Note: blue highlighted bullet points = lecture notes, red bullet points = discussion questions

Chapter 2
Science, Matter, Energy, and Systems
Core Case Study
● Controlled experiment:
○ 1. Identify key variables
■ Examples: water loss and soil nutrient content that might change after trees are
cut down
○ 2. Set up two groups: experimental (chosen variable is changed in a known way) and
control (chosen variable is not changed)
● F. Herbert Bormann and Gene Likens (1963)
○ Goal: compare the loss of water and soil nutrients from an area of uncut forest (control
site) and an area of cut forest (experimental site)
○ Experiment:
■ 1. Built dams so that all surface water leaving each forest had to flow across a
dam → measure volume and dissolved nutrient content
■ 2. Measured amounts of water and dissolved nutrient content flowing from
control site = undisturbed mature forest stores water and retains chemical
nutrients
■ 3. Compared to experimental site, where they cut down trees and sprayed area
with herbicide to prevent regrowth (uh…)
○ Conclusion:
■ Amount of water flowing out of forest increased
■ Excess water erodes soil and removes dissolved nutrients

2.1: What Do Scientists Do?

Scientists Collect Evidence to Learn How Nature Works
● Science = field of study focused on discovering how nature works and using that knowledge to
describe what is likely to happen in nature
○ Based on assumption that events in the natural world follow orderly cause-and-effect
patterns
○ Cause-and-effect patterns can be understood through careful observations, measurements,
and experiments
● Scientific method:
○ Identify a problem → find out what is known about the problem → ask a question →
perform an experiment → analyze data → propose hypothesis → perform experiment →
if hypothesis is accepted, it becomes a scientific theory
● Scientific hypothesis = testable explanation of collected data
○ “If… then…”
● Model = approximate physical or mathematical representation used to understand or explain
behavior of complex natural systems
● Scientific theory = well-tested and widely accepted scientific hypothesis
Scientists Are Curious and Skeptical
● Peer review = scientists publish details of their methods, results, and reasoning + other scientists
evaluate what they published AKA self-correcting

Critical Thinking and Creativity Are Important in Science

● Thinking critically:
○ Be skeptical
○ Evaluate evidence and hypotheses from a variety of reliable sources
○ Identify and evaluate personal assumptions and distinguish between facts and opinions
before coming to a conclusion

Theories and Laws Are the Most Important and Certain Results of Science
● Scientific theory is a big deal: it has been tested widely, supported extensively, and accepted
mostly
● Scientific law/law of nature = well-tested, widely accepted description of observations of what
we find always happening in the same way in nature
○ Example: law of gravity, Law of Conservation of Energy, second law of thermodynamics
○ You can break societal law but you can’t break scientific law

Science Can Be Reliable, Unreliable, and Tentative

● Reliable science = data, hypotheses, models, theories, and laws accepted by most scientists
considered experts
● Unreliable science = scientific results and hypotheses that have not undergone peer review or
have been discarded after peer review
● Tentative science = preliminary scientific results that have not undergone adequate testing and
peer review
○ Sometimes will become reliable, sometimes won’t

Science Has Limitations

● 1. Scientific research can’t prove that any scientific theory is absolutely true
○ Always a degree of uncertainty
○ Scientists have to establish a high probability to certainty
○ Scientists do not use the word “proof” because it implies “absolute proof”
■ Example: You can’t say, “Science has proven that cigarettes cause lung cancer,”
but you can say, “Overwhelming evidence from thousands of studies…”
● 2. Scientists are not always free of bias
○ High standards for evidence and peer review try to prevent this
● 3. Many systems in the natural world have variables with complex interactions that you can’t
account for
○ In response, scientists develop mathematical models that take into account interactions of
many variables
● 4. Science involves use of statistical tools
● DQ: Does that mean scientific results are not valid or useful?
2.2 What is Matter and What Happens When it Undergoes Change?
Matter Consists of Elements and Compounds
● Matter = anything that has mass and takes up space
○ 3 physical states: solid, liquid, gas
○ 2 chemical forms: elements and compound s
● Element = fundamental type of matter with a unique set of properties that cannot be broken down
into simpler substances
○ Example: gold, mercury
● Compounds = combination of two or more different elements held together in fixed proportions
○ Most of matter are compounds

Elements and Compounds Are Made of Atoms, Molecules, and Ions

● Atom = basic building block of matter, smallest unit of matter that an element can be divided and
still have its distinctive chemical properties
● Atomic theory = all elements are made up of atoms, the most widely accepted scientific theory in
chemistry
● Atoms have 3 types of subatomic particles
○ Neutrons = no electrical charge
○ Protons = positive electrical charge
○ Electrons = negative electrical charge
● Nucleus = center of atoms with one or more protons and usually one or more neutrons
○ Electrons are outside of nucleus
● Atomic number = number of protons in atom’s nucleus
● Electrons have < mass than protons and neutrons
● Atom’s mass is concentrated in nucleus
● Mass number = total number of neutrons and protons in nucleus
● Atoms have same number of proteins in its nucleus but different number of neutrons and
therefore mass numbers
● Isotopes = forms of an element having the same atomic number but different mass numbers
● Molecule = second building block of matter, a combination of two or more atoms of the same or
different elements held together by chemical bones
○ Basic building blocks for compounds
○ Examples: water, hydrogen gas
● Ion = third building block of matter, atom or group of atoms with one or more net positive or
negative electrical charges resulting from loss or gain of negatively charged electrons
○ Chemists identify using superscript to indicate number of positive or negative electrical
charges
● Ions measure acidity, which measures comparative amounts of hydrogen ions vs. hydroxide ions
○ Pure water has equal number of H+ and OH- ions, is a neutral solution, and has a pH of 7
○ Hydrogen > hydroxide ions = acidic solution, pH less than 7
○ Hydroxide > hydrogen ions = basic solution, pH greater than 7
● Chemical formula = shows number of each type of atom or ion in a compound
Organic Compounds Are the Chemicals of Life
● Organic compounds = contain at least two carbon atoms combined with atoms of one or more
other elements
● Hydrocarbons = compounds of carbon and hydrogen atoms
○ Examples: methane (main component of natural gas)
● Simple carbohydrates (simple sugars) = contain carbon, hydrogen, and oxygen
○ Examples: glucose, which plants and animals break down to obtain energy
● Polymers = form when simple organic molecules (monomers) are linked together by chemical
bonds
○ 1. Carbohydrates
■ Example: glucose
○ 2. Proteins
○ 3. Nucleic acids
■ Examples: RNA, DNA (formed by monomers called nucleotides) → used for
reproduction

Matter Comes to Life through Cells, Genes, and Chromosomes

● Cells = fundamental structural and functional units of life
● Cell theory = idea that all living things are composed of cells, most widely accepted scientific
theory in biology
● Genes = segments of DNA that contain instructions/codes/genetic information for making
specific proteins
○ Each coded unit of information leads to a trait that passes from parent to offspring
● Chromosome = double helix DNA molecule wrapped around one or more proteins
● DQ: How are we different from each other?

Physical and Chemical Change

● Physical change = no change in chemical composition
○ Example: cutting up pieces of aluminum foil, melting ice, boiling water
● Chemical change/chemical reaction = change in chemical composition
○ Chemical equation shows how chemicals Are are arranged in a chemical reaction
○ Example: when coal is burned, C + O2 → CO2

Law of Conservation of Matter

● Law of conservation of energy = whatever matter undergoes a physical or chemical change, no
atoms are created or destroyed
○ Demonstrated through balanced equations
○ DQ: How do you explain, “You are what you eat”?

2.3 What is Energy and What Happens When it Undergoes Change?

● Energy = capacity to do work or to transfer heat
● Work = done when any object is moved a certain distance (force x distance)
● Moving/kinetic energy = energy associated with motion
○ Examples: flowing water, speeding car, electricity, wind
 ○ Forms of kinetic energy:
■ Heat/thermal energy = total kinetic energy of all moving atoms, ions, or
molecules
● Hotter an object is, the faster the motion
● Temperature = measure of average heat or thermal energy
● When two objects at different temperatures make contact, heat flows
from warmer object to cooler object (like touching a hot stove)
■ Electromagnetic radiation = energy travels from one place to another as waves
formed from changes in electrical and magnetic fields
● Each form has wavelength and energy content
○ Wavelength = distance between successive peaks or troughs in
the wave
○ Short wavelengths have more energy than long
● DQ: What is the energy form of sunlight:
○ Electromagnetic radiation, in case you forget why you put this
here…
● Stored/potential energy = stored and potentially available for use
○ Examples: rock held in hand, water in a reservoir behind a dam, chemical energy stored
in carbon atoms of coal or molecules of food
● Electromagnetic radiation from the sun makes up 99% of the energy that keeps us warm and
supports the plants that we and organisms eat
● Commercial energy = energy sold in the marketplace
○ Makes up the remaining 1% of energy we use
○ 90% of commercial energy used comes from burning of nonrenewable fossil fuels (oil,
coal, natural gas)
■ Fossil fuels = formed over many years as layers of decaying remains of ancient
plants and animals exposed to intense heat and pressure

Energy Varies in Its Quality

● Energy quality = measure of the capacity of energy to do useful work
● High-quality energy = concentrated energy that has a high capacity to do useful work
○ Examples: high-temperature heat, concentrated sunlight, high-speed wind, energy
released when burning wood/gasoline/natural gas/coal
● Low-quality energy = little capacity to do useful work
○ Examples: moving molecules in the atmosphere or ocean → greatly dispersed and has
such a low temperature

Energy Changes Are Governed by Two Scientific Laws

● First law of thermodynamics/law of conservation of energy = when energy is converted from one
form to another in a physical or chemical change, no energy is created or destroyed
○ When we run out of energy, we lose energy quality = amount of energy available for
performing useful work
● Second law of thermodynamics = when energy is converted, we end up with lower-quality or
less-usable energy
 ○ Usually takes the form of heat that flows into the environment
○ Random motion of air or water molecules disperses heat, decreasing temperature to the
point where energy quality is too low

What Are Systems and How Do They Respond to Change?

Systems and Feedback Loops
● System = set of components that function and interact in some regular way
○ Examples: cell, human body, forest, economy, car, earth
● 3 key components:
○ Inputs
○ Flows/throughputs
○ Outputs
● A system becomes unsustainable if throughputs > availability of environment to provide the
required inputs and to absorb/dilute the system’s outputs
● Feedback = any process that increases (positive) or decreases (negative) change
● Feedback loop = occurs when output of matter, energy, or information is fed back into a system
as input and leads to changes
○ Positive = causes system to change in the same direction
■ Example: when researchers removed the vegetation from a stream, they found
that flowing water caused erosion and loss of nutrients, which caused more
vegetation death
■ Ecological tipping point = when a natural system becomes locked into a positive
feedback loop, the system can change so drastically that it suffers severe
degradation and collapse
● Minimum viable population = lower bound on the population of a
species that can survive in the wild
○ Negative/corrective = causes system to change in opposite direction
■ Example: thermostat, which measure temperature of house and turns on heating
or cooling to achieve desired temperature
■ Example: recycling aluminum
● When aluminum is recycled, it becomes an input that reduces the need
for mining aluminum