Chemicals are Your Friends-Well Most of Them Anyway

As a chemist, one of the hardest things that I deal with is the fact that most people HATE chemistry. It seems to be the most hated of all the sciences. And of all of the chemistry classes people take in university, the one they hate the most seems to be organic chemistry. This adds to my heartbreak because that is the type of chemist I am. I love chemistry and I really love organic chemistry. You don’t spend 11 years in university studying something that you only have tepid feelings about. So when the first thing people say to me after they find out I am a chemist is “ugh, I hated chemistry,” I start to feel defensive. “Oh ya, well…I hate your chosen profession…you…accountant.” This is of course made worse by idiots who have no clue what chemistry is and want to scare you with “chemicals” and making them sound like something nefarious that Snidely Whiplash is pouring into your water supply.

Here’s the thing: not all chemicals are bad. Actually most of them are great. In fact, you sitting there, reading this, you are a giant, walking, talking chemical reactor. Your cells use chemical energy to function. Your food is all chemicals. Your body is doing some pretty complex chemistry just to make your heart beat. The chemical bonds in fats, proteins, and sugars are broken down and put back together in important ways that allow you to survive. Chemistry is life.

There are some chemicals that are terrible for you, both man made and natural. Strychnine comes to mind as a chemical that is not so good for you. Botulinum toxin, produced by the bacterium C. botulinum, causes botulism-not a good chemical, unless you’re the bacterium. Man made chemicals are an interesting mix: we make them to solve certain problems, but they might also create a few problems of their own. Here’s a quiz for you: name the chemical that you think has saved the most lives? I am talking of hundreds of millions of lives. What did you guess? Did you guess DDT? That’s right, the pesticide DDT has actually saved the most lives. It is the most effective chemical in killing malaria-carrying mosquitoes. It is also inexpensive compared to alternate pesticides, which is matters greatly, since the vast majority of people impacted by malaria are in the developing world. Now, I am not advocating for the use of DDT. Its environmental impact is severe. But I do think it highlights some of the complexities regarding what makes a chemical “good” or “bad”.

Now when people hear chemical names, they sometimes get scared because they think “well that sounds like a toxic compound I do know, so this must be bad too”. I remember hearing a woman say that the traces of tertiary butylhydroquinone in fryer oil was harmful to human health because “butyl” is like the lighter fluid “butane”. These two compounds are so different, it is kind of like saying Michael and Michelle at your office are practically the same person because their names are so close. I hear variations of this argument a lot. “This chemical is ALMOST the same as a really bad one, therefore it must also be bad.” The thing is, when you look at the periodic table, the different between each type of element (all 118 of them) differ only by one single proton. But that proton makes a huge difference. Just like changing one proton in an atom changes the element, changing one atom in a molecule can drastically change that molecule.

Take a deep breath in, let it out. Are you still alive? Great! That is because what you breathed in was mostly nitrogen gas (and some oxygen of course, but mostly nitrogen.) The nitrogen in our atmosphere is comprised of two atoms of nitrogen bonded together with three bonds (triple bonded). That nitrogen floats around not killing anyone, perfectly happy and inert. Now, let’s change one of those nitrogen atoms to carbon. So instead of two nitrogen atoms triple bonded together we have one carbon atom triple bonded to one nitrogen atom. Take a deep breath of this compound and now you’re dead. See one carbon atom triple bonded to one nitrogen atom is cyanide.

So the moral of this post is that not all chemicals are bad. Don’t believe anyone who says they have something for you that is “chemical-free” because they are lying. If you have questions about chemicals, especially additives and preservatives, send me a message: I would love to answer your chemistry questions, especially if your source is food babe, Gwyneth Paltrow, or Dr. Oz: you deserve someone who actually knows what they are talking about.

I love chemistry!


Pharmaceuticals-How Are They Produced?

I thought I would talk a little about pharmaceuticals. Chances are you take some, know someone who takes them, and have all complained about their prices. A few years ago while I was in grad school I took a pharmaceutical chemistry class taught by scientists from Gilead, and I must say it was very enlightening. I thought I would share some of the lessons I learned and some of the key problems that face those charged with making these chemicals that many people depend on.
Let’s start with a poignant news story. What would you do if you were suddenly unable to get a hold of a medication that you require? When a company decides to stop producing a compound, what can be done? Is that right or wrong? How should medications be priced? These are questions that are very difficult to answer.
To understand a little bit about the complexity of the issues with the pharmaceutical industry I think it is first important to understand how these medications are produced. I know I found it eye opening. Guess how long it takes to produce a drug? 0-5 yrs? 5-10 yrs? 10-15 yrs? 15-20 yrs? If you guessed 15-20 yrs, then you would be correct. It takes 20 years and (as of 2008) $1.7 billion to develop a SINGLE drug. 
The timeline:
Discovery/Preclinical Trials
Time: 1-3 years
In this time, the company will begin by identifying a medical need, such as anti-HIV medications, and then study that disease to determine where drugs can target the disease and the possible interactions of the drug. This is where potential contenders for a drug are determined. This amounts to some 30 000 chemical compounds will be screened! These preclinical trials will involve pharmacodynamics and pharmacokinetics.
Pharmacodynamics: studies how a drug interacts with a target-this is the impact of the drug on the body. Is the drug going to do what is was intended to do? Is it going to do something else? 
Pharmacokinetics: this is how a drug is transported to the target-this is really looking at the impact of the body on the drug. This looks at four things: absorption, distribution, metabolism, and excretion. Remember, your body is one self contained complex chemical reactor. I think one excellent example of the importance of studying this effect is the notorious thalidomide. There are two versions of thalidomide: R and S. One is an anti-emetic (R) while the other causes birth defects (S). Yes it is possible to separate the two and give a person only the version that DOES NOT cause birth defects; however, once in the body, the drug is inter-converted to the other form (a process called racemisation).
Any potential drug will be screened for toxicity using two species: one rodent and one non-rodent. They will be tested for single and repeated dosing. They will be tested by various delivery methods. (Side note: a 14-day rat trial costs $250 000.)
During this time, chemists will be answering the questions of: can the drug be made? How many steps (hint: more steps, more costly, more trouble)? What are the yields (not all chemical conversions give 100% yield-actually very few give 100%)? Is chemical manufacturing possible, feasible, and affordable? 
After all of this, about 100-200 of the 30 000 compounds will make it on to the next step. 
Safety Review
Time: about 30 days 
This is where the pharmaceutical company is trying to get approval from human clinical trials. All of the information gleaned in the preclinical trials must be presented to the regulatory bodies, including the synthetic routes for production. This is also the time that a company will take out a patent on a compound (a process in the tens of thousands of dollars for each one). 
Clinical Trial: Phases 1, 2, 3:
Time: 2-10 years
This is where the human trials begin. 
Phase 1: 
– 10-100 volunteers
– months to 1 year
– involves “proof of concept” and determines whether the drug is adequate, safe, tolerable. 
– 50-70% of the compounds (that made it to clinical trial) will be abandoned. 
Phase 2:
– 50-500 patients 
– 2 years
– 60% of the compounds (that made it to phase 2) will be abandoned
Phase 3:
– 500-2000 patients
– 3-5 years
– only 4-10% of compounds will succeed
Time: up to 7 years
This is the stage where regulatory bodies determine if a drug is safe enough and effective enough to sell to the population. 
Now if you have been keeping track, we are about 15 years from when the patent was filed to the point that the drug can be sold. A patent is only good for 20 years; therefore, a company only has about 5 years to recover the cost of the production. This also means that drugs that are currently hitting the market were just getting out of preclinical trials in 1998.
During this time, optimisation is ongoing to make the manufacturing process safer, cheaper, and more efficient. However, if the process is changed too much, it may mean that a company will need to refile their drug for approval. 
There is lots of interesting chemistry in pharmaceutical production. I think I will leave that for another entry, but if you have found this interesting, please check out these course notes for reference material.  

I originally published this on Chemistry is Awesome

The Trouble With Science Communication

I dedicate this post to Dr. Brent Rudyk and Nathaniel O’Coin.

The other day Nathaniel asked me “What is the Canadian Light Source?” He has a friend who was recently doing research at the CLS and didn’t know what it was. His friend was doing near-edge x-ray absorption spectorscopy. I hit a communication block: how do I explain this? I mean, I know what the technique is; I had a number of colleagues while I was in grad school making trips to the CLS and yet I found myself struggling to explain what CLS and near-edge x-ray spectroscopy is. I mentioned it on facebook and my friend, Dr. Rudyk, came back with a GREAT explanation: “CLS is a synchrotron, where highly intense, tunable x-rays are created by bending near light speed electrons. X-ray absorption near-edge spectroscopy (XANES) is the process of promoting a core electron into conduction states and analyzing the resulting “edge-jump” and the general vicinity of the jump.” I was excited. I couldn’t have said it better. I immediately recalled the classes I discussed it in. But here’s the problem: Nathaniel still didn’t quite understand. See he has no chemistry or science background, meaning that the terms “conduction state”, “edge-jump” still didn’t help him understand what was going on.

This whole situation really demonstrates the challenge in communicating science to a non-technical audience. My friend Brent is a wonderful teacher, easy to talk to, and is a great communicator, and yet, his perfect description of XANES and CLS still didn’t help Nathaniel understand. How do we, as scientists, make our explanations more accessible to non-technical audiences without coming off as condescending? This is what the mission of Curiosity Science is all about. I hope that those of you who follow with interest bare with us as we learn to talk about science most accessibly and I hope that other scientists interested in contributing to the project recognise the challenge and the wonderful opportunity that we have.

So with all of this in mind: here is my attempt at explaining the CLS and XANES-really I am just editing Brent’s answer because it really is one of the best explanations I have read. The Canadian Light Source is located at the University of Saskatchewan in Saskatoon, Saskatchewan. It is a synchrotron, which is a source of light generated by accelerating electrons to nearly the speed of light (2.99 x 10^8 m/s) and then bending these electrons using very powerful electro-magnets. As the electrons bend, they emit intense, highly focused beams of light. This light is at different energies: some are x-rays, others are infrared or ultraviolet. These beams that come off allow scientists to do various experiments depending on the wavelength of light.

Different wavelengths of light have different energies. X-ray is much more intense energy than infrared. When an atom absorbes an x-ray, there is enough energy to kick an electron that is closer to the nucleus of an atom to a higher energy state (excited state). These are the core electrons and require a lot more energy to excite or remove compared to electrons located farther away from the nucleus of an atom. The different types of electrons have very specific energies that are required to excite them, this gives rise to the “absorption edge” because in the actual spectrum it looks like a vertical line, like the edge of a cliff. The specific “edges” that one would see in a spectrum are element specific. You can therefore tell what elements are present, what their oxidation state is etc.

So there you go. There is a little bit about the CLS and what you can do with it. The CLS is a pretty cool, state of the art research centre. It is definitely a claim to fame for the University of Saskatchewan and the City of Saskatoon.

Also, Thanks Brent, for helping me in trying to explain XANES to the world. Let me know if I missed something!

Welcome to Curiosity Science!

Hello Folks and welcome to Curiosity Science!
I previously wrote a blog called Chemistry is Awesome, where I answered your chemistry questions in a non-technical, jargon-free manner. It was fun, but I found myself stymied by the fact that science is so much more than just chemistry and many of the things I wanted to share involved other sciences on top of chemistry alone. I wanted to share all science because really Science is Awesome.
Enter Curiosity Science. This is for anyone curious about any type of science. Science impacts all of us. It isn’t meant for just a handful of people who spent years studying it. Science is meant for everyone. Again, this is a place to fine jargon-free, non-technical answers and information on the science that happens every day.
Do you have science questions? Contact us: Do you want to #askanexpert a question? Send us an email or tweet @thecuriosityscience.
Curiosity Science Mission: to bring great science to every curious mind without the technical jargon. Hope you join us for our 13 week mission!