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15/10/14
1
Week 2 lectures‐ review
Scien7fic reasoning in biology, hypothesis tes7ng, methods of study
1. Reduc7onism
• The scien)fic approach of reducing complex systems to simpler components that are more manageable.
• Ex. 1. Understanding the func7oning of a tree by looking only at the cells of that tree.
• Ex. 2. Understanding the structure of DNA allowed Franklin, Watson and Crick (in 1935) to infer how inheritance might work.
2. Francis Bacon (1561‐1626) Father of Induc7ve Reasoning Bacon’s induc7ve approach included ‘the careful observa)on of nature with a systema)c accumula)on of data to draw upon’. New natural ‘laws’ (or descrip7ons of paWern) were then created based on the knowledge of par7cular findings through ‘tes)ng and experimenta)on to determine if they were consistent with the observa)ons from nature.’
Inductive Reasoning • Inductive reasoning draws conclusions through the
logical process of induction • Repeating specific observations can lead to important
generalizations – Example 1. “the sun always rises in the east” – Example 2. The water at the beach has always been about 24 degrees in July. It is July. The water will be about 24 degrees.
– Inductive reasoning goes from observations to conclusion
© 2011 Pearson Education, Inc.
3. Deductive Reasoning and Hypothesis Testing (Plato, Descartes)
• Deductive reasoning uses general premises to
make specific predictions • For example, if organisms are made of cells
(premise 1), and humans are organisms (premise 2), then humans are composed of cells (deductive prediction)
• Deductive reasoning goes from general to specific
© 2011 Pearson Education, Inc.
4. Hypothe7co‐deduc7ve method (AKA: THE scien7fic method, ‘H‐D method’)
Karl Popper (1902‐1994)
He wrote: The Logic of Scien7fic Discovery (1934) (in a hurry to get an academic post outside of Nazi‐run Europe)
Take‐home from this book is no7on of falsifiability and that falsifiability separates science from non‐science
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Questions That Can and Cannot Be Addressed by Science
• A hypothesis must be testable and falsifiable – E.g. 1. a hypothesis that ghosts fooled with a
broken flashlight and their presence explains why it cannot be turned on, cannot be tested;
– E.g. 2. Reincarnation cannot be tested (or more importantly, cannot be falsified!)
• Supernatural and religious explanations are outside the bounds of science
© 2011 Pearson Education, Inc. From www.undsci.berkeley.edu
Types of Data • Data are recorded observations or items of
information; these fall into two categories – Qualitative data, or descriptions rather than
measurements • For example, Jane Goodall’s observations of
chimpanzee behavior – Quantitative data, or recorded measurements,
which are often organized into tables and graphs and because they are often variable, analysed with statistics! Also comes in various forms.
© 2011 Pearson Education, Inc.
A Case Study in Scientific Inquiry: Investigating Mimicry in Snake Populations
• Many poisonous species are brightly colored, which warns potential predators
• Batesian mimics are harmless species that closely resemble poisonous species
• Henry Bates (1861) hypothesized that this mimicry evolved in harmless species as an evolutionary adaptation that reduces their chances of being eaten
© 2011 Pearson Education, Inc.
From Pfennig et al. 2001, Nature
Quan7ta7ve data
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120
White Oak Red Maple White Ash Eastern White Cedar
Percent dead
Percent alive
Other forms of quan7ta7ve data
Counts (e.g., number of flowers, which can then be expressed as percentages) Con7nuous data (e.g., heights, masses) Binary responses (e.g., yes/no; presence/absence)
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Experimental Controls and Repeatability • A controlled experiment compares an
experimental group (e.g., the artificial kingsnakes) with a control group (e.g., the artificial brown snakes)
• Ideally, only the variable of interest (the effect of coloration on the behavior of predators) differs between the control and experimental groups
• A controlled experiment means that control groups are used to cancel the effects of unwanted variables
• A controlled experiment does not mean that all unwanted variables are kept constant
© 2011 Pearson Education, Inc.
Model organisms in Ecology and Evolu7on
Drosophila melanogaster (fruit fly) Arabidopsis thaliana (Mouse‐ear cress)
Second case study: What pollinates arc7c plants? Start with an observa7onal study,
con7nue with a field experiment Hypothesis 1: Bees will be primary pollinator (because we know that they are the most important plant pollinators on earth) Hypothesis 2: Ants will be primary pollinators (because they were seen most commonly on the plants and the plants have some features that make them candidates for ant pollina7on, and can move more easily in windy environments) Lin (2013). M.Sc. Thesis, Trent University. Conducted his research in Ivvavik Na7onal Park, Yukon
Test organism (not necessarily a ‘model’ organism):
Buffaloberry, Soapberry et al. (Sheperdia canadensis)
Which of ants or flies pollinate arc7c plants (or neither, or both)? Conduct
field experiment Hypothesis: Ants will pollinate the plants because they were more numerous and not as affected by high arc7c winds Test: Exclude ants, exclude bees and flies, control
Results (shown in a bar graph) from two different sites in the park (replicated!): fruits were produced only (almost)
when flies were able to visit!
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Week 3. Interspecific interac7ons
Tip: How to remember the difference: Think ‘interna7onal’ means more than one na7on…so ‘interspecific interac7ons means interac7ons between two or more species
Interspecific (Burmese python with White‐tailed deer prey) Intraspecific (figh7ng Am. Robins)
Characterizing interac7ons (examples)
• Preda7on: +/‐ Means + effect on survival and reproduc7on of predator, ‐ effect on survival and reproduc7on on prey.
• Mutualism: +/+. Posi7ve for both species that interact (or individuals within a species)
• Reminder (survival + reproduc7on = fitness)
Compe77on: Interspecific (‐/‐) • Two forms: interference and exploita)ve • Interference compe77on is direct physical compe77on for resources between individuals.
• Exploita7ve compe77on is indirect, when one species reduces resources for the other (e.g., shared resources)
Compe77ve Exclusion
• Gause (1934) first proposed this concept:
Compe77ve Exclusion Principle
Two species compe7ng for the same limi7ng resources cannot coexist permanently in the
same place.
(even a slight reproduc7ve advantage through more efficient feeding,
reproduc7on, etc. will eventually lead to local elimina7on of the inferior compe7tor)
What IS a niche?
• “n‐dimensional hyperspace” (Hutchinson 1957)
Black Fly Larvae
Basically…where an organism lives…
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Some other terms some7mes used to categorize preda7on:
Par7al preda7on: E.g., A bird lays 14 eggs, only 9 are eaten. Micro‐preda7on: E.g., A very small organism (predator) eats part of a bigger organism (prey) Sea
squirts
4.3 mm
Osman et al. 1992.
Whereas preda)on accounts for MOST of the mortality in vertebrates (e.g, frogs, birds, rep7les, mammals)
And natural selec7on favours those
who survive (and subsequently reproduce!) There are many an)‐predator adapta)ons.
(a) Cryptic coloration (b) Aposematic coloration
Canyon tree frog Poison dart frog
(c) Batesian mimicry: A harmless species mimics a harmful one. (d) Müllerian mimicry: Two unpalatable species mimic each other.
Hawkmoth larva Cuckoo bee
Yellow jacket
Green parrot snake
Categoriza7on of some an7‐predator adapta7ons (defensive colora7ons):
Includes ‘mechanical’ and ‘chemical’ defenses Figure 54.5
Other adapta7ons for herbivory
• Special sensory organs, specialized diges7ve systems and teeth.
“An7‐herbivory” adapta7ons
• Include secondary compounds/metabolites: broad name for chemicals that protect plants against herbivory (among other poten7al func7ons)
Structural protec7on: Without herbivores: Galapagos Opun7a (Prickly Pear cactus): shrubby, bigger fruits, fewer soser spines
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Varying defini7ons of ‘symbiosis’
• Your textbook uses broader defini7on(+/‐ and +/+) to include any rela7onship between 2 or > 2 species where they live in direct and in)mate contact with each other.
Common endoparasites:
Spiny‐headed worms
Roundworms
Tapeworms
Figure 54.7
(a) Acacia tree and ants (genus Pseudomyrmex)
(b) Area cleared by ants at the base of an acacia tree
Classic example of mutualism: Ants are aggressive and s7nging. Ants feed on nectar produced by the tree and on swellings at 7ps of leaflets. Trees benefit because ants aWack anything that touches tree, remove fungal spores, small herbivores and debris.
“plant‐ants”
“ant‐plants”
Commensalism: +/0: When the water buffalo move they scare up insects which are then discovered and eaten by the caWle egrets. No cost to waterbuffalo.
Figure 54.8
Figure 54.9
(a) Salt marsh with Juncus (foreground) (b) With Juncus Without Juncus
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Num
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peci
es
Facilita7on (+/+) or (0/+)
Black rush (Juncus gerardi) facilitates in at least three ways: (1) makes the soil more hospitable for other species (2) helps prevent salt buildup by shading soil surface, reducing evapora7on, (3) prevents soil from becoming oxygen depleted as it transports oxygen to its belowground 7ssues.
Measuring biodiversity!
• Various measures:
• The simplest (AND most understandable) is ‘species richness’
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Species diversity measures: most common
2. Shannon‐Weiner diversity index (H or H’)
H = ‐(pA*ln pA + pB*ln pB + pC*ln pC +……..) Where A, B, C … are the species in the community, p is the rela7ve abundance of each species and ln is the natural logarithm.
Figure 54.10
Community 1 A: 25% B: 25% C: 25% D: 25%
Community 2 A: 80% B: 5% C: 5% D: 10%
A B C D
Example forests: which do you think is more diverse?
Sample calcula7ons of H
Forest 1 (with equal propor7ons of all 4 species of tree): H = ‐4 (0.25 * ln 0.25) = 1.39 Forest 2 (with unequal propor7ons of all 4 species of tree) H = [0.8* ln 0.8 + 2 (0.05* ln 0.05) + 0.1 * ln 0.1] = 0.71
Therefore, Forest 1 is more diverse.
H = ‐(pA*ln pA + pB*ln pB + pC*ln pC +……..)
What else affects biodiversity?
• Energy • Water • Disturbance • Invasive species • Preda7on • Succession • Biogeographic factors (the stuff of Biogeography!)
Energy (+) can limit the number of species and the food chain length
Experiment: Added and subtracted leaf liWer to tree hole communi7es in communi7es
Spiny‐tailed skink
More moisture (+) on slope means more invertebrates
From:Seagle and Sturtevant 2005, Ecology
Chose dry (up slope) and wet (down slope) sites and measured soil moisture and invertebrates.
Rela7ve soil moisture
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Disturbance (+)
Distance from edge of woodlot 50 m into woodlot)
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50 50
50 50 MaWlack 1993, Biol. Cons.
Invasive species (‐): Dog‐strangling vine (vincetoxicum rossicum) on Trent campus. What is H?
Predation (+) EXPERIMENT
RESULTS
With Pisaster (control)
Without Pisaster (experimental)
Year ’73 ’72 ’71 ’70 ’69 ’68 ’67 ’66 ’65 ’64 1963
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Num
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Classic experiment: Removal of star fish from inter7dal sites in Washington state (Paine 1974)
Area (hectares; log scale)
Num
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0.1 1 10 100 103 104 105 106 107 108 109 1010 1
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1,000
Figure 54.26 Biogeography (Variable effects on biodiversity: one factor is area of habitat)
LLIN Week 4a. Ecologists at work.
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Most mosquitoes caught near top of net because of plume from heads of subjects so if there are holes at the top (regardless of size) the nets should be replaced!
Week 4 b.
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Week 5. Week 6.
Basic concepts from Prof. Dorken’s week 6. lectures
Semelparous versus iteroparous Metapopula7ons Logis7c growth Density‐dependence versus density‐independence