There are 5 universal elements in bio active molecules; carbon, nitrogen, oxygen, sulfur and phosphorous. Phosphorous has same 5 electron outer shell as Nitrogen in the periodic table, and sulfur has the same shell as oxygen. They naturally bonds to carbon polymers such as proteins. In N2, the two nitrogen atoms form a triple bond. It is because of nitrogen’s small size that it is able to form pπ-pπ bonds with itself and is surprisingly stable. This property is not exhibited by atoms such as phosphorus. Thus, phosphorus is more reactive than nitrogen. Author Isaac Asimov once called phosphorus "life's bottleneck," because it makes up 1 percent of an organism but is only present in 0.1 percent of minerals on Earth. 

https://www.sciencenews.org/article/phosphorus-earth-earliest-life-forged-lightning-chemistry

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The phosphorus of the primitive Earth was present as phosphates. The primitive Earth was deficient in the total available phosphorus until a sufficient quantity of phosphorus weathered from the igneous rocks in which it was entrapped.  One path to bio accessible phosphorous is through lightening strikes. 

https://pubmed.ncbi.nlm.nih.gov/917502  &https://www.gondwanatalks.com/l/did-lightning-provide-phosphorus-to-ancient-life/

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The best guess was that it all started with the "primordial soup"  hot or cold. New research shows that precursors of ribonucleotides, amino acids and lipids can all be derived by a reducing reaction that adds carbon and nitrogen compounds to hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use ​hydrogen sulfide as the reductant. 

https://phys.org/news/2015-03-chemists-riddle-life-began-earth.html

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A cell is a isolated biochemical factory. Cell walls are made of phospho-lipids, with the hydrophilic phosphate head and two  hydrophobic (polyethylene like) tails. The 2 tails, means that they do not naturally form spherical tail-in micelles, but instead self assemble into roughly flat bilayers.  A bilayer lipid isolates the water in the cell from the outside world. There are portals that allow passage into and out of the cell, and receptors for messaging. Inside the cell are the  template (DNA) with a sugar phosphate backbone, the means for replication, and to generate energy using tri-phosphate to di-phosphate cycles.  

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Primitive protocells were the precursors to today's unicellular organisms. Although the origin of life is largely still a mystery, in the currently prevailing theory, known as the RNA world hypothesis, early RNA (single helix) molecules would have been the basis for catalyzing organic chemical reactions and self-replication.

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The energy transfer molecule in cells is ATP - a "triphosphate". The core process in metabolism is oxidation using energy from ATP to remove acid groups from precursors. In the case of photosynthesis in plants, light is absorbed and reacts with water to make ATP and oxygen is the byproduct.  The ATP is then used to fix carbon from carbon dioxide into biomolecules.

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Once there was a process for building biomolecules, a process evolved for using biomolecules as food by  breaking them down by oxidation in the citric acid cycle to create ATP that could be used for locomotion, sensing, and replication by  the creation of specialist molecules such as proteins. 

 

The most earliest  common ancestor  was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. A thermophile is an organism that thrives at relatively high temperatures, between 41 and 122 °C (106 and 252 °F).   Thermophiles are found in various geothermally heated regions of the Earth, such as hot springs like those in Yellowstone National Park and deep sea hydrothermal vents, as well as decaying plant matter, such as peat bogs and compost.

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The enzymes in thermophiles function at high temperatures and are a  component in DNA replication, even  used  in PCR. PCR employs two main reagents—primers (which are short single strand DNA fragments known as oligonucleotides that are a complementary sequence to the target DNA region) and a DNA polymerase (thermophile enzyme).

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Bacteria evolved from thermophiles and  are microbes with a cell structure simpler than that of many other organisms. Their control centre, containing the genetic information, is contained in a single loop of DNA. Some bacteria have an extra circle of genetic material called a plasmid rather than a nucleus. The plasmid often contains genes that give the bacterium some advantage over other bacteria. For example it may contain a gene that makes the bacterium resistant to a certain antibiotic.

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The fossil record starts around 3.5By years ago with cyano-bacteria in the form of Stromatolites, which are layers of sand and rock glued together by residues from cyano-bacteria. Cyano-bacteria absorbed carbon dioxide and seeded the earth with oxygen. Cyano-bacteria are unicellular. All the oxygen that makes the atmosphere breathable for aerobic organisms originally comes from cyanobacteria or their later descendants.

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Around  2.5 B years ago, there was a great extinction  from Arcaic to Protozic eras "Great Oxygen Event" caused ironically  by increasing oxygen levels which killed the first photosynthetic microbes that were making oxygen. Before the extinction, there are cycles of increasing microbe levels (euchorytes)  followed by die offs. The cycles are signaled by alternating black and red iron oxide deposits in rocks. Eventually, the photosynthesizers evolved resistance and iron gets depleted resulting in much higher oxygen levels even in the deepest oceans, killing of any non-photosynthetic life such as deep ocean vent species. Excess oxygen in the atmosphere depleted methane which is a strong warming gas, so the earth cools into a sever ice age 717 M years ago killing off photosynthesizers. In total  99% of life was killed off. The thaw that followed led to the "Avalon Expolsion" 635-538 M years ago leading to macroscopic life as Ediachrons such as multi-segment worms. Sponges have survived until today. 

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Jellyfish were the first with basic locomotion. Around 550 M ago at the start of the Cambrian, egg laying molluscs   with exoskeletons, and copper based blood that flows throughout  the body. Within the molluscs are a staggering variety of insects, and shellfish. By 420 years ago the cephalons, squid and octopus, evolved closed circulation that delivered oxygen to key organs. Octopus show remarkable intelligence and are a true intelligent alien. The hard exoskeleton limits the size of insects. The soft exoskeletons limit the protection against predators and their load bearing capability. 

 

The evolution of fish began about 450 million years ago with lampreys and then  early fish with  developed the skull and the vertebral column, leading to the first craniates and vertebrates. 

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Around 400 M years ago,  a great increase in fish variety occurred.   It was from the lobe-finned fish that the first amphibians (tetrapods) evolved as four-limbed vertebrates .  Meanwhile, the insects ruled on land until the fish evolved into amphibians.  

 

The earliest known proto-reptiles originated around 312 million years ago during the Carboniferous period, having evolved from advanced 4 legged frog like animals which became increasingly adapted to life on dry land. Their hard shelled eggs allowed reproduction away from water and led to mass occupancy of land. There are  two major clades of reptiles , synapsids which became mammals, the other being the sauropsids (which includes reptiles, dinosaurs and birds). Synapsids have a single temporal fenestra, an opening low in the skull roof behind each eye orbit, leaving a bony arch beneath each; this accounts for their name.[7] The distinctive temporal fenestra developed about 318 million years ago when synapsids and sauropsids diverged, but was subsequently merged with the orbit in early mammals. Lystrosaurus, of the Synapsids, survived the Permian-Triassic extinction, 252 million years ago, as a small 20lb burrowing animal. They were then by far the most common terrestrial vertebrates, accounting for as many as 95% of the total individuals in some fossil beds, until being decimated by the dinosaurs.  The Lystrosaurus marks the point at which the evolutionary line leading to mammals  separates from todays reptiles and birds. They (dinosaurs) have roughly 80% of DNA in common with humans, which accounts for the recognizable "architecture" of   skeletons. Evidence from crocodiles and their extinct relatives suggests that  elevated metabolisms could have developed in the earliest archosaurs, which were the common ancestors of dinosaurs and crocodiles. 

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The devastating Permian–Triassic extinction event (252 M years ago) wiped out an estimated 96% of all marine species and 70% of terrestrial vertebrate species. The scientific consensus is that the main cause of extinction was the large amount of carbon dioxide emitted by the volcanic eruptions that created the Siberian Traps, which elevated global temperatures, and in the oceans led to widespread anoxia and acidification. The Siberian traps are a massive igneous rock outflow covering 7 M squ km. 

Aridification induced by global warming was the chief culprit behind terrestrial vertebrate extinctions. There is enough evidence to indicate that over two thirds of terrestrial labyrinthodont amphibians, sauropsid ("reptile") and therapsid ("proto-mammal") taxa became extinct.  Lystrosaurus  a pig-sized herbivorous dicynodont therapsid, constituted as much as 90% of some earliest Triassic land vertebrate fauna was the largest surviving community.  

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Archosaurs (which included the ancestors of dinosaurs and crocodilians) were initially rarer than therapsids, but they began to displace therapsids in the mid-Triassic. In the mid to late Triassic, the dinosaurs evolved from one group of archosaurs, and went on to dominate terrestrial ecosystems during the Jurassic and Cretaceous. This "Triassic Takeover" may have contributed to the evolution of mammals by forcing the surviving therapsids and their mammaliform successors to live as small, mainly nocturnal insectivores; nocturnal life probably forced at least the mammaliforms to develop fur, better hearing and higher metabolic rates, while losing part of the differential color-sensitive retinal receptors reptilians and birds preserved.  The dinosaurs had offspring that were self sufficient straight out of the egg, whereas the mammals had extend periods requiring feeding by parents to survive. This vulnerability seems to contributed to the dinosaurs predatory dominance. 

 

There is evidence that survivors of the Permian extinction were warm blooded based on isotopes of oxygen in the bones and teeth. The assumption is that they were better able to survive the temperature changes associated with the extinction. 

https://theconversation.com/more-than-252-million-years-ago-mammal-ancestors-became-warm-blooded-to-survive-mass-extinction-79961

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​The evolution of mammals has passed through many stages   By the mid-Triassic, there were many synapsid species that looked like mammals. 

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• gradual development of a bony secondary palate.  This as a prerequisite for the evolution of mammals' high metabolic rate, because it enabled these animals to eat and breathe at the same time.  

• the dentary gradually becomes the main bone of the lower jaw.

• progress towards an erect limb posture, which would increase the animals' stamina.  

 

By the late Triassic period (ca 210 mya), mammalian ancestors were endothermic (requiring fluid to replace incubatory water losses of eggs), very small in size (making large eggs impossible), and had rapid growth and limited tooth replacement (indicating delayed onset of feeding and reliance on milk)

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The lineage leading to today's mammals split up in the Jurassic; synapsids from this period include Dryolestes, more closely related to extant placentals and marsupials than to monotremes, as well as Ambondro, more closely related to monotremes.[1] Later on, the eutherian and metatherian lineages separated; the metatherians are the animals more closely related to the marsupials, while the eutherians are those more closely related to the placentals. Since Juramaia, a small  shrew like animal, the earliest known eutherian, lived 160 million years ago in the Jurassic, this divergence must have occurred in the same period.

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Mass extinction events cause an explosion of evolutionary change. Numerous ecological niches are suddenly empty of both competition and predators. New herbivores and insectivores can flourish, eventually leading to new predators, and new balanced ecosystems

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Dinosaurs diverged from their reptile ancestors during the Middle to Late Triassic epochs, roughly 230 million years. The Triassic/Jurassic extinction (volcanic)  event, 205 M years ago,  left fairly untouched;  plants, crocodylomorphs, dinosaurs, pterosaurs and mammals. The fabulously diverse dinosaurs dominated for over 200My. 

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The dinosaurs were egg layers. The egg limits the amount of energy available to the fetus before birth, at which point it needs to be able metabolize adult food.  The ancestral mammals, led to Monotremes as egg layers who suckle their young, and marsupials who give birth to a "fetus" that suckles and develops in a protected pouch. The most successful were the Eutherans who are placental mammals who develop inside the mothers body directly fed using mother blood through a  placenta. After birth the placentals suckled their young. These variants allowed unlimited access to energy and over 2 years of development  before metabolizing adult food. These variants appeared while dinosaurs dominated.

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The K-T meteor 66My ago changed the trajectory of evolution.  Nothing larger than 50 lbs survived  an explosion  that released the same energy as 100 teratonnes of TNT more than a billion times the energy of the atomic bombings of Hiroshima and Nagasaki.

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Shrews survive the meteor,  mammal species explode, and birds   evolved as the survivors of the dinosaur line.

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The role of extinctions can be seen in diversity, measured as the count of different "families" changing overtime.  The similarities between species from their common ancestor can be seen in  their limb bone structure. 

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Next the line of primates appears around 50 My ago.  Tropical rain forest is really the perfect habitat for the development of high intelligence such as in primates.  Living in the tree tops keeps most predators away, and the tropics  provide  food year round. The development of higher intelligence seems to be associated with a long time to maturation, and one child per birth focuses development resources. All of these require attentive parenting and few predators to ensure survival.  Large size is the other factor to dissuade predators. Primates evolved all the physical attributes of grip, muscularity, agility, and prehensile tails that are required to be a large tree dweller.

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Around 6-7 My ago, Hominids who were bipedal, split from the Great Apes.  At the "Cradle of Humanity" site near Johannesburg,  The Sterkfontein Caves were the site of the discovery of a 2.3-million-year-old fossil Australopithecus africanus. The Rising Star Cave system contains the Dinaledi Chamber (chamber of stars), in which were discovered fifteen fossil skeletons of an extinct species of hominin, provisionally named Homo naledi. Dated at 335–236K yrs ago, they cohabited with homo erectus. Naledi has similar brain size to Australopithecus (& gorillas) and appears to be a sophisticated community with  a ritual burial chamber, including stone tools, fire and wall engravings. Homo naledi was around 5 ft tall, walked upright, with chimp looking faces, longer arms than humans but with human (not chimp - tree living) hands with opposable thumbs.  Early small brained hominids seem to have many characteristics that we think of as "human", and have hung around as a distinct group even up to the arrival of homo sapiens. 

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Early human ancestors came close to eradication in a severe evolutionary bottleneck between 800,000 and 900,000 years ago, according to scientists. A genomics analysis of more than 3,000 living people suggested that our ancestors’ total population plummeted to about 1,280 breeding individuals for about 117,000 years. Scientists believe that an extreme climate event could have led to the bottleneck that came close to wiping out our ancestral line.

https://www.theguardian.com/science/2023/aug/31/population-collapse-almost-wiped-out-human-ancestors-say-scientists

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The ice ages since 400 M years ago, required species to adapt quickly in order to thrive. The ice ages forced animals to migrate in response to climate change which probably made it difficult for new predators to get established. Humans became effective predators, very different from the Great Apes. This helped the early humans to thrive. 

 

By 200Ky ago homo sapiens appeared with 99.5% of the DNA of the common Great Ape ancestor. The earliest homosapiens skeleton "Omo1" was from  195K years ago, dated by Argon levels in the local environment,  was found  in Ethiopia. Prime distinguishing feature in skeleton is facial shape within the brain case; smaller jaw bone, rounder brain case, brow ridge. Structures have been confirmed through DNA.

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Around 40Ky, modern humans must have shared the planet with at least four other human cousins: Homo erectus, the Neanderthals, a strange, small-brained human found only on the island of Flores in Indonesia, affectionately known as the Hobbit; and most recent of all, species X: a separate human genetic lineage identified in 2010 only by DNA extracted from a finger bone found in a Siberian cave. There is also evidence of interbreeding between different human variants, particularly Homosapiens and Neanderthal.

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The increasing size of the brain case is one of the most notable changes in the evolving humans as seen in these skulls at the "cradle of humanity" in South Africa.  There is also evidence that intelligence also seems to be linked to an alternative source of changes in DNA.  DNA changes by mutation, and also courtesy of "transposons" that  move sections of DNA around by writing the information back into a cells DNA, presumably changed which bits get expressed.  The DNA sequence of  hundreds of individual neurons from human cadavers show that cells in the same brain are, indeed, genetically distinct from one another. This suggests a new level of specialization in brain cells. 

https://www.newyorker.com/tech/annals-of-technology/the-strangers-in-your-brain

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We became bipedal which Dawin suggested freed up our hands to use weapons. 

In another notable change we became "naked apes". The most popular explanation is that it allowed much more heat dissipation, which was needed  for our large brains and the need to be a relatively large (50-100 Kg) long distance athlete in open grasslands. Our nearest relatives, the apes, lived in shady tree environments. The density of eccrine glands explains Homo sapiens’ prodigious perspiration abilities. In hot conditions, most people can easily sweat one liter per hour or 12 liters a day. Our highest recorded rates, about 3.5 liter per hour, top those of chimpanzees by between five and ten times .

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Fur loss may have occurred when our ancestors switched from prey to predator. Around two million years ago hominins like Homo erectus became hunters, probably tracking game for long hours in hot, open environments. This is evident from butchered animal bones, found at Homo erectus sites. Furthermore, the species seems to have been a far better endurance athlete than its predecessors based on skeletal features that indicate enhanced running and walking abilities, like long legs, modern feet and a bigger attachment for the butt muscle.

https://www.discovermagazine.com/planet-earth/why-humans-lost-their-hair-and-became-naked-and-sweaty

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The early humans were hunter - gatherers who spent their travelling around following food sources.  There are many surviving native communities that survived to modern times such as native americans, eskimos.  

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During the last ice age, from (c. 115,000 – c. 11,700), hunter gatherers leave Africa and populate all the major land masses using land bridges formed by ice and low sea levels.

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Native residents of the Americas first appeared 10-20,000 years ago over the Bearing Straight. In Southern US, the Clovis people 11,500 to 10,800 BCE,  had distinctive hunting equipment such as the "Clovis Point" arrowhead made from flint (natural quartz). 

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The scientific revolution changed the trajectory of life on earth through modern medicine, hygiene and nutrition.

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Pre industrial revolution the population increased at 0.15% a year, post it has increased to 1.7% a year equivalent to 3 children per couple per generation. This has lead to  the massive consumption of land for food and fossil fuels. 

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