Comprehensive Biology of Life: Principles, Hierarchy, and Evolution

Fundamentals of Biology and the Definition of Life

• Biology is defined as the scientific study of living organisms. This field encompasses various aspects of life, including structure, function, biochemistry, regulatory processes, growth, development, and evolution.

• Life is a complex concept to define because it exists in highly diverse forms. These forms exhibit varying patterns of living and dying. For example, animal cuttings cannot grow or survive as plant cuttings do. If plant cuttings, such as flowers from a florist, are placed in water near a sunny window, they will continue to grow and bloom before eventually withering, demonstrating that they are still alive.

• The most basic unit of life that exhibits all specific properties of life is the cell.

• All life on Earth shares a specific set of foundational properties:

  • A common set of chemical components.

  • A common set of cellular structures.

  • A common hierarchy of complexity.

  • A common fundamental set of genes.

  • A common ancestry.

The Diversity and Classification of Life Forms

• Life is organized into groups—such as bacteria, plants, and algae—based on similarities in biological processes.

• The majority of life on Earth exists as single-celled (unicellular) organisms. These include:

  • Bacteria.

  • Archaea.

  • Protists.

  • Yeasts (a type of fungi).

  • Certain types of algae.

• Unicellular life requires microscopes for observation, revealing an immense diversity of physical and molecular adaptations.

• Multicellular life is visible to the naked eye and is generally classified into three major groups:

  • Animals.

  • Plants.

  • Fungi.

• Cellular structures are used to differentiate life into two primary categories:

  • Prokaryotes: These organisms have simpler, less complex internal structures. All members of the domains Bacteria and Archaea are prokaryotes.

  • Eukaryotes: These organisms possess complex internal cellular structures. While all multicellular life forms (animals, plants, fungi) are eukaryotes, the group also includes some unicellular organisms, such as protists and yeasts.

Emergent Properties and the Biological Hierarchy

• Life is characterized by the concept of emergence. An emergent property is a novel, complex property that exists only when individual parts are combined together in specific ways; these properties are not present when the parts are analyzed in isolation. It shows greater complexity than predicted by the simple addition of its individual parts.

• A non-biological example of emergence is a bicycle. While individual parts (wheels, chains, pedals) cannot perform the function of transportation on their own, they become functional in a complex way when correctly assembled.

• Biologists organize the complexity of life into a hierarchical structure. Interactions at lower levels allow for the prediction of interactions at higher levels. The primary hierarchy includes:

  • Atoms: The fundamental building blocks of matter; their interactions allow for the formation of molecules.

  • Molecules: Chemical structures consisting of two or more atoms.

  • Organelles: Functional components within cells.

  • Cells: The basic unit of life.

  • Tissues: Groups of similar cells working together.

  • Organs and Organ Systems: Structures composed of multiple tissues performing specific functions.

  • Organisms: Individual living entities.

  • Populations: Groups of the same species in a specific area.

  • Communities: Interacting populations of different species.

  • Ecosystems: All living things in an area interacting with the non-living environment.

  • Biosphere: The global sum of all ecosystems.

The Central Dogma of Life

• The Central Dogma describes the universal process of protein synthesis which unites all life on Earth. All organisms use the same method to produce proteins, allowing DNA from one organism to potentially be used to synthesize proteins in a completely unrelated organism.

• The process involves specific molecular instructions:

  • DNA (Deoxyribonucleic acid): Contains regions that provide instructions for making RNA molecules.

  • Transcription: The process by which DNA provides instructions for the synthesis of RNA. It is important to note that DNA does not "turn into" RNA.

  • Translation: the process where the RNA sequence is used to assemble a protein.

• The fundamental flow of information within all cells follows this pattern:     $\text{Sequence of DNA} \rightarrow \text{Sequence of RNA} \rightarrow \text{Proteins}$

Evidence for Common Ancestry

• Genetic evidence strongly supports the hypothesis that all life on Earth evolved over a long period from a single common ancestor. This ancestor is often referred to as LUCA (Last Universal Common Ancestor).

• LUCA was likely a bacterium that lived near a deep-sea hydrothermal vent approximately $4$ billion ($4 \times 10^9$) years ago.

• Despite the immense diversity of life, all organisms share common DNA and the same genetic code for essential cellular functions, such as translation.

• Venn diagrams of shared genes illustrate this relatedness. For example, a comparison of three plant species—$Oryza\,sativa$, $Arabidopsis\,thaliana$, and $Populus\,trichocarpa$—reveals significant genetic overlap:

  • $Oryza\,sativa$ unique genes: $18000$

  • $Arabidopsis\,thaliana$ unique genes: $4000$

  • $Populus\,trichocarpa$ unique genes: $9000$

  • Overlap between $Oryza$ and $Arabidopsis$: $75$

  • Overlap between $Oryza$ and $Populus$: $600$

  • Overlap between $Arabidopsis$ and $Populus$: $1600$

  • Central overlap shared by all three species: $21000$ genes (representing approximately $38\%$ of the genes involved).

Phylogeny and the Three Domains of Life

• A phylogeny (phylogenetic tree) is a diagram used to illustrate the genetic relatedness between various taxa. A taxon (plural: taxa) is a group of similar and related organisms, such as a species.

• Structure of a Phylogeny:

  • Base: Represents the last common ancestor of all lineages in the tree.

  • Branches: Represent evolutionary lineages.

  • Nodes (Branch Points/Dichotomies): Represent a common ancestor between two or more taxa.

  • Branch Ends: Represent current-day (extant) taxa.

• The three primary domains of life are:

  1. Bacteria: Unicellular prokaryotes that are commonly encountered in daily life.

  2. Archaea: Unicellular prokaryotes that often inhabit extreme environments, such as hydrothermal vents. Despite both being prokaryotic, Bacteria and Archaea are not very closely related and occupy distinct branches on the phylogeny of life.

  3. Eukarya: The domain containing all eukaryotic organisms, which can be either unicellular or multicellular.

Questions & Discussion

• How are increasing levels of complexity that form from smaller parts classified?

  • They are classified as emergent properties.

• Why are viruses not considered alive based on shared biological properties?

  • Viruses are not considered alive because they cannot perform metabolic actions and lack a metabolism of their own.

• What is the most basic unit of life exhibiting all life properties?

  • The cell is the most basic unit of life.

• How does the Central Dogma describe the use of information in DNA?

  • The sequence of DNA codes for the sequence of RNA, which in turn codes for proteins.

• What provides the strongest evidence for the current classification of the three domains of life?

  • The degree of similarity of DNA and RNA between organisms serves as the strongest evidence.

• Where is the common ancestor of all species in a phylogenetic tree located?

  • The common ancestor is located at the base of the tree.

• What does a branch point or dichotomy represent in a phylogeny?

  • It represents a common ancestor shared between two taxa.

• Which domains of life are exclusively unicellular and prokaryotic?

  • The domains Bacteria and Archaea are entirely unicellular and prokaryotic.