Developments in scientific research follow improvements in analysis and deduction—improvements in analytical techniques allowing the detection of trace amounts of substances has led to advances in the understanding of plant hormones and their effect on gene expression.
In this case, the NOS statement is referring to the use of genomics to analyse gene expression in plants. Some of the earliest experiments into tropisms were conducted by none other than Charles Darwin, whose 1880 book The power of movement in plants represented the first attempt to synthesise available evidence on tropisms and included many of his own experiments in this field. As developments in technology increased, the role of hormones became increasingly important and better understood.
Hormones influence gene expression; by detecting changes in gene expression, we can determine the role of hormones in this process. DNA sequences have been analysed to determine how these change in response to hormone exposure and mRNA levels (evidence of transcription and hence gene expression) can also be detected, pinpointing the cells that are responding to these hormones. Scientists have detected a range of common short sequences of nucleotides, from four to twelve bases in length. Different combinations of these appear to be linked to specific hormones and allow the genes to be affected by different classes of hormones. Details on some of these nucleotide sequences can be seen in the table below (Plants in Action). Experiments have revealed that plant hormones can act extremely fast – with mRNA changes detected as quickly as 2-5 minutes from exposure.
The advances in microarray analysis of DNA and mRNA was thus critical to our improved understanding of how plant hormones work.
Jennifer J. Holland, Diana Roberts, Emmanuel Liscum; Understanding phototropism: from Darwin to today, Journal of Experimental Botany, Volume 60, Issue 7, 1 May 2009, Pages 1969–1978, https://doi.org/10.1093/jxb/erp113 Web. Accessed 6 Feb, 2018.
“Modiﬁed Gene Expression.” Plants in Action, 1st ed., Australian Society of Plant Physiologists, 1998, plantsinaction.science.uq.edu.au/edition1/?q=content/9-2-4-modi-ed-gene-expression. Web. Accessed 6 Feb, 2018.
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.
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.
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.
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.
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….
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.
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.
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.
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 .
Compare and contrast the use of light and electron microscopes . (This links to topic 1.2 – Understanding: • Electron microscopes have a much higher resolution than light microscopes)
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.
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.).
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!
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:
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!
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:
NOS statement for 6.1 – Use models as representations of the real world—dialysis tubing can be used to model absorption in the intestine.
This becomes: Outline how dialysis tubing can be used to model absorption in the intestine (3).
“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.
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.
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.
Falsification of theories with one theory being superseded by another—plant families have been reclassified as a result of evidence from cladistics.
The use of DNA sequences to classify organisms has been an important breakthrough in classification. Previously, species were classified primarily on morphology (physical characteristics), which works some of the time but is less useful in other situations. Thus seemingly unrelated organisms have been grouped more closely together and those that were thought to be very closely related have been found to be more distant. Carl Woese used gene sequencing to not only overturn the existing dogma of the 5-Kingdom system, but to also propose that Archaea are more closely related to humans (eukaryotes) than to other prokaryotic bacteria. This was a major paradigm shift in microbiology and has since been recognised as “…one of the 20th century’s landmark achievements in biology…” by Dr. Nigel Goldenfeld (“Carl Woese | Carl R. Woese Institute For Genomic Biology”).
In another example, the Figwort family of flowering plants, underwent a dramatic recent reclassification. The figworts were a large family classified under the family Scrophulariaceae and included the popular snapdragons and foxgloves. Using three genes found in the chloroplast, researchers were able to determine that there were significant differences in lineage and so an entire family had to be reclassified into six families. See Olmstead et al. (2001), full text available online, for the full scientific story.
Butter-and-eggs, or Linaria vulgaris, is a close relative of the snapdragon, and no longer in the Scrophulariaceae
The monkey flower is a traditional snapdragon to many people, but is now in a more obscure family – the Phrymaceae.
n.a. ” Carl Woese | Carl R. Woese Institute For Genomic Biology”. Igb.illinois.edu. University of Illinois, 2016. Web. 25 Apr. 2016.
Essig, F. “Whatever Became of the Snapdragon Family?”. BotanyProfessor. Botanyprofessor.blogspot. April 5, 2012. Web. April 25, 2016.
Olmstead, Richard G., Claude W. dePamphilis, Andrea D. Wolfe, Nelson D. Young, Wayne J. Elisons, and Patrick A. Reeves. Disintegration of the Scrophulariaceae. Am. J. Bot. February 2001 88:348-361. Web. Accessed April 25, 2016.
Developments in scientific research follow improvements in apparatus—sources of 14C and autoradiography enabled Calvin to elucidate the pathways of carbon fixation.
At the beginning of the 20th-century, the scientific understanding of photosynthesis was centred on the combination of Carbon Dioxide with chlorophyll to produce formaldehyde as an intermediate before being converted to a carbohydrate (Benson). This view predominated up to the discovery of radioactive Carbon-14 by Kamen and Benson in 1940 (Benson).
In 1945, C14 became readily available to researchers in the US. A young researcher in California, Melvin Calvin, was told by a senior scientist at the University of California-Berkley that he should start to do something interesting with it. So began a research focus that led to the Nobel Prize in Chemistry in 1961 “for his research on the carbon dioxide assimilation in plants” (“Melvin Calvin-Facts”).
The shape of the apparatus Calvin used led to it being called the “lollipop” experiment. The central “lollipop” contained a suspension of algae, to which was introduced the radioactive carbon. Periodically, a sample of the algae was released into the tube below (the stick of the lollipop) where it was immediately killed by a solution of alcohol. The compounds could then be analysed through chromatography. By using the radioactively labelling isotope of carbon, it was possible to trace the path the isotope took and by analysing the intermediate compounds the researchers were able to determine what happened to the carbon – where was it absorbed and what was it used for? The series of experiments helped identify the sequence of carbon compounds produced in the Calvin Cycle and also disproved the idea that chlorophyl fixes carbon.
These experiments were carried out be many individuals over a period of nearly 15 years and in some ways it seems unfair that Calvin tends to receive all the credit (as well as a solo Nobel Prize). A personal report by Andrew Benson (available here) gives a good idea of the collaborative nature of this process.
Benson, A. Following the path of carbon in photosynthesis: a personal story. Photosynthesis Research. 73: 29–49, 2002. Web. April 20, 2016.
Looking for patterns, trends and discrepancies—patterns of chromosome number in some genera can be explained by speciation due to polyploidy.
Polyploidy is a condition of possessing more than two sets of chromosomes. This duplication typically occurs during meiosis and may result in triploid (3n), tetraploid (4n) or even hexaploid (6n) offspring. This sounds potentially devastating (think of the effects of just having one extra chromosome!) but is thought to be a key driving factor in speciation in some organisms. Up to 1 in 100,000 flowering plants are polyploid, showing a high degree of tolerance. In fact, over 75% of flowering plant species may be recent polyploids! Common polyploids include potatoes, bananas, cotton, wheat and watermelon.
Although it also can occur in amphibians and fish, mammals and birds are typically less tolerant, with an estimate of 10% of spontaneous miscarriages in humans being due to polyploid embryos (Woodhouse et. al.).
The advantages of polyploidy include:
The extra sets of alleles mean that the offspring is less likely to be affected by recessive mutations
it promotes heterozygosity, which can make the hybrid offspring more fit than the parents
the extra sets of genes may evolve new functions over time
it seems to increase asexual reproductive ability, which could be advantageous under some conditions.
Potential disadvantages include:
the extra genetic material affects the surface area to volume ratio of the nucleus and the cell, disrupting many important processes
disruption to normal mitotic and meiotic divisions
negative effects on gene expression and interaction
n.a. Polyploidy. University of Texas at Austin. The Chen Laboratory. 2016. 28 August. 2018
n.a. Speciation. Bioninja. N. p., 2016. Web. 7 Apr. 2016.
Woodhouse, M., Burkart-Waco, D. & Comai, L. Polyploidy. Nature Education 2(1):1. 2009. Web. April 7, 2016.