All posts by huanyi01pd2014

Soil Chemistry

The large-scale deforestation of tropical rainforest has had a great impact towards the environment, from the loss of habitats, to driving climate change. However what one often neglects is destruction of soil as a result of deforestation. Recently while watching a documentary about the deforestation in the Amazon I’ve noticed that the deforested areas were like deserts, which strongly contrasted with the lush lives among the rainforest floors. This is seen in the image below taken by John Michael Fay of National Geographic.

Figure 1: Deforested Amazon Rainforest (Fay, J.M., n.d. )

This led me to my question, what is the main factor(s) which determine the health of the soil or the extent of soil degradation?

Rainforest soil have little or no nutrients as they are rapidly used up by the flourishing plant life (Sayre, 1994). However a tropical rainforest has its own nutrient cycle, where it recycles the nutrients released by the decomposition of the organic matter on the forest floor. The Nitrogen cycle and Water cycles within the Tropical Rainforest, are the 2 major cycles which allows the rich existence of life among the forest (Witherick, M.E., 2010).

As learned from GCSE Biology, Nitrogen is a essential element for all living things. This is because the enzymes in and living organism which facilitates all kinds of reaction and processes is a form of protein. And from IB Chemistry we know that a protein molecule is identified by the functional group of an amine.

Figure 2: A Protein Molecule (University of New Mexico, n.d.)

Although the air is composed of 79% Nitrogen gas, but it is in a chemical form which is inaccessible to the  majority of living organisms. (Kiera, S., 2009). This form of Nitrogen can be converted to the usable form of nitrates and nitrites through Nitrogen Fixation, a process limited to some microorganisms. (Nitrogen Cycle, n.d.). The nitrogen fixation mechanism is undergone exclusively with prokaryotes using the complex enzyme of nitrogenase and can be seen from the following equation (Deacon, J., n.d.):

N2 + 8H+ + 8e + 16 ATP ↔ 2NH3 + H2 + 16ADP + 16 Pi

As seen with the visible layer of humus and rotting leaves of the rainforest floor,the hot and humid climate of the rainforest, this creates an ideal condition for decomposition. The decaying leaves, animal and insect droppings are decomposed by fungi and bacteria, which releases Ammonium (NH4+). Then through the process of Nitrification by bacteria, nitrate and nitrite compounds can be formed and assimilated into plants. This cycle is represented in the following diagram by Sierra Kiera, 2009:

Figure 3: The Nitrogen Cycle (Sierra Kiera, 2009).

Water is also an essential substance for all living organism as it is a component of aerobic respiration. The water cycle consist of the processes of: evaporation, precipitation, transpiration, through flow, surface runoff. In the diagram below by BBC Bitesize, it shows the uniqueness of the water cycle and the features that help the rainforest retain and store the precious water.

Figure 4: The Rainforest Water Cycle (BBC, n.d.)

These cycles are examples of close systems. As we have just learned in Chemistry, the closed system allows the rainforest to sustain a natural occurring equilibrium of its nutrient usage and creation and water storage and transfer. By removing the trees from the cycle, we are in fact “opening” the system, creating an imbalance in nature, interfering with the equilibrium. Since the trees are a large store of water in the cycle and prevent direct rainfall, the removal of the trees will cause the rain to wash away any nutrients and physically erode the soil. Since there are no more decaying roots and leaves from trees, there will be a lack of supply to nitrogen, which inhibits the growth of other organism. Also the lack of decomposition of these organic substances, will cause problems with water retention. Water plays a vital role not just in aerobic respiration but assimilating important dissolved minerals such as calcium and magnesium into plants. Due to the copious amount of rain in a tropical climate, the remaining nutrients in the soil is quickly washed away, leaving a sheet of bare land with no capability of plant growth.

In conclusion, the ratio of organic matter in soil is a major factor in determining the fertility of the soil. The decomposers (fungi and bacteria), the amount of nutrients, the decaying matter, and the water retention rate are all necessities in soil for the growth of plants. (Lewandowski, A., 2002). With the lack of either component, the soil can be easily susceptible to erosion, degrading the soil, in the long-run causing desertification. This poses a threat to the available arable land available for crops and other agricultural use, which directly affects our supply of food.


Sayre, April Pulley. Exploring Earth’s Biomes: Tropical Rainforest. New York: Henry Holt and Company, Inc, 1994, pp.1-56

Nitrogen Cycle. (n.d.). Microbiology The Beginning. Retrieved September 5, 2013, from

Kiera, S. (2009, October 13). Nitrogen Cycle in the Rainforest. Biology of Tropical Rainforest. Retrieved September 5, 2013, from

ACEER. (n.d.). Water Cycle. West Chester University. Retrieved September 5, 2013, from

Lewandowski, A. (2002). Organic Matter Management – Soil Scientist. University of Minnesota Extension. Retrieved September 5, 2013, from

BBC. (n.d.). BBC – GCSE Bitesize: Rainforest water and nutrient cycles. BBC – Homepage. Retrieved September 5, 2013, from

Deacon, Jim. “The Microbial World: The Nitrogen cycle and Nitrogen fixation.” Biology. The University of Edinburgh, n.d. Web. 5 Sept. 2013. <>.

Witherick, M. E., & Milner, S. (2010). Edexcel IGCSE geography. Harlow: Edexcel.

BBC – GCSE Bitesize: What are enzymes?. (n.d.). BBC – Homepage. Retrieved September 10, 2013, from

Image Citations:

“Biological Macromolecules.” UNM Biology Department Home Page. N.p., n.d. Web. 5 Sept. 2013. <>.

Fay, J.M., n.d. Retrieved from:

The Hole in Our Ozone

Remember back in 2006 when there was a big panic about the news of a hole in our ozone? However as time past, the talks about this hole gradually died down. Recently I came across a news article that states, “Some scientists believe the ozone layer, protecting earth from the sun’s ultraviolet radiation, could be recovering.” (Valente, 2012). At the moment since Earth is the only known home for human beings, it is important for us to understand and protect the environment we call home for our future generations. Therefore I decided to do some further research and reading into our Earth’s Ozone layer.

For those of you who don’t know what the Ozone is, here is a brief summary. The Ozone layer is a thin layer of gas that naturally occurring in the Earth’s stratosphere, an area roughly 20-50km above the Earth’s surface. (Figure 1) This layer of ozone protects us from the harmful UV radiation from the sun. (Wilson, 2013) UV radiation has high energy and a short wavelength therefore it can penetrate the skin, manipulating DNA, which in result can cause cancer and other skin disorders. (Office of Air and Radiation, 2010).

The location of the Stratosphere
The location of the Stratosphere (Figure 1)

What exactly is the Ozone layer made of? How does it prevent the penetration of UV radiation? The ozone is composed of the 3 different allotropes of oxygen, O, O2, and O3. These atoms and molecules undergo the Ozone Oxygen Cycle, where the molecules are broken down into atoms and atoms rejoin to make molecules. (Wilson, 2013). Here are some photographical representations of this process:

Under UV light, O2(g) ---> 2 O(g)
Under UV light, O2(g) ---> 2 O(g)
O(g) + O2(g) ---> O3(g)
O(g) + O2(g) ---> O3(g)

Both processes are exothermic. The light energy from UV light is transferred in to thermal energy or heat therefore being absorbed, preventing it from reaching the Earth’s surface. (NASA, 2008)

The Ozone hole is found above Antarctica and covers averagely around 17.9 million square kilometers. (Welch, 2012). (Figure 2)The hole is not a physical or literal hole but an area where there is severe depletion of Ozone. As National Geographic states, “Chlorofluorocarbons (CFC) used by industrialized nations for much of the past 50 years, are the primary culprits in ozone layer breakdown.” Because CFC’s are quite nonreactive as they are they are nontoxic, noncorrosive, nonflammable, and very stable. They were found in fire extinguishers, as propellants in aerosols, solvents in electronics manufacture, coolants for refrigerators and air conditioners and as foaming agents in plastics.

Biggest measured hole, Sept 22 2012, 21.2 million square kilometers
Biggest measured hole, Sept 22 2012, 21.2 million square kilometers

CFC’s easily rise to the stratospheric level on earth. In Antarctica, especially during the cold winter nights where there is no sunlight, a polar vortex, strong circular winds, isolates the air in the polar region that traps the CFC in the stratosphere.  (Carver, 1998) When the sun finally comes out again, and the UV light hits the clouds of CFC’s it breaks it down into atoms of chlorine and bromine. These acts as catalyst in the destruction of ozone

O3—>O2 + O

Cl + O3—>ClO + O2

ClO + O—>Cl + O2

According to the U.S. Environmental Protection Agency, One chlorine atom can break apart 100,000 ozone molecules, and bromine is 40 times more destructive. These atoms destroy much of the ozone over Antarctica, by causing an imbalance of ozone to the natural cycle. (Wilson, 2013). Luckily as of 2000, the Montreal protocol demands the removal of CFC in production of products. However even after regulations have been put into place for the ban of these harmful chemicals, the hole hasn’t had significant improvements. Paul Newman, a chemist from NASA predicts, “the ozone layer above Antarctica likely will not return to its early 1980s state until about 2060.”(LiveScience, 2012)


LiveScience. (2012, Oct 25). Antarctic Ozone Hole Is The Second Smallest Since It’s Been 20 Years. Huffington Post. Retrieved from:

Valente, M. (2012, Nov 24). Hopes grow on shrinking ozone hole. Aljazeera. Retrieved from:

Welch, C. (2012). The Ozone Hole (weblog). Retrieved from:

Wilson, T.V. (2013). Can We plug the hole in the ozone layer? HowStuffWorks. Retrieved from:

National Geographic. (n.d.). Ozone Depletion. National Geographic:Environment. Retrieved from:

Carver, G. (1998). Part III. Science of the Ozone Hole. University of Cambridge Centre for Atmospheric Science. Retrieved from:

Office of Air and Radiation. (2010, June). UV Radiation. U.S Environmental Protection Agency. Retrieved from:

University of Wisconsin. (2008, Sept. Chemical of the Week: Ozone. Retrieved from:

National Weather Service. (2007). Layers of the Atmosphere. National Oceanic and Atmospheric Administration. Retrieved from: