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The Immune System: Your Own Person Military

     This post has taken me quite awhile to write, but here is the starting point for our journey to understanding vaccines: the immune system! You can think of your immune system like your own personal army protecting you from outside threats. With this in mind, the first term that we should define is pathogen: an agent that causes disease. Your immune system is designed to protect you from pathogens. 

    Now, at first glance this definition seems pretty straight forward; however, defining a pathogen can actually be kind of a tricky process.  For example, staphylococcus aureus is normally a pretty harmless skin bacteria, but if your skin gets damaged or the staph gets into a spot it really shouldn't be, now it can cause disease. This means that staph is not always a pathogen. This also means that it can take awhile for your immune system to recognise a pathogen is present and thus the infection can take root before your immune system can respond, and thus you get something the picture on the right, which is an MRSA infection.



      The idea with vaccines is to get your immune system to immediately recognise a pathogen and destroy it before it has a chance to cause disease. So who is involved in this very important immune army? We have antibodies, T cells, and B cells. T cells and B cells are also referred to as "white blood cells".  (The oxygen carrying blood cells are called red blood cells.) There is a difference between T cells and B cells in where they are produced and how they interact with antigens, but for simplicity, I am not going to delve into the differences. We are just going to focus on B cells and antibodies. 

Antigen: This is a marker on a cell that causes a response from your white bloods (B and T). This could be a protein on the cell membrane. Whatever it is, it tells your immune system that this cells is a foreign invader and needs to be dealt with. 

Antibodies: Little Y-shaped proteins that bind to antigens. These are specific to the antigen on a specific pathogen. They are secreted proteins. They roam around your blood system and will bind to the antigen on the pathogen they are specific for when they come across them. This marks the pathogen and allows your white blood cells to destroy it. If you have had a disease, you keep the antibodies that you formed when you were infected and it prevents you from being reinfected.  (Antibodies are also referred to as immunoglobulin or immune globulin.) 

To summarise: your white blood cells (B and T cells) are your body's Swiss army. They are exist to prevent pathogens from invading your body and killing you. When you get a disease, your white blood cells wage war, and usually win. (Again, Swiss army-fierce when engaged.) Your immune system produces antibodies that bind to specific markers on pathogens, called antigens, and this marks pathogens, making them easily removed from your body. If you have never had a disease before, you will end up creating antibodies. If you have had a disease before, then you will already have antibodies, immediately marking the disease cells and preventing you from getting it again. 

   The idea with vaccines is that you trick your immune system into thinking that it has the disease. It produces antibodies, so that when you are exposed to the actual disease, your immune system immediately marks the pathogens BEFORE they can cause disease and they are destroyed by your white blood cells. 

   I said above that your immune system usually wins, so why do we even care about this? Well, just because your immune system may win, it doesn't mean that it does not suffer some losses. For example: measles, you may not die, but you may end up losing your hearing. Mumps: you may actually lose your ability to reproduce. Polio: you may be paralysed for life. And of course, you can actually die. The flu causes over 100 000 deaths world wide every year, and that doesn't even count the millions who have died in massive flu pandemics prior to the advent of the vaccine. 

Coming Up Next: Vaccines: How They are Produced

    

More on Ebola

    I have already written about the approval of experimental drugs, but it seems that the waters are getting muddier as the ebola outbreak continues to cause problems in Western Africa. One of the most disappointing things that I have seen is that the FDA (US Food and Drug Administration) is now saying that there are cases of fraudulent ebola treatments being sold online. 

    If the problem was not bad enough, now people are trying to cash in on the mass hysteria and sell compounds that have not undergone any testing. You may be asking, "how is this different than using experimental drugs?" Well the difference comes in the form of the fact that the "experimental drugs" that have been approved for use have already undergone preclinical testing by regulated pharmaceutical companies and have been approved for stage 1 human clinical trials. The compounds that are being sold online fall outside the regulated pharma industry, their efficacy and safety have not been tested at all. The best case is that these compounds will do nothing, at worst these compounds will cause more damage. 

  The reason the FDA exists is to prevent this. It is there to protect consumers, and in a disaster such as this ebola outbreak, the consumers are an even more vulnerable population. This vulnerability requires regulatory bodies, such as the FDA or WHO, to be more vigilant of fraudsters looking to make a quick buck.

   While these stories make it seem like the human race is filled with a bunch of greedy bastards with no compassion, take a look at the work by volunteers and employees of organisations like the Internation Federation of the Red Cross Red Crescent for examples of people willing to make a difference and help their fellow humans. 

Experimental Ebola Drugs Now Approved for Use

     The recent Ebola outbreak in western Africa has been something that has captured the world's attention, especially with its high death toll. The question has been how to treat the disease as currently there is no vaccine and the drugs are experimental. On Tuesday, the World Health Organisation met to discuss the ethical implications of using experimental drug treatments on ebola patients. The BBC shared an article earlier this week explaining some of the issues. 

    If you need a bit of a refresher on how pharmaceuticals are produced, check out an earlier blog I wrote on how pharmaceuticals are produced. There are a lot of regulations to go through and only about 1% of the compounds that make it successfully through the animal trials (such as the ebola drugs) are likely to make it through the human clinical trials. 

    The other huge challenge with these experimental drugs is that there are limited supplies. Canada has committed 1000 doses of the experimental vaccine.
But why only 1000 doses when so many people are affected? Why can't we just give out more doses? Well this all goes back to how these compounds are produced and the regulations that surround their production. 

     Early in the testing cycle of pharmaceuticals, you don't need tens of thousands of kg of product, so only about 1-10 kg of product are produced. While clinicians are testing the efficacy of the drug on patients (or animals-depending on phase), process chemists are testing the synthetic pathway. This pathway has to be cost efficient, it has to follow the regulations of good manufacturing practices, and it has to be scalable. Of course, all of this has to be safe. What works on a research lab bench is not always safe or practical on the large scale of production in the pharmaceutical industry. 

    Finding a drug/vaccine, making sure it works, making sure it works in human trials are only part of the testing that happens. The synthesis is also important. Every synthetic reaction has by products. Not only do you have to test the safety of the product that you want, you also have to test the safety of the by-products of the reaction. You have to demonstrate that they are being removed effectively. This process also needs to be approved by the regulatory bodies. The process is continually optimised during the life time of the drug. 

   Synthesis also takes are really long time. I remember teaching a postdoc in the lab I did my PhD in how to do a simple esterification reaction. (He was not from a synthetic background.) I remember him being shocked at how long making the compound took, even though it was one step. He figured it would be a couple hours of work and it ended up taking him 2 days to synthesise, isolate, and purify the compound. This is why I found it funny when people figured that the H1N1 flu vaccine circumvented proper testing and regulation when, during the mass outbreak, all of the sudden the vaccine was available for that strain within a couple weeks. It wouldn't have even been physically possible to come up with a new vaccine in two weeks, but let's save influenza for another blog entry in this vaccine series.

Dear Pro-Vaxxers: Let's Lay Off Jenny McCarthy

         Vaccinations: I am guessing that by clicking on this entry you are expecting either some fear-mongering piece on how vaccinating your kid will make them more sick than the disease and it is all pseudo-science or you are expecting a self-righteous piece on how vaccines are safe and those not vaccinating your kids are guilty of child abuse and you are responsible for the deaths of babies. 

         Sorry to disappoint, but this particular blog is my attempt to recognise that people who offer trepidation about vaccination do have some valid questions and they should not be mocked for asking them. I am writing to the pro-vaxxers: we have the science on our side, let's maybe stop calling people who question it idiots and maybe instead help them understand. By being combative, we are not doing anything to stem the anti-vax movement, and that is something that impacts all of us.

       The anti-vax movement can be traced back easily to Andrew Wakefield's fraudulent studies on a relationship between autism and the MMR vaccine. I don't really feel like going too much into Andrew Wakefield as I would equate him to the Bernie Madoff of science. There have been no less than 16 000 peer reviewed papers by reputable scientists in everything from epidemiology to chemistry who have since studied vaccines and found that there is no link whatsoever and we should all line up and get the shot. The damage done by this study is upsetting.

      So why then are people still buying into the "anti-vax" movement? I would have to say that such a study simply caused people to ask questions that previously they just accepted: what is in these vaccines? Why do I have to get so many? How are they tested? How do we KNOW they are safe? It obviously didn't help that high profile celebrities like Jenny McCarthy and Jim Carey were often seen at anti-vax rallies and Jenny McCarthy even wrote the introduction to Andrew Wakefield's book. 

Ah, Jenny McCarthy-she is really why I am writing this particular entry because recently she has backed off her "anti-vax" stance writing an op-ed piece for the Chicago Sun Times stating “I believe in the importance of a vaccine program and I believe parents have the right to choose one poke per visit. I’ve never told anyone to not vaccinate.” Well you know the internet, this immediately caused a backlash of people calling her a hypocrite, citing every "anti-vax" statement she ever made. There is even a website called Jenny McCarthy Bodycount which shows the number of preventable deaths caused by previously eradicated diseases. 

      I am a staunch pro-vaxxer. It is in the interest of public health that we get vaccinated. It is how we will cure diseases and ensure no one ever gets them. Seriously, if you are the kind of person donating money to any sort of disease cure, chances are some of that money is going toward finding vaccines. With all this in mind I was utterly disappointed to see the reaction toward Jenny McCarthy's change. DEAR PRO-VAXXERS: THIS IS WHAT WE WANT! We want people to realise that vaccines are important to the health and safety of everyone in society. We want people who were previously anti-vax to take comfort in the science of vaccines and recognise their importance and feel comfortable in choosing vaccination for them and their children. People are not likely to do that if they see someone like Jenny McCarthy get completely torn apart for changing their mind. I, for one, think it was a brave move of Jenny McCarthy to write a piece explaining that she now has a more "pro-vax" stance.

      As a matter of fact, there have been studies to show that in the face of all the evidence, people are less likely to change their minds. We are not going to make easier by being jerks when someone decides to change their minds. 

"Dumbledore says people find it far easier to forgive others for being wrong than being right," said Hermione.  (Harry Potter and the Half Blood Prince, page 95)

      I really feel that as scientists we need to be more accessible as experts. We need people to start realising that we are the "real doctors" and that there are more resources out there to get the answers than their general practitioner physician. Don't get me wrong, physicians are great. They are great at what they do but they are not experts. They refer you to oncologists, surgeons, dermatologists, etc., when you need an expert for a medical malady. This works the same for research. Physicians are not experts. They rely on the work of experts and yet they are the ones that have to field the questions. Let's help physicians out and get the experts out there because an immunologist is much more suited to addressing the question of "why do I have to get my baby vaccinated every 2 months?" than your public health nurse or general physician. Again, let me stress: public health nurses and physicians are great-but they are not the only resource.

       All of this has inspired me to dedicate a series of my blog entries just to vaccines and their importance. I hope to provide peer-reviewed, cutting-edge research answers to the way vaccines work, why we need them and why they are important. Ms. McCarthy states in her op-ed that maybe the vaccine schedule that the doctor prescribes is too much. Well Ms. McCarthy, there is actually a reason for that schedule. It is important to ensure the efficacy of the vaccinations and I am going to write about why it is important to get your vaccines on schedule, as well as many other things so that you, and other concerned parents like you, can get the most accurate, scientific data out there to allay your concerns.  

     So for all of you, pro or anti-vax, I hope you keep reading my series with an open mind to learning something new. For all of you pro-vaxxers: please be kind when talking about the vaccine debate. I know that it can be frustrating, but remember that much of it started with simple questions, which is something that as scientists, we embrace. We have the science on our side; we don't need to resort to childish name calling or "anti-vax shaming". Shaming has never been a winning strategy. We are not trying to win a debate. We are trying to provide information that makes parents feel that they are doing the right thing by vaccinating their children. For all of you anti-vaxxers: please keep an open mind to peer-reviewed science. You should always feel comfortable asking questions about why your child is receiving any kind of treatment, but you should also know where to get answers that are based on fact. Unfortunately the internet is a big place and anyone can post whatever they like. It can be a challenge just to sort out what sources are valid and which ones are not. Vaccination is about more than just you and your child, though: it is about community health.

Next: The Immune System: What Exactly are We Designing Vaccines For?

    

Science Policy and Communication

One of my favourite topics to get up on my soapbox about is science policy and that not enough of the policy makers have a true understanding of science. Now part of my usual rant with has to do with the fact that I am not blaming the policy makers for this, but rather chiding the apathy of the scientific community for not being more active in the policy making role. And that isn't entirely the fault of the scientific community either. Have you ever seen "question period" in the House of Commons? I would rather slide down a banister of razor blades and land in a pool of alcohol than participate in that. 

For me, I just want people to understand small things like what you read on the internet isn't necessarily factual or that medical doctors aren't experts in science and scientific studies are still done by humans and can have mistakes.

Things that can help people learn to read science without spending 11 years in university (yes, I spent 11 years in university study science and chemistry) are nicely summed up in this Nature article. We are at a point where information is so easily accessible. Now it is time to learn how to sort and process that information in a meaningful way. 

I personally love talking about science and all things science so that I can learn and I can teach. It is one of my favourite things to get other people as passionate for science as I am. And if I can teach you something then I feel my job here is done. Hence why I have this blog. I may not be able to write often, but I do love when I get the chance to write about something I love as much as science. 

Biodiesels

I am currently writing my dissertation for my Ph.D. entitled "The Use of Canola Oil as a Carbon Feedstock in the Synthesis of Value-Added Materials". One of the things that happens when writing a dissertation is that you do a lot of reading about interesting points tangential to your actual project. Since I am working with canola oil, I devoted a special section of my introduction to biodiesels, since 80% of the biodiesels used in the EU are made of canola oil. (They call it rapeseed, but it is canola oil.) I thought I would share some of the chemistry of biodiesels.

First, let's start with a little history. Did you know that diesel engines were originally designed to run on a renewable fuel source? In 1900, Rudolph Diesel presented his engine, which was powered by peanut oil, believing that biomass fuel was the future of the engine. However, come the 1920s, engines were altered to use the lower viscosity petrodiesel which was much cheaper to produce. This remains one of the huge challenges in sustainable development: economics. How much are you willing to pay for fuel because while the $1.30/L (Canadian pumps in Alberta) is pretty steep, it is still cheaper than biobased fuels because of the mass production infastructure. But I digress; this is a chemistry blog. 

Peanut oil is not technically a biodiesel. Biodiesels are transesterified vegetable oils resulting in fatty acid esters, most commonly the methyl ester. The vegetable oil is reacted with an excess of methanol in the presence of an acid or base catalyst (industrially it is usually the base sodium methoxide) to produce 1 equivalent of glycerol and 3 equivalents of fatty acid methyl esters. These are referred to as FAMEs. What is awesome about biodiesels is that they can be used directly in compression engines without modification to the engine and they can also be blended with petrodiesels because they are completely soluble. Because they come from plants, the carbon dioxide and water produced by the burning of the fuel are taken back up by the plants resulting in overall reduction in emissions. There is also a reduction in carbon monoxide, sulphates, particulate, and total hydrocarbon emissions. Which is all pretty great. 

But of course there are some major drawbacks. First, cost. As I have alluded, price plays a big role in industrialisation and biodiesels are currently a lot more expensive to produce compared to petrodiesel. Second, poor cold performance. This is actually a concern with diesels in general. But these longer chain fuels begin to solidify at higher temperatures. Huge problem in a place like Edmonton, Alberta where in the winter it is common to get temperatures well below -10 C. This is also why diesel engine vehicles require a block heater. Fuels need to remain liquid and low in viscosity to actually perform well. Third, and I think this is really important, is that the greenhouse gas (GHG) emission savings is much lower than expected, failing the sustainability requirements. The EU's Renewable Energy Directive (RED) demands a 35% reduction in GHG emissions compared with petrodiesels for biodiesels. They have estimated that canola-based biodiesels result in a "typical" 45% reduction while commonly using the default number of 38% in GHG savings. 

However, a recent study by Gernot Pehnelt and Christoph Vietze refutes these claims and points to GHG savings of, at best, 29.7%.  The authors claim there was a lack of transparency in the calculations performed by the European Commission. Running a life cycle analysis using the same basic methodology and background data as RED, and only utilising publicly available and published data in their calculations, the authors were unable to replicate the numbers reported by RED. Further, these calculations did not take into account for any of the other environmental or social impacts associated with using available agriculture land for fuel, which they argue would further decrease the sustainability of canola oil biodiesel. 

Another huge concern with biodiesels is that glycerol is produced as a by-product. The global production of glycerol has grown exponentially, well passed the global demand for this chemical. 

As we move toward a more sustainable future, it is important to recognise that the after over one hundred years of industrialisation based on petroleum fossil fuels, our journey has no quick solutions. It will be a long and complex movement, but with every step, even the smallest, we are that much closer to a sustainable future. This must be a global movement.

References:

Brown, B. A. Ph.D. Dissertation, University of Alberta, Not Yet Published.

 

Bart, J. C. J.; Palmeri, N.; Cavallaro, S. Biodiesel science and technology; Woodhead Publishing Ltd.: Boca Raton, FL, 2010.

Huber, G. W.; Iborra, S.; Corma, A. Chemical reviews 2006, 106, 4044–98.

Cheng, J. Biomass to Renewable Energy Processes; Taylor and Francis Group: Boca Raton, FL, 2010.

Ragauskas, A. J.; Williams, C. K.; Davison, B. H.; Britovsek, G.; Cairney, J.; Eckert, C. A.; Frederick, W. J.; Hallett, J. P.; Leak, D. J.; Liotta, C. L.; Mielenz, J. R.; Murphy, R.; Templer, R.; Tschaplinski, T. Science (New York, N.Y.) 2006, 311, 484–9.

Spellman, F.; Bieber, R. The Science of Renewable Energy; CRC Press, Taylor and Francis Group: Boca Raton, FL, 2011.

The Economic Impact of Canadian Grown Canola and its End Products on the Canadian Economy; 2011.

Knothe, G. Energy & Environmental Science 2009, 2, 759.

Gilbert, N. Nature 2012.

 

Pehnelt, G.; Vietze, C. Jena Economic Research Papers 2012, 39, 1–35.