vernacular arose and still persists because it enables discourse about the inner lives of people as they interact with one another. Great for survival, but not so much for scientific discourse. We easily convince ourselves of the connection between behavior and mental states. Over time, the more subtle distinctions are lost and we end up thinking that names/terms are literal. Folk psychology often serves as a starting point for scientific inquiry into the mind and behavior. Because it is entwined into our vernacular language regarding the mind, our mental-state words provide labels for meaningful categories of experience. Behavior did not emerge to serve the subjective mind. It came about to enhance fitness-to keep organisms alive so reproduction can occur.

Early Life (Bacteria like)

By 3.5bya bacteria had emerged. They run or tumble to get around. Motility has both costs and benefits. It requires flagella, and flagella movement is metabolically expensive. On a positive note, it adds leverage in food acquisition and avoiding harm. Their movements are called taxic behaviours – toward useful or away from harmful substances. Chemo and photo receptors. Less tumbling occurs when an attractant is detected. Straight towards the substance. With repellants, tumbling increases, changing direction and withdrawing. Electrolytes and water are also balanced within the cell to prevent excess or deficiency.

When animals have low electrolytes they seek out salt. When they have too much they seek water to clear. Animals also have thermoregulation inside and behavior. Bacteria do this by reconfiguring certain biochemical processes to adjust their physiology and to match their external temperature.

Sex evolved as a modification of cell division in single-cell protists and would not exist without the asexual solution to reproduction that bacteria have used for billions of years. They may not have sex but they can be social. In the case of creating biofilm, they can communicate by generating electrical signals, which they use to coordinate feeding and reproduction and to attract new members.

Bacteria can acquire information about the world and use it to change future behavior. They form internal molecular representations of environmental conditions (temp, O2 levels) and use them to predict environmental conditions later.

Survival Tactics

Approach and withdrawal may be universal simply because they are subject to the laws of physics, not because they reflect psychological motivations (polarity, temperature, entropy, etc?). The evolution of nervous systems in animals provided novel options for approach and withdrawal beyond simple taxic responses. They can be implemented in a more precise way and the added complexity resulted in behavioural quirks. We withdraw from danger and are attracted to sexual desire and food. Emotional states should not be called upon to explain behavior. They are mediated by different brain circuits.

RNA or DNA?

Gerald Joyce believes RNA was developed first, which jump-started evolution, but needed to create DNA to support a large genome.

Self-replicating RNA and DNA molecules, according to this model, were initially free-floating, but were later compartmentalized. Allowing protein products of DNA and RNA to be confined and used by the structures inside. Perhaps first in the pores of a rock, not sustainable, until a lipid structure was created. This allowed them to move, replicate, and evolve. Possibly these early cells would collect resources, which would facilitate reaching a threshold where the whole cell would divide due to a limit within the lipid casing. Might be polarity or pressure.

Alternatively, RNA/DNA could appear after biological entities could support metabolism. Günter Wächtershäuser proposed a version of this metabolism-first theory in which hot water from volcanoes flowed over mineral-rich rocks to ignite (catalyze) chemical reactions that fused simple carbon-based compounds into larger ones. The reforming of materials could have formed a basic protocell. This was met with critique saying the volcano vents would be too hot for life, but Mike Russell and Bill Martin solved this problem with the alkaline hydrothermal vent theory. It is widely accepted that the early oceans were cold and acidic due to abundance of positively charged chemicals. The water would go through cracks to the mantle, get heated, and flow over carbonate and pyrite vents making it more alkaline – creating a negative charge. This alkaline fluid would get trapped in the vents, separated from the acidic ocean by a foam barrier consisting of iron sulfide. Hydrogen and carbon dioxide could construct formaldehyde or acetate with iron sulfide as a catalyst. Once it could leave the pore as a lipid encased protocell it could self-replicate.

Either theory could be the case, or in tandem. Regardless, they both provide reasoning behind the importance of a negative charge inside cells and lipid membranes.

Life Beginning

Life as we know it began about 3.8billion years ago. By 3.5bya, LUCA’s descendants had diverged to form bacteria. Archaea then branched off. One reason for their longevity is they are able to live under many different climatic conditions. They survive on land, air, and water. Bacteria thrive in moist, warm recesses of our body, but also snow and ice, and in deep-sea vents. Some archaea can survive up to 200degrees Fahrenheit, in waters of high salt concentration, and even acid.

The survival and wellbeing of any cell depends on the active exchange of molecules between the outside world and the cytoplasm, by passage of the cell membrane. The membrane is selective and this discretionary permeability is dependent on the molecular composition of the membrane.

Once inside the cytoplasm, externally acquired ingredients contribute to the complex chemical reactions that make enzymes and other proteins used in energy generation, maintenance of fluid and ion balance, regulation of inner temperature, and control of cell movements in acquiring nutrients and defending against harm. Metabolism generates waste that must be excreted through the cell membrane, often with the help of transporters.

Bacteria and archaea have a cell wall as well as membrane to protect them. The wall allows more chemicals through, except large toxins, to move freely through. Its rigid shape prevents the cell from collapsing when water leaves, and from exploding when it enters.

The cell membrane maintains the balance of charge between inside and out. This chemical balance (acid out, alkaline in) is essential for sustaining the inner workings of metabolism.

Tyler Volks point out that cells are self-generated dynamic entities that at any given moment are always on the cusp between persisting and perishing. They manage to survive by using metabolism to stay ahead of the game. When metabolic waste is expelled, the result is a loss of molecules. To compensate, cells also use metabolism to grow new molecules. If the exchange is at least equal, the cell can persist in its present form. More molecules = growth and protection against perishing. But a cell can only grow so much, as a larger cell requires more nutrients, and the cell runs up against a basic principle of physics. As a sphere gets bigger, its interior increases to a greater degree than its surface area. This makes it harder for the surface to keep the flow of nutrients enough to sustain the ever-larger interior. So, it divides and starts again. Mitosis. Vertical gene transfer involves passing genes from parent to offspring. Horizontal gene transfer takes genes from other organisms. Genetic mutations also contribute to variability.

Using antibiotics to destroy the membrane of a bacteria can only work as long as they aren’t using horizontal gene transfer and undergoing mutations.

Organelles

2bya Eukarya appeared. In bacteria and archaea, DNA floats freely within. Eukaryotes, it is isolated from the rest of the cytoplasm. Eukarya = true kernel. Nucleus is surrounded by a nuclear membrane. Membrane enclosed structures inside are called organelles. One of these organelles is mitochondria. Dedicated energy machines that are more efficient than the energy producing capacities available to prokaryotes.

The endoplasmic reticulum and golgi apparatus are involved in the manufacture and regulation of proteins made under instructions from the DNA in the nucleus.

Because Eukaryotes don’t have a rigid cell wall they require a system of filaments, made of proteins, that form an inner scaffold called the cytoskeleton. Prokaryotes have a cytoskeleton but it is less elaborate, as it doesn’t need to form the cell shape. The EK uses it as a chemical transport system that facilitates communication between the different parts of the cell. They are large so need the communication. They also needed other changes that are related to metabolism to support their larger cell volume. Which is the role mitochondria play.

It is believed the change occurred with in-folding the cell membrane in archaeal cells to create a nucleus. Making the nucleus the control center, DNA instructing RNA to undergo protein synthesis. Also, the archaeal cell engulfed a bacteria without the bacteria being digested. The long term relationship became mutually beneficial – or symbiotic. This became the Last Eukaryotic Common Ancestor (LECA).

Nick Lane suggests that prior to this, Archaeal cells lived on gases – hydrogen and C02. Once it had the bacteria, it was able to utilize the energy produced. The endosymbiotic theory (Lynn Margulis).

Creating Energy

Animals obtain energy from carbon containing compounds by consuming and digesting other organisms (animals, plants, fungi). Fungi get energy by releasing digestive chemicals externally, then consuming. The end result being glucose, which is delivered to cells for mitochondria to use oxygen to break down into energy. Cellular respiration.

Plants mainly make energy using chloroplasts, which capture sunlight, in a process called photosynthesis. Water is absorbed from the roots and CO2 extracted by leaves are broken down to yield glucose, which is stored as starch and used as fuel. Plants also have mitochondria to make energy in darkness.

The by-product of photosynthesis is oxygen. When photosynthetic organisms multiplied rapidly, the atmosphere contained sufficient oxygen to foster a growth spurt of O2 dependent organisms. Tyler Volk calculated that the recycling of CO2 between O2-breathing and photosynthetic organisms increased global photosynthesis by 200-fold vs when it was supplied by volcanoes and rock weathering. Protista also fall under the multicellular category.

Energy and Size

EK’s ability to increase in size created the first true predators and prey. Lane suggests there is a limit on energy produced per gene and that EK can generate 200,000x more per gene than PK (Energy demand vs cell size limit). Preventing them from growing. Mitochondria to the rescue y’all. The first major bump in O2 occurred 2bya, before the arrival of EK. Thought to have resulted, in part from Photosynthetic PK. The second rise was 800mya. Making it possible for even larger, energy demanding multicellular organisms (animals, plants, and fungi) and contributed to diversification. Mitochondria solved the energy problem, the cytoskeleton solved the structure problem, and the transporter proteins the carriage problem.

Most animal phyla have only been around 500my and distinct animal species tend to only last 1-4 my before becoming extinct. So, PK wins out. PK diversified biochemically, enabling them to adapt to environmental changes without having to change structurally.

Sex

Sex began with unicellular protists – the entire organism essentially a free-roaming sperm or egg cell. Genetic markers of sexual reproduction indicate that the genetic capacity for sex is universal in EK. Some that don’t have sex now may have the lost the ability over time. There are energetic costs to sexual reproduction.

When the sperm and egg meet up, they physically fuse so that the sperm can fertilize the egg. Genes are mixed via recombination. New cells divide and replicate and get differentiated with chemical signals to make skin, muscle, organs, etc (somatic cells).

Horizontal gene transfer can occur in EK. GMO issues are based on the concern that genes from food may be transferred to us and alter our genome.

Asexual reproduction is continuous and fast compared to sexual reproduction. Sex is also inefficient – producing many gametes that get wasted and the recombination process. The advantages are genetic variability during environmental changes. The population as a whole can adapt. As humans we tend to attribute sexual motivation as a psychologically stimulating event when it is not necessarily so in other organisms.

Most DNA is contained in the nucleus, some is in the mitochondria. In sexual reproduction the nuclear genes are mixed but the mitochondria DNA is passed mainly from one parent (usually mother). Creating the Mitochondrial Eve Hypothesis.

A negative aspect of taking in bacteria, or mitochondria, is the extra free radical release. The fact that transmission is limited to just the female parent may reduce the free radical damage, eliminating physiological conflict, making it easier for two genomes to exist. Sperm are more behaviorally active than eggs and produce more free radicals, potentially damaging mitochondria over time.

Colonies

Colonies are not true multicellular organisms, as their cells are not officially components of a single unitary body. But a certain type of colony launched multicellularity. They adhere to one another and use chemical secretions to stay attached (adhesion molecules) and to communicate with one another (signaling molecules).

Kelp and seaweed are examples of EK colonies. Slime molds (amoeba) have the ability to move across the landscape using highly efficient routes. Colonies form because group existence offers advantages over unicellular life. Safety in numbers, moving as a unit, protection against predators. Survival chores can also be divvied up and specialized. Suppressing the expression of genes that aren’t needed saves energy.

Defectors are a problem in colonies. Moochers take what they need and give nothing back and migration means the new colony needs to express genes to protect themselves again.

Cells in different tissues depend on each other and can’t survive without the cooperation. Survival of the individual cell becomes subsidiary to survival of the overall organism, and mandatory cooperation results. Colonies are the transitional step between unicellular and multicellular organisms. Clonal colonies eliminated defection compared to aggregating colonies with different parents. Karl Niklas believes the jump to clonal colonies was created plants, fungi, and animals.

Cell Adhesion

Two key requirements for multicellular life are cell to cell adhesion and cell to cell communication. The reason unicellular colonies can’t achieve this status is because of the lack of sustained cooperative relationship between individual cells. According to Niklas, two evolutionary steps are required to progress to a multicellular organism. First, an alignment of fitness phase has to occur in which genetic similarity among cells prevents conflict between them, thus enhancing cooperation. A unicellular bottleneck. It starts as a single cell and all others are generated from it (zygote). The export of fitness stage, fitness must become interdependent with minimal physiological conflict. Fitness is transferred from the individual to the organism as a whole. Functions are programmed in the genome. Defection cannot occur and it all hinges on sex and the way the egg is fertilized to make diverse genes from both parents.

To survive as a multicellular organism, the individual cells must give up their sovereignty and reproducibility (similar to human civilization except the offspring are given up as a tribute to the system at a deficit). Organisms with harmful genetic mutations tend to die before reproducing and genes are shuffled to lessening impacts from harmful ones.

Autoimmunity has some strong contrasts with a society that has given too much power to those who eliminate defectors. Self-destructive tendencies and false positives.

Flagella

The leading explanation for animals is the Colonial Flagellating Hypothesis. Ernst Haeckel. Plants, fungi, and animals each have a protist ancestor. The protist ancestor of animals is an ancient extinct protozoan that is also believed to be the ancestor of protozoa called choanoflagellates.

Flagella movements, called beats, involve wavelike undulations. Cilia rotate rather than undulate. Choanoflagellates are predators, feeding off bacteria. They can control the motion of their movements towards nutrients or away from threats with flagellum by generating electrical signals that cause beating movements. They feed by creating water currents, pulling bacteria toward them and trapping within their collar made of membranes. Then absorbed into the cell.

Asexual reproduction is the norm but they also sexually do under certain conditions. When food supply is limited, cell survival is challenged, and asexually produced offspring that are smaller or larger than normal are produced. They become gametes. Small are sperm and large are eggs. When they fuse they can create genetically diverse offspring.

Cell to cell adhesion happens in colonies and communication is possible. The simplest choanoflagellate colony consists of individual cells forming a sphere, with flagella facing outwards. When cell bodies release chemicals inside, the flagella move in a coordinated beating fashion. Nutrients are then transported across adhesion bridges. One issue is cells can’t feed and divide at the same time. Since they are predators, they need to actively keep feeding. Cell specialization fixed this. Female gametes move to the center of the cell under bad conditions and sperm fertilize. They almost become multicellular but they don’t end up being interdependent.

Ancestral choanoflagellates used electrical signaling to move, like muscle contraction. Also to communicate to other cells like neurons. They also have the genes that animals use to form neurons. Sponges are believed to be the first animals but were unable to build a nervous system (didn’t need one).

Animals

Animals differ by consuming other organisms and are motile. Creating predator prey driven evolution. They also developed nervous systems and muscles, which greatly extended their behavioral options. 

Sponges are thought to be the first animals. Fossil records for them aren’t great though, since they have soft bodies that don’t fossilized well. They belong to parazoa with placazoa (also tissueless). Trichoplax is the only known placazoan left. All animals with tissues that form organs and systems belong to a metazoan subsystem called Eumetazoa. Two early ones were Ctenophora (comb jellies) and Cnidaria (hydra, jellyfish, sea anemone, and corals)

Today, more than 99% of animals are bilaterally symmetrical. Most are descended from the same flatworm ancestor (acoel 540mya). Last common bilateral ancestor (LCBA). The Cambrian Explosion between 540my-480mya expanded bilateral species. All sea dwelling.

Sponge

The sponge has a choanocyte, similar to unicellular choanoflagellates (flagellum and collars). They line the outside and pinacocytes protect the body but are not tightly connected like our skin. Some sponges develop a shell made of calcium carbonate. The space between the outer surface and inner cavity is called the mesophyll, and contains an endoskeleton made of spongin. The endoskeleton in some sponges also has mineralized particles of calcium carbonate that add support. Since they are stationary, they release noxious chemicals into their surroundings, and with external calcified barbs to deter consumption. They also expel sediment and waste by inflating and collapsing to force it out. Controlled by myocytes. Thought of as precursors to muscles but without nerves.

New Body Plans

Choanocytes capture and amoebocytes absorb and transport. Eumetazoan animals that followed had cells that formed digestive tissues, organs, and systems. The cnidarian descendants of sponges had a specialized mouth organ connected to a digestive system. Cavlier-Smith argues sponges are the only animal to evolve multicellularity without changing the absorptive feeding. Some must have evolved a new body plan for feeding. Specialized cells that formed appendages with sharp barbs that could catch and transfer food, through the mouth and into a specialized internal digestive organ – a gut, which formed by sealing the body pores.

Jellyfish use tentacles to search for food. They are home to cnidocyte cells. When contact is made, they activate, but only if the chemistry of the object is indicative of prey. A barb unfolds and attaches, injects toxins to immobilize, then delivers it to the mouth and gut. There, gastrodermal cells release chemicals to digest and make energy. Tentacles are used in sexual reproduction. The male hands the female sperm. They can also engage in hermaphroditic fertilization. Complex movements of tentacles and body require tissues that can rapidly respond to sensory information when engaging in survival activities. Muscle would help to contract faster but can’t activate fast enough with diffusion of chemicals. So, neurons evolved in tandem with muscles.

Neurons

Like all cells, neurons have a cell body, but additional nerve fibers. One is an axon, which extends out of the cell body and enables the cell body to send messages over long distances to other neurons. Dendrites extend out like antennae for short distances and receive messages transmitted from axons of other neurons. It adds an electrical step between the chemical one to transmit signals faster. In its most fundamental sense, a nervous system is a sensory-motor integration device. Inputs come in the form of messages from sensory receptors specific to key stimuli (light, sound, touch, odors, tastes) and the outputs involve motor effectors. The most basic job of a nervous system is to connect sensory receptors with motor effectors.

In a sponge’s youth, they are mobile. The outer body surface of larval sponges has cilia, which is used to move around. Swimming cells have short cilia and cover most areas. They beat constantly, causing random, undirected movements that keep it moving and afloat. Steering cells have long cilia, which are concentrated at one end. Sensitive to light, which causes it to bend, directing movement toward light sources. They probably evolved basic neurons to move quickly and then got rid of them at maturity. By having lots of cells they could divvy up roles. Possibly clustering muscle cells and sensory ones together for efficiency. Next, growing an extension of the sensory body outward. This could work with diffusion until too slow. Needed axons for rapid communication.

Sponges apparently have the genes necessary for synaptic vesicles but don’t have the molecular signals to activate them in a coordinated fashion in development. In humans, neurons and skin cells both arise from the ectoderm layer. A more complex neural net led to more complex and specialized behavior. A jellyfish neural net seems to display the early plans of complex bodies and brains.

It has been suggested that the key factor for the Cambrian explosion of animal bodies was the advent of the nervous system-based learning. Nervous systems made learning sophisticated and flexible. Leading to the ability to explore new niches. The evolutionary arms race would have accelerated, creating unprecedented changes to the body. Furthering Bauplan diversification.

Predator Prey Accelerated Bilateral Shape

650mya animal life was dominated by aquatic organisms with asymmetric or radial bodies that lacked a nervous system, or at best had a simple one (cnidarians and ctenophorans). Then around 630mya, a new body style – bilateral symmetry appeared. They went on to acquire nervous systems that sported a collection of neurons in the head – a brain, which could evaluate the environment and behave in ways more complex than ever. During the Cambrian Explosion 543-480mya, brainy bilaterals were numerous and diverse. By 400mya, some invertebrates had invaded the land (in particular millipedes). 350mya they were joined by amphibians, the first vertebrates to live by breathing atmospheric oxygen.

Instead of having tentacles to grab floating nutrients, like a polyp, or drifting down randomly with the mouth facing down, like medusae, bilateral animals are mobile and have a preferred method of locomotion. Forward is a direction that emerges from the shape of a bilateral body.

Bilaterals were the first to have a head, and the direction that head faces is forward. It is also the location of key sensory organs (eyes, ears, nose) that guide forward moving behaviors in the search for food, drink, shelter, or mates and away from danger. Predator-prey interactions accelerated complexity in bilateral animals, allowing chase and escape.

Eumetazoans, are animals with tissues (radial and bilateral) that are a result from specialized cells. Daughter cells divide, to give rise to identical cells that collect together in a single layer to form a hollow sphere called a blastula. This folds inwards to form the gastrula, with distinct layers of embryonic cells (where specialized cells are made from).

Radials are diploblasts, as they have two embryonic cell layers, while bilaterals are triploblasts, having three. In radials they are the ectoderm and endoderm. The outside covering or skin and the gut. They also have mesoglea, but it is not made of living tissue.

Bilaterals also have a mesoderm – which lies between the ectoderm and endoderm and generates additional cells. A coelom, where the gut and other inner organs reside.

Radials have one opening for the gut and anus. Bilateral eumetazoans have a separate input and output. There is also a nervous system. Cnidarians are basic and lacks or has minimal control over body movements. Some motor coordination but not by the way of central headquarters. This is where newer bilaterals developed a brain to integrate information from sensory organs, such as paired eyes, to movement.

Scientists believe the Last Common Bilateral Ancestor (LCBA) was a primitive worm. It is thought that the LCBA emerged as a modification of the cnidarian larval body, and inherited a diffuse nervous system and an incomplete gut.

During the early life of bilaterals, the blastula folds inward forming the gastrula, and the fold gives rise to an opening that becomes the digestive tract (protostomes – mouth first). Most invertebrates belong to this group. The rest are anus first (deuterostomes – mouth second). A unique set of invertebrates that are ancestors of vertebrates. By 580mya they had both appeared.

The proto-deutero ancestor (PDA), came after LCBA, which arose about 630mya from radial. The PDA is thought to be Nephrozoa, the clade when coelom appeared. Including proto and deutero – practically all existing animals.

Protostomes are divided into two groups: flatworms, annelids (segmented worms), and mollusks (clams, oysters), and the other arthropods (insects, arachnids, crustaceans) and roundworms. They are defined by whether it grows continuously or sheds its body and starts fresh at some point. Genetic analysis shows mollusks have more in common with deutero than arthropods and roundworms. Suggesting annelids and mollusks offer advantages as model systems for understanding human function and disease, despite worms and fruit flies being more popular in genetic studies.

Chordates

Chordates – No other organism has a notochord. A flexible, hollow rod made of cartilage that runs along the axis of the chordate body along its dorsal side, or back. A primitive skeleton that supports the body against the pull of gravity – the skin and some inner body parts hang from it. The gelatinous filling at its hollow center enables its body to be flexible and to engage in undulatory swimming movements. Annelid worms, ancestors of which were early protostomes, possess a longitudinal muscle, called the axochord.

Protostomes and cephalochordate deuterostomes inherited from the PDA a central nervous system consisting a brain and nerve cord, as well as a structural support chord (an axochord in protostomes, and a notochord in chordates). With evolution of vertebrates, the notochord gave way to the spine (vertebral column), and the dorsal nerve cord became the spinal cord.

In embryonic life, all vertebrates possess a dorsal notochord, which is then replaced by a vertebral column as the embryo matures. The gelatinous interior becomes the soft material inside the disks between the vertebrae. When a disk is herniated, the material squeezes out, and with the loss of this cushion, inflammation and compression of nerves can result, leading to sciatica and back pain.

Vertebrata

There are approximately 28 bilateral phyla with distinct Bauplan features. 27 are invertebrates, including 23 groups of protostomes and 4 deuterostomes. One vertebrate phylum.

To hunt the ocean waters, while swimming, the capacity for fast, agile swimming, to catch prey and avoid being eaten is required. Having a vertebral structure that can move, provided the flexibility. The vertebral column is attached to the brain, anchors the rest of the skeleton, limbs, muscles, and organs. Just like the notochord did for invertebrate chordates.

An animal’s Bauplan unfolds in early life under the control of its genes. A family of genes called homeobox genes are major players in body construction. These are found in all multicellular organisms. The subset – hox genes, play roles in developing bilateral bodies. Hox genes direct the construction of basic structural features that all protostomes and deuterostomes, all bilaterals, share, such as symmetry along the anterior-posterior axis. They regulate other genes that initiate the construction of specific structures, such as legs and arms, at specific times in embryonic life. Also, organs and size of different body parts. Also nervous systems. Conservation of the Hox genes is what gives all bilaterals their common Bauplan features. The variation in expression of genes between different phyla that contribute to the unique body designs. Protostomes and invertebrate deuterostomes have one cluster of Hox genes, while vertebrates have four sets. This helped them develop complexity.

Jaws and Lobes

530mya a Haikouella preceded fish as the first vertebrate. It was transitional between a notochord and a primitive vertebral column – a notochord with segments.

Fish appeared 520mya during the Cambrian Explosion. The first fish didn’t have bones, but skeletons made of cartilage, making their subgroup cartilaginous fish. They initially lacked jaws. Mouth always open, with stationary primitive teeth as a filter. Active predators that ate while swimming forward (filter forward, filter sand, attach to other animals and sucking out nutrients). Breathed through gills to extract oxygen. Lampreys and hagfish haven’t changed much here.

510mya parts of the gills became a jaw with muscles and teeth.

The largest subset of jawed fish are the ones whose skeletons are made of bones. Appeared around 480mya, more varied diets, with some being carnivores, herbivores, and omni. Early bony fish diverged into animals commonly referred to as ray-finned fish. Bony fish use gills to breathe and fill their swim bladder with air, giving them buoyancy, meaning they can breathe stationary. Sharks must keep moving to keep oxygen over gills. Some sharks can take a break by staying stationary in a moving current of water. The other group is the lobe-finned fish. They split from ray-finned about 440mya and are mostly extinct, but are the kind of fish that subsequent vertebrates evolved from.

Lobe-finned fish have fins made of a single bone surrounded by hunks of muscle tissue. They had two paired sets of these lobes on the ventral side and could use them to walk across the ocean floor and plant their position in currents. This aided their ability to hunt aquatic invertebrates or other fish. The precursor to limbs.

Water Escape and Mammal Ancestors

375mya a Fishapod (Tiktaalik) diverged. A lobe-finned fish equipped with some novel Bauplan accoutrements. Joints added to the stilt-like limbs, enabling smooth walking movements. In addition to gills, they possessed primitive lungs, allowing occupation of warm, shallow water with low O2. The first terrestrial tetrapods.

Amphibians were next and could inhabit both water and land. Frogs are familiar examples that start as tadpoles underwater as vegetarians who use gills, then they develop lungs as a carnivorous adult. However, they couldn’t leave the water without plants getting there first to release O2. Plants got there 50mya earlier as a by-product of photosynthesis.

The first animals to invade land were invertebrate protostomes, like millipedes, which were vegetarian. They lived off mossy growths on rocks. The amphibians would eat them. In response to protostomes eating the plants, they diversified, which was made possible by CO2 exhalation from animal respiration. With more plants to eat, terrestrial protostomes also diversified, in the form of insects and spiders. Amphibians reigned supreme without competition.

As vertebrate life diversified on land, carnivorous dietary options opened up, but so did the chances of being eaten. Amphibians needed to stay close to water to reproduce, but without sexual intercourse. Fish and amphibian eggs are encased in jellylike membranes and are laid in water. Males then release sperm upon them (external sexual reproduction).

By 330mya a new class of tetrapods emerged, amniotes. The fetus develops in an internal, fluid-filled sac and with lungs that extracted oxygen from the air rather than water. Maturing in the female these vertebrates could get away from water. The egg would be laid and hatch on land. This meant external genitalia was required. Genitalia bearing animals make up the remaining vertebrates – reptiles, birds, and mammals.

Reptiles first, their long limbs made them more mobile than amphibians. They split to give rise to birds and mammals. In both birds and mammals, their spatial range of foraging greatly increased, putting additional pressure on the brain to expand to accommodate the challenges involved.

Synapsids were the first group of reptiles to branch off from basal amniotes, about 310mya. These are mammal-like reptiles. They included fierce predators and herbivores. Some were large with fins on their backs and bony armor, others with saber teeth. A second group split off that were small sauropsids. They were no match until about 250mya, the Earth heated, and much of the animal and plant life on land and in the sea perished in a mass extinction.

The most important synapsids that survived were the cynodonts. The size of a large dog and features that showed more hints of mammals we know today (changes in skeletons, jaw, eye socket, ears, hair, and internal body temperature control). The first warm blooded animals. They split into herbivores and carnivores and expanded their territory into a variety of niches and climates. By 210mya they were true mammals.

Surviving sauropsids remained in the background until they spawned dinosaurs about 230mya. The oceans were a hospitable home and they became large sea predators. Eventually some returned to land and became the dominant terrestrial predators. Ancestors of alligators, crocodiles, lizards, snakes, as well as birds. Birds are basically flying reptiles with feathers.

Mammals got wrecked by dinosaurs and had to become nocturnal, surviving on less food and small to avoid them. Tiny shrew-like creatures, living in dense forests.

65mya, 50lb or heavier animals were wiped out. Probably a meteor which produced a cloud of dust which blocked the sun and disrupted photosynthesis. Smaller reptiles, birds, and mammals were impacted less because they needed less to survive. Christine Janis argues it was the small size resulting from not being able to compete that allowed them to survive. “A small animal could be flexible; it could swim, climb, dig, run, or jump as its conditions required. A larger animal had to specialize-and the greater the specialization, the harder it is to alter its body plan to adapt to a changing environment.”

The massive continental drift was around the extinction of dinosaurs, and mammals began to evolve separately and diversify. Further diversification occurred by way of a land bridge between Asia and North America.

Most mammals are of the placental variety (fetus in until breaks, releasing fluid), including rodents, felines, canines, farm animals, flying mammals, marine mammals, and primates.

Humans Incoming

Reptiles replace teeth, while mammals are born without and replace once. Meaning they need to nurse with mammary glands since they can’t chew. It also meant they could protect the infants in a home area. Some other mammalian traits already existed from cynodonts – legs under instead of to the side to facilitate breathing while running (reptiles can’t). It also made oxygen available for metabolism, and internal heating. The first warm-blooded, or endotherms, able to maintain a core stable body temperature under variations in external temperature. They also probably had fur, which reduced some of the metabolic burden.

Also, converted the 3 chamber reptile heart to 4, they had a powerful O2 delivery system to the tissues to make energy. This internal temperature may have helped them survive the global cooling. Birds independently acquired a warm blooded body. Cynodonts had a double-jointed jaw, out of which hearing capacities developed.

Being nocturnal, early mammals had less need for color vision and developed night vision. Swapping color receptors (cones) for light receptors (rods). Of the mammals, only primates reclaimed complex color vision. Early mammals also developed expanded capacities for smell, facilitated by high oxygen intake though the nose, as well as sound processing enhancements. Reptiles and amphibians mainly hear low frequencies. All because of the jaw converting into a sophisticated eardrum and middle ear bones that helped turn sounds into neural messages to send the brain.

Olfactory and auditory processing systems changed to accommodate the increased importance of these modalities over vision in early mammals, and the visual system had to specialize for night vision.

Primates emerged roughly 70mya. Their diet included leaves, flowers, nuts, and fruits, and had the ability to grasp with hands and feet, enabling tree climbing. To forage and escape predators. Their eyes moved to the front of their face, making binocular vision and depth perception, which are important for leaping and grasping. Moved mostly with two legs, making arms available for swinging, steering and manipulating items.

Early primates were prosimians (lemurs and tarsiers). Two other groups were anthropoids (monkeys and apes) and hominids (humans). Anthropoids emerged to shift to day time feeding because of the fovea (region of the retina with a concentration of cone cells). Daytime was still risky but their high-acuity vision meant they could detect predators easily.

Getting bigger, they reverted to all fours again and needed more energy. Depending on fruit was high energy but unpredictable with competition. These pressures increased brain size, and new brain areas, enhancing cognitive capacities and making possible survival based on intelligence as much as brawn.

Humans 6mya had undergone considerable diversification. They could stand upright but were nothing special. Preyed on by large animals but preyed on smaller ones. Homo had sapiens, ergaster, neanderthalensis, and erectus. 10,000 years ago they were extinct and Homo sapiens were all that was left.

It’s thought that about 70,000-30,000ya genetic mutation allowed a rewiring for for abstract thought and language. Perhaps Neanderthals and sapiens both possessed the ability for symbolic thought and language.