Why is the Sky Blue?

By Scott Mattison (@FoolsPizza)

Blue Sky

At some point, every parent is asked why the sky is blue. A good way to explain this to a five year old is to ask them what colors make up white light, in case you forgot its the rainbow. Remind them the colors of the rainbow (red, orange, yellow, green, blue, indigo, and violet). Then explain that the air we breathe actually changes the way light moves. This is because air is made up of molecules that the light hits and changes the light’s direction. Finally, you can simply explain that the inner part of the rainbow (blue, indigo, and violet) move through the air the best to reach our eyes, giving the sky its blue color.

For the kid that keeps asking, “why” you can give them the simple answer to this question: an effect known as Rayleigh Scattering caused by small molecules in the atmosphere is what gives the sky it’s blue color. Rayleigh scattering causes shorter wavelengths to be scattered a lot more (1/wavelength^4).  Remember the colors of the rainbow from longest wavelength to shortest wavelength are red, orange, yellow, green, blue, indigo, and violet. Blue being a shorter wavelength means blue light dominates the scattered light coming from the sky.

A tricky question a kid could ask is, “why the sky isn’t violet?” This is a great question. Violet is the shortest wavelength of light we can see, so if shorter wavelengths are preferentially scattered, why isn’t the sky violet? The answer to this question is actually really cool and makes light really fun to study!

To fully explain to your (hypothetical?) child why the sky isn’t violet, first you should talk a bit more about how light scatters. The two most common ways that light scatters are Mie Scattering and Rayleigh Scattering. Mie’s solution to the scattering of light allows us to model the movement of light as it interacts with particles, like dust and water, that are similar size or larger than the wavelength. With Mie scattering, light is mostly scattered along the direction it originally hit the particle, and the effect is not wavelength dependent.

Light undergoing Mie Scattering

Rayleigh scattering, as we have already mentioned, is what gives the sky its blue color. Rayleigh scattering occurs when light interacts with particles much smaller than the wavelength size. Light that undergoes Rayleigh scattering is equally scattered in every direction. Rayleigh scattering is exponentially stronger with shorter wavelengths, meaning short blue, indigo, violet end of the spectrum is much more strongly scattered than the red, yellow, green end of the spectrum.

Light Undergoing Rayleigh Scattering

Now that your (again, hypothetical ) kid knows how light scatters, you can help them begin to build an understanding of why the sky is blue. Light that is Mie scattered will mostly continue moving in the direction it was moving. So if you let your kid look at the sun (a terrible idea), they will see the effects of Mie scattering (especially if there are clouds in the way). However, if you kid looks at the rest of the sky, light that has been Mie scattered is going to keep moving away from their eyes. So overhead, Rayleigh scattering is dominant, giving the sky its blue color.

Up to this point you have only really explained to your kid the short answer for why is the sky blue. The second part of this answer relies on a the second way that light can interact with matter, absorption. I have previously talked a little about the absorption of light when I tried to figure out how to attach a laser to a shark. Here though, I am going to focus on how our bodies use the absorption of light to help us perceive the world around us.

The eyes of most people detect light via rods and cones. Rods and cones absorb light and convert the energy absorbed into a signal sent to your brain. Rods are responsible for non-color specific and night vision, whereas cones provide you with your perception of color. Most people have 3 types of cones in their eyes, one for the detection of shorter wavelengths, violet to blue, one for the perception of longer wavelengths, orange and red, and one for the perception of the middle wavelengths, green and yellow.

Rods and Cones
The light absorbance of rods and cones. Image Source: Wikipedia

Now, what colors make up white light? There are two answers to this question the first is shown on the album cover to Pink Floyd’s dark side of the moon. As we pointed out at the start, white light is made up of all of the colors of the rainbow. The second answer to this question is more familiar to anyone who works with colors on a computer. We can simulate white light with simply an even combination of red, green, and blue. In fact, we can actually simulate most colors by manipulating combinations of red, green, and blue.

So now we can get back to the question at hand, why is the sky blue? While Rayleigh scattering does preferentially scatter violet light over blue light, our eyes are far more sensitive to blue light. Additionally, Rayleigh scattering is occurring in the sky for all wavelengths of visible light, shorter wavelengths are merely scattered more. In fact what we are seeing as the color blue is really our eyes average out all of the wavelengths present in the sky and creating the perception of blue light.

Now that your inquisitive (possibly hypothetical) child has likely completely lost interest you can explain that all color is merely how our eyes perceive the world. This is why individuals who are colorblind may not realize it until much later in life. Then you can go show them other cool optical illusions that are so good are fooling us.

Lunar Light as a Trigger for Werewolf Transformations

By Scott Mattison (@FoolsPizza)

Most people are familiar with the idea of a werewolf, a human with the ability to shapeshift into a wolf or humanoid wolf monster.There are many variations of the concept of a werewolf, but most versions center around the notion that the full moon acts as the catalyst for the transformation. Completely ignoring the fact that such a transformation would require a rapid reorganization of several body systems, the time has come to ask the hard question: Are there any unique properties of a full moon that could cause such a transformation?

Now, you may be thinking that werewolves are magic, and clearly there is no need for science to try to explain magic. However, as scientists, it is important to question the unknown and develop a deeper understanding of our world. While werewolves may not be real, it is still fun to think of the answers as a what if scenario. [As a side note, if there is an entire magical community running around like in the Harry Potter books, they are colossal jerks for not sharing all of the medical breakthroughs that magic would bring.]

Does the full moon possess any unique qualities that could trigger the transformation from human to wolf? In many descriptions of werewolves, lycanthropy is a curse passed down by the bite of another werewolf. This curse may be some form of virus, similar to rabies, but I will leave that discussion to those more suited towards it.

As a general note, some stories involving werewolves treat the transformation as a timed process that occurs with the cycle of the moon, regardless of the presence of moonlight. Timed processes such as this are called lunar rhythms. Lunar rhythms are really neat, but this blog post will focus more on the moon and moonlight itself.

Most stories of werewolves involve the transformation typically only occurs at night during a full moon. The fact that the transformation only occurs at night is very important as full moons are often visible in the daylight. In fact some months, the full moon occurs entirely during the day. This tells us one of two things 1) it is not the shape of the moon that is triggering the transformation or 2) bright sunlight acts as an inhibitor to the transformation process.

Furthermore, many accounts of the transformation describe the individual only changing after being bathed in moonlight, and not requiring the individual to look at the moon. This observation further supports the idea that the shape of the moon is not triggering the transformation process. Confirmation of the existence of a blind werewolf would be required to fully confirm this theory. However, finding such a specimen may prove challenging.

This leads us to the idea that moonlight is what acts as the primary catalyst for the transformation. It is very possible for a virus to introduce an optically sensitive component to cells of the body. In fact there is a whole field of science, known as optogenetics, which allows scientists to introduce light-based control of muscle and nervous cells through genetic engineering. In that case, what is special about the light of a full moon? Well, during a single lunar cycle, lunar brightness increases exponentially as the moon waxes and decreases exponentially as the moon wanes. This means that during a lunar cycle, the full moon is the brightest. 

There are two big issues with the hypothesis of lunar brightness. The biggest issue is that if the transformation is caused by a brightness threshold alone, then a werewolf would transform anytime they walked out into the sunlight, as the moon is simply reflecting the light of the sun. This actually relates back to one of our observations earlier, bright sunlight may act as an inhibitor to the werewolf transformation. This would mean our virus is introducing some form of optically sensitive molecule that is activated at a certain threshold of light, but deactivated in some way by bright sunlight.

Sunlight blocks the transformation of a person into a werewolf.

This isn’t too far fetched as the sun is roughly 400,000 times brighter than the full moon. Alternatively, there could be some spectral shift of the light reflected by the moon relative to the sun that triggers the transformation. The moon isn’t a perfect reflector and does absorb some wavelengths more strongly than others. The reduction of one wavelength beneath a certain threshold may be the requirement for the transformation to occur instead.

The second biggest issue is that the brightness of the full moon varies between lunar cycles depending on the angle between the moon and the earth, the distance between the moon and the earth, and the presence of small particles in the atmosphere. Interestingly, these changes are noteworthy because they do actually coincide with certain descriptions of werewolves.

Some accounts of werewolves describe the potential for the change to occur on the days preceding and following a full moon. This could be due to the moon being closer to the earth (so that it takes up more of the sky) or at a point higher in the sky (so that it is traveling through less atmosphere). Furthermore, many accounts of werewolf encounters describe the transformation occurring as the moon appeared from behind the clouds. This is in agreement with the theory that a certain optical threshold must be reached to cause the werewolf transformation.

In conclusion, we propose that lycanthropy is caused by the introduction of an a molecule that responds to light into the host’s cells. This molecule is activated by light above a certain intensity threshold and inhibited by the presence of bright sunlight. Thus, if werewolves are real and follow the rules discussed above any individual who has been bitten by a werewolf need only to wear a thick layer of sunscreen on the nights leading up to and following the full moon to prevent their transformation.

Author’s Note:

Major Spoilers for “Harry Potter and the Prisoner of Azkaban” Follow so if you haven’t read a 19 year old book (or watched a nearly 14 year old movie) stop reading here

My wife and I had a long debate on whether or not the werewolves in the Harry Potter books follow lunar rhythms. Through most of the books it is implied the transformation occurs whether or not the individual is exposed to moonlight during a full moon, thus implying a lunar rhythm. However, in the third book Lupin doesn’t transform until the moon comes out from behind a cloud and bathes the party in moonlight; implying moonlight is the catalyst for the transformation. So either the cloud moment is just meant as dramatic flair and he would have transformed at that exact moment either way (which could is probably true, but annoyingly coincidental) or the cloud moment is the answer and Lupin should never transform if he simply locked himself in a basement or dungeon. Either way we were definitely overthinking the whole situation.

Arming Sharks with Laser Beams: A Warm Meal or Seared Meat?

by Scott Mattison (@Fools Pizza)

An update drawing of our hypothetical shark. (Credit to @AndersonEvolve for correcting the number of gills a shark typically has)

Last time, we determined a theoretically useful wavelength (500 nm) for arming sharks with a laser beam. This wavelength was useful as it would provide a decent transmission range through salt water. There are still three more major challenges facing the successful completion of our design (and several other smaller ones).

Laser is actually an acronym for light amplification through stimulated emission of radiation. Stimulated emission is the release of a photon of light as an electron relaxes from an excited energy state back to a ground state after absorbing energy. This means that when one photon goes in, two photons come out, generating additional light. Stimulated emission was predicted in Einstein’s quantum theory of radiation, and the first laser was built in 1960 by Theodore Maiman.

Stimulated Emission
A simplified rendering of stimulated emission using two energy levels.

The big take away of stimulated emission is that to build a laser, we typically need electrons to be in an excited state. There are several different materials that can give light amplification through this method including glasses infused with rare earth elements, semi-conductor materials, dyes, and even various gases like carbon dioxide and Helium Neon.

There are important considerations for selecting  the type of laser for a specific application. In our case, we are going to be operating a laser in the ocean, without an easy method for retrieval. Fortunately, as we are subcontracting for an evil organization, money is not a major consideration. However, the movements of the shark and harsh conditions of the ocean would require a stable laser source, and we need this source to be fairly small, as we do not want the laser to interfere with the shark’s ability to swim. Most importantly, we want to be able to cook a fish from a distance. From the American National Safety Institute standard Z136.1, we can determine the maximum safe exposure for skin to a laser beam. We will assume that we want the fish to cook in under 0.1 seconds as both the shark and fish will likely be moving. This means that we will require a laser intensity of over 6 W/cm2 just to pass the safety threshold of laser exposure. Likely, a high powered diode pumped solid state laser could provide the power and stability we need at our target wavelength; however, there are still a few more issues to consider.

The second major challenge is building a laser that can actually cook a fish underwater. Lasers are excellent at providing targeted heating. That is what makes lasers great tools for precision cutting, which is why we have laser cutters and use lasers for targeted treatment of cancers. Unfortunately, despite what movies and television shows tend to depict (looking at you Big Bang Theory), this means lasers are not good at doing more than targeted heating. With a laser, the shark isn’t going to get a warm meal, instead it will simply sear meat in one location. In fact, if we increase the laser power to increase heating, we are more likely to cut the fish in half than actually cook it (think laser cutter). We could work around this using beam steering components, but even if we could steer the beam to hit the shark’s meal, our laser wouldn’t penetrate deeply enough into the fish without burning away the outer layers (this would also probably smell terrible).

If this wasn’t enough of a problem, our final challenge is powering this laser, underwater. A laser diode runs typically with no better than 20% efficiency. This means to output 1 watt of optical power, the laser requires 5 watts of electrical power. Obviously, to save energy (and increase competitive advantage), the laser would not be operating constantly and instead would use some form of motion tracking to switch on and off. Even under these conditions, the laser would require a very powerful battery in order to operate effectively. Currently, finding a  lightweight and durable power source that the shark can carry around  and provide a long enough operational lifetime to make the efforts worthwhile is a tough challenge. This might be the final deal breaker in our arming sharks with laser beams scenario.

So far we have really only discussed the large number of technical challenges to arming sharks with laser beams to provide a warm meal. We have completely ignored the ethical dilemmas (short answer: it’s bad) and whether the laser would even provide a competitive advantage to the shark (it won’t). Additionally, we haven’t even discussed how to actually arm the sharks with lasers. Based on this low level of analysis, we can conclude that following the ideas of a person who calls himself Dr. Evil might be a bad idea.

Arming Sharks with Lasers

by Scott Mattison (@FoolsPizza)

In the immortal words of Dr. Evil: “Every creature deserves a warm meal.” To meet this call to action, we have devised a method for efficiently providing sharks with laser beams. To accomplish this, we are going to have to design a high energy laser source that is capable of being submerged in water.

Rendering of proposed design (not to scale)

I will preface this blog post with the knowledge that someone has in fact put a laser onto a shark. As the laser used could not even blind a fish, much less cook one, I do not think it meets our demands.

Building a working laser isn’t that hard; however, designing a laser to attach to a shark has some special challenges. I am going to break down some of the design process over a few posts. Ignoring the ethics of the matter (it’s bad) or if we this is even a good thing for the sharks (it’s not), the first thing we need to do is decide what wavelength of light we want the laser to be.

For this decision, and many future ones, the most important variable that we face is that we will be working in the ocean. You may have noticed that the ocean is blue, at least in the deeper parts. Despite a somewhat odd popular opinion, the ocean is not blue because it is reflecting the sky. In fact the ocean and the sky are actually blue for completely different reasons. To understand this we will have to talk a bit about physics of how light interacts with the environment.

There are many ways light can interact with the world, but the two methods that primarily define how we observe the world are scattering and absorption. Scattering of light in the atmosphere due to small particles, known as Rayleigh scattering, preferentially scatters shorter wavelengths of light than longer wavelengths. Rayleigh scattering is what gives the sky its blue coloring. Readers who are familiar with wavelengths of visible light may be thinking that blue isn’t the shortest wavelength, and asking why isn’t the sky violet. This question is an answer for another time, but the short answer is: colors are crazy.

Unlike the sky, the ocean is blue because of absorption. Absorption occurs as an interaction between light and the electrons of molecules. If the energy level of photon of light is equivalent to the energy difference between two electron energy levels then the electrons may absorb that photon. Without delving too much into the quantum mechanics here, the electron configurations of water make it absorb light of longer wavelengths (more red) better than it absorbs light of shorter wavelengths (more blue).

Water does not absorb light so strongly that we see these effects on a small scale, hence a glass of clean water will appear clear instead of blue. However, over a distance of several meters this absorption starts to become very pronounced. When scuba diving, the deeper a diver goes into the water the less color they will be able to see. In fact, during deep water scuba certification you actually take a color chart down with you as you dive and get to observe the loss of color first hand.

Since absorption takes place over such a long distance, in smaller bodies of water and in bodies of water with a lot of sediment and debris, scattering begins to play a larger role in the appearance of the water. Scattering is why a lot of lakes and beaches will appear brown or green in color instead of blue as light is being scattered back from within the water before the absorption process can play a significant enough role to make water appear blue.

So, what does this all mean for our shark and its warm and tasty meal? Well for starters, this means that we will want to select our wavelength of light based on our desired operating distance. I am not a marine biologist; however, it may be reasonable to assume that we want our shark to be able to cook a warm meal from at least 100 feet away. Based on this distance and the absorption levels of light by water, we are going to want to match the wavelength of our light source to the absorption of the ocean and go for a light source that is shorter.

Absorbance of visible light by water. Horizontal axis is wavelength in nanometers and the vertical axis is absorbance in inverse meters. This figure is reproduced from Wikipedia all rights belong to the original authors.

Looking at the graph above, there is a minimum absorbance around 420 nm, but for reasons we will discuss in more detail in my next post, we want to select a wavelength of light that will penetrate more deeply into biological tissues. Despite biological tissues being mostly water, as a general rule, longer wavelengths penetrate more deeply than shorter wavelengths. This is why two-photon microscopy has taken on such a large role in biological imaging as it uses two photons of a longer wavelength to excite a fluorescent molecule in the same way as a single photon of half the wavelength would. This phenomenon allows researchers to probe fluorescent molecules much deeper in biological tissues. For our shark, this means we are going to need to strike a balance between long wavelengths of imaging depth and short wavelengths for effective range.

Assuming we want half of our light from our laser to hit our shark’s target at a range of 100 feet, we can use what is referred to as the Beer-Lambert law to calculate the maximum acceptable absorbance of water.

Beer Lambert 2

The equation above gives the simplified form of the Beer-Lambert law where we assume half of the initial photons hit their target. α in this case is the absorbance and Δx is the distance the light traveled through some absorbing medium (water).


Next, we can determine our Δx in meters from feet with a simple unit conversion. Also we can use two neat properties of the natural logarithm to simplify our equation and make it easily solvable. 

Finally we can solve our equation to determine the maximum value we can have for absorbance.

Our answer (0.0227 inverse meters) comes out to be very close to a wavelength of 500 nm (found using the graph above), meaning we will be arming our shark with a laser that would appear very teal-blue upon observation. Tune in to my next blog post for a rousing discussion of building an actual laser that will operate well underwater.

Signals from Noise

by Scott Mattison (@FoolsPizza)

Imagine paying almost $20 to go to see the newest Marvel movie. The previews finally end and your movie starts, only parts of the screen are randomly dark. Likely, you would be upset and would either ask the theatre to fix the error or demand your money back. What if I told you the lasers that provide the light for imaging technologies like confocal microscopy and two-photon fluorescence microscopy had that exact problem?

Lasers enable scientists to easily capture incredibly detailed images of biological tissues and cells that were previously challenging, if not impossible, to achieve. One of the earliest challenges that had to be solved when using lasers for biological imaging was how to reduce an effect referred to as “speckle”.

If you have a laser pointer at home, you can observe speckle just by shining it at the wall; if you look at the spot made by the laser, you will see some areas that are bright and other areas that are dim. This is speckle!

Speckle is the result of two paths of light interacting with one another. In some cases, the two paths combine to make a brighter light whereas in other cases the two paths combine and cancel each other out. More specifically, this interaction is called interference. Interference causes speckles that appear as a grainy pattern of bright and dark spots.

A simulated example of speckle originating from a laser beam illuminating a wall

As you can imagine, when you are trying to capture a detailed image of the inner workings of a cell, speckle is not desirable as this grainy pattern can degrade your image quality. In this regard, we consider speckle to be noise within our images. Luckily, scientists and engineers have worked over many years to find creative ways to reduce and remove speckle in imaging applications. As cool and interesting as a lot of these methods are, I am not  here to talk about how we can reduce speckle in our images, I am here to talk about how we can utilize it. However, before we can discuss how we can use speckle to our advantage, we need to know a bit more about it first.

When a beam of light interacts with a rough surface, light that bounces off this surface and the different paths will interfere with one another, creating a random speckle pattern. If neither the light source nor the rough surface move, the speckle pattern will remain constant. Any movement of the rough surface will cause corresponding changes to the speckle pattern that is generated. Now, we can start to see how we can utilize speckle to our advantage.

By tracking changes in speckle patterns, researchers can determine the movement of a sample over time. This technique has been used to monitor how tissue reacts when a specific force is applied. From this, properties related to the tissue such as its strength or how well it recovers after being changed can be determined. This approach has the potential to allow doctors to differentiate between healthy and cancerous tissues or identify unhealthy regions of blood vessels.

Tracking movement of tissues isn’t all speckle can do. By simply observing changes in speckle over time, researchers have demonstrated that we can actually tell the difference between the movements of liquids and solids. This has led to amazing techniques for mapping out small networks of blood vessels within the body, and has even allowed researchers to image blood flow in the brain!

To me, speckle is an awesome example of what makes research so powerful. We had this noise source in our images that was really slowing down progress in research. Instead of just finding a way to solve this problem (which we did), researchers have found a way to take that noise and make something useful out of it, a signal.