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Matt’s Holiday Nightmare

Learning Outcomes

surfing on Bells Beach, Victoria

When you complete this set of modules you should be able to:

    • Explain what is meant by ‘exponential growth’ and generation (doubling) time
    • Explain why logarithms are used to plot bacterial growth curves
    • Describe the phases of growth in a bacterial culture
1: What causes cholera?
2: Build the basic growth equation
3: Draw exponential growth
4: How long until 1 million bacteria?
5: All we need now is data
6: Looking at data
7: Log transformation straightens out exponential growth
8: Do ALL curves get "straightened" by taking the log?
9: Phases of bacterial growth
10: A test for exponential growth
11: And the answer is...
12: To recap
13: Some more practice
14: Extended problem: Exponential growth ends
15: Summary


Matt Gets Messy: In search of Exact Doubling Time »
NAVIGATION
  • Measurement
    • Basic Lab Techniques
      • 1: Metric Review
      • 2: Choose your weapon
      • 3: Read your weapon
      • 4: Can you read this pipette?
      • 5: Summary
    • Straight Lines/ Standard Curves
      • 1: Line graphs
      • 2: Straight lines
      • 3: A straight line has only one slope
      • 4: Slopes and spectros
      • 5: Standard curve-the wavelength
      • 6: Standard curve-making and using
      • 7: Beer’s Law
      • 8: The plug and chug method
      • 9: Try a biology example
      • 10: Summary
    • Logs and pH
      • 1: When size matters
      • 2: There must be a better way!
      • 3: The log is the power!
      • 4: What about other numbers?
      • 5: And what about SMALL numbers?
      • 6: Your turn with other numbers
      • 7: Antilogs
      • 8: Measuring the power of an earthquake
      • 9: Measuring acidity
      • 10: Differences in acidity: Here are two problems
      • 11: Summary
    • Calculating Molar Weight
      • 1: What is a mole?
      • 2: How much does a mole weigh?
      • 3: Molar weights made easy
      • 4: …but not quite that easy
      • 5: Using the Periodic Table
      • 6: Water
      • 7: Practice with sulfuric acid
      • 8: …and caffeine
      • 9: Going backwards
      • 10: …and rubies
      • 11: Summary
    • The Size of Things
      • 1: Tall (and small) tales
      • 2: Metric conversions: step to the right, step to the left
      • 3: 3 Worlds: Milli, Micro, Nano
      • 4: Focus on the microworld
      • 5: Practise measuring in the microworld
      • 6: Next stop … the nanoworld
      • 7: End of the line… the picoworld
      • 8: Summary
  • Visualisation
    • A Graphing Primer
      • 1: The case of the confusing axes
      • 2: Choose your x and y carefully
      • 3: Practise labelling the axes
      • 4: Next step: ranging the axes
      • 5: Practise ranging the axes
      • 6: Next step: scale the axes
      • 7: Practise determining labelled interval distance
      • 8: How to scale axes
      • 9: Finally fill in the axes
      • 10: Summary
    • Log Transformations
      • 1: Logs of graphs and Graphs of logs
      • 2: Method 1: log then graph
      • 3: The curvy line turned into a straight line!
      • 4: To transform or not to transform?
      • 5: Method 2: graph then log
      • 6: Graphing bigger (and smaller) numbers
      • 7: Try it out
      • 8: Just add realism
      • 9: Summary
    • Chopping up Plasmids
      • 1: Three thieves and a beaded necklace
      • 2: And the moral is?
      • 3: A real plasmid
      • 4: Practice with restriction sites
      • 5: What’s wrong with these gels?
      • 6: Playing with plasmids
      • 7: Other weird things
      • 8: Summary
  • Cellular Processes
    • Introduction to Diffusion
      • 1: Measuring movement
      • 2: Directed vs undirected movement
      • 3: Measuring movement using flux
      • 4: Gradients and diffusion
      • 5: Visualising the gradient
      • 6: Fick’s First Law
      • 7: The gradient in Fick’s First Law
      • 8: A familiar equation for Fick’s First Law
      • 9: Graphing Fick’s First Law
      • 10: How does flux depend on distance?
      • 11: A fragrant example
      • 12: General transport equations and Fick’s First Law
      • 13: Summary
    • Time to Diffuse
      • 1: Fick’s second law: … is about “time to diffuse”
      • 2: A very useful formula
      • 3: Time-to-diffuse increases dramatically
      • 4: General functions and Diffusion
      • 5: Biological applications
      • 6: Why do rhinos have lungs and amoebas don’t?
      • 7: Diffusion is efficient in small organisms but not big ones
      • 8: Why we have lungs
      • 9: How many macrophages does it take to kill a virus?
      • 10: You need a lot of macrophages – or one smart one!
      • 11: Summary
    • Diffusion through a Membrane
      • 1: Review of diffusion equations
      • 2: The two-compartment model
      • 3: What does continuous mean?
      • 4: Examples of permeability
      • 5: A formula for permeability
      • 6: The area of the membrane
      • 7: The final equations
      • 8: Rate of flux
      • 9: A metaphor
      • 10: Continuous curves
      • 11: Discrete curves
      • 12: Iterating the discrete curve
      • 13: Summary
    • Osmosis
      • 1: Osmosis is a special kind of diffusion
      • 2: Putting the Os into Osmolarity
      • 3: Calculating osmolarity
      • 4: Osmolarity adds up
      • 5: Which way will water flow?
      • 6: …and how fast?
      • 7: What else can the equations tell us?
      • 8: Where does it all end?
      • 9: Drink your water
      • 10: Sharks, alligators and goldfish
      • 11: Summary
    • The Nernst Potential
      • 1: Getting through membranes
      • 2: Going with the flow
      • 3: Permeability is key!
      • 4: Meet the neighbourhood
      • 5: Getting groovy with gradients
      • 6: Some real numbers
      • 7: The Goldman Equation
      • 8: Playing with the Goldman Equation
      • 9: The Nernst Equation
      • 10: Taking Nernst for a test drive
      • 11: More about Nernst
      • 12: How about those logs?
      • 13: Pumps and channels
      • 14: At equiliubrium? Or far from it?
      • 15: Opening the gate
      • 16: The action potential and the Goldman equation
      • 17: Action potential and the Nernst equation
      • 18: Summary
  • Microbiology
    • Matt’s Holiday Nightmare
      • 1: What causes cholera?
      • 2: Build the basic growth equation
      • 3: Draw exponential growth
      • 4: How long until 1 million bacteria?
      • 5: All we need now is data
      • 6: Looking at data
      • 7: Log transformation straightens out exponential growth
      • 8: Do ALL curves get “straightened” by taking the log?
      • 9: Phases of bacterial growth
      • 10: A test for exponential growth
      • 11: And the answer is…
      • 12: To recap
      • 13: Some more practice
      • 14: Extended problem: Exponential growth ends
      • 15: Summary
    • Matt Gets Messy: In search of Exact Doubling Time
      • 1: In search of … the exact doubling time
      • 2: Finding doubling time with general numbers
      • 3: Logarithms = Exponent-busters
      • 4: Now let’s try out our knowledge of logs
      • 5: More exponent busting
      • 6: World Population
      • 7: Growth of technology
      • 8: How long before the oysters are unsafe?
      • 9: Summary
    • Methods for Counting Bacteria
      • 1: Recap the story
      • 2: Count them all?
      • 3: Direct count
      • 4: Light scatter (spectrophotometer)
      • 5: The dilemma of the dead cell
      • 6: Viable plate count
      • 7: Comparison of methods
      • 8: Summary
    • Viable Plate Count… or how to count to a million
      • 1: Why we need to dilute
      • 2: Setting the stage: Diluting Cold Press Coffee
      • 3: Working out the dilution
      • 4: Overall dilution
      • 5: Design a dilution scheme
      • 6: How to scale up
      • 7: Count a plate!
      • 8: Why we plate more than one dilution?
      • 9: Picking the plate to count
      • 10: Putting it all together
      • 11: Quickies
      • 12: Is the water safe?
      • 13: Summary
  • Probability and Statistics
    • Normal Distributions and the Scientific Method
      • 1: The Scientific Method
      • 2: What makes a Good Procedure?
      • 3: Normal Fish
      • 4: More about normal distributions
      • 5: Visualising a normal distribution
      • 6: Testing Fish2Whale
      • 7: Exploring the Fish2Whale Distribution
      • 8: Overlapping Distributions
      • 9: Summary: The End for now…
    • Bar Graphs and Standard Error
      • 1: Beyond the scatterplot
      • 2: Practice with quantitative and qualitative
      • 3: How to make a bar chart
      • 4: How to make a fancier bar chart
      • 5: Info lost and found
      • 6: Error bars
      • 7: Practice with error bars
      • 8: And another way: the standard error
      • 9: The same graph both ways
      • 10: Summary
    • BLAST and (Im)probability
      • 1: Combinatorics
      • 2: Combining letters into words
      • 3: Many names for large numbers
      • 4: Four-letter alphabet
      • 5: How many base sequences?
      • 6: How many AA sequences?
      • 7: Division
      • 8: How many ways can you make a protein?
      • 9: To be or not to be… in blast
      • 10: Blast: do try this at home
      • 11: Summary
    • Basic Rules of Probability
      • 1: Introduction
      • 2: All Life’s a Game
      • 3: The Law of OR
      • 4: Some Fine Prints
      • 5: What if you violate the fine print?
      • 6: More game shows
      • 7: What are the chances?
      • 8: The Law of AND
      • 9: More fine prints
      • 10: Examples of independent events
      • 11: What if you violate the fine print?
      • 12: Summary
      • 13: Practice with dice
      • 14: Practice with coins
      • 15: What else can probability do?
      • 16: To Curl or not to Curl
      • 17: Surviving the numbers game
      • 18: Gaining an edge
      • 19: Hanging on for dear life
    • Mice with Fangs: Intro to Punnett Squares
      • 1: Introduction
      • 2: The Punnett Menu
      • 3: Creating combinations Chez Punnett
      • 4: Insults by the dozen
      • 5: Punnett menu revisited
      • 6: Onwards to Genetics
      • 7: Recap of genetics vocab
      • 8: Can this marriage be saved?
      • 9: Vampire fangs
      • 10: Example: Mr Spock and Jax
      • 11: Example: Mr Spock and Nurse Chapel
      • 12: And you thought we were done!
      • 13: The dreaded double hybrid
      • 14: Another dihybrid cross
      • 15: Summary
    • More Mice with Fangs: Intermediate Punnett Squares
      • 1: Introduction
      • 2: A Punnet Insult Generator
      • 3: Quick Recap of Genetics Vocab
      • 4: Reviewing the Dreaded Double Hybrid
      • 5: Not all double crosses are dihybrids!
      • 6: Ms Heterozygote meets Mr Recessive
      • 7: Fuzzy meets Fangy
      • 8: Back to Probability
      • 9: Really big Punnett Squares
      • 10: Summary
  • Statistical Tests
    • Chi-squared Tests
      • 1: Do those shoes fit?
      • 3: The day is saved … or not
      • 2: Dilbert’s three-day work week
      • 7: What’s a p-value?
      • 8: What’s a Lookup Table?
      • 4: What you observe vs what you expect
      • 5: The chi-squared equation
      • 6: Give it a try
    • Goodness of Fit Tests
      • 1: Do those shoes fit?
      • 2: Dilbert’s 3 day work week
      • 3: The day is saved . or not
      • 4: The Brute Force method
      • 5: Computer = brute force
      • 6: What’s your threshold for pain?
      • 7: Sick-day sistribution
      • 8: A brief recap of the Brute Force Method
      • 9: The Brute Force method again
      • 10: Using arithmetic instead of Brute Force
      • 11: One small correction
      • 12: How big is big?
      • 13: Degrees of Freedom
      • 14: The magic lookup table
      • 15: The answer, finally
      • 16: Summary of chi-square
      • 17: Another example for chi-square
      • 18: So, which method do you like better?
      • 19: Applications
      • 20: Example 1: Testing for a dihybrid ratio
      • 21: Example 2: Habitat selection (ecology)
      • 22: Review and Words of Wisdom
    • Testing Differences with the T-Test
      • 1: How to convince your boss
      • 2: Looking at the data
      • 3: Estimating averages
      • 4: How do we measure variation? If you said standard deviation…
      • 5: How accurate are our estimates?
      • 6: Combining errors
      • 7: Getting to t-calc
      • 8: A general formula for t-calc
      • 9: Degrees of freedom
      • 10: The bottom line (finally)
      • 11: Give it a try
      • 12: Once more for luck
      • 13: The big picture