The Nature of Science Design of Controlled Experiments

The Nature of Science Design of Controlled Experiments

Lesson Rationale Based on personal observations while grading AP Free-Response questions and the debrief which ended the conference, most students have a poor understanding of the design of controlled experiments.

Lecture reviews of the: essential nature of science
Lesson Milestones Lecture reviews of the: essential nature of science generally accepted elements of the scientific method construct of a controlled experiment basic statistical analysis tools from Appendix B: Statistics Primer

Lesson Milestones Tasks Accomplishment and review of the 2013 AP Free Response question, Fruit Fly Choice Chamber

Science as a means of understanding the natural word Scientific method
Key Concepts Science as a means of understanding the natural word Scientific method Designing a Controlled Experiment Statistics (Chi Square Test) Appendix B

Describe what science can do and what it cannot do.
Learning Objectives Describe what science can do and what it cannot do. Define the terms observation and data. Define and develop a hypothesis. Explain how scientists test a hypothesis using generally accepted steps to a scientific method. Distinguish between manipulated and responding variables.

Explain the terms falsifiable and reproducibility.
Learning Objectives Distinguish between the colloquial and scientific meanings of the terms theory and law. Explain the terms falsifiable and reproducibility. Calculate a Chi-square analysis and use the result to justify acceptance or rejection of a null hypothesis.

Matrix for Planning and Assessing Scientific Inquiry
Materials Matrix for Planning and Assessing Scientific Inquiry AP Free Response, Fruit Fly Behavior AP Handout of Equations

AP Investigations – None Chi-Square Lab
AP Investigation/Lab AP Investigations – None Chi-Square Lab

Read Appendix B: Statistics Primer
Assignments Read Appendix B: Statistics Primer Focus – Step 5: Inferential Statistics

How do these pictures relate to each other?
Discussion Study tying vaccine to autism was fraud, report says Andrew Wakefield, colleagues altered facts about patients in their research, analysis shows updated 4 minutes ago LONDON — The first study to link a childhood vaccine to autism was based on doctored information about the children involved, according to a new report on the widely discredited research. The conclusions of the 1998 paper by Andrew Wakefield and colleagues was renounced by 10 of its 13 authors and later retracted by the medical journal Lancet, where it was published. Still, the suggestion the MMR shot was connected to autism spooked parents worldwide and immunization rates for measles, mumps and rubella have never fully recovered. A new examination found, by comparing the reported diagnoses in the paper to hospital records, that Wakefield and colleagues altered facts about patients in their study. The analysis, by British journalist Brian Deer, found that despite the claim in Wakefield's paper that the 12 children studied were normal until they had the MMR shot, five had previously documented developmental problems. Deer also found that all the cases were somehow misrepresented when he compared data from medical records and the children's parents. Called 'an elaborate fraud' Wakefield could not be reached for comment despite repeated calls and requests to the publisher of his recent book, which claims there is a connection between vaccines and autism that has been ignored by the medical establishment. Wakefield now lives in the U.S. where he enjoys a vocal following including celebrity supporters like Jenny McCarthy. Deer's article was paid for by the Sunday Times of London and Britain's Channel 4 television network. It was published online Thursday in the medical journal, BMJ. In an accompanying editorial, BMJ editor Fiona Godlee and colleagues called Wakefield's study "an elaborate fraud." They said Wakefield's work in other journals should be examined to see if it should be retracted. Last May, Wakefield was stripped of his right to practice medicine in Britain. Many other published studies have shown no connection between the MMR vaccination and autism. But measles has surged since Wakefield's paper was published and there are sporadic outbreaks in Europe and the U.S. In 2008, measles was deemed endemic in England and Wales. Copyright 2011 The Associated Press. All rights reserved. This material may not be published, broadcast, rewritten or redistributed. How do these pictures relate to each other?

Discussion

Discussion 2011 – 118 cases of measles reported in the United States 89% of those (105) patients had not been vaccinated

What Science Is and Is Not
Science – from the Latin word scientia, meaning “knowledge” Until the Enlightenment (18th century) science was defined as any recorded knowledge

“We may well discover from science many interesting answers to the question ‘How does life work?’ What we cannot discover, through science alone are the answers to the questions ‘Why is there life anyway?’ and ‘Why am I here?’ “ - Dr. Francis S. Collins, The Language of God

Science – Investigate and understand the natural world, explain events, and use explanations to make useful predictions. Process of reaching an understanding of the natural and physical world. Requires a combination of open- mindedness to new evidence and skepticism. Scientific understanding changes with new discoveries – new evidence.

Three things that set science apart: Deals only with the natural world. Collects and organizes information in an orderly way, looking for patterns and connections between events. Proposes explanations for events that can be tested by experiments.

Faced with a problem or question, scientists seek a solution through testing. What is the process of finding the solution? There is no one way; no one method But there are some generally accepted guidelines that constitute what is called the scientific method.

A means of gaining knowledge about the natural world by
Scientific Method Scientific method A means of gaining knowledge about the natural world by making observations, posing hypotheses, and conducting experiments to test those hypotheses. Glossary, Hillis

Scientific observation should be done in an orderly way.
Scientific Method Observation Information, gathered by the senses, about structures, processes and events. Scientific observation should be done in an orderly way. What can I see, hear, sense in any way? What can I measure?

Two categories of data: Qualitative data Quantitative data
Scientific Method Observation Data – information; evidence; recorded observations and measurements, either in words or numbers. Accurate data is the evidence that leads to conclusions and useful predictions. Two categories of data: Qualitative data Quantitative data

Descriptions of appearance, impressions, etc., no numbers
Scientific Method Qualitative data Descriptions of appearance, impressions, etc., no numbers Involves a judgment made by the observer. Quantitative data Expressed as numbers, obtained by measuring or counting. Mass, weight, number of individuals, size in centimeters, etc.

Known as anthropomorphism
Scientific Method Qualitative data frequently taken in studies of animal behavior in the wild. The challenge is to describe the animal behavior in an objective manner. Unscientific observers frequently attribute human qualities and motivations to animals. Known as anthropomorphism

Let’s say you’ve collected some data. How do you…
Scientific Method Let’s say you’ve collected some data. How do you… Interpret the data and develop an explanation of the event? Form an idea of how and why something works?

Develop the tentative idea into a hypothesis In science, a hypothesis
Scientific Method Develop the tentative idea into a hypothesis In science, a hypothesis Is a tentative answer to a well-framed question; an explanation on trial A predication that can be tested We all use hypotheses in solving everyday problems

Observations Question Hypothesis #1: Dead batteries Hypothesis #2:
LE 1-25a Observations Question Hypothesis #1: Dead batteries Hypothesis #2: Burnt-out bulb

Test falsifies hypothesis Test does not falsify hypothesis
LE 1-25b Hypothesis #1: Dead batteries Hypothesis #2: Burnt-out bulb Prediction: Replacing batteries will fix problem Prediction: Replacing bulb will fix problem Test prediction Test prediction Test falsifies hypothesis Test does not falsify hypothesis

About writing a hypothesis… A valid hypothesis Contains a prediction
Scientific Method About writing a hypothesis… A valid hypothesis Contains a prediction And the predication can be tested in some way A valid and correct hypothesis Is supported by the evidence gathered by the test The predication came true!

The hypothesis was not supported by the evidence gathered by the test.
Scientific Method This means that you can have a valid, but ultimately incorrect hypothesis. The hypothesis was not supported by the evidence gathered by the test.

Hypotheses are often written in an “If…then” format
Scientific Method Hypotheses are often written in an “If…then” format If this is done, then the result will be… “If…then” helps the student construct a valid hypothesis One that contains a prediction

Observe, measure, or experiment to test the hypothesis
Scientific Method Observe, measure, or experiment to test the hypothesis Did the prediction come true? Test will help scientists conclude if the evidence will either support or not support the hypothesis.

The test of a hypothesis is an experiment.
Scientific Method The test of a hypothesis is an experiment. Actions or observations taken to test a hypothesis A more defined and structured experiment is known as a controlled experiment All variables except the variable being tested are kept unchanging, or controlled.

Design of a Controlled Experiment
An experiment in which a sample is divided into two groups whereby the experimental groups are exposed to manipulations of an independent variable while one group serves are as untreated control. The data from the various groups are then compared to see if there are changes in a dependent variable as a result of the experimental manipulation. Glossary, Hillis

All variables, except the variable being tested for the hypothesis, are kept unchanging, controlled, or constant Goal is to make the only difference between the two groups the variable whose influence is predicted in the hypothesis

Variables Factors in an experiment that can change Temperature, light, time, materials, etc. Many variables can be acting at the same time Constant variable which is deliberately maintained at a predetermined value during the experiment Example: using an incubator to control temperature while growing bacterial cultures

Two critical variables that apply to the hypothesis: Manipulated variable, or independent variable – is deliberately changed. Responding variable, or dependent variable – is being observed and changes in response to the manipulated variable. The hypothesis must connect directly to these two variables!

There are also two “groups” involved in a controlled experiment Experimental group Control group

Experimental Group: Group or sample that is experimented on sample that is subjected to the manipulated variable Control Group: Another group or sample that is not experimented on, but in every other way exactly alike to the first group sample not subjected to manipulated variable that is used as comparison with experimental group.

Randomization If the design requires sampling of a population – which is likely – such samples must be randomly selected

Figure B1 Sampling From a Population

About ready to start the controlled experiment… Will the “If this happens, this should be the result” prediction hold true? Must be able to compare the results of the experimental and control groups Must show that a phenomena occurs after a certain treatment is given, and it does not occur when the treatment is withheld.

Did the data support the predication made by the hypothesis? If yes, hypothesis is valid But are any new questions raised? If no, hypothesis is invalid Is it possible to rework the hypothesis or is an entirely new hypothesis necessary?

Conclusion The place where you got tired of thinking. Valid hypothesis may allow scientists to predict outcomes, or make general statements, for much larger groups.

Multiple trials build confidence in results Conduct the experimental several times using the same procedure. If results are consistent, shows the first time was not a fluke.

Reproducibility All scientists must be able to do the experiment done by one scientist. Predictions are tested by experiments which can be reproduced by others to see if the same results occur. Publishing and Peer Review Fellow scientists must be able to critique the experiments and results.

Science is not fair Not open to all ideas and explanations. Must be driven by the evidence.

Once an explanation is out in the scientific community… frequently finds application to related fields and other similar investigations.

A common misconception
Truth be said, impossible to keep everything constant except one variable in field experiments. Very difficult for highly regulated laboratory experiments. Control groups also used to cancel the effects of environmental variables that cannot be controlled or eliminated.

When (Controlled) Experiments are Not Possible
At times your situation does not allow you to test a hypothesis: Technology needed for test does not yet exist Ethical and legal restrictions on human testing Laboratory setting may cause bias in results Too many variables exist; can’t control them If you want to observe animal behavior in the wild, then observe them in the wild, not the laboratory

Let’s discuss the word theory for a moment.
How a Theory Develops Even though a valid hypothesis exits, the next step is not a brand, new scientific theory. Scientific meaning of the word theory is often misunderstood by students and the general public. Let’s discuss the word theory for a moment.

How a Theory Develops Theory “A well tested explanation that unifies a broad range of observations.” - Dr. Kenneth Miller

How a Theory Develops “All scientific theories represent a framework for making sense out of a body of experimental observations. But the primary utility of a theory is not just to look back, but to look forward. A viable scientific theory predicts other findings and suggests approaches for further experimental verification.” - Dr. Francis S. Collins

Is there a process to developing a theory?
How a Theory Develops Is there a process to developing a theory? A hypothesis or set of hypotheses have been tested – repeatedly and by ideally different investigators – and have not been contradicted by evidence. Now an explanation develops which explains of all or much of the data we have and offers valid predictions that can be further tested.

How a Theory Develops In science, a theory can never be proven true, because we can never assume we know all there is to know. Instead, theories remain standing until they are disproved by new evidence, at which point they are thrown out altogether or modified to fit the additional data.

Newton’s theory of universal gravitation Cell theory
How a Theory Develops There are theories which have such a great body of supporting evidence they are essentially “proven” in the scientific sense: Newton’s theory of universal gravitation Cell theory Heliocentric theory Atomic theory Can you ever imagine these theories being proved wrong or falsified?

Vital part of science philosophy and practice.
How a Theory Develops Falsifiability A theory is scientific if it leaves open the possibility of being proven wrong or false. Vital part of science philosophy and practice. With the discovery of new evidence, even theories long held may be discarded and replaced by better theories.

How a Theory Develops Falsifiability It must be possible to make an observation that would show the hypothesis to be false. If an observation is impossible, then falsifiability is not possible. Therefore, the theory or hypothesis is not scientific.

Theory: Colloquial Meaning Speculation; a guess
How a Theory Develops Theory: Colloquial Meaning Speculation; a guess “Oh, it’s just a theory.”

Oh, it’s just a theory… "Evolution is a 'theory', just like gravity. If you don't like it, go jump off a bridge." Anonymous Distinguish between the everyday, colloquial meaning of theory and the scientific meaning. In this case, for over 150 years the theory of evolution has been well supported by the evidence and no other scientifically derived theory has taken its place.

How a Theory Develops "It doesn't matter how beautiful your theory is, it doesn't matter how smart you are. If it doesn't agree with experiment, it's wrong" - Richard Feynman

How a Theory Develops "The story of a theory's failure often strikes readers as sad and unsatisfying. Since science thrives on self-correction, we who practice this most challenging of human arts do not share such a feeling. We may be unhappy if a favored hypothesis loses or chagrined if theories that we proposed prove inadequate. But refutation almost always contains positive lessons that overwhelm disappointment, even when [...] no new and comprehensive theory has yet filled the void." Stephen Jay Gould ( ), "Bully for Brontosaurus", The Face of Miranda (1991)

Sometimes you hear of scientific laws Laws are not:
How a Theory Develops Sometimes you hear of scientific laws Laws are not: the same as theories the next rung up on the ladder from theories

Observations that continue to fit the evidence
How a Theory Develops Laws are Observations that continue to fit the evidence Never contradicted by evidence Appear everywhere in the universe Unchanged since first discovered, since the beginning of the universe and likely will remain so Simple in that they are typically expressed in a simple mathematical equation

How a Theory Develops For example, Newton’s Laws of Motion or Boyle’s Gas Law, or the law of conservation of energy

Why discuss obsolete theories?
History shows that science will discard or change even strongly held theories if new evidence comes to light. Emphasize

Video Summation Creative review of the philosophy of science: Symphony of Science – The Poetry of Reality.

A final thought on scientific investigation
Occam's Razor (also spelt Ockham's Razor), is a principle attributed to the 14th century English logician and Franciscan friar, William of Ockham. In its simplest form, Occam's Razor states that one should make no more assumptions than needed. Put into everyday language, it says The simplest explanation is the best.

A final thought on scientific investigation
Better said: When multiple explanations are available for a phenomenon, the simplest version is preferred.

Summation

The Reader’s Perspective
The AP Biology Exam The Reader’s Perspective

AP Biology Exam: Reader Perspective
Distribute handout, AP Reader Experience Take a moment to read. Review the memo in class.

AP Biology Exam: Reader Perspective
Distribute the handout, AP Free Response Questions 2013 Take a moment to read quickly through the questions. Now let’s focus on question #1…

Question 1: Fruit Fly behavior
Drospholia melangaster

You did not need to know anything about the fruit fly itself…

..except their size and affinity for sugary solutions. But even without these two facts, it could be answered!

What was essential: Clear understanding of the nature of science, and How to set up a controlled experiment! First a few stories, a lesson on controlled experiments, then you’ll answer this question!

Distribute worksheet, AP Biology Free Response Question #1, Fruit Fly Choice Chamber 2013

Process You will write your answer to subparts (a) through (e) within 22 minutes in class Then a teacher led review of the answer Followed with peer scoring using the actual scoring rubric and class discussion Final scoring by teacher after class

But wait…There’s more about the fruit fly! Part (d) requires you to perform a Chi- Square test, but you likely do not know what that is… Lets walk through an introduction to this important statistical tool, then we’ll get back to answering the fruit fly free response question.

Chi-Square Test AP Biology Chapter 15

Every controlled experiment must consider the errors that can be made.
Sources of Error Every controlled experiment must consider the errors that can be made. Scientific instruments are not perfect; there will always be that “margin of error.” Random events happen Are the samples chosen large enough and/or actually representative of all the subjects? Statistical tools exist to help take into account the error.

Chi-square test is one of those tools
Should there be a difference between observed results and predicted or expected results, Chi-square allows investigator to judge the influence of simple, random chance. If Chi-square indicates that the difference is likely not due to chance, then the investigator will know to look for other influencing factors.

Which alleles go to which gamete?
Chi-Square Test Example: Random chance is a major determinant in the inheritance of alleles (different versions of the same gene) Which alleles go to which gamete? Which gamete combines with which gamete? Could other factors or errors be influencing results?

We begin with understanding that…
Chi-Square Test Biologists need a statistical tool which helps judge the probability that random chance influenced an outcome, such as a genetic cross. We begin with understanding that… Hypothesis leads to certain prediction of data. Experiment results in observed data.

What you expect to see based on your hypothesis (predictions)
Chi-Square Test The following equation calculates the likelihood that the difference is due to chance alone Observed results What you can observe during the course of an experiment; Data you collected Expected results What you expect to see based on your hypothesis (predictions)

Can typically be determined from simple rules of probability.
Chi-Square Test Expected results Can typically be determined from simple rules of probability. Plug into the formula the expected and observed result, determining the Chi-Square value X2 Now let’s check our understanding for a moment…

Remember what the Chi-Square test is:
A statistical test that compares data collected in an experiment (observed) to data that was predicted by the hypothesis and expected as results. If any difference does exist between the observed and expected results, it could simply be due to random chance. We call outcome the null hypothesis.

Chi-Square Test Null hypothesis (H0). Any difference between the observed results and the expected results is not significant and due to random chance alone. If the Chi-Square test leads us to accept the null hypothesis, then the difference is due to random chance. If the Chi-Square test leads us to reject the null hypothesis, then the difference is due to another factor and not chance.

Let’s say we have a calculated Chi-Square value X2 What’s next?
Chi-Square Test Let’s say we have a calculated Chi-Square value X2 What’s next? We need to decide an acceptable probability that the observed results, and thereby the Chi- Square value X2, are caused by chance alone. We need to know two things Degrees of Freedom Probability value

Chi-Square Distribution Table
Chi-Square Test Chi-Square Distribution Table The degrees of freedom (df) and probability (p) values are seen in this table. The Chi-Square values are seen in the boxes representing a cross between df and p.

Chi-Square Test Chi-Square Distribution Table Degrees of Freedom (left column) is determined by one less than the number of possible outcomes in the experiment (df = n – 1). For example, in a coin toss, there are two possible outcomes – heads or tails. Therefore, the df is one (1).

Chi-Square Test Chi-Square Distribution Table Notice the grey-shaded column. Biologists usually use a probability (p) value of 0.05., which sets the threshold of significance. In other words, it is the threshold for rejecting or accepting the null hypothesis.

Chi-Square Test Chi-Square Distribution Table Another way of saying it is this: p=0.05 is setting a hypothesis that the difference between observed data and expected data is entirely due to chance.

Chi-Square Test Chi-Square Distribution Table If the Chi-Square value falls within a column with a higher probability value than the 0.05 value, we can say the hypothesis could be correct, at least from a statistical standpoint.

Chi-Square Test Chi-Square Distribution Table If the Chi-Square value falls within a column with an equal or lower probability value than the 0.05 value – the 0.01 probability column, then you cannot accept the null hypothesis – something other than random chance is at work.

Chi-Square Test

Figure B12 The Chi-Square Goodness-of-Fit Test

Now let’s complete part (d) of the fruit fly free- response question
Chi-Square Test Now let’s complete part (d) of the fruit fly free- response question

Summation Following Chapter 8, Inheritance, Genes, and Chromosomes, their will be a lab which examines Chi-Square testing once more. As you can see, Chi-Square does pop up in the AP Exam.

Summation

Figure B11 The t-test

The Nature of Science Design of Controlled Experiments

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