Experimental Design Notes

• Need to take a sample of bean plants to represent the population of all bean plants

• Need to get a representative sample

• Statistics:

•  helps sample small portions of habitats, communities, biological populations to draw conclusions about the larger population
• Measures differences of the relationships between the sets of data
• Compare small populations of bean plants in sunlight vs. shade
• Depends on sample size, mathematically form conclusion with a level of confidence

• In science, level of confidence is usually around 95%, can never be 100
• Statistics- can be describe conditions in countries around the word
• Data can heighten our awareness of global issues

• Ex. Poverty level of the world
• At least of 80 percent of the world live off of 10 used

• Descriptive Stats

•  numerical summaries of data
• Mean:  average of data points
• Range: measure of the spread of data. Finds the difference between largest and smallest value
• Standard Deviation: measure of how a data set is spread out around the mean

• Error bars: graphical representation of the variability of data
• Can be used to show range of data or standard deviation

• In normal distribution 68 percent of all values lie within in + or – 1 of SD of the mean and 95 if values lie within in plus or minus 2 of SD of the mean
• Plotting the number would likely result in a bell curve
• Most data won’t have perfect distribution
• Flat bell curve: data is spread out widely from the mean
• Tall and narrow bell curve: data is close to the mean
• SD tells how tightly data points are clustered around the mean
• Data close together: small SD
• Data far apart: Larger SD
• Tells how many extremes are in the data
• More extremes = larger SD
• Few extremes = small SD

Scientific Method

• 2 forms- Biologist use 2 main types of scientific inquiry

• Discovery science
• Hypothesis based science

• Discovery Science

• Describes natural structures and processes
• Observation and analysis of data
• Conclusions through inductive reasoning using observation
• Ex. Jane Goodall and chimpanzee behavior

• Hypothesis Based

• Potential answer to a well framed question
• Educated guess based on experiment and data available from previous experiments and discovery science

• Theory: a hypothesis that is supported by an overwhelming amount of data and results

• Attempts to explain nature
• Underlines most scientific research
• Allow scientists to modify their conclusions as new inform become available

• 5 steps

• Observations
• Ask questions
• Form hypothesis
• Make predictions
• Test the prediction using additional observations or by conducting experiments

• 2 ways to test hypo.

• Controlled experiments
• Advantages
• All factors other than the one hypo to be causing the effect can be kept constant
• Comparative method

Stats 2

• Reliability of the Mean

• Variance is other measure of dispersion
• 1 method calculate standard error

• Standard Error

• Allows for calculation of the 95 percent confidence interval
• CI used to indicate relativity of an estimate
• Degrees of freedom = n-1
• Calculated 955 of it can be plotted as error bars on a graph
• Smaller CI more reliable the data staminate
• Determines if there’s a significant difference between sets of data

• T-test

• Only valid for certain situations
• 2 group tests
• Only have 2 samples to compare
• Assumptions
• Normal and not skewed distribution
• SD for both samples is similar

• Null hypothesis- the hypothesis of no difference or no effect

• Probability that chance alone could make a difference have an effect
• 5% = difference is due to chance 5% of the time

• Degree of freedom = sum of total number of sample sizes of both groups

• Steps

• Calculate degree of freedom
• V1 + V2 -1 = DF
• Look at t values and match degree of freedom now with t value column
• Values lie between 1 and 5 percent
• Reject null hypothesis when P is 5 or less

Microscopy

        

• History

• 1st century Ad glass as invented, Roman observed it and tested
• Experimented with different designs
• Thick in the middle and thin outwards
• Discovered that holding lens over an object made it larger
• Magnifying glass
• 1590, 2 Dutch spectacle makers, Zaccharias and Hans Janssen put more then one lens together and looked through saw object larger
• More novelty than function
• Anthony Van Leeuwenhoek
• Simple hand held microscope
• Made better lenses by grinding small glass balls into thin lenses magnification = 270x
• Using it, saw bacteria, yeast, blood cells
• 17th century, compound microscope 1+ lens invented to enhance resolution and magnification
• Robert found basic unit of life- cells

• 2 functions

• Enlarge image, can be seen with naked eye or camera
• Contrast details stand out

• Light Microscopy

• Intact cells low magi. Limits of relation are 200 nanometers
• Classic light microscope method – bright field
• Uses pure white light
• 2 series of lenses- objective and ocular lens
• Total magi of a compound microscope is the product of magi of ocular and objective lens

• Increase contrast

• Cells absorb little visible light
• Little contrast available
• Staining is used to increase contrast

• Phase Contrast Microscopy

• Made to see improved contrast differences in between and surrounding medium
• Can see cell without staining
• Based on principle that cells slow speed of light passing through specimen
• Result is difference of phase between the cell and its surroundings
• Difference is amplified by a special ring in the objective lens of the microscope
• Leads to dark image on light background

• Dark-field

• Light micro where light reaches specimen form the side only the specimen looks light
• Better contrast than bright field and phase contrast microscopes

• Fluorescence microscope

• Uses electrons to image cells and cell structures
• 2 types
• TEM transmission electron microscope
• SEM scanning electron microscope

• TEM

• Uses electromagnets to act as lenses
• Works as a vacuum and filled of cameras so that a micrographs can be taken
• Typically used to examine inside of a cell
• Resolving power is greater than light micro
• Must use thin section because of electron beams don’t penetrate very well resolving power - .2 nanometers?

• SEM

• Used to look at external features
• Surface image only
• Coat specimen with thin film of heavy metal like gold
• Electron beam then directed into the specimen and scans back and forth across it
• Electron moved by the metal are collected to produced an image
• Wide range of magnification 15x-100,000x

• Parts of microscope

• Specimen control
• Stage where specimen rests
• Clips used to hold the specimen still
• Micromanipulator device that allows you t move the specimen in controlled small increments along the x and y axis
• Illuminating sheds light on the specimen
• Lamp light source
• Condenser lens that aligns and focuses form the lamp onto the specimen
• Diaphragm apertures alters the amount of light that reaches the condenser used to enhance contrast of lens

• Lens

• Objective lens gathers light from the specimen
• Ocular transmits and magnifies image from the objective lens to you eyes

• Focus

• Coarse focus know used to bring object o the focal plane of the object lens
• Fine focus know used to make fine adjustments to focus the image

Seed Germination

• Seed dormancy

• In seeds, development and activity may be suspended
• Dormant seeds don’t divide, expand or differentiate
• Seed dormancy must be broken for the embryo to begin developing

• Germination

• Beginning of growth
• Growth in a seed calls it a seedling
• Process where the seed begins to grow

• Seed Germination Dependency

• Internal and external
• Water
• Temperature
• Oxygen
• Light

• Start of Germination

• Begins with water- called imbibitions
• Seed takes up water, undergoes metabolic changes
• Activates bio chemical process resulting in protein synthesis
• Oxygen = seed metabolism and energy production
• Seeds that are waterlogged or buried too deeply in soil won’t get enough oxygen needed

• Steps of Germination

• Seed gets water, seed coat bursts
• Chemical energy provides the energy needed for the embryo to enlarge and push out of the seed coat
• Tip of root comes out first and anchors plant and lets plan absorb minerals and water form soil

• Plant Vocab

• Cotyledon: embryonic leaf inside the seed
• Monocotyledon:  one of two major groups of plants has only 1 cotyledon ex onions corn lilies
• Diacotyledon: other major group of plants, 2 cotyledons, beans, castor oil plant

• Monocot Germination

• Primary root pierces seed coat and grows downward
• Primary leaf grows up and is protected by the coleptile, hallow cylindrical structure
• When the seedling is above round the coleptile stops growing

• Dicot Germination

• As embryo grows seeds out shoot called a radical
• Radical becomes primary root and grows
• Hypocotyls then emerges and lifts grouping tip
• With light, hypocotyls straightens and cotyledons spread apart to expose the primary leaves