Comprehensive Notes on Evolution and Foundations of Biology

Diversity of Life and Unifying Characteristics

• Millions of species exist on Earth, encompassing a vast range of diversity.
• Key questions: What are unifying characteristics of life? How should we approach studying this massive system?

The Study of Life and Science

• Biology describes the study of living things and associated processes.
• The field is incredibly broad due to the diversity of life.
• Science, more generally, uses numerous branches of study of nature applied in this endeavor, such as mathematics, physics, and chemistry.

Back to Biology: Broad Categories of Life

• Living things share certain characteristics that can be examined in several broad categories:
  • Structure
  • Function
  • Growth
  • Development
  • Reproduction

Organization and Hierarchical Complexity

• One fundamental characteristic of living things is that they are organized.
• The scale of biological organization is vast and massively complicated.
• Because biological systems are complex, a piece-by-piece approach is often used to study them.

Layered Analysis and Reductionism

• Layers on layers: examining a system component by component is a common approach.
• This piece-by-piece approach describes the principle of reductionism.
• Reductionism: looking at biological systems at varying levels of complexity; these studies are useful and often necessary.

Emergent Properties: The Limits of Reductionism

• An incomplete picture arises if we only examine individual components; some characteristics arise from interactions among multiple components and become evident at higher levels of organization.
• Emergent properties describe those characteristics that result from multiple components working together and reveal themselves at higher levels of organization.

Systems Thinking: Completing the Half

• Completing the half: the study that examines interactions between multiple components to understand emergent properties.
• Emphasizes the collaborative, integrative nature of the scientific process (systems biology).

What Are We Trying to Learn? Structure and Function

• Biological research can be broken down into two broad inquiries relating to structure and function.
• Structure relates to the way something is and its components.
• Function describes interactions with other components and energy exchange.

Life at the Most Basic Level: Cells

• The smallest unit of organization that encompasses all characteristics of life is the cell.
• Cells can act independently or as part of larger, more complex organisms.

The Cell: Prokaryotic vs Eukaryotic

• The two major flavors of living cells differ in complexity:
  • Prokaryotic organisms are relatively simple and lack membrane-bound organelles.
  • Eukaryotic cells are more complex and often form multicellular organisms.
• Implications: differences in cellular organization relate to complexity, size, and capabilities.

Prokaryotes: Simple and Successful

• Prokaryotic organisms are single-celled and lack membrane-bound organelles.
• They are structurally simpler than eukaryotes but incredibly successful and diverse.

Eukaryotes: More Complex and Often Multicellular

• Eukaryotic organisms possess membrane-bound structures.
• They are often significantly larger and may be unicellular or multicellular.

How Cells Do What They Do: Genetic Information

• The structure and function of cells are dictated by the expression and transmission of genetic information.
• The molecule responsible for encoding these instructions is DNA (deoxyribonucleic acid).

DNA: The Basics

• DNA is made up of 4 different nucleotides: Adenine (A), Thymine (T), Guanine (G), Cytosine (C).
• They have specific pairings arranged on a strand: $A ext{-} T ext{ and } G ext{-} C.$

DNA Organization and Genes

• Found in the nucleus in eukaryotes, DNA is organized on chromosomes.
• On chromosomes, genes are specific sequences that code for proteins.

Proteins: The Workhorses of Life

• Proteins provide essential structural elements and form the primary cellular machinery.
• They are made up of amino acids arranged in sequence.
• Amino acids are coded by 3-letter sequences (codons) on DNA within a gene.

Gene Expression: What Gets Read and When

• Gene expression describes which genes, and their associated proteins, are being read and manufactured at a given time.
• The precise set of expressed genes at any time depends on a wide range of factors (developmental stage, environment, regulation, etc.).

The Genomic Revolution: Genomes

• The entire collection of genes in an organism is its genome.
• We now have full genome sequences for a variety of organisms, including humans.
• Much work remains to understand precisely how these sequences interact with one another.

Energy and Life: Metabolism and Energy Use

• Among the universal characteristics of life is the use and transfer of energy.
• These processes are fundamental to growth, maintenance, and reproduction of cells.
• Many genes are geared toward providing the necessary machinery for these processes.

Metabolism: The Chemical Machinery of Life

• Energy use and transfer are performed through a variety of chemical reactions collectively referred to as metabolism.
• Metabolic reactions are responsible for everything from DNA replication to the generation of ATP.

ATP: The Energy Currency

• ATP is the energy currency used to drive metabolic processes, from cellular signaling to chemical synthesis.
• ATP is useful because of its energy-rich phosphate bonds.

Recurring Themes: Conserved Elements Across Life

• DNA and ATP are universal in living things.
• The production and use of DNA and ATP are conserved across organisms, pointing to shared ancestry.

Evolution: A Foundational Perspective

• “Nothing in biology makes sense except in the light of evolution.” —Theodosius Dobzhansky
• Evolution may be defined as a change in heritable characteristics over time.

Evolution in Action

• Organisms have changed over the course of the history of life on the planet.
• These changes occur at all levels of biological organization.

Darwin and Natural Selection: A Mechanism

• A paradigm shift occurred with the establishment of Darwin’s Theory of Natural Selection.
• It describes the process by which specific, heritable variations are likely to be preserved across generations.
• The story has grown more complex with new discoveries.

Solving the Mystery with Science

• The things organisms do, what they are made of, and how they came to be are all complicated.
• We use the scientific method to come to a better understanding.

What Is Science? The Scientific Method

• Science is a systematic approach to acquiring knowledge.
• The scientific method has allowed us to describe and understand nature.

How Does It Work? The Role of Inquiry

• At the crux of science is evidence, i.e., a search for information relating to some natural phenomenon.

Reproducibility in Science

• What sets science apart from other forms of inquiry is a structure emphasizing reproducibility: others must be able to examine phenomena in the same way and arrive at the same conclusion.

Observations and Data in Scientific Inquiry

• Scientists make a series of carefully recorded observations.
• Observations come in a variety of flavors.
• The structured recording of observations provides data (singular: datum).

Types of Data

• Data may be recorded as specific numerical values, known as quantitative data.
• Those data not practically reduced to numerical values are recorded as qualitative data.
• Continuous data may manifest as any value, and are theoretically infinite in their outcome; these are widely used and help reduce ambiguity.
• Discrete data are those that fall into some predefined numerical category; important in biology and elsewhere.

Induction and Deduction: Big to Small Logic

• Induction draws broad conclusions from specific observations.
• Deduction makes specific predictions from generalizations.

The Foundations: Hypotheses, Theories, and Inquiry

• The foundation of science emphasizes a testable explanation: a hypothesis.
• A hypothesis is tested using data collected during experiments.
• A scientific theory is a broad, well-established principle supported by a variety of hypotheses.

Science in Practice: Collaboration and Innovation

• Science is designed as a collaborative process.
• It benefits from new technologies that enable formulation and testing of new hypotheses.