Author Archives: brittgow

About brittgow

Science and maths teacher at a small, rural school in Victoria, Australia. One husband, two children and three dogs on a sheep and cattle farm. Interests are: Education for Sustainability, web 2.0, beautiful gardens and good food.

Genetically Modified Organisms

Our last Area of Study in Unit 4 Biology is: 

“How do Humans impact on biological processes?”

Key knowledge: 

DNA manipulation:
• the use of enzymes including endonucleases (restriction enzymes), ligases and polymerases
• amplification of DNA using the polymerase chain reaction
• the use of gel electrophoresis in sorting DNA fragments, including interpretation of gel runs
• the use of recombinant plasmids as vectors to transform bacterial cells.

Biological knowledge and society:
• techniques that apply DNA knowledge (specifically gene cloning, genetic screening and DNA profiling) including social and ethical implications and issues
• the distinction between genetically modified and transgenic organisms, their use in agriculture to increase crop productivity and to provide resistance to insect predation and/or disease, and the biological, social and ethical implications that are raised by their use
• strategies that deal with the emergence of new diseases in a globally connected world, including the distinction between epidemics and pandemics, the use of scientific knowledge to identify the pathogen, and the types of treatments
• the concept of rational drug design in terms of the complementary nature (shape and charge) of small molecules that are designed to bind tightly to target biomolecules (limited to enzymes) resulting in the enzyme’s inhibition and giving rise to a consequential therapeutic benefit, illustrated by the Australian development of the antiviral drug Relenza as a neuraminidase inhibitor
• the use of chemical agents against pathogens including the distinction between antibiotics and antiviral drugs with reference to their mode of action and biological effectiveness.

Genetically modified organisms – 

Insect resistant (‘Bt’) cotton

Insect resistant (‘Bt’) corn

Herbicide tolerant (‘Roundup ready’) canola

Iron-fortified wheat

Golden rice

Drought-tolerant wheat

‘Round up’ resistant soy beans

Chapter 13 – DNA tools and techniques

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Genetic tools (Restriction enzymes, ligases and DNA probes and primers): These tools are used as genetic scissors (restriction enzymes), genetic glue (ligases – to stick DNA fragments together) and genetic markers (probes that recognise and attach to specific sequences of DNA with a fluorescent or radioactive marker) Gene Technology video (1 of 6)  (YouTube, 9.05min)

DNA amplification: Using a Polymerase Chain Reaction (PCR) researchers can create many copies of DNA in a test tube. Access the Image Source link for a self-paced Virtual Laboratory activity that demonstrates the process of PCR using animations. Gene Technology video (2 of 6)  (YouTube, 9.54min)

Gel Electrophoresis: This technique is used to separate fragments of DNA according to their size – longer fragments with a large number of base pairs travel more slowly through the substrate (agarose gel), while shorter fragments with a smaller number of base pairs travel a greater distance. A buffer solution is added to the apparatus and DNA fragments are ‘cut’ at specific sites using restriction enzymes and loaded, together with a fluorescent dye, in ‘wells’ at the negative end of the apparatus.  An electric charge is applied and the negatively charged DNA fragments are attracted to the positive end of the gel matrix. Gel Electrophoresis on YouTube. and Gene technology (3 of 6) (YouTube, 9.41min)

DNA recombination: Scientists are able to insert fragments of DNA from one organism into another organism, bringing together genetic material from various sources. Recombinant DNA produces genetically modified organisms, that may add desirable characteristics to food crops, for example

DNA sequencing: DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. DNA Sequencing on YouTube.  and Gene technology (4 of 6) (YouTube, 9.59min) and Gene Technology (5 of 6) (YouTube, 6.53)

DNA profiling: Also called DNA fingerprinting, this technique compares DNA from victims, suspects and crime scenes to determine which samples have the most in common. How does DNA fingerprinting work from the Naked Science Scrapbook (YouTube). 

Gene cloning: Molecular cloning is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms. Gene cloning in plain English on YouTube. 

Genetic screening: Used to identify  genetic disorders or potential risk of disease. For example, when a family has a history of females suffering from breast cancer, a genetic screening test can identify the presence or absence of a particular gene that indicates susceptibility to this cancer. Pro-active treatment may include removal of the breasts to prevent the disease. 

Genetically Modified Organisms (GMO) and transgenic organisms: When genetic engineering is used to insert specific sequences of DNA into host organisms.

Gene transformation: “In molecular biology, transformation is the genetic alteration of a cell resulting from the direct uptake, incorporation and expression of exogenous genetic material (exogenous DNA) from its surrounding and taken up through the cell membrane.” Bacterial transformation by zabaaz on YouTube.

Hominoids, hominids and homonins – what’s the difference?

 

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Primates: (Order Primate) includes all species with prehensile (grasping digits) with opposable thumbs. They also have forward facing eyes with binocular vision, a well-developed cerebral cortex and bicuspid teeth. This includes all the new world monkeys (such as spider monkeys) and old world monkeys (macaques), as well as the Greater and Lesser apes.

Hominoids: refers to the broad term for great and lesser apes which includes gibbons, orangutans, gorillas, chimpanzees and humans. They have no tail, an upright gait and arms shorter than their legs.

Hominids: includes just the great apes, orangutans, gorillas, chimpanzees and humans

Hominins: Refers to the bipedal human species and their relatives.  such as the following:

  • Sahelanthropus tchadensis (Tournai) – mix of human and chimp features, small brain, may have been bipedal (6.5 mya)
  • Ardipithecus ramidus – Primitive teeth, probably bipedal (4.5mya)
  • Australopithecus afarensis (Lucy) – Walked upright, about 1.2m – 1.4m tall , basic stone tools (3.5mya)
  • Homo habilis (Handy man) – More advanced stone tool making and use, brain size half of modern humans (2 mya)
  • Homo ergaster – Small face and teeth, advanced tool use and may have used fire (2.5mya)
  • Homo erectus (Java man) – Modern features, but with a visible brow ridge, brain size 60-70% of modern humans (1 mya)
  • Homo heidelbergensis – Found in Europe, brain size very similar to modern humans, advanced tool use (1 mya)
  • Homo neanderthalensis – Stocky, adapted to cold, tool use, social structures, rudimentary language possible, brain size slightly larger than modern humans. (500, 000 ya)
  • Homo floresiensis (the hobbit) is known from fossils discovered in Indonesia and co-existed with Homo sapiens. (17,000 – 95,000 ya)
  • Homo sapiens (including the sub-species Denisovans) (present day)

The Australian Museum has some good information about how the definitions for these terms have changed over time, causing lots of confusion for students and scientists alike. New technologies, such as CT scans and DNA analysis, have given us new evidence to support different theories of human evolution than from fossil morphology alone.

The Science of Human Evolution (YouTube, 54.42min) is an interesting video that describes the features of various human ancestors, based on their fossil remains.

Evolution from Ape to Man (YouTube, 50.43min) is another video that describes how the search for the “missing link” in human evolution was based on flawed thinking and how scientists have changed their theories depending on the evidence that becomes available.

Human face evolution in the last 600 million years (YouTube, 1.07min) shows an animated progression of facial features from our distant ancestors to the modern human face we recognize today.

Great Human Odyssey (YouTube, 1hr 52.06min) describes how human ancestors migrated out of Africa and developed skills, technology and talent to survive in almost every environment across the globe.

Modern humans may have interbred with Neanderthals and Denisovans (YouTube, 10.54min) – an excellent segment from Catalyst on ABC with the evidence that modern humans have DNA in common with neanderthals and Denisovans indicating that modern humans may have interbred with these species.

Determining relatedness between species

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Unfortunately I will be unable to take some classes this week, due to commitments inside and out of the school. During Period 5 on Tuesday I would like you to continue with reading and answering the review questions for Chapter 11. Please make sure you understand all the key terms and definitions for this chapter by studying the Quizlet for this Chapter 11 – Determining relatedness between species. The chapter review questions for Chapter 11 are due by Friday 18th August.

The following two weeks we will be working on Chapter 12 – Human change over time (due Friday 1st September). The Quizlet for Chapter 12 -Human change over time needs to be completed.  We will also start studying for the next SAC (Wednesday 6th September) which is a written report assessing the following outcome:

Outcome 1: Analyse evidence for evolutionary change, explain how relatedness between species is determined, and elaborate on the consequences of biological change in human evolution.

Assessment: A report using primary or secondary data. The assessment task may be written or multi-modal. (approximately 50 minutes or not exceeding 1000 words)

You will be using resources from the Australian Museum – Human Evolution website, including the virtual skulls of various  hominoids (all primates), hominids (great apes) and hominims (humans and their ancestors). 

Mutations and Population genetics

We have started Unit 4 by looking at a broad overview of the process of evolution over time – how the fossil record shows that species have changed over time. Embryology and comparative anatomy also provides evidence for evolutionary change. But what are the mechanisms that cause this change? The fundamental unit of phenotypical change is the gene, so in this part of the course we will investigate change at the genetic level.

In this section of Unit 4: Area of Study 1 we will learn about the following:

Population genetics is the study of distributions and changes in allele frequency in a population, as the population is subject to the four main evolutionary processes:

  • Natural selection
  • Genetic Drift
  • Mutation
  • Gene flow (by migration or distribution of pollen and seeds)

Variation between individuals and species and polymorphism: In any normal population there is some variation between individuals – a box of apples may have individual apples that are slightly different sizes and shapes with slightly different colour variations, even when they come from the same tree. So, not all variation is caused by genetic differences. It may be environmental differences that result in the variation – for example, the amount of light, temperature or soil nutrients in the case of plants or the nutrition and experiences provided to animals. Some characteristics , such as height or wing length might show continuous variation, while other characteristics can be clearly separated into different categories (discontinuous variation). An example of discontinuous variation in humans might be the ability to roll one’s tongue – you can either do this or you can’t – there is no blending, or in-between characteristic. Polymorphism occurs when two or more clearly defined phenotypes are present in the population. A classic example is the light and dark coloured morphs of the peppered moth. The ABO blood grouping is an example in human populations.

Inherited variations: We know that the DNA molecule, present in every cell of living organisms, codes for proteins that determine the phenotype of an organism. DNA is passed from one generation to the next through reproduction, which can occur asexually or sexually (with the production of gametes (meiosis) and fusion of sperm and egg). So, families of individuals tend to look more alike than non-related individuals due to these inherited characteristics. This was seen in our work with pedigree trees, showing how genetic diseases can be passed on through several generations.

Mutations – sources of variation: The source of these variations is genetic mutations. Genetic mutations may be spontaneous or may be induced by exposure to mutagenic agents (X-rays and Gamma rays and some chemicals, such as benzene and mustard gas).

Gene pool, gene flow, genetic drift (by chance): The gene pool is the set of all genetic information in a population, while gene flow describes how genes leave and arrive in a population by death and emigration or births and immigration. Genetic drift is the change of gene frequencies due to random sampling.

Polygenes, polygenetic traits: Polygenes are non-allelic genes that together influence a phenotypic trait – often the precise loci of these genes is unknown to biologists. Examples of polygenetic traits in humans are height, weight and skin colour.

Mitochodrial DNA: Mitochondrial DNA is a single, circular strand of DNA found in the mitochondria of eukaryotic cells. In most species, mitochondrial DNA is inherited solely form the mother. In humans, mitochondrial DNA was the first significant part of the human genome to be sequenced.

Founder and bottleneck effects:The founder effect is the lost of genetic variation that occurs when a new population is established by a small group of individuals from a larger population. The people of Easter Island and Pitcairn Island show limited genetic variability (small gene pools) due to this effect. A similar effect is the bottleneck effect, when large numbers of a population are removed, leaving a small gene pool.  As a species, cheetahs have famously low levels of genetic variation. In fact, cheetahs are so closely related to each other that transplanted skin grafts do not evoke an immune response. This can probably be attributed to a population bottleneck they experienced around 10,000 years ago, barely avoiding extinction at the end of the last ice age. However, the situation has worsened in modern times. Habitat encroachment and poaching have further reduce cheetah numbers, consequently snuffing out even more genetic variation and leaving cheetahs even more vulnerable to extinction.

 

Changes in the genetic make-up of a population

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Good introduction from BBC Earth: How do we know evolution is real?

Evidence for evolution:

Tree of Life Resources:

YouTube Videos:

 

Unit 4: How does life change and respond to challenges over time?

 

Area of Study 1: How are species related? 

Outcome 1: “On completion of this unit the student should be able to (1) analyse evidence for evolutionary change, (2) explain how relatedness between species is determined, and (3) elaborate on the consequences of biological change in human evolution.”

Evidence for evolutionary change is abundant in the fossil record, biogeography (distribution of species across the earth), developmental biology and structural morphology. This area of study will allow us to investigate these four types of evidence.

Paleontologists have unearthed a wide range of evidence that provides a record of the change in the number of different species and the particular characteristics of those species over time. The fossil record demonstrates that living organisms first evolved in aquatic environments and gradually moved onto land. After plants had successfully colonized terrestrial habitats and converted a percentage of carbon dioxide into oxygen, animals were able to survive out of the oceans and freshwater environments. Evidence for these changes lies in the relative ages and absolute dating of fossils in different parts of the world.

Other evidence is provided by the similarities between living species – homologous structures in vertebrates, for example – and the similarities in developmental biology among different species. These similarities suggest that living organisms descended from a common ancestor and that species that are more closely related in the family tree have a more recent common ancestor. This evidence is supported by genetic research which confirms evolutionary relationships between species.

 

The Immune System – Like fighting invaders on the Great Wall

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First line of defence (innate immunity): This is like a moat and castle walls, preventing invasion by foreigners. There are physical and chemical barriers to infection.

Second line of defence (innate immunity): If the foreign materials breach the first line of defence, an infection forms. This is the inflammation (heated battle) where invaders are being killed indiscriminately.

Third line of defence (active immunmity) : The last line of defence is the active, specific response by trained killer cells (ninjas!) that recognise their targets and actively seek them out and destroy them. They may be proteins or pathogens that have taken over the reproductive capacity of the cell (prions and viruses, for example), so the infected cell must be destroyed.