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.

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1.4 Membrane Transport

Experimental design—accurate quantitative measurement in osmosis experiments are essential. (3.1)

This is one of the NOS that is relatively easy to incorporate into your learning.  Prescribed practical 2 is Estimation of osmolarity in tissues by bathing samples in hypotonic and hypertonic solutions; when you do this lab, you get a first-hand experience in why these measurements are important.

In my class we use potatoes and sucrose solutions of 0.1-0.5M, plus distilled water. We cut them into approximately equal-sized “chips” and place them in test tubes containing each of the six solutions.  Next class (or within 24h) we then remove them, measure again and investigate the changes.

While the potatoes are bathing in the solutions, we discuss the NOS as a class.  Here are some of our talking points:

  • The movement of water, which will influence the change in size of the potatoes, is likely to be small. Thus accurate measurements are needed to demonstrate that there has indeed been change, rather than just random variation.
  • Following on from this, the more measurements that can contribute to the data, the more accurate picture we might have – thus we need to accurately measure length, height, width and mass.
  • Accurate replicates will enable us to process the data to investigate any changes with confidence.
  • Measuring grams/mm requires careful attention to the uncertainties attached to those measurements.
  • While qualitative data is still important, it is less objective than accurate quantitative measurements.
  • These measurements need to be coupled with carefully controlled variables to allow the most accurate conclusion to be drawn.

 

Content, Practicals and the Nature of Science

As I have mentioned at various times on this blog, I think one of the challenges with the new syllabus is the idea that the NOS represents an “add-on” that will somehow impact teaching and learning.  Some of them certainly are new concepts and content, but some are also linked directly to either content, lab-work or both.  In these cases, making the connections is easy and can help reinforce what the students are already learning.  Some examples that would work here include (IBO,2014).:

1.4 Membrane transport Experimental design—accurate quantitative measurement in osmosis experiments are essential. (3.1)
This links to Practical 2:  Estimation of osmolarity in tissues by bathing samples in hypotonic and hypertonic solutions. 

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.

2.9 Photosynthesis Experimental design—controlling relevant variables in photosynthesis experiments is essential. (3.1)

4.3 Carbon cycling Making accurate, quantitative measurements—it is important to obtain reliable data on the concentration of carbon dioxide and methane in the atmosphere. (3.1)
See my post on Carbon Database Analysis

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)

9.1 Transport in the xylem of plants Use models as representations of the real world—mechanisms involved in water transport in the xylem can be investigated using apparatus and materials that show similarities in structure to plant tissues.
This links to Practical 7 – Measurement of transpiration rates using potometers.

With a bit of planning, a single lesson can combine content, practical work and the Nature of Science.  Further, linking NOS to an experiment can help reinforce understanding in a much more effective way. As you begin to work towards the IA, these then provide additional inspiration for students to develop their own investigations.

In terms of preparing for examinations, students should draw on their experience with these practical experiments. This looks especially important for the new Paper 3, which includes a Section A with unseen data based on the core/AHL syllabus, but could also be important on the other papers as well.

I could envisage the following sorts of short-answer questions (to be clear, I have made these up myself!):

  • Outline the use of models in:
    • measuring transpiration in plants
    • showing how absorption in the small intestine works
  • Explain the need to control variables when designing experiments to measure photosynthesis
  • Outline the importance of collecting adequate quantitative data when conducting osmosis experiments/measuring the rate of reaction in enzyme experiments.
  • Explain the importance of quantitative data in providing evidence to support climate change

Remember to look back over your experimental notebooks or old lab reports here – this does not require so much in terms of memorisation of facts but rather the process and justification of experimental procedures.

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

1.6 Mitosis and Cyclins

Serendipity and scientific discoveries—the discovery of cyclins was accidental (1.4)

The NOS  section in the Biology guide tells us that: “Scientists also have to be ready for unplanned, surprising, accidental discoveries.” (p6)  I see this as an opportunity to discuss the human side of the scientific process.  It is also another good time to link science (biology) to TOK. In TOK, we typically think of the natural sciences as being objective, neutral and based predominantly on Reason as a way of knowing. Meticulous observations, carefully planned experiments and independent verification are seen as the hallmarks of science and what gives it a greater sense of certainty than other areas of knowledge such as the human sciences or history. However, while these are important aspects of science, this ignores the fact that science is practiced by humans and as such, is prone to all the messiness that comes from being human.  Further, that like any human endeavour, luck, imagination and creativity are also key parts.

The discovery of cyclins was indeed a serendipitous event. Tim Hunt, who shared the Nobel Prize in Physiology or Medicine in 2001 for this discovery, said in his Nobel lecture…”I did not set out on my scientific career with the intention of studying the cell cycle, and had no idea that the winding road of discovery would lead in that direction.”(p1).  He began his career studying protein synthesis and took to spending summers in  the Marine Biological Laboratory at Woods Hole, Massachusetts, conducting research on mitosis in sea urchins.  It was this work that led to the discovery of the cyclins, proteins that were first identified because they peaked in concentration during interphase and then declined rapidly just before cell division.

While Hunt and his fellow researchers were demonstrating all the traits of the scientific method: – well-designed experiments testing out hypotheses – they had no idea of what they might discover and the joy of the unknown is an integral part of science at all levels.

References

Hunt, T. 2001. Protein synthesis, proteolysis and cell cycle transitions. Nobel Lecture.  http://www.nobelprize.org/nobel_prizes/medicine/laureates/2001/hunt-lecture.pdf

IB. 2014. Biology Guide: First Exams 2016. Peterson House, Cardiff.

Jackson, P. K. 2008. The Hunt for Cyclin. Cell. 134; 199-202.

Pulverer, B. n.d. Surfing the cyclin wave.  Nature.  http://www.nature.com/celldivision/milestones/full/milestone12.html

1.1 Cells – an Introduction Part 2.

Ethical implications of research—research involving stem cells is growing in importance and raises ethical issues

A prescribed title essay in TOK recently (May 2014) was about the extent that ethics should limit the production of knowledge in the natural sciences. Stem cells was the natural choice of an example for many students who chose this. This topic is the perfect vehicle to link TOK explicitly into the biology classroom and in doing so, allows for some wonderful discussion about this topic.  This year, we used a modified Tug for Truth as a way of structuring the discussion.

Screen Shot 2015-02-04 at 9.22.36 PM

Tug for Truth is part of the Visible Thinking truth routines from Harvard’s Project Zero.  You can download PDFs for all of the different routines from their website.  The lesson plan for the Tug-for-Truth suggests picking a controversial topic and then “tugging” the truth by mentioning either true or false claims.  In our case, one side tugged in favour of fewer restrictions on stem cell research and the other side called for tighter restrictions.  Each side had to justify their claim, thereby moving the “rope” in their direction.  The stronger or better-reasoned the claim, the greater the tug. Focusing on TOK allowed students to use the Ways of Knowing to frame their claims – emotion was one that was used consistently.

For students, there are a range of great websites available for understanding the stem cell debate and what researchers are discovering: try the University of Utah’s excellent Stem Cells information page, this detailed fact-sheet from Euro Stem Cells  and this summary of research advances from the Genetics Policy Institute.

1.5 The Origin of Cells

1.5  Testing the general principles that underlie the natural world—the principle that cells only come from pre-existing cells needs to be verified.

If Cell Theory tells us that all cells come from pre-existing cells, then where did the first cell come from?  What a wonderfully intriguing question!  What is the origin of life?

This is a topic that dovetails nicely with TOK, as it helps establish the process by which the natural sciences develop knowledge.  Although we cannot, of course, travel back to the early years of the earth, we can develop hypotheses and test them experimentally, discarding those for which the evidence does not support.  I think this NOS is also important because it emphasises that biologists can attempt to answer even the most perplexing questions through the scientific process.

Pasteur demonstrated that new cells could not spontaneously arise – they must therefore develop from existing cells.

http://www.sumanasinc.com/webcontent/animations/content/scientificmethod.html
http://www.sumanasinc.com/webcontent/animations/content/scientificmethod.html

Urey and Miller demonstrated that inorganic compounds could become organic under the right environmental and atmospheric conditions.

http://highered.mheducation.com/sites/9834092339/student_view0/chapter26/animation_-_miller-urey_experiment.html
http://highered.mheducation.com/sites/9834092339/student_view0/chapter26/animation_-_miller-urey_experiment.html

And, my favourite, the endosymbiotic theory – we all have prokaryotes inside us!

Ongoing research, demonstrated in the excellent Exploring Life’s Origins website, provides evidence of how protocells and membranes may have evolved.  It all fits rather nicely with the new Crash Course Big History series, of which episode 5 is on the origin of life.

1.3 Membrane Structure

Falsification of theories with one theory being superseded by another—evidence falsified the Davson-Danielli model.

As we saw with Watson and Crick, models play an important role in developing knowledge in biology.  This is particularly important when studying microscopic structures. Davson (a physiologist) and Danielli (a chemist) proposed a model in 1935 that was based on twin layers of protein surrounding the membrane – a protein bilayer.

Diagram of the Davson-Danielli model (Eichman)
Diagram of the Davson-Danielli model (Eichman)

This was based on studies dating back to the 1890s that had established a phospholipid bilayer surrounding cells. Their model appeared to be confirmed by subsequent electron micrographs taken in the 1950s that showed a darker band, thought to be protein, surrounding a lighter  core of phospholipids.

Electron micrograph supporting the Davson-Danielli hypothesis (Childs)
Electron micrograph supporting the Davson-Danielli hypothesis (Childs)

Developments in microscopy techniques, however, soon led to the revision of this theory and its replacement with the Singer-Nicholson model, which is the basis of our understanding today. They based their model on Freeze-Fracture techniques, which involved rapidly freezing cells and then fracturing them. This fracture plane is between the phospholipid bilayer.  Visible in these micrographs were a series of bumps or protrusions – which turned out to be the integral proteins embedded within the membrane.  The structure of the proteins themselves were also able to be studied in more detail and it was revealed that they were globular, rather than fibrous,  and thus unlikely to be find in a structural role. From this developed our modern understanding of a fluid, phospholipid bilayer containing a range of peripheral and integral proteins within it.

Freeze-Fracture Image (Childs)
Freeze-Fracture Image (Childs)

The current TOK Guide tells us that:

The methods of the natural sciences based on observation of the world as a means of testing hypotheses about it are designed to reduce the effects of human desires, expectations and preferences, in other words they are considered objective. (p36).

In what ways does this example demonstrate this? Why is it important to understand theories that are no longer used? If our understanding of science is dependent on technology, and technology is continually advancing, will we ever arrive at a single, final understanding of the natural world?

Sources:

Historical Development of Membrane Structure:

Childs, G. “Membrane Structure and Function.” Membrane Structure and Function. N.p., 19 July 2001. Web. 27 Jan. 2015.  http://163.178.103.176/Fisiologia/general/activ_bas_3/Membrane%20Structure%20and%20Function.htm

Eichman, P. “From the Lipid Bilayer to the Fluid Mosaic: A Brief History of Membrane Models.” SHiPS Resource Center || History of Biological Membranes. SHiPS Resource Centre, n.d. Web. 26 Jan. 2015. <http://www1.umn.edu/ships/9-2/membrane.htm&gt;.

Original Published Articles

Danielli, J. F., and H. Davson. “A Contribution to the Theory of Permeability of Thin Films.” Journal of Cellular and Comparative Physiology 5.4 (1935): 495-508. Wiley Online. Web. <http://onlinelibrary.wiley.com/doi/10.1002/jcp.1030050409/abstract&gt;.

Singer, S. J., and G. L. Nicolson. “The Fluid Mosaic Model of the Structure of Cell Membranes.” Science 175.4023 (1972): 720-31. Web. 27 Jan. 2015. <http://life.umd.edu/cbmg/Faculty/song/688D/Paperdiscussion/Singer%20and%20Nicolson%201972.pdf&gt;.

Other:

Allott, Andrew, and David Mindorff. Biology: Course Companion. Oxford: Oxford UP, 2014. Print.

Diploma Programme Theory of Knowledge Guide. Publication. Cardiff: IB, 2013. Print.