Hydrological optics and light capture in the aquatic enviroment.

October 23, 2014 in Uncategorized

This essay shall discuss hydrological optics, how light behaves in water, and light capture in particular the package effect and how it influences the absorption spectra. The radiation we commonly call light lies between 400-700 nm and coincidently is the same wave length for both photosynthesis and human sight, this gives us an easily comparable spectrum to deal with as I may compare to both colour of the light (ie. Red or blue) or the wavelength. Light is greatly influenced by the medium in which it travels through so the behaviour in water is significantly different to the behaviour in the atmosphere however we must consider the basic behaviours of light in the atmosphere before we approach such topics as absorption and scattering.

Photons travel at a speed of 3*10[8]ms[-1] and on a summer day in direct sunlight 1m[2] will receive 10[21]quanta s[-1]. Although light often behaves as a particle it also as wave like properties, the wavelength of light can be found by c/v or the speed of light divided by the frequency.

The energy of light is not constant but changes with the frequency of the waves and can be found by E=hv where h= 6.63*10[-34] (planks constant) consequently red light only has 57% of the energy as blue light (700nm/400nm respectively) (Falkowski and Raven 1997). Radiant flux, Φ, is the time rate of the flow of radiant energy (expressed as W(Js[-1]) or quanta s[-1]). If it is appropriate to indicate radiant flux as a function of ᴓ or ɸ then it can be expressed by L(ᴓ,ɸ) (where ᴓis the zenith angle and ɸ is the azimuth angle). The radiant intensity, I, is the measure of radiant flux per unit of angle in a specific direction and is given by the equation: I=dɸ/dW. Irridance, E, is the radiant flux per unit area of a surface (W (or quanta s[-1]) m[-2]) and is given by the equation E=dΦ/ds. Ed = ∫_2π▒〖L(ᴓ,Φ)cos⁡〖ᴓ dw〗 〗 is the irridance due to downwelling light. Eu=∫_(-2π)▒〖L(ᴓ,Φ)cos⁡ᴓdw 〗 is the irridance due to upwelling light (with allowance made for ᴓ{90,180})(Kirk 1986).

If we move aside from theory then the radiation fields have varying irridance and scalar irridance values with the photosynthetic range, this range effects the extent to which photosynthesis can take place, this is expressed as the variation of irridance or scalar irridance per unit spectral distance across the spectrum (Wm[-2]nm[-1]). It is possible to understand the radiance distribution over all angles at any point in a medium by simply understanding the angular structure of the light on the point. Even this comes with its problems as if we were to use only 5͘͘͘͘͘͘͘· intervals this would represent 1369 separate radiance values, as this quantity is impractical we use 3 average cosines: upwelling light/ downwelling light/ total light, and the irridance reflectance to as a more approachable technique. Photons are either absorbed or they scatter when entering the aquatic medium, the absorption and scattering properties of the given aquatic medium are given by the: absorption coefficient, scattering coefficient and the volume scattering coefficient- these are inherent optical properties as there magnitude only depends on the specific substances comprising the medium.Some of the incident light from the beam is absorbed by the medium, the fraction of incident flux which is absorbed divided by the thickness of the thin layer of medium is the absorbtion coefficient, a. Some of the incident light is scattered by the medium, the fraction of incident flux scattered by the thin layer of medium divided by the thickness of the medium is the scattering coefficient, b. expressing these two ideas quantitatively we can obtain two equations: A=Φa/Φo or B=Φb/Φo- where Φo is the radiant flux incident of the beam, Φa is the radiant flux absorbed by the medium, Φb is the radiant flux scattered by the medium(Kirk 1986).

Now the light has reached the organism, the light must be captured for photosynthesis, this light must be in the specific absorption spectrum. The absorption spectrum may be expressed by absorptance, A, percent absorption, absorbance, D (D=-log⁡〖(1-A)〗) – the parameter of light absorption depends on the purpose of the absorption. The absorbance spectrum depends on the chlorophyll/ carotenoids/ billiproteins composition in the thylakoids- the fundamental light harvesting system. The size or shape of the chloroplasts, whether there is a single cell or colonies as well as pigment composition all influence the specific absorption coefficient per unit pigment. To determine the absorbance spectrum of a single thylakoid is to indirectly calculate it by dispersing chloroplasts into particles which eliminate size and shape influencing the absorbance spectrum. Absorbance spectrum of a cell or colony, suspension or segment of a thalllus or leaf will differ significantly from the dispersed thylakoid fragments thus the peaks are less pronounced and have specific absorption per unit pigment. This phenomenon is due to the package effect which is where pigment molecules are contained within discrete packages within chloroplasts, this lessons the effectiveness of which the light is collected from the field. The package effect is greatest when absorption is greatest(Kirk 1986).

Due to the nature of the package effect you can conclude the identity: Dsus/Dsol<1 or the absorbance of the suspension is less than the absorbance of the solution. If there are n particles per ml and the medium is illuminated by a parallel beam of light the j[th] particle (in solitude) absorbs proportionally α[j]A[j], where α[j] is the projected area of particle in the direction of the beam and A[j] is the particle absorption (fraction of light incident on it which is absorbed). The standard natural logarithm of absorbance is: ln⁡〖1/(1-A)〗 which becomes: ln⁡〖1/(1-α[j]A[j])〗 with the j[th] particle the subject. If you apply beers law for 1 cm path length the equation: ∑_(j=1)^n▒〖α[j]A[j]〗= nᾱĀ is reached where ᾱĀ is the average absorption cross-section. The base-10 logarithm of the suspension is given by Dsus=0.434nᾱĀ. If the pigment was in a solution then the concentration would be: nCṼmg ml[-1] where Ṽ is the average volume of the particles and C is the pigment concentration within the particles. The absorbance due to the dispersed pigment is: Dsol=0.434nCṼy where y is the specific absorption coefficient (absorption coefficient due to the pigment at concentration 1mg ml[-1]). Combining the equations we can see that Dsus/Dsol=ᾱĀ/CṼy is true so therefore can conclude that ᾱĀ/CṼy<1. If the particles only absorb weakly then Dsus≈Dsol and ᾱĀ≈CṼy. If we keep the values of α and Ṽ constant but increase either C, by increasing the pigment concentration in the particles, or y, by changing the wavelength to a more intensely absorbed wavelength, the value of CṼy will increase. As C or y increases so does A however A cannot increase in direct proportion as when A reaches a value nearing 1 there is less leeway to increase in value. This causes the obvious discrepancy between spectrum of the particle suspension and the corresponding solution as absorbtion increases by individual particles increases(Kirk 1986).

This essay has discussed the behaviour of light in and out of the water medium and how the particular water medium will influence the intensity of light before reaching any organism. I have briefly covered the pigments and thylakoids which capture the light but have looked in more detail at the way the pigments are arranged influences the absorption spectrum with some basic calculations to show how changing the concentrations of pigments and the specific wavelength can influence the specific absorption graph.


Kirk, J.T.O. (1986). Light and photosynthesis in aquatic ecosystems

Falkowski, P.G., Raven, J.A. (1997). Aquatic photosynthesis

Great White Shark VS Saltwater Crocodile

October 20, 2014 in Uncategorized

Although rare, it is certainly not unheard of for humans to be attacked by aquatic animals. The question is, what marine species of animal is most dangerous to us humans?

Figure 1: A Great White Shark (Carcharodon carcharias) and a Saltwater Crocodile (Crocodylus porosus). nationalgeographic.com

Sharks will continuously come up on simple Google searches of deadly marine animals, as well as in books, surveys and documentaries. The chances of being attacked by a shark are one in 1.5 million (ISAF). Even though the odds are very little, the public are lead to believe that the main cause of these rare attacks are mainly because of the Great White Shark (Carcharodon carcharias). This is down to a number of movies about unrealistic shark attacks and a large amount of attention the media gives sharks, such as Shark Week on the Discovery Channel. However, sharks are not the only animals around the coast line that prove to be a threat to humans. In some places around the world, such as Australia, Southeast Asia and eastern India, similar locations to where white sharks are found, there are other active and dangerous animals in the water and around the waters edge, such as the Saltwater Crocodile (Crocodylus porosus), the largest reptile in the world.


Figure 2: A table showing recorded attacks on humans by Saltwater Crocodiles, 1971-2004. Caldicott, D.G (2005).

An advantage that the Saltwater Crocodile has that the Great White Shark does not is that the Saltwater Crocodile can inhabit the land as well as water, increasing the chances of human interaction. Although not strictly aquatic, the Saltwater Crocodile will spend its time waiting in the shallow waters of rivers and waterholes, waiting for prey to come to the edge. When given the opportune moment, the crocodile will grab its prey from the shoreline and drag it underwater, drowning it. The average size of Saltwater Crocodiles to be recorded is between 3 to 4m  however, individuals have been found to be seven metres long, proving why the Saltwater Crocodile is the largest reptile in the world (Ryan, 1998).

Figure 2. shows a recording of numbers of Saltwater Crocodile attacks in different conditions. The table states that 76.7% of nonfatal attacks were during the day and 23.3% of nonfatal attacks were at night. This would suggest that the crocodiles were more likely to attack during the day, also when most humans are active, leading to an increase of chances of interaction between both. However, Fig.2. also shows that 50% of fatal attacks were during the day and the other 50% during the night. This shows that a Saltwater Crocodile’s behaviour is somewhat unpredictable and would attack unprovoked at any time of day. Although it has to be taken into consideration that some cases shown on Fig.2 are listed as unknown time of day. (Caldicott, 2005). Their unpredictable behaviour allows them to surprise their prey when hunting. It is also this behaviour which leads to attacks on humans and makes them contenders for being one of the most dangerous animals to humans. Similarly, Great white sharks have hunting techniques to surprise their prey, their dark grey colouring on their dorsal side allows them to blend in with the rocks on the seabed, while their white ventral side camouflages them from underneath to blend in with the surface of the water as the light reaches it (Peschak et.al 2006).

Great White sharks, the largest predatory fish, have been recorded to grow to six meters long (Bruce et.al, 2006), smaller than recorded saltwater crocodiles. This alone could intimidate a human due to the average size comparison. Steven Spielbergs’ 1975 film ‘Jaws’ was an interpretation of Peter Benchleys’ novel with the same title published in 1974, a story about a great white shark found to be hunting humans in a popular holiday destination. This has created a misconception about Great White Sharks, that they will prey on every human they come across. Found across the world nearing to warmer climates and the equator, Great White Sharks can be seen closer to the shore rather than out in the ocean in order to find prey (Last & Stevens 2009). This mimics Benchleys’ behaviour of the Great White Shark coming into human civilizations such as shores however, the odds mentioned above conclude that Great White Sharks do not actively prey on humans like in Benchleys’ novel.

Figure 3: Showing the number of shark species known to have attacked a human. The Great White Shark (Carcharodon carcharias) has a much larger total. Florida Museum of Natural History, University of Florida .

Records show that there have been approximately 279 White Shark attacks on humans since 1580, 78 of these attacks have been recorded as fatal (ISAF). This can be seen in Figure 3. This same record, created by the Florida Museum of Natural History, University of Florida, shows that the majority of shark attacks recorded have been from White Sharks. Although, when compared to other species of sharks, the White Shark looks to be the most deadly to humans, the witnesses and victims of the attacks could easily mistake the species of shark, assuming that it is a Great White Shark because of the nature they have been perceived to show.  It is less likely that another species of crocodile would be mistaken for a Saltwater Crocodile when attacking due to the area they populate and their size, making witness appeals and records of attacks more reliable than White Shark attacks.

Figure 4: A graph comparing the amount of attacks by different species of Crocodile. 2008-2013 – theconversation.com

Both species of animalia, the Great White shark (Carcharodon carcharias) and the Saltwater Crocodile (Crocodylus porosus) are specifically mentioned to be deadly in ‘A Colour Atlas of Dangerous Marine Animals’ (Auerbach et.al, 1990), an illustrated book providing information and records of the species believed to be a danger to humans. The question of which of the two is more dangerous to humans is unclear due to the rarity of attacks however, by looking at evidence such as records of attacks,  (figure 3 and figure 4) and learning the behaviour of both species, it can be assumed that the less known Salt water crocodile tops the Great White Shark as most dangerous marine species out of the two.


Auerbach, P.S, Campbell, D.R, Halstead, B.W (1990). A Colour Atlas of Dangerous Marine Animals. London: Wolfe Medical Publications.

Bruce, B.D, Stevens, J. D,  Malcolm H (2006) Movements and swimming behaviour of white sharks (Carcharodon carcharias) in Australian waters. Volume 150, Number 2.

Caldicott, D.G (2005). Crocodile Attack in Australia: An Analysis of Its Incidence and Review of the Pathology and Management of Crocodilian Attacks in General. Adelaide, Australia: Elsevier. 143–159.

ISAF Statistics on Attacking Species of Shark. Florida Museum of Natural History, University of Florida http://www.flmnh.ufl.edu/fish/sharks/statistics/species3.htm

Last, P.R & Stevens, J.D (2009). Sharks and Rays of Australia. 2nd ed. Melbourne: CSIRO. p176-177. http://www.publish.csiro.au/samples/Sharks%20and%20Rays%20of%20Australia.pdf

Peschak, T.P, Scholl, M.C (2006). South Africa’s Great White Shark. Cape Town: Struik. p19.

Ryan, C (1998) Saltwater Crocodiles as Tourist Attractions, Journal of Sustainable Tourism 6:4, 314-327 – http://www.tandfonline.com/doi/pdf/10.1080/09669589808667319

Shark Week on discovery channel – http://www.discovery.com/tv-shows/shark-week/#!/sun


Figure 1: Great White Shark http://animals.nationalgeographic.com/animals/photos/great-white-sharks/

Figure 1: Saltwater Crocodile http://animals.nationalgeographic.com/animals/reptiles/saltwater-crocodile/

Figure 2: Caldicott, D.G (2005). Crocodile Attack in Australia: An Analysis of Its Incidence and Review of the Pathology and Management of Crocodilian Attacks in General. Adelaide, Australia: Elsevier. 143–159.

Figure 3: ISAF Statistics on Attacking Species of Shark. Florida Museum of Natural History, University of Florida http://www.flmnh.ufl.edu/fish/sharks/statistics/species3.htm

Figure 4: http://theconversation.com/croc-attacks-a-new-website-with-bite-20671