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Free Textbooks!

July 28, 2013

Every college student knows that the cost of textbooks can be exceedingly high. For a short but interesting discussion of this topic, check out this article. As you can see from the attached graphic (taken from the linked article), the cost of textbooks has risen much faster than the consumer price index (aka inflation). There are various reasons put forward to explain this, but whatever the cause the end result is that students are left paying very high prices which they often can’t afford.

Rising textbooks costs (see linked article for source).

Rising textbooks costs (see linked article for source).

What can you do about this as a student? There are a number of creative options which you can try with varying degrees of success, including obvious ones like buying second hand books. Another option, though, is to use a free book. More and more textbooks are showing up on the internet as freely distributed materials. Of course, some of these are pirated and illegally uploaded (and downloaded!) but many are specifically written and/or posted online as free.

In preparation for my upcoming statistics course, I did some looking around on the internet and found a site called OpenIntro. This organization was founded by a Harvard professor and a Google analyst with the aim of providing free, open source textbooks to students. It sounds too good to be true, but the site really does provide high quality educational texts free of charge, written specifically for OpenIntro. At the moment, the only free textbook is on statistics, but it is a well written, 400 page text authored by professors from Harvard and Duke universities, complete with graphics and problem sets. I currently use this book as the main textbook for my statistics course within the chemical and biosciences coop program. It can be downloaded free of charge as a PDF at the OpenIntro website. I recommend that anyone with an interest in stats have a look at the site and see what they think of the book. We can only hope that free open source textbooks are the way of the future! – Michael Judge.

Chemical of the Week: Tetrodotoxin

July 23, 2013

Tetrodotoxin (TTX) is a very powerful nerve toxin found in the puffer fish and some other marine animals such as starfish.

TTX works by interfering with the ability of nerve membranes to transport sodium. Ingestion of small amounts of TTX produces a feeling of numbness in the face along with a floating sensation. Larger amounts can produce paralysis and death, although “large” is relative here, since less than a milligram can be fatal.

The tetrodotoxin molecule.

The tetrodotoxin molecule.

Puffer fish (or “fugu”) is considered a delicacy in Japan and even though only carefully trained chefs are allowed to prepare it, 179 deaths were reported in a ten year period due to eating fugu. Interestingly, TTX has been proposed by one anthropologist as an ingredient in the potions of voodoo practitioners in Haiti. The theory is that a victim is given TTX and slips into a paralytic coma indistinguishable from death, only to be revived later as the living dead, or a zombie! Fans of the Simpsons will remember that Homer once believed he was suffering from fugu poisoning.

Course FAQ: Organic Chemistry

July 21, 2013

Q. Just what exactly is organic chemistry?

A. In the early days of chemistry, scientists found they could extract interesting compounds from substances sourced from living systems, such as butter, animal fat and so on. For this reason, these isolated chemicals generally became known as “organic.”. Today, organic chemistry is more generally considered to be the study of chemicals which are primarily based on carbon (although there are a few exceptions, such as carbon dioxide, which is not considered organic). The vast majority of chemicals are organic by this definition, including vitamins, proteins, pesticides, plastics and many others.

Organic chemistry involves understanding the structures and names of these compounds as well as how they react and how they are synthesized.

Cadbury's creme eggs. How do they get that yolk such a bright yellow?

Cadbury’s creme eggs. How do they get that yolk such a bright yellow?

Q. Why do we study organic chemistry?

A. In many ways, organic chemistry is the gateway to the study of many other sciences, including biochemistry and biology. A good knowledge of the basics of organic chemistry lets you understand how living systems function, since biological systems are mostly made of organic compounds.

In addition, many industrial processes are essentially organic chemistry. The paint and coating, nutraceutical and pharmaceutical industries all involve organic reactions, for example.

As well, some knowledge of organic chemistry is also useful in just about any field of science for practical reasons. A lot of organic compounds are used as solvents, for example, so its helpful to know the difference between ethanol, methanol and isopropanol.

Q. What do we learn in the lectures?

A. All kinds of things! We begin with a brief study of how organic molecules are put together, by talking about bonding and electron structures. We then learn how to name organic compounds using the formal naming system devised by IUPAC.

As well, we learn about the most common reactions of organic chemicals. We’ll discuss how some everyday organic compounds are made, such as polyethylene, aspirin and 2,4-D.

The fascinating effects of isomerism are also considered. Isomers are chemicals which have the same atoms but different properties depending on how the atoms are put together. For a good intro to isomerism, check out this video.

Finally, the course also teaches the theory and practice of some common lab techniques, such as distillation.

Q. What about labs?

A. There are five to six lab sessions in each of the two organic chemistry courses. In these labs, you will apply the theory and see the results in action. Experiments include synthesizing interesting chemicals, such as a bright red dye (an azo dye: see the photo above and the note below!). You will also learn many standard organic lab techniques, such as distillation, recrystallization and melting point analysis. If you ever wanted to start making moonshine whiskey in your backyard shed, this is your starting point! (just kidding, please don’t start making moonshine in your shed.)

Q. Is it tough?

A. Organic chemistry can be challenging, but it’s doable! The subject matter is not extremely difficult, but it requires dedication and good study habits since there is a bit of memorization required in some places to be able to use the nomenclature system and also to recall the various reactions. However, if you can remember that positive and negative charges attract each other, you have just conquered about half of organic chemistry.

Note: the image shows Cadbury’s Easter Creme Eggs, which were recently involved in a scandal when the treat was found to contain an azo dye after the company had promised to remove it.

Interesting News from the World of Science: A Safer Painkiller?

July 17, 2013

The active ingredient in Tylenol and many other painkillers is a drug known as acetaminophen (or sometimes paracetamol). Acetaminophen has been around for a long time and works pretty well, but it’s well known that this particular drug is highly toxic to the liver when taken in overdose or when the patient’s liver function is already compromised (this is why you do NOT take Tylenol for a hangover!). In the U.S., for example, acetaminophen is believed to be responsible for about half of all cases of acute liver failure.

Acetaminophen (top) and new potential replacements (bottom).

Acetaminophen (top) and new potential replacements (bottom).

The liver toxicity occurs because liver enzymes metabolize the drug into a harmful compound known as an iminoquinone. This metabolization has nothing to do with the pain killing function of acetaminophen and so a drug which is not metabolized in this way but still works to reduce pain would be beneficial.

A recent publication in ACS Medicinal Chemistry Letters details preliminary attempts to synthesize analogues of acetaminophen which still work like acetaminophen but don’t generate toxic metabolites. These are based on tweaking the acetaminophen structure to add two heterocycles in place of the single benzene ring in the original structure.

The new drugs are still in the preliminary stages and it’s not yet known if they will work. There is a precedent, however, the even more popular painkiller ASA (i.e. Aspirin) is based on tweaking the structure of an older drug.

 

Chemical of the Week: 2,4-D (The enemy of dandelions everywhere!)

July 16, 2013

2,4-dichlorophenoxyacetic acid (2,4-D) is a widely used synthetic herbicide. It affects only “broadleaf” plants (typically the plants we consider weeds) and not grasses or most crops, hence it can be widely applied without harming desirable vegetation. This chemical mimics natural plant hormones and causes rapid, uncontrolled growth of broadleaves, leading to death of the plant. Pure 2,4-D is actually relatively insoluble in water and so other forms, such as esters and salts, are now more widely used.

The 2,4-D structure.

The 2,4-D structure.

2,4-D is applied so commonly that a 2003 study found that 63% of homes contained traces of this chemical in household dust! It was also a component of the infamous Agent Orange herbicide used during the Vietnam War. Exposure of military personnel to Agent Orange was subsequently connected to a wide variety of health problems. Currently, it is believed that these health issues were actually more likely due to the presence of other chemicals present in Agent Orange, such as traces of dioxin.

A Look Back at 2012/13: Science Goes to Tim’s!

July 10, 2013

Who says data has to be dull? During the Fall 2012 session of the Chemical and Biosciences Data Analysis course, students had the opportunity to satisfy their curiosity concerning whatever subject they were interested in by using a statistical technique known as Analysis of Variance or ANOVA. Simply put, ANOVA compares two or more groups of numbers to see if there is a difference between them. Often, each of the groups is associated with a variable and so the test really tells you if one or more variables has some kind of effect. You can use ANOVA to test for the effect of just about any variable on just about anything you choose.

A generic cup of coffee (just in case there are any copyright issues!)

A generic cup of coffee (just in case there are any copyright issues!)

OK, so maybe that doesn’t sound all that interesting, but the fun part is choosing your variables!

Second year students were given the task of asking any question they wanted to and using ANOVA to find out the answer. They came up with some very creative questions, including …

  • which weapon in a video game gives the best score on a tough level?
  • do I answer math questions better after I run up a flight of stairs?
  • does my cat prefer to play with string, bottle caps or twist ties?
  • which brand of juice does my son prefer?
  • which artificial sweetener tastes best?

Perhaps the most vital question of all, though, was “Which Tim Horton’s on campus has the shortest line up and when?” Students clocked wait times at our two locations at both 9 a.m. and 1 p.m. Surprisingly, the ANOVA test showed there were no statistically significant differences in wait times based on either the location or the time. Actually, this result is not surprising because most people will tell you that no matter which grocery line up you’re in, it’s the slowest. Now at least we know the best location to go to; whichever one is closer, since it doesn’t really make a difference.

 

Chemical of the Week: Androstenedione (the home run hormone)

July 9, 2013

Androstenedione (or “andro”) is a naturally occurring human hormone which is produced in the body as a precursor to other hormones such as testosterone and estradiol. Andro does not appear to be anabolic (does not promote muscle growth) but it can possibly enhance sports performance by temporarily raising testosterone levels in the body (meaning it falls into the category of compounds known as “androgenic”).

The structure of androstenedione.

The structure of androstenedione.

Andro was legal in North America up until the end of the 1990’s and was used by popular sports figures such as Mark McGwire who, in 1998, broke the record for most home runs hit in a season. So perhaps it does help! It’s not recommended as  a sport supplement, however; as with other androgenic compounds, it carries the risk of side effects ranging from liver problems to cancer.

Student Work Experience: Rachel Molloy

July 3, 2013

My name is Rachel Molloy and I was lucky enough to get a Summer Student Co-Op position at the Public Health Agency of Canada’s National Microbiology Laboratory.
The main objective for this position is to perform biological inventories of enteric bacterial pathogens that are considered level two pathogens. The lab I work in is accredited to ISO 17025. While performing my everyday duties I have been able to exercise and refine my skills in the areas of laboratory notebook keeping, standard operating procedures, GLP’s, MSDS’s, PSDS’s, Microsoft Office and general organization.

Rachel at work (photo property of the Public Health Agency of Canada's National Microbiology Laboratory)

Rachel at work (photo property of the Public Health Agency of Canada’s National Microbiology Laboratory)

I am also receiving training in a variety of laboratory techniques that are used to do basic surveillance and for outbreak investigations, including molecular and genetic methods plus classical microbiology and tissue culture.

There are also many other services available at the National Microbiology Laboratory that I have taken full advantage of when I am not hard at work. There is a library on site with tons of science related literature and lots of seminars available on the science of infectious diseases (I attended one recently about the role of proteomics in HIV research).

The staff here are friendly and educated. I participate in my unit’s weekly meetings and have found the whole experience to be very welcoming.

I am grateful for those at the National Microbiology Laboratory for the wonderful experiences that I continue to have, and for Red River College for providing me the chance to have those experiences.

 

Chemical of the Week: Theobromine

July 3, 2013

Theobromine is an alkaloid chemical produced by the cacao plant and thus is found in chocolate. Its molecular structure is very closely related to that of caffeine and it has some of the same properties – such as acting as a stimulant – albeit to a lesser extent.

The theobromine molecule.

The theobromine molecule.

Although one might expect to find bromine in this chemical, its name is actually derived from the Greek phrase “food of the gods” which is a pretty good description of chocolate!
In addition to being a weak stimulant, theobromine also has some other physiological effects. It can act as a diuretic and has been found to be better than codeine at stopping persistent coughs, due to its effect on the vagus nerve. Theobromine is also responsible for the fact that chocolate is toxic to dogs and some other animals.

Research in the Chemical and Biosciences Program: Pharmaceuticals in Wastewater

June 26, 2013

Did you know that more than half of a dose of the common antibiotic amoxicillin moves right through the body and is excreted unchanged? That drug ends up in the sewer system and eventually at the local wastewater treatment plant, along with hundreds of other pharmaceutical compounds, antibacterials and related chemicals. Most municipal wastewaterAssorted_Pills_3 plants receive a constant stream of so-called micropollutants such as amoxicillin, present at levels in the part per billion or part per trillion range. Since these plants aren’t built to remove micropollutants, they pass right through and end up in our rivers and lakes. This is a growing concern, since many of these pollutants can eventually affect aquatic life and may also appear in drinking water supplies.

Michael Judge and Karanveer Singh of the Chemical and Biosciences program are currently working on a project, funded by the college Applied Research Department and the National Research Council of Canada, which is examining possible methods of removing micropollutants from wastewater. The project involves an extensive literature review of the existing methods, as a first step towards formulating a more ambitious research endeavor to investigate optimized removal processes. In addition, Karanveer is carrying out preliminary research into the optimization of high pressure liquid chromatography (HPLC) as a means of following the removal of selected micropollutants.