9.2 Transport in the Phloem

Developments in scientific research follow improvements in apparatus—experimental methods for measuring phloem transport rates using aphid stylets and radioactively-labelled carbon dioxide were only possible when radioisotopes became available.

This NOS is another example that fits nicely into the syllabus content.  In 9.2, students are asked to analyse …data from experiments measuring phloem transport rates using aphid stylets and radioactively-labelled carbon dioxide. We can learn about this process through the NOS to understand how it works and why it enables us to understand the flow of sap through the phloem.  Two for the price of one!

Radioisotopes have been encountered before in your IB Biology studies. They become widely available to researchers after the second world war.  As the molecules that are radioactive can be traced, it became possible to track the flow of these molecules through cells, tissues and organisms over time.

Phloem transport is based on high hydrostatic pressure.  Thus if the phloem can be punctured, the contents should continue to exude out. If the plant is exposed to radioactively labelled carbon dioxide, the sap can be tested for the presence of the isotopes and the rate of translocation can then be estimated.

Image from D. Fischer, Plants in Action.

The use of the aphids can be summarised as follows (base on the images above; Plants in Action; image D. Fischer):

Top Image: Aphid feeding, inset is the stylet (St) penetrating to the phloem (p)
Image a: feeding aphid with stylet penetrating the plant
Images b-d: the stylet is removed from the aphid (they would be anaesthetised beforehand – there are some links here to the use of animals in experiments)
Image e: phloem sap starts to accumulate from the stylet.

The droplet of phloem sap can then be analysed for traces of the isotope to determine transport rate.  Aphids can be placed along the length of the plant stem to show transport along various distances.

Sources:

Fischer, D. “Collection of Sap from Aphid Stylet.” Plants in Action, University of Queensland, 2018, plantsinaction.science.uq.edu.au/content/522-techniques-collect-phloem-sap. Digital image. Feb 1, 2018.

“5.2.2 – Techniques to Collect Phloem Sap.” Plants in Action, Australian Society of Plant Scientists, 2018, plantsinaction.science.uq.edu.au/content/522-techniques-collect-phloem-sap. Online Textbook. Feb 1, 2018.

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11.2 Movement

Developments in scientific research follow improvements in apparatus—fluorescent calcium ions have been used to study the cyclic interactions in muscle contraction

 In a review article of the use of Calcium imaging in physiology studies, Russell notes that calcium ions are:

“…an ubiquitous intracellular messenger that regulates multiple cellular functions such as secretion, contraction, cellular excitability and gene expression in all organ systems.” (Russell, 1605)

We have encountered them in detail in looking at synapses and muscle contraction in animals and also their role in the formation of the cell wall in plants.  Clearly calcium is an important element whose roles range wider than just making healthy bones and teeth!

Advances in technology enable us to collect data that is otherwise outside the the abilities of human perception; this provides the evidence to develop theories.  In 1962 it was reported that scientists had extracted a Ca²⁺-sensitive bioluminescent protein from the jellyfish, Aequoria victoria.  and gave it the name “aequorin”. Aequorin emits light when it reacts with calcium and this can be detected experimentally by illumination with different types of radiation. In many cases, a light microscope can be used to view it and it can be photographed or filmed as well.

Aquorea victoria (Sierra Blakely)

In topic 11.2 we learn about the role of calcium from the sarcoplasmic reticulum binding to troponin and thus triggering the contractile cycle of actin and myosin.  A recent study (Desai et al.) used calcium fluorescence to tag individual molecules of myosin in order to image how single filaments of myosin interact with ATP and Calcium to activate the actin.  The team were able to determine that two myosin heads are needed to activate the actin filament and that 11 Myosins bind as part of a regulatory unit.

As technology advances, our understanding of biological processes grows deeper and more complex. This in turn either provides additional evidence in support of existing theories or may suggest alternative explanations.  And so science moves on….

Sources:

Allott, Andrew, and David Mindorff. Biology: Course Companion. Oxford, Oxford University Press, 2014.

Blakely, Sierra. “ Aequorea Victoria .” Aequorea Victoria , Wikipedia, 17 Feb. 2017, en.wikipedia.org/wiki/Aequorea_victoria. Accessed 20 Apr. 2017.

Desai, Rama, Michael A. Geeves, and Neil M. Kad. “Using Fluorescent Myosin to Directly Visualize Cooperative Activation of Thin Filaments.” The Journal of Biological Chemistry 290.4 (2015): 1915–1925. PMC. Web. 20 Apr. 2017.

Russell, James T. “Imaging Calcium Signals in Vivo: a Powerful Tool in Physiology and Pharmacology.” British Journal of Pharmacology, vol. 163, no. 8, 2011, pp. 1605–1625., doi:10.1111/j.1476-5381.2010.00988.x.

Zimmer, Marc. “Green Fluorescent Protein.” Green Fluorescent Protein – The GFP Site, Connecticut College, 18 Aug. 2015, http://www.conncoll.edu/ccacad/zimmer/GFP-ww/GFP-1.htm. Accessed 20 Apr. 2017.

2.2 Water

Use theories to explain natural phenomena—the theory that hydrogen bonds form between water molecules explains the properties of water.

Theories in biology are explanations for how the natural word works. They can be broad statements that incorporate facts and laws and must be testable through experimentation or observation.  In our everyday conversation we may use theory as a synonym for “educated guess” but in the scientific context theories are far more rigorous and comprehensive.

Consider these observations of water in the lab (you may well have done all of these at some point!):

1. We can use a pipette to pile drops of water onto a coin.  The water does not spill off immediately but piles higher and higher.
2. With great care, we can float a paper clip on top of a glass of water. Adding a drop of detergent causes the paperclip to immediately sink.
3. If we heat and cool samples of ethanol and water, the water heats up more slowly, boils at a higher temperature and cools down more slowly than the ethanol.

Water drops on a penny (Purvis)

Paperclip on water (Villaneuva)

 

Observations in the natural world, such as insects that seem to walk across water or the absorption of water by a plant add to the idea that water appears to be a rather unusual liquid and must have particular properties in order to explain these features.

Based on our observations and experiments, we need to review other scientific theories and ideas to help develop a theory – in this case, atomic theory and the properties and behaviour of electrons.  This then develops into a coherent theory explaining our observations and results as a consequence of hydrogen bonding that takes place between water molecules.

The red lines show the attraction between the electron-rich Oxygen atom and the electron-poor Hydrogen atom (Gould)

We cannot “see” a hydrogen bond and cannot prove absolutely that they exist.  However, the theory of hydrogen bonds and how they function explains all of the above observations and more about the properties of water and has withstood experimental and observational testing.  We can accept this (or any) theory as correct if there is evidence for it, if it has predictive power, if it has not yet been falsified, and if it explains natural processes.

 

Sources

Allott, Andrew, and David Mindorff. Biology: Course Companion. Oxford, Oxford University Press, 2014.

Gould, S.E. “Hydrogen Bonds: Why Life Needs Water.” Scientific American Blog Network, Scientific American, 6 Aug. 2013, blogs.scientificamerican.com/lab-rat/httpblogsscientificamericancomlab-rat20110802hydrogen-bonds-why-life-needs-water/. Accessed 20 Apr. 2017.

Purvis, David. “Water Drops on a Penny.” Dr. Dave’s Science, 2015, drdavesscience.com/free-science-activities/. Accessed 20 Apr. 2017.

VILLANUEVA, A. “Floating Paperclip on Water.” Understanding Biology, Blogspot, 27 Jan. 2010, understanding-biology.blogspot.com/2010/01/floating-paper-clip-cohesion-surface.html. Accessed 20 Apr. 2017.

 

1.2 Ultrastructure of Cells

Developments in scientific research follow improvements in apparatus—the invention of electron microscopes led to greater understanding of cell structure.

Although lenses had been used for magnification earlier, it was Anton van Leeuwenhoek, a Dutch draper of the 17th-century, who developed the first true microscope in his workshop in Delft. Cunningly arranged from lenses he polished and ground himself, he was able to view objects at up to 270x magnification and became the first person to observe and describe bacteria, yeast and the microorganisms in water, amongst others.

Anton van Leeuwenhoek’s microscope. The specimen was placed on the spike and the screw was turned to focus. (History of the Microscope)

Microscope design continued slowly but was radically improved by the discovery in the 1860s by Ernst Abbe of the Abbe sine condition. This is necessary in order for a lens to focus on and produce a very clear sharp image. One of Abbe’s sketches below shows a compound microscope not very different to those we use in the lab today.

The Abbe refractometer (Paselk)

After WW1 the demand for laboratory work led to an explosion in the production of microscopes and they became indispensable  to the modern lab.  However, as Abbe himself noted, the theoretical resolution of a light microscope is limited to 200nm, owing to the distance of wavelengths of light.  The usual assumptions is a wavelength size of 550nm (now where have we seen that before?!) Thus even with the improvements made in lens quality and construction, a light microscope will always be limited to that resolution and a maximum magnification of somewhere around 1000-2000 times, under the very best circumstances. In order to improve this, an illumination source that could overcome this limitation had to be sourced.

This was overcome in 1931 by Max Knoll and Ernst Ruska at the Berlin Technische Hochschule by using a beam of electrons. By the end of the decade, a resolution of 10nm had been achieved and by 1944, 2nm. This brought closer the goal of atomic resolution. Further developments included the Scanning Electron Microscope (1965) which allowed for precise three-dimensional images and opened up yet further possibilities for research.

With such high resolution, it was now possible to explore a whole new world at the cellular and molecular level, allowing research into some of the very fundamental processes of living organisms. As we have seen before, developments in technology can drive scientific research forwards at a very fast pace. The majority of content learned in IB Biology across nearly all the topics has been informed by the power of electron microscopes.

Possible Questions to think about (Note these are my own and not from any IB exams!):

Outline how technology has improved scientific research using a named example [3].

Compare and contrast the use of light and electron microscopes [4].  (This links to topic 1.2 – Understanding: • Electron microscopes have a much higher resolution than light microscopes)

 

Sources:

Palucka, Tim. “Overview of Electron Microscopy.” History of Electron Microscopy, 1931-2000, History of Recent Science and Technology, 2002, authors.library.caltech.edu/5456/1/hrst.mit.edu/hrs/materials/public/ElectronMicroscope/EM_HistOverview.htm. Accessed 27 Feb. 2017.

Paselk, Richard A. “The Evolution of the Abbé Refractometer.” The Evolution of the Abbé Refractometer, Humboldt State University , Sept. 1999, www2.humboldt.edu/scimus/Essays/EvolAbbeRef/EvolAbbeRef.htm. Accessed 27 Feb. 2017.

“Van Leeuwenhoek Microscope.” A Complete Microscope History – Who Invented the Microscope?, History of the Microscope, 2010, http://www.history-of-the-microscope.org/history-of-the-microscope-who-invented-the-microscope.php. Accessed 23 Feb. 2017.

“Who Invented the Microscope? A Complete Microscope History.” History of the Microscope, History of the Microscope, 2010, http://www.history-of-the-microscope.org/history-of-the-microscope-who-invented-the-microscope.php. Accessed 27 Feb. 2017.

5.1 Evidence for Evolution

Looking for patterns, trends and discrepancies—there are common features in the bone structure of vertebrate limbs despite their varied use.

This Nature of Science statement fits neatly into the syllabus content for this topic.  One of the applications for 5.1 is – “Comparison of the pentadactyl limb of mammals, birds, amphibians and reptiles with different methods of locomotion.” (IBO, p67). Thus understanding the importance of the pentadactyl limb as an example of a homologous structure should allow you to understand it as an example of seeking patterns, trends and discrepancies.

All amphibians, birds, reptiles and mammals descended from a common ancestor that had a tetrapod (4-legged) body plan and lived some 360 million years ago. However, as the different vertebrate groups then radiated outwards, this basic structure became adapted for different functions, some more radically than others.  Snakes have lost their legs, birds developed their forelegs into wings and whales and icthyosaurs returned to the water, with fore limbs adapted for paddling. However, despite these differences in function, an analysis of anatomy shows the same underlying structure.

The pattern is the repeated form of bone and limb structure (1 long bone-2 shorter bones-smaller bones-5 digits); the trend is that this developed among all four tetrapod classes and the discrepancies are the evolution of different functions and forms (wings-flying; flippers-swimming; arms-grasping etc. )

Homologous Tetrapod Limbs (University of California Museum of Palaeontology)

 

As Stephen Jay Gould wrote, “Why should a rat run, a bat fly, a porpoise swim and I type this essay with structures built of the same bones unless we all inherited them from a common ancestor? (Gould, 258).

 

Gould, Stephen Jay. Hen’s Teeth and Horses Toes. New York, Penguin. 1990. Print.

“Homologous Tetrapod Limbs (4 Of 6)”. Evolution.berkeley.edu. University of California, Museum of Paleontology, 2016. Web. 24 May 2016.

IBO. Biology guide: First assessment 2016. Cardiff, IBO. 2014. Print.

2.1 Molecules to Metabolism

Falsification of theories—the artificial synthesis of urea helped to falsify vitalism.

A popular theory during the 18th and 19th centuries, though it can be traced back to the ancient Greeks, was the idea of Vitalism.  Vitalism states that:

…living organisms are fundamentally different from non-living entities because they contain some non-physical element or are governed by different principles than are inanimate things. (Bechtel and Richardson)

It was particularly associated with the idea of a vital force that provided the “spark” of life separating the living from the non-living.

In 1828, the German chemist Friedrich Wöhler synthesised organic urea from inorganic cyanic acid and ammonium. Although it is now doubted that Wöhler expressly set out to falsify vitalism, his results nevertheless showed that organic molecules can be produced without the need for a non-specific “force” – providing an important milestone in understanding quantitative chemistry, isomerism and biochemistry.

As a scientific theory, Vitalism fails on two principal fronts: it offers no predictive value and there are no tests or experiments which could be used to demonstrate its existence or function.

References

Bechtel, W. and Richardson, R. Vitalism. mechanism.ucsd.edu. 1998. Web. May 24, 2016.

Kinne-Saffran and Kinne R.K.H. Vitalism and Synthesis of Urea: From Friedrich Wöhler to Hans A. Krebs. Am J Nephrol 1999; 19:290–294.

7.2 Transcription and Gene Expression

Looking for patterns, trends and discrepancies—there is mounting evidence that the environment can trigger heritable changes in epigenetic factors.

This is highly topical given some recent events in the science news. But firstly, for a primer on epigenetics, check out Sci Show for their episode on Epigenetics.

Epigenetics is essentially “…genetic control by factors other than an individual’s DNA sequence.” (Simmons). These factors are thus important in the switching on or off of particular genes. While this happens throughout life, particularly during embryonic development, it is the growing body of evidence of environmental influence during adulthood that is particularly exciting.

A recent study investigating the genomes of obese men and obese men before and after bariatric surgery detected epigenetic effects coded in men’s sperm (Donkin et al.).  The environmental factors of obesity, as well as recovery from obesity, seem to effect the genes coded in the sperm, thus influencing the genome of future offspring. These genes seem to be linked to appetite control, providing intriguing insights into how obesity may become genetic and not just environmental.

If the environment affects genes and these changes are passed on to offspring, rather than the genes you were born with and inherited from your parents, then there are some very interesting possibilities that emerge for evolution.   As one scientist commented, this is a “…provocative start to asking some really interesting questions,” (Simmons).  Consider some of these yourself – it makes you rethink topic 5!

Sources

Donkin, Ida et al. ‘Obesity And Bariatric Surgery Drive Epigenetic Variation Of Spermatozoa In Humans’. Cell Metabolism (2015): -. Web. 10 Dec. 2015.

Simmons, D. (2008) Epigenetic influence and disease. Nature Education 1(1):6

Zusi, K. ‘Obesity Alters Sperm Epigenome | The Scientist Magazine®’. The Scientist. N. p., 2015. Web. 9 Dec. 2015.

6.4 Gas Exchange

Obtain evidence for theories—epidemiological studies have contributed to our understanding of the causes of lung cancer. (1.8)

In 1964, the US Public Health Service published a report on the links between smoking and health that has since been recognised as a turning point in public health.  The conclusion of the report was clear: “Cigarette smoking is a health hazard of sufficient importance in the United States to warrant appropriate remedial action.” (Dela Cruz, C. S) This was based in large part on two large-scale epidemiological studies completed in 1950.

One study, in the US, found that 96.5% of lung cancers in a study group of 605 patients were in men who were moderate to heavy smokers for many years (Wynder and Graham). The other, in the UK, found an association between lung cancer and smoking cigarettes and between cancer development and the amount of smoking (Doll and Hill).

Additional research establishing the nature of the 50 carcinogens and 400-500 major constituents of cigarette smoke provided the supporting data to establish this causation (Dela Cruz, C. S). It is now estimated that a heavy smoker has between a 10-30 fold greater risk of developing lung cancer than a non-smoker (Dela Cruz, C. S).

Now, this is not meant to be a History of Science section, or a study of epidemiology, but an analysis of the Nature of Science.  So what can we determine from this?

Well, Theories are the backbone of science, establishing explanations for observable phenomena that are supported by experimental data and evidence. Until such evidence was established, tobacco companies could brush aside health concerns because of a lack of data – it could be genetic, environmental, the product of other health concerns etc etc. Large scale studies that established causal links between cigarette use and lung cancer determined that smoking was the key cause and thus public health policy and laws were able to move in the direction of reducing smoking.

The adult per capita cigarette consumption in the US, 1900-2006 (Dela Cruz, C.S)

The graph above shows the dramatic effect that the studies outlined above had on smoking, as well as on social and legal factors such as taxes and bans on advertising.  One could extend this aspect into some TOK-territory by examining advertising and cigarettes: Australia has some of the most restrictive laws regarding cigarette packets and warnings, which could lead to some interesting knowledge questions.

Ultimately, it is the collection experimental data that leads to the formations of theories which can then be used to explain observations.  The power of science is that these theories can then be used to support legislation to protect the public against powerful interests.

Sources:

Dela Cruz, Charles S., Lynn T. Tanoue, and Richard A. Matthay. ‘Lung Cancer: Epidemiology, Etiology, And Prevention’. Clinics in Chest Medicine 32.4 (2011): 605-644. Web. 4 Dec. 2015.

Doll, Richard, and A. Bradford Hill. “Smoking and Carcinoma of the Lung.”British Medical Journal 2.4682 (1950): 739–748. Print.

Wynder EL, Graham EA. Etiologic factors in bronchiogenic carcinoma with special reference to industrial exposures; report of eight hundred fifty-seven proved cases. A M A Arch Ind Hyg Occup Med.1951;4(3):221–235

2.3 Carbohydrates and Lipids

Evaluating claims—health claims made about lipids in diets need to be assessed. (5.2) (IBO; 39)

This NOS links nicely to to syllabus knowledge statements:

1. Unsaturated fatty acids can be cis or trans isomers. (IBO; 39)

2. Application: Scientific evidence for health risks of trans fats and saturated fatty acids. (IBO; 39)

3. Application: Evaluation of evidence and the methods used to obtain the evidence for health claims made about lipids. (IBO; 39)

The concept of evaluating claims also lends itself to TOK.  Thus it is possible to teach necessary content, the NOS and provide TOK integration, all in the one lesson.  This is the best way, in my opinion, to incorporate the NOS (or TOK for that matter)- not as “additional content” but complementary to the learning that is already going on.

The first lesson involves covering the understandings: the molecular structure of fatty acids, the differences between saturated and unsaturated FAs and the difference between cis and trans unsaturated FAs.  This covers the content needed.  In our next lesson, the students are placed in groups and have one of the following four articles allocated to them:

We should ban Trans Fats – The Guardian

Dairy Products Don’t Cause Heart Disease– The Guardian

Are Fats Bad? – New York Times

Butter is Back – New York Times

As part of their reading, the students are asked to identify the First Order Knowledge Claims made in the article.  These are claims about knowledge within specific subject areas – for instance, Trans fats increase the risk of heart disease.

The students then share their knowledge claims on the board, using the Sustainability Compass (Compass Education). The board is divided into the four compass points (N, E, S, W), representing the four key dimensions of sustainability: Nature, Economy, Society, and Well-being. This adds another layer to the discussion by having the students incorporate systems thinking – environmental effects of industrial animal farming, econmoic impacts of chronic health problems, the personal impacts of diet choices and lifestyles etc.

The Sustainability Compass (Compass Education

The next part is, as a class, to select 3-5 of these First Order Knowledge Claims and identify the TOK concepts and vocabulary that match them best and to then develop them into Second Order Knowledge Claims.  These are the focus of TOK – claims about the nature of knowledge.  Students must be able to distinguish between first and second order claims as a central part of their TOK course. The final task is to develop the second order knowledge claims into appropriate knowledge questions (open-ended, general and about knowledge) – which are cornerstone of the TOK presentation and essay.

Ideally, we do this in one 85-minute lesson, though if you set the reading for homework it would be possible to complete this in a shorter period.

Thanks to Camille Garewal (@CDolmont) for pictures and inspiration for this post.

Sources:

IBO. Biology Guide: First Assessment 2016. IBO, 2014.

“Compass and Accelerator Tools.” Compass Education, AtKisson, 10 Aug. 2017, http://www.compasseducation.org/resources/compass-and-accelerator/.

IBO. Theory of Knowledge Guide: First Assessment 2015. IBO, 2013.

“Sustainability Compass.” Accelerator Pro, AtKisson, 2017, atkisson.com/tools/.

4.3 Carbon Cycling and 4.4 Climate Change

Making accurate, quantitative measurements—it is important to obtain reliable data on the concentration of carbon dioxide and methane in the atmosphere. (IBO, 63) 

Assessing claims—assessment of the claims that human activities are producing climate change. (IBO, 65)

Climate change continues to be the subject of much debate in certain sections of the media and the world, despite the proliferation of evidence that supports both rapid climate change and the human role in driving it.  As these two NOS states, and as we learn in TOK, claims must be assessed and their evidence evaluated to determine their truth.

The best place to begin is to explore the website for the Intergovernmental Panel on Climate Change (IPCC), the global body that synthesises the climate research and produces reports at intervals of 5-6 years.  The Fifth Assessment Report was published between September 2013 and November 2014. The reports are provided in PDF and can be daunting!  However, the Summary for Policymakers  provides a nice overview of the main results of the review, including details on greenhouse gas emissions, temperature change, ocean acidification, snow and ice cover and changes in animal and plant behaviour and life-cycles.

A good activity for the students is adapted from Stephen Taylor’s page at i-biology.  Students can access a range of different databases from the CDIAC to examine carbon emissions.  I have the students collect data for both the last 5 years and for the entirety of the database they have chosen.  The longer the database, the more clearly the trend is displayed.  Students can then practice their graphing and analysis skills using spreadsheets.  With the new IA Guidelines allowing for database analysis, this could be a good starting point for an investigation.

Student Task Sheet

We finished our sequence of classes with a great discussion on the precautionary principle.  This is no longer explicitly required in the new syllabus but has great links to TOK and also to the idea of verifying data. We used the Visible Thinking Truth Routine – Claim, Support, Question– to examine two different articles with an opposing view of the PP. We ended up debating what certainty level is required for proof in the natural sciences – a nice end to the topic.

Source:

Biology Guide: First Assessment 2016. Cardiff: IBO, 2014. Print.

“Carbon Cycle.” BioNinja, 2017, http://www.ib.bioninja.com.au/standard-level/topic-4-ecology/43-carbon-cycling/carbon-cycle.html.