01_introduction.pdf

Biology 199 Introduction to Biological Thinking: an introduction to how biologists pose questions, conduct studies, design experiments, analyze data, evaluate evidence, and communicate scientific information... Mesoamerican Ethnobotany...

Biology 199 Introduction to Biological Thinking: an introduction to how biologists pose questions, conduct studies, design experiments, analyze data, evaluate evidence, and communicate scientific information... Mesoamerican Ethnobotany Mesoamerica plants and people of Mesoamerica and how they connect with the rest of the world The “big three plus one” of Mesoamerican food plants: Squash Corn/maize Beans Peppers/chilis Mesoamerica: is a culturally defined region areas that supported highly developed societies in pre-Columbian times Encompasses present-day: Central & southern Mexico Belize Guatemala El Salvador Pacific coast of Honduras Pacific coast of Nicaragua Pacific coast of northern Costa Rica Map from Wikipedia Ethnobotany: literally, culture & plants scientific study of the (myriad) relationships that exist between plants & people bridges anthropology and botany minimal skill set required for a practicing ethnobotanist: knowledge of local culture to gain access to & confidence of informants language skills/linguistics to connect local and scientific names of plants to understand cultural context of plant use botany identification skills, knowledge of plant relationships knowledge of plant structure and plant chemistry Ethnobotany = the study of plant uses by people culture-based plant use probably predates origin of humans as a species, case in point: Chausiki, the sick Chimp a case of herbal self-medication by a sick chimpanzee; first observed by: Mohamedi Seifu Kalunde, a Tanzanian traditional herbalist Michael Huffman, an American biologist one day, Chausiki’s behavior indicated illness Huffman, M., et. al. 1996. lethargic, inattentive to infant son Ethnobotany and zoopharmacognosy of Vernonia amygdalina, a medicinal plant used dark urine by humans and chimpanzees. loose stools Proceedings of the International stiff posture Compositae Conference, Kew 2:351-60. Chausiki self-medicated herself: harvested a plant stem, extracted pith tissue spent 20 minutes sucking pith next day healthy vigor had returned the medicinal plant: Vernonia amygdalina, local common names: goat-killer bitter leaf pith tissue known to be less toxic than other stem tissues http://www.mhhe.com/biosci/pae/botany/ botany_map/articles/article_04.html Plant used by Chausiki: Vernonia amygdalina compounds present in pith have: antiparasitic activity has bitter-tasting leaves antitumor activity much contemporary folk-medicine use in Africa antibacterial activity Presumably, molecules from pith cells cured a parasitic or bacterial infection in Chausiki Vernonia amygdalina home.scarlet.be/~tsh77586/Latham2.htm  Society for Economic Botany scientific society hosts an annual meeting publishes: “Economic Botany” (scientific journal) “Plants & People” (Society for Economic http://www.ethnobotany.org/ Botany newsletter)  Thinking like a scientist: Inductive vs. deductive reasoning: Inductive Multiple Pattern General specific recognition conclusion observations Induction: using information/knowledge of small scope to generate large general principles (small to large) Deductive Accept or Existing Formulate Collect Analyze reject theory hypothesis data data hypothesis Deduction: using general principles to test hypotheses about specific phenomena (large to small)  Thinking like a scientist/biologist: inductive vs deductive reasoning Theory of organic evolution General principal Large body size benefits warm-blooded or theory animals in cold climates Black-capped Chickadees of New England Fitness is fitness Hypothesis will be larger than heritable varies Carolina Chickadees of Virginia & Carolinas Populations Organisms are Earth is are variable adapted to old environment Observation Catch and weigh specimens of (experiment) both species; analyze results Reproductive capacity Fit survive to exceeds environment reproduce carrying capacity more often Does data obtained support or than non-fit Confirmation contradict the hypothesis? Induction: Deduction: general principles developed by finding hypotheses: repeated patterns in data, from: generated from general principles direct observation of nature tested by observation or experiment or results of many, related experiments i.e, by collection of data many cases lead to a general principle confirmed or rejected based on data associated w/ descriptive/comparative science (Abduction: general principles found by a combination of induction and deduction)  Scientific method in experimental science The Scientific is a reiterative (repeated successively) process (interpret this diagram as the beginning of multiple cycles) Method Observation/ measurement Hypothesis Experiment (start here) More observations, more measurements Confirm vs reject hypothesis Repeat, indefinitely Consistent results from series of related experiments may lead to general, broad insights An example of experimental biology: Acetabularia & the genetic control of development Where does the genetic material of the cell reside? nucleus? cytoplasm? These were open questions in the early 20th C What is the genetic material? proteins? nucleic acids? (gametes develop inside cap cells) Acetabularia – Mermaid’s Wine Cup siphonous green alga – an enormous single cell, 2-4 cm long just one nucleus, located in “foot” region, during early development development: “foot” → stalk → cap → reproductive structures (in the cap) cap morphology varies by species (therefore presumed to be under genetic control) What we know now about Acetabularia growth and development Genetic material of the cell consists of DNA molecules located in the nucleus Genetic information is expressed by: portions of DNA (genes) are copied as mRNA mRNA enters cytoplasm, directs the synthesis of proteins with assistance of ribosomes fully synthesized proteins fold into active forms and play roles in cell function many different genes produce many different proteins in a coordinated sequence general overview: genes in from the nucleus control cellular growth and development Acetabularia development is controlled by: DNA → mRNA → protein (the central “dogma” of cell/ molecular biology) Successive activation of genes produces a series of proteins that control all activities of the cell But these basic ideas were not known in the 1930s!  Hammerling – 1930 – Experiments with dissected fragments, also Acetabularia (part 1) from nearly mature cell http://8e.devbio.com/article.php?ch=2&id=2 (before cap forms): 80 (but soon dies) removal of nucleus from nearly mature cell (before cap forms) cap forms, but cell soon dies tip → new cap, but soon dies stalk → no regeneration foot → total regeneration w/ full reproductive potential Hammerling – 1930s Nucleus Stalk Experiments with transplant (cytoplasm) Acetabularia (part 2) expmt transplant http://8e.devbio.com/ expmt article.php?ch=2&id= 280 med. cren. cyto. cyto. discoid cap med. lobed cap cren. nucleus nucleus & stalk removed cren. med. cren. cap cap cap med. cren. cap med. cyto. cyto. cren. med. cytoplasm cytoplasm Conclusion? Where does genetic control of cap med. med. cren. shape reside? nucleus cren. nucleus nucleus cytoplasm? nucleus nucleus?  Comparative/descriptive/discovery science – e.g., family placement of Picrodendron Since late 1600s, relationships not well resolved Generic status uncertain (multiple hypotheses): Juglans L. (walnuts) Rhus L. (sumacs) Schmidelia L. (= Allophyllus L.) Picrodendron Planchon Family placement uncertain (multiple hypotheses): Anacardiaceae Sapindaceae Terebinthaceae Simaroubaceae Picrodendraceae Juglandaceae Euphorbiaceae Picrodendron baccatum: small tree native to Burseraceae Bombacaceae Bahama Islands, Cuba, Hispaniola, Jamaica The basic process: observe, describe, compare, interpret W.J.Hayden’s Masters Thesis: new comparative anatomical data for Picrodendron and poorly known hypothesized relatives Relationships of Picrodendron revealed by inductive reasoning (Hayden 1976): Picrodendron: leaf anatomy All consistent with comparable structures of plants classified in wood anatomy Euphorbiaceae subfamily Oldfieldioideae pistillate flower morphology All structural data +/- discordant with anatropous ovule & obturator comparable structures of plants in other genera and families once thought to be pollen close relatives of Picrodendeon (Biogeography also supported the same conclusion: anatomically similar plants of Euphorbiaceae subfamily Oldfieldioideae occur in Venezuela and Mexico) Therefore, Picrodendron is best classified with Euphorbiaceae subfamily Oldfieldioideae Three decades later, several DNA sequence studies have confirmed classification of Picrodendron with genera formerly classified in Euphorbiaceae subfamily Oldfieldioideae These plants are now classified as family Picrodendraceae Comments on Scientific Method: Limited to repeatable, measurable phenomena “Proof” is elusive; successful hypotheses withstand repeated testing, but can never be proven in an absolute sense (Karl Popper) Scientific knowledge is thus tentative, potentially subject to disproof Nevertheless, we possess many very successful hypotheses about nature that are treated operationally as fact  Scientific Method: Theories “It’s just a theory!” But “theory” is not used In Science, a theory this way in everyday language. is a series of interrelated, successful hypotheses that In everyday language, seem to describe accurately “theory” is more or less some aspect of nature, i.e., equivalent to which theories verge on FACT component of the scientific method? Science often advances by balancing creative open-mindedness and skeptical inquiry: skeptical inquiry open-mindedness scientific method factual knowledge (creativity, imagination) (deduction) (induction) scientific knowledge is generally regarded as tentative or provisional everything we know is potentially falsifiable periodically, in the history of science, status-quo models of reality are overturned it is thus useful to consider creative, new, radical, “out-of-the-box” ideas but such ideas should be considered from perspective of skeptical inquiry and subject to critical testing (i.e., experiment or observation) science policy, however, should be informed by best available current data/knowledge Different types of scientific literature: Primary research paper (primary literature) Review paper Books Textbooks Research monographs Reports Submitted to governmental agencies Released by organizations, etc. Abstracts of talks/posters presented at scientific meetings Markers of quality: Peer review Journal impact factor (reflects average annual citations of articles in recent issues of the journal) Components of a (primary literature) scientific paper: Double-funnel metaphor of a scientific paper: Title Authors Introduction starts w/ broad general overview and concludes with the specific context of the Abstract study, Including statement of purpose and/or Introduction hypotheses being tested Materials and methods Materials & Methods – narrow, specifics of what Results, including tables, figures was done Results – narrow, just the newly obtained data Discussion Discussion starts narrow and focused on the Literature cited specifics of the study but proceeds to ever (Appendices) more general and far-reaching implications Unifying themes in biology: evolution genetics central dogma of molecular biology: DNA-RNA-protein cell theory structure and function hierarchical organization & emergent properties homeostasis open systems processing matter & energy... in geology: immensity of geological time continental drift law of superposition (and cross-cutting relationships) (law of superposition also applies to archeology)  Unifying themes of biology; hierarchical levels of organization: reductionism holism emergent properties biosphere cells w/ (ecosystem) community chloroplasts chloroplast population thylakoid membrane organism chlorophyll (Myriophyllum molecule aquaticum)  Unifying themes of biology: evolution, phylogeny See: https://www.evogeneao.com/learn/tree-of-life evolution Analysis of similarities and differences among organisms yields phylogenetic trees (cladograms) Shared derived characteristics (synapomorphies) are most important in revealing relationships Biodiversity Phylogenetic trees provide “a means to harness biological information diversity unity for interpretation or prediction” (differences) (similarity) (Keeling et al. 2005).  Thinking like a scientist/biologist: everything has multiple contexts or perspectives big picture holistic biology critical thinking (ideas) details reductionism content (facts) biosphere textbooks, review articles levels of biological organization primary literature biological molecules Perspectives: time Geological Prehistory Historic Present Future Past Time Successful scientists/biologists must have facility in recognizing the appropriate general context of facts and ideas  Ethnobotany is composed of freely intertwined branches from seemingly disparate areas of knowledge: science, art, and humanities Consilience - Wm. Whewell (19th C, philosophy of science): unity of knowledge, linking facts and principles from different disciplines to form a broad comprehensive theory that spans all realms of knowledge Book by E. O. Wilson: “Consilience: The Unity of Knowledge” (1998) attempt to bridge conflict between science and humanities assertion: science, art and humanities will ultimately reveal that the world is orderly and explainable by a small number of natural laws E. O. Wilson, October 16, 2007 Image from Wikimedia Commons Is widespread consilience among diverse academic disciplines a reasonable expectation?  Personal motivational contexts for engagement in science: disciplinary context (abstract, idealized state, “service to something larger than self”) community context (colleagues, professional societies, scientific journals, “status among peers”) self (individual scientist, curiosity, “careerism”) Ethics (in science): science is practiced by fallible (imperfect) human beings science is a social endeavor and, as such, it is subject to the mores and ethical codes of society yet science aims to uncover universal truths how does universal truth emerge from socially embedded imperfection?  “Service to something larger than self” Fronticepiece, Hortus Cliffortianus, 1737, by Linnaeus: Mother Earth, seated at center, holding keys to the realms of Nature, served by those who bring to light knowledge of plant diversity (including Cliffort, bust upper left) Carl Linnaeus 1707 - 1778 Humans are transforming planet Earth...... What sort of Earth shall we pass along to our children, grandchildren, great grandchildren?  Ethnobotany as a window to environmental issues: much of our “human footprint,” is agricultural land producing: food beverages fiber wood, lumber biomass fuels medicine rubber, resins dyes flowers, ornamental plants these (above) are all ethnobotany! “In the lower 48 states, humans have converted 54% of the total land into cities and suburbs, and 41 % into various forms of agriculture. That’s an astounding 95% of total land Aerial view, confluence of the Stanislaus and San Joaquin dedicated to man-made use.” rivers, California Central Valley, east of Tracy. © Copyright 2007 Roy Tennant, FreeLargePhotos.com Estimated growth of human population (ca 2.5 billion in 1951) since the end of the last Ice Age: (ca 4.5 billion in 1980) 22 August 2022 estimate: 7,969,234,695 (ca 6 billion in 2000) 27 August 2023 estimate: 7,993, 885,222 (see: http://www.census.gov/popclock/) 24 August 2024 estimate: 8,172,491,015 http://www.biology.iupui.edu/biocourses/N100H/ch39pop.html