Module 2: Science, Matter, Energy, and Systems

Chris Merkord

Module 2: Science, Matter, Energy, and Systems

• How scientists study the natural world

• Evidence, hypotheses, theories, and laws

• Matter, energy, and their transformations

• Systems thinking and feedbacks in nature

• Links to sustainability and environmental change

Credit: The Sourcebook for Teaching Science

Learning Objectives

By the end of this module, you should be able to:

• Describe how scientific knowledge is developed and evaluated

• Distinguish hypotheses, theories, and scientific laws

• Explain basic properties of matter and energy

• Apply the laws of conservation and thermodynamics

• Describe systems, feedback loops, and tipping points

• Connect physical and biological principles to environmental issues

How Do Scientists Learn About Nature?

• Explain how the natural world works
• Focus on cause-and-effect relationships
• Rely on observation, evidence, and testing
• Scientific knowledge develops over time

Science Starts with Questions

• Observations of nature
• Questions about patterns or changes
• Focus on measurable variables
• Common in environmental systems

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Using Experiments to Test Ideas

• Identify key variables
• Compare outcomes under different conditions
• Control group (no change)
• Experimental group (variable altered)

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Example: Forests and Water Loss

• Forested vs. deforested watersheds
• Water flow and nutrient loss measured
• Dams used to capture runoff
• Controlled field experiment

What the Experiment Showed

• Forests retain water efficiently
• Forest soils retain nutrients
• Deforestation increases runoff (30–40%)
• Increased erosion and nutrient loss

What Do Scientists Do?

• Collect data
• Identify patterns
• Develop explanations
• Test ideas with evidence

Figure 1: Examples of scientists doings science.

The Scientific Process (Simplified)

• Observation
• Question
• Hypothesis
• Prediction
• Test / experiment
• Analyze results
• Revise or repeat

Hypotheses

• Tentative explanations
• Testable and falsifiable
• Based on observations
• Supported or rejected by data

Scientific Theories

• Broad explanations of natural phenomena
• Supported by extensive evidence
• Repeatedly tested
• Widely accepted by scientists

Scientific Laws

• A description of a consistent pattern in nature
• Often expressed mathematically
• Describes what happens, not why it happens
• Highly reliable and repeatable
• Revised only with new evidence
• Laws are not “proven theories”
• Theories do not graduate into laws
• They answer different questions:
  • Laws: What happens?
  • Theories: Why and how does it happen?

Classic examples:

• Newton’s laws of motion
• Laws of thermodynamics
• Law of conservation of matter
  • Matter is neither created nor destroyed in physical or chemical changes
  • Atoms are rearranged, but the total amount of matter remains constant

Hypotheses vs. Theories vs. Laws

• Hypothesis: tentative, testable idea
• Theory: well-supported explanation
• Law: consistent description of behavior
• Different roles, not levels of certainty

Evaluating Scientific Knowledge

• Peer review
  Independent evaluation by other scientists in the field

• Replication of results
  Findings can be reproduced using the same methods

• Transparent methods
  Clear description of data, methods, and analyses

• Strength of evidence
  Multiple lines of evidence support the same conclusion

Manuscript peer review process. Source: Understanding Peer Review in Science, Anne Helmenstine / Science Notes.

Limits of Science

• No absolute proof
  Scientific conclusions are always open to revision

• Measurement uncertainty
  Observations and measurements contain inherent error

• Potential for bias
  Scientists are human and can be influenced by assumptions

• Peer review reduces bias
  Independent review helps identify errors and bias

What Is Matter and What Happens When It Undergoes Change?

• Matter is anything that has mass and occupies space
• Composed of atoms, ions, and molecules
• Forms elements and compounds
• Exists in three physical states: solid, liquid, or gas
• Matter is rearranged during physical and chemical changes
• Cannot be created or destroyed (law of conservation of matter)

Matter Consists of Elements and Compounds

• Elements
  Substances made of one type of atom
• Compounds
  Combinations of two or more different elements
• Elements cannot be chemically broken down
• Represented by chemical symbols (e.g., H, O, C)

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

An Atom Is the Basic Building Block of Matter

• Smallest unit of an element that retains its chemical properties
• Composed of protons, neutrons, and electrons
• Protons and neutrons form the nucleus
• Electrons occupy regions surrounding the nucleus

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Atomic Number, Atomic Mass, and Element

Atoms differ in numbers of subatomic particles

• Atomic number determines the element

  • Number of protons in the atomic nucleus

• Mass number

  • Total number of protons and neutrons in the nucleus of an element’s atoms

• Element

  • A pure substance that consists only of atoms with the same number of protons

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Why Electrons Matter (shell model)

• Electrons occupy energy levels (shells) around the nucleus
• Outer-shell electrons determine how atoms interact
• Atoms with incomplete outer shells are chemically reactive
• Atoms gain, lose, or share electrons to become more stable
• Chemical reactivity controls nutrient availability, toxicity, and pollutant behavior in the environment

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Ions

• Atoms with a net electric charge

• Formed when atoms gain or lose electrons

• Loss of electrons → positively charged ion (cation)

• Gain of electrons → negatively charged ion (anion)

• Ionic form affects solubility, mobility, and biological availability in the environment

Copyright: adapted with permission from OpenStax Biology for AP Courses, OpenStax, and Rice University

Ionic Bonds

• When an atom loses or gains electrons, it becomes electrically charged

• Charged atoms are called ions

• Ionic bonds are formed between oppositely charged ions (transfer of electrons)

Copyright: adapted with permission from OpenStax Biology for AP Courses, OpenStax, and Rice University

Covalent Bonds

• Sharing of electrons between atoms to form covalent bonds.

• Stronger and much more common than ionic bonds in the molecules of living organisms.

• Commonly found in carbon-based organic molecules, such as our DNA and proteins.

• Also in inorganic molecules like H2O, CO2, and O2.

• One, two, or three pairs of electrons may be shared, making single, double, and triple bonds, respectively. More bonds = stronger; triple bonds are the strongest

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

So, why care about ions and compounds?

• So, understanding the chemistry of ions and compounds allows us to measure them.

Remember the trees in the valley?

• Scientists learned how to measure nitrate and nitrite ions in water to determine the concentration of these ions

  • Reduce nitrate with zinc and react with naphthylethylenediamine under acid conditions to produce a red compound - 550mn.

• Determined that lack of trees washed out nitrates from the soil, increasing in concentration in the water runoff.

Acids and Bases

• Acid

  • A chemical compound that donates H+ ions to solutions.

  • Aqueous solutions with a pH less than 7 are said to be acidic

• Base

  • A compound that accepts H+ ions and removes them from solution.

  • Aqueous solutions with a pH greater than 7 are basic or alkaline.

• Pure water has a pH very close to 7

• If an equal number of these ions are present in a solution the pH will not change as it is said to be buffered.

A pH Scale

• To describe the acidity of a solution, we use the pH scale.

• Bases have a high pH, so they have a low concentration of H+

• Acids have a low pH, so they have a high concentration of H+

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Organic compounds are the chemicals of life

• Organic compounds have at least two carbon atoms and various other elements

  • Hydrocarbons: contain carbon and hydrogen atoms

  • Simple carbohydrates: contain carbon, hydrogen, and oxygen

  • Polymers: simple organic compounds (monomers) chemically bonded together

Polymers are essential to life

• What are the major types of polymers?

  • Complex carbohydrates: two or more monomers of simple sugars such as glucose

  • Proteins: formed by amino acids (that are monomers)

  • Nucleic acids: such as DNA and RNA that are formed by nucleotides (that are monomers)

The structure of DNA: The best known biomolecule

• DNA is composed of two helical strands of nucleotides
• Each nucleotide has three components:
  • Phosphate group
  • Five-carbon sugar (deoxyribose)
  • Nitrogenous base (A, T, C, or G)
• Base sequence stores genetic information

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Matter Comes to Life Through Cells, Genes, and Chromosomes

• Cells
  Smallest units of life in all organisms

• Genes
  DNA sequences that encode functional traits

• Chromosomes
  Long DNA molecules containing many genes

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Matter undergoes physical, chemical, and nuclear changes

• Physical changes
  Change form or state (e.g., ice to water) without changing chemical identity

• Chemical changes
  Rearrangement of atoms to form new substances

• Chemical equations
  Represent reactants, products, and conservation of atoms

A chemical equation: Coal –> CO2

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

Cannot create or destroy atoms

• Law of conservation of matter
  Matter is neither created nor destroyed in physical or chemical changes

• Atoms are rearranged, not created or lost

• Balanced chemical equations
  Ensure the same number of each type of atom on both sides of a reaction

A chemical equation: Coal –> CO2

Copyright: OpenStax Biology for AP Courses, OpenStax, and Rice University

What Is Energy and What Happens When It Undergoes Change?

• Energy
  The ability to do work or transfer heat

• First law of thermodynamics
  Energy is conserved; it changes form but is not created or destroyed

• Second law of thermodynamics
  Energy transformations result in lower-quality, less usable energy

Energy

• Energy
  Ability to do work or transfer heat

• Work
  Occurs when energy moves or changes form

• Work = force × distance

• Examples:

  • Moving an object
  • Heat transfer from a hot surface

Source: Dr. Anne Marie Helmenstine, University of Tennessee at Knoxville

Energy Comes in Many Forms: Kinetic Energy

• Kinetic energy
  Energy associated with motion

• Includes:

  • Thermal energy — motion of particles that produces heat
  • Electromagnetic energy — energy carried by waves

• Example:

  • Wind kinetic energy turns turbines
  • Converted to electrical energy

From Wikimedia Commons, a freely licensed media file repository

Energy comes in many forms: potential energy

• Potential energy
  Stored energy that has the capacity to do work

• Example:

  • Water stored behind a dam

• Potential energy can be converted to kinetic energy

  • Flowing water spins turbines
  • Turbines generate electrical energy

Aerial view of Cheoah Dam in North Carolina illustrating potential energy stored in reservoir water and its conversion to kinetic energy for hydroelectric power generation. Image credit: Wikimedia Commons, Cheoah Dam aerial – near Robbinsville, North Carolina.

Some Types of Energy Are More Useful Than Others

• High-quality energy
  Concentrated energy with high capacity to do work
  • Examples: high-temperature heat, concentrated sunlight, strong wind
• Low-quality energy
  Dispersed energy with limited ability to do work
  • Example: heat lost to the environment

Solar Energy and Earth Systems

• Solar energy arrives as electromagnetic radiation
• Spans a range of wavelengths (the electromagnetic spectrum)
• Primary energy source for:
  • Climate and weather
  • Photosynthesis
  • Ecosystems and food webs
• Drives most natural processes on Earth

The electromagnetic spectrum showing the range of electromagnetic radiation by wavelength and energy, from radio waves to gamma rays, illustrating how solar energy reaches Earth across multiple wavelengths. Source: NASA, via Wikimedia Commons.

Human Energy Use: Commercial Energy

• Commercial energy
  Energy extracted, processed, and sold by humans

• Includes:

  • Fossil fuels (coal, oil, natural gas)
  • Electricity
  • Nuclear and renewable sources

• Most commercial energy currently comes from fossil fuels

  • Nonrenewable
  • Major environmental and climate impacts

Classification of energy sources into conventional (nonrenewable) and nonconventional (renewable) categories, illustrating common examples of each type. Source: BYJU’S, Conventional and Nonconventional Sources of Energy.

ExxonMobil oil refinery in Baton Rouge, Louisiana, illustrating large-scale petroleum refining infrastructure used to process crude oil into fuels and other products. Source: Wikimedia Commons, Exxon Mobil oil refinery – Baton Rouge, Louisiana.

What Are Systems and How Do They Respond to Change?

• A system is a set of interacting components that function together

• Examples: cell, organism, forest, economy, car, Earth

• Most systems include:

  • Inputs of matter, energy, and information
  • Flows (throughputs) within the system
  • Outputs of products, wastes, and degraded energy (often heat)

Living and Nonliving Systems

• Nonliving systems
  • Do not grow or adapt to environmental change
    
  • Function remains largely fixed
• Living systems
  • Respond to environmental change
    
  • Adjust size, structure, and behavior
• Systems become unsustainable when:
  • Inputs are used faster than they are replenished
    
  • Outputs exceed the environment’s capacity to absorb or dilute them

Ecological System Feedback Loops

• Feedback loop
  Occurs when a system output feeds back as an input, influencing future system behavior

• Positive feedback
  Amplifies change, pushing the system further in the same direction

• Negative feedback
  Dampens change, promoting stability

• Example of positive feedback:

  • Vegetation loss increases erosion and nutrient loss
  • Poor soil conditions cause further vegetation decline
  • System becomes increasingly degraded over time

Alternative ecosystem trajectories showing how compounding disturbances can push ecosystems toward different stable states (Amazonian forests). Source: Wikimedia Commons, Alternative ecosystem trajectories for Amazonian forests that transition due to compounding disturbances.

Ecological Tipping Points

• Tipping point
  A threshold beyond which a system shifts rapidly to a new state

• Often triggered by sustained pressure or positive feedbacks

• After a tipping point:

  • Change can be difficult or impossible to reverse
  • System structure and function may fundamentally change

• Examples:

  • Forest to grassland transitions
  • Coral reef collapse

Alternative ecosystem trajectories showing how compounding disturbances can push ecosystems toward different stable states (Amazonian forests). Source: Wikimedia Commons, Alternative ecosystem trajectories for Amazonian forests that transition due to compounding disturbances.

Negative (Corrective) Feedback Loops

• Negative feedback loop
  Counteracts change and promotes system stability

• Example: thermostat

  • Measures temperature
    
  • Turns heating or cooling on or off to maintain a set point

• Environmental example: aluminum recycling

  • Used cans become inputs rather than waste
    
  • Reduces mining and manufacturing demand
    
  • Lowers energy use, pollution, and material extraction
    

Illustration of an ecological feedback loop showing how changes in one part of an ecosystem feed back to influence other components, either amplifying or stabilizing system behavior over time. Credit: MyLearning.org, “Ecological Interactions: Closing the Loop.”