Using the Nature of Science in Class

With my current grade 11s, we have not spent much time on the nature of science in class.  Although resources are provided in their notes, we have focused more on experiments and content.  Having just finished our second unit and the end of unit test, I developed this resource as an introductory activity that students worked on in groups of three.

The resource is adapted from one of the many wonderful templates provided at the #TMSouthHistorians blog: https://tmsouthhistorians.wixsite.com/tmsouthhistorians/copy-of-blog-resources and often shared through @Jmosley_history – this is the A-B Starter.

 

I chose NOS prompts from topics 5.1, 5.2, 5.3, 10.3, 4.1, 2.1, 2.2, 2.3, 2.4, 2.5 and 8.1, which make up the first two units I teach – Diversity of Life and Chemistry of Life.  I had the students work together with no resources to begin with and try to identify links to the syllabus topics, TOK and to using the five categories of NOS to help organise the different ideas.  I tried to emphasise that they didn’t need to try and memorise new content but to discuss how these link to the knowledge they already have.  The task seemed to work well and got them more engaged than if we were just learning the content of the statements.  I hope to eventually develop templates for each unit that I teach.

 

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2.4 Proteins

Looking for patterns, trends and discrepancies—most but not all organisms assemble proteins from the same amino acids.

Part of the universality of life is the observation that all living organisms construct proteins out of the same pool of 20 amino acids.  These 20 were identified in a rapid era of discovery after the development of partition chromatography in 1943.  However, this has now been expanded to include two additional amino acids – selenocysteine and pyrrolysine, giving a total of 22 amino acids.

Selenocysteine, as the name suggests, is similar to the amino acid cysteine but it has a Selenium atom as part of its side-chain (R-Group). It is a highly reactive and potentially dangerous substance – cells have to use some tricky metabolic pathways in order to prevent it from moving freely and building up in the cytoplasm.   It is used in certain redox reactions and has been found in all three domains of life, although it is not universal amongst them

Pyrrolysine is rarer, having only been found in some species of Archaeans and bacteria. It is structurally similar to lysine, but with the addition of a a pyrroline ring to the side-chain. It’s role and possible existence in other organisms is the focus of many ongoing studies.

Both of these amino acids are not encoded in the DNA – they are instead encoded by the stop codons UGA for selenocysteine and UAG for pyrrolysine and expressed via interactions with specific tRNA molecules, a process known as cotranslation. The biochemistry involved is fairly complex and difficult to summarise for IB biology purposes, but if you are interested the links below are a good place to start.

In summary, then:

  • all living organisms use the traditional 20 amino acids to construct proteins and code for these amino acids in their DNA
  • all three domains of life (thought not every species in them) also use a 21st amino acid selenocysteine in some proteins (humans included)
  • Archaeans and bacteria have developed a mechanism to use a 22nd amino acid, pyrrolysine.
  • both of these amino acids are not coded for in the DNA but are expressed through the use of a stop codon and tRNA
  • the presence of Selenocysteine in all three domains strongly suggests it was present in the last universal common ancestor, and is thus a very ancient biochemical pathway

 

Selenocysteine and pyrrolysine are powerful examples of the versatility inherent in the genetic code. (Rother and Krzycki).

Like so many aspects of biology, once a rule is determined, the incredible variety of life shows us an exception.

For an interesting TOK-linked discussion, consider this quote, also from the Rother/Krzycki article:

They further provide examples of how precedent, though valuable, is not always the best predictor in scientific investigation…

What do the authors mean by this?  Does this mean that inductive reasoning is not always a reliable form of reason? What other examples from science can you think of to illustrate this quote?

Sources:

Das, Gunajyoti & Mandal, Shilpi. (2013). Nearest-Neighbor Interactions and Their Influence on the Structural Aspects of Dipeptides. Biochemistry research international. ResearchGate. Accessed on 2 October, 2018
https://www.researchgate.net/figure/Chemical-structures-of-selenocysteine-Sec-and-pyrrolysine-Pyl_fig1_258037372

Dinmann, J. (2012). Control of gene expression by translational recoding. Advances in Protein Chemistry and Structural Biology via ScienceDirect. Accessed on 2 October, 2018. https://www.sciencedirect.com/topics/neuroscience/pyrrolysine

Gutiérrez-Preciado, A., Romero, H. & Peimbert, M. (2010) An Evolutionary Perspective on Amino Acids. Nature Education. Accessed on 2 October, 2018.
https://www.nature.com/scitable/topicpage/an-evolutionary-perspective-on-amino-acids-14568445

Rother, Michael, and Joseph A. Krzycki. “Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea.” Archaea 2010 (2010): 453642. PMC. Web. 2 Oct. 2018.

2.5 Enzymes

Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. (3.2)
This links to Practical 3 – Experimental investigation of a factor affecting enzyme activity.

Working with enzymes is something that all biology students get very familiar with over their studies!  This is particular true in the new syllabus as Practical 3 requires an enzyme experiment and they are popular as topics for the IA.

IMG_2768
Testing the effect of substrate concentration on potato catalase.

Although there are several other practical-themed NOS statements, this one makes particular reference to the idea of reliability and replicates.  In terms of assessment this is most likely to appear in the Section A of Paper 3, when students are provided with experimental scenarios and have to apply their knowledge. However, it is also important for the IA.  The chosen investigation must design a methodology that will collect sufficient data, the data must be processed with appropriate awareness of uncertainties, and the reliability of the results reviewed and evaluated in the conclusion and evaluation.

This is thus an important lesson to not just experience the practical side of biology, but to understand the importance of replicates and how this impacts the IA.  So what could this look like? Here are a few ideas:

  • If an enzyme-based experiment, aim for five variations of the independent variable (five different pHs; five different temperatures etc). As enzyme experiments are invariably time-based, this will allow you to plot a graph with more confidence (five data points rather than, say, three).
  • Try to repeat each variation five times.  This will provide enough data to calculate the average and standard deviation. Of course there are more processing options than this (think rate of reaction) but these two are the basics.
  • The conclusion/evaluation needs to then assess how the range of the independent variable, the sample size and the processed data contribute to the reliability of the experiment. The more replicates you have, the more robust this section will be.
  • There are always time constraints on how many replicates you can collect – so factor this into your methods.  If your experiment is only collecting data for three minutes for each run, then you should be able to get more replicates (and you will be expected to collect more data).  If, in contrast, you are collecting data for more than an hour per experiment, then you will need to be aware of this.
  • Finally, remember that design, processing and evaluation are all relative to the specific experiment you carried out – so always think in terms of the context for your investigation and the resources available to you.

 

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.

 

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.

H-bonds
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.

 

Best Holiday Read 2016

Like all good biology teachers, I try to load up my summer reading list with the latest science books.  One book in particular stands out this year and I think it deserves its own blog post!  Described as a “biography of the gene”, The Gene by Siddhartha Mukherjee is a phenomenal book.  Beautifully written (the author, a cancer physician and researcher, has a genuine literary touch) it is a fascinating overview of our understanding of the gene.  It takes us from the first Aristotelian musings on inheritance all the way forward to today’s latest insights into genetics and molecular biology.  All the famous geneticists from the Nature of Science are in here: Mendel, Darwin, Morgan , Watson, Crick, Franklin, Sanger and too many more to list.  In fact, the book is the perfect compendium for IB Biology students!  The narrative is lively and engaging and the individual personalities of the scientists leap off the page. It is worth making time for, even in the busy schedule of an IB student.

the-gene-9781476733500_lg

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.

2.8 Respiration and Ethics

Assessing the ethics of scientific research: the use of invertebrates in respirometers has ethical implications.

The use of animal models in biological experiments has a long history. Indeed, many of our most important discoveries were made possible by using animal test subjects. However, using animals at any time during an experiment has ethical implications that need to be evaluated.

Any scientific research involving animals will have to satisfy an ethics board as to the justification for using and/or experimenting on animals. Two key issues that scientists have to consider might include: what suffering or pain will the animal experience and are there alternatives to using animals?  There is a process in the UK called the 3R’s – replacement, refinement and reduction of the use of animals in research (Festing, S. and Wilkinson, R.).  This process, while acknowledging that animals may be required in certain circumstances, aims to ultimately reduce these to only the most essential experiments.

There is often a difference in concern between invertebrates and vertebrates in terms of what ethical rules apply to them.  Most people probably care less about the fate of cockroaches or crickets in a respirometer experiment than about the use of mammals in medical research.  However, it is still important to evaluate the ethical use of invertebrates in the same way as vertebrates. In addition to the issues of pain/suffering and replacement, we should consider:

  • whether the animals can be released back into their natural habitat
  • whether it is ethical to remove them in the first pace
  • whether we can minimise any pain or suffering that may take place in the experiment.

The IBO has published a document on the use of animals in experiments and it is very clear that any animal (invertebrate or not) must be treated ethically and must not be subject to any suffering or environment outside its normal range. This link from the Nuffield Foundation outlines an experiment based on this; take note of their ethical issues paragraph after the methods.

Sources:

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

Festing, Simon, and Robin Wilkinson. The Ethics Of Animal Research. Talking Point On The Use Of Animals In Scientific Research. EMBO Reports 8.6. 2007: 526-530. Web. 27 Jan. 2016.