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.

1024px-Aequorea4
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.

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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.

 

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.

van-leeuwenhoek-microscope1
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.

abbe1874-refrac
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.).

dipomerr
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!

screen-shot-2017-02-09-at-12-17-53-pm
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:

screen-shot-2017-02-09-at-12-58-42-pm
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.

screen-shot-2017-02-03-at-9-21-49-am

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

screen-shot-2017-02-03-at-8-12-13-am

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!

screen-shot-2017-02-03-at-8-19-56-am
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?

Screen Shot 2017-02-03 at 9.30.34 AM.png

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/

5.2 Natural selection

Use theories to explain natural phenomena—the theory of evolution by natural selection can explain the development of antibiotic resistance in bacteria. (2.1)

Evolution occurs at both the micro and macro levels.  Macroevolution is the eye-catching form, where we see species changing into dramatically new ones. This process though takes time and is not directly observable. 

Microevolution, while less “glamorous” is no less interesting. Indeed, it has applications that are amongst the most serious concerns in health, medicine and agriculture. This is the ability of populations of bacteria, protists, fungi, insects or plants to evolve resistance to antibiotics, drugs, pesticides and other chemicals used to control them. 

The resistance of bacteria to antibiotics has occurred at an incredible rate, as the image below shows:

antibiotic-timeline
Image from CDC.gov

What is particularly concerning about this is shown in the following graph – the number of antibiotics being developed approved continues to decline, which leaves fewer options for treatment.

Understanding the process of evolution is critical to estimating the number and type of new drugs that are needed to combat them.  It is thus necessary to understand that antibiotic use represents a very strong selection pressure. Given the reproductive potential of bacteria (more offspring are born than can survive) and the variation that is possible (through both mutation and horizontal gene transfer) it should therefore come as no surprise that populations rapidly evolve resistance.  Evolution and natural selection are thus not the dated musings of a 19th-century naturalist, but of critical importance to health problems of the 21st-century: in the US alone, over 2 million illnesses and 23,000 deaths per year are directly attributed to evolved resistance.

From an assessment perspective, antibiotic resistance in bacteria is a great example to use when responding to and extended response question on evolution/natural selection.

Sources:

“About Antimicrobial Resistance | Antibiotic/Antimicrobial Resistance | CDC “. Centers for Disease Control and Prevention. Cdc.gov., 2016. Web. 11 Dec. 2016.

“Microevolution”. Understanding Evolution. University of California Museum of Paleontology.Evolution.berkeley.edu. 2016. Web. 11 Dec. 2016.

6.1 Digestion and Absorption

Use models as representations of the real world—dialysis tubing can be used to model absorption in the intestine. (1.10)

Models are an essential part of the scientific method and have been discussed in our biology syllabus in topics ranging from Neural Development, the human brain, DNA structure and membranes.

Models allow scientists to represent an idea that is difficult, or impossible to experience directly. By their nature they are simplifications of the real world processes they describe, but they are still extremely useful as a means of explaining processes, making predictions, testing hypotheses and analysing data. Think of the importance of models of climate change or fisheries populations – these models have direct impacts on economics, politics and society.

In 6.1 we are discussing the use of models in the digestive system.  A classic middle-school demonstration is to use visking, or dialysis, tubing to demonstrate the workings of the digestive system.  An example experiment using starch, iodine and Benedict’s solution shows how this might work. The inside of the model gut originally contains both starch and glucose. However, testing over time shows that after 15 minutes, the gut still contains starch, however the liquid outside the “gut” tests positive for glucose.  The movement of glucose out of the gut and into the surrounding fluid, while the larger starch molecules stay behind, helps demonstrate the need to reduce the size of polysaccharides before they can be absorbed and used by the body.

It would be useful to review the different NOS statements on models and develop some common ideas about the use of models in biology.  Turn each statement into a question using an appropriate command term and try to develop some short-answers. For example:

  1. NOS statement for 6.1 – Use models as representations of the real world—dialysis tubing can be used to model absorption in the intestine.
  2. This becomes: Outline how dialysis tubing can be used to model absorption in the intestine (3).

Sources:

“Evaluating Visking Tubing As A Model For A Gut | Nuffield Foundation”. Nuffieldfoundation.org. N. p., 2016. Web. 11 Dec. 2016.

“Scientific Modelling “. Sciencelearning Hub. The University of Waikato. 2016. Web. 9 Dec. 2016.

9.4 Reproduction in plants

Paradigm shift—more than 85% of the world’s 250,000 species of flowering plant depend on pollinators for reproduction. This knowledge has led to protecting entire ecosystems rather than individual species.

Albert Einstein is claimed to have said: “If the bee disappears from the surface of the earth, man would have no more than four years to live.” (Quote Investigator). While it appears he did not actually ever say this, it is a remarkably prescient observation about the role that pollinators play in continuing the survival of plants.

While wind, water and explosive propulsion do work for some flowering species, the majority rely on animal pollinators. The co-evolution of pollinators with the plants they pollinate means that, in many cases, species may be pollinated by only a select few animals.  Should the animals decline in population, so will the plants.

A recent example in New Zealand reminds us of this (Biello). The endemic flowering shrub Rhabdothamnus solandri, or New Zealand gloxinia, relies primarily on the bellbird (Anothornis melanura) and stitchbird (Notiomystis cincta) to pollinate its flowers.  These birds have long beaks and tongues to access the long, tubular flowers of the shrub.  However, the bellbird and stitchbird have recently become extinct on New Zealand’s North island. To investigate this impact on the flower, researchers conducted a study on three smaller offshore islands, where the birds were still present. The results were alarming – in the absence of the two birds on the North island, just 22% of of flowers produced fruit and had only 37 seeds per flower. This compares to the the islands that still have the birds, where they produced 232 seeds per flower and 58% produced fruit. In order to save this flower, we must also save the birds.

rhabdothamnus_solandri___taurepo__new_zealand_gloxinia-006

New Zealand Gloxinia – Rhabdothamnus solandri. 

 

A paradigm shift represents a radical change in thinking based on new evidence.  Understanding that protecting birds, for example, will also protect plants, is an important change in thinking from purely looking at the conservation of single species. Conservation methods that focus on ecosystems as a holistic unit reflect our increased understanding of the way animals and plants in particular are inter-related.

Sources:

Biello, David. “For Want Of A Pollinator, A Flower May Be Lost–Or A Forest”. Scientific American. N. p., 2016. Web. 13 Oct. 2016.

“If The Bee Disappeared Off The Face Of The Earth, Man Would Only Have Four Years Left To Live | Quote Investigator”. Quoteinvestigator.com. N. p., 2013. Web. 13 Oct. 2016.

“T.E.R:R.A.I.N – Taranaki Educational Resource: Research, Analysis And Information Network – Rhabdothamnus Solandri (Taurepo) “. Terrain.net.nz. N. p., 2016. Web. 14 Oct. 2016.

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. )

Vertebrate limb
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.