Information

1.1: What Our Ancestors Knew - Biology


Skills to Develop

  • Describe how our ancestors improved food with the use of invisible microbes
  • Describe how the causes of sickness and disease were explained in ancient times, prior to the invention of the microscope
  • Describe key historical events associated with the birth of microbiology

Clinical Note - PART 1

Cora, a 41-year-old lawyer and mother of two, has recently been experiencing severe headaches, a high fever, and a stiff neck. Her husband, who has accompanied Cora to see a doctor, reports that Cora also seems confused at times and unusually drowsy. Based on these symptoms, the doctor suspects that Cora may have meningitis, a potentially life-threatening infection of the tissue that surrounds the brain and spinal cord.

Meningitis has several potential causes. It can be brought on by bacteria, fungi, viruses, or even a reaction to medication or exposure to heavy metals. Although people with viral meningitis usually heal on their own, bacterial and fungal meningitis are quite serious and require treatment.

Figure (PageIndex{1}): (a) A lumbar puncture is used to take a sample of a patient’s cerebrospinal fluid (CSF) for testing. A needle is inserted between two vertebrae of the lower back, called the lumbar region. (b) CSF should be clear, as in this sample. Abnormally cloudy CSF may indicate an infection but must be tested further to confirm the presence of microorganisms. (credit b: modification of work by James Heilman)

Cora’s doctor orders a lumbar puncture (spinal tap) to take three samples of cerebrospinal fluid (CSF) from around the spinal cord (Figure (PageIndex{1})). The samples will be sent to laboratories in three different departments for testing: clinical chemistry, microbiology, and hematology. The samples will first be visually examined to determine whether the CSF is abnormally colored or cloudy; then the CSF will be examined under a microscope to see if it contains a normal number of red and white blood cells and to check for any abnormal cell types. In the microbiology lab, the specimen will be centrifuged to concentrate any cells in a sediment; this sediment will be smeared on a slide and stained with a Gram stain. Gram staining is a procedure used to differentiate between two different types of bacteria (gram-positive and gram-negative).

About 80% of patients with bacterial meningitis will show bacteria in their CSF with a Gram stain.1Cora’s Gram stain did not show any bacteria, but her doctor decides to prescribe her antibiotics just in case. Part of the CSF sample will be cultured—put in special dishes to see if bacteria or fungi will grow. It takes some time for most microorganisms to reproduce in sufficient quantities to be detected and analyzed.

Exercise (PageIndex{1})

What types of microorganisms would be killed by antibiotic treatment?

Most people today, even those who know very little about microbiology, are familiar with the concept of microbes, or “germs,” and their role in human health. Schoolchildren learn about bacteria, viruses, and other microorganisms, and many even view specimens under a microscope. But a few hundred years ago, before the invention of the microscope, the existence of many types of microbes was impossible to prove. By definition, microorganisms, or microbes, are very small organisms; many types of microbes are too small to see without a microscope, although some parasites and fungi are visible to the naked eye.

Humans have been living with—and using—microorganisms for much longer than they have been able to see them. Historical evidence suggests that humans have had some notion of microbial life since prehistoric times and have used that knowledge to develop foods as well as prevent and treat disease. In this section, we will explore some of the historical applications of microbiology as well as the early beginnings of microbiology as a science.

Fermented Foods and Beverages

People across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. Discoveries from several archeological sites suggest that even prehistoric people took advantage of fermentation to preserve and enhance the taste of food. Archaeologists studying pottery jars from a Neolithic village in China found that people were making a fermented beverage from rice, honey, and fruit as early as 7000 BC.2

Production of these foods and beverages requires microbial fermentation, a process that uses bacteria, mold, or yeast to convert sugars (carbohydrates) to alcohol, gases, and organic acids (Figure (PageIndex{12})). While it is likely that people first learned about fermentation by accident—perhaps by drinking old milk that had curdled or old grape juice that had fermented—they later learned to harness the power of fermentation to make products like bread, cheese, and wine.

Figure (PageIndex{2}): A microscopic view of Saccharomyces cerevisiae, the yeast responsible for making bread rise (left). Yeast is a microorganism. Its cells metabolize the carbohydrates in flour (middle) and produce carbon dioxide, which causes the bread to rise (right). (credit middle: modification of work by Janus Sandsgaard; credit right: modification of work by “MDreibelbis”/Flickr)

The Iceman Treateth

Prehistoric humans had a very limited understanding of the causes of disease, and various cultures developed different beliefs and explanations. While many believed that illness was punishment for angering the gods or was simply the result of fate, archaeological evidence suggests that prehistoric people attempted to treat illnesses and infections. One example of this is Ötzi the Iceman, a 5300-year-old mummy found frozen in the ice of the Ötzal Alps on the Austrian-Italian border in 1991. Because Ötzi was so well preserved by the ice, researchers discovered that he was infected with the eggs of the parasite Trichuris trichiura, which may have caused him to have abdominal pain and anemia. Researchers also found evidence of Borrelia burgdorferi, a bacterium that causes Lyme disease.3 Some researchers think Ötzi may have been trying to treat his infections with the woody fruit of the Piptoporus betulinus fungus, which was discovered tied to his belongings.4 This fungus has both laxative and antibiotic properties. Ötzi was also covered in tattoos that were made by cutting incisions into his skin, filling them with herbs, and then burning the herbs.5 There is speculation that this may have been another attempt to treat his health ailments.

Early Notions of Disease, Contagion, and Containment

Several ancient civilizations appear to have had some understanding that disease could be transmitted by things they could not see. This is especially evident in historical attempts to contain the spread of disease. For example, the Bible refers to the practice of quarantining people with leprosy and other diseases, suggesting that people understood that diseases could be communicable. Ironically, while leprosy is communicable, it is also a disease that progresses slowly. This means that people were likely quarantined after they had already spread the disease to others.

The ancient Greeks attributed disease to bad air, mal’aria, which they called “miasmatic odors.” They developed hygiene practices that built on this idea. The Romans also believed in the miasma hypothesis and created a complex sanitation infrastructure to deal with sewage. In Rome, they built aqueducts, which brought fresh water into the city, and a giant sewer, the Cloaca Maxima, which carried waste away and into the river Tiber (Figure (PageIndex{3})). Some researchers believe that this infrastructure helped protect the Romans from epidemics of waterborne illnesses.

Figure (PageIndex{3}): (a) The Cloaca Maxima, or “Greatest Sewer” (shown in red), ran through ancient Rome. It was an engineering marvel that carried waste away from the city and into the river Tiber. (b) These ancient latrines emptied into the Cloaca Maxima.

Even before the invention of the microscope, some doctors, philosophers, and scientists made great strides in understanding the invisible forces—what we now know as microbes—that can cause infection, disease, and death.

The Greek physician Hippocrates (460–370 BC) is considered the “father of Western medicine” (Figure (PageIndex{4a})). Unlike many of his ancestors and contemporaries, he dismissed the idea that disease was caused by supernatural forces. Instead, he posited that diseases had natural causes from within patients or their environments. Hippocrates and his heirs are believed to have written theHippocratic Corpus, a collection of texts that make up some of the oldest surviving medical books.6 Hippocrates is also often credited as the author of the Hippocratic Oath, taken by new physicians to pledge their dedication to diagnosing and treating patients without causing harm.

While Hippocrates is considered the father of Western medicine, the Greek philosopher and historian Thucydides (460–395 BC) is considered the father of scientific history because he advocated for evidence-based analysis of cause-and-effect reasoning (Figure (PageIndex{4b})). Among his most important contributions are his observations regarding the Athenian plague that killed one-third of the population of Athens between 430 and 410 BC. Having survived the epidemic himself, Thucydides made the important observation that survivors did not get re-infected with the disease, even when taking care of actively sick people.7 This observation shows an early understanding of the concept of immunity.

Marcus Terentius Varro (116–27 BC) was a prolific Roman writer who was one of the first people to propose the concept that things we cannot see (what we now call microorganisms) can cause disease (Figure (PageIndex{4c})). In Res Rusticae (On Farming), published in 36 BC, he said that “precautions must also be taken in neighborhood swamps

. because certain minute creatures [animalia minuta] grow there which cannot be seen by the eye, which float in the air and enter the body through the mouth and nose and there cause serious diseases.”8

  • Give two examples of foods that have historically been produced by humans with the aid of microbes.
  • Explain how historical understandings of disease contributed to attempts to treat and contain disease.

The Birth of Microbiology

While the ancients may have suspected the existence of invisible “minute creatures,” it wasn’t until the invention of the microscope that their existence was definitively confirmed. While it is unclear who exactly invented the microscope, a Dutch cloth merchant named Antonie van Leeuwenhoek (1632–1723) was the first to develop a lens powerful enough to view microbes. In 1675, using a simple but powerful microscope, Leeuwenhoek was able to observe single-celled organisms, which he described as “animalcules” or “wee little beasties,” swimming in a drop of rain water. From his drawings of these little organisms, we now know he was looking at bacteria and protists. (We will explore Leeuwenhoek’s contributions to microscopy further in Chapter 2.)

Nearly 200 years after van Leeuwenhoek got his first glimpse of microbes, the “Golden Age of Microbiology” spawned a host of new discoveries between 1857 and 1914. Two famous microbiologists, Louis Pasteur and Robert Koch, were especially active in advancing our understanding of the unseen world of microbes (Figure (PageIndex{5})). Pasteur, a French chemist, showed that individual microbial strains had unique properties and demonstrated that fermentation is caused by microorganisms. He also invented pasteurization, a process used to kill microorganisms responsible for spoilage, and developed vaccines for the treatment of diseases, including rabies, in animals and humans. Koch, a German physician, was the first to demonstrate the connection between a single, isolated microbe and a known human disease. For example, he discovered the bacteria that cause anthrax (Bacillus anthracis), cholera (Vibrio cholera), and tuberculosis (Mycobacterium tuberculosis).9 We will discuss these famous microbiologists, and others, in later chapters.

Figure (PageIndex{5}): (a) Louis Pasteur (1822–1895) is credited with numerous innovations that advanced the fields of microbiology and immunology. (b) Robert Koch (1843–1910) identified the specific microbes that cause anthrax, cholera, and tuberculosis.

As microbiology has developed, it has allowed the broader discipline of biology to grow and flourish in previously unimagined ways. Much of what we know about human cells comes from our understanding of microbes, and many of the tools we use today to study cells and their genetics derive from work with microbes.

  • How did the discovery of microbes change human understanding of disease?

Key Concepts and Summary

  • Microorganisms (or microbes) are living organisms that are generally too small to be seen without a microscope.
  • Throughout history, humans have used microbes to make fermented foods such as beer, bread, cheese, and wine.
  • Long before the invention of the microscope, some people theorized that infection and disease were spread by living things that were too small to be seen. They also correctly intuited certain principles regarding the spread of disease and immunity.
  • Antonie van Leeuwenhoek, using a microscope, was the first to actually describe observations of bacteria, in 1675.
  • During the Golden Age of Microbiology (1857–1914), microbiologists, including Louis Pasteur and Robert Koch, discovered many new connections between the fields of microbiology and medicine.

Footnotes

  1. 1 Rebecca Buxton. “Examination of Gram Stains of Spinal Fluid—Bacterial Meningitis.” American Society for Microbiology. 2007. http://www.microbelibrary.org/librar...ial-meningitis
  2. 2 P.E. McGovern et al. “Fermented Beverages of Pre- and Proto-Historic China.” Proceedings of the National Academy of Sciences of the United States of America 1 no. 51 (2004):17593–17598. doi:10.1073/pnas.0407921102.
  3. 3 A. Keller et al. “New Insights into the Tyrolean Iceman's Origin and Phenotype as Inferred by Whole-Genome Sequencing.”Nature Communications, 3 (2012): 698. doi:10.1038/ncomms1701.
  4. 4 L. Capasso. “5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.” The Lancet, 352 (1998) 9143: 1864. doi: 10.1016/s0140-6736(05)79939-6.
  5. 5 L. Capasso, L. “5300 Years Ago, the Ice Man Used Natural Laxatives and Antibiotics.” The Lancet, 352 no. 9143 (1998): 1864. doi: 10.1016/s0140-6736(05)79939-6.
  6. 6 G. Pappas et al. “Insights Into Infectious Disease in the Era of Hippocrates.” International Journal of Infectious Diseases 12 (2008) 4:347–350. doi: http://dx.doi.org/10.1016/j.ijid.2007.11.003.
  7. 7 Thucydides. The History of the Peloponnesian War. The Second Book. 431 BC. Translated by Richard Crawley. http://classics.mit.edu/Thucydides/p....2.second.html.
  8. 8 Plinio Prioreschi. A History of Medicine: Roman Medicine. Lewiston, NY: Edwin Mellen Press, 1998: p. 215.
  9. 9 S.M. Blevins and M.S. Bronze. “Robert Koch and the ‘Golden Age’ of Bacteriology.” International Journal of Infectious Diseases. 14 no. 9 (2010): e744-e751. doi:10.1016/j.ijid.2009.12.003.

Glossary

microbe
generally, an organism that is too small to be seen without a microscope; also known as a microorganism
microorganism
generally, an organism that is too small to be seen without a microscope; also known as a microbe

Contributor

  • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at https://openstax.org/books/microbiology/pages/1-introduction)


3.1. You buy things we don’t need because stores know how to use our fears against you.

3.1.1. Fear helped our ancestors with their chances of survival

3.1.1.1. They had to move fast when a threat came along, so now our brains do the same in the right circumstances.

3.1.2. The amygdala is the part of the brain that fear comes from.

3.1.2.1. This survival-driven fear instinct is so powerful that it even has the ability to slow down the rational thinking parts of our brain.

3.1.2.2. Companies know this, and they play on it frequently.

3.1.2.3. One security company aired a commercial that utilized this mechanism perfectly.

3.1.2.3.1. While a mother is making dinner in the kitchen, her children play outside. But the mom doesn’t notice the man who is eerily watching the kids.

3.1.2.3.2. The scare-factor of this ad was enough to make people go out and purchase the company’s security devices.

3.1.2.4. Some businesses use our fears against us by exaggerating how afraid we are of becoming something we don’t want to.

3.1.2.4.1. They can do this by making the issues we have to deal with seem much worse than they actually are.

3.2. Addiction can happen to anyone, and companies know the process well and exploit it to get you to buy.

3.2.1. Many of us can’t live without our phones or favorite foods.

3.2.1.1. This is a classic symptom of an addiction.

3.2.2. One study found out the extent of the effect that young Americans cell phone use has on their brains.

3.2.2.1. When 18-25-year-old’s devices ring, the region of the brain associated with being in love lights up.

3.2.2.2. In other words, you are in love with your phone, and it’s not by chance.

3.2.3. Shopping has these same effects but is also a little more sinister.

3.2.3.1. The high we can get from making purchases releases dopamine, which gives a feeling of well-being.

3.2.3.2. But this urges us to want more, so we spend more. It can be a difficult cycle to break.

3.2.4. Food companies know this effect well

3.2.4.1. That’s why they load their foods with unhealthy fats and sugars.

3.2.4.2. You get the same dopamine rush and next time you come back, you need more to get the same fix, so you buy more.

3.2.5. Research on rats addicted to food and cocaine has some alarming results.

3.2.5.1. In rats hooked on food, the effects of the craving continued seven times longer than the rats with drug addictions

3.2.5.2. Companies know this and will not hesitate to use your body’s ability to get addicted against you

3.3. You make some purchases because of fake peer pressure that vendors create.

3.3.1. It’s human nature that we like to follow what others are doing.

3.3.1.1. Our ancestors survived better in communities, which were easier to get into if you fit in well.

3.3.2. We learn how to use certain items based on what we see others do with them.

3.3.2.1. It’s also hard for us to avoid conforming when everybody else is following a set pattern.

3.3.2.2. We tend to want what we see most people have.

3.3.2.3. Research confirms all three of these truths about peer pressure.

3.3.3. There might be products that you own that you think you just have to have.

3.3.3.1. Without even knowing it you may think you need that iPhone or designer brand handbag because everybody else does.

3.3.3.2. But these fancy items don’t mean that you’re unique or in fashion, it’s you succumbing to businesses taking advantage of your psychology without you knowing it.

3.3.4. Reviews are one of the best tools companies use to fake peer pressure.

3.3.4.1. Have you purchased an item on Amazon that had the most and highest reviews?

3.3.4.1.1. Up to 25% of them are fake!

3.3.5. We also go crazy for items on bestseller lists because we think it means they have value.


Part 1 Outline

  1. The fundamental unity of life
  2. A nested hierarchy of species
  3. Independent determination of the historical phylogeny
    • Statistics of incongruent phylogenies
  4. Intermediate and transitional forms
    • Reptile-birds
    • Reptile-mammals
    • Ape-humans
    • Legged whales
    • Legged seacows
  5. Chronology of common ancestors
  • References

Studying the GCSE Applied Science (Double Award) provides insight into, and experience of how science works whilst stimulating learners' curiosity and encouraging them to develop an understanding of science, its applications and its relationship to the individual and society. It should also prepare candidates to make informed decisions about further study and training opportunities in applied science.

This WJEC GCSE Applied Science (Double Award) specification will enable learners to develop:

  • essential knowledge and understanding of different areas of science and how they relate to each other
  • knowledge and understanding of science and its applications
  • interest in, and enthusiasm for science, including developing an interest in further study and careers associated with science
  • competence and confidence in a variety of practical, mathematical and problem solving skills
  • understanding of the scientific process
  • practical, problem-solving, enquiry and scientific modelling skills and understanding in laboratory, and work-related contexts
  • understanding of the relationships between data, evidence and explanations and their ability to evaluate scientific methods, evidence and conclusions
  • understanding of how society makes decisions about scientific issues
  • communication, mathematical and technological skills in scientific contexts

What students will learn and the weighting of the exam

ENERGY, RESOURCES and the ENVIRONMENT

Written examination:

1 hour 30 minutes

22.5% of qualification

Exam in the summer of Year 10

This unit includes the following topics:

1.1 Energy and life

1.1.1 The cell and respiration

1.1.2 Obtaining the materials for respiration

1.2 Modern living and energy

1.2.1 Underpinning energy concepts

1.2.2 Generating electricity

1.2.4 Building electric circuits

1.3 Obtaining resources from our planet

1.3.1 Obtaining clean water

1.3.3 Producing useful compounds in the laboratory

SPACE, HEALTH and LIFE

Written examination:

1 hour 30 minutes

22.5% of qualification

Exam in the summer of Year 10

This unit includes the following topics:

2.1. Our planet

2.1.1 Our place in the Universe

2.1.3 Transfer and recycling of nutrients

2.2. Protecting our environment

2.3. Health, fitness and sport

2.3.1 Factors affecting human health

2.3.2 Diagnosis and treatment

2.3.4 Exercise and fitness in humans

FOOD, MATERIALS and PROCESSES

Written examination:

1 hour 30 minutes

25% of qualification

Exam in the summer of Year 11

ACTIVITY 1 - Carrying out a practical investigation in an applied scientific

context (45 marks)

Learners will formulate a plan, analyse and evaluate data, under a high level of control. Learners must work individually and no teacher feedback or assistance is

allowed. When obtaining results, learners will be permitted to work in groups of no more than three, under a limited level of control (provided their plans are sufficiently similar). Teacher assistance should not normally be required but may be given if

equipment failure occurs. Activity 1 will be completed in three sessions of 60 minutes duration.

ACTIVITY 2 - Analysis of data in an applied scientific context (15 marks)

Activity 2 will be carried out under a high level of control and will be completed in one

session of 60 minutes duration. Learners must work individually and no teacher feedback or assistance is allowed.

Learners will analyse data which will allow them to develop the skills that enable them to:

  • use mathematical methods to analyse data
  • draw evidence-based conclusions
  • assess the quality of evidence given
  • evaluate methods
  • suggest improvements.

TASK BASED ASSESSMENT

20% of qualification

Exam in the summer of Year 11

The assessment consists of three activities:

ACTIVITY 1 - Carrying out a practical investigation in an applied scientific

context (35 marks)

Learners will formulate a plan, analyse and evaluate data, under a high level of

control. Learners must work individually and no teacher feedback or assistance is

allowed. When obtaining results, learners will be permitted to work in groups of no more than three, under a limited level of control (provided their plans are sufficiently similar). Teacher assistance should not normally be required, but may be given if equipment failure occurs. Activity 1 will be completed in three sessions of 60 minutes duration.

ACTIVITY 2 - Analysis of data in an applied scientific context (15 marks)

This will be carried out under a high level of control and will be completed in one session of 60 minutes duration. Learners must work invididually and no teacher

feedback or assistance is allowed.

Learners will analyse data which will allow them to develop the skills that enable them to:

  • use mathematical methods to analyse data
  • draw evidence-based conclusions
  • assess the quality of evidence given
  • evaluate methods
  • suggest improvements

ACTIVITY 3 - Risk assessment (10 marks)

This will be carried out under a high level of control and will be completed in one session of 60 minutes duration. Learners must work invididually and no teacher

feedback or assistance is allowed.

Learners will assess risks associated with the collection of numerical and other data

and manage risks when using practical techniques, carrying out standard procedures

and solving practical problems. They will develop the skills to enable them to:

  • use chemical 'safety sheets' to identify chemical hazards
  • identify the risks that arise from carrying out procedures
  • suggest control measures to reduce risk
  • carry out risk assessments
  • follow health and safety procedures to manage risk.

PRACTICAL ASSESSMENT

10% of qualification

This assessment will be undertaken between Jan-Feb of Year 11

Each task comprises two sections:

Section A - Obtaining results (6 marks)

Learners will be permitted to work in groups of no more than three, to obtain results from

a given experimental method. This will be carried out under a limited level of control i.e.

learners may work with others to obtain results but they must provide their own

responses to the questions set. Teacher assistance should not normally be required, but

may be given if equipment failure occurs. Section A will be completed in one session of

Section B - Analysing and evaluating results (24 marks)

Learners will be assessed on their ability to analyse and evaluate the data obtained in

section A. They will require access to their section A assessment in order to complete

this. Section B will be carried out under a high level of control i.e. learners must work

individually. This section is to be completed with no teacher feedback or assistance

allowed and under formal supervision. Section B will be completed in one session of 60

In Units 1-3 exams, learners must:

Demonstrate knowledge and understanding of scientific ideas, processes, techniques

Apply knowledge and understanding of scientific ideas, processes, techniques and

Analyse, interpret and evaluate scientific information, ideas and evidence, including

  • make judgements and reach conclusions
  • develop and refine practical design and procedures

The table below shows the weighting of each assessment objective for each unit and

the qualification as a whole.

Key vocabulary:

Essential words for students to be able to explain and use

The document from the link below is essential in allowing pupils access to key terms used in the development and evaluation of specified practicals. It is an invaluable revision resource in preparation for Unit 3 &ndash the practical assessment.

There are many skills listed in the exam syllabus. Please see Appendix A and B of the syllabus for a summary of the mathematical and practical skills required. Use the link below.

Additional Resources

Please use the link below to access

  • a Padlet platform with revision links for each topic
  • exam syllabus
  • WJEC Question Bank link &ndash past paper and mark scheme access
  • Careers in STEM links
  • Revision guide links

Please note &ndash a QR code will be provided in parents evening and in each newsletter. This QR code will provide additional resoucres to aid revision. These resources cannot be linked to this document due to copyright issues as the website is open to the general public.

How parents can help

Provide your child with a scientific calculator

Actively encourage your child to use the resource link above. Familiarise yourselves with what is available in the resource link above and help your child to plan how they will best use the material provided.

Ask your child to show you their GCSE Pod accounts and their school email. This way you will know that he/she is actively using the valuable resources that will help them to revise effectively.

Extra-curricular opportunities & visits

To be announced as and when opportunites arise.

Science Ambassadors represent the department. When positions become available, pupils will be invited to put forward their application.

Science Ambassadors will be trained in the use of Virtual Reality headsets, they will then run a VR after school club for pupils.

A STEM book club runs for Science Ambassadors.

Homework expectations

Homework will be set by individual teachers at a time which best suits the scheme of work. This should be completed to the best of the pupils&rsquo ability.

Applied Science Single Award

Purpose of the course

Studying the GCSE Applied Science (Single Award) to provides insight into, and experience of how science works, whilst stimulating learners' curiosity and encouraging them to develop an understanding of science, its applications and its relationship to the individual and society. This GCSE is not designed to enable progression to level 3 qualifications in Science.

This WJEC GCSE Applied Science (Single Award) specification will enable learners to develop:

  • knowledge and understanding of key areas of science and its application
  • interest in, and enthusiasm for science
  • competence and confidence in a variety of practical, mathematical and problem solving skills
  • understanding of the scientific process
  • practical, problem-solving, enquiry and scientific modelling skills and understanding in laboratory, and work-related contexts
  • understanding of the relationships between data, evidence and explanations and their ability to evaluate scientific methods, evidence and conclusions
  • understanding of how society makes decisions about scientific issues
  • communication, mathematical and technological skills in scientific contexts.

What students will learn and the weighting of the exam

SCIENCE IN THE MODERN WORLD

Written examination: 1 hour 30 minutes

40% of qualification

Exam in the summer of Year 10

This unit includes the following topics:

1.1 Modern living and energy

1.1.1 Underpinning energy concepts

1.1.2 Generating electricity

1.1.4 Building electric circuits

1.2 Obtaining resources from our planet

1.2.1 Obtaining clean water

1.2.3 Producing useful compounds in the laboratory

1.3 Our planet

1.3.1 Our place in the Universe

1.3.3 Transfer and recycling of nutrients

1.4 Protecting our environment

SCIENCE TO SUPPORT OUR LIFESTYLES

Written examination: 1 hour 30 minutes

30% of qualification

Exam in the summer of Year 11

This unit includes the following topics:

2.1 Health, fitness and sport

2.1.1 Factors affecting human health

2.1.2 Diagnosis and treatment

2.1.4 Exercise and fitness in humans

2.2 Controlling processes

2.2.1 Controlling chemical reactions

2.2.2 Controlling nuclear reactions

TASK BASED ASSESSMENT

20% of qualification

Assessment to be undertaken between Nov-Dec of Year 11

ACTIVITY 1 - Carrying out a practical investigation in an applied scientific

context (45 marks)

Learners will formulate a plan, analyse and evaluate data, under a high level of control. Learners must work individually and no teacher feedback or assistance is

allowed. When obtaining results, learners will be permitted to work in groups of no more than three, under a limited level of control (provided their plans are sufficiently similar). Teacher assistance should not normally be required but may be given if

equipment failure occurs. Activity 1 will be completed in three sessions of 60 minutes duration.

ACTIVITY 2 - Analysis of data in an applied scientific context (15 marks)

Activity 2 will be carried out under a high level of control and will be completed in one

session of 60 minutes duration. Learners must work individually and no teacher feedback or assistance is allowed.

Learners will analyse data which will allow them to develop the skills that enable them to:

  • use mathematical methods to analyse data
  • draw evidence-based conclusions
  • assess the quality of evidence given
  • evaluate methods
  • suggest improvements.

PRACTICAL ASSESSMENT

10% of qualification

Assessment to be undertaken between Jan-Feb of Year 11

Section A - Obtaining results (6 marks)

Learners will be permitted to work in groups of no more than three, to obtain results

from a given experimental method. This will be carried out under a limited level of control i.e. learners may work with others to obtain results but they must provide their

own responses to the questions set. Teacher assistance should not normally be required,

but may be given if equipment failure occurs. Section A will be completed in one

session of 60 minutes duration.

Section B - Analysing and evaluating results (24 marks)

Learners will be assessed on their ability to analyse and evaluate the data obtained

in section A. They will require access to their section A assessment in order to

complete this. Section B will be carried out under a high level of control i.e. learners

must work individually. This section is to be completed with no teacher feedback or

assistance allowed and under formal supervision. Section B will be completed in one

session of 60 minutes duration.

In Unit 1 and Unit 2 exams, learners must:

Demonstrate knowledge and understanding of scientific ideas, processes, techniques and procedures

Apply knowledge and understanding of scientific ideas, processes, techniques and procedures

Analyse, interpret and evaluate scientific information, ideas and evidence, including in relation to issues, to:

  • make judgements and reach conclusions
  • develop and refine practical design and procedures

The table below shows the weighting of each assessment objective for each unit and the qualification as a whole.

Key vocabulary:

Essential words for students to be able to explain and use

The document from the link below is essential in allowing pupils access to key terms used in the development and evaluation of specified practicals. It is an invaluable revision resource in preparation for Unit 3 &ndash the practical assessment.

There are many skills listed in the exam syllabus. Please see Appendix A and B of the syllabus for a summary of the mathematical and practical skills required. Use the link below.

Additional Resources

Please use the link below to access

  • a Padlet platform with revision links for each topic
  • exam syllabus
  • WJEC Question Bank link &ndash past paper and mark scheme access
  • Careers in STEM links
  • Revision guide links

Please note &ndash a QR code will be provided in parents evening and in each newsletter. This QR code will provide additional resources to aid revision. These resources cannot be linked to this document due to copyright issues as the website is open to the general public.

How parents can help

  • Provide your child with a scientific calculator
  • Actively encourage your child to use the resource link above. Familiarise yourselves with what is available in the resource link above and help your child to plan how they will best use the material provided.
  • Ask your child to show you their GCSE Pod accounts and their school email. This way you will know that he/she is actively using the valuable resources that will help them to revise effectively.

Extra-curricular opportunities & visits

  • To be announced as and when opportunites arise.
  • Science Ambassadors represent the department. When positions become available, pupils will be invited to put forward their application.
  • Science Ambassadors will be trained in the use of Virtual Reality headsets, they will then run a VR after school club for pupils.
  • A STEM book club runs for Science Ambassadors.

Homework expectations

Homework will be set by individual teachers at a time which best suits the scheme of work. This should be completed to the best of the pupils&rsquo ability.

BTEC Science

Double Award Science

Purpose of the course

WJEC Double Award Science encourages learners to develop confidence in, and a positive attitude towards, science and to recognise its importance in their own lives and to society. Studying GCSE Science (Double Award) provides the foundations for understanding the material world. Scientific understanding is changing our lives and is vital to the world&rsquos future prosperity, and all learners should be taught essential aspects of the knowledge, methods, processes and uses of science. They should be helped to appreciate how the complex and diverse phenomena of the natural world can be described in terms of a small number of key ideas relating to the sciences which are both inter-linked and are of universal application.

  • the use of conceptual models and theories to make sense of the observed diversity of natural phenomena
  • the assumption that every effect has one or more cause
  • that change is driven by differences between different objects and systems when they interact
  • that many such interactions occur over a distance without direct contact
  • that science progresses through a cycle of hypothesis, practical experimentation, observation, theory development and review
  • that quantitative analysis is a central element both of many theories and of scientific methods of inquiry.

Year 10 modules

What students will learn and the weighting of the exam

Written examination: 1 hour 15 minutes

15% of qualification

Exam in the summer of Year 10

This unit includes the following topics:

1.1 Cells and movement across membranes

1.2 Respiration and the respiratory system in humans

1.3 Digestion and the digestive system in humans

1.4 Circulatory system in humans

1.5 Plants and photosynthesis

1.6 Ecosystems and human impact on the environment

CHEMISTRY 1

Written examination: 1 hour 15 minutes

15% of qualification

Exam in the summer of Year 10

This unit includes the following topics:

2.1 The nature of substances and chemical reactions

2.2 Atomic structure and the Periodic Table

2.4 The ever-changing Earth

2.5 Rate of chemical change

Written examination: 1 hour 15 minutes

15% of qualification

Exam in the summer of Year 10

This unit includes the following topics:

3.2 Generating electricity

Year 11 modules

What students will learn and the weighting of the exam

Written examination: 1 hour 15 minutes

15% of qualification

Exam in the summer of Year 11

This unit includes the following topics:

4.1 Classification and biodiversity

4.2 Cell division and stem cells

4.4 Variation and evolution

4.5 Response and regulation

4.6 Disease, defence and treatment

CHEMISTRY 2

Written examination: 1 hour 15 minutes

15% of qualification

Exam in the summer of Year 11

This unit includes the following topics:

5.1 Bonding, structure and properties

5.3 Metals and their extraction

5.4 Chemical reactions and energy

5.5 Crude oil, fuels and carbon compounds

Written examination: 1 hour 15 minutes

15% of qualification

Exam in the summer of Year 11

This unit includes the following topics:

6.1 Distance, speed and acceleration

Unit 7 PRACTICAL ASSESSMENT

2 Practical assessments: 1 hour each. Both followed by a written exam: 1 hour each. 10% of qualification overall

Exam any time from the first week of January to the second week of February in Year 11

This assessment gives learners the opportunity to demonstrate their ability to work scientifically. This will include experimental skills and strategies and skills in analysis and evaluation.

The tasks will be externally marked by WJEC and will change on an annual basis.

Key assessments

In Units 1 and Unit 6 exams, learners must:

Demonstrate knowledge and understanding of scientific ideas, processes, techniques

Apply knowledge and understanding of scientific ideas, processes, techniques and

Analyse, interpret and evaluate scientific information, ideas and evidence, including

  • make judgements and reach conclusions
  • develop and refine practical design and procedures

The table below shows the weighting of each assessment objective for each unit and

the qualification as a whole.

In Unit 7, learners must complete Section A and Section B

Section A - Obtaining results (6 marks)

Learners will be permitted to work in groups of no more than three, to obtain results from a given experimental method. This will be carried out under a limited level of control i.e. learners may work with others to obtain results but they must provide their own responses to the questions set. Teacher assistance should not normally be required, but may be given if equipment failure occurs. Section A will be completed in one session of 60 minutes duration.

Section B - Analysing and evaluating results (24 marks)

Learners will be assessed on their ability to analyse and evaluate the data obtained in

section A. They will require access to their section A assessment in order to complete

this. Section B will be carried out under a high level of control i.e. learners must work

individually. This section is to be completed with no teacher feedback or assistance

allowed and under formal supervision. Section B will be completed in one session of 60 minutes duration.

Key vocabulary:

Essential words for students to be able to explain and use

The document from the link below is essential in allowing pupils access to key terms used in the development and evaluation of specified practicals. It is an invaluable revision resource in preparation for Unit 3 &ndash the practical assessment.

There are many skills listed in the exam syllabus. Please see Appendix A and B of the syllabus for a summary of the mathematical and practical skills required. Use the link below.

Additional Resources

Please use the link below to access

  • a Padlet platform with revision links for each topic
  • exam syllabus
  • WJEC Question Bank link &ndash past paper and mark scheme access
  • Careers in STEM links
  • Revision guide links

Please note &ndash a QR code will be provided in parents evening and in each newsletter. This QR code will provide additional resoucres to aid revision. These resources cannot be linked to this document due to copyright issues as the website is open to the general public.

How parents can help

  • Provide your child with a scientific calculator
  • Actively encourage your child to use the resource link above. Familiarise yourselves with what is available in the resource link above and help your child to plan how they will best use the material provided.
  • Ask your child to show you their GCSE Pod accounts and their school email. This way you will know that he/she is actively using the valuable resources that will help them to revise effectively.

Extra-curricular opportunities & visits

  • To be announced as and when opportunities arise
  • Science Ambassadors represent the department. When positions become available, pupils will be invited to put forward their application
  • Science Ambassadors will be trained in the use of Virtual Reality headsets, they will then run a VR after school club for pupils
  • A STEM book club runs for Science Ambassadors

Homework expectations

Homework will be set by individual teachers at a time which best suits the scheme of work. This should be completed to the best of the pupils&rsquo ability.

Separate Award Science - Biology

Purpose of the course

Studying GCSE Biology provides the foundations for understanding the material world. Scientific understanding is changing our lives and is vital to the world&rsquos future prosperity, and all learners should be taught essential aspects of the knowledge, methods, processes and uses of science. They should be helped to appreciate how the complex and diverse phenomena of the natural world can be described in terms of a small number of key ideas relating to the sciences which are both inter-linked, and are of universal application. These key ideas include:

  • the use of conceptual models and theories to make sense of the observed diversity of natural phenomena
  • the assumption that every effect has one or more cause
  • that change is driven by differences between different objects and systems when they interact
  • that many such interactions occur over a distance without direct contact
  • that science progresses through a cycle of hypothesis, practical experimentation, observation, theory development and review
  • that quantitative analysis is a central element both of many theories and of scientific methods of inquiry.

What students will learn and the weighting of the exam

CELLS, ORGAN SYSTEMS and ECOSYSTEMS

Written examination: 1 hour 45 minutes

45% of qualification

Exams in the summer of Year 10

This unit includes the following topics:

1.1 Cells and movement across membranes

1.2 Respiration and the respiratory system in humans

1.3 Digestion and the digestive system in humans

1.4 Circulatory system in humans

1.5 Plants and photosynthesis

1.6 Ecosystems, nutrient cycles and human impact on the environment

VARIATION, HOMEOSTASIS and MICRO-ORGANISMS

Written examination: 1 hour 45 minutes

45% of qualification

Exams in the summer of Year 11

This unit includes the following topics:

2.1 Classification and biodiversity

2.2 Cell division and stem cells

2.4 Variation and evolution

2.5 Response and regulation

2.6 Kidneys and homeostasis

2.7 Micro-organisms and their applications

2.8 Disease, defence and treatment

PRACTICAL ASSESSMENT

Practical assessment: 1 hour. Written exam: 1 hour. 10% of qualification

Exam any time from the first week of January to the second week of February in Year 11

This assessment gives learners the opportunity to demonstrate their ability to work scientifically. This will include experimental skills and strategies and skills in analysis and evaluation.

The tasks will be externally marked by WJEC and will change on an annual basis.

Key assessments

In Unit 1 and Unit 2 exams, learners must:

Demonstrate knowledge and understanding of scientific ideas, processes, techniques

Apply knowledge and understanding of scientific ideas, processes, techniques and

Analyse, interpret and evaluate scientific information, ideas and evidence, including

· make judgements and reach conclusions

· develop and refine practical design and procedures

The table below shows the weighting of each assessment objective for each unit and

the qualification as a whole.

Section A - Obtaining results (6 marks)

Learners will be permitted to work in groups of no more than three, to obtain results from a given experimental method. This will be carried out under a limited level of control i.e. learners may work with others to obtain results but they must provide their own responses to the questions set. Teacher assistance should not normally be required, but may be given if equipment failure occurs. Section A will be completed in one session of 60 minutes duration.

Section B - Analysing and evaluating results (24 marks)

Learners will be assessed on their ability to analyse and evaluate the data obtained in

section A. They will require access to their section A assessment in order to complete

this. Section B will be carried out under a high level of control i.e. learners must work

individually. This section is to be completed with no teacher feedback or assistance

allowed and under formal supervision. Section B will be completed in one session of 60 minutes duration.

Key vocabulary:

Essential words for students to be able to explain and use

The document from the link below is essential in allowing pupils access to key terms used in the development and evaluation of specified practicals. It is an invaluable revision resource in preparation for Unit 3 &ndash the practical assessment.

There are many skills listed in the exam syllabus. Please see Appendix A and B of the syllabus for a summary of the mathematical and practical skills required. Use the link below.

Additional Resources

Please use the link below to access

  • a Padlet platform with revision links for each topic
  • exam syllabus
  • WJEC Question Bank link &ndash past paper and mark scheme access
  • Careers in STEM links
  • Revision guide links

Please note &ndash a QR code will be provided in parents evening and in each newsletter. This QR code will provide additional resoucres to aid revision. These resources cannot be linked to this document due to copyright issues as the website is open to the general public.

How parents can help

Provide your child with a scientific calculator

Actively encourage your child to use the resource link above. Familiarise yourselves with what is available in the resource link above and help your child to plan how they will best use the material provided.

Ask your child to show you their GCSE Pod accounts and their school email. This way you will know that he/she is actively using the valuable resources that will help them to revise effectively.

Extra-curricular opportunities & visits

To be announced as and when opportunites arise

Science Ambassadors represent the department. When positions become available, pupils will be invited to put forward their application

Science Ambassadors will be trained in the use of Virtual Reality headsets, they will then run a VR after school club for pupils

A STEM book club runs for Science Ambassadors

Homework expectations

Homework will be set by individual teachers at a time which best suits the scheme of work. This should be completed to the best of the pupils&rsquo ability.

Separate Award Science - Chemistry

Purpose of the course

Studying GCSE Chemistry provides the foundations for understanding the material world. Scientific understanding is changing our lives and is vital to the world&rsquos future prosperity, and all learners should be taught essential aspects of the knowledge, methods, processes and uses of science. They should be helped to appreciate how the complex and diverse phenomena of the natural world can be described in terms of a small number of key ideas relating to the sciences which are both inter-linked, and are of universal application.

  • the use of conceptual models and theories to make sense of the observed diversity of natural phenomena
  • the assumption that every effect has one or more cause
  • that change is driven by differences between different objects and systems when they interact
  • that many such interactions occur over a distance without direct contact
  • that science progresses through a cycle of hypothesis, practical experimentation, observation, theory development and review
  • that quantitative analysis is a central element both of many theories and of scientific methods of inquiry.

What students will learn and the weighting of the exam

CHEMICAL SUBSTANCES, REACTIONS and ESSENTIAL RESOURCES

Written examination: 1 hour 45 minutes. 45% of overall qualification

Exams in the summer of Year 10

This unit includes the following topics:

1.1 The nature of substances and chemical reactions

1.2 Atomic structure and the Periodic Table

1.4 The ever-changing Earth

1.5 Rate of chemical change

CHEMICAL BONDING, APPLICATION OF CHEMICAL REACTIONS and

ORGANIC CHEMISTRY

Written examination: 1 hour 45 minutes. 45% of qualification

Exams in the summer of Year 11

This unit includes the following topics:

2.1 Bonding, structure and properties

2.3 Metals and their extraction

2.4 Chemical reactions and energy

2.5 Crude oil, fuels and organic chemistry

2.6 Reversible reactions, industrial processes and important chemicals

PRACTICAL ASSESSMENT

Practical assessment: 1 hour. Written exam: 1 hour. 10% of qualification

Exam any time from the first week of January to the second week of February in Year 11

This assessment gives learners the opportunity to demonstrate their ability to work scientifically. This will include experimental skills and strategies and skills in analysis and evaluation.

The tasks will be externally marked by WJEC and will change on an annual basis.

Key assessments

In Unit 1 and Unit 2 exams, learners must:

Demonstrate knowledge and understanding of scientific ideas, processes, techniques

Apply knowledge and understanding of scientific ideas, processes, techniques and

Analyse, interpret and evaluate scientific information, ideas and evidence, including

  • make judgements and reach conclusions
  • develop and refine practical design and procedures

The table below shows the weighting of each assessment objective for each unit and

the qualification as a whole.

Section A - Obtaining results (6 marks)

Learners will be permitted to work in groups of no more than three, to obtain results from a given experimental method. This will be carried out under a limited level of control i.e. learners may work with others to obtain results but they must provide their own responses to the questions set. Teacher assistance should not normally be required, but may be given if equipment failure occurs. Section A will be completed in one session of 60 minutes duration.

Section B - Analysing and evaluating results (24 marks)

Learners will be assessed on their ability to analyse and evaluate the data obtained in

section A. They will require access to their section A assessment in order to complete

this. Section B will be carried out under a high level of control i.e. learners must work

individually. This section is to be completed with no teacher feedback or assistance

allowed and under formal supervision. Section B will be completed in one session of 60 minutes duration.

Key vocabulary:

Essential words for students to be able to explain and use

The document from the link below is essential in allowing pupils access to key terms used in the development and evaluation of specified practicals. It is an invaluable revision resource in preparation for Unit 3 &ndash the practical assessment.

There are many skills listed in the exam syllabus. Please see Appendix A and B of the syllabus for a summary of the mathematical and practical skills required. Use the link below.

Additional Resources

Please use the link below to access

  • a Padlet platform with revision links for each topic
  • exam syllabus
  • WJEC Question Bank link &ndash past paper and mark scheme access
  • Careers in STEM links
  • Revision guide links

Please note &ndash a QR code will be provided in parents evening and in each newsletter. This QR code will provide additional resoucres to aid revision. These resources cannot be linked to this document due to copyright issues as the website is open to the general public.

How parents can help

  • Provide your child with a scientific calculator
  • Actively encourage your child to use the resource link above. Familiarise yourselves with what is available in the resource link above and help your child to plan how they will best use the material provided.
  • Ask your child to show you their GCSE Pod accounts and their school email. This way you will know that he/she is actively using the valuable resources that will help them to revise effectively.

Extra-curricular opportunities & visits

  • To be announced as and when opportunites arise
  • Science Ambassadors represent the department. When positions become available, pupils will be invited to put forward their application
  • Science Ambassadors will be trained in the use of Virtual Reality headsets, they will then run a VR after school club for pupils
  • A STEM book club runs for Science Ambassadors

Homework expectations

Homework will be set by individual teachers at a time which best suits the scheme of work. This should be completed to the best of the pupils&rsquo ability.

Separate Award Science - Physics

Purpose of the course

Studying GCSE Physics provides the foundations for understanding the material world. Scientific understanding is changing our lives and is vital to the world&rsquos future prosperity, and all learners should be taught essential aspects of the knowledge, methods, processes and uses of science. They should be helped to appreciate how the complex and diverse phenomena of the natural world can be described in terms of a small number of key ideas relating to the sciences which are both inter-linked, and are of universal application. These key ideas include:

  • the use of conceptual models and theories to make sense of the observed diversity of natural phenomena
  • the assumption that every effect has one or more cause
  • that change is driven by differences between different objects and systems when they interact
  • that many such interactions occur over a distance without direct contact
  • that science progresses through a cycle of hypothesis, practical experimentation, observation, theory development and review
  • that quantitative analysis is a central element both of many theories and of scientific methods of inquiry.

What students will learn and the weighting of the exam

ELECTRICITY, ENERGY and WAVES

Written examination: 1 hour 45 minutes

45% of qualification

Exams in the summer of Year 10

This unit includes the following topics:

1.2 Generating electricity

1.6 The total internal reflection of waves

FORCES, SPACE and RADIOACTIVITY

Written examination: 1 hour 45 minutes

45% of qualification

Exams in the summer of Year 11

This unit includes the following topics:

2.1 Distance, speed and acceleration

2.4 Further motion concepts

2.9 Nuclear decay and nuclear energy

PRACTICAL ASSESSMENT

Practical assessment: 1 hour. Written exam: 1 hour. 10% of qualification

Exam any time from the first week of January to the second week of February in Year 11

This assessment gives learners the opportunity to demonstrate their ability to work scientifically. This will include experimental skills and strategies and skills in analysis and evaluation.

The tasks will be externally marked by WJEC and will change on an annual basis.

Key assessments

In Unit 1 and Unit 2 exams, learners must:

Demonstrate knowledge and understanding of scientific ideas, processes, techniques

Apply knowledge and understanding of scientific ideas, processes, techniques and

Analyse, interpret and evaluate scientific information, ideas and evidence, including

· make judgements and reach conclusions

· develop and refine practical design and procedures

The table below shows the weighting of each assessment objective for each unit and

the qualification as a whole.

Section A - Obtaining results (6 marks)

Learners will be permitted to work in groups of no more than three, to obtain results from a given experimental method. This will be carried out under a limited level of control i.e. learners may work with others to obtain results but they must provide their own responses to the questions set. Teacher assistance should not normally be required, but may be given if equipment failure occurs. Section A will be completed in one session of 60 minutes duration.

Section B - Analysing and evaluating results (24 marks)

Learners will be assessed on their ability to analyse and evaluate the data obtained in

section A. They will require access to their section A assessment in order to complete

this. Section B will be carried out under a high level of control i.e. learners must work

individually. This section is to be completed with no teacher feedback or assistance

allowed and under formal supervision. Section B will be completed in one session of 60 minutes duration.

Key vocabulary:

Essential words for students to be able to explain and use

The document from the link below is essential in allowing pupils access to key terms used in the development and evaluation of specified practicals. It is an invaluable revision resource in preparation for Unit 3 &ndash the practical assessment.

There are many skills listed in the exam syllabus. Please see Appendix A and B of the syllabus for a summary of the mathematical and practical skills required. Use the link below.

Additional Resources

Please use the link below to access

· a Padlet platform with revision links for each topic

· WJEC Question Bank link &ndash past paper and mark scheme access

Please note &ndash a QR code will be provided in parents evening and in each newsletter. This QR code will provide additional resoucres to aid revision. These resources cannot be linked to this document due to copyright issues as the website is open to the general public.

How parents can help

Provide your child with a scientific calculator

Actively encourage your child to use the resource link above. Familiarise yourselves with what is available in the resource link above and help your child to plan how they will best use the material provided.

Ask your child to show you their GCSE Pod accounts and their school email. This way you will know that he/she is actively using the valuable resources that will help them to revise effectively.

Extra-curricular opportunities & visits

To be announced as and when opportunites arise

Science Ambassadors represent the department. When positions become available, pupils will be invited to put forward their application

Science Ambassadors will be trained in the use of Virtual Reality headsets, they will then run a VR after school club for pupils

A STEM book club runs for Science Ambassadors

Homework expectations

Homework will be set by individual teachers at a time which best suits the scheme of work. This should be completed to the best of the pupils&rsquo ability.


Friday, February 1, 2013

A comment on the distribution of residuals (and data) for phylogenetic ANOVA

I get inquiries (with some regularity) about "testing for normality in phylogenetic (i.e., species) data" before phylogenetic regression or ANOVA or about "satisfying the assumptions of parametric tests," by which is usually meant the assumption of normality.

I could probably write a whole paper about this (à la Revell 2009 or Revell 2010), but instead I'll make the simple point: we do not expect normality of the dependent (or independent, for continuous x) variables in phylogenetic data. Instead, what we do expect is multivariate normality of the residual error in y given X (or, equivalently, normality of y given X, controlling for the tree). This is actually a generally under-appreciated property of non-phylogenetic parametric statistical tests - but it is one that is entirely logical. Think: do we expect normality of human height, say, in order to fit an ANOVA model in which height depends on sex? Of course not, the response variable (height) is bimodal. ANOVA is appropriate to test for an effect of sex on height so long as the residual error in height controlling for sex is normal (and, like many such tests, may be fairly robust to mild violations of this assumption). Phylogenetic data are just a little more complicated because even after controlling for our main effects, the residual error can still be bi- or multi-modal due to phylogenetic correlations.

We can still test the parametric assumptions of our model - and I applaud those inclined to do so, as this is relatively seldom done in comparative studies. In the example below, I will first simulate data under the assumptions of the generalized phylogenetic ANCOVA test normality of the response variable, y (it should fail) and my continuous covariate, x2 (it should fail) fit the phylogenetic ANCOVA model anyway, and then test normality of the residuals (these should fail, because the residuals are phylogenetically autocorrelated, see Revell 2009) mathematically "remove" the phylogeny, following Butler et al. (2000), and test for normality again (this time, it should pass). For normality testing, I'm using the Lilliefors (Kolmogorov-Smirnov) test, implemented in the R package nortest. A significant result means the data are not normally distributed.

This is the distribution of our effect on the tree.

> # now simulate data under an arbitrary ANCOVA model
> # the same principle applies to regression or ANOVA
> x1 x2 e y # is y normal? (should fail)
> lillie.test(y)

Lilliefors (Kolmogorov-Smirnov) normality test

data: y
D = 0.1049, p-value = 0.00149

> # is x2 normal? (should fail)
> lillie.test(x2)

Lilliefors (Kolmogorov-Smirnov) normality test

data: x2
D = 0.1113, p-value = 0.0005154

> # fit the model
> fit fit
Generalized least squares fit by REML
Model: y

x1 + x2
Data: data.frame(x1, x2, y)
Log-restricted-likelihood: 40.7237

Coefficients:
(Intercept) x11 x12 x2
1.7388578 1.8929459 3.9681291 0.8418073

Correlation Structure: corBrownian
Formula:

1
Parameter estimate(s):
numeric(0)
Degrees of freedom: 128 total 124 residual
Residual standard error: 0.9261019
> # are the residuals normal? (should fail)
> lillie.test(residuals(fit))

Lilliefors (Kolmogorov-Smirnov) normality test

data: residuals(fit)
D = 0.1156, p-value = 0.0002458

> # are the residuals controlling for phylogeny normal?
> # (should pass)
> lillie.test(chol(solve(vcv(tree)))%*%residuals(fit))

Lilliefors (Kolmogorov-Smirnov) normality test

data: chol(solve(vcv(tree))) %*% residuals(fit)
D = 0.0694, p-value = 0.1371