1. The Scientific Method Timothy G. Standish, Ph. D.

2. What is Science? “Sci” = Knowledge “ence” = The condition of Explanation of natural phenomena through observation and experimentation A method of gaining knowledge (the scientific method)

3. The Scientific Method The Scientific method relies on two types of reasoning: Inductive reasoning - The drawing of generalized conclusions from a collection of data, this is the type of reasoning used when coming up with a theory Deductive reasoning - Elimination of possibilities until only one or a very few remain. Hypotheses are testable statements that must be true if a theory is true, thus if the hypothesis is not true, the theory can be deducted from the set of possible theories.

4. Data Hypothesis Theory Pass Beliefs Induction Fail The Scientific Method Deduction Test (Experiment)

5. Error Data The Scientific Method Does Not Always Provide Definitive Answers Truth Time Present Science Old Theory

6. Ockham’s Razor: The law of economy or parsimony When looking at data, it is usually possible to come up with a number of different theories, some of which are more complicated than others Scientists generally agree that the most simple theory or explanation of data is most probably true This preference for the most simple theory is called Ockham’s Razor, the law of economy or parsimony William of Ockham was a 14th century English monk to whom “Entia non sunt multiplicanda entia praeter necessitatem” (Don’t multiply entities except by necessity) is attributed Others including Aristotle had invoked this principle before Ockham, but he stands out for his repeated and sharp use of the “razor”

7. Understanding Science Scientists must understand the difference between facts (data) and interpretation (theory) Fact - Chimpanzees and humans have DNA that is 98 - 99 % identical Interpretation 1 - Chimpanzees and humans share a common ancestor Interpretation 2 - Chimpanzees and humans share a common Designer Most data is open to multiple interpretations Theory ≠ Fact

8. Reductionism Organisms are too complex to study as a whole, so biologists break them down to their components to determine how the parts work. Knowing each part’s workings gives insight on the whole organism. Understanding the digestive system, requires study of the digestive organs. Understanding the esophagus, stomach and intestines helps us understand the system. Cells, the fundamental units of life, can be understood in light of the biochemicals (proteins, lipids, carbohydrates etc.) from which they are made. All biochemicals are coded for ultimately through DNA

9. Emergent Properties Biological systems are more than just the sum of their parts, the combination of parts produce “emergent” properties only present because of the combination and not intrinsic to any single part. A wheel is not a transportation device and neither is a bicycle frame, put them together with a few other parts and they become a bicycle. The heart would not pump blood if it was only the ventricles contracting, or just valves ensuring blood flows in only one direction. Combination of ventricles and valves moves blood through the heart and out to the body.

10. Biologist’s Dilemma Life is too complex to study as a whole, thus reductionism must be used to simplify biological systems to the point they can be understood The “simple” components that make up living things have emergent properties present only when they are combined together. In other words, the whole is greater than the sum of the parts Understanding how the components work does not necessarily tell us how the organism works.

11. Ernst Haeckel One of Darwin’s most ardent promoters “The Monera (for instance, chromacea and bacteria), which consist only of this primitive protoplasm, and which arise by spontaneous generation from these inorganic nitrocarbonates, may thus have entered upon the same course of evolution on many other planets...” “First simple monera are formed by spontaneous generation, and from these arise unicellular protists...” Both quotes are from The Riddle of the Universe at the close of the Nineteenth Century by Haeckel.

12. Reductionism Again Our understanding of cells at the molecular level reveals a world of complexity unimagined by Haeckel and others of his age. Cells are not “primitive protoplasm,” but a myriad of complex molecular machines each of which is immensely unlikely to have come about spontaneously. Haeckel’s naive faith in spontaneous generation now seems laughable in the light of knowledge generated by scientists practicing reductionism.

13. Genetics In one sense, genetics could be considered to be the ultimate exercise in reductionism on the part of biologists. Genes serve as the blue print for life. All proteins are defined by genes, and all other macromolecules are made by proteins. All emergent properties are ultimately defined by genes

14. Interdisciplinary Science In this class, we will look at DNA and proteins, methods for studying them and the central role that these two macromolecules play in cells. All this will be done within the context of the scientific method.