Directed Research in Biology

  1. Designing the Research Project
    1. The Literature Review
      1. Purpose of a Literature Review
        1. Identifying Knowledge Gaps
          1. Understanding Current State of Field
            1. Informing Research Design
            2. Formulating Search Queries
              1. Identifying Keywords and Phrases
                1. Subject-Specific Terminology
                  1. MeSH Terms
                  2. Using Boolean Operators
                    1. AND, OR, NOT Operations
                      1. Parentheses for Complex Searches
                        1. Wildcard Characters
                      2. Using Scientific Databases
                        1. PubMed
                          1. Advanced Search Features
                            1. MeSH Database
                            2. Web of Science
                              1. Citation Searching
                                1. Impact Factor Information
                                  1. Research Areas Classification
                                  2. Scopus
                                    1. Author Profiles
                                      1. Institutional Affiliations
                                        1. Citation Analysis
                                        2. Google Scholar
                                          1. Broad Search Capabilities
                                            1. Citation Tracking
                                              1. Author Profiles
                                              2. Specialized Databases
                                                1. GenBank for Sequence Data
                                                  1. Protein Data Bank (PDB)
                                                    1. Ecological Databases
                                                  2. Critically Evaluating Scientific Papers
                                                    1. Assessing Study Design and Methods
                                                      1. Experimental Design Quality
                                                        1. Sample Size Adequacy
                                                          1. Control Group Appropriateness
                                                          2. Interpreting Results and Conclusions
                                                            1. Statistical Significance vs Biological Significance
                                                              1. Data Presentation Quality
                                                                1. Conclusion Validity
                                                                2. Identifying Bias and Limitations
                                                                  1. Selection Bias
                                                                    1. Measurement Bias
                                                                      1. Confounding Variables
                                                                    2. Identifying Knowledge Gaps
                                                                      1. Recognizing Unanswered Questions
                                                                        1. Contradictory Findings
                                                                          1. Methodological Limitations
                                                                            1. Unexplored Areas
                                                                            2. Assessing the State of the Field
                                                                              1. Emerging Technologies
                                                                                1. Future Directions
                                                                              2. Synthesizing Information
                                                                                1. Organizing Findings Thematically
                                                                                  1. Conceptual Frameworks
                                                                                    1. Chronological Organization
                                                                                      1. Methodological Groupings
                                                                                      2. Creating Concept Maps or Summaries
                                                                                        1. Visual Representation
                                                                                          1. Relationship Mapping
                                                                                            1. Summary Tables
                                                                                          2. Using Reference Management Software
                                                                                            1. Importing and Organizing References
                                                                                              1. Database Import Functions
                                                                                                1. Manual Entry
                                                                                                  1. Folder Organization
                                                                                                  2. Generating Citations and Bibliographies
                                                                                                    1. Citation Style Selection
                                                                                                      1. In-text Citation Insertion
                                                                                                        1. Bibliography Formatting
                                                                                                    2. Formulating a Research Question
                                                                                                      1. Moving from a Broad Topic to a Specific Question
                                                                                                        1. Brainstorming and Narrowing Focus
                                                                                                          1. Mind Mapping Techniques
                                                                                                            1. Progressive Refinement
                                                                                                              1. Feasibility Assessment
                                                                                                              2. Aligning with Available Resources
                                                                                                                1. Equipment Availability
                                                                                                                  1. Time Constraints
                                                                                                                    1. Budget Considerations
                                                                                                                  2. Criteria for a Good Research Question (FINER Framework)
                                                                                                                    1. Feasibility
                                                                                                                      1. Technical Feasibility
                                                                                                                        1. Resource Requirements
                                                                                                                          1. Time Frame Realism
                                                                                                                          2. Interest
                                                                                                                            1. Personal Motivation
                                                                                                                              1. Scientific Importance
                                                                                                                                1. Societal Relevance
                                                                                                                                2. Novelty
                                                                                                                                  1. Original Contribution
                                                                                                                                    1. Methodological Innovation
                                                                                                                                      1. Conceptual Advancement
                                                                                                                                      2. Ethics
                                                                                                                                        1. Ethical Considerations
                                                                                                                                          1. Regulatory Compliance
                                                                                                                                            1. Risk Assessment
                                                                                                                                            2. Relevance
                                                                                                                                              1. Scientific Significance
                                                                                                                                                1. Practical Applications
                                                                                                                                                  1. Field Advancement
                                                                                                                                              2. Developing a Testable Hypothesis
                                                                                                                                                1. The Null Hypothesis (H₀)
                                                                                                                                                  1. Definition and Role
                                                                                                                                                    1. No Effect Statement
                                                                                                                                                      1. Statistical Testing Framework
                                                                                                                                                        1. Default Position
                                                                                                                                                        2. Examples in Biological Research
                                                                                                                                                          1. Treatment Effect Hypotheses
                                                                                                                                                            1. Correlation Hypotheses
                                                                                                                                                              1. Difference Hypotheses
                                                                                                                                                            2. The Alternative Hypothesis (H₁)
                                                                                                                                                              1. Directional vs Non-Directional Hypotheses
                                                                                                                                                                1. One-tailed Tests
                                                                                                                                                                  1. Two-tailed Tests
                                                                                                                                                                    1. Hypothesis Selection Criteria
                                                                                                                                                                  2. Making Specific, Falsifiable Predictions
                                                                                                                                                                    1. Operational Definitions
                                                                                                                                                                      1. Variable Measurement
                                                                                                                                                                        1. Precise Terminology
                                                                                                                                                                          1. Quantifiable Outcomes
                                                                                                                                                                          2. Predicting Measurable Outcomes
                                                                                                                                                                            1. Expected Results
                                                                                                                                                                              1. Magnitude Predictions
                                                                                                                                                                                1. Direction of Effects
                                                                                                                                                                            2. Principles of Experimental Design
                                                                                                                                                                              1. Identifying Variables
                                                                                                                                                                                1. Independent Variables
                                                                                                                                                                                  1. Manipulated Factors
                                                                                                                                                                                    1. Treatment Conditions
                                                                                                                                                                                      1. Predictor Variables
                                                                                                                                                                                      2. Dependent Variables
                                                                                                                                                                                        1. Response Variables
                                                                                                                                                                                          1. Outcome Measures
                                                                                                                                                                                            1. Measured Parameters
                                                                                                                                                                                            2. Controlled Variables
                                                                                                                                                                                              1. Constant Conditions
                                                                                                                                                                                                1. Standardized Procedures
                                                                                                                                                                                                  1. Environmental Controls
                                                                                                                                                                                                  2. Confounding Variables
                                                                                                                                                                                                    1. Identifying Confounders
                                                                                                                                                                                                      1. Controlling Confounding
                                                                                                                                                                                                        1. Statistical Adjustment
                                                                                                                                                                                                      2. The Importance of Controls
                                                                                                                                                                                                        1. Positive Controls
                                                                                                                                                                                                          1. Known Response Controls
                                                                                                                                                                                                            1. Method Validation
                                                                                                                                                                                                              1. System Functionality
                                                                                                                                                                                                              2. Negative Controls
                                                                                                                                                                                                                1. No Treatment Controls
                                                                                                                                                                                                                  1. Blank Controls
                                                                                                                                                                                                                    1. Sham Controls
                                                                                                                                                                                                                    2. Internal vs External Controls
                                                                                                                                                                                                                      1. Within-Study Controls
                                                                                                                                                                                                                        1. Historical Controls
                                                                                                                                                                                                                          1. Concurrent Controls
                                                                                                                                                                                                                        2. Replication and Sample Size
                                                                                                                                                                                                                          1. Determining Adequate Replication
                                                                                                                                                                                                                            1. Biological Replication
                                                                                                                                                                                                                              1. Technical Replication
                                                                                                                                                                                                                                1. Statistical Requirements
                                                                                                                                                                                                                                2. Power Analysis
                                                                                                                                                                                                                                  1. Effect Size Estimation
                                                                                                                                                                                                                                    1. Alpha and Beta Errors
                                                                                                                                                                                                                                      1. Sample Size Calculation
                                                                                                                                                                                                                                    2. Randomization and Bias Reduction
                                                                                                                                                                                                                                      1. Random Assignment
                                                                                                                                                                                                                                        1. Randomization Methods
                                                                                                                                                                                                                                          1. Stratified Randomization
                                                                                                                                                                                                                                            1. Block Randomization
                                                                                                                                                                                                                                            2. Blinding and Double-Blinding
                                                                                                                                                                                                                                              1. Single-Blind Studies
                                                                                                                                                                                                                                                1. Double-Blind Studies
                                                                                                                                                                                                                                                  1. Observer Bias Prevention
                                                                                                                                                                                                                                                2. Designing Pilot Studies
                                                                                                                                                                                                                                                  1. Purpose and Benefits
                                                                                                                                                                                                                                                    1. Feasibility Testing
                                                                                                                                                                                                                                                      1. Method Optimization
                                                                                                                                                                                                                                                        1. Effect Size Estimation
                                                                                                                                                                                                                                                        2. Interpreting Pilot Data
                                                                                                                                                                                                                                                          1. Preliminary Results
                                                                                                                                                                                                                                                            1. Method Refinement
                                                                                                                                                                                                                                                              1. Full Study Planning
                                                                                                                                                                                                                                                          2. Creating a Research Proposal
                                                                                                                                                                                                                                                            1. Structure of a Proposal
                                                                                                                                                                                                                                                              1. Introduction and Background
                                                                                                                                                                                                                                                                1. Problem Statement
                                                                                                                                                                                                                                                                  1. Literature Context
                                                                                                                                                                                                                                                                    1. Rationale Development
                                                                                                                                                                                                                                                                    2. Statement of the Problem
                                                                                                                                                                                                                                                                      1. Research Gap Identification
                                                                                                                                                                                                                                                                        1. Significance Justification
                                                                                                                                                                                                                                                                          1. Urgency Assessment
                                                                                                                                                                                                                                                                          2. Research Question and Hypotheses
                                                                                                                                                                                                                                                                            1. Primary Questions
                                                                                                                                                                                                                                                                              1. Secondary Questions
                                                                                                                                                                                                                                                                                1. Hypothesis Formulation
                                                                                                                                                                                                                                                                                2. Review of Relevant Literature
                                                                                                                                                                                                                                                                                  1. Current Knowledge Summary
                                                                                                                                                                                                                                                                                    1. Methodological Review
                                                                                                                                                                                                                                                                                      1. Gap Analysis
                                                                                                                                                                                                                                                                                      2. Proposed Methods
                                                                                                                                                                                                                                                                                        1. Experimental Procedures
                                                                                                                                                                                                                                                                                          1. Detailed Protocols
                                                                                                                                                                                                                                                                                            1. Equipment Requirements
                                                                                                                                                                                                                                                                                              1. Quality Control Measures
                                                                                                                                                                                                                                                                                              2. Data Collection Methods
                                                                                                                                                                                                                                                                                                1. Sampling Strategies
                                                                                                                                                                                                                                                                                                  1. Measurement Techniques
                                                                                                                                                                                                                                                                                                    1. Data Recording Systems
                                                                                                                                                                                                                                                                                                    2. Data Analysis Plan
                                                                                                                                                                                                                                                                                                      1. Statistical Methods
                                                                                                                                                                                                                                                                                                        1. Software Requirements
                                                                                                                                                                                                                                                                                                          1. Analysis Timeline
                                                                                                                                                                                                                                                                                                        2. Expected Outcomes and Significance
                                                                                                                                                                                                                                                                                                          1. Anticipated Results
                                                                                                                                                                                                                                                                                                            1. Scientific Contribution
                                                                                                                                                                                                                                                                                                              1. Broader Impacts
                                                                                                                                                                                                                                                                                                              2. Timeline and Feasibility
                                                                                                                                                                                                                                                                                                                1. Project Milestones
                                                                                                                                                                                                                                                                                                                  1. Critical Path Analysis
                                                                                                                                                                                                                                                                                                                    1. Risk Assessment
                                                                                                                                                                                                                                                                                                                    2. Budget and Resources
                                                                                                                                                                                                                                                                                                                      1. Personnel Costs
                                                                                                                                                                                                                                                                                                                        1. Equipment and Supplies
                                                                                                                                                                                                                                                                                                                          1. Indirect Costs
                                                                                                                                                                                                                                                                                                                          2. Potential Pitfalls and Alternative Approaches
                                                                                                                                                                                                                                                                                                                            1. Risk Identification
                                                                                                                                                                                                                                                                                                                              1. Contingency Plans
                                                                                                                                                                                                                                                                                                                                1. Alternative Methods

                                                                                                                                                                                                                                                                                                                          Previous

                                                                                                                                                                                                                                                                                                                          1. Foundations of Scientific Inquiry

                                                                                                                                                                                                                                                                                                                          Go to top

                                                                                                                                                                                                                                                                                                                          Next

                                                                                                                                                                                                                                                                                                                          3. Conducting the Research