Bio evolution notes

These are notes taken during RPI's BIO 1010 course, relating to a review of evolution and life.

It is recommended to use Ctrl F or the equivalent search function to find the relevant section, as these notes are quite long.

The scientific method

• Independent variable - what is varied
• Potentially confounding (control) variables - what is kept constant
• Dependent variable - what is measured
• Experimental group (treatment) - the group that has been subjected to the differing independent variable
• Control group (treatment) - the group that has not been subjected to the differing independent variable
• Experimental units - the unit that the experimental group is tested on
• Replicates - repeated experiments carried out to improve accuracy
• Scope of inference - how general the results of an experiment are; with more replication the scope is greater

Evolution

Formation of Earth

Billions of years ago, a supernova explosion created a nebula in where the solar system is today. While the majority of the gases in the solar system gathered to form the sun, the cloud of rocks and dust clumped together to form planets, which became rounded because of gravity. Earth itself was formed around 4.5 billion years ago. Due to the molten conditions on Earth at the time, heavy elements such as iron sank deep inside the Earth, and lighter elements floated to the top - this is called the iron catastrophe. This in turn created Earth's molten inner core, which created Earth's magnetic field, protecting it from damaging solar radiation.

Stages of Earth

Black Earth (4.5 BYA)

• Earth was hot molten rock that began to cool and solidify to basaltic rock (modern-day oceanic crust)
• Nothing survived from this stage

Gray Earth (4.3 BYA)

• Intense heat and pressure in the early Earth causes new minerals to form
• Granite becomes the foundation of our continents
• No life yet

Blue Earth (3.8 BYA)

• Earth cools enough for liquid water; water is a universal solvent which allows for organic chemistry to take place
• Zircon crystals which could have only formed in the presence of water provides evidence that liquid oceans were present by 4.3 billion years ago
• Life began at around 3.8 billion years ago; stromatolite fossils dated to 3.5 billion years ago

Red Earth (3.5 BYA)

• Photosynthesizing microbes released a large amount of oxygen, rusting iron and causing it to sink to the bottom of the sea
• Oxygen also causes the formation of more minerals

White Earth (540 MYA)

• Earth plunged into a deep freeze, life is nearly wiped out
• Volcanic activity melts the Earth and destabilizes the atmosphere

Green Earth (520 MYA - present)

• Diversity of life exploded
• Life creates and sculpts its surroundings

The origin of life

Building blocks of life

All elements are forged in the interior of stars. Stars fuse lighter elements (such as hydrogen and helium) into heavier elements, up to iron. Elements are heavier than iron are produced by supernovae. Many carbon-based molecules are brought to Earth by asteroids and comets, and early oceans allow basic organic compounds to form.

Complex biomolecules

The Stanley-Miller experiments in the 1950s showed that a simulation of the atmosphere of early Earth (composed of water vapor, ammonia, methane, and hydrogen), combined with water, heat, and lightning, was able to synthesize simple organic compounds including amino acids. Simple organic compounds combined to form more complex organic compounds. RNA became the original self-replicating molecule, used to encode genetic information. Later, proteins and DNA formed.

Membrane enclosure

The cell membranes of all living organisms are made of phospholipid bilayers that are composed of fatty acids. The head is hydrophilic and the tail is hydrophobic. When exposed to water, the bilayer spontaneously forms a two-layered sheet with the tails pointing toward the center. The membrane is permeable, allowing RNA nucleotides (building blocks of RNA) to enter. With the combination of RNA and membranes, protocells form. While not life, they do have similar characteristics, such as growth and division.

Selection and evolutionary change

The replication of RNA molecules within the protocell creates an osmotic gradient; the cell membrane stretches grabs fatty acids from the membranes of cells with lower RNA replication rates. Therefore, protocells with higher rates of RNA synthesis grow faster, and outcompete protocells with little or no RNA. The replication process of RNA causes better versions of RNA that in turn get better at replicating.

Protocells vs living cells

Protocells are not living cells, but they had many characteristics similar to modern-day living cells, such as lipid bilayer cell membranes, RNA composed of nucleotides.

Potential life outside of Earth

Scientists believe that life can exist on worlds other than Earth, especially on planets in a star's habitable zone, which corresponds to the range of orbital distances where liquid water can exist on a planet's surface. We detect planets by looking for dips in brightness of a star, which indicate planets transiting (crossing in front of) the star. Space telescopes we use for this purpose include TESS, Kepler, and JWST. The Fermi Paradox is the question of why we haven't found life yet if there are so many planets out there.

Emergence

Emergence is the property of a system that has different properties than the sum of its parts. For example, the neurons in the brain are each not conscious, but billions of neurons attached together allow human beings to think, reason, and be self-aware. Life is the ultimate emergent property.

Due to the increase in entropy in every physical system as demanded by the 2nd law of thermodynamics, highly ordered systems all inevitably decay into disordered systems. Life escapes this process by constantly taking in energy from its environment - this is called a metabolism.

The definition of life

Something is considered alive if it satisfies the following characteristics:

• Growth
• Response
• Heredity
• Homeostasis (regulates its internal state)
• Metabolism (converting / using energy to perform a function)
• Reproduction
• Order

Early evolution of life

Hadean Eon

Protocells emerge at the start of the Hadeon eon (4 BYA). Bacteria becomes the first type of life to arise (3.8 BYA).

Archean Eon

Archaea becomes the second domain of life, thriving in extreme environments (3.7 BYA). Later on, (initially anaerobic) photosynthetic bacteria such as Aquifex.

Great oxidation event

Aerobic cyanobacteria develop and form stromatolites (3.5 - 3 BYA). Eukaryotes (complex cells with nucleus and membrane-bound organelles) develop from archea and appear (2.7 BYA).

Endosymbiotic theory is used to explain how eukaryote cells formed - various prokaryotic cells that shared a symbiotic relationship engulfed each other to form the first eukaryotic cells.

Universal features of life

All living cells are:

• Enclosed by a membrane
• Store hereditary information in DNA
• Replicate DNA and use RNA for DNA transcription
• Have ribosomes and proteins to catalyze cellular reactions

Photosynthesis

Early on in the atmosphere, there was no oxygen, as oxygen is highly reactive. After oxygen levels rose, aerobic respiration became the dominant form of metabolism within cells. Chloroplasts primarily perform photosynthesis in plants.

Snowball earth

Due to the increase in oxygen from the great oxidation event, greenhouse gases are reduced dramatically, causing the entire planet to cool down and freeze over. Volcanic activity melted the ice and returned Earth to normal temperatures (~650 MYA).

Ediacaran

The most ancient complex organisms are from the Ediacaran (600 - 540 MYA), and all lived in the oceans and didn't have shells. There is very little we know about them.

The Cambrian explosion

Most of the Ediacaran life forms were extinct by 540 MYA. In their place, thousands of new species emerged in the Cambrian Explosion. These species developed modern body plans, hard shells, locomotion, nervous systems and sensory organs. Theorized causes of the Cambrian explosion include increased oxygen, increased minerals due to weathering, and the development of vision.

Tiktaalik

At 360 MYA, the species Tiktaalik appeared, a transitory animal between ocean and land animals. Fully land-bound creatures appeared soon after.

Early history of evolutionary theory

In 1798, Malthus proposes that many more individuals are born than can possibly survive. Erasmus Darwin proposes that 1800 that all life must be derived from one original ancestor, and slowly changed to become their current forms. Lamarck then proposed that evolution occurs by passing on acquired traits (which was later disproven). Charles Darwin corrects this theory by realizing that competition leads to advantageous traits to be preserved, causing new species. Alfred Russel Wallace similarly published his idea that any advantageous trait would eventually be dominant.

However, there was an issue - the Cambrian explosion was noted by its abruptness and exceptionality, and there was no fossil record indicating an Ediacaran ancestor to the new species of the Cambrian. It is possible that the reason is due to the fact that not much rock preserving fossil evidence survives from that time period.

Natural selection

Natural selection, or "survival of the fittest", is based on several mechanisms:

• Overproduction of offspring - organisms produce more offspring than will survive
• Genetic variation - offspring each have different traits, caused by genetic variation, causing some offspring to be poorly adapted and some to be well adapted to the environment
• Environmental pressures - offspring face challenges surviving in their environment
• Differential survival & reproduction - offspring that are well adapted to the environment survive and potentially reproduce

Origins of variation

Nearly all genes have multiple forms (alleles), which encode the information to generate the phenotype (observed characteristics). For instance, humans that have the red hair allele leads to the phenotype of red hair.

Mutations are usually negative (and thus are not passed on as these individuals don't survive to reproduce) but those that are neutral or useful are passed on, causing genetic variation. Most traits follow a normal distribution within a population, as trait are determined by the additive effects of many genes. Evolutionary change cannot take place without variation.

Forms of selection

Galapagos finches

During Charles Darwin's voyage aboard the HMS Beagle, he studied the fauna of the Galapagos islands. There were 14 species endemic to the islands, and Darwin realized that they were all descended from one species.

During a 1978 study of Geospiza fortis, directional selection was demonstrated after a drought that favored the selection of larger-beaked finches.

Coevolution

Predator and prey evolve together over time, as different species place selection pressures on each other. For example, modern-day Pronghorn are very fast due to coevolution with now-extinct large predators. New Zealand's terrestrial birds are nocturnal due to an extinct large eagle that drove birds into the night.

Sexual selection

In many species, it is typical that the females of the species chose who they wanted to mate with, due to them metabolically using far more resources in the production of offspring. To showcase an individual's favorable genes to pass on to offspring (health, strength, and fitness), and in turn favorability to mate with, many species exhibit elaborate and exaggerated characteristics - such as the tails of peacocks.

Genetic drift

Genetic drift is the random changes in a gene pool in a population.

Genetic drift plays a very important role when a population is bottlenecked (few members survive). Genetic drift means that the population is vulnerable, as there is not a lot of genetic variation, so any random change spreads easily in the population and cause the population to die off.

Genetic drift also causes the founder effect - when small members of a large population move to a new location, genetic diversity also decreases. So the genetics of the population reflect those of the initial members.

Classification of species

The binomial nomenclature system is the standardized system used to classify organisms. A species is generally defined as a group of individuals that can interbreed naturally and produce viable offspring.

Causes of speciation

Species can form from three main ways.

Ring species

An original population can populate around different sides of a geographic barrier and spread around the geographic barrier, but by the time the two isolated populations meet, they can no longer interbreed, producing two new species. This is called a ring species.

Mass extinctions

Mass extinctions have caused many species to grow extinct. The Permian extinction event, occurring 200 million years ago, caused 95% of species to go extinct. The K-T (cretaceous-tertiary) extinction event 65 MYA separate the age of reptiles and the age of mammals. An iridium layer at the K-T boundary in the geological record suggests that the K-T extinction event was caused by an asteroid.

Mass extinctions usually cause a radiation of life, as they leave many niches unoccupied by competitors, allowing new species to fill them.

Evidence for evolution

• Life shares a lot of common genetic information and has molecular commonalities, suggesting it evolved from a universal common ancestor
• There is fossil evidence of life changing from one type to another (e.g. Tiktaalik, Archaeopteryx)
• Anatomically, various different organisms exhibit various homologous morphologies (forms and structures)
  • Note: homologous structures are structures with similar structure and differing function, versus analogous structures are structures with different structure and similar function

Characteristics of primates

Primates are distinguished by having a grasping hand, binocular vision, a large brain, parental care, and sociality. They evolved 80-75 MYA, and have diversified with time. A 47-million year old fossil known as "Ida" was earliest ancestor of humans.

Hominid fossils have been found in different locations around the world. So scientists initially proposed the multiregional hypothesis, which stated that modern-day humans evolved from different species around the world. This has since been disproven with mitochondrial evidence, in which we now believe all modern-day humans originated in Africa and spread around the world.

The first step in human evolution was Australopithecus Afrarensis (or "Lucy") 3.2 MYA, which was the first ape to develop bipedalism - standing on its two feet. The second step was Homo Habilis 2.3 MYA, which had a precision gripping hand for tool-making. This started the pattern of brain growth and complex social behavior for humans. Then came Homo Erectus 1.9 MYA, which moved out of Africa. They innovated building shelters for themselves, and fire. Next, came Homo Neanderthalensis 200,000 years ago, who were almost completely human. They exhibited traits of altruism, burial of their dead, stone tools, art, and likely spoken language. Modern-day humans came out of Africa soon after, likely interbred with Neanderthals, and developed agriculture 10,000 years ago.