Comprehensive Biology Classification and Research Methodology Study Guide

Characteristics of the Kingdom Animalia

• Multicellularity Requirement: All organisms classified within the kingdom Animalia are multicellular. There is no such thing as a unicellular animal.

• Distinguishing Unicellular Organisms: Organisms such as the amoeba find themselves excluded from the animal kingdom because they are unicellular, even though they may exhibit animal-like behaviors like movement and consumption.

Biological Classification and Taxonomy

• Increasing Specificity: Biological classification moves from broad categories to highly specific ones to differentiate organisms. An example is the classification of the American black bear:
  • Phylum: Chordata. Members of this phylum possess a backbone. This classification excludes organisms like butterflies, insects, and sponges.
  • Class: Mammalia. Mammals are characterized by several traits:
    • Nursing: They nurse their young.
    • Hair: Mammals possess hair. Even aquatic mammals like dolphins have hair in the form of eyelashes.
    • Thermoregulation: They regulate their body temperature internally rather than externally.
  • Order: Carnivora. These organisms are consumers that eat meat.
  • Family: Ursidae.
  • Genus: Ursus.
  • Species: americanus.

Binomial Nomenclature and Scientific Naming Conventions

• System of Naming: Every organism is identified by its genus and species names. This is the scientific name.

• The Genus: This is the first part of the scientific name. It must always be capitalized.

• The Species: This is the second part of the name. It must always be lowercase.

• Formatting Rules:

  • Typed Text: When typing a scientific name, it must always be in italics.
  • Handwritten Text: When writing a scientific name by hand, it must be underlined to signify its status as a scientific name.

• Examples of Binomial Names:

  • Brine Shrimp: Artemia salina. In this name, Artemia is the genus and salina is the species.
  • Humans: Homo sapiens. Homo is the genus. Historically, other species existed within the same genus, such as Homo habilis and Homo erectus, but Homo sapiens is the last remaining species of the genus.

The Three Domains of Life

All living things on Earth are categorized into three primary domains: Bacteria, Archaea, and Eukarya.

• Domain Bacteria:

  • Cell Type: Prokaryotic. They lack membrane-bound organelles.
  • Structure: Single-celled (unicellular).
  • Role in Human Health: While some bacteria cause harm, a vast majority are beneficial, particularly for gut health. There are more bacterial cells on or within a human body than there are human cells.
  • Ecological Functions: Bacteria are essential for decomposing matter and were crucial in creating oxygen in the atmosphere to allow for evolution.

• Domain Archaea:

  • Cell Type: Prokaryotic.
  • Extremophiles: These organisms thrive in extreme environments, including:
    • Hydrothermal Vents: Deep ocean fissures where magma emerges.
    • Polar Ice Caps: Environments of extreme cold.
    • The Dead Sea: High-salinity environments.
    • Yellowstone Geysers: Environments of extreme heat.
  • Association with Humans: There are no known human diseases associated with Archaea because they live in extreme conditions that do not match the medium-temperature "buffet" environment of the human body.

• Domain Eukarya:

  • Cell Type: Eukaryotic.
  • Organelles: Every organism in this domain possesses a nucleus and membrane-bound organelles, including lysosomes, peroxisomes, the Golgi apparatus, and mitochondria.

The Four Kingdoms of Domain Eukarya

• Kingdom Animalia:

  • Metabolism: Consumers.
  • Organization: Exclusively multicellular.

• Kingdom Plantae:

  • Metabolism: Photosynthetic.
  • Organization: Exclusively multicellular; there are no unicellular plants.
  • Structures: They possess cell walls (containing cellulose) and specialized plant tissues such as roots and leaves.

• Kingdom Fungi:

  • Metabolism: Decomposers. They break down living or dead matter (e.g., leaf litter, yeast infections, athlete's foot, or mold on strawberries).
  • Organization: Can be unicellular (such as yeast) or multicellular.
  • Structures: They possess a cell wall.

• Kingdom Protista:

  • Catch-all Kingdom: Historically used for organisms that did not fit into the other three kingdoms.
  • Subgroups:
    • Protozoans (Animal-like): For example, the amoeba. They move using structures like pseudopods and hunt bacteria or algae. They are not animals because they are unicellular.
    • Algae (Plant-like): These are photosynthetic and contain green pigments. They can be unicellular, colonial, or large multicellular structures like kelp/seaweed. They are not plants because they lack true roots (instead having holdfasts that do not absorb nutrients) and true leaves (instead having blades).
    • Slime Molds (Fungal-like): Organisms that resemble fungi in behavior or structure.
  • Evolutionary Significance: It is theorized that protozoans gave rise to animals, algae gave rise to plants, and slime molds gave rise to fungi. This is supported by genetic analysis.

Introduction to Biological Research

• Library Resources: Arapahoe Community College (ACC) provides access to five librarians through the library website (arapahoe.edu/library). Support is available through:

  • Hours: Monday through Thursday from $8:00$ to $7:00$; Friday from $8:00$ to $5:00$.
  • 24/7 Chat: A global network of English-speaking librarians (including some in Spain and the UK) is available at all hours.
  • Appointments: $30$-minute time slots are available in person, via Zoom, or at the Castle Rock location (if booked at least $1$ day in advance).

• The Research Pyramid: In biological science, research focuses on the top of the pyramid: scholarly and peer-reviewed sources.

  • Primary Research: This is research conducted by the person who published it. It involves original experiments (e.g., studying tarantula mating habits).
  • Literature Reviews: Papers where a researcher collects and synthesizes existing research from many sources over a period, such as the last $10$ years.
  • Peer Review: A process where expert scientists scrutinize a researcher's work before publication to check for bias, data accuracy, and sound conclusions. Most peer-reviewed literature is written at a very high level (doctoral level), unlike most daily media which is written at an $8\text{th}$ grade reading level.

Navigating Academic Databases for Scientific Research

• Credo Reference: A digital encyclopedia useful for background information, definitions (e.g., defining photosynthesis), and collecting keywords. It includes a "Mind Map" tool to find related scientific terms like Artemia salina (instead of just using the common name "brine shrimp").

• ScienceDirect: A high-end database for primary research articles in natural sciences.

• Search Strategies:

  • Quotation Marks: Use for exact phrases ($"hatch rates"$) to prevent the database from searching terms separately.
  • Boolean Operators: Use $AND$ to connect different concepts and $OR$ to connect synonyms ($"Artemia salina" \text{ OR } "brine shrimp"$).
  • Date Filtering: Research should typically be limited to the last $5$ to $10$ years to ensure the information is current.
  • Preprints: Some articles may be dated in the future (e.g., $2026$ or $2027$). These are preprints that have not yet fully passed peer review and should be treated with caution.

Structure and Evaluation of Primary Research Articles

• Essential Sections:

  • Abstract: A short summary paragraph of the entire article.
  • Introduction: Provides context and background.
  • Materials and Methods (or Methodology): A technical, detailed account of the experiment. If this section is missing, the paper is likely not primary research.
  • Results: A clear report of what the experiment proved.
  • Discussion: An analysis of the findings and potential for future research.
  • Conclusion: A summary of the final findings and their implications.
  • References: A list of sources. Researching "forward and backward" involves checking an article's references to find more relevant, though potentially older, papers.

• Effective Reading Strategy: To avoid reading unnecessary $50$-page documents, researchers should read in the following order: Abstract $\rightarrow$ Introduction $\rightarrow$ Conclusion (or Results). If those sections are relevant, then read the entire article.

Citation Standards and Technical Writing in Biology

• APA Style: All natural science research uses the American Psychological Association (APA) citation style.

• Citation Tools and Precautions:

  • Database citation generators can be helpful but must be checked for accuracy.
  • Special scientific symbols (e.g., the degree symbol $90^{\circ}$) can sometimes "break" citation robots, resulting in incorrect characters.
  • Author Limits: In APA, you must list up to $20$ authors. The term et al. is only used for citations with $21$ or more authors.

• Technical Writing Guidelines:

  • Voice: Scientific writing is objective and fact-led rather than personal. It prioritize facts over personal opinion.
  • Quoting vs. Paraphrasing: Direct quotes should never be used in primary research or review papers. All information must be paraphrased into the researcher's own words to demonstrate understanding, followed by an author-date citation.
  • Citing Lab Manuals: Lab manuals and digital resources must be cited heavily throughout lab reports.

Questions and Discussion

• Question: In biological research, is it okay to use a source that might be older, like from $2000$?

• Response: A source from $2000$ is over $24$ years old. Generally, for current background information, more recent research from the last few years is preferred.

• Question: When doing research on the 24/7 library chat, can I ask them about specific class assignments?

• Response: The 24/7 chat librarians do not know specific instructors or course-specific pre-labs. Users should ask specific research questions about topics (e.g., "I am researching brine shrimp hatch rates") rather than referring to "Dr. Bauer's lab."

• Question: Should lab reports include direct quotes?

• Response: No. Direct quotes should be avoided. Information should be paraphrased to show mastery of the material, which helps verify the student has actually learned the content.

• Question: Is it necessary to put a link for a general Google search in the pre-lab?

• Response: Yes, for the general search portion of the assignment, the URL should be included alongside the citation information.