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BIOL1020H Week 2: Lectures 1 & 2 

Outline Biology: a defini@on  Scien@fic reasoning in biology: a short history Hypothesis tes@ng  Methods of study A case study in scien@fic inquiry 

•  Biology is the scientific study of life •  Biologists ask questions such as

– How does a single cell develop into an organism? – How does the human mind work? – How do living things interact in communities?

•  Life defies a simple, one-sentence definition •  Life is recognized by what living things do

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Figure 1.3

Order

Evolutionary adaptation

Response to the environment

Reproduction

Growth and development

Energy processing

Regulation

Early formula@ons (and KEY players) of the scien@fic method (all sciences)  1.  Reduc@onism 2.  Induc@ve reasoning  3.  Deduc@ve reasoning 4.  Popperian Hypothe@co‐

deduc@ve method 

1. Reduc@onism 

•  The scien)fic approach of reducing complex systems to simpler components that are more manageable. 

•  Ex. 1. Understanding the func@oning 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. 

The Power and Limitations of Reductionism

•  Studying tree physiology allows an understanding of water transport at the cellular level

•  Also, studying the molecular structure of DNA helps us to understand the chemical basis of inheritance

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Systems biology: scaling up from the results of reduc@onist inves@ga@ons 

The approach that a_empts to model the dynamic behaviour of the whole biological system based on the study of the interac@ons among the system’s parts.   For example: how might increasing a crop’s water supply affect the process of storage of molecules essen@al for human nutri@on 

2. Francis Bacon (1561‐1626) Father of Induc@ve Reasoning  Bacon’s induc@ve approach included ‘the careful observa)on of nature with a systema)c accumula)on of data to draw upon’. New natural ‘laws’ (or descrip@ons of pa_ern) were then created based on the knowledge of par@cular 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

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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

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4. Hypothe@co‐deduc@ve method (AKA: THE scien@fic method, ‘H‐D method’) 

Karl Popper (1902‐1994) 

He wrote: The Logic of Scien@fic Discovery (1934) (in a hurry to get an academic post outside of Nazi‐run Europe)  

Take‐home from this book is no@on of falsifiability and that falsifiability separates science from non‐science 

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

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Steps of the hypothe@co‐deduc@ve method 

1.  Iden@fy a broad problem statement 2.  Define a problem statement 3.  Develop hypotheses (best guess) (plus 

predic@on..a step that is not always, but should be included in these steps!) 

4.  Determine measures 5.  Data collec@on 6.  Data analysis 7.  Interpreta@on of data (e.g., do data fit with 

your hypotheses and predic@ons?) 

Do you learn more if you support or reject an hypothesis?? 

•  All species of tree die.  (Support hypothesis). This could lead to trying to figure out what general climate or atmospheric event might cause tree death) 

•  Only one species of tree die. (Reject hypothesis). This observa@on leads to the next hypothesis that there is a species‐specific agent that is killing the tree species.  

•  You can proceed just as quickly when you reject your ini@al hypothesis as if it is supported! 

From www.undsci.berkeley.edu 

DDE concentra@ons in faeces (guano) coincided with ini@al popula@on declines in 

Chimney Swij 

From www.undsci.berkeley.edu 

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Migration routes and wintering grounds of three northern wheatears breeding in Alaskan (AK) and one in the eastern Canadian Arctic (CN; grey dot, breeding area, blue, autumn migration,

orange, spring migration, dashed lines indicate uncertainty in migration...

Bairlein F et al. Biol. Lett. doi:10.1098/rsbl.2011.1223

©2012 by The Royal Society

But how did early biologists work? 

Darwin used mostly observa@ons, also ar@ficial breeding experiments. Most early biologists (also called natural 

philosophers) were ardent naturalists 

What IS known about Polar Bears to understand link with climate? •  Climatology •  Bear physiology •  Bear popula@on biology •  Bear systema@cs •  Winter behaviour •  Habitat selec@on •  Sex roles and sex ra@os •  Reproduc@ve biology •  Geomorphology •  Diet •  Nutri@on •  Responses to environmental varia@on (including both human and natural) 

•  In other words….  We need to understand their natural (or life) history… 

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You will need to know something about your study organism! 

Understanding the interac@on between a species and its environment has been termed the study of ‘autecology’    “Autecology, also called Species Ecology,  is the study of the interac@ons of an individual organism or a single species with the living and nonliving factors of its environment. Autecology is primarily experimental and deals with easily measured variables such as light, humidity, and available nutrients in an effort to understand the needs, life history, and behaviour of the organism or species.” Encyclopedia Britannica, online.   Note: You are NOT doing ‘Synecology’, the study of the structure and func@on of ecological communi@es. 

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.

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Figure 1.23

Quan@ta@ve data 

0 

20 

40 

60 

80 

100 

120 

White Oak  Red Maple  White Ash  Eastern White Cedar 

Percent dead 

Percent alive 

Other forms of qualita@ve data 

Counts (e.g., number of flowers, which can then be expressed as percentages)  Con@nuous data (e.g., heights, masses)   Binary responses (e.g., yes/no; presence/absence) 

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

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From Pfennig et al. 2001, Nature 

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•  This hypothesis was tested with the venomous eastern coral snake (Micrurus fulvius) and its mimic the nonvenomous scarlet kingsnake (Lampropeltis elapsoides)

•  Both species live in the Carolinas, but the kingsnake is also found in regions without venomous coral snakes

•  If predators inherit a (local) avoidance of the coral snake’s coloration, then the colorful kingsnake will be attacked less often in the regions where coral snakes are present

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Figure 1.25

Scarlet kingsnake (nonvenomous)

Key

Range of scarlet kingsnake only (allopatry) Overlapping ranges of scarlet kingsnake and eastern coral snake (sympatry)

Eastern coral snake (venomous)

Scarlet kingsnake (nonvenomous)

North Carolina

South Carolina

Field Experiments with Artificial Snakes •  To test this mimicry hypothesis, researchers made

hundreds of artificial snakes: – An experimental group resembling kingsnakes – A control group resembling plain brown snakes

•  Equal numbers of both types were placed at field sites, including areas without poisonous coral snakes

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Figure 1.26

(a) Artificial kingsnake

(b) Brown artificial snake that has been attacked

•  After four weeks, the scientists retrieved the artificial snakes and counted bite or claw marks

•  The data fit the predictions of the mimicry hypothesis: the ringed snakes were attacked less frequently in the geographic region where coral snakes were found

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Figure 1.27

Ar.ficial kingsnakes 

Brown ar.ficial snakes 

Percen

t of to

tal a9acks 

on ar.ficial sna

kes 

83%  84% 

100 

80 

60 

40 

20 

0 

Coral snakes absent 

Coral snakes present 

17%  16% 

RESULTS 

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Sta@s@cal analysis of results 

•  Why? Because these results could have occurred due to chance alone.  

•  We use sta@s@cs to determine whether the results are probable due to chance alone.  

“The mean propor@on of ringed replicas a_acked was significantly greater in allopatry (0.654 ± 0.107) than in sympatry (0.083 ± 0.116; P= 0.009, 2‐tailed Wilcoxon two‐group test).” 

Experimental Controls and Repeatability •  A controlled experiment compares an

experimental group (the artificial kingsnakes) with a control group (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

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•  In science, observations and experimental results must be repeatable (but they are often NOT repeated, unless there is a very strong financial or medical consequence to the research).

•  Why??

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Communica@ng Science! 

•  Science is a highly social ac@vity 

•  Coopera@on makes science proceed more rapidly (e.g., mul@ple labs looking for Ebola vaccine) 

•  Science without communica@on is not science! 

Nega@ve results are PROBABLY underrepresented in the published literature (and ojen sit in electronic files for years or in unpublished theses).   Model organisms in Ecology and 

Evolu@on 

Drosophila melanogaster (fruit fly)  Arabidopsis thaliana (Mouse‐ear cress) 

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In Conserva@on Biology we have our own ‘model organisms’ (also called 

‘Flagship species’) 

Atelopis varius (Harlequin Frog)  Affected by airborne toxins, decline in habitat, change in climate, breathes through skin so sensi@ve to air quality. 

Loxodonta africana (African Elephant)   And (unfortunately) many more…. 

Second case study: What pollinates arc@c plants? Start with an observa@onal study, 

con@nue with a field experiment  Hypothesis: Bees will be primary pollinator (because we know that they are the most important plant pollinators on earth)   Method: Observe plants from a distance to determine what hangs out on the plant’s flowers.   Lin (2013). M.Sc. Thesis, Trent University. Conducted his research in Ivvavik Na@onal Park, Yukon 

    

Test organism (not necessarily a ‘model’ organism): 

Buffaloberry, Soapberry et al.   (Sheperdia canadensis)  Ivvavik Na@onal Park, Yukon 

Visitors to arc@c Buffaloberry over 40 hours of observa@on 

Did we accept or reject our hypothesis? 

Bees will be primary pollinator (because we know that they are the most important plant pollinators on earth)  

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Which of ants or flies pollinate arc@c 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 arc@c winds  Test: Exclude ants, exclude bees and flies, control      

Results from two different sites in the park (replicated!): fruits were produced only (almost) when flies were able to 

visit! 

Did we accept or reject our hypothesis? 

    

Ants will pollinate the plants because they were more numerous in our observa@onal study on the plants and not as affected by high arc@c winds  

Plant‐animal interac@ons, niche theory and more next week! 

Manatee (Trichechus manatus)  feeding on hydrilla, an introduced species.