How Bioluminescence Works

Bioluminescence is the ability of a living organism to emit light; a phenomenon which has intrigued humans for thousands of years and allowed them to invent mystical and magical stories behind these beacons of light. We might have decided that these lights serve a magical purpose, but evolution has found many uses for this process from protection, all the way to communication.  The chemical mechanism behind these bioluminesent photons is a very simple one, though not the same in all organisms, they share some of the same basic principles.  Taking the firefly as an example, the compound which acts as it's light bulb is called luciferin, and the reaction begins with molecular oxygen and ATP, with the help of the enzyme luciferase, turning luciferin into a dioxetane derivative (mechanism of this can be seen here)¹.

Once this dioxetane derivative is formed the emission of light reaction is ready to occur spontaneously. This happens in a concerted reaction releasing CO₂ and producing an excited ketone. The electron of the excited ketone then falls in energy to create a photon and end with the final product of oxyluciferin.

The newly created oxyluciferin is then enzymatically recycled into luficerin by this mechanism here².

References:
1.  Aldo Roda Chemiluminescence and Bioluminescence: Past, Present and Future, p. 57, Royal Society of Chemistry, 2010, ISBN 1-84755-812-7
2.   Keiko Gomi and Naoki Kajiyama. Oxyluciferin, a Luminescence Product of Firefly Luciferase, Is Enzymatically Regenerated into Luciferin. J. Biol. Chem. 2001 276: 36508-36513. July 16, 2001, doi:10.1074/jbc.M105528200

Why are Flamingos Pink?

This is a question that many children will ask their parents at some point, and if the child is chemically literate this is what the parents could tell them.  Flamingos primarily eat crustaceans and algae from their aquatic environment, which we usually see them standing in, and in their food, there is what is known as carotenoid pigments. Carotenoids are made from fats, and the incorporated into the chloroplasts of algae to serve as light absorbing pigment.  Then the algae get eaten by the crustaceans or flamingos, the carotenoids get passed on into these animals.  Usually when a molecule is eaten, it breaks down, but something such as a pigment will absorb into your bloodstream and not break down, so when a flamingo eats these, the pigments enter the blood stream and then eventually come out in their feathers.  Now for flamingos, the primary pigments which get absorbed and end up in their feathers, are Canthaxanthin (the molecule below), astaxanthin and  phoenicoxanthin ¹. Canthaxanthin is a molecule which gives of a bright violet colour when it is crystallized  but when it is incorporated into flamingo feathers, it is diluted to give a vibrant pink.

References:
1. Fox, D., and T. Hopkins. "Comparative Metabolic Fractionation of Carotenoids in Three Flamingo Species." Comparative Biochemistry and Physiology 17.3 (1966): 841-56.

Ricin: A Potent Poison

Now I don't really talk about anything on this site that deals with anything biochemistry related, but I will make this an exception due to the state of current events. Ricin might be a word that you have heard recently in the new, about the poising attempt on President Obama by an Elvis impersonator.  For those who don't know what Ricin is, it is a protein originating from the same plant that gives you castor oil. It's job in the body is a nasty one, as it inhibits protein synthesis (which is pretty much everything important in a cell), more specifically it acts upon the ribosome (a small organelle which synthesizes proteins). It's categorization of inhibitor is a Ribosome Inactivating Protein, which cynically has the acronym RIP.  Although this is a very deadly poison (a gram worth to kill), there does exist an antidote, but the survivors will have major organ damage and will have a shortened life expectancy.

Source:
Wikipedia

Biology 12 BC Study Guide

I just realized that I still have my ginormous study guide that I made back in high school when I was determined to get 100% in biology (of which I didn't achieve unfortunately) because I was certain that I wanted to go into medicine.  I'm not joking when I say this thing is large, it is 31 pages long, and now you must think "Wow, this guy was really cool in high school, spending his friday nights making study guides".  It is true that I would compulsively make elaborate study guides, mainly for the sake of keeping all of my information organized. Enough of the bantering of my crazy educational antics, here is the study guide:

BC Biology 12 Study Guide

I wish luck to all of you high schoolers who download this!

Should Search Engines Block Queries to The Anarchist's Cookbook?

This thought came to me when I decided to search for The Anarchist's Cookbook to calm my curiosity of how easy it is for anyone to get a hold of it. When I searched Google for it, the first page presented me a number of places where I could purchase the book, along with a full pdf file of the book. I was quite surprised when I found it so quickly, and quite disturbed at that as well. I am fully against internet censoring to the extent of websites being shut down (other than that of illegality issues), but I believe that search engines such as Google, Bing, and Yahoo should take a step towards assuring that the average internet user cannot obtain information like this.

The problem that I have with The Anarchist's Cookbook is not the fact that it explains how to make explosives, I think it's good information for people who know what they are doing, such as chemists, but I have a problem with the fact that it is written for the average person, who has had no safety training in handling chemicals. It explains how to get certain chemicals from off the shelf products in order to construct bombs, and other such dangerous weapons, rather than having to get chemicals from a supplier such as Sigma-Aldrich, who makes it impossible for the average person to obtain. If someone really wanted to hurt someone, they should have to gain the knowledge first before jumping right to making the explosive from a set out procedure. In that time planning it out, they could very well change their mind. An example of this is the Drano Bomb, where kids can make a bomb out of common household items, which can cause serious damage, as reported here. Reports have been made of people loosing fingers while holding the water bottle, which is an unexpecting object to be a bomb since we see bottles littered all the time.

In the end, we have to ask ourselves if information like this should be free to the public, through being written in layman’s terms, rather than in academic terminology that could only be understood with four years of post secondary education, along with the understanding and appreciation of what we are dealing with.

Ponderings Of Where Science Education Should Go

Just as a forefront, I don't want to make myself out to be an expert in the educational studies; these are merely my observations and thoughts of where I believe we should be heading with our public elementary and high schools.

A step back from memorization

A key part in education right now is the preparation for standardized tests, to reshape a student to be able to answer predictive questions, selecting students who aren't well rounded, but excel solely in this category, while leaving their creativity behind. This method doesn't teach children to ask questions because they soon realize that there is only one right answer, where in the real world a person needs to ask themselves questions in order to problem solve, or to see a problem all together. I can't tell you the number of times I have heard an arts student say that they didn't like science because there was only one right answer, and that they preferred to have an objective look on their topics. But this here, is the beauty of science; anyone can disprove anything that is considered “true” with sufficient evidence, creating a paradox in how we test the subject. If education can step back from the emphasized learning of knowledge and spend more time exploring the beauty of the scientific method, people won't be as afraid of science. I'm not necessarily saying that I think everyone should go into the sciences because of this, but people who are in other fields shouldn't have a fear of it.

In line with this, there may also be a problem with this method for the upcoming generation who are surrounded with more and more electronic gadgets connected to all human information. With an increasing dependence on technology, the need of memorizing small details diminishes proportional to the easiness of accessing the information [1]. In fact, it has been proven that if the information is easily accessed, our mind will refrain from storing it in our long term memory. From this, we may see a change with our next generation in their ability to hold long term memories of small facts. Because of this, we need to push for a stronger investment in the creativity and imagination of students. It was Einstein who stated that "Imagination is more important than knowledge. Knowledge is limited. Imagination encircles the world”.

Consequences of the current education system

One key result of this is the fact that 3rd year genetics is considered to be one of the toughest courses for biology undergraduates, but for other majors such as mathematics, physics, and chemistry it seems easier because of their problem solving experience. Up to that point in university biology students are made to only know memorization as the medium of education. They aren't made to problem solve, create, or learn the scientific method until later in their degree; all they are doing is building up their knowledge to be able to problem solve later. As much as this method has worked for years and years, I believe that we can do better in educating students so that when they do get to their first genetics class, they have the problem solving skills to be able to excel in the course.

As have just finished my undergrad, i have witnessed a slew of grad students who eagerly boast in their academic excellence, while in their T.A. duties saying things such as "Wow, you don't know that", and refuse to teach an elemental concept. This power trip blocks the process of education; being in an employee of an academic institute, they are there to help educate and build the body of science, but instead think selfishly in looking at their academic achievements. They are the kind of people who were bred out of this academic competition that exists in a capitalistic society, a concept of every man/woman for themselves, only yielding the best of the best. But these people fail to see what science really is. They fail to see that it is a body of knowledge that is dependent of everyone working as a whole.

Ending Comments

It will be tough to be subjective through a land of no standardized tests, creating a lot of issues in how to test the mass number of students without multiple choice. The recourses to mark thousands of objective tests at a time are just not here unless we can find a testing method in the future that both appeases this method along with the practicality of marking.

I'm not necessarily saying that we should put all of our teaching into the creativity process because we will still need to have memorized a great deal to get anywhere in the scientific world. Our brains rely on connections to get anywhere, which requires us to have this knowledge in our memory. We need to see the comparisons that the computers are unable to see, this also being known as human intuition.

References
[1]Sparrow, Betsy, Jenny Liu, and Daniel Wegner. "Google Effects on Memory: Cognitive Consequences of Having Information at Our Fingertips." Science333.6043 (2011): 776-778.

Internet Detox

I have decided to take a break from the internet for a week. This is because I have made a really deep addiction to constant flowing information and I need to disconnect myself from this addiction. It all stems from the last year, being stuck in bed with only one outlet to the outside world.

Any post that I make in the next week will be on my phone, as all I will limit myself to is email, and this blogger app.

Wish me luck

Antoine Lavoisier's Understanding of Caloric and the Properties of Water

The process of science is a wonderful thing, which is what drives me into trying to understand the history of science.  My recent dive into this is reading Antoine Lavoisier's Elements of Chemistry, as it is one of modern chemistry's first textbook written by one of it's fathers. Now this isn't the easiest piece of literature to read, not because of the language, it excels in that category, but the font chosen makes the s's appear as f's. Difficulties aside, here is a quote I fell in love with, showing his understanding of the cohesion of water molecules before there was an understanding of hydrogen bonds, and heat before there was an understanding of molecular kinetic energy.

It is, perhaps, more natural to suppose, that the particles of caloric have a stronger mutual attraction than those of any other substance and that these latter particles are forced asunder in consequence of this superior attraction between the particles of the caloric, which forces them between the particles of other bodies, that they may be able to reunite with each other.  We have somewhat analogous to this idea in the phenomena which occur when a dry sponge is dipt into water: The sponge swells; its particles separate from each other; and all its intervals are filled up by the water.  It is evident, that the sponge, in the act of swelling, has acquired a greater capacity for containing water than it had when dry.  But we cannot certainly maintain, that the introduction of water between the particles of the sponge has endowed them with a repulsive power, which tends to separate them from each other; on the contrary, the whole phenomena are produced by means of attractive powers; and there are, first, The gravity of the water, and the power which it exerts on every side, in common with all other fluids; 2dly, The force of attraction which takes place between the particles of the water, causing them to unite together; 3dly, The mutual attractions of the particles of the sponge with each other; and, lastly, The reciprocal attraction which exists between the particles of the sponge and those of the water.  It is easy to understand, that the explanation of this fact depends on properly appreciating the intensity of, and connection between, these several powers.  It is probable, that the separation of the particles of bodies, occasioned by caloric, depends in a similar manner upon a certain combination of different attractive powers, which, in conformity with the attractive powers, which, in conformity with the imperfection of our knowledge, we endeavour to express by saying, that caloric communicates a power of repulsion to the particles of bodies.

Just as a background fact, Caloric was Lavoisier's term for kinetic energy, and at that time was considered to be a fluid or gas that would flow through matter, making it either hot or cold.  Just as heat flows from hot to cold, Caloric would flow from a hotter material to a cooler one until it reaches an equilibrium.  All of these observations, now obvious to us, were new and exciting for the scientists at the time, and to think there was a fluid that flows dictating temperature wasn't far off from the truth considering that matter with more kinetic energy expands according to PV = nRT.

I recommend this read to anyone interested in the history of our chemical body of knowledge, or to show respect to the people who worked undyingly hard to make these pivotal discoveries.

References:
Lavoisier, Antoine Laurent. Elements of Chemistry, in a New Systematic Order, Containing All the Modern Discoveries. New York: Dover Publications, 1965. Print.

For Those Students Who Have Trouble in Drawing Tetrahedrals

Just a relay of a blog post I found on Master Organic Chemistry explaining the difficulties in viewing 2D representations of the Tetrahedral.

Find it Here.

When the Catholic Church and Science Get Along

I asked myself yesterday, while watching TV, what is used to make the papal smoke turn either white or black, and how do they make sure there is no false alarm.  In my research I found that they previously used wet straw to make the black smoke and nothing added to make the white smoke. But in an article by The Guardian, I found that they now use an electronic smoke machine, starting in 2005, where potassium perchlorate (KClO₄), anthracene (3 fused benzene rings), and sulphur is used to make the black smoke, while potassium chlorate (KClO₃), lactose and a pine resin is used to make the white smoke.

So how does this work?

Black
The anthracene (from tar) helps the burnt carbon from the paper flow upwards in the smoke instead of remaining in the ash.  The KClO₄ is used to aide the combustion of the paper to create the chunks of carbon. What carries all of this upward is the water that is generated in the chemical reaction of combustion. Just think of it as the burnt carbon as being graphite, which produces a back colour.

White
What creates the white smoke is the existence of unburnt paper, or other unburnt fuel, rising up with the heat.  The paper is thermally broken apart in a process called pyrolisis, leaving small white particles of unburnt cellulose, or from the added resin, rising up as the combustion product of H₂O rises out of the chimney. Just think of the particles of unburnt fuel being like table sugar, which gives off a white colour.

References:
Via: The Guardian

Egyptian Blue: Calcium Copper Silicate

In a recent article by Scientific American, a story is told of Calcium Copper Silicate (Egyptian Blue) being the first artificial pigment made by humans, and soon to be utilized, once again, as a nano ink for biomedical imaging.  I'm not going to go over the details of the article, but I will present some background information of this soft blue colour.

Being the first recorded synthetic pigment, you may ask how it was originally synthesized.  The first procedures, in 3000 B.C., involves the heating of sand, calcium carbonate, copper, and an alkali substance to obtain this blue pigment having a composition of CaCuSi₄O₁₀.  The reaction below is a general understanding of the reaction, where the molecules can be variable in a number of different ways.

Cu₂CO₃(OH)₂ + 8SiO₂ + 2CaCO₃ → 2CaCuSi₄O₁₀ + 3CO₂ + H₂O

The blue colour comes from the absorption of the copper, which can range from the blue, seen above, to a much darker blue, depending on how pure the mixture is. But what wasn't known at that time, was that when irradiated with visible light, the compound emits IR photons, which is the property that will conduct the imaging technologies.

References:
Via: Scientific American
Wikipedia

What is Triclosan and Why is it Being Banned?

Triclosan has been in the media recently, in it's battle with regulation in its existence in many cleansing products.  In a recent article by the C&EN News they reported that "Minnesota state agencies will be able to purchase only soaps and detergents that are free of the antibacterial ingredient triclosan. State officials say they are concerned that the chemical has been linked to endocrine disruption and the growing threat of antibiotic resistance."

What is Triclosan, and how long have we been in contact with this reportedly "harmful" chemical? 
It has been used commonly in many different products since 1972 when it first became apparent that it reduced bacterial activity.  Such products as toothpaste, mouthwash, deodorant, trash bags, kitchen tools, and many other areas where antibacterial products seemed appropriate for manufacturers to use for preserving their products, or making their cleaning products more affective.

Why is it being banned?
It is being banned for a number of reasons.  First of all, as mentioned by C&EN, the risk of upsetting endocrine function.  This hasn't necessarily been proven in human subjects (other than slightly affecting the immune system, which may be due to the vast number of bacteria in, and around the body ¹), but it has been reported that the North American Bullfrog's endocrine system becomes compromised under low doses of Triclosan ².  Another reason is that it has been proven that it decreases bacterial species diversity, in other words, selects for antibiotic resistance.  The third reason is that it can be harmful to the environment for the reasons stated above (i.e. disrupting aquatic bacteria), along with Triclosan's byproducts such as dioxins being harmful.

How to avoid using products with Triclosan?
If you don't wish stay free of this product, read labels, and educate yourself of what is in the products you are using. It may also be listed under trade names of UltraFresh, Amicor, or BioFresh.

References:
Via: C&EN
1. Erin M. Rees Clayton, Megan Todd, Jennifer Beam Dowd, Allison E. Aiello. "The Impact of Bisphenol A and Triclosan on Immune Parameters in the U.S. Population, NHANES 2003–2006". Environ Health Perspect 119 (3): 390–396. doi:10.1289/ehp.1002883

2. Nik Veldhoen, Rachel C. Skirrow, Heather Osachoff, Heidi Wigmore, David J. Clapson, Mark P. Gunderson, Graham Van Aggelen and Caren C. Helbing. "The bactericidal agent triclosan modulates thyroid hormone-associated gene expression and disrupts postembryonic anuran development". Aquatic Toxicology 80 (3): 217–227. doi:10.1016/j.aquatox.2006.08.010