History of Life on Earth

Age of the Earth

• Earth is approximately $4.5$ billion years old.

Evidences that Earth existed for a long time

• Fossils - Some dry land today was covered by oceans

• Many layers of rock - Rocks layers represent the order rocks and fossils appeared thus they traced the history on earth

Timeline of Lifeforms

1. 4.6 - 3.8 BYA - Due to violent environment: meteorites, volcanic eruptions.
   (Zircon Crystal)

2. 3.5 BYA - Discovered in sedimentary rock formation called stromatolites
   (Prokaryotes) / common ancestor

3. 3.0 BYA - First photosynthetic organism that emitted blue green algae
   (Cyanobacteria)

4. 2.0 BYA - Influx of multicellular organism occurred 1.2 billion years ago
   (Eukaryotic)

5. 500 MYA - Paleozoic era, they became dominant specifically cambrian and ordovician
   (Trilobite & Cephalopods)

6. 251 - 65.5 MYA - Mesozoic era, the age of reptiles, and periods: Triassic, Jurassic, Cretaceous
   (Reptiles)

7. 250 TYA - Cenozoic era, the age of mammals and recent life based on paleontological evidence
   (Homo erectus)

Geologic Time Scale

• Organized from largest to smallest: Eon, Era, Period, Epoch.

• Understanding this scale helps comprehend organism evolution and environmental impact.

Key Eras

• Precambrian: Earliest geological time with trace fossils appearing.

• Mesozoic: Known as the age of reptiles; significant for the extinction of dinosaurs.

• Cenozoic: Known as the age of mammals; mammalian dominance began here.

Important Events in Geologic Time

• Formation of Pangea during the Mesozoic Era.

• The asteroid impact that led to the extinction of dinosaurs.

Major Organisms and Evolution

• Cyanobacteria appeared around $3.0$ billion years ago, significant for photosynthesis.

• The oldest known materials on Earth date back to around $4.6$ billion years ago, coinciding with the formation of the Earth.

The Four Theories

1. Spontaneous generation - life came from non living things

2. Biogenesis - life only came from other living things

3. Cosmogenesis - life on earth came from another part of our solar system/galaxy

4. Special creation - all religious belief

The philosophers

• Aristotle, Greek - Abiogenesis theory/Spontaneous generation (idea of life can appear on non-living things)

• Fransesco Redi, italian 1886 - disproved Spontaneous generation “maggot on a flask”

• John Needham, english 1748 - tried to prove spontaneous generation can occur under right conditions “boiled broth to kill organism in it”

• Lazzaro Spallanzani, italian 1767 - did an experiment to verify Needham’s theory

• Louis Pastuer - convinced most scientist the spontaneous generation could not occur.

Lesson 4.1 : Change in Population

Artificial and Natural selection
Key Concepts/ Definition

Evolution and Selection Mechanisms

• Natural selection favors traits that improve survival and reproductive success in changing environments (e.g., finch beak variations to exploit different food sources).

• Artificial selection is based on selective breeding to enhance desirable traits in plants and animals, improving production efficiency (e.g., domestication of pigs, bean varieties).

• Both natural and artificial selection cause changes in population structure by altering gene frequencies over generations.

Genetic Mechanisms Affecting Population Structure

• Mutation introduces new genetic variants:

  • Advantageous mutations increase fitness.

  • Deleterious mutations reduce fitness.

  • Neutral mutations have no effect on fitness but may persist in the population.

• Genetic drift can randomly reduce genetic diversity, especially in small populations (illustrated through beetle color variants wiped out by chance).

• Founder effect refers to the loss of genetic variation in the new population that was established by a very few individuals from a larger population.

• population bottleneck events drastically change genetic structure due to reduced population size or initial genetic pool.

• Recombination during meiosis shuffles DNA segments, creating genetic diversity critical for evolution.

Summary of Population Genetics Components

Evolution

Core Concepts of Evolution

• Evolution is continuous, not a completed event culminating in humans or any species as a final product.

• It involves descent with modification, where traits are passed from ancestors to descendants with variations.

• Organisms better adapted to their environments have higher chances of survival and reproduction, contributing to evolutionary change.

Species and Speciation

• Species are defined by Ernst Mayer as groups of interbreeding natural populations that are reproductively isolated from other such groups. Members of a species are capable of producing fertile offspring.

• Speciation is the evolutionary process through which populations evolve to become distinct species, arising from existing species.

Reproductive Isolation Mechanisms

Reproductive isolation is key to speciation. It prevents gene flow between populations and can be categorized into pre-zygotic and post-zygotic mechanisms.

Pre-zygotic Isolation (Prevents fertilization)

• Geographic or Ecological Isolation: Species live in different areas or habitats, preventing encounters.

• Temporal or Seasonal Isolation: Different reproductive timings prevent mating (e.g., plants flowering in different seasons).

• Behavioral Isolation: Differences in mating behaviors or courtship patterns (e.g., distinct bird songs).

• Mechanical Isolation: Incompatibility in reproductive organs prevents mating.

• Gametic Isolation: Incompatibility between sperm and egg prevents fertilization, sometimes due to immune responses.

Post-zygotic Isolation (Occurs after fertilization)

• Hybrid Inviability: Fertilized eggs fail to develop properly (e.g., tiger-leopard crosses result in miscarriage).

• Hybrid Sterility: Hybrids are sterile due to abnormal gonad development or chromosome segregation (e.g., mules from horse and donkey).

• Hybrid Breakdown: First-generation hybrids are viable, but subsequent generations are weak or sterile.

Modes of Speciation

Charles Darwin and the Development of Evolutionary Theory

• Charles Darwin (1809–1882) was an English naturalist who formulated the theory of natural selection as the mechanism of evolution.

• He observed variation among individuals within species and recognized that some variations conferred survival advantages.

• Darwin noted the struggle for existence in nature, where individuals with advantageous traits (stronger, faster, more attractive) were more likely to survive and reproduce.

• His famous voyage aboard the H.M.S. Beagle (1831–1836), especially observations from the Galápagos Islands, provided critical evidence for his revolutionary ideas.

• Darwin’s theory, published in On the Origin of Species (1859), argued that species evolve over time through natural selection, where advantageous heritable traits become more common.

• He introduced the term descent with modification, emphasizing common ancestry and the accumulation of changes over generations.

• Darwin’s concept viewed life as a tree of life, contrasting with Lamarck’s linear progression (ladder) of species.

Historical Figures in Evolutionary Thought

Phylogeny and Evolutionary Relationships

• Phylogeny is the evolutionary history of a group of organisms, tracing their ancestry and relationships.

• It integrates molecular data (DNA sequences) and anatomical features.

• Phylogenetic trees visually represent these relationships, showing a common ancestor at the root and branching lineages representing species divergence.

Key Terminology

Summary of Genetic Engineering and Related Concepts in General Biology

Core Concepts in Genetics and Genetic Engineering

• Genetics is the branch of biology that studies DNA, genes, and how traits are inherited by offspring.

• Genetic engineering involves the artificial manipulation, modification, and recombination of DNA or other nucleic acids to alter organisms or populations, aiming to enhance organism capabilities beyond natural limits.

Genetic Engineering Techniques

The document outlines several techniques used in genetic engineering and related biological manipulations:

Detailed Explanation of Selected Techniques

• Selective Breeding/Artificial Selection: Breeders choose parents with desired physical traits to produce offspring carrying those traits, enhancing characteristics in crops or animals.

• Hybridization: Involves crossing genetically different plants or animals to combine beneficial traits, exemplified by Burbank’s hybrid potato.

• Inbreeding: Maintains specific traits by breeding genetically similar individuals but can lead to complications such as reduced fertility.

• Gene Splicing: Enables precise manipulation of DNA by cutting and inserting sequences, facilitating the study of gene function and creation of novel proteins.

• Gel Electrophoresis: Separates molecules by size and charge, crucial for genetic fingerprinting, gene analysis, and evolutionary studies.

• Recombinant DNA Technology: Involves combining DNA from different organisms; plasmids (small circular DNA molecules) are commonly used as vectors for gene transfer.

Matching Genetic Engineering Techniques with Descriptions

Genetically Modified Organisms (GMOs) and Transgenic Organisms

• GMOs/Transgenic Organisms are those whose genetic material has been altered using genetic engineering techniques.

Examples of GMOs include:

Benefits of Genetic Engineering

• Improvement of crop quality and yield, leading to enhanced food production.

• Production of pharmaceuticals and drugs for treating diseases.

• Development of biofertilizers and biopesticides to support sustainable agriculture.

• Bioremediation applications to address environmental pollution.

Applications of Genetic Engineering Techniques

• Medicine Production: Recombinant DNA technology allows mass production of hormones (e.g., insulin), vaccines, and other therapeutic proteins.

• Agriculture: Enhanced crops with pest resistance, improved nutritional qualities, and higher yields.

• Environmental Management: Use of genetically modified organisms to clean pollutants or improve soil quality.

• Scientific Research: Techniques like gel electrophoresis and gene splicing facilitate understanding of genetics, protein function, and evolutionary relationships.

Summary Table: Genetic Engineering Techniques and Uses

Summary: Processes Involved in Genetic Engineering

This content provides a comprehensive overview of genetic engineering, focusing on the principles, historical development, techniques, and applications, particularly recombinant DNA (rDNA) technology. It emphasizes the limitations of traditional breeding, the advent and milestones of genetic engineering, and the stepwise processes involved in producing genetically modified organisms (GMOs), with detailed examples such as Bt corn and transgenic animals.

Key Concepts and Background

• Selective Breeding has historically been the primary method for crop improvement in the Philippines (e.g., rice, corn, cabbage, sugarcane) and animal domestication (e.g., dogs from gray wolves). However, classical breeding methods have limitations, especially for traits like disease resistance (e.g., stem rust in wheat), which are difficult to introduce through traditional means.

• Genetic Engineering is defined as the direct manipulation of an organism’s genes in a laboratory setting to express desired traits. This contrasts with selective breeding by enabling the transfer of genes across reproductive barriers, thus allowing traits to be introduced between reproductively incompatible organisms.

• The core technique used in genetic engineering is Recombinant DNA (rDNA) technology, which involves adding, deleting, overexpressing, or underexpressing specific genes to achieve desired phenotypic outcomes.

Historical Timeline of Genetic Engineering

• 1972: Cohen and Boyer successfully introduced a plasmid segment into a different bacterial plasmid, making Escherichia coli the first transgenic organism.

• 1974: Jaenisch created the first transgenic animal, a mouse.

• 1977: Genentech produced human somatostatin protein in genetically modified E. coli.

• 1983: Bevan, Flavell, and Dell-Chilton developed the first transgenic crop, tobacco.

Principles of Recombinant DNA Technology

• DNA is considered the blueprint of life, encoding instructions for protein synthesis.

• Proteins determine the phenotypic traits of organisms.

• Genetic engineering involves:

  • Identification of a gene of interest (e.g., a gene conferring pest resistance).

  • Isolation of the gene using biochemical tools.

  • Insertion of the gene into a host organism to express the desired trait.

Case Study: Bt Corn

• Corn is a major agricultural crop susceptible to infestation by corn borers (genus Ostrinia), which can cause significant crop damage.

• Through rDNA technology, the Bt toxin gene (cry1Ab gene) from Bacillus thuringiensis is introduced into corn.

• The cry protein produced by Bt corn creates holes in the gut of corn borers, thereby protecting the crop from infestation.

• This modification makes Bt corn resistant to corn borers, leading to improved crop yield and reduced pesticide use.

Detailed Process of Genetic Engineering

1. Identification of the Gene of Interest

   • Example: The Bt gene (cry1Ab) encodes a protein toxic to specific pests.

2. Isolation of the Gene

   • Use of restriction enzymes (endonucleases) to cut DNA at specific sequences.

   • Pioneers: Werner Arber studied bacterial restriction enzymes; Hamilton Smith and Daniel Nathans demonstrated the ability of restriction enzymes to cut DNA at specific sites.

   • Example: EcoRI enzyme from E. coli recognizes and cuts the sequences 3’CTTAAG and 5’GAATTC.

3. Insertion of the Gene into a Vector

   • DNA ligase is used to join the gene of interest with a plasmid or other vector.

   • The recombinant DNA (plasmid + gene) is introduced into a bacterial cell.

4. Methods for Introducing Foreign Genes into Host Cells

   • Microprojectile bombardment (gene gun): DNA-coated gold particles are shot into target cells.

   • Electroporation: Uses electrical pulses to increase cell membrane permeability.

   • Agrobacterium tumefaciens-mediated transformation:

     • A. tumefaciens naturally inserts its Ti plasmid into plant genomes, causing crown gall tumors.

     • This mechanism is exploited to insert foreign genes (e.g., cry1Ab) into crop genomes.

5. Transformation of Host Organism and Regeneration

   • Bacteria harboring recombinant plasmids are used to infect plant cells or tissues.

   • Transformed plant cells are cultured to regenerate whole plants expressing the desired trait.

Summary of Essential Steps for Producing Transgenic Crops Using rDNA Technology

Other Examples of Genetic Engineering Applications

• Transgenic Mice: Created for research and biomedical applications by introducing foreign genes.

• Transgenic Bacteria (e.g., E. coli): Engineered to produce human proteins such as somatostatin.