Themes in the Study of Life: Scientific Method I. Introduction A. The science of biology is enormous in scope. 1. It reaches across size scales from submicroscopic molecules to the global distribution of biological communities. 2. It encompasses life over huge spans of time from contemporary organisms to ancestral life forms stretching back to nearly four billion years. B. As a science, biology is an ongoing process. 1. As a result of new research methods developed over the past few decades, there has been an information explosion. 2. Technological advances yield new information that may change the conceptual framework accepted by the majority of biologists. C. With rapid information flow and new discoveries, biology is in a continuous state of flux. There are, however, enduring unifying themes that pervade the science of biology: 1. A hierarchy of organization 2. Emergent properties 3. The cellular basis of life 4. Heritable information 5. The correlation between structure and function 6. The interaction of organisms with their environment 7. Unity in diversity 8. Evolution: the core theme. 9. Scientific process: the hypothetico-deductive method D. Life is organized on many structural levels E. A characteristic of life is a high degree of order. Biological organization is based on a hierarchy of structural levels, with each level building on the levels below it. PowerPoint Slide #2 Slide #3 Atoms Complex biological molecules Subcellular organelles Cells Tissues Organs Organ systems Complex organisms F. There are levels of organization beyond the individual organism: 1. Population Localized group of organisms belonging to the same species. 2. Community Populations of species living in the same area. Page 1 of 18 Slide #4 Themes in the Study of Life: Scientific Method 3. Ecosystem An energy-processing system of community interactions that include abiotic environmental factors such as soil and water 4. Biomes Large scale communities classified by predominant vegetation type and distinctive combinations of plant s and animals Biosphere The sum of all the planet's ecosystems. II. Each level of biological organization has emergent properties A. Emergent property = Property that emerges as a result of interactions between components. 1. With each step upward in the biological hierarchy, new properties emerge that were not present at the simpler organizational levels. 2. Life is difficult to define because it is associated with numerous emergent properties that reflect a hierarchy of structural organization. B. Some of the emergent properties and processes associated with life are: 1. Order. Organisms are highly ordered, and other characteristics of life emerge from this complex organization. 2. Reproduction. Organisms reproduce; life comes only from life (biogenesis). 3. Growth and Development. Heritable programs stored in DNA direct the speciesspecific pattern of growth and development. 4. Energy Utilization. Organisms take in and transform energy to do work, including the maintenance of their ordered state. 5. Response to Environment. Organisms respond to stimuli from their environment. 6. Homeostasis. Organisms regulate their internal environment to maintain a steadystate, even in the face of a fluctuating external environment. 7. Evolutionary Adaptation. Life evolves in response to interactions between organisms and their environment. C. Because properties of life emerge from complex organization, it is impossible to fully explain a higher level of order by breaking it into its parts. D. Holism = The principle that a higher level of order cannot be meaningfully explained by examining component parts in isolation. 5. Page 2 of 18 Slide #5 Themes in the Study of Life: Scientific Method 1. An organism is a living whole greater than the sum of its parts. 2. For example, a cell dismantled to its chemical ingredients is no longer a cell. E. It is also difficult to analyze a complex process without taking it apart. F. Reductionism = The principle that a complex system can be understood by studying its component parts. 1. Has been a powerful strategy in biology. 2. For example, Watson and Crick deduced the role of DNA in inheritance by studying its molecular structure. G. The study of biology balances the reductionist strategy with the goal of understanding how the parts of cells, organisms and populations are functionally integrated. III. Cell's are an organism's basic units of structure and function A. The cell is an organism's basic unit of structure and function. 1. Lowest level of structure capable of performing all activities of life. 2. All organisms are composed of cells. 3. May exist singly as unicellular organisms or as subunits of multicellular organisms. B. The invention of the microscope led to the discovery of the cell and the formulation of the cell theory. 1. Robert Hooke (1665) reported a description of his microscopic examination of cork. 2. Hooke described tiny boxes which he called "cells" (really cell walls). The significance of this discovery was not recognized until 150 years later. 3. Antonie van Leeuwenhok (1600's) used the microscope to observe living organisms such as microorganisms in pond water, blood cells and animal sperm cells. 4. Matthias Schleiden and Theodor Schwann (1839) reasoned from their own microscopic studies and those of others, that all living things are made of cells. This formed the basis for the cell theory. 5. The cell theory has since been modified to include the idea that all cells come from preexisting cells. C. Over the past 40 years, use of the electron microscope has revealed the complex ultrastructure of cells: Page 3 of 18 Slide #6 Themes in the Study of Life: Scientific Method 1. Cells are bounded by plasma membranes that regulate passage of materials between cell and its surroundings. 2. All cells, at some stage, contain DNA. D. Based on structural organization, there are two major kinds of cells: prokaryotic and eukaryotic. E. Prokaryotic cell = Cell lacking membrane-bound organelles and a membrane-enclosed nucleus. 1. Found only in the Kingdom Monera, the bacteria and blue-green algae. 2. Generally much smaller than eukaryotic cells. 3. Contains DNA that is not separated from the rest of the cell, as there is no membranebound nucleus. 4. Lacks membrane-bound organelles. 5. Almost all have tough external walls. F. Eukaryotic cell = Cell with a membrane-enclosed nucleus and membrane-enclosed organelles. 1. Found in protists, plants, fungi and animals. 2. Subdivided by internal membranes into different functional compartments called organelles. 3. Contains DNA that is segregated from the rest of the cell. DNA is organized with proteins into chromosomes that are located within the nucleus, the largest organelle of most cells. 4. Cytoplasm surrounds the nucleus and contains various organelles of different functions. 5. Some cells have a tough cell wall outside the plasma membrane (e.g. plant cells). Animal cells lack cell walk G. Though structurally different, eukaryotic and prokaryotic cells have many similarities, especially in their chemical processes. IV. The continuity of life is based on heritable information in the form of DNA A. Biological instructions for an organism's complex structure and function are encoded in DNA, 1. Each DNA molecule is made of four types of chemical building blocks called nucleotides. 2. The linear sequence of these four nucleotides encodes the precise information in a gene, the unit of inheritance from parent to offspring. 3. An organism's complex structural organization is specified by an enormous amount of coded information, Page 4 of 18 Slide #7 Slide #8 Slide #9 Slide #10 Themes in the Study of Life: Scientific Method B. Inheritance itself is based on: 1. A complex mechanism for copying DNA. 2. Passing the information encoded in DNA from parent to offspring. C. All forms of life use essentially the same genetic code. 1. A particular nucleotide sequence provides the same information to one organism as it does to another. 2. Differences among organisms reflect differences in nucleotide sequence. V. Structure and function are correlated at all levels of biological organization A. There is a relationship between an organism's structure and how it works. Form fits function. 1. Biological structure gives clues about what it does and how it works. 2. Knowing a structure's function gives insights about its construction. 3. This correlation is apparent at many levels of biological organization. (See Campbell, Figure 1.7) VI. Organisms are open systems that interact continuously with their environments A. Organisms interact with their environment, which includes other organisms as well as abiotic factors. 1. Both organism and environment are affected by the interaction between them. 2. Ecosystem dynamics include two major processes: a) Nutrient cycling. b) Energy flow. VII. Regulatory mechanisms ensure a dynamic balance in living systems A. No such thing as “balance of nature” – the biosphere is constantly changing but may be considered in a dynamic balance, that is short term B. Most regulation is by negative feedback mechanisms or homeostasis Page 5 of 18 Slide #11 Slide #12 Slide #13 Themes in the Study of Life: Scientific Method Positive or Runaway Feedback Negative Feedback Upward Deviation (+) Set point Downward Deviation C. D. E. VIII. A. B. C. Set point (-) Positive or Runaway Feedback Negative Feedback Feedback 1. Any return to the set point is negative feedback 2. Any deviation further away from the set point is positive feedback There is no connotation of good or bad in the terms negative and positive Example: Thermoregulation Diversity and unity are the dual faces of life on Earth Biological diversity is enormous. 1. Estimates of total diversity range from 5 million to over 30 million species. 2. About 1.5 million species have been identified and named, including approximately 260,000 plants, 50,000 vertebrates and 750,000 insects. To make this diversity more comprehensible, biologists classify species into categories. Taxonomy = Branch of biology concerned with naming and classifying organisms. 1. Taxonomic groups are ranked into a hierarchy from the most to least inclusive category: kingdom, phylum, class, order, family, genus, species. 2. The kingdoms of life recognized in the fivekingdom system are: Monera, Protista, Plantae, Fungi and Animalia. (See Campbell, Figure 1. 10) 3. A six-kingdom system recognizes two prokaryotic groups and divides the Monera into the Archaebacteria and Eubacteria. Page 6 of 18 Slide #14 Themes in the Study of Life: Scientific Method Slide #15 D. There is unity in the diversity of life forms at the lower levels of organization. Unity of life forms is evident in: 1. A universal genetic code. 2. Similar metabolic pathways (e.g. glycolysis). 3. Similarities of cell structure (e.g. flagella of protozoans and mammalian sperm cells). IX. Evolution is the core theme of biology A. Evolution is the one unifying biological theme. 1. Life evolves. Species change over time and their history can be described as a branching tree of life. 2. Species that are very similar share a common ancestor at a recent branch point on the phylogenetic tree. 3. Less closely related organisms share a more ancient common ancestor. 4. All life is connected and can be traced back to primeval prokaryotes that existed more than three billion years ago. B. In 1859, Charles Darwin published On the Origin of Species in which he made two major points: Page 7 of 18 Slide #16 Themes in the Study of Life: Scientific Method 1. X. Species change, and contemporary species arose from a succession of ancestors through a process of "descent with modification." 2. A mechanism of evolutionary change is natural selection. C. Darwin synthesized the concept of natural selection based upon the following observations: 1. Individuals in a population of any species vary in many inheritable traits. 2. Populations have the potential to produce more offspring than will survive or than the environment can support. 3. Individuals with traits best suited to the environment leave a larger number of offspring, which increases the proportion of inheritable variations in the next generation. This differential reproductive success is what Darwin called natural selection. D. Organisms' adaptations to their environments are the products of natural selection. 1. Natural selection does not create adaptations; it merely increases the frequency of inherited variants that arise by chance. 2. Adaptations are the result of the editing process of natural selection. When exposed to specific environmental pressures, certain inheritable variations favor the reproductive success of some individuals over others. E. Darwin proposed that cumulative changes in a population over long time spans could produce a new species from an ancestral one. F. Descent with modification accounts for both the unity and diversity of life: 1. Similarities between two species may be a reflection of their descent from a common ancestor. 2. Differences between species may be the result of natural selection modifying the ancestral equipment in different environmental contexts. The Nature of Science A. Studying Natural Phenomenon 1. Diversity of ways 2. Rules, definitions and approaches 3. Zen, poet, musician, novelist 4. What is truth? Does anyone have a monopoly on truth? Page 8 of 18 Slide #17 Slide #18 Slide #19 Themes in the Study of Life: Scientific Method 5. Is there a correct way to study natural phenomena? Science is one approach 1. Science is a method and not a belief! a) Science does not claim to be able to answer or explain everything b) Science changes constantly, altering explanations (theories) to conform to empirical evidence 2. Religion is a belief and requires faith and claims answers and explanations for all things. a) Definition of faith: unquestioned belief, reliance, trust b) Based on unchanging dogma or doctrine without supporting evidence B. faith (fāth) noun 1. Confident belief in the truth, value, or trustworthiness of a person, an idea, or a thing. 2. Belief that does not rest on logical proof or material evidence. See synonyms at belief, trust. 3. Loyalty to a person or thing; allegiance: keeping faith with one's supporters. 4. Often Faith Theology. The theological virtue defined as secure belief in God and a trusting acceptance of God's will. 5. The body of dogma of a religion: the Muslim faith. 6. A set of principles or beliefs. ]1 1Excerpted from The American Heritage Dictionary of the English Language, Third Edition Copyright © 1992 by Houghton Mifflin Company. Electronic version licensed from Lernout & Hauspie Speech Products N.V., further reproduction and distribution restricted in accordance with the Copyright Law of the United States. All rights reserved. Page 9 of 18 Themes in the Study of Life: Scientific Method 3. Empirical evidence - evidence based on scientific experimentation em·pir·i·cal (ĕm-pîrʹ ĭ-kəl) adjective 1. a. Relying on or derived from observation or experiment: empirical results that supported the hypothesis. b. Verifiable or provable by means of observation or experiment: empirical laws. 2. Guided by practical experience and not theory, especially in medicine. C. Science is a method and is based on definitions not empirical evidence, that is a tautology In logic an empty or vacuous statement composed of simpler statements in a fashion that makes it logically true whether the simpler statements are factually true or false; for example, the statement Either it will rain tomorrow or it will not rain tomorrow. D. E. Science versus technology versus medicine Science is experimentation, gathering empirical evidence XI. Misuses of science A. BELIEVE TO BE TRUE VERSUS KNOW TO BE TRUE 1. Cranberry juice example - common practice from a clinical note, 1962, on ONE sixty-six year old woman a) No scientific evidence for this "traditional" practice b) Not enough hippuric acid to lower acidity of urine to kill any bacteria in "cranberry cocktail" - straight cranberry juice will pucker a person for 723 days! 2. Common cold and myths, nutrition of crust on bread 3. Nutrition myths - "You can't prove it doesn't work therefore it must be valid." - illogical 4. "Allergies" - lack of understanding of meaning 5. Sugar "addiction" or "allergy" (Woman who claimed she was allergic to sodium!) B. Low sample size, n C. Anecdotal and testimonial evidence - true believers 1. Chiropractic 2. Iridology 3. Herbal Life D. Spurious conclusions Page 10 of 18 Slide #20 Slide #21 Themes in the Study of Life: Scientific Method 1. Marijuana, alcohol and driving - U. of Washington study 2. Rockefeller quote to his Sunday school class 3. Billy James Hargis and chromosomes 4. Feingold and nutrition for hyperactivity E. Science and political gain 1. Stalin & Lysenko 2. Racists F. Overuse of science - Cigarette industry and evidence for lung cancer G. "She makes housekeeping into a science." meaningless, being orderly and organized is not necessarily a scientific activity but it helps H. If someone makes a claim about something it is up to him or her to present the evidence to support the claim it is NOT up to the listener to disprove it. I. Typical signs of fraudulent claims include: 1. Products advertised as effective against a wide range of ailments 2. Use of terms like scientific breakthrough, miraculous cure, ancient remedy, etc. 3. Impressive sounding terminology to disguise a lack of good science 4. Claims the government or the medical profession have conspired to suppress the product 5. Testimonials instead of facts and figures 6. Product availability from only one source XII. Science as a process of inquiry often involves hypothetico-deductive thinking A. As the science of life, biology has the characteristics associated with science in general. B. Science is a way of knowing. It is a human endeavor that emerges from our curiosity about ourselves, the world and the universe. Good scientists are people who: 1. Ask questions about nature and believe those questions are answerable. 2. Are curious, observant and passionate in their quest for discovery. 3. Are creative, imaginative and intuitive. 4. Are generally skeptics. C. The key ingredient of the scientific process is the hypothetico-deductive method, which is an approach to problem-solving that involves: 1. Asking a question and formulating a tentative answer or hypothesis by inductive reasoning. Page 11 of 18 Slide #22 Themes in the Study of Life: Scientific Method 2. D. E. F. G. Using deductive reasoning to make predictions from the hypothesis and then testing the validity of those predictions. Hypothesis = Educated guess proposed as a tentative answer to a specific question or problem. Inductive reasoning = Making an inference from a set of specific observations to reach a general conclusion. Process of deriving general principles from particular facts or instances Deductive reasoning = Making an inference from general premises to specific consequences, which logically follow if the premises are true. 1. The process of reasoning in which a conclusion follows necessarily from the stated premises; inference by reasoning from the general to the specific 2. Usually takes the form of If.. then logic. 3. In science, deductive reasoning usually involves predicting experimental results that are expected if the hypothesis is true. Useful hypotheses have the following characteristics: 1. Hypotheses are possible causes. Generalizations formed by induction are not necessarily hypotheses. Hypotheses should also be tentative explanations for observations or solutions to problems. 2. Hypotheses reflect past experience with similar questions. Hypotheses are not just blind propositions, but are educated guesses based upon available evidence. 3. Multiple hypotheses should be proposed whenever possible. The disadvantage of operating under only one hypothesis is that it might restrict the search for evidence in support of this hypothesis; scientists might bias their search, as well as neglect to consider other possible solutions. 4. Hypotheses must be testable via the hypothetico-deductive method. Predictions made from hypotheses must be testable by making observations or performing experiments. This limits the scope of questions that science can answer. 5. Hypotheses can be eliminated, but not confirmed with absolute certainty. If repeated experiments consistently disprove the predictions, then we can assume that the hypothesis is false. However, if repeated experimentation supports the deductions, we can only assume that the hypothesis may be true; accurate predictions can be made from Page 12 of 18 Slide #23 Themes in the Study of Life: Scientific Method H. I. J. K. L. false hypotheses. The more deductions that are tested and supported, the more confident we can be that the hypothesis is true. Another feature of the scientific process is the controlled experiment which includes control and experimental groups. Control group = In a controlled experiment, the group in which all variables are held constant. 1. Controls are a necessary basis for comparison with the experimental group, which has been exposed to a single treatment variable. 2. Allows conclusions to be made about the effect of experimental manipulation. 3. Setting up the best controls is a key element of good experimental design. Variable = Condition of an experiment that is subject to change and that may influence an experiment's outcome. Experimental group = In a controlled experiment, the group in which one factor or treatment is varied. Science is an ongoing process that is a selfcorrecting way of knowing. Scientists: 1. Build on prior scientific knowledge. 2. Try to replicate the observations and experiments of others to check on their conclusions. Page 13 of 18 Slide #24 Themes in the Study of Life: Scientific Method 3. M. N. O. XIII. A. Share information through publications, seminars, meetings and personal ommunication. What really advances science is not just an accumulation of facts, but a new concept that collectively explains observations that previously seemed to be unrelated. 1. Newton, Darwin and Einstein stand out in the history of science because they synthesized ideas with great explanatory power. 2. Scientific theories are comprehensive conceptual frameworks that are well supported by evidence and are widely accepted by the scientific community. Biology is a multi-disciplinary science that requires knowledge of chemistry, physics and mathematics. Process which outlines a series of steps used to answer questions. 1. Is not a rigid procedure. 2. Based on the conviction that natural phenomena have natural causes. 3. Requires evidence to logically solve problems. Scientific method - "Organized common sense" Hierarchy of scientific method 1. Observation 2. Question 3. Hypothesis a) Most important part of experiment b) A question that must be capable of being answered yes or no c) Must match experiment 4. Experimental design a) The experiment is designed to test the hypothesis, that is when the experiment is done can the hypothesis be answered "yes" or "no" b) Experiments are not designed to prove anything or to discover anything but to test an hypothesis c) Variable - a good experiment has only ONE variable (mouse & hairspray example) d) Controls - need as many controls as necessary to ensure that there is only one variable e) If at all possible results should be quantified Page 14 of 18 Themes in the Study of Life: Scientific Method f) g) Numbers can be tested statistically Results should be in tabular or graphic form - no subjective interpretation of data (data is plural, datum is singular) 5. Conclusion a) Here is where the results can be discussed b) Discussion must have to do with the hypothesis and results, not something unrelated B. Possible errors of interpretation 1. Anthropomorphism - ascribing human attributes to nonhuman animals (love, hate, greed, remorse etc) 2. Teleology - (tee-lee-ahl'-uh-jee) a) "Birds evolved wings so they could fly" b) "The course of evolution is toward the perfection of a species" c) Have to be able to live with the concept of "IS" without an ultimate purpose attached to it Teleology is the study of things or events in terms of their purposes or ends. From ancient times to the present, many philosophers and scientists have thought that various natural processes could be explained only in terms of the purposes that they were achieving or in terms of the ends or goals that they were reaching. In Aristotle's physics, four types of explanation were offered, but the most important one was in terms of the purpose (Greek: telos), or final goal, of physical change. For Aristotle all processes of change were purposeful. From the examination of the world in terms of purpose and the discovery of such apparent purposes, a teleological argument for the existence of God was worked out, an argument claiming that the purposes found in nature required a purposeful Designer, or God. In the development of modern science, one of the first contentions of Galileo Galilei and Rene Descartes was that purposes could neither be known nor discovered. Although scientists have progressively removed teleological inquiry from one branch of the study of nature after another, the central issue remains: whether teleological explanation is necessary to account for the behavior of living or conscious beings or whether all of their behavior can be explained without it. RICHARD H. POPKIN Bibliography: Collins, James, Interpreting Modern Philosophy (1972); Hull, David, Philosophy of Biological Science (1974); McFarland, J. D., Kant's Concept of Teleology (1969); Taylor, Charles, The Explanation of Behaviour (1964); Woodfield, Page 15 of 18 Slide #25 Themes in the Study of Life: Scientific Method Andrew, Teleology (1976); Wright, Larry, Teleological Explanations (1976). 3. 4. Subjectivity versus objectivity Bias versus prejudice a) Bias - a view point based on past experience and not necessarily apparent to the individual - not a planned sort of thing and is largely unavoidable b) Prejudice - a view point held in disregard to facts that contradict it C. Double-blind studies for humans 1. Power of suggestion 2. Placebo effect XIV. Probability A. Rules of probability are by definition 1. Absolute certainty = 1 2. Absolute uncertainty = 0 3. Most probabilities fall somewhere in between the two extremes 4. Sum rule - the probability that one or another of two independent events will occur is the sum of their separate probabilities a) Probability that a coin flip will come up with a head or a tail: 1/2 + 1/2 = 1 b) Probability that a role of a die will turn up a five or a six: 1/6 + 1/6 =1/3 5. Product rule - if two events are independent of each other, the probability of their coinciding is the product of their individual probabilities 6. Odds of a game a) Probability of getting a head on a coin toss and of getting a head on a second toss is: B. C. 1/2 X 1/2 = 1/4 (1/2)2 b) Probability of a male (0.50) with blood type A (0.40) and being born in June (1/12): 0.50 X 0.40 X 0.084 = 0.0168 The results and interpretations of experiments are subject to statistical analysis Mathematical calculations of probability versus "seat of pants predicting" - Vegas trap 1. Coin flip 2. Role of dice, one die, two dice 3. Gambling Page 16 of 18 Slide #26 Slide #27 Themes in the Study of Life: Scientific Method a) b) c) d) License plates Birthdays Odds of a game - Vegas The "Gambler's Fallacy" - the odds of a game will change with time XV. Normal Distribution A. Curve below – mean = 5, standard deviation = 1 Slide #28 Normal (Gaussian) Distribution or Bell Shaped Curve 0.45 Mean = 5 0.4 0.35 Standard Deviation = 1 0.3 0.25 0.2 0.15 0.1 0.05 0 10.0 9.5 9.0 8.5 8.0 7.5 7.0 6.5 6.0 5.5 5.0 4.5 4.0 3.5 3.0 2.5 2.0 Normal distribution synonyms 1. Gaussian curve 2. Bell shaped curve C. Very important in testing if there is a significant difference between two sets of data D. "Laws of Nature" 1. Too simplistic way of viewing natural phenomenon 2. A scientific statement (theory) is a probability statement and not necessarily true a) The theory can be used to make predictions and formulate more experiments but should never be accepted as absolute b) Scientific inquiry would cease if so called laws were accepted as immutable c) Challenge to the law must be presented with evidence, however XVI. Science and technology are functions of society A. Science and technology are interdependent. 1. Technology extends our ability to observe and measure, which enables scientists to 1.5 1.0 0.5 0.0 B. Page 17 of 18 Slide #29 Themes in the Study of Life: Scientific Method B. C. work on new questions that were previously unapproachable. 2. Science, in turn, generates new information that makes technological inventions possible. 3. For example, Watson and Crick's scientific discovery of DNA structure led to further investigation that enhanced our understanding of DNA, the genetic code, and how to transplant foreign genes into microorganisms. The biotechnology industry has capitalized on this knowledge to produce valuable pharmaceutical products such as human insulin. We have a love-hate relationship with technology. 1. Technology has improved our standard of living. 2. The consequence of using technology also includes the creation of new problems such as increased population growth, acid rain, deforestation, global warming, nuclear accidents, ozone holes, toxic wastes and endangered species. 3. Solutions to these problems have as much to do with politics, economics, culture and values as with science and technology. A better understanding of nature must remain the goal of science. Scientists should: 1. Try to influence how technology is used. 2. Help educate the public about the benefits and hazards of specific technologies. Page 18 of 18