Science and Life Notes

How Science is Done

  • Science is the process of studying the natural world through observation and experiment.
  • "Natural Sciences"

Objectives (Scientific Method)

  • List and use the steps of “The Scientific Method.”
  • Identify experimental variables:
    • Experimental variables.
    • The experimental group(s) vs. control groups.
  • Scientific opinion: Why is it important to know how science is done?
  • Know the difference between scientific fact, hypothesis, theory, and law.
  • How does the general usage of “theory” differ from its use in science?
  • Distinguish science from pseudoscience.

Vocabulary (scientific method)

  • Theory, hypothesis, scientific fact
  • Experimental variables (independent, dependent & standardized)
  • Control group/s (positive vs. negative control groups)
  • Experimental group/s
  • Scientific method, pseudoscience, law

Science and Biology

  • Science: process of studying the natural world through observation and experiment.
  • Biology: “life” ”study” science of life
  • Biologist: scientist who studies life (uses the scientific method to test hypothesis about life)

The Scientific Process

  • Hypothesis-based
  • The Scientific Method
  • Scientific Inquiry

Steps of the Scientific Method

  1. Observation
  2. Forming causal questions
  3. Hypothesis
  4. Test of hypothesis
  5. Collect data and interpretation of results
  6. Conclusions
  7. Documentation/Publishing
  8. Peer review
  • Order may vary

Hypothesis Testing

  • Is the hypothesis testable?
  • Can it be falsified?
  • In much of science, you look to disprove something.
  • Observation- plants are green
  • Results of experimentation often lead to more questions.
    • What about plants that are not green? yellow
  • Controls

Observation

  • The scientific method often begins with observations

Forming Causal Questions

  • "Problem"
  • Best expressed as an "open-ended" question

Hypothesis

  • A testable educated guess to answer the question.
  • Has to be testable!

Hypothesis and Prediction

  • Hypothesis leads to prediction
  • Predictions
  • Wording of hypothesis as an if/then statement
  • Predictions can help in refining your experiment

Test of Hypothesis

  • Research (experimental, observational)
  • Experiment- procedure to determine if hypothesis is/isn’t valid
  • To be “science” we need to test it

Experimental Variables

  • The independent variable: the single variable you change, and/or the unknown
  • The dependent variables: the variables that are being measured
  • The standardized variables: variables kept constant
  • Note: your textbook calls these “controlled variables”
  • Why just one thing changed?
  • Experiment- I will alter orientation of dirtied silverware and run through the dishwasher and check for cleanliness.

Experimental Group & Control Group/s

  • Experimental group: group exposed to the independent variable. You observe this group for changes (dependent variables)
  • Control group: group NOT exposed to the independent variable. Or where the independent variable is kept constant. You do observe both groups for changes (dependent variables). Acts as a reference for comparison with exp. group

Categories of Controls

  • Positive control: test where you know the outcome should show results. What would be a positive control for my experiment?
  • Negative control: test where you know the outcome should not show results. What would be a negative control for my experiment?
  • Why would you do these types of controls?

Experiment Example

  • Material and Methods: To test rattling is an indication of incandescent light bulb function, the following experiment was performed.
  • The bulbs used were twenty Sylvania 100Watt incandescent bulbs, lot 328A, manufacture date 1-26-202a. Prior to experiment, each bulb was shaken and determined not to rattle (see protocol below)
  • Ten bulbs were screwed into separate, identical lamp fixtures (Ledu Brass Swivel Arm Lamp model #839465) and illuminated in a 22∘C22^{\circ} C temperature controlled room.
  • Lamp bulbs were video monitored until they were observed to suddenly brighten then stop working. These bulbs were then shaken by a shaker machine at an oscillation of 120 shakes per second……
  • How big should sample size be?

Data Collection and Interpretation

  • Determine how you will measure changes (number of colonies, size of growth, etc.) and what they mean.
  • Best to use objective means of measuring

Conclusions

  • (Comparing the observed to the expected results)
  • Did I prove my hypothesis?
  • Basically 2 possible outcomes:
    • results support hypothesis
    • results do not support hypothesis
  • Error analysis. Was my experiment any good? How can I improve on any future experiments?

Documentation, Publishing, and Peer Review

  • Steps of the scientific method (continued)
  • Write it up (Documentation/Publishing)
  • Peer review- Helps to keep scientists and science honest
  • How?
  • Google “retractions in science” “Applied Science”
  • More than 10,000 research papers were retracted in 2023 — a new record

Example Experiment: Moderna mRNA Vaccine

  • 3,700 kids 12-15
  • 2/3 were given 2 doses of vaccine.
  • The other 1/3 were given 2 does of a placebo.
  • Health was monitored since mid March, 2021.
  • Results: Experimental group 0 infected. Control group 4 infected.
  • not a “Human challenge”
  • May 2021

Science as a Process

  • Science is a process - answers lead to more questions.
  • Experimental conclusions accumulate.
    *Observations made during experiment

Example: Backed-Up Kitchen Sink

  • Observation- the kitchen sink is backed up
  • Question- why is the kitchen sink backed up?
  • Hypothesis #1- stuff in the garbage disposal is preventing the water from draining
  • Problems- not really have a good control group
  • Final conclusion :(

Scientific Fact, Hypothesis, Theory & Law

  • Fact- a phenomena that can be directly and repeatedly observed or measured. Cannot be rationally argued against…….
  • Hypothesis - “a testable educated guess”; a tentative explanation of phenomena. Has to be testable.
  • Theory - a widely accepted explanation of natural phenomena; has stood up to thorough & continual testing. (i.e. Theory explains facts). “explains why something happens”. Consensus!
  • Law - a statement of what always occurs under certain conditions. “explains what is happening” . Can usually be defined mathematically. (i.e. A theory that can be defined mathematically).
  • Note: not the same thing as a legal law

Scientific Theories

  • Scientific Theories: a widely accepted explanation of natural phenomena; has stood up to thorough & continual testing.
  • Why are theories not “facts”? Theories explain facts
  • A Theory is what scientists are most sure about. “Best” explanation of facts. Meaning that that is what the science supports

Unifying Theories in Biology

  • Cell theory: cells are the fundamental units of life
  • Biogenesis: the principle that living organisms are generated only by other living organisms.
  • Gene theory: genes determine cell structure/function.
  • Heredity theory: an organism’s characteristics are a result of genes inherited from its parents.
  • Evolution: Is a process by which species come to possess genetic adaptations to their environment. Its mechanism is natural selection.
    • (this should actually be a “theory of natural selection”).
  • Evolution is a fact. Why?

Obstacles to Good Science

  1. Facts are limited to what questions are asked
  2. Limited to our current understanding.
  3. Conflicts of interests. Who is paying for research? Selective ignorance of evidence
  4. Communication. How information is disseminated. i.e. who and where published. Why are scientific journals not all public access? Peer review- time, $, etc.

Examples of Research Funding Issues

  • NIH halts 100100 million study of moderate drinking that was funded by the alcohol industry. May 2018
  • 2024 The truth about alcohol. Is it healthy? - UCHealth Today
  • Where are the references? “Research”

Limits of Science

  • Science is not the only way to answer questions.
  • Science is limited to things that can be measured.
  • How scientific opinions differ from Political, public, historical, religious, personal?

Critical/Scientific Thinking

  • Making sense of scientific or marketing claims

Pseudoscience

  • “Ideas put forth as scientific when they are not scientific.”
  • Hoax science
  • Junk science
  • Fraudulent science
  • Fringe - or alternative science
  • Alternative facts?
  • Fake news?

Homework

*Due; always check the lecture schedule, but recall lecture “topic homeworks” are due Wednesday’s
*Remember to post to and view the discussion board topic "Is it science or pseudoscience?“ You get points for postingJ
*You will pick Three of the topics from the discussion board and research to determine which is science and which is pseudoscience (or not, or is it something "other")
*Statement or summery of topic.
*Is the statement supported by science or not (pseudoscience) or… something else?
*What is the source of your information?
*Cool reading (not requires:) “Never shower in a thunderstorm” by Anahad O'Connor

Key Takeaways

  • The “scientific method” helps organize the process of doing testing.
  • To be science, conclusions need to be made via testing of hypotheses.
  • A good experiment has controls.
  • “Theory” is the best explanation of fact.
  • Be skeptical of claims.

Quiz Examples

  • Experiment 1: Grammar and spelling effects on roommate judgment.
    • Standardized variable/s
    • Independent variable/s
    • Dependent variable/s
    • What is the experimental group and control group in this experiment?
  • Experiment 2: Effectiveness of messages to reduce vaccine misperceptions.
    • Standardized variable/s
    • Independent variable/s
    • Dependent variable/s
    • What is the control group in this experiment?
  • Experiment 3: Effect of women's tears on men's testosterone levels.
    • Standardized variable/s
    • Independent variable/s
    • Dependent variable/s
    • What is the control group in this experiment?

Dispelling Dogma

  • Acupuncture cures migraine pain
  • Global warming is controversial
  • Stress causes stomach ulcers
  • Stress causes gray hair
  • Organic food is better for you
  • Cell phones cause brain cancer
  • Boys are better at math than are girls.
  • Immunization vaccinations are full of toxins

What is Life?

  • Life is unified
  • Life is diverse

Objectives (unity and diversity of life)

  • Living things are unified- List and explain the characteristics that define “life”.
    • Ex. Emergent properties are seen in living organism.
  • Living things are diverse- list (but don’t yet explain) the 3 domains and 6 kingdoms of life.
  • What is a “species”?
  • The “Linnaean system of classification” is used to organize and name different species of living organisms.
  • Know the levels of classification in this system.
  • Be able to correctly write a scientific name.

Vocabulary (Unity and Diversity of Life)

  • Cell
  • The 3 Domains (Eukarya, Archaea, Bacteria)
  • Emergent properties
  • Growth and development
  • Heredity
  • Homeostasis
  • The 6 Kingdoms (plants, animals, protists, bacteria, archaea, fungi)
  • Linnaean system of classification
  • Metabolism
  • Natural-selection
  • Organization

Defining Life

  • All living things exhibit multiple properties or characteristics in combination. i.e. having all these characteristics define “life”
  • I. Life is unified
  • How can life be defined?
  • What is life?
  • Well…. I’ll know it when I see it.

Characteristics of Life

  • Order and Emergent properties
  • Reproduction / Heredity
  • Growth and Development
  • Energy Processing (Metabolism)
  • Regulation/Homeostasis
  • Sensing and Responding
  • Evolve (change over time)

Order and Emergent Properties

  • Complex and Ordered- living organisms are complex (built up from simple to complex)
    • chemical (atom -> molecule -> macromolecule)
    • organelle
    • cell*
    • tissue
    • organ
    • organ system
    • multicellular organism

Cellular Organization

  • Cell- “the basic unit of life”
  • All living organisms are composed of one or more cells
  • Eukaryote cell- larger, complex (ex. Plants, fungi, you)
  • Prokaryote cell- small, simple (ex. Bacteria)

Emergent Properties

  • Each level of organization exhibits Emergent Properties
  • Ex. Capillaries transport blood
  • Ex. How do brain cells make thought?
  • structure/function
  • “the whole is more than the sum of its parts”

Emergent Properties Across Levels

  • Emergent properties are seen throughout increasing levels of organization
    • chemical (atom -> molecule -> macromolecule)
    • organelle
    • cell*
    • tissue
    • organ
    • organ system
    • multicellular organism
    • Population
    • Community
    • Ecosystem
    • Biosphere

Reproduction and Heredity

  • Characteristics are passed from parent to offspring.
  • DNA via chromosomes

Growth and Development

Energy Processing (Metabolism)

  • Metabolism – Why do organisms need energy?
    • Ex. need energy for Homeostasis
  • How do organisms obtain energy?

Energy Flow in Ecosystems

  • Through ecosystems; Energy (flow one-way) Chemicals (recycled)
  • Note: the ultimate source of energy for ecosystems is usually _
  • Fundamental concept in ecology

Regulation/Homeostasis

  • Maintain internal balance
  • Ex. Thermoregulation- Human body temperature is ~37∘C37^{\circ}C (~98.6∘F98.6^{\circ}F)
  • Ex. Osmoregulation- Bacteria cell
  • What happens if homeostasis is lost?

Sensing and Responding

  • Sense and respond to the environment
  • Bacteria moving towards higher sugar concentration

Evolutionary Adaptations

  • Evolve- over time, living organisms “evolve”
  • Evolution Definition: Change in gene frequency within a population over time
  • Charles Darwin “On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life.”
  • Published 1859

Darwin's Theory of Evolution

  • Individuals differ, more offspring are born than can survive, resources are limited.
  • Those individuals that are better able to obtain resources have a higher chance of survival and reproduction thus passing on beneficial genes.
  • Natural Selection- Environmental challenges and complex interactions with other organisms. (select) individuals. (selects against other)
  • Natural selection acts on individuals. Over time, this will lead to changes in the composition of the population (i.e. leads to evolution of population)
  • Reproduction is a very important part

Natural Selection

  • Within a given environment, those genetic adaptations that increase an individual’s success (increased reproductive success) are passed on to their offspring.
  • This process is known as “natural selection”
  • Natural selection is the driving force of evolution
  • Where do new traits come from within populations?

Evidence for Evolution

  • Facts explained by the theory of evolution via Natural Selection
    • Biogeography
    • Fossil record
    • Comparative anatomy
    • Comparative embryology
    • Biochemistry and molecular biology
    • Direct observations of natural selection

What is Alive?

  • Which satisfy all the characteristics of living organisms?
  • Rock? Fire? Computer? You? Bacteria? (ex. Salmonella) Virus? (ex. Avian Flu virus) Earth? Raw vs. baked potato? Not dead
  • Homeostasis vs Equilibrium

Unity of Life

  • Features shared by all life
    • The characteristics of life
    • Are composed of one or more cells
    • Cells are surrounded by a plasma membrane
    • DNA-as genetic material
    • DNA replication (semi-conservatively)
    • Central dogma (DNA>RNA>protein)
    • Glycolysis

Diversity of Life

  • Species: “members of a population that look similar and are able to actually or potentially interbreed in nature à producing fertile offspring”.
  • How many different species are there?
  • How are these species organized?

Species Concept Limitations

  • What about organism that do not “breed” (those with just asexual reproduction)?
  • female horse + male donkey -> mule

Domains and Kingdoms of Life

  • 3 Domains of life are subdivided into 6 Kingdoms of life
  • Biologist separate and classify organisms based on shared characteristics (based upon evolutionary relationships)
  • Organisms between the 6 kingdoms are very different

The Three Domains of Life

  • Bacteria - unicellular prokaryotes
    • Kingdom Eubacteria
  • Archaea - unicellular prokaryotes
    • Kingdom Archaebacteria
  • Eukarya - eukaryotes
    • Kingdom Protista
    • Kingdom Plantae
    • Kingdom Animalia
    • Kingdom Fungi
  • Be able to list the 3 domains & The 6 kingdoms of living organisms

Archaea and Bacteria Domains

  • Domain Bacteria
    • Only one kingdom: Bacteria kingdom (10,00010,000 species)
  • Domain Archaea
    • Only one kingdom: Archaebacteria kingdom (1,0001,000 species)

Archaea Habitats

  • Archaea some species live in “extreme” habitats

Eukarya Domain

  • Eukarya domain with 4 kingdoms
    • Animalia
    • Fungi
    • Plantae
    • Protists

The Three Domains of Life (cont.)

  • III. Eukarya - eukaryotes
    • Kingdom Fungi
    • Kingdom Plantae
    • Kingdom Animalia
    • Kingdom Protista

Biodiversity and Systematics

  • Life on earth is diverse, yet similar.
  • Systematist’s place organisms into groups based upon evolutionary relationships.
  • Recall: Broadest, most inclusive group is the domain.
  • Organisms are further separated using the Linnaean system of classification
    • Named after Linnaeus
    • Domain -> Kingdom -> Phylum -> Class -> Order -> Family -> Genus -> Species

Linnaean System Example

  • Domain: Eukarya
  • Kingdom: Animalia
  • Phylum: Chordata
  • Class: Mammalia
  • Order: Primates
  • Family: Hominid
  • Genus: Homo
  • Species: sapiens
  • Scientific name of this organism?

Scientific Names

  • Scientific names are “binomial” (composed of two parts) the genus and species
  • Homo sapiens or Homo sapiens
  • Underline form if handwritten
  • For class, be able to correctly write out a scientific name
  • Why not just use common names?

Ethical Considerations

  • Are the cells used in in vitro fertilization (IVF) alive? Are they human? Are they a person?
  • Are human 1n egg cells alive? 1n sperm?

Key Takeaways (Life)

  • Defining “life” is challenging.
  • There are many types of living organisms.
  • These are categorized based on evolutionary relationships.
  • Linnaean system of classification is handy.
  • Know how to format scientific names

Quiz Example (Fungus)

  1. Using the proper nomenclature of the Linnaean hierarchy system of classification, fill in the blanks (b-g) below for this mushroom? (I have filled-in some of it for you).
    • Domain EUKARYA
    • FUNGI
    • BASIDIOMYCOTA
    • AGARICOMYCETES
    • BOLETALES
    • BOLETACEAE
    • SPONGIFORMA
    • Species SQUAREPANTSII
  2. What is the common name for this mushroom? If you know it.
  3. What is the scientific name of this organism? (format correctly)

Quiz Example (Stink Bug)

  • Using the proper nomenclature of the Linnaean hierarchy system of classification, fill in the blanks (b- g) below for this invasive brown marmorated stink bug (I have filled-in some of it for you).
  1. Domain ?
  2. ?
  3. ARTHROPODA
  4. INSECTA
  5. HEMIPTERA
  6. PENTATOMIDAE
  7. HALYOMORPHA
  8. Species HALYS