The philosophy of science

1. The philosophy of science The nature of scientific knowledge, methods of reasoning and hypothesis construction

2. What is Science? • Very complex • Not well understood by the public • Sometimes purposely misrepresented • Taught how to do science, but not taught what science is • The most powerful tool/methodology humans have ever created to understand nature

3. What is Science? • Science is a lie detector (Brian L. Silver) • Science is the organized, systematic enterprise that gathers knowledge about the world and condenses the knowledge with testable principles (E.O. Wilson) • The central aim of science is to render the complexities of the universe transparent, so that we can see through them to the simplicities beneath (Cohen & Stewart)

4. What is Science? • Simple dictionary style definition • Activity, process • Science = Scientific method • Define by characteristics (6)

5. 1- Human Construct • People do science • The idea of science can change • Can influence the quality of the products of science • Full of other human constructs • Species • Population • Community • Ecosystem • Biodiversity

6. 2- Dynamic Process • Process of science • Deduction (H-D method)- General to specific • Induction- Specific to general • Tools of science • Methods • Statistical tools • Technology

7. 3-Tentative • Scientific conclusions • Confidence in those conclusions is constantly tested • Viewed by some as a weakness of science • Differing connotations of same terms

8. 4-Testable • Hypotheses need to be susceptible to being falsified • Can never PROVE anything • Data can suggest that a hypothesis, idea, conceptual model, etc. has merit or not

9. 5- Empirical Evidence • Objective • Transparent • Observable (at least indirectly) • Repeatable • In opposition to • Opinion (from authority) • Anecdotal evidence (over generalizing) • Personal experience

10. 6-Natural phenomena explain natural world • As opposed to using supernatural causes to explain the natural world • A result of • Scientific ideas needing to be testable (i.e. falsification vs. confirmation) • Data needing to be empirical • Science has its limitations • Utility bound by the natural world

11. What is Science?

12. Methods of Reasoning Induction (Inductive Inference) Deduction (Hypothetical-D) • Generalizing from specific results • Results of specific study hold true in more general spatial and temporal context • Holds no claim on “truth” • Criticized for lack of reliability • Workhorse of science • Only true way to gain new insight • Provides fuel for further deduction • Specific question from general theory • Grounded in theory • Positing a hypothesis • Deducing outcomes (if…then) • Testing predictions • Logically supported truth-seeking • Increases reliability of knowledge • Can increase power of inferences made in induction

13. …In my view it would be just as sensible for the two ends of a worm to quarrel (Whitehead) You @$$! @#$$$%! Deduction Induction

14. Retest inferences gained through induction with another H-D method…and so on Don’t leave a hanging inference! As process continues without “disproof” the hypothesis is on it’s way to becoming part of theory or a theory in and of itself

15. SCIENCE requires BOTH • Title • Abstract • Introduction • Literature review • Objectives • Hypothesis (H-Deductive) • Methods • Results • Conclusion • Generalize • Infer (Inductive) Typical Layout of a scientific journal article

16. Hypothesis Generation Non-scientific Scientific • Tautological (vacuously true) • “We hypothesized occupied habitat would differ from habitat selected at random • Descriptive • “Our objectives were to examine and home range sizes of gray partridge in South Dakota • Not-testable • My totem protects me from evil spirits • Null hypothesis* • statistical hypothesis • a priori false • Not-testable • Gause’s principle of Competitive Exclusion • STILL have scientific value • Models- on principles of nature • can be advanced as deductions and used in hypothesis testing • Poincare- assumption, something taken as true, or imagined for argument’s sake • Hutchinson Niche Theory- the niche is an imaginary phenomenon- provides a construct • Research/ Alternative*

17. Research Hypothesis • Whether (If)? • existential, the existence of pattern or phenomenon • How? • how do migratory animals navigate? • Why? • ask for purpose reason or cause • winter hare populations declined because of winter food shortages • What is the cause? • A caused B only if A occurred, B occurred and B would not have occurred without A (can’t test) • What’s the cause of the cause and so on…what caused winter food shortages • Could have several causes • Correlation does not imply causation which requires

18. Research Hypothesis: Construction

19. The Null Hypothesis: The Strawman • Widely applied in scientific research • NOT a true hypothesis • Used for statistical analysis • Set-up to be rejected or accepted • Accepted= Research hypothesis is false • Rejected= Research hypothesis is supported • Null hypothesis* • statistical hypothesis • a priori false

20. Create Experiment • Sample Size- # Aquariums, # fish in each? • Fish Species- Mix? All the same? • Oxygen curve- Speed high to low? How low? • Other considerations? (time, money) UCR Fish LCR Fish

21. P-value • Are we finished? • Null- LCR fish and UCR fish will exhibit the same surface brathing • Research- LCR fish will exhibit less surface breathing, and begin surface breathing later • Accept or reject the null?

22. NO! Is the DIFFERENCE significant? Time to first surface breath # surface breath sin 20 minutes • Compare means • 5.28 (LCR) • 1.88 (UCR) • Are they significantly different? • Unpaired t test results • Statistical significance: • P value < 0.0001 • Cut-off < 0.05 •   t = 6.565 • Reject the Null of no difference • Supports our hypothesis • Compare means • 4.15 (LCR) • 4.25 (UCR) • Are they significantly different? • Unpaired t test results • Statistical significance: • P value < 0.0771 • Cut-off < 0.05 •   t = 1.182 • Accept the Null of no difference • Reject our hypothesis http://www.graphpad.com/quickcalcs/ttest1.cfm?Format=C

23. Results • Correct prediction: LCR fish will start surface breathing later than UCR fish (p<0.0001) • Incorrect prediction: Reject our hypothesis the UCR fish will surface breath less often than UCR fish (p<0.0771) • Partial support for our hypothesis that LCR fish have evolved specific adaptations to living in an oxygen poor environment • Why no evidence of fewer surface breaths? • Design Flaw? • Physiological constraint?

24. Results- Often Misunderstood Terms • P-value • Theoretical probability of obtaining a larger test statistic (more extreme) given the null hypothesis is true, if the experiment were repeated at infinitum • Ignore what is insignificant and study further what is significant • Chance would only produce the significant effect “once in 20 trials” is arbitrary but convenient • Type l error-a true null hypothesis is rejected-finding significance where there is none • probability of a type I error= alpha level • at alpha=0.05, the probability of a type 1 error = 1-0.95=5% • Type II error-false null hypothesis is rejected- failing to find significance where it exists • probability of type II error= beta level • power= the probability of not committing a type ll error  

25. Good Reads (with caution) • [BOOK] Chapters 1-3 in Guthery’ Primer on natural Resource science • Wildlife science: gaining reliable knowledge (Romesburg1981) • [BOOK] An Introduction To Experimental Design And Statistics For Biology (Heath 1995) (used $30) • On the Past and Future of Null Hypothesis Significance Testing (Robinson and Wainer 2002) • The insignificance of statistical significance testing (Johnson 1999) • Suggestions for Presenting the Results of Data Analyses (Anderson et al. 2001)

26. Proposal: 1) Intro/Funnel Evolutionary adaptations of fish living in an oxygen-poor environment: Does evolution provide insurance against environmental degradation? • Evolution via natural selection is a unifying principle within the biological sciences. As environmental degradation increases on a global scale, research as shown that the ability of some species to adapt quickly to changing environments may offer some insurance against species loss. This phenomenon, termed the portfolio effect, is of particular importance due to the predicted changes of global warming. The Cache River, located in Southern Illinois, has experienced a different type of degradation. Engineers bisected the river in half in 1913 separating the Upper Cache River (UCR) from the Lower Cache River (LCR), which consequently experiences extreme periods of decrease oxygen availability. With this reproductive barrier in place, the fish community in the LCR may have evolved an increased ability to survive in oxygen-poor environments. We set out to determine if microevolution is occurring within the LCR fish community because of their low oxygen environment and to investigate if such adaptations are a hedge against further environmental degradation.

27. Proposal: 1) Intro/ Lit-Review • Natural Selection & Adaptation (theory) • Sympatric speciation • Reproductive barriers • Micro-evolution • Portfolio Effect (theory) • Evidence of Micro-evolution in other environments • As a hedge against global warming • As a hedge against nutrient pollution • As a hedge against decreased oxygen • Environmental Degradation • Effects of Decreased oxygen • Study Description

28. Proposal: 1) Intro/Study Description • Study Site • CRW background • Specifics on Cache River • Known effects on fish community • Objectives • To determine if microevolution is occurring within the LCR fish community as a result of their low oxygen environment… • to understand if such adaptations are a hedge against further environmental degradation. • Hypothesis • Overtime, the fish community in the LCR has evolved an enhanced ability to survive in oxygen-poor habitat • Predictions • If fish in the LCR have evolved an enhanced ability to survive in oxygen-poor habitat, then they will exhibit less surface breathing than UCR fish in an oxygen-poor environment • If fish in the LCR have evolved an enhanced ability to survive in oxygen-poor habitat, then they will begin surface breathing later than UCR fish in an oxygen-poor environment

29. Proposal: 2) Methods • Experimental Design • Capturing fish • Seining • Number, species, etc. • Transport • Aquarium Set-up • Number in each tank, etc. • Water • Oxygen levels • Data acquisition • Monitoring • Recording UCR Fish LCR Fish

30. Proposal: 3) Results • Compare Means: LCR vs. UCR • Hypothesis 1 • T-test • Significant difference? • P-value • Meaning if accept/reject • Hypothesis 2 • T-test • Significant difference? • P-value • Meaning if accept/reject

31. Proposal: 4) Discussion • What each result would mean • Have adapted to low oxygen • Have NOT adapted to low oxygen • Mixed results, clear/unclear • Next steps and further research • Potential issues (often titled “Considerations”) • Fish species • Design mistakes • O2 curve mistakes • Broader implications • Is adaptation good insurance against environmental degradation?

32. Outline- Due Tuesday March 6th • Title of Study • Abstract (200 words or less) • Introduction • Funnel Paragraph • Literature Review • Your Study: objectives & hypothesis • Methodology • Research design • Data analysis plan • Expected results • Discussion • References