Topic 4. Ecology

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4.1 Ecosystems

Lesson 1

Ecology is the study of living things, their environment, and the relationships between them.

DeepEcoNOS: Deep Ecology is a kind of philosophy, which proposes that humankind are an integral part of ecological systems, and that we should feel apart of the ecology around us – instead of acting as arbitrators or manipulators of ecosystems.Arne Naess (founder of the Deep Ecology Movement) 


Food web and Food chains

A food chain shows the feeding relationships between a number of organisms. The arrows represent the flow of organic nutrients and energy. A food web is a branching food chain.

 Figure 1: Foodweb from Manuel Antonio park, Costa Rica

food web


Stages in a food chain:

  • Producer – Produces organic compounds, from inorganic ones.
  • Primary consumer – Feeds on, and thereby obtains the nutrients / energy from, a producer
  • Secondary consumer – Feeds on, and thereby obtains the nutrients / energy from, a primary consumer
  • Tertiary consumer – Feeds on, and thereby obtains the nutrients / energy from, a secondary consumer

These stages are called trophic levels.

Exercise: Extract two food chains from the Manuel Antonio food web, identifying a producer, primary consumer, secondary consumer, and tertiary consumer.

Further descriptions:

  • Predator – an organism that hunts and kills for food, it’s prey.
  • Top predator – an organism that is a predator, and has not predators itself
  • Detritivores and saprophytes – organisms that feed on dead and decaying organic material (eg. ants and fungi). These are not normally shown in a food web, but they are significant.
  • Autotrophs – obtain inorganic nutrients from the abiotic environment (from the non-biological surroundings) eg. Plants
  • Heterotrophs – obtain organic nutrients from other organisms.
  • Detritivores are different to saprophytes because their digestion of detritus is internal ( they eat it), like ants. Saprophytes secrete digestive enzymes and digest detritus outside of their bodies, like fungi.

Exercise: From the Manuel Antonio park, select a top predator, an autotroph, and two heterotrophs which are in competition with each other for the same food source.


Bonus Activity: try the word quiz

Species and communities

Species are groups of organisms that can interbreed to produce fertile offspring. A population is a group of organisms of the same species, living together at the same time eg. the squirrel monkeys of Manuel Antonio park.

A community is a group of different species living together at the same time eg. the monkey community of Manuel Antonio park (Howler monkey population, Squirrel monkey population, and white-faced Cappucin population).

Ecology Birdwatching Task:

  • Watch the bird feeder time-lapse (you might want to choose x0.25 the speed).
  • Give each kind of bird a letter and write a brief description eg. Bird A is large and brown, with a brown beak
  • Make a simple table to record how many birds of each type you think appeared at the bird feeder in the time captured.
  • Discuss any ‘uncertainty’ you might have about your counting.
  • Report back to the class.


 This also needs to be turned into a suitable graph.

Lesson 2 – Using Chi-squared

Fundamental Question: How can we tell if the distribution of organisms is random, or significantly altered by one or more factors?

Lesson Objectives: Learn how to apply the Chi-squared test.


  • Chi-squared test. A stastical test applied to find if the distribution of organisms (eg. moss on a tree) is significantly different with respect to a certain factor (eg. north or south).
  • Null hypothesis. The assumption that the distribution can be explained by chance and is not significantly varied with respect to that factor.
  • Alternative hypothesis. The assumption that the distribution with respect to a certain factor varies significantly.

The Chi-squared test (called X2 as X is the old greek letter Chi, pronounced ‘Kigh’) is a statistical test used to see if a particular distribution occurs by chance or Is there really more moss growing on the North or South side of trees compared to other plants like Lianas, or is it just random?

In order to work the test ‘assumes’ is no significant difference (aka the null hypothesis), and then sets out to try and prove that there actually is a significant difference.

Question: Is the occurrence of moss significantly different from the growth of other epiphytic plants such as Lianas?

Note: an epiphyte is a plant which utilises another plant as a habitat, without taking anything away from the host plant. Orchids, bromeliads, and Llianas are all epiphytes. This distinguishes it from a parasitic plant, which will feed on the host tree.

  • Null Hypothesis (given the symbol Ho): Yes, it is just by chance
  • Alternative Hypothesis (given the symbol Ha): No, it is not just chance where the moss and other epiphytes grow.
image credit

image credit moss and lichen growing on the side of a tree


Step one: Set up your categories: North, South, how much moss, how many other epiphytes

Step two: Arrange the categories into a table, adding a row and a column for totals.

Screen Shot 2017-01-31 at 11.23.23 AM


Step three: Add the data, adding totals for each row and column. Notice the bottom right hand corner will contain the grand total of all the lichen and moss found. This data is called the observed values

Screen Shot 2017-01-31 at 11.24.03 AM

Step four: Calculate the expected values for each category , using the formula Expected value = row total x column total / grand total. For example a category would be Moss growing on the North side of the tree, and the expected value would be 13×10 / 20 = 6.5. For mathematical purposes we would leave the number without rounding to 7, even though half a plant doesn’t make sense. Add these to the table you have made, using parentheses to signify an expected value.

Screen Shot 2017-01-31 at 11.31.53 AM

Step five: Using the formula X2 = (the sum of all the Observed – Expected)squared, divided by the expected. Calculate Chi-squared. The formula is written below:

Screen Shot 2017-01-31 at 11.34.54 AM


Step six: Looking up the critical Chi-squared value in the Chi-squared table

Degrees of freedom is 1 (number of rows-1) x (number of columns -1).

We can see that for 95% confidence, a value of 3.81 is required for Chi-squared to reject the null hypothesis.

Therefore in this case as our calculated value of Chi-squared is less than 3.81, we retain the null hypothesis. According to this data, there is nothing different about the way that moss grows on a tree trunk compared to other epiphytes. 


Need to see more examples? Watch this video


 Class activities (to do in class)

Activity:  Learning to use a basic X2 test (pronounced Chi-squared). You will be expected to look for gender bias based on response to a valid question that will generate categorical data (choose a question that has only two answers eg. Do you prefer using an iPad or a laptop in class)

2) Draw a table separating out the possible categories your data will fall under

eg.     IPad      Laptop



3) Collect the data from our class, asking your classmates for cooperation in our example

4) Calculate the expected values if the null hypothesis was true eg. there is no gender bias in students who prefer working with iPads or laptops). To do this you can use the formula row total x column total / grand total (intuitively, the expected result for female students who like iPads will be the total number of people who like iPads x the fraction of people who are female).

5) Calculate the Chi – squared value. You can use an excel spreadsheet to make this faster, as it will do some of the calculating for you.

6) Work out the degrees of freedom. Number of rows -1 x Number of columns -1. eg. 1 in my example.

7) Check the Chi-squared value against the tabulated values on the powerpoint slide. You can see that the values have different probability ratings. eg. if your value exceeds the published value at p > 0.05, this means that there is a 95% certainty that the null hypothesis is wrong and there is a significant difference.

Still lost? Download chi-squared worked example and go through it, asking questions if needed.


Lesson 3 – Chi-squared lab

Down load lab instructions: the quadrat lab


4.2 – Energy losses

lesson one: Energy losses

Objectives: Understand how energy losses occur in food chains; both within and between trophic levels. Understand how this limits the length of food chains. Recall that energy is lost in food chains, while nutrients can be recycled.

Key words:

  • Entropy: the concept that systems tend to become disorganised if left to their own devices. This applies to the flow of energy in food chains, that begins as chemical energy in a highly organised bio-molecules and ends up as highly scattered heat energy moving by convection and radiation.
  • Pyramid of energy: a graphical representation of the energy level in each trophic level.
  • Trophic level: the feeding level eg. producer

Introduction: the image shows the thermal profile of a human body. It can be concluded that heat loss by radiation occurs constantly, and is particularly associated with the ‘core of the body’ including the thoracic cavity where many vital organs are found. This energy is generated by aerobic respiration, and in fact one of the functions of cellular respiration is to maintain a constant body temperature – even it means wasting a little heat energy.

Energy flows in a food chain from producers to consumers to top consumers. Ultimately energy is released to the environment and escapes into the Earth’s atmosphere as heat energy.

image credit:

image credit:

This is in contrast to nutrients, which are recycled through the work of decomposers and may pass through the same food chain many times. Producers convert light energy into chemical energy through the process of photosynthesis (some other producers also harness the energy in chemical reactions, they are called chemoautotrophs). Chemical energy flows through food chains through the result of feeding.


Energy losses

Although this varies in different ecosystems, around 90% of energy is often lost in a feeding relationship between trophic levels. So if a person subsists on apples, only 10% of the energy in the apple trees ends up being available to the human.


Energy losses in ecosystems may occur:

  • 1. Between trophic levels (during feeding)
  • 2. Within trophic levels (energy is consumed by the organism)

1. Between trophic levels

Energy losses that occur between trophic levels are due to the incomplete ingestion, incomplete digestion, and uneaten organisms.

Incomplete ingestion – using the context of the apple trees, the human does not eat the whole apple tree. Only the apple. Therefore most of the energy available in the apple trees is not accessed.

Incomplete digestion – Using the context of the apple trees, some parts of an apple cannot be digested, such as the seeds. They would count as fibre. Therefore the energy in them is not available to the human.

Uneaten organisms – The human does not feed from every apple tree. Some apple trees are not fed upon, and of course even on those that are, some apples are not eaten.


2. Energy loss within trophic levels

Energy losses that occur within trophic levels are due to the organism digesting the food and then using the energy in respiration for cellular processes eg. muscle contraction. When this happens the chemical energy stored in the food is converted into ATP in the process of respiration. The reason this is necessary is that the energy in chemicals like glucose is not readily available. Adenosine Tri-Phosphate reality breaks down into Adenosine Di-phosphate, yielding a packet of energy that can be instantly used for muscle contraction, molecule synthesis, cellular movement e.t.c.


The second law of thermodynamics states that energy changes (from one form to another), are never 100% efficient. Ultimately this means that the energy is lost as heat energy ( mostly as radiation).





The energy obtained by an organism tends to be stored as chemical energy, in the body. This not only includes storage carbohydrates such as glycogen (animals), or starch (plants), but proteins and lipids as well, as well structural components like bones and hair. This means that the mass of the organisms in a trophic level, can represent the energy stored at that trophic level.

P= Energy stored at a trophic level, in grams per year.


Pyramids of Energy

A pyramid of energy represents the energy found at a particular trophic level. This consists of a kind of horizontal bar chart, where the energy at each trophic level is shown by the area (length) of the bar. The units of a pyramid of energy are often kilojoules / m2 / year.


Class activities A:

Problem: Should salmon farming be carried out using fish feed, or soy as a source of food for the salmon

  1. Draw the two possible food chains
  2. Using graph paper, make two pyramids of energy to show each food chain
  3. Discuss the problem, using your pyramids of energy to defend your answer.


Food chain soy

  • Energy in Soy 50,000 KJ m-2yr-1
  • Energy in Salmon 7,000 KJ m-2yr-1

Food chain fish meal

  • Energy in plankton 80,000 KJm-2yr-1
  • Energy in fish meal 2,500 KJm-2yr-1
  • Energy in salmon 200 KJm-2yr-1


Class activities B:

Some students were asked Demonstration of Energy losses using the ‘blind paper toss model’.They stood in four rows, facing the same way. The front row were given paper balls and asked to toss them over their shoulders at the group behind. Any students in the second row who caught them, were considered to have been successful feeders. Any who did not catch a paper ball are effectively eliminated, and have to sit down. This continues until the fourth row.

Discussion of model.

  • Does this model produce a pyramid of energy?
  • Why does this occur?
  • How does this accurately model energy flow through food chains, and therefore explain the pyramid shape shown by ecological pyramids.
  • Conversely, what are the limitations of this model.
  • Can you make suggested refinements to this model, perhaps including energy loss within a trophic level? or the inclusion of decomposers?

Recommended questions IB Oxford 

Page 214 questions 1, 2, 3

Page 216 questions a, b, c

 Page 219 questions 1, 2, 4, 5

Socratic discussion question: Discuss: If a Cappucin monkey eats a fig, at what point will it actually access the energy in the fruit?



Introduction from recent news: the world’s biggest ever Mesocosm. Biosphere 2.

A mesocosm is a mini-ecosystem in closed system. A closed system means that only energy can be exchanged across the boundary, and not matter. This means that light energy can come in, and heat energy out, but you can’t add food or water to a mecososm once it has been set up.

Mesocosms can be aquatic, or terrestrial.

Your challenge? Make a successful mesocosm in the lab. I suggest that you:

-choose the type of mecocosm you want to make (terrestrial or aquatic)

-choose the community you want to include (which species)

-think carefully about how those species might interact in a stable way

-ethics: how can you prevent an organism from suffering as a result of a mesocosm experiment.

-choose the abiotic components

-Hint: what will the community need in order to survive?

Download this document for the mesocosm Project:


Check out this strange story of one of the world’s most successful mecososms.

Figure below: A conceptualised energy flow diagram can be developed (note that energy is ultimately lost to space and not recycled)


4.3 Carbon cycling


Lesson 1: Carbon cycle and measuring changes in the carbon cycle.

Big questions: Why is it that energy cannot be recycled in a food chain, while nutrients can?

Objectives: Know the basic components of the carbon cycle. Distinguish between a source, a sink, and a reservoir. Carry out basic calculations using fluxes. Realise that methane is another gas that contains carbon, and is significant in the context of global warming.


  • Source – a process that releases a substance eg. combustion of fossil fuels releases carbon dioxide into the atmosphere.
  • Sink – a process that removes a substance eg. photosynthesis removes carbon dioxide from the atmosphere
  • Reservoir- a store of a substance eg. the atmosphere stores carbon dioxide.
  • Flux – any movement of a substance eg. carbon. Usually used in a quantitative context eg. combustion of fossil fuels releases 6 gigatonnes of carbon a year.



Spend some time playing the carbon cycle game

(click here Be prepared to share something that you learned from the exercise.

Activity 1: The carbon cycle.

Study the diagram below. You may wish to make a copy.

Screen Shot 2016-09-01 at 6.57.57 AM

Instructions: After studying the carbon cycle above, in your own notes

  • a) Make a list of sources and sinks of atmospheric carbon dioxide
  • b) Make a list of reservoirs (pools of Carbon), and fluxes (movement of carbon between pools). This may take the form of a table.
  • Check your list with others.
  • Check the summary at the bottom of the page

Activity 2. Fluxes of methane 

First watch this bizarre video. This is the kind of environment where methane is produced naturally – a peat bog. That is, permanently flooded soil.


Environments that produce methane (methanogenesis) are characteristed by:

  • flooded conditions
  • acidic soils
  • low oxygen concentrations
  • relatively slow rates of decomposition

Peat is a kind of soil characterised by layers of slowly decomposing vegetation, because of acidic conditions and / or a high soil water content. A peat bog is an area of wetlands that contain peat.

Atmospheric methane levels are raised by:

  • Methanogenesis – by archaen bacteria (other bacteria contribute by making the substances which arcane bacteria use to make methane, namely hydrogen, carbon dioxide and acetate)

Atmospheric methane levels are lowered by:

  • Oxidation – converted to carbon dioxide and water in the atmosphere, in a process involving free radicals (free radicals are highly reactive molecules which have unpaired electron pairs).

Methane is also produced in the intestines of many animals, including humans – this is carried out by the same bacteria found in peat bogs.

Activity 3 – Methane vs. carbon dioxide


You will debate the relative importance of methane:

  • read the following document on methane:

Debate with the people at your table. Should we be more focussed on carbon dioxide, or methane in our strategy to combat global warming.

Summarise in one single statement your conclusion regarding the relative importance of carbon dioxide and methane in climate change.


Recommended question of the day: Interpreting data on atmospheric CO2 concentrations. Data-based questions Page 221 1-4

before answering the question it is recommended you watch a clip from the movie An Inconvenient Truth.


Fluxes of carbon – summary (for help with activity 1).

Atmospheric carbon dioxide levels are raised by:

  • Combustion – producing Carbon, Carbon monoxide and Carbon dioxide gases (and H2O)
  • Respiration – releasing Carbon dioxide (and H20)
  • Acid erosion of limestone – releasing Carbon dioxide (and H2O and producing a salt)

Carbon dioxide levels are lowered by:

  • Dissolving in the ocean – forming hydrogen carbonates, and carbonic acid
  • Reef building – which produces calcium carbonate
  • Photosynthesis – which produces organic compounds like glucose

4.4 Climate change

Lesson one- Understanding the link between global warming and the enhanced greenhouse effect

Objectives: Explain how the enhanced greenhouse effect can lead to global warming.


  • Global warming: An overall increase in global temperatures.
  • Greenhouse effect: the reabsorption of long-wave radiation (heat) by greenhouse gases.
  • Greenhouse gas: a gas than can re-absorb long-wave radiation and therefore contribute to the greenhouse effect.
  • Climate change: Changing of regional weather patterns.
  • Long-wave radiation: radiation with a relatively long wavelength (infra-red, or heat).
  • Short-wave radiation: radiation with a relatively short wavelength (visible light, ultra-violet light)

The greenhouse effect is a natural process which is important in maintaining a global average temperature which is suitable for life  (15 degrees C). Without the greenhouse effect, the average temperature would be a freezing -18 degrees C (according to NASA).

How does it work?

  1. A mixture of long and short-wave radiation from the sun reaches the Earth’s surface.
  2. Some of the short-wave radiation is reflected back into space.
  3. The radiation that reaches the Earth’s surface causes it to warm, and emit long-wave radiation
  4. Greenhouse gases re-absorb long-wave radiation, trapping it in the Earth’s atmosphere.
  5. This raises the Earth’s atmosphere to an average temperature which is suitable for life.

Simple explanation:


Another explanation:


The Enhanced Greenhouse Effect

It has been shown through studies of the Earth’s history that sometimes the average temperature of the Earth’s atmosphere can rise because of increased levels of greenhouse gases. The most important greenhouse gases have been carbon dioxide and water. Other greenhouse gases include methane, and oxides of nitrogen (eg.nitrous oxide NO2).

Although there are other factors that may also affect the changes in global temperature (eg. sunspot activity), there is currently a global concern that the climate is changing because of global warming, due to an enhanced greenhouse effect (more greenhouse effect), because of anthropogenic sources of atmospheric carbon dioxide and methane.

The two most important pieces of evidence for this are:

1) Manua Loa Observatory, Hawaii. 57 years of data on changes in atmospheric CO2



Q) Why is there a seasonal change (fluctuation?)

Q) What is the overall change?

Q) What evidence is there that this is causation?


2) Ice core data, such as the European project for ice coring, which combine northern atmosphere average temperature and carbon dioxide levels

image credit: British antarctic survey

image credit: British antarctic survey

Q.) Describe the trends shown in the data above

Q.) Evaluate this data as evidence of man-made global warming.

 Lesson two- Understanding the argument for global warming

Objectives: to evaluate counter-claims against the theory of man-made global warming. To learn that scientific arguments should be made using data from reliable sources, should not be biased, and should include uncertainties.


  • Global warming: An overall increase in global temperatures.
  • Climate change: Changing of regional weather patterns.
  • Ozone-layer depletion: A reduction in the amount of ozone at the stratospheric level. This is a separate issue to global warming


Activity A: Watch extracts from Al Gore’s film: the Inconvenient truth, and from the film ‘The great global warming swindle’. Try and list key claims made, and the evidence presented to support the claims. Try and have arguments from both sides.

Steps of a scientific argument:

1- Isolate the part of the claim relating to scientific theory

2-Discern the evidence backing the claim

3-Evaluate the source of the claim


The great global warming swindle

Debunking the great global warming swindle

And this on the CO2 and temperature relationship

The Effects Of Global Warming

Global warming means an average increase in atmospheric temperatures worldwide. This does not mean that the temperature will increase in every country however, the implications are far more complex and involve regional changes in climate (climate change).

Effects which have already been detected include:

-Melting of polar ice cap (Arctic)

-Melting of alpine glaciers (eg. Kilimanjaro). What are the global implications of this loss? (hint: see photo below)

-Rising sea levels

-Decreasing pH of surface layer of world’s oceans due to dissolving CO2. This has the effect of dissolving the carbonate skeleton of coral reefs

-Changing weather patterns (this can cause crop yields to improve or to decline in a specific area)

-Changes in migration behaviour eg. birds may not move in the way they used to during summer / winter

-Changes in species ranges ie. where species can live. Two examples of this would be that mosquitoes and other pests would be able to extend further north, and predators may be able to hunt further north than they used to.

-Species extinction eg. Golden Toad in Monteverde

– More extreme weather events eg. tsunamis, hurricanes. This is because of the relationship between energy flow between the atmosphere and the world’s oceans.

-Acidification of oceans, leading to decalcification and weakening of coral reefs

-Bleaching and die-off of coral reefs, due to temperature rises of more than 2 degrees C in the ocean.


Lesson 2 – Global warming simulation lab


Extra materials:

Revision powerpoint



Climate change and Global warming

this is a simple and colourful explanation of how the enhance greenhouse effect can lead to global warming. It comes from the documentary ‘An Inconvenient Truth’ by Al Gore.



The role of CO2 in global warming.



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