Origin of Life, Geologic Time, and Mass Extinctions

Origin of Life: Four Overlapping Stages

• Stage 1: Pre-Cellular Production of Monomers: Nucleotides and amino acids (a.a.'s) were produced prior to the existence of cells.

• Stage 2: Polymerization of Monomers: Nucleotides and a.a.'s became polymerized to form DNA, RNA, and proteins.

• Stage 3: Enclosure in Membranes: Polymers became enclosed in membranes.

• Stage 4: Evolution of Cellular Properties: Polymers enclosed in membranes evolved cellular properties.

• Fundamental Requirements: Life requires an intricate interplay between DNA, RNA, and proteins. Living cells arise from pre-existing cells.

Cosmic and Earth Timeline

• $13 - 17 \text{ bya}$: The Big Bang formed the universe.

• $4.6 \text{ bya}$: Our solar system formed.

• $4.55 \text{ bya}$: Earth formed.

• $4 \text{ bya}$: Earth had cooled sufficiently for its outer layers to solidify and for oceans to form.

• $4 - 3.5 \text{ bya}$: Life emerged on Earth.

Early Earth Conditions and the First Biomolecules

• Primitive Earth Reducing Atmosphere Hypothesis:

  • Primitive Atmosphere Composition: Consisted primarily of $H<em>2O$ vapor, $N</em>2$, $CO<em>2$, with small amounts of $H</em>2$ and $CO$.

  • Oxygen Levels: Characterized by little free oxygen, thus termed a "reducing atmosphere."

  • Temperature: Initially too hot for liquid water.

  • Cooling and Condensation: As Earth cooled, water vapor condensed to form liquid water, leading to the concept of a "primordial soup."

• Abiotic (Prebiotic) Synthesis (Oparin and Haldane, 1920s):

  • Proposed the spontaneous formation of organic molecules.

  • Monomers evolved and subsequently joined to form polymers.

• First Biomolecules: Miller-Urey Experiment (1953):

  • Experimental Setup: Simulated primitive atmospheric gases (e.g., $H<em>2O$, $H</em>2$, $CH<em>4$, $NH</em>3$) and strong energy sources (e.g., electrical sparks to mimic lightning).

  • Results: Demonstrated that biochemicals could be produced from simple nonbiological sources, yielding compounds such as Hydrogen Cyanide (HCN), Formaldehyde ($CH_2O$), glycine, other amino acids, sugars, and nitrogenous bases.

  • Recent Perspectives: More recent research suggests a neutral environment (with $CO$, $CO<em>2$, $N</em>2$, $H_2O$) could also produce organics, indicating that organic molecules can be synthesized under a variety of conditions on primitive Earth.

Alternative Mechanisms for Organic Molecule Formation

• Deep-Sea Vent Hypothesis (1988):

  • Location: Proposed that key organic molecules arose at deep-sea hydrothermal vents.

  • Conditions: Superheated water (around $300 \text{ }^\circ\text{F}$), rich in $H_2S$ and metal ions, mixed with cold seawater.

  • Mechanism: Organics formed within the distinct temperature gradient around these vents.

• Extraterrestrial Hypothesis:

  • Source: Suggests that organic carbon, including amino acids and nucleic acid bases, arrived on Earth from asteroids and comets, effectively stocking the "prebiotic soup."

  • Evidence: Meteorite studies, particularly of carbonaceous chondrites, reveal significant amounts of organic carbon.

  • Controversy: Debate exists as to whether these organics could have survived the intense heat of atmospheric entry and impact.

The First Cells and the RNA World

• Protobionts – Cell-like Structures:

  • Characteristics: Possessed a boundary (e.g., a membrane), contained polymers with genetic information, and polymers with enzymatic functions.

  • Key Property: Capable of self-replication.

• Chemical Selection – The RNA World Hypothesis:

  • Role of RNA in Protobionts: RNA is hypothesized to have played a central role due to its ability to:

    • Store genetic information.

    • Possess the capacity for replication.

    • Exhibit enzymatic functions (acting as ribozymes).

• Stromatolites:

  • Description: Mats of mineralized cyanobacteria, providing ancient fossil evidence of early life.

• Clay Hypothesis:

  • Mechanism: Simple organic molecules polymerized on solid surfaces like clay, mud, or inorganic crystals to form more complex organic structures.

• Transition: The RNA World was eventually replaced by the more stable and efficient DNA/RNA/Protein World.

Advantages of the DNA/RNA/Protein World

• Information Storage:

  • DNA's Role: DNA took over the primary informational role from RNA, allowing RNA to diversify into other functions (e.g., tRNA, mRNA, rRNA).

  • Stability: DNA is inherently less susceptible to mutations and is more chemically stable than RNA, ensuring more reliable information storage.

• Metabolism and Other Cellular Functions:

  • Protein Catalysis: Proteins offer significantly greater catalytic potential and efficiency compared to ribozymes (RNA enzymes).

  • Diverse Functions: Proteins can perform a vast array of other essential cellular tasks, including forming the cytoskeleton, facilitating transport, and providing structural support.

Understanding Earth's History Through Fossils

• What are Fossils: Fossils are the preserved remains and traces of past life.

• Paleontology: The scientific study of the fossil record.

• Formation of Fossils:

  • Most fossils are traces of organisms embedded within sediments.

  • Sediment is gradually converted into sedimentary rock.

  • This rock forms recognizable strata (layers) in a stratigraphic sequence.

• Stratigraphic Principles:

  • Strata of the same age typically contain similar fossil assemblages.

  • This principle aids geologists in determining the relative dates of embedded fossils, even when geological upheavals have disturbed the rock layers.

Factors Affecting the Fossil Record

Absolute Dating: Radiometric Techniques

• Radiometric Dating: A method for determining the absolute age of fossils and rocks.

• Half-life ($t_{1/2}$):

  • Definition: The specific length of time required for half of the radioactive atoms in a sample to decay into a stable daughter product.

  • Stability: Half-life is unaffected by external factors such as temperature, light, or pressure.

  • Dependability: All radioactive isotopes exhibit a dependable half-life, ranging from mere seconds to billions of years.

• General Formula: Calculated using the remaining fraction of the radioisotope and its half-life.

• Key Radioactive Isotopes and Their Half-lives:

• Practice Problems:

  1. Question: What fraction of the original $C^{14}$ remains in a sample after $11,460$ years?

     • Solution: $11,460 \text{ yrs} / 5730 \text{ yrs/half-life} = 2 \text{ half-lives}$. After $2$ half-lives, $1/4$ of the original $C^{14}$ remains.

  2. Question: How old is a sample that contains $25\%$ of its original $K^{40}$?

     • Solution: $25\%$ remaining means $2$ half-lives have passed. The half-life of $K^{40}$ is $1.25 \text{ byrs}$. So, the age is $2 \times 1.25 \text{ byrs} = 2.5 \text{ billion yrs}$.

  3. Question: An anthropologist claims a specimen is $30,000$ years old. It contains a $C^{14}$ to $N^{14}$ ratio of $1:7$. Is his claim valid?

     • Solution: A $1:7$ ratio implies $1/8$ of original $C^{14}$ remains ($1/(1+7)$). This is $3$ half-lives ($1/2^3$). The age is $3 \times 5730 \text{ yrs} = 17,190 \text{ yrs}$. The claim of $30,000$ years is not valid.

  4. Question: How many half-lives have elapsed to yield a sample with $125$ atoms of $C^{14}$ and $375$ atoms of $N^{14}$?

     • Solution: Total atoms (original parent) = $125 + 375 = 500 \text{ atoms}$. Remaining $C^{14}$ = $125 \text{ atoms}$. Fraction remaining = $125/500 = 1/4$. This means $2$ half-lives have passed.

  5. Question: If the $U^{235}:Pb^{207}$ ratio in a zircon in a sandstone was found to be $1:3$, how old is the zircon?

     • Solution: A $1:3$ ratio implies $1/4$ of original $U^{235}$ remains. This corresponds to $2$ half-lives. Age = $2 \times 713 \text{ million yrs} = 1.426 \text{ billion yrs}$.

  6. Question: If the $K^{40}:Ar^{40}$ ratio in a zircon in a granite was found to be $1:7$, how old is the sample?

     • Solution: A $1:7$ ratio implies $1/8$ of original $K^{40}$ remains. This corresponds to $3$ half-lives. Age = $3 \times 1.25 \text{ billion yrs} = 3.75 \text{ billion yrs}$.

Geologic Time Scale and Mass Extinctions

• Earth's History: Spans approximately $4.55 \text{ bya}$ to the present.

• Mass Extinction Events: Significant periods of rapid and widespread loss of biodiversity. The geologic record indicates several major mass extinctions, including events where $85\%$, $83\%$, $95\%$, $80\%$, $76\%$ of marine species vanished, and a currently unfolding Sixth Mass Extinction.

• Changes in Organisms Result From:

  1. Genetic changes (evolutionary processes).

  2. Environmental changes (natural or anthropogenic).

• Patterns of Change Correlated With:

  • Climate/Temperature fluctuations.

  • Atmospheric composition changes.

  • Movement of land masses (Continental drift at $1-10 \text{ cm/yr}$).

  • Major floods or glaciations.

  • Volcanic eruptions.

  • Meteorite impacts.

• Precambrian Time: Comprises the Hadean, Archaean, and Proterozoic Eons, covering approximately $87\%$ of geologic time. The Ediacaran period marks its end.

Precambrian Time (approx. $4.5 \text{ bya}$ to $543 \text{ mya}$)

• Duration: Encompasses approximately $600 - 4,500 \text{ mya}$. Includes the Hadean, Archaean, and Proterozoic Eons (about $87\%$ of geologic time).

• Atmospheric Conditions: Initially little or no atmospheric oxygen, meaning a lack of an ozone shield which allowed intense UV radiation to bombard Earth's surface.

• First Cells: Came into existence in aquatic environments.

  • Prokaryotes: Appeared around $3.5 \text{ bya}$.

  • Cyanobacteria: Left many ancient stromatolite fossils. These organisms were crucial as they added the first significant amounts of oxygen to the atmosphere through photosynthesis, leading to the evolution of aerobic species.

• Eukaryotic Cells: Arose around $2.5 \text{ bya}$, explained by the Endosymbiotic Hypothesis.

• Multicellularity: Arose around $1.5 \text{ bya}$.

Ediacaran Period (approx. $600 - 540 \text{ mya}$)

• Timing: The very end of the Proterozoic Eon.

• Life Forms: Appearance of multicellular animals, including sponges. Characterized by unusual soft-bodied, mudflat-dwelling animals with no internal organs, shells, or bones.

• Yilingia spiciformis: A newly discovered fossil (2018) from Southern China, measuring $27 \text{ cm} \times 2.5 \text{ cm}$. It possessed a segmented, cylindrical body and showed similarities to some Cambrian animals.

• End Event: A mass extinction event occurred at the end of this period.

Phanerozoic Eon (Current Eon, $543 \text{ mya}$ to Present)

Paleozoic Era ($543 - 248 \text{ mya}$)

• Key Feature: Experienced $3$ major mass extinction events.

  Cambrian Period ($543 - 490 \text{ mya}$) - "Cambrian Explosion"

  • Climate: Warm, wet climate with sufficient oxygen and no ice at the poles.

  • Biodiversity: Witnessed the rapid appearance and diversification of nearly all existent animal phyla. Many marine invertebrates with shells flourished. The first vertebrates appeared around $520 \text{ mya}$.

  • Causes of Diversity: High diversity may be attributed to:

    • Favorable environment (high oxygen levels).

    • Evolution of Hox genes, which control body plan development.

    • A "Predator/Prey Arms Race," driving the evolution of defenses like shells and promoting reef-building.

  • Burgess Shale Organisms: Famous for preserving diverse, exquisitely detailed soft-bodied organisms from this period.

  • New Discovery - Titanokorys gainesi (2021): A massive new radiodont (primitive arthropod) discovered in the Burgess Shale, measuring half a meter long, with a 3-part carapace, multifaceted eyes, a tooth-lined mouth, and spiny claws, earning it the moniker "swimming head."

  Ordovician Period ($490 - 443 \text{ mya}$)

  • Climate: Warm temperatures, very moist atmosphere with high $CO_2$ levels; all continental landmasses were north of the tropics.

  • Marine Life: Diverse marine invertebrates flourished, including trilobites, brachiopods, bryozoans, conodonts (earliest vertebrates), red and green algae, primitive fish, cephalopods, corals, crinoids, and gastropods.

  • Land Invasion: Primitive plants and arthropods began to colonize land.

  • Mass Extinction: An abrupt climate change, likely caused by extensive glaciation, resulted in a mass extinction event where $60\%$ of marine invertebrates perished at the end of this period.

  Silurian Period ($443 - 417 \text{ mya}$)

  • Climate: Stable climate as glaciers melted.

  • Life Forms: Significant diversification of vertebrates (especially fish) and plants; coral reefs made their appearance. A large-scale colonization of terrestrial environments by plants (notably seedless vascular plants) and animals (arthropods) occurred.

  Devonian Period ($417 - 354 \text{ mya}$) - "The Age of Fishes"

  • Climate: Northern regions were dry, while southern regions were wet (oceans).

  • Terrestrial Life: Many more terrestrial species emerged. Gymnosperms (seed plants) made their debut. Insects also emerged.

  • Vertebrate Evolution: Tetrapods (four-limbed vertebrates), specifically amphibians, began to emerge. Invertebrates continued to flourish in the oceans.

  Carboniferous Period ($354 - 290 \text{ mya}$)

  • Geological Feature: Characterized by the formation of rich coal deposits globally.

  • Climate/Environment: Cooler conditions with land covered by vast forested swamps.

  • Biological Diversification: Plants and animals further diversified significantly. Very large plants and trees were prevalent. Flying insects evolved. Amphibians were prevalent.

  • Key Evolutionary Innovation: The amniotic egg emerged, marking the appearance of reptiles, allowing them greater independence from water for reproduction.

  • ### Permian Period ($290 - 248 \text{ mya}$)

    • Continental Drift: The supercontinent Pangaea formed, leading to significant environmental changes.

    • Climate: Interior regions of Pangaea became dry with pronounced seasonal fluctuations.

    • Plant Life: Forests shifted to domination by gymnosperms.

    • Animal Life: Amphibians remained prevalent, but reptiles became the dominant terrestrial vertebrates. The first mammal-like reptiles appeared.

    • Mass Extinction: The end of the Permian Period witnessed the largest known mass extinction event in Earth's history, causing the disappearance of an estimated $95\%$ of marine species.

Mesozoic Era ($248 - 65 \text{ mya}$) - "Age of Reptiles"

• Climate: Consistently hot climate with dry terrestrial environments and little to no ice at the poles.

  Triassic Period ($248 - 201 \text{ mya}$)

  • Plant Life: Gymnosperms were dominant.

  • Reptiles: Reptiles were abundant, and the first dinosaurs made their appearance.

  • Mammals: The first true mammals evolved, though they remained small and relatively inconspicuous.

  Jurassic Period (54 million-year span, $201 - 145 \text{ mya}$)

  • Dinosaurs: Achieved enormous size and diversified extensively, becoming the dominant terrestrial life forms.

  • Mammals: Remained small and largely insignificant in the ecosystem.

  • Birds: The first birds appeared.

  • ### Cretaceous Period (80 million-year span, $145 - 65 \text{ mya}$)

    • Dinosaurs: Began a precipitous decline toward the end of the period.

    • K-T Extinction (Cretaceous-Tertiary): A major mass extinction event at the end of this period, attributed to a combination of a large meteorite impact and intense volcanism, leading to the demise of non-avian dinosaurs.

    • Mammals: Began an adaptive radiation, moving into habitats vacated by the disappearance of dinosaurs, setting the stage for their dominance in the succeeding era.

Cenozoic Era ($65 \text{ mya}$ through today) - "Age of Mammals"

• Periods: Encompasses the Paleogene, Neogene (formerly Tertiary), and Quaternary Periods.

• Climate Shift: Tropical conditions gradually gave way to a colder, drier climate.

• Biological Diversification:

  • Mammals: Continued their adaptive radiation, filling diverse ecological niches.

  • Birds, Fishes, Insects: Also diversified significantly.

  • Flowering Plants: Were already diverse and plentiful, continuing their evolutionary success.

• Quaternary Period ($1.8 \text{ mya}$ to today):

  • Primate Evolution: The evolution of primates began during the Cenozoic.

  • Age of Man (Hominids): Homo sapiens appeared approximately $130,000$ years ago.

Primate Evolution

• Lineage: Includes lemurs, tarsiers, monkeys, apes, and humans.

• Ancestry: All descended from tree-dwelling organisms.

• Arboreal Adaptations (for climbing trees):

  1. Rotating shoulder joint, allowing for a wide range of arm movement.

  2. Big toe and thumb widely separated from other digits, enabling grasping.

  3. Stereoscopic vision (forward-facing eyes for depth perception).

• Other Unique Primate Traits: Larger brain size relative to body size, typically one offspring per pregnancy, and an upright body posture.

• Human Evolution (Homo Lineage):

  • Key Evolutionary Changes: Bipedalism (walking on two legs) and a significant increase in brain size.

  • Distinguishing Feature: Fully opposable thumb, enhancing dexterity and tool use.

  • Ancestral Lineage: Examples include Australopithecus, H. habilis, H. erectus.

  • Non-Ancestral Lineages: Neanderthals and Denisovans represent distinct, related hominin groups that co-existed with early Homo sapiens.

The Sixth Mass Extinction (Holocene/Anthropocene Extinction)

• Current Crisis: Earth is currently experiencing the most severe wave of species die-offs since the extinction of the dinosaurs $65 \text{ million years ago}$.

• Anthropogenic Impact: Human activities are the primary driver of this extinction event, leading to drastic changes in ecosystems and species populations.

• Land Animals Biomass Shift:

  • Previously, $100\%$ of vertebrates were wildlife.

  • Currently, only $3\%$ of land animal biomass consists of wildlife; the remaining $97\%$ is composed of humans, pets, and livestock.

  • Animal populations have decreased by an average of $80\%$ since $1900$.

• Humans as "Global Superpredators": Human population growth and consumption patterns designate humans as a dominant force impacting global ecosystems.

• Atmospheric $CO_2$ Levels:

  • Human activities have increased atmospheric $CO_2$ by $50\%$.

  • This human-induced rise is greater than the natural increase observed at the end of the last ice age $20,000 \text{ years ago}$ (NOAA).

  • Permian extinction levels: $2,000-3,000 \text{ ppm}$.

  • Today's $CO_2$ level: $413 \text{ ppm}$ (but rising rapidly).

• Recent Declines (Since Dawn of Human Civilization):

  • $83\%$ of wild mammals have vanished.

  • $80\%$ of marine mammals have vanished.

  • $50\%$ of plants have vanished.

  • $15\%$ of fish have vanished.

  • (Source: Bar-On, Yinon M; Phillips, Rob; Milo, Ron (2018). "The biomass distribution on Earth". Proceedings of the National Academy of Sciences. 115 (25): 6506–6511.)

  • Many species face imminent extinction, potentially within $10-15$ years.

• Living Planet Report 2022 Findings:

  • Vertebrate Decline: An average of $69\%$ decline in monitored populations ($32,000$ populations) of mammals, birds, amphibians, reptiles, and fish between $1970$ and $2016$.

  • Regional Hotspots: Most significant declines observed in tropical subregions of the Americas ($94\%$ decline) and Africa ($66\%$ decline).

  • Freshwater Vulnerability: Freshwater biodiversity is declining faster than terrestrial or oceanic biodiversity (an $83\%$ decline).

  • Megafauna: Large-sized species (megafauna) are particularly vulnerable to extinction.

• Extinction Risk (Survival Probability):

  • Plant extinction risk is comparable to that of mammals and higher than for birds.

  • Over $1/5$ of wild species are at risk of extinction this century due to climate change alone.

• Primates on the Brink: Examples include Grauer's Gorilla, Aye-Aye, Northern Sportive Lemur, Pygmy Tarsier, Rondo dwarf galago, and Slow Loris.