BIO1130 Slide Deck - The Scientific Method PDF

Topic 1 THE SCIENTIFIC METHOD 2 Learning objectives Define science and explain what the scientific method entails and why it is important Distinguish the types of science, and types of reasoning, and outline both of their roles in the scientific method Differentiate between h...

Topic 1 THE SCIENTIFIC METHOD 2 Learning objectives Define science and explain what the scientific method entails and why it is important Distinguish the types of science, and types of reasoning, and outline both of their roles in the scientific method Differentiate between hypothesis vs. prediction vs. theory Explain why science proceeds via rejecting, not proving, hypotheses Summarize the characteristics that distinguish science from non-science Explain confounding variables and the role of controls in addressing them Explain the concept of inferential strength and extrapolation, and how these relate to observational vs. manipulative studies Outline the four requirements for science to result in knowledge acquisition Demonstrate concepts from above via the case study on the evolution of human skin colour 3  Definitions Biology: the intellectual and practical activity encompassing the systematic study of the structure and behaviour of the natural world through observation and experimentation Scientific method: an approach to knowledge acquisition that seeks to ensure that our understanding is based on evidence (i.e., data acquired through observation and experimentation) 4 Two types of science Descriptive: seeks to characterize ‘patterns’ (i.e., to describe the physical and/or natural world) Hypothesis-testing: concerned with testing one or more causal explanations for an existing pattern (i.e., to explain observations of the physical and/or natural world) 5 Both types of science are important to the scientific method descriptive science provides the grist for the hypothesis-testing science mill (i.e., it provides patterns and may suggest possible explanations) hypothesis-testing science interprets patterns and, in doing so, provides direction as to where to look for other patterns Descriptive science Hypothesis-testing science 6  Example: eutrophication in freshwater lakes 1) Descriptive study reveals a pattern: 3) An experiment manipulating [K] finds no effect, rejecting this hypothesis. Primary production 4) Characterize more patterns; Is primary production correlated with something else? Is [K] correlated with this? Potassium [K] concentration 2) Hypothesis: [K] is a limiting nutrient such that increasing availability fosters increased algal growth. 7  The scientific method Descriptive science Biological hypothesis Deduction Descriptive Induction Hypothesis-testing science science Predictions Study Inference Data Conclusions (statistical (patterns) (support or reject biological hypothesis) hypothesis testing) 8  Induction Specific observations (patterns) are synthesized to produce a general statement or conclusion (reasoning from the particular to the general) Even if all the axioms are true, the conclusion is not necessarily true. Inductive reasoning is often the source of biological hypotheses, but is ideally not used to test them This bird is a swan & it is white. And this bird is a swan & it is white. ∴ All swans are white 9  The scientific method Descriptive science (biological) hypothesis Deduction Descriptive Induction Hypothesis-testing science science Predictions Study Inference Data Conclusions (statistical (patterns) (support or reject biological hypothesis) hypothesis testing) 10  Deduction in hypothesis-testing science Hypothesis: a causal explanation for a given pattern Prediction: a statement of what will be observed under specified conditions (i.e., those of the study we’re going to do) if the hypothesis is true. A prediction only exists within the context of a hypothesis and a particular study The scientific method uses deduction to derive predictions and hence to test hypotheses 11  Deduction A form of reasoning from one or more general statements (premises) to a logical conclusion There is no uncertainty: if the premises are true then the conclusion necessarily follows (i.e., it must be true) It can be represented by a syllogism: – Premise 1: All birds have feathers. – Premise 2: All robins are birds. – Deduction: Therefore, all robins must have feathers. 12  Deduction With respect to testing a scientific hypothesis, predictions must follow deductively from hypotheses Syllogisms can also be presented as if…then statements – If hypothesis X is true, – and a study of type Y is performed, – then result Z will be observed. 13  What makes a “scientific” hypothesis? According to Sir Karl Popper, in addition to being causal all scientific hypotheses must also be refutable, at least in principle A refutable hypothesis is one for which there are possible outcomes that are inconsistent with it I.E., it can be falsified (in theory) The ‘hypothesis’ that the fossil record of life on earth was created by god is not falsifiable. There is no observation that could refute the existence of a supernatural being. It is therefore not a scientific hypothesis. Why must hypotheses be refutable? 14  Science proceeds by falsifying hypotheses Popper argued that science best proceeds by eliminating hypotheses, not proving them, because you cannot prove a hypothesis “When you have eliminated the impossible, Watson, whatever remains – however improbable – is the truth.” Sherlock Holmes, Hypotheses The Sign of Four Pattern we want to explain 15 A logical fallacy: you can’t prove a hypothesis If H then P Humidity is high this morning because it rained last night (H). P observed If it rained last night, the garden will be wet (P). The garden is wet (i.e., P is observed). ∴ H true Therefore, the high humidity is because it rained last night. This argument is invalid because the conclusion can be incorrect even if P follows deductively from H and P is observed. Why? Because H is not the only potential cause of P. So, observing the prediction SUPPORTS, but does not prove, the hypothesis. 16  But you CAN disprove a hypothesis If H then P Humidity is high this morning because it rained last night (H). P NOT observed If it rained last night, the garden will be wet (P). The garden is NOT wet (i.e., P is not observed). ∴ H false Therefore, the high humidity is NOT the result of rain last night. This argument is valid because the prediction follows deductively from the hypothesis. So, a failure to observe the prediction falsifies the hypothesis. 17  Example: why the bathroom light doesn’t work Hypotheses Power What we want off to house to explain Bulb burnt out Light switch is on, but there’s no light Short in circuit 18  Hypotheses and predictions Hypothesis: a statement about the cause of some pattern Prediction: the pattern one will see in the results of a particular study if the hypothesis is true Inference: – if predicted pattern is observed, hypothesis is supported (but not proven) – if predicted pattern is not observed, the hypothesis is rejected (falsified). 19  The scientific method Descriptive science (biological) hypothesis Deduction Descriptive Induction Hypothesis-testing science science Predictions Study Inference Data Conclusions (statistical (patterns) (support or reject biological hypothesis) hypothesis testing) 20 Type of study Separate from the type of science, there are two types of study: 1) Observational - researcher observes/measures/characterizes, but does not alter, the system 2) Manipulative (aka an ‘experiment’) - the researcher changes something and compares what happens to a control (i.e., unmanipulated) treatment, or one or more other treatments with different values of the manipulated variable The type of study is independent of the type of science. Don’t confuse them! 21 Examples of the two types of study 2) Manipulative (experiment) 1) Observational study Primary production Phosphorous concentration 22 All combinations exist for types of science and study Type of science Type of study Descriptive Hypothesis-testing When do hummingbirds Measure the correlation between arrive in the spring? chlorophyll content and phosphorus Observational Where are the areas of across many lakes to test the highest biodiversity? hypothesis that P is limiting Fun science. What Classic experiment to test happens when I…? predictions of a hypothesis. Manipulative Treatments are compared to each other or to a control. 23  Practice Hyperlink (click here), or: Q1: Correlates of marijuana use among under undergraduate students. 24 24  Observational vs. manipulative studies: why do we care? Inferential strength is a measure of how strongly the results support the conclusions. All else equal (caution, it never is), manipulative studies have greater inferential strength than observational studies Why? Because manipulative studies better control for confounding variables. This is why you often hear that “correlation doesn’t imply causation”. 25  Confounding variables A separate, often unknown, variable that may be responsible for the observed pattern. Statistically, a third variable that is correlated with the independent variable and which may be causing the association between the dependent and independent variables. Lake primary productivity (dependent variable) Potassium conc. Phosphorous conc. (independent variable) (confounding variable) 26 Consider a manipulative experiment The independent variable (e.g., potassium conc.) is actively changed by the researcher, so confounding differences are FAR less likely When a potential confound exists, it can be addressed via appropriate controls A control is an experimental procedure or treatment level designed to minimize the effects of confounding variables. 27  Example: effects of an oncolytic virus on tumour growth in mice Biological question: can a tumour-killing virus effectively reduce tumour growth rate in vivo? Procedure: inject a virus suspension into spontaneous tumour mouse model and track tumour growth Design question: what are the appropriate controls? – A second set of mice that don’t receive the virus injection? – Something better? 28  All else is often not equal: extrapolation Studies, especially manipulative experiments, are almost always conducted on ‘model' systems that are smaller in scale, and/or simplified, compared to the system of interest Drawing inferences from results of studies on model systems requires that we assume that the model system behaves similarly to the actual system of interest This is called extrapolation, and the more extrapolation that is required, the lower the inferential strength Observational studies often involve far less extrapolation than manipulative studies 29  Common types of extrapolation Extrapolation is common and often extreme: Interspecies (very common in biomedical studies – e.g., rates as models for humans) From experimental indicators (that which we measure or estimate) to system properties of real interest (e.g., from expression levels to protein levels, from species richness to “biodiversity”, etc.) Spatial and temporal scales In vitro to in vivo 30 30 Practice Hyperlink (click here), or: Q2: Which of the following affect(s) the inferential strength of a study? 31 31  The scientific method Descriptive science (biological) hypothesis Deduction Descriptive Induction Hypothesis-testing science science Predictions Study Inference Data Conclusions (statistical (patterns) (support or reject biological hypothesis) hypothesis testing) 32  Statistical hypothesis testing In almost every study, we want to know if a pattern in the results is real (i.e., is it the result of chance – i.e., random sampling variation – or is it a repeatable, biological phenomenon?) This is the field of statistical hypothesis testing Don’t confuse this with scientific hypothesis testing. Descriptive science also often include statistical hypothesis testing to determine if any observed patterns are real It’s very important but poorly named. It should be called something other than hypothesis testing (e.g., ‘statistical inference’) 33  Summary – the scientific method Falsifiable hypotheses are derived (often inductively) from patterns arising from previous observation and experimentation Deductive predictions are tested via observational and/or manipulative studies with appropriate controls Statistical inference is used to determine whether predicted patterns are present in the results Inference is made to support or reject hypothesis based on this evidence 34  Science and knowledge acquisition Knowledge acquisition requires researchers to be: Rational (i.e., guided by reason): employ the scientific method to ensure inference are based on the evidence Remain always skeptical of hypotheses and evidence: – seek to repeatedly and carefully scrutinize patterns (i.e., are they real?) and hypotheses (Are they reasonable? Consistent with data?) – be willing to reject or modify hypothesis based on the evidence Strive to be objective: unbiased by preconceived notions, beliefs, ideologies, experiences, etc.) Be methodologically materialistic: restrict assumptions and explanations to the material world (i.e., the supernatural is not considered because it is not falsifiable and hence not scientific) 35  Science vs. Pseudo-science Studies that seek only to confirm beliefs are not science (Popper called them pseudo-science) Consider the hypothesis the world is flat: – One seeking to confirm this hypothesis could find (apparent) evidence in support of it, and if this fits with your preconceived notion there may be little incentive to do an exhaustive search for additional evidence that might refute it – But one seeking to disprove this hypothesis would only need show that one deductive prediction it makes is false to reject it – Observations interpreted as evidence of a flat earth are also consistent with a spherical earth (i.e., they don’t reject a spherical earth) 36  Hypothesis vs. theory A hypothesis that has survived many attempts at falsification is referred to as a theory (e.g., the theory of evolution) A scientific theory is an explanation of some aspect of the natural or physical world that has been repeatedly tested via the scientific method. It has withstood this rigorous scrutiny such that it constitutes accepted scientific knowledge This is very different that the everyday usage of theory as ‘speculation’ 37  Case study: skin colour evolution in humans Casual observation and more rigorous descriptive studies show geographic variation in skin colour. Why? What’s causing this? Biasutti (1941) By en:User:Cburnett, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=2866948 38 Modified from “The Evolution of Human Skin Color” by A. Prud’homme-Généreux. 2011. National Center for Case Study Teaching in Science, Univ. at Buffalo, State Univ. of New York  A biological hypothesis Humans and chimpanzees shared a common ancestors 6-7 Mya Chimpanzees are light-skinned but covered by dark hair Evidence suggests that early humans left the cover of trees for the open savannah where there is little shade Humans lost much of their body hair (possibly because of selection to facilitate evaporative cooling to dissipate heat) UV light causes DNA mutations Melanin, a pigment produced by skin cells, absorbs UV light, shielding cells from UV-induced DNA damage Hypothesis: variation in human skin colour evolved from selection for increased melanin in areas of high UV exposure because this reduces UV- induced DNA damage (i.e., skin cancer) 39  Testing the hypothesis: an observational study Global UV Index Lighter skin Darker skin National Oceanic and Atmospheric Administration. Retrieved 18 Oct 2009 Barsh (2003) from Relethford (1997) Evidence is consistent with (i.e., supports) the hypothesis It remains possible that another hypothesis makes the same prediction As scientists, we remain skeptical and objective 40 Problem Skin cancer generally arises late in life, long after reproduction, and is usually not fatal Jablonski & Chaplin (2000) argued that selection for increased melanin resulting from decreased cancer risk will therefore be very weak Prof. Nina Jablonski …and that the cancer-protecting function of melanin is unlikely to be the primary selective agent favouring increased melanin (i.e., it may have contributed weakly or not at all) 41  Folate Folate (folic acid) is an essential nutrient for DNA synthesis and is especially important during pregnancy when DNA replication rates are very high in the fetus Blood folate in people exposed (‘Patients’) or Folate deficiency causes anemia in not (‘Normals’) to UV light for 9h/d for 3 mothers, serious neural defects in the months. developing fetus, and increases risk of Correction to video: miscarriage melanin reduces the loss of FOLATE due to UV- Melanin protects against UV-induced induced degradation. breakdown (i.e. photolysis) of folate in the skin 42 Branda & Eaton (1978) Science New hypothesis Hypothesis: humans evolved increased melanin (and hence darker skin) in areas of high UV exposure because this protected them from UV- induced degradation of folate This can explain the evolution of darker skin in humans following hair loss, but it CANNOT, on its own, explain the evolution of light skin (i.e., there is no advantage of light skin, so darker skin should eventually evolve everywhere) 43 Vitamin D3 UVB is critical for the synthesis of vitamin D3 which starts in the skin D3 is needed for calcium absorption and hence bone growth; deficiencies can lead to immobilization, developmental deformities, and death In northern latitudes, dark skin can cause D3 deficiency Hypothesis: selection in more extreme latitudes favours lighter skin to increase vitamin D production Vitamin D3 44  Jablonski & Chaplin (2000) Insufficient UVB to synthesis in D3 in light, moderate and dark skin Sufficient UVB to synthesis Insufficient UVB to synthesis D3 in even dark skin in D3 in moderate to dark skin 45 Support Previously observed broad association between skin colour and latitude is consistent with this hypothesis Additional support: Females require more D3 than males during pregnancy and while breast feeding. And across human populations, females consistently have slightly lighter skin colour than males on average. D3 can also be obtained through certain foods including fisher liver oil. Indigenous populations at extreme latitudes (e.g., Inuit) have darker skin but historically also had diets rich in such foods. 46 Overall Current evidence strongly supports this hypothesis that skin colour has diverged evolutionarily among human populations in response to selection arising from environmental differences A trade-off exists between selection for darker skin to reduce folate photolysis and selection for paler skin to facilitate vitamin D3 synthesis (when D3 cannot be obtained through diet) Effects of melanin in reducing skin cancer by protecting from UV-induced mutation probably contributed little to the evolution of current differences in skin colour 47 Topic 2 DARWIN AND THE THEORY OF EVOLUTION 48  Learning objectives Summarize the history of evolutionary thinking up to Darwin, including the ‘argument from design’ Explain how changing views of geology and fossil evidence set the stage for Darwin Outline Lamark’s theory of evolution, including his mechanism of acquired characters Describe the key observations Darwin made during his voyage on the Beagle and how they influenced his thinking Detail Darwin and Wallace’s key insights – i.e., evolution AND natural selection – and the evidence presented for each (you should be able to define evolution and explain what natural selection is) Summarize the evidence for common descent that comes from homology, vestigial organs, fossils, biogeography Explain what experimental evolution is and how it provides evidence for evolution Differentiate between artificial and natural selection Be able to counter several common misconceptions about evolution Outline how Müllerian and Batesian mimicry work and explain their differences Explain why creationism and intelligent design are not scientific 49 Outline 2.1 Setting the stage - evolutionary thinking prior to Darwin (with an aside about sexism and discrimination) 2.2 Darwin and the voyage of the Beagle Lock & Whitfield creator 2.3 Darwin’s insights: evolution and natural selection QS:P170,Q26242255, Charles Darwin 1877, marked as public domain, more details on Wikimedia Commons 2.4 Evidence for, and misconceptions about, natural selection 50  2.1 Setting the stage – thinking before Darwin Human cultures have a diversity of creation stories that purport to explain how the world arose and came to be as it is Prior to 6th-7th century BCE, these provided the only answers to grand questions concerning the world and our place in it This began to change with early Greek philosophers, some of whom sought systematic explanations based on natural, rather than supernatural, processes Hypotheses were formulated, but were not subjected to refinement or rejection through skeptical and objective testing Aristotle (384-322 BCE) did emphasize the importance of direct observation of nature and argued that principles must agree with the facts (i.e., observations) But most Greek philosophers viewed the world as eternal and unchanging, incompatible with evolution 51 From Greeks to medieval scholars Aristotle did recognize certain similarities among organisms and arranged life (and the physical world) into a linear sequence of increasing complexity in his Scala Naturae – the Great Chain of Being European scholars in the Middle Ages and Renaissance adapted this to a Christian view of creation An ‘argument from design” was promoted, which dates back to at least the early Greeks but was famously accepted by medieval scholar St. Thomas Aquinas (1224-1274) and influentially formulated by William Paley (1743-1805) via the ‘watchmaker analogy’ – It argues that the complex structures of living things, and the remarkable adaptations of plants and animals, are evidence of an intelligent designer 52 Natural theologians & classification Fig. 26.4, Campbell Biology, 3rd Canadian Edition. 2021. Pearson Starting in the 1600’s, natural theologians dissatisfied with Aristotle’s Scala Naturae began developing systematic classification systems based on similarity of organisms E.g., John Wray’s 1691 “The Wisdom of God Manifested in the Works of Creation” provided the first systematic classification of plants Carl Linnaeus (1707-1778), a Swedish physician, zoologist and botanist, who developed a taxonomic system in which all organisms are arranged in hierarchical groupings based on similarity, with lower groups nested within higher ones Linnaeus, Wray and others had no theoretical reason why this should be the case other than believing it represented a divine plan 53  A young earth James Ussher by Sir Peter Lely, marked as public domain, more details on Wikimedia Commons Christianity also introduce the idea that the earth was young (i.e., creation was relatively recent) In 1664, Archbishop James Ussher used Old Testament genealogies to calculate that god created the world on Oct. 26, 4004 BC at 9am! The idea was widespread – Isaac Newton dated creation at 3998 BCE This sort of thinking about fixed species created by a divine power and a young earth was widespread up to the time of Darwin 54  Changing ideas But at the time that Archbishop Ussher was making his calculations, a radical shift was beginning in geology toward the idea of a very old earth By the 18th century, it was clear that sedimentary rocks had been laid down under ancient oceans In 1795, James Hutton argued that the way rock strata were aligned, and how the processes of erosion and sedimentation worked (and also fossil evidence), Charles Lyell - Pillars of Pozzuoli, marked as public indicated that the world must be inconceivably old domain, more details on Wikimedia Commons Charles Lyell (1830) sought to explain existing geological features by appealing to the geological processes we currently observe, arguing that they must have operated over very long periods of time in a slow, gradual manner (uniformitarianism as opposed to catastrophism)  Fossils played a crucial role In the early 1800’s, by comparing the anatomy of living species with that of fossils, French naturalist Georges Cuvier established the fact of extinction – there were species in the fossil record that were not living today (e.g., mastodons, Irish elk) Some of the most spectacular of these were discovered by a remarkable British Georges Cuvier (1769-1832); Georges_Cuvier.jpg; Unknown derivative paleontologist, Mary Anning (1799-1847) work: Beao, Georges Cuvier, marked as public domain, more details on Wikimedia Commons Extinction challenges the idea that the earth flora and fauna have been constant, opening the door to both change and long periods of time over which it can occur Autographed letter concerning the discovery of plesiosaurus, from Mary Anning; sketch of plesiosaurus. Wellcome Collection. Attribution 4.0 International (CC BY 4.0) 56  Aside: Historical sexism in evolutionary biology Evolutionary biologists generally reflect the attitudes and biases of the societies they are part of Historically, this included the widespread notion that females were intellectually inferior to males Ironically, this was ‘supported’ by pseudoscientific data and paradigms emanating from evolutionary biology Scholarship was therefore actively prohibited in women and those engaging in it experienced discrimination and others forms of maltreatment 57  Sexism in evolutionary biology today The face of science is changing; many prominent evolutionary biologists today are women and the contributions of women are many and varied Progress is being made, but problems nevertheless remain. For example: – there is a paucity of women in academic and institutional leadership positions – the role of women in driving science forward is still not equally represented – women continue to experience sexual harassment at work – systematic biases remain in evaluations of research and teaching, impacting career advancement – support for child rearing is insufficient Want more information? This is a great paper (free online): Wellenreuther, M. & S. Otto. 2015. Women in evolution – highlighting the changing face of evolutionary biology. Evolutionary Applications 9: 3-16. https://doi.org/10.1111/eva.12343 58  Aside: Historical sexism in evolutionary biology The scientific achievements past women made, despite the historical barriers they faced, have also traditionally been underrecognized, including in courses and textbooks This need not, and should not, continue; their contributions deserve to be recognized and doing so may provide inspiration and will make our field richer and stronger for the diversity of voices 59  Mary Anning From a working-class family on the British south coast; no formal education Learned paleontology because her family collected and sold fossils LONG list of important discoveries (e.g., first correctly identified ichthyosaur skeleton, played a key role in showing that coprolites are fossilised faeces) Mary Anning; Credited to 'Mr. Grey' in Crispin Tickell's book 'Mary Anning of Lyme Regis' (1996), Mary Anning painting, marked as public domain, more details on Wikimedia Commons She knew more about fossils and geology than many of her wealthy fossilists clients; scholars from around the world consulted her to discuss anatomy and classification Treated as an outsider in the scientific community; scientific descriptions of the specimens she found were published by her male colleagues to which she sold the specimens, often with no mention of her Royal Society named her 1 of the 10 most influential women in the history of British science Learn more: https://en.wikipedia.org/wiki/Mary_Anning 60  Ideas on evolution before Darwin Several scholars proposed the idea that life had changed over time: – Georges-Louis Leclerc, Comte de Buffon (1707-88), a French nobleman who thought the earth had formed from debris when a comet struct the sun, which took 70,000y to cool and the oceans and continents to form. He thought life was composed of organic particles and the mold that structures them could change in new habitats. – Erasmus Darwin (1731-1802; Charles’ grandfather) proposed that all life had transformed and diversified over millions of years, that humans initially walked on four limbs and, remarkably, that we had descended from another primate species – Robert Chambers (1802-1871), a Scottish geologist, proposed that species changed over time, and this was slow and gradual, but his scientific reasoning, including on the mechanism was, according to Darwin, confused and inadequate But none developed a full-blown theory of evolution 61  Lamark’s theory of evolution Jean-Baptiste Lamark (1744-1829) was an expert on plants and invertebrates Provided the first detailed theory of evolution Jean-Baptiste de Lamarck; Charles Thévenin artist. QS:P170,Q979783, marked as public domain, more details on Wikimedia Commons In Zoological Philosophy (1809) he proposed that new, more complex species descended gradually from older, less complex ones He suggested (incorrectly) that this occurred via the inheritance of acquired characters: that traits acquired during the lifetime of an individual, due to the continued use or disuse of structures, are passed on to their progeny Lamark’s legacy was not that he postulated an incorrect mechanism of evolution, but rather that he proposed one at all AND that he connected it to environmental fit (i.e., to explain what we now refer to as adaptation) 62 Outline 2.1 Setting the stage - evolutionary thinking prior to Darwin (with an aside about sexism and discrimination) 2.2 Darwin and the voyage of the Beagle Lock & Whitfield creator 2.3 Darwin’s insights: evolution and natural selection QS:P170,Q26242255, Charles Darwin 1877, marked as public domain, more details on Wikimedia Commons 2.4 Evidence for, and misconceptions about, natural selection 63  Darwin – a short sketch Born February 12th, 1809 Father was a medical doctor, mother was from the Wedgwood family (porcelain) Married (1838) his cousin Emma Wedgwood (1808-1896) and had 10 children Neglected his medical studies at U. Edinburgh so his father sent him to Cambridge to do a BA with the goal of becoming an Anglican clergyman While completing his degree, he developed an interest in natural history: taxidermy, insect collecting, botany, etc. Became close friends with botany prof John Henslow Planned to visit Tenerife after graduating George Richmond artist QS:P170,Q25561, George Richmond to study tropical natural history so took a - Emma Darwin - 1840, marked as public domain, more details on geology course in preparation Wikimedia Commons George Richmond artist QS:P170,Q25561, Charles Darwin by G. Richmond, marked as public domain, more details on Wikimedia 64 Commons  The Beagle Shortly after completing his BA, received a letter from Henslow proposing him R. T. Pritchett, PSM V57 D097 HMS beagle in as a gentleman and unofficial naturalist on board the HMS Beagle with captain the straits of magellan, marked as public domain, more details on Wikimedia Commons Robert FitzRoy Left in 1831 on a planned 2 year voyage to map the coastline of S. America Trip lasted 5 years, during which he suffered from acute sea sickness, and he visited 3 continents and various islands Spent most of his time on land, collecting fossils of extinct organisms, observing and preserving local fauna and flora; he experienced the ecological complexity of the jungles of Brazil and studied the geology of S. America 65  Voyage of the Beagle Cape Verde islands Fig. 22.5 The voyage of the HMS Beagle (December 1831- October 1836); Campbell Biology, 3rd Canadian Edition. 2021. Pearson. 66  Geological observations Darwin began the expedition thinking like a good protestant: believing in catastrophism (e.g., the Great Flood) FitzRoy gave him a copy of Charles Lyell’s Principles of Geology Mount Vesuvius; I, Pastorius, CC BY 2.5 This, along with his recent geology course, focussed his attention on geological questions – In the Cape Verde Islands, he saw beds of sedimentary rock that had been uplifted volcanically and then curved down as the land later subsided – Off the coast of Chile he experienced firsthand how the land was elevated several feet by an earthquake, and observed marine fossils at 3000m in the Andes – He studied coral reefs, realizing that the continued growth of coral and a sinking seabed would eventually form atolls When he returned five years later, he was in total agreement with Lyell and Hutton’s uniformitarianism 67  Fauna of the Galápagos islands An archipelago of ~21 volcanic islands around the equator ~970km off the coast of Ecuador Often, the fauna on each island was similar but distinct and resembled a species in S. America RAF-YYC from Calgary, Canada; CC BY-SA 2.0 Nicolas Völcker, Wikimedia Commons, CC-BY-SA Galápagos marine iguana, the only iguana to live Galápagos mockingbirds varied slightly from in a marine environment island to island yet were all similar to the mockingbirds of S. America. 68 Fauna of the Galápagos islands Striking variation in shells morphology among islands 200px-Gal%C3%A1pagos_Giant_Tortoise Mfield, Matthew Field, http://www.photography.mattfield.com, Galapagos giant tortoise Geochelone elephantopus, CC BY-SA 3.0 Giant Galápagos Tortoise (15 different subspecies on the Islands) 69  Fauna of the Galápagos islands Collected and preserved birds from many islands, thinking they were blackbirds, grosbeaks, finches, and wrens On Darwin’s return the samples were given to John Gould, a famous English ornithologist Gould reported that they were ALL "a series of ground Finches” which were so peculiar as to form an entirely new group of 25 distinct forms, John Gould (14.Sep.1804 - 3.Feb.1881), Darwin's finches by Gould, marked as public domain, more details on found only in the Galápagos, but closely allied to finches from S. America Wikimedia Commons Fig. 22.6, Campbell Biology, 3rd 70 Canadian Edition. 2021. Pearson.  Inconsistencies with creationism In the Galápagos he also saw sea lions distinct from anywhere else in the world but similar to California sea lions Overall, Darwin was struck by the fact that: Casey Klebba, Galapagos, sea-lion, female (by Casey Klebba), CC BY-SA 4.0 – species on different islands in extremely similar habitats were sometimes distinct – species on the islands were closely allied to forms on the ‘nearby’ continent – the fauna and flora of Africa, Europe, Australia and South America had relatively few species in common, even in remarkably similar habitats. – the animals and plants of the temperate zones of S. America resembled the species living in the tropical zones of S. America as opposed to species in temperate Europe – fossil mammals in S. America that no longer exist were similar to present-day species (e.g., extinct giant vs. extant three-toed sloths) He concluded that these observations were inconsistent with creationism  Transmutation of species By the voyage home, Darwin was convinced that: – the earth was VERY old – that current geological patterns were the result of slow, ongoing processes (which we can observed in action today) operating over long time periods More importantly, he was also convinced that species are not ‘fixed’ but rather change (‘transmute’) …but he lacked a natural mechanism to explain how He developed this after returning to England in 1836, in what he described as “the busiest two years of his life”, providing one of the most fundamental insights in the history of science  Practice Hyperlink (click here), or: Q13: How did geologic and fossil evidence influence Darwin’s thinking about evolution? 73 Outline 2.1 Setting the stage - evolutionary thinking prior to Darwin (with an aside about sexism and discrimination) 2.2 Darwin and the voyage of the Beagle Lock & Whitfield creator 2.3 Darwin’s insights: evolution and natural selection QS:P170,Q26242255, Charles Darwin 1877, marked as public domain, more details on Wikimedia Commons 2.4 Evidence for, and misconceptions about, natural selection 74  Prior to publishing his ideas Darwin was sure that evolution must be based on the gradual accumulation of slight changes He had the basic pieces of his theory in place by the late 1830, but it was 23 years after the return of the Beagle before he published it (we don’t know why he took so long) But during that time he: Anthonyeatworld at the English Wikipedia, Down House, CC BY-SA 3.0 – Arranged experts to describe his collections, consulted with them, & published reports on these – Published a book about his journey on the Beagle (Journal and Remarks, 1839; aka The Voyage of the Beagle), which brought him considerable fame and respect – Published papers and books on geology, including his first paper which showed that S. American landmass was slowly rising (which Lyell enthusiastically backed and presented to the Geological Society of London) and a book about the formation of coral atolls – Became an internationally recognized expert on barnacles, spending 8 years studying and publishing on them; also studied orchids, earthworms and other species – Married and raised a large family; moved to Down House 16 miles outside of London – Developed his ideas about evolution and natural selection, and amassed evidence in support of these 75  Alfred Russell Wallace In 1858 while working on the Origin, Darwin received a letter from Alfred Russell Wallace that essentially set out the same theory Wallace was a brilliant natural historian, geographer and collector who identified many new species of birds and insects Wallace had spent years in the jungles of S. America and the Malay Unknown author, Alfred Russel Wallace 1862 - Project Gutenberg eText 15997, marked as public domain, more details on Wikimedia Commons Archipelago, gathering plants and animals that he sold to collectors He kept careful records of everything he saw and reflected on these, coming to the same basic conclusions as Darwin concerning evolution and a mechanism to explain it (i.e., natural selection) Wallace asked Darwin to forward the paper to Lyell and, if he thought it worthy, for it to be presented to the Linnean Society  Presentation of their ideas In July 1858, Darwin and Wallace’s letters were jointly read at a meeting of the Linnean Society and later published in their journal Surprisingly, neither drew much immediate attention (the President later described 1858 as a year “which has not…been marked by any of those striking discoveries London Stereoscopic and which at once revolutionise…” Photographic Company (active 1855-1922), Alfred-Russel- Wallace-c1895, marked as public domain, more details on Wikimedia Commons It wasn’t until the next year when Darwin published his book that the world took note Wallace and Darwin became friends after Wallace’s return to the UK and Wallace never expressed any bitterness toward Darwin  (Source: Wikimedia Commons) The Origin ‘On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life’ was published on 24 November 1859 Written for non-specialists All 1250 copies sold on the first day; went through 6 editions in Darwin’s lifetime, Darwin shortly before publication; the final published in 1872 and containing a new chapter dedicated to criticisms of Charles_Darwin_seated.jpg: Henry Maull (1829–1914) and his theory (generally from creationists) John Fox (1832–1907) (Maull & Fox) derivative work: Beao, Charles Darwin seated crop, marked as public domain, more details on Wikimedia Commons A survey by academic booksellers, publishers and librarians in the United Kingdom voted it the most influential academic book ever written; “a book which has changed the way we think about everything” Darwin’s “one long argument” Darwin and Wallace had two main insights: 1) Descent with modification (‘common descent’) All species have descended, with modification, from one or a few common ancestors; in other words, species do not arise from independent acts of creation, but they evolve from pre-existing species 2) Natural selection Natural selection is the mechanism underlying much of this evolution; it explains how the characteristics of organisms change over time, and it explains the remarkable fit between organisms and their environment (i.e. adaptation) 79 What is Evolution? Originally (Darwin): ‘descent with modification’, meaning change in the characteristics (i.e., traits/phenotypes) of a populations over time. More modern definition: a change in a heritable character in a population over time. Or even better: a change in allele frequency in a population over time. (An allele is just a particular form or variation of a gene.) Populations evolve, individuals do not. 80  1) Descent with modification/common descent Darwin reasoned that humans, and all other species, are related like individuals in a family tree – i.e., a branching tree of life In other words, all species are connected with one another because they have evolved from one or a few common ancestors Lamark Darwin Bergstrom and Dugatkin (2016) Evolution, 2nd ed., Norton & Company 81  Descent with modification The very fact that Linnaeus could classify species into nested groups based on similarities is because of descent with modification (i.e., evolution), Darwin argued Fichier:Darwin tree.png Darwin’s first phylogenetic tree from Darwin (1859) – the only figure in The Origin his notes (1837) 82  ‘tips’ representing extant (i.e., present-day) Phylogenetic trees species (here some of the Galapagos finches) ‘root’ representing the common ancestor (here a finch from South America) Fig. 1.20, Campbell Biology, 3rd Canadian Edition. 2021. Pearson 83 Tree-thinking Fig. 22.17, Campbell Biology, 3rd Canadian Edition. 2021. Pearson 84 Evidence of common descent: a) homology Homology – originally referred to curious similarities in structure despite differences in function Darwin argued that similarity in structure when function differs is very hard to explain via ‘special creation’, but makes complete sense if the species descended from a common ancestor that possessed that trait Darwin’s interpretation is so widely accepted that homology is now defined as similarity due to inheritance from a common ancestor 85  Example – structural homology “What could be more curious than that the hand of man formed for grasping, that of a mole, for digging, the leg of a horse, the paddle of a porpoise and the wing of a bat, should all be constructed on the same pattern and should include similar bones and in the same relative positions?” —Darwin (1859) Fig. 22.15, Campbell Biology, 3rd Canadian Edition. 2021. Pearson 86 Example – developmental homology similar traits present in different species at a particular stage of their development Fig. 22.16 Campbell Biology, 3rd Canadian Edition. 2021. Pearson 87  Evidence of common descent: b) vestigial structures Vestigial structure are remnants of structures that served a function in an ancestor File:Membrana nittitante.jpg Undeveloped hind legs in a baleen whale; Vestigial Structures. (2022, June 8). https://bio.libretexts.org/@go/page/13473 http://upload.wikimedia.org/wikipedia/commons/thumb/d/d0/Bird_blink-edit.jpg/440px-Bird_blink-edit.jpg Hindlegs in a boa constrictor (Source: Stefan3345 - Own work, CC BY-SA 4.0, https://commons.wikimedia.org/w/index.php?curi d=46072277 Nictitating membrane (3rd eyelid) in humans; Toby Hudson, Bird blink-edit, CC BY- SA 3.0 88 Evidence of common descent: c) fossils Demonstrated the fact of extinction, meaning species change through time (i.e., they aren’t fixed and immutable) Darwin further argued that descent with modification helped explain the fossil record: – Species should change slowly and the fossil record provides evidence of this (e.g., fossils of extinct species often resembled living species in the same areas) Decent with modification predicts the fossil record should include ‘transitional species’ that bridge morphological ‘gaps’ between existing groups Few of these had been discovered in Darwin’s lifetime, and he took pains to explain why these may be rare; many have subsequently been found 89  Example – transitional forms of cetaceans Figs. 22.19 & 22.20, Campbell Biology, 3rd Canadian Edition. 2021. Pearson 90 Evidence of common descent: d) biogeography Darwin and Wallace travelled the world and were struck by the strong patterns they observed in the geographic distribution of species: Living species tend to be similar to others geographically nearby (and to fossil species in the same area) In other words, species that resemble each other tend to be clustered in time and space (Wallace 1855) This all makes sense if similarity is due to descent from a common ancestor 91  Descent with modification (i.e., evolution) Was accepted soon after publication of The Origin; Darwin’s second book on evolution, The Descent of Man and Selection in Relation to Sex, published 12 yr later in 1871, generated far less controversy Massive amounts of evidence of common descent have accumulated since Darwin’s time, in particular from DNA sequencing; the evidence is overwhelming “No reliable observation has ever been found to contradict the general notion of common descent. It should come as no surprise, then, that the scientific community at large has accepted evolutionary descent as a historical reality since Darwin’s time and considers it among the most reliably established and fundamentally important facts in all of science.” T. Ryan Gregory (2008) doi:10.1007/s12052-007-0001-z 92  Practice Hyperlink (click here), or: Q14: Support for evolution comes from which of the following observations? Q15: What is meant by 'nested groups' in Linnaean classification and how do this support evolution? 93 Darwin’s “one long argument” Darwin’s had two main insights: 1) Descent with modification All species have descended, with modification, from one or a few common ancestors; in other words, species do not arise from independent acts of creation, but they evolve from pre-existing species 2) Natural selection Natural selection is the mechanism underlying much of this evolution; it explains how the characteristics of organisms change over time and it explains the remarkable fit between organisms and their environment 94  2) Natural selection – inspiration from Malthus English clergyman Thomas Malthus argued, in “An essay on the principle of population”, that policies to help the poor were doomed because population growth would always outstrip food production Population size Thomas Malthus (1766-1834); John Linnell artist, QS:P170,Q250732, Resource limitation – Thomas Robert Malthus Wellcome L0069037 -crop, CC BY 4.0 population growth is checked by war, famine, disease, etc. Time 95 Natural selection Darwin (and Wallace) realized that all organisms must experience the same thing Individual members must compete, directly or indirectly, consciously or unconsciously, for the limited resources needed to survive and reproduce And any trait that better enables them to do this will cause those bearers to leave more offspring than others lacking the trait Because offspring are more likely to have the trait, the trait will become proportionately more common in future generations 96  Critical ingredients for natural selection Observation 1 – There is excess fertility such that more offspring are produced than the environment can support. Inference 1: there must be a fierce struggle for existence among members such that only a (sometimes very small) portion of offspring survive to reproduce. Observation 2 – Individuals vary (i.e. no two are exactly the same) Inference 2: success in the struggle for existence is not random but depends, in part, on traits facilitating it. This is the process of natural selection. Observation 3 – Much of this variation is heritable Inference 3: Across generations, traits that increase success will become more common. This is evolution by natural selection. 97  Natural selection Is a process that occurs when certain conditions are met; i.e., it is deductive reasoning. If these conditions are met, then this outcome must occur in a given situation If: 1) Individual vary in a trait 2) There is a non-random association between the trait and an individual’s reproductive success (i.e., their ability to survive and reproduce relative to other individuals in the population; also known as their ‘Darwinian fitness’) 3) The trait is heritable* Then: The trait will evolve (i.e., its frequency or value will change across generations) 1 & 2 are necessary for natural selection to occur 1, 2 & 3 are necessary for natural selection to produce evolutionary change 98  anonymous, Herbert Spencer, marked as public Natural selection domain, more details on Wikimedia Commons Is, in brief, the differential reproductive success of individuals due to differences in phenotype Is NOT a tautology (a statement that is necessarily true by definition) – If you don't get any better, you'll never improve; graphic images; free gift; boys will be boys – “survival of the fittest” —Herbert Spencer, Principles of Biology (1864) If ‘fit’ refers to individuals endowed with traits that improve their survival, then ‘survival of the fittest’ is “Survival of those that survive best”. This IS a tautology, but it is NOT the definition of natural selection. In evolutionary biology, fitness is a measure of the capability of an individual (genotype) to contribute to the next generation, i.e., its reproductive success Still unclear how natural selection works? Watch this short but excellent video: https://www.youtube.com/watch?v=0ZGbIKd0XrM 99  Darwin’s evidence for natural selection 1) Deductive reasoning – if these conditions exist (and observation indicates they clearly are), it’s the necessary outcome Pigeon breeds; 2) It is consistent with the observation that organisms are so well suited to Karl Wagner creator QS:P170,Q18511685, Wm19342a, marked as public domain, more details on Wikimedia Commons survive and reproduce in their environments (i.e., it explains adaptation) 3) An analogy with artificial selection – Darwin noted that, for thousands of years, humans have shaped the evolution of various animals and plants by systematically breeding those with desire characters, producing crops, livestock, companions, etc. – He called this artificial selection – Darwin presented the example of pigeon breeding, which was extremely popular in his day – Artificial selection produces varieties and varieties can ultimately become new species as differences accumulate 100 Artificial selection Figs. 22.9, Campbell Biology, 3rd Canadian Edition. 2021. Pearson 101  Practice Hyperlink (click here), or: Q16: How do artificial and natural selection differ? 102 Natural selection was not widely accepted at first While evolution (i.e. descent with modification/common descent) was soon accepted, natural selection as the primary cause was not Several objections were raised including: – No new species had been produced via artificial selection, only varieties (Darwin saw no distinction between varieties and species and presented numerous examples in The Origin of disagreement among naturalists; he Unknown author, Man is But a Worm, viewed species as the result on continued divergence of varieties.) marked as public domain, more details on Wikimedia Commons – Precursors of complex organs (e.g., the eye) are unlikely to have been advantageous (Darwin dealt with this in an entire chapter of The Origin, showing how early stages could be advantageous.) 103 Natural selection was not widely accepted at first – Ongoing debate about the earth not being sufficiently old (Lord Kelvin estimated 15-20 million years but was later proved wrong) – Natural selection will exhaust variation, halting further evolution (Inheritance was not understood in Darwin’s time and his idea amounted to a blending of the two parents; Engineer Fleeming Jenkin used this to attack natural selection on the basis that variation would be lost.) – Direct evidence was lacking. In the 50 yr after the Origin, only a couple of studies had been done showing natural selection in action 104  Example #1: Batesian mimicry (observational evidence) Henry Walter Bates surveyed the Amazon rainforest with Wallace in 1848 While Wallace collections were lost when his ship caught fire Bates came back later, having sent 14,712 specimens (mostly insects) Described situations in which a presumed palatable butterfly species gained protection from predators by resembling an abundant unpalatable species; later became known as ‘Batesian mimicry’ J. Thomson, Henry Walter Bates, marked as public domain, more details on Wikimedia Commons Hover fly (Source: Judy Gallagher The highly poisonous pufferfish, www.flickr.com/photos/52450054@N04/9686230960; Canthigaster valentine (top) and its edible CC BY 2.0) mimic, Paraluteres prionurus (bottom). Source: Caley & Schluter (2003) doi: 105 10.1098/rspb.2002.2263  Example #2: Experimental evolution Evolution by natural selection was observed on short timescales in Darwin’s day From 1880-1887, William Dallinger conducted an experiment in which he raised a species of protozoan at increasing temperatures Dallinger gradually increased the temperature causing most, but not all, individuals to die W. H. Dallinger or an unknown illustrator, Dallinger Incubator J.R.Microscop.Soc.1887 p193, They flourished initially at 16C, but over the 7 yr he managed to evolve populations marked as public domain, more details on Wikimedia Commons that survived temperatures in excess of 66C (and that died at the original 16C) This is known as experimental evolution: a technique in which biotic and/or abiotic conditions are manipulated in replicate populations under controlled conditions and the evolutionary outcome is studied Question: is this an example of artificial selection? 106  Example #2: Bumpus sparrows – selection in action On Feb. 1, 1898, Herman Bumpus collected 87 male and 49 female sparrows immobilized by a serve ice and snowstorm in Providence, RI 36 males and 28 females subsequently perished while others survived Female House sparrow (Passer domesticus) Photo by DAVID ILIFF. License: Bumpus determined sex of each bird and measured 9 morphological on each CC BY-SA 3.0 Compared to those that died, the surviving birds differed in several traits, indicating selection on these (or correlated) traits Data have been reanalyzed multiple times as statistical methods for quantifying selection have advanced over the years, but all find evidence of natural selection 107 Outline 2.1 Setting the stage - evolutionary thinking prior to Darwin (with an aside about sexism and discrimination) 2.2 Darwin and the voyage of the Beagle Lock & Whitfield creator 2.3 Darwin’s insights: evolution and natural selection QS:P170,Q26242255, Charles Darwin 1877, marked as public domain, more details on Wikimedia Commons 2.4 Evidence for, and misconceptions about, natural selection (and evolution) 108  Maturation of Darwin/Wallace’s theory Darwin & Wallace suggested natural selection as an explanation consistent with observations (e.g., adaptation, biogeography), but direct demonstrations of selection in action in nature were lacking Our understanding of natural selection, and evolution more generally, has come a long way since Evolutionary theory has matured as researchers continue to learn, examine new data (e.g., DNA, field, lab, fossil), test and refine more nuanced hypotheses – heredity is a crucial element that was not understood in Darwin’s time. The rediscovery of Mendel’s work in the 1900’s changed this (see Topic 3). – The Modern Evolutionary Synthesis of the 1930’s and 40’s integrated genetic, micro- and macroevolution into a single, coherent framework But descent with modification and natural selection remain as foundational concepts at the heart of modern-day evolutionary biology 109  More recent evidence for natural selection Since the modern evolutionary synthesis of the 1930’s and 40’s, overwhelming evidence of natural selection in action has accumulated from observational and manipulative studies in the lab and in nature in an enormous diversity of species from microbes to large mammals We’ll discuss two examples here; see Fig. 22.13 in Campbell for another. We’ll see even more when we talk more about natural selection in detail in Topic 4 – microevolution Peppered moth (Biston betularia) File:Biston.betularia.7200.jpg Chiswick Chap, Biston.betularia.7200, CC BY-SA 3.0 File:Biston.betularia.f.carbonaria.7209.jpg Martinowksy, Lichte en zwarte versie berkenspanner, CC BY-SA 3.0 Chiswick Chap, Khaydock, Peppered moths c2, CC Biston.betularia.f.carbonari 110 BY-SA 3.0 a.7209, CC BY-SA 3.0 Contemporary evidence – Müllerian mimicry in Heliconius In 1879, Herman Müller proposed selection would favour shared warning signals in two distasteful butterfly species because it spreads the selective burden of educating predators Observational studies and theory supported the idea, but natural selection for müllerian mimicry had never been demonstrated in the field Durrell Kapan (2001) provided an elegant test by taking advantage of the unusual polymorphism of Heliconius cydno alithea H. sapho H. cydno alithea Image: Marcus Kronforst and Krushnamegh Kunte https://cns.utexas.edu/news/heliconius-species H. eleuchia 111 Contemporary evidence – Müllerian mimicry in Heliconius This is hypothesis-testing science using a manipulative experiment (recall Topic 1!) Hypothesis: the resemblance of H. cydno to different local co-models (the pattern we wish to explain) is due to preferential predation (causing a higher probability of death) of morphs that don’t match the local co-model compared to those that do (the cause) They also set out to test a second hypothesis about density of individuals, but we’ll ignore that. 112 Contemporary evidence – Müllerian mimicry in Heliconius Experiment: capture yellow and white H. cydno from two source sites and release them at other sites that are dominated by yellow or white co-models; track their subsequent survival H. sapho co-model yellow morph H. cydno alithea white morph Image modified from: Marcus Kronforst and Krushnamegh Kunte https://cns.utexas.edu/news/heliconius-species H. eleuchia co-model 113 Contemporary evidence – Müllerian mimicry in Heliconius Prediction: recall, this is what you expect to see in the results of your study IF the hypothesis is true: resighting rate following introduction will decline faster in H. cydno morphs whose wing colour does not match the locally dominant co-model compared to morphs whose wing colour matches the local co-model If you watch the video: I talk about a 2nd hypothesis concerning densities. Ignore this. If you do try to follow along, when talking about prediction 2 I say that cyndo morphs were introduced at different frequencies at different sites, whereas I should have said different DENSITIES (i.e., more or fewer of them were introduced at different sites). 114 Contemporary evidence – Müllerian mimicry in Heliconius Results: Ignore this panel. Kapan (2001) https://doi.org/10.1038/35053066 Predators eliminated rare morphs more rapidly when they deviated from the local co-model, consistent with the hypothesis: i.e., selection for Müllerian mimicry 115  Practice Hyperlink (click here), or: Integrating Topics 1 and 2 – Q17: a study design to test Batesian mimicry. 116  Misconceptions about evolution 1) Natural selection is not goal driven nor progressive. – it has increased complexity and specialization in some lineages over time, but not in others, and this is not a ‘goal’ of evolution E.g., present-day tapeworms have lost their digestive system; snakes have lost their limbs; the earliest birds had teeth – it has no goal; it’s wrong to say that natural selection: ‘acts for the purpose of…’ ‘in order to…’ ‘so that…’ ‘is trying to…’ – it is just a process that occurs when certain conditions are met – it makes organisms ‘better’ only in the sense of improving fit to their current environment 117 Misconceptions about evolution Lamarkian thinking incorrectly implies linear progression toward some goal Humans are not an endpoint or goal of evolution No organism is ‘higher’ or ‘lower’ than another, just different Much more accurate: Inaccurate: 118 Misconceptions about evolution 2) Natural selection does not act ‘for the good of the species’. Selection arises from variation in relative, not absolute fitness (we’ll talk about this more later) While altruistic traits can and do sometimes evolve, natural selection can, and often does, favour traits that are detrimental to a population/species – E.g., evolutionary conflicts of interest (i.e., when traits that maximize fitness in one individual are costly to the other); E.g., parent-offspring conflict, sexual conflict, tragedy of the commons (i.e., selection favours traits that lead to overexploitation of resources) – Example: see the video I previously suggested about simulating natural selection: https://www.youtube.com/watch?v=0ZGbIKd0XrM CC BY-SA 3.0 By Johanna L. Rönn, Uppsala U. from Photo by Chris Friesen, https://commons.wikimedia.org/ http://news.nationalgeographic.com/news courtesy of Oregon State 119 w/index.php?curid=245319 /2009/02/photogalleries/spiky-beetle- Univ.; cc-by-sa-2.0 genitals/photo3.html, CC BY-SA 1.0  Misconceptions about evolution 3) Natural selection does not result in perfection. Natural selection does improve fit of organisms to their environment, but there are many reasons why perfection is not the outcome including: biotic environments evolve, and often ‘coevolve’, meaning a moving target that, in some cases, actively thwarts adaptation (e.g., arms race between predators and prey) We’ll discuss more reasons in Topic 5 (Adaptation). 120  Misconceptions about evolution Other misconceptions about evolution and natural selection are common This is a great resource for identifying and correcting these: https://evolution.berkeley.edu/evolibrary/misconceptions_faq.php 121  The Theory of Evolution Reasonable scientific debate concerning the fact of evolution ended in the late 1800’s Whether natural selection was largely responsible was challenged until the 1930’s when the ‘modern evolutionary synthesis’ provided a genetic basis for evolution Th. Dobzhansky and united micro- and macroevolutionary ideas Source: wikipedia Evolution by natural selection is now considered fact (a ‘theory’ in scientific terms) and it is arguably the greatest unifying idea in biology: “Nothing in biology makes sense except in the light of evolution.” —Theodosius Dobzhansky, 1973 122 Evolution and religion: fundamentalist Christians I want to talk about examples of conflict arising from a relatively small but vocal and well- organized Christian fundamentalists: the proponents of creationism/intelligent design I focus on these because: a) they are highly prevalent in North America; 2) I am most familiar with them I take no issue with anything intrinsic to Christianity (or any other religion) that accommodates the scientific method and what we learn from it (and many due, including the mainstream Christian religions) I DO take issue when any religious belief is used to reject scientific evidence and rational scientific thought, including the scientific method itself 123  Evolution and religion Despite the scientific consensus, many people do not ‘believe’ in evolution to this day This is most pronounced for those who interpret sacred texts literally (e.g., the Bible) To deny evolution on this ground requires rejecting much of science – physics, astronomy, geology, biology – as well as the scientific method itself There are a diversity of beliefs about the origins of life, from literal belief in the creation stories (e.g., Genesis) through to the purely materialistic account of science The main Christian churches hold a position of ‘theistic evolution’ in which God works through natural laws with little or no direct intervention Catholic Church accepts physical evolution but invokes supernatural creation of the soul Religious that do not assume a single deity (e.g., Buddhism, Hinduism) tend to see evolution as compatible with their belief in a continually transforming earth 124  Evolution vs. creationism Creationism is the belief that nature and the universe originated from supernatural acts of divine creation; intelligent design is a pseudo-scientific rebranding of creationism based on the ‘argument from design’ (i.e., the watchmaker analogy) As a hypothesis for explaining the diversity of life on earth, adaptation, biogeography and the fossil record, etc., neither are scientific because they cannot be refuted – One can always postulate that a supernatural power created life and the earth in a way to make it look like evolution occurred Such an ‘explanation’ adds nothing to our understanding; arbitrary assumptions to fit any and all observation is NOT knowledge as it is neither skeptical, objective, nor refutable 125  Evolution vs. creationism Some proponents of intelligent design are well versed in various sciences, allowing them to formulate what appear as highly sophisticated and convincing arguments These arguments are pseudo-science as they seek to confirm, not reject, pre-conceived ideas and they lack the necessary criteria for knowledge acquisition: i.e., rationality, skepticism, objectivity, and (obviously) methodological materialism (Topic 1) Their arguments are lengthy and detailed, but none provide strong evidence against the modern theory of evolution A few good resources (there are HEAPS): – https://en.wikipedia.org/wiki/Intelligent_design#Scientific_criticism – National Academy of Sciences, Engineering & Medicine’s “Science and creationism” https://www.nap.edu/catalog/6024/science-and-creationism-a-view-from-the-national-academy-of – Scientific American’s ‘15 Answers to Creationist Nonsense’ https://www.scientificamerican.com/article/15-answers-to-creationist/ 126  Evolution and religion Many scientists see no conflict between evolution and religious faith; Pope John Paul II agreed in 1996 – A common view is that science and religion are separate domains, one concerned with explaining the natural and physical world and the other with interpreting the meaning of human life What motivates the controversy? Unclear, but some suggest it may be the discomfort about what evolution means for human morality and behaviour – “I think if you teach children that they evolved from apes, then they will start acting like apes.” (Louisiana State hearings on evolution, 1981) – “It is foolish and naïve to believe that what children are taught about who they are, how they got here, doesn’t have anything to do with what they conclude about why they are here and what their obligations are, if, in fact, they have any obligations, and how they should live” (National Public Radio, 1995) 127  Misuses of evolution Evolution and natural selection have sometimes been misused to justify abhorrent policies/beliefs – racial segregation was justified by supposed innate (i.e., evolved) differences – eugenics (e.g., compulsory sterilization of mentally ill) was justified as aiding natural selection – ‘social Darwinism’ applied the concept of natural selection to sociology, economics and politics, often to justify competition, struggles between nations and racial groups, and inspiring genocides such as the Holocaust The scientific justification for these is baseless Neither evolution nor natural selection justify any moral position; philosophers call such misuses the ‘naturalistic fallacy’ (claiming that what is justifies what should be) An understanding of evolution does change our perspective, hopefully by promoting awareness of our continuity with the living world and the importance and value of biological diversity 128 Topic 3 GENETICS AND THE MODERN EVOLUTIONARY SYNTHESIS Note: I assume you have a basic understanding of meiosis, but if you want a review see Chp. 13 of Campbell and/or the video in the ‘Additional Resources’ slide at the end of this lecture. 129  Learning objectives Compare/contrast blending vs. particulate inheritance Outline the core ideas in Weismann’s germ plasm theory Explain Mendel’s three ‘laws’ of inheritance using modern genetic terminology and outline the core tenant of Mendel’s that remains true despite inheritance usually being more complex Map phenotype to genotype under different scenarios of dominance Draw a Punnett square to determine genotypes of offspring from specific crosses of two parental genotypes Use the addition and product rules of probability, and Punnett squares, to calculate probabilities of specific genotypes from given crosses Be familiar with modern genetic terms (e.g., locus, gene, allele, heterozygote, homozygote, phenotype, genotype) Explain the ways in which inheritance is often more complex than a simple ‘one locus-2 allele’ Mendelian model Describe the two reasons why many traits exhibit continuous variation. Calculate allele frequencies from genotype/phenotype frequencies or the reverse (by assuming HW) Understand the conceptual basis of HW expected genotype frequencies – i.e., Why are they p2, 2pq, q2? What assumptions are necessary for this to be true, and what does it mean if genotype frequencies differ from this? Conduct a test for HW genotype frequencies for a locus with two alleles: calculate expected # of individuals of each genotype under HW, compare these with observed # of individuals, and make an appropriate inference 130 Outline 3.1 Early theories of inheritance 3.2 Mendelian inheritance of simple traits 3.3 Inheritance is more complex 3.4 Re-discovery of Mendel and the Modern Evolutionary Synthesis 3.5 Hardy-Weinberg 131  Squididdily at en.wikipedia, Blending inheritance, CC BY-SA 3.0 3.1 Early theories of inheritance Blending inheritance Theory that phenotypes in offspring are an average (i.e., blend) of their two parents. Darwin had a version of this he called pangenesis in which all parts of the body produce particles of hereditary information (‘gemmules’) which accumulate in the gonads and are transferred to offspring. Environmental impacts could alter gemmule production, allowing for a Lamarkian idea of transmission of acquired characters Fleeming Jenkin argued that blending inheritance made natural selection ineffective because variation would soon be lost Experiments by Francis Galton on rabbits (1869-1871) were inconsistent with Darwin’s model of inheritance and the hypothesis fell out of favour 132 August Weismann A German (1834-1914), considered by some as one of the most notable evolutionary theorists after Darwin First grappled with evolution vs. creationism and came to the conclusion that many Unknown author, August Weismann, marked as biological observations made complete sense in an evolutionary, but not creationist, public domain, more details on Wikimedia context Commons Did experiments convincing him that Lamarkian inheritance of acquired characters didn’t work In 1892 developed his germ plasm theory for multi-cellular organisms proposing that heritable information was transmitted only by the germ cells in the gonads (i.e., the reproductive cells or gametes); all the other cells of the body – somatic cells – do not transmit such information, serving only to carry out all the bodily functions necessary for the transmission of the germ cells 133 The germ plasm theory germ cells produce somatic cells (the soma) anew each generation information flows from germ cells to somatic but not the other way the soma is disposable; the germ plasm is (potentially) immortal Ian Alexander, Weismann's Germ Plasm, CC BY-SA 4.0 134  The germ plasm theory Situation is different in plants, corals, and sponges In these taxa, germ cells are produced by somatic cells (e.g., vegetative meristems in plants) and changes (i.e., mutations) in those somatic cells can affect subsequent germ cells derived from them, and hence be transmitted across generations 135 Schmid-Siegert et al. 2017. https://doi.org/10.1038/s41477-017-0066-9 Outline 3.1 Early theories of inheritance 3.2 Mendelian inheritance of simple traits 3.3 Inheritance is more complex 3.4 Re-discovery of Mendel and the Modern Evolutionary Synthesis 3.5 Hardy-Weinberg 136  Who was Gregor Mendel? Augustinian friar, born in part of the Austrian empire (today Czech Republic) From a farming family and struggled to pay for his education; became a monk in part because it provided free education Twice failed the exams to become a high school teacher; received training in Gregor Mendel, 1822- physics at University of Vienna 1884; Unknown author, marked as public domain, more details on Wikimedia Commons Now recognized as the founder of modern genetics From 1856-1863, Mendel cultivated and tested thousands of pea plants Analyzed his data with exemplary scientific rigour, developing mathematical predictions of his hypotheses to compare with observed results – he employed some of the principle of the scientific method From this he developed his principles of heredity 137  Mendel’s success Several of his choices were extremely judicious (lucky?): Many varieties of garden peas were available, they are easy to artificially cross and to grow, they have a short generation time and produce many descendants B. Ebbesen; CC BY-SA 3.0 He chose to work with discrete (binary polymorphisms) characters rather than quantitative (i.e., continuously variable) ones (e.g., size), and he used true-breeding (aka pure-breeding) plants He had the foresight to follow several successive generations of plants and record their traits, and crossed various combinations which provided insight into recessive characters 138 By LadyofHats, reworked by Sciencia58; CC0, https://commons.wikimedia.org/w/index.php?curid=82940368  Typical breeding experiment in a typical experiment, Mendel mated (crossed) two contrasting, true-breeding varieties parents are the P (parental) generation offspring of P generation are called F1 (first filial) generation When F1 individuals self- or cross-pollinate with other F1 hybrids, F2 generation is produced Fig. 14.,3 Campbell Biology, 3rd Canadian Edition. 2021. Pearson 139  Mendelian inheritance Observed that F1 plants were not a blend of the parents, but resembled one and not the other But the trait of the other parent, missing in the F1, reappeared in the F2; that is, the hereditary ‘factor’ wasn’t diluted or destroyed In the F2, there was consistently an approximate 3:1 ratio of the two phenotypes Mendel observed this pattern for 7 different traits Table 14.1, Campbell Biology, 3rd Canadian Edition. 2021. Pearson 140  Mendel’s model of particulate inheritance Mendel proposed a model in which heredity was controlled by ‘factors’ Distinct forms of these factors account for variation in phenotype Every individual has two factors, one inherited from each of their parents Example: life cycle of humans. Fig. 13.4 Campbell Biology, 3rd Canadian