Mushroom Coral as a Sunscreen

In an episode of Man vs. Wild that I was watching, a Mushroom Coral's mucus was used as a sunscreen, so me as a chemist interested in cosmetics, I wanted to know what photoprotecting chemicals were in this mucus.  The coral Fungia fungites and a couple other species gained this ability to protect themselves because they would grow in shallow water of the Adaman Sea where a lot of UV radiation penetrates through the clear water.  First looking at this ability one would expect the coral to synthesize these molecules, but it turns out that the culprits are tiny symbiotic dinoflagellates. In a paper from 1999 by Brown¹ studying the makeup of the mucus required for photoprotection, they look at the concentration of xanthophylls in the mucus, the primary photoprotector. Their study looked at how the concentrations of xanthophylls varried throughout the day, and showed that it is best to harvest the mucus at noon when the xanthophylls are at their peak concentration.

So finally to the chemistry of all of this. The molecule shown above is called diatoxanthin, which is a type of xanthophylls, and this is the molecule mostly responsible for filtering out the harmful rays.  So how does this happen? Well molecules and atoms absorb light one way or another through absorbing the photons, resulting in electron excitation, and in this case, the molecule absorbs in the UV portion of the electromagnetic spectrum. So what happens after the diatoxanthin molecules become excited? Well biology has found a solution for that, which has been named the Xanthophyll Cycle. It's job is to convert all the used up diatoxanthin back into diatoxanthin.

References:
1. Fitt, W. K., R. P. Dunne, S. W. Gibb, D. G. Cummings, I. Ambarsari, B. E. Brown, and M. E. Warner. "Diurnal Changes in Photochemical Efficiency and Xanthophyll Concentrations in Shallow Water Reef Corals : Evidence for Photoinhibition and Photoprotection." Coral Reefs (1999): 99-105.

4-Methylimidizole, a Pepsi Additive

Recently the news has been discussing Pepsi's additive 4-methylimidizole in the caramel colouring of their popular drinks, with the fact that the Centre for Environmental Health has deemed it unsafe. Now should you go into your fridge right now and toss all of your Pepsi into the garbage? No. Although a study that was performed in 2007 gave results showing that 4-methylimidizole has carcinogenic properties in mice and rats, keep in mind that this is at an extremely high dose (115mg/kg of body weight) and the dosage that a normal consumer will receive showed no effects.

So why is this molecule in Pepsi in the first place? It comes with the additive caramel colour, which is produced by a separate manufacturer and is listed as Caramel Colour on the ingredients list.  This molecule is made as a product of the Maillard Reaction, the browning of food, and in this case being the reaction to produce the caramel colour. But the problem with their method in producing the caramel colour is that they use a method with a higher concentration of ammonia, which incidentally ends up producing more 4-methylimidizole than other methods. Since this has come out, the US caramel colour manufacturers have changed their recipe to adhere to the people's reaction, lowering the overall concentration of 4-methylimidizole.  This has yet to change the formulation in other parts of the world though.

How the Internet is Changing Your Brain

I was introduced to this video on Academic Earth in relation to my post about where science education should go, and it goes without saying that they harmonize each other very well. Please watch this 2 minute video, and it will open your eyes to what our technology is doing to our brains.

Created by AcademicEarth.org

Why do Onions Make You Cry?

Cutting onions is arguably the worst part of cooking, the burning irritation you get in your eye becomes unbearable so much as to take a break mid way through chopping.  So why is this? This is all to do with mixing molecules in the onion cells that aren't supposed to be together, an enzyme named Allilinase and a molecule called Allilin.  Think of this like the type of adhesive that has two parts that you need combine together to make the glue active.  When we cut onion we start the chain of reactions allowing the Allilin to come in contact with Allilinase to turn the Allilin into Sulfenic Acid and this Sulfenic Acid turns into syn-Propanethial-S-oxide though the enzyme Lachrymatory Factor Synthase.

This syn-Propanethial-S-oxide is what everyone hates because this is the irritant that when combined with the moisture in your eyes gives you that pain and your body tells your tear ducts to try and wash it out.

References:
Something about Science

Why Does Garlic Sometimes Turn Blue?

I've noticed sometimes when I cook garlic in butter that the garlic will turn blue after a while, and I had to ask myself why this happens.  After finding out that it is safe and poses no loss of taste, I sighed and continued reading.  It seems to be due to the presence of sulfates within the garlic, a component of what gives it such a pungent smell.  What happens is that the sulfates combine with the copper ions present in the butter, water, or cooking equipment to create something known as Copper (II) sulfate, or CuSO₄. This new compound is what gives off that bright blue colour.

So you may ask now if there are any precautions to be taken to avoid receiving this colour.  Luckily science has gained us much information about this process.  The main component of this phenomena is an enzyme present within the garlic that catalyzes this reaction, and can be deactivated simply by heating at high temperatures, or by letting the garlic age.

Hydrangeas and their Variety of Colour

Hydrangeas (Hydrangea macrophylla) have been known to form in a range of colours, from red, to purple, to blue, with having nothing to do with the genetics of the plant. So, if this colour difference isn't due to the genes, it must be due to certain environmental factors, and as it turns out, it is all to do with the pH and other properties of the soil. The more acidic the soil, and the greater [Al³⁺] in the soil, the more blue the sepals of the hydrangea will become. So why is this? Let's start with looking at the pigments which govern the colour of the sepals. The major pigment found in Hydrangeas (along with a number of other plants) is called Myrtillin, also known as delphinidin 3-glucoside, which is part of a group of molecules called anthocyanin.

But odly, this molecule assumes a red colour in acidic conditions and blue in basic conditions¹ (opposite to that of the soil conditions) and the pH within the sepals is usually slightly acidic, with little variation, so the blue colouring must have something to do with the Al³⁺. Through much research, Kondo et al. ², came up with a model proposing that the aluminum acts as a bridge to coordinate the Myrtillin to other copigments pigments known as acylquinic acids, which produces this blue colour.

While this is how the blue colour is formed, it can be safely assumed that the red colour is merely caused by Myrtillin by itself without any co-pigments or metal chelation.  A question which hasn't been answered yet is what the pH of the soil has to do with all of this.  The low pH allows there to be more free aluminum ions within the soil, to allow there to be more [Al³⁺] taken up into the plant.

References:
Second figure from 1.
1. K. Yoshida, M. Mori and T. Kondo, Nat. Prod. Rep., 2009, 26, 884–915.
2. T. Kondo, Y. Toyama-Kato and K. Yoshida, Tetrahedron Lett., 2005, 46, 6645–6649.

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.