Today is Thursday, September 4 th , 2014

1. In This Lesson: Unit 0 Nature of Science and Scientific Method (Lesson 1 of 1) Today is Thursday,September 4th, 2014 Pre-Class: Take out your homework. We’re going to be discussing your scientific method definitions in lab groups soon. Note: The syllabus receipt and guided reading can go in the Turn-In Box on the black cart. Show me your calculator and I’ll check you off.

2. Today’s Agenda • The real meaning behind the scientific method. • A horse that could count. • Evolution Pre-Test. • Where is this in my book? • Page 16 and following…

3. By the end of this lesson… • You should be able to orient yourself in scientific history. • You should be able to describe the scientific method from a “purpose” standpoint (not memorization of the steps).

4. Evolution Pre-Test • Before we start, let’s just get this pre-test out of the way. • Remember, though it doesn’t directly count for your grade, it’s important that you try your best. • The feedback is very real.

5. Evolution Pre-Test • Username: • [firstnamelastname]832 • Password: • Gleicher[house/apt #] Important Buttons How to Save for Later Change Question

6. In the beginning… • Okay, let’s be honest here: Science is young. • Think about your other classes – languages have been around for a long time, math dates back quite a ways, and history is quite literally ancient. • Science? Yeah, it started in earnest with the ancient Greeks, but it’s been through a lot, and it shows its youth every once in a while. • Here’s what I mean…

7. Middle Ages:Geocentrism vs. Heliocentrism • Geocentrism: The Earth is the center of the solar system. Don’t mind that Galileo guy with “proof” otherwise. • Heliocentrism: The Sun is the center of the solar system. http://en.wikipedia.org/wiki/File:Justus_Sustermans_-_Portrait_of_Galileo_Galilei,_1636.jpg

8. Renaissance:Spontaneous Generation • Maggots come from rotting meat, rats come from leaky roofs, mice come from sweaty underwear. • Even Jan van Helmont, the guy who coined the word “gas,” had it wrong: • “If you press a piece of underwear soiled with sweat together with some wheat in an open mouth jar, after about 21 days the odor changes and they ferment, coming out of the underwear and penetrating through the husks of wheat into mice. But what is more remarkable is that mice of both sexes emerge, and these mice successfully reproduce with mice born naturally from parents...But what is even more remarkable is that the mice which come out of the wheat are not small mice, not even miniature adults or aborted mice, but adult mice emerge!” • Jan van Helmont(not being very science-y)

9. 1891: Clever Hans • A horse that can perform basic arithmetic:

10. Today: • Jenny McCarthy citing a discredited paper to claim that vaccines lead to autism. • A sizable chunk of the population denying climate change in the face of real data. • Evolution deniers. • And the icing on the cake of willful ignorance: Learn with Shiloh.

11. So…now what? • In the words of Dr. George Mehler, “YOU are the vanguard of the enlightenment.” • In other words, it’s up to you folks out there to take a discerning and objective look at the world. • Don’t believe all you’re told, don’t believe all you see, and demand proof at all times. • This is hard to do. Don’t believe me? • Observation Test • Stroop Test

12. The Scientific Method • We now get to the scientific method. • How do you remember it? • Here’s how I like to present it: • Identify problem • Form hypothesis • Design/perform experiment • Gather/analyze data • Draw conclusion • Don’t memorize it. Ever.

13. The Scientific Method • What does it mean? • Head to your lab tables (I’ll show you where you sit in a second) and discuss your homework. Try to get a real conversation going.

14. The Scientific Method • The scientific method is the way to avoid things like counting horses and celebrities/politicians posing as scientists. • You need to feel it, not memorize it. • To help you do that, here are a few experiments. Figure out the flaws, if any.

15. Experiment #1: The Pepsi Challenge • This was a marketing technique (and use of the scientific method) by Pepsi. • In the test, a “test taker” is given two blank cups, one of which contains Pepsi, one Coca Cola. He/she doesn’t know which is which. • The “test taker” tries a sip or two of each and decides which he/she likes better. Most people seem to take Pepsi. • Is this a valid experiment? http://www.stephendenny.com/wp-content/uploads/2010/03/pepsi-challenge.jpg

16. Experiment #1: The Pepsi Challenge • Turns out, not quite. • True, people really do pick Pepsi more, but: • It’s not a double-blind study. • The experimenter knows which is which. • It’s not a full drink. • People prefer Pepsi in small quantities because it’s sweeter, but for a whole drink Coke is chosen. http://www.stephendenny.com/wp-content/uploads/2010/03/pepsi-challenge.jpg

17. Experiment #2: UPenn’s Myopia Study • In the late 1990s, the University of Pennsylvania Medical Center finds that children who often sleep with the lights on tend to develop myopia later in life. • Buy it?

18. Experiment #2: UPenn’s Myopia Study • Penn forgot to look at one really important thing: • The kids’ parents. • Oddly, parents with myopia tend to leave the lights on for their kids more than other parents. • That, however, doesn’t cause myopia. It’s genetic. • Conclusion: Kids with myopia come from parents with myopia.

19. Experiment #3: Chantix™ • Chantix™ is a prescription medication for quitting smoking. • Because apparently telling people on the package that it’s going to kill them isn’t enough. • An independent, double-blind study (more on that in a second) found that 11.9% of people on Chantix™ were not smoking after 24 weeks on the prescription. • Good results or no? http://spinfuel.com/vaping-news/wp-content/uploads/2014/06/chantix.jpg

20. Experiment #3: Chantix™ • Turns out…you can’t be sure if that’s good or not. • You need to know the rate of success on a placebo. • If I inform you that in this same study, 11.9% on Chantix™ stopped after 24 weeks but 2.3% stopped on a placebo, is it good now? • Actually, we’re still not sure. That’s something we’ll look at later this year. http://spinfuel.com/vaping-news/wp-content/uploads/2014/06/chantix.jpg

21. Lessons • Experiment #1 – Pepsi Challenge: • Double Blind Study – make sure both the participant and the researcher interacting with the participant don’t know which treatment group (variable/control) the participant is in. • Experiment #2 – UPenn Myopia: • Correlation Does Not Equal Causality – just because two things appear to have a relationship (sleeping with lights on and myopia) doesn’t mean they’re actually connected. • Experiment #3 – Chantix™: • Analyze Your Data – Don’t make conclusions without data, and make sure you’re comparing to a control or baseline.

22. Features of a Good Experiment • High sample size (n) • In other words, they tested a lot of subjects. • Has a control group and variable groups • An un-modified sample and a sample being tested. • Only one variable tested at a time • Sources of error are minimized. • Can be repeated by others • Procedure is clear.

23. Example Experiment • Hypothesis: • Spiders given caffeine build asymmetrical webs. • Experiment: • Gather 100 spiders of same species. • High sample size, no additional variables. • Give 50 spiders caffeine and water, give other 50 plain water. • Control group (plain water) and variable group (caffeine and water). • Record procedure clearly • Repeatability.

24. Controls and Constants • By the way, don’t forget that controls are different from constants. • Constants are things kept the same in an experiment. Sometimes constants are referred to as “controlled variables.” • Example: All spiders used in the experiment were the same species. • Controls are the test subjects treated “normally.” • Example: Spiders not given any kind of “treatment” like caffeine.

25. Spiders on Drugs • Scientists actually did this test. • NASA scientists! • Here’s what they found: • Normal spiderweb

26. Spiders on Drugs • Caffeine: • Mescaline/peyote:

27. Spiders on Drugs • Marijuana: • Benzedrine/Speed:

28. Spiders on Drugs • Sleeping Pills

29. The first one? • LSD

30. Other Quick Vocabulary Reminders • Placebo – Something designed to look like a “treatment” but that doesn’t actually do anything. • Also called a sugar pill. • TED: Eric Mead – The Magic of the Placebo • Independent Variable – What the researcher changes to create the control and variable groups. • Think something like “Chantix or placebo.” • Dependent Variable – What the researcher measures to carry out the experiment. • Think something like “quitting rate of smokers.”

31. Other Quick Vocabulary Reminders • Hypothesis – An informed “guess” as to the relationship between variables. • More on this in a few slides. • Theory – A hypothesis that has been accepted essentially as fact. A wealth of data and experiments support it as accurate. • If someone says, “Well, I don’t know, it’s just a theory,” s/he probably doesn’t know what “theory” means.

32. Other Quick Vocabulary Reminders • Sample size • How many subjects were tested. • Generally, if you give 50 smokers Chantix and 50 smokers a placebo, your sample size is 50, not 100. • Sample size is given by n (n=50 for the above example). • Significance • If you say a conclusion is “significant,” you better have statistics to back it up. • If you have not actually done a mathematical analysis of your data, do not use the word significant. At all.

33. “Significant” is Significant • To put it another way: • Two baseball players each get one at bat. • The first (Player 1) hits a home run. • The second (Player 2) strikes out. • Is Player 1 significantly better? • No. • One at bat each (n=1) is simply not enough to determine a statistical significance. • We would need a lot more, along with some statistical tests (more in the next unit) to make that claim. • Does Player 1 appear to be better? • Sure. But don’t say Player 1 is significantly better.

34. About Hypotheses • It’s natural for students to say things like, “My hypothesis was correct.” • Don’t. And I better not see that phrase in your lab reports. • In science, we eitheraccept a hypothesis or reject it. They’re neither right nor wrong. • Additionally, there’s something called the null hypothesis. Let’s see what that means.

35. The Null Hypothesis • Suppose you think that sugar in coffee will make the coffee sweet. • That’s a deduction, by the way. • The null hypothesis, then, is that sugar has no effect on coffee. • The null hypothesis is always “no relationship.” • Key:When you reject your own hypothesis, you are accepting the null hypothesis.

36. One last thing… • By some definitions, there are actually three scientific methods. • The most familiar to you is the one we just talked about – the classical method. • Developed in part by that Galileo dude. • There are also: • Observational Method (Discovery) • Synthesis Method

37. Other Scientific Methods • Observational: • Sometimes you just need to discover something. • Synthesis • Using the already-published work of other scientists. • Watson and Crick didn’t experiment!

38. Isaac Newton: • “If I have seen further it is by standing on the shoulders of giants. • (referencing the synthesis method, in part)

39. The Relationship is Circular Classical (Experiments) Publish the Results Publish the Results Observations Synthesis Publish the Results

40. Closure: Labeling the Experiment • A biologist thinks that exercising is good for mice. • He takes 20 two-week-old mice and gives them all identical cages and identical diets, and he keeps them in the same room. • 10 mice also receive an exercise wheel. The other 10 receive an exercise wheel that does not spin. • He records their life spans and compares. • What is the hypothesis? • What is the sample size? • What are the constants? • What is the control (or control group)? • What is the variable (or variable group)? • What’s the independent variable? • What’s the dependent variable? • Could anything have been done better?

41. Closure: Answers • Hypothesis • Mice that exercise live longer. • Sample Size • 10 (20 total mice, but in two groups of 10). • Constants • Same age, same room, same cage, same exercise wheels. • Control • Mice with a non-spinny wheel. • Variable/Treatment Group • Mice with a spinny wheel. • Independent Variable • Exercise or no exercise. • Dependent Variable • Life span. • Improvements • Same litter of mice, bigger sample size.

42. Closure: Bad Science? • Bad Science: • TED: Ben Goldacre – Battling Bad Science • Publication Bias: • TED: Ben Goldacre – What Doctors Do Not Know About the Drugs They Prescribe • Science Denial: • TED: Michael Specter – The Danger of Science Denial

43. Closure: Abstract Reading • The “abstract” of a scientific paper is usually a short summary of all of the procedures and findings of the researchers. • Take a look at this one and let’s see what we can interpret:

44. No effects of gluten in patients with self-reported non-celiac gluten sensitivity after dietary reduction of fermentable, poorly absorbed, short-chain carbohydrates. • Abstract • BACKGROUND & AIMS: • Patients with non-celiac gluten sensitivity (NCGS) do not have celiac disease but their symptoms improve when they are placed on gluten-free diets. We investigated the specific effects of gluten after dietary reduction of fermentable, poorly absorbed, short-chain carbohydrates (fermentable, oligo-, di-, monosaccharides, and polyols [FODMAPs]) in subjects believed to have NCGS.

45. No effects of gluten in patients with self-reported non-celiac gluten sensitivity after dietary reduction of fermentable, poorly absorbed, short-chain carbohydrates. • METHODS: • We performed a double-blind cross-over trial of 37 subjects (aged 24-61 y, 6 men) with NCGS and irritable bowel syndrome (based on Rome III criteria), but not celiac disease. Participants were randomly assigned to groups given a 2-week diet of reduced FODMAPs, and were then placed on high-gluten (16 g gluten/d), low-gluten (2 g gluten/d and 14 g whey protein/d), or control (16 g whey protein/d) diets for 1 week, followed by a washout period of at least 2 weeks. We assessed serum and fecal markers of intestinal inflammation/injury and immune activation, and indices of fatigue. Twenty-two participants then crossed over to groups given gluten (16 g/d), whey (16 g/d), or control (no additional protein) diets for 3 days. Symptoms were evaluated by visual analogue scales.

46. No effects of gluten in patients with self-reported non-celiac gluten sensitivity after dietary reduction of fermentable, poorly absorbed, short-chain carbohydrates. • RESULTS: • In all participants, gastrointestinal symptoms consistently and significantly improved during reduced FODMAP intake, but significantly worsened to a similar degree when their diets included gluten or whey protein. Gluten-specific effects were observed in only 8% of participants. There were no diet-specific changes in any biomarker. During the 3-day rechallenge, participants' symptoms increased by similar levels among groups. Gluten-specific gastrointestinal effects were not reproduced. An order effect was observed. • CONCLUSIONS: • In a placebo-controlled, cross-over rechallenge study, we found no evidence of specific or dose-dependent effects of gluten in patients with NCGS placed diets low in FODMAPs.

47. Citation • Biesiekierski, J. R., Peters, S. L., Newnham, E. D., Rosella, O., Muir, J. G., & Gibson, P. R. (2013). No effects of gluten in patients with self-reported non-celiac gluten sensitivity after dietary reduction of fermentable, poorly absorbed, short-chain carbohydrates. Gastroenterology, 145(2), 320-328.