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.

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.

 

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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.

11.3 The Kidney and Osmoregulation

Curiosity about particular phenomena—investigations were carried out to determine how desert animals prevent water loss in their wastes.

Water, water, every where,

And all the boards did shrink;

Water, water, every where,

Nor any drop to drink.

The Rime of the Ancient Mariner

As a zoology major at university, I spent many hours pouring over Knut Schmidt-Nielsen’s classic text, Animal Physiology. He was  widely regarded as the father of comparative physiology and made groundbreaking contributions to the discipline of  Ecophysiology, the study of how animal physiology is adapted to the environment. A group of animals that came in for particular notice in many of his studies were the desert rats (Dipodomys sp.).

Merriam’s Kangaroo Rat (Dipodomys merriami) (Dr. Lloyd Glenn Ingles, 1999)

These rats eat only dry food, principally seeds, yet almost never drink water, even if it is available. Their habitat, the deserts of SW North America, see little rainfall and baking temperatures. How is this possible?

Firstly, a primer on water balance (adapted from Schmidt-Nielsen, 1962). Animals gain water through either drinking free water, water in their food and the water produced from the oxidation of glucose in respiration (metabolic water). Water is lost from the body by evaporation from the skin and lungs, in urine and in feces.  In order to survive without drinking water and on a dry-food diet, these animals must therefore minimise their water loss. As this topic is linked to 11.3 (Osmoregulation) we will focus on their kidney adaptations.

We learn when studying topic 11.3 that the Loop of Henle is crucial in allowing the development of a urine that is hyperosmotic to the blood plasma. Desert rats have a proportionally very long Loop of Henle and a thicker medulla, which allows for the establishment of even more concentrated urine.  Additionally, as a small animal, their high metabolic rates mean they have more densely packed mitochondria and transport pumps throughout the nephron, allowing the maintenance of a concentration gradient.

The result is that various species of desert rats can excrete a urine that is up to 16 times the concentration of their blood plasma and over four times more concentrated than seawater!

adapted from Willmer et al. 2011

With a greater amount of solute in the urine, proportionally less water is needed to excrete it. These rodents also take it a step further by producing very dry, pellet-like feces.  They also ingest their feces to reabsorb what little water is in them.  They are therefore able to survive only by using metabolic water and the water in their food – a useful adaptation for the desert.

But the curiosity doesn’t end there!  Schmidt-Nielsen wanted to know if they could survive on drinking seawater.  Seawater has a concentration of between 1000-1200 mOsm/L. If a human drank 1 litre of seawater, they would need 2 litres of urine to flush out the excess sodium chloride, thus leading to dehydration very quickly.  But given the ability of the desert rat kidney’s to concentrate the urine, he reasoned that they should be able to do it.

Firstly, to induce thirst, he fed the rats on a diet of soybeans. These are high in protein and produce a lot of urea that needs to be removed.  Normally, the rats don’t drink water so they need to be induced to do this; the high protein diet accomplishes this. He then provided different groups of rats seawater, freshwater and no water. The results are displayed below:

The results of providing sea water to desert rats (Schmidt-Nielsen 1962).

Amazingly, the rats provided with sea water showed no change in body weight after 2 weeks, almost exactly the same as those provided with fresh water.  Proof of the tremendous concentrating power of their kidneys, and more specifically, their loops of Henle.

And remember, should you ever be stuck on a becalmed ship or wrecked on a desert island, don’t drink the water!

Sources

Coleridge, Samuel Taylor. “The Rime of the Ancient Mariner .” Poetry Foundation, Poetry Foundation, http://www.poetryfoundation.org/poems-and-poets/poems/detail/43997.

Ingles, Dr. Lloyd Glenn. “Merriam’s Kangaroo Rat (Dipodomys merriami)”  University of Texas, El Paso. museum2.utep.edu/chih/theland/animals/mammals/dipomerr.htm, 1999. Web. 9 Feb. 2017.

Schmidt-Nielsen, Knut. “Comparative Physiology of Desert Mammals.” Agricultural Experimental Station, vol. 21, Dec. 1962, animalsciences.missouri.edu/research/bec/Brody%20Memorial%20Lectures%201/Lecture%202%20Knut%20Schmidt-Nielsen.pdf.

Willmer, Pat, et al. Environmental Physiology of Animals. 2nd ed., Malden, Mass., Blackwell Publ., 2011.

Nature of Science – the First Two Years

WordPress alerted me recently that I have had this blog now for two years! It started as a way to help me try to get my head around the new Nature of Science components of the syllabus and its readership grew very slowly – I think it was mostly my own students who used it for the first six months or so. But it has grown steadily since the first examination period last May and I hope it will continue to be useful to IB Biology students.
I thought it might be interesting to see some of the blog statistics (I teach science, after all!)  from the first two years and see what it tells us. I would love to hear back from students or teachers who use the blog to find out what works and what doesn’t and what I should add or do more of.

Views

Readership grew slowly over 2015 (988 views), which makes sense as that was the last exam period for the old syllabus.  However things picked up in 2016, which recorded just under 7000 views for the year.  Already, 2017 has nearly surpassed the whole of 2015.

Excluding the home page/archives, which tops the list at over 4000 views, here is the top ten most visited pages at the blog:

There is a clear difference between the top 4 (average of 551 views) and the remainder of the top ten.  No doubt this is due to cyclins, Harvey, Davson-Danielli model and Florey and Chaim appearing on either the specimen, May or November exam papers. Students should be aware, though, that what was on a previous paper is no guarantee of what will be on the next one – there is a lot of content in the biology syllabus and students should make an effort to review across all topics, rather than just a handful. I would imagine that there might be some new NOS questions and topics on the next exam paper.

Most Views

No surprises here!  The most views in a day was set on May 3, 2016 – the day before the biology exams!

I wonder what happened on May 4?

I imagine that Sunday 30 April 2017 might surpass this!

Interestingly, there was not a similar spike in the November exams – perhaps because there are fewer students?  For the entire month of November, according to the country data, the only November session country in the top ten was Singapore.

Who Visits?

This is still amazing to me – that something I publish can be read and used by students from 109 countries on every inhabited continent! The top ten countries in order are: USA, Cambodia, Canada, the UK, Hong Kong, Singapore, UAE, Germany, Australia and Switzerland.  Not surprising, as according to the May 2016 Statistical Bulletin, the USA (1), Canada (2), UK (3) and Hong Kong (10) are all in the top ten countries for IB candidates. It would be great to hit every country with an IBDP program!

How do they get here?

Besides search engines (the biggest source of visitors- 2676 in 2016) most people hear about the blog via twitter (168 views over 2016).  I know a lot of high school students don’t necessarily use twitter so I need to think of some other ways to engage with them – any ideas would be welcome!

So there it is – two years of data on the Nature of Science blog.  It would be remiss of me as a science teacher not to review the numbers and use them to help guide the site forwards.

Thanks to all who have followed, commented, liked or retweeted the blog – what began as a way to help my own students has developed into something much larger and I hope I can continue to make this a valuable resource for students and teachers worldwide.

As always, please let me know what you think!

Personalities!

Here are some flashcards I put together on Quizlet identifying the scientists that are mentioned in the NOS. While it is unlikely that you would have a question asking you to name a specific scientist or the conditions under which their work took place, it is definitely helpful to be able to link names to topics and to their area of work.

https://quizlet.com/130283945/flashcards/embed

https://quizlet.com/197507130/nature-of-science-examples-flash-cards/

https://quizlet.com/197503111/nature-of-science-key-terms-flash-cards/

Image from:

Famous Scientists. 2018. https://www.famousscientists.org/