The Germ Guy: Confessions of a Mercurial Microbiologist



A Moment That Changed The World…

Late last year, something unbelievable happened. As news spread, the world woke up to a new reality. Nothing would ever be the same again.

Most people were shocked by the revelation, as it was thought to be impossible. Yet a handful of people knew this would occur. Almost no one believed in them but they continued on tirelessly. They did everything they could to skew the odds in their favour. They hacked what was once thought to be an impenetrable defense and used viral tools to ensure success. In the end, their efforts paid off and these once slighted individuals reaped the rewards with almost sinful delight.

If you haven’t already guessed what that event was, I’ll fill you in…

(The Ebola Vaccine was 100% Effective!)

Believe it or not, vaccination proved to be perfect in the most recent clinical trial. For researchers, public health officials, and even the World Health Organization, this was a hallmark moment. It was time for a…


If you hadn’t heard of this incredible news, you can’t be blamed.  The article came out right before Christmas. Most people including the media were rightfully focused on the festive season of the Holidays. They also were dealing with the hangover of another world-changing event that happened six weeks earlier…

trump-pres(Which, if you didn’t know, culminates today…)

If you think about it, there were similarities between these two events. The premise of a President Trump or a 100% effective vaccine was considered ludicrous just a year before. Although both had shown themselves to be capable of achieving these heights, few really believed they would succeed. Yet, as the human tallies came in, the picture became clear. At the end of it all, there was only one word to describe what had occurred…


But there is one significant difference between these two announcements. One has created a significant amount of debate, backlash, and concern while the other has created a sense of hope not seen since…

hope(Susan Lucci’s Winless Streak Ended…)

Putting the parallels with American politics and daytime soap operas aside, there are three reasons behind the optimism from the Ebola vaccine. The first and most obvious is a future in which epidemics like the one seen in 2014-2016 may never happen again. After everything the people in the West African nations of Guinea, Sierra Leone, and Liberia went through (and yes, America), this announcement provides…

relief(Some welcome relief…)

The second has to do with the ability of a vaccine to protect. For what might be the first time, there is an option with 100% effectiveness. This has always been the goal of researchers but until recently, figuring out how to develop the perfect candidate has been nearly impossible. A new benchmark has been set against which future vaccines will be evaluated. Granted, finding a way to protect against Ebola is much easier than say…

flu(A constantly evolving virus…)

Yet even flu researchers are getting closer to a universal vaccine that may one day protect us against all possible variations of this more common – and possibly more troublesome – pathogen.

The final reason deals with the nature of the vaccine. It was made through a combination of different genetic engineering processes. The virus used isn’t even Ebola but one that is harmless to humans. Although it is officially known as a recombinant, some might prefer to call it a…

gmo(Genetically Modified Organism…)

As you probably know, there is a significant amount of debate on GMOs with good reason. These products have entered the agricultural industry and the food marketplace without much consultation or information being given to the public. Not surprisingly, some have reacted quite negatively to this and called for an all out ban on genetic engineering.

But thanks to this vaccine, we can realize not all genetically modified organisms are bad. After all, if you want to look at a GMO, all you need to do is…

timberlake(You are not a clone…)

Perhaps this good news GMO story may balance the scales a little. Maybe those calling for an end to this technique will realize it only can hurt scientific advancement and put other discoveries such as this vaccine in peril.

I hope all people will understand the need for genetic engineering in health and medicine and appreciate the potential it brings. Most importantly, I wish all those who are skeptical of scientific research understand for the most part, the work, while at times seemingly out of touch with reality, ultimately is attempting to improve our world and make it a better place for all.

Okay, I know that may have sounded like an…

inaurgural(Inaugural speech…)

But as this day only comes once every four years, I figured it would be worth the risk.

If you want to read more on the vaccine, you can check out the World Health Organization for more details:  Final trial results confirm Ebola vaccine provides high protection against disease.

A Bacterial Bakery Trick…

It’s a common practice for bakers. They arrive early in the morning, spend hours slaving in the back, and eventually get all the freshly made breads, cakes, pastries and buns organized in displays. Then, when the time is right, they invite the world to enjoy the wares of their labour by…

bakery(Opening The Door…)

If you happen to be walking by at just the right time, the attraction can be almost irresistible. The aroma coming from the freshly baked goods can stop you in your tracks and lead to an unexpected diversion into the store.

Scientifically speaking, this attraction is caused by a phenomenon known as odorant perception. An aromatic molecule called a volatile organic compound enters the nose or the mouth and interacts with the cells resting inside. As this happens, olfactory nerves sense the molecule and send a signal…

aroma(To the brain…)

Here’s where it gets interesting. The scent first is interpreted as either pleasant or repulsive. After the decision is made, a neurological signal is transmitted to the rest of the body to move. Pleasant aromas tell our bodies to get closer to the smell while those considered to be foul force us to move away.

If we rely on instinct alone, our bodies heed the command and we head, if only slightly, in the appropriate direction. If the smell is strong enough, it may even overcome our current mental plans. This is most common in repulsion, when being overtaken by a horrific odour causes us to move away quickly.

But, those clever bakers use the opposite reaction to their advantage. If they can make those wonderful aromas as strong as possible, people will fall victim to instinct and…

bakery2(Pick Up A Few Things…)

Odorant perception isn’t only for humans. Researchers have found other species rely on this phenomenon. Mice have it, fruit flies have, even worms have it. The response to external odours appears to be conserved in evolution…at least in animals. Until recently, no one quite knew if the use of volatile scents could attract or repel bacteria.

A few weeks ago, that changed when a team of researchers from McMaster University discovered a bacterial species capable of using odours to signal other members of the same species. It’s known as Streptomyces and it is the source for many antibiotics – think streptomycin. But the bacterium also has a rather fascinating capability. It can change the way it looks and functions over time…

streptomyces(Here’s the life cycle…)

The bacterium also likes to explore its environment in search of nutrients. However, this is no easy task. Those cells designated with the burden of exploring may encounter a long and arduous trip. They may have to travel great distances (millimetres) from the colony. They may face unspeakable challenges including giant chasms (agar cracks), rushing rivers (condensation), and of course, great mountains…

rock2(…or as we call them, small stones)

Depending on where the new resources are eventually found, these brave bacteria may be isolated in a brand new world without any means to signal the colony.

But thanks to this paper, there really is no reason to fret. We now know Streptomyces can use the same method as bakers to let their colleagues know food has been found and that more cells should come.

Here’s how it works. Upon finding the nutrients, the bacteria create a volatile organic compound – an aroma – that can travel through the air back to the colony. This airborne chemical reaches home base and informs the other members about the new source of food. Other explorers are then sent off like pilgrims to join these brave scouts and ensure the population continues to thrive in this new, rural area of the world.

At the end of the day, the explorers are joined by their peers, the colony extends and much like those who found new food at the bakery…

rock3(Everybody wins!)

There is, however, one particular difference between the lure of the baker and the signal from the explorer cells. That happens to be the nature of the volatile organic compound causing the attraction.

Humans tend to love chemicals such as maltol and methianol, which give off that fresh bread aroma. We simply cannot resist. But the bacteria have no interest in these molecules. For them, nothing is more delightful than trimethylamine. It’s what drives them to explore and is the key to their movement in this paper. For those who are not familiar with this scent, it’s most commonly associated with…

deadfish(Rotting fish…)

Guess it’s true that there are different strokes for different folks…or in this case, bacteria.

If you want to read more on how Streptomyces uses volatiles to communicate, you can read the entire paper. It can be found here:
Streptomyces exploration is triggered by fungal interactions and volatile signals

Three Germy Cheers For The Appendix!

Sometimes a study comes out and you have no option but to get excited because the topic is simply…


Okay, so maybe the appendix isn’t exactly what you might consider headline news. After all, it’s long been considered an evolutionary artifact with no real use in humans. Yet, in the city of Glendale, Arizona, a research team at Midwestern University have revealed this tiny organ may indeed serve a valuable purpose.

It may be a safe house for friendly bacteria…

skeptical(Yeah, I know it sounds sketchy…)

This theory has been around for about a decade but no one has ever been able to explain it in a credible manner. Thankfully, that’s what the researchers as Midwestern University set out to do in a very systematic and painstaking way.

They took genomic information from 533 different species, all of which had some indication of an appendix. Some of them were definitive while others were more sketchy in nature. Some of the more obvious ones (and one non-existent one in G) can be seen here…

(Can you guess which animals they are?)

With the species in place, the team then went about organizing them in a timeline of evolution in the hopes of finding some reason for this intestinal tag. They did this by comparing a variety of different gastrointestinal structures, such as the cecum area. Scores were made based on the shape, size, and function of each part of anatomy. Then environmental factors were thrown into the mix, such as latitude and longitude, population density, and diet.

By the time it was all said and done, I’m sure they were not in the mood for….

ribbit2(Singing and Dancing…)

But, the results paid off as they were able to develop several links between evolution and the appendix. Most were anatomical in nature but one significant link got me in the mood for some MALT!

malt2(Not that kind…)

The appendix is rich in two forms of immune tissue, gastrointestinal associated lymphatic tissue (GALT), and mucosal associated lymphatic tissue (MALT).

kermit2(Get it?)

Both these immune types are specifically designed to help us deal with whatever comes into the gastrointestinal tract. Having more GALT & MALT can also be good for our friendly bacteria. The cells in this area help to stimulate the growth of several beneficial species through a variety of chemical cross-talk mechanisms.

In essence, having that appendix might help ensure you have a healthy and diverse microbial population that is…

telus-frog(Sitting Pretty…)

Of course, all of these theories are still up for debate. Even this study suggests there are many questions to be answered before we can truly say the appendix is a microbial safe haven. Yet, this study adds to the theory that as we evolved through time, our bodies learned how microbes are for the most part our friends and wanted to be sure we loved them biologically.

Now if only we could love them emotionally like we do….

frog-kiss(You get the idea…)

For more on the paper, which sadly is not open-access but I felt definitely worth discussing, you can read more at ScienceDaily: Appendix may have important function, new research suggests.

Oh, and as for those intestinal drawings, here are the answers:
(A) Wombat (Vombatus ursinus);
(B) Brushtail possum (Trichosurus vulpecula);
(C) Rabbit (Oryctolagus cuniculus);
(D) North American beaver (Castor canadensis);
(E) Rock hyrax (Procavia habessinica);
(F) Orangutan (Pongo pygmaeus);
(G) Bush-tailed phascogale (Phascogale tapoatafa).


Have A Happy Holiday Season!

It’s that time of the year again. Everyone is winding down from the year that has been and finding time to relax and wear something a little more comfortable…

christmas-suit(Or stylish…)

However you choose to mark these next few days, with family, friends, or as I have done for many years in the past…

lab(In the lab…)

I wish you – and of course your germs – a most wonderful time.

Oh, and if you do happen to venture out on Monday to take in the madness that is…

(Boxing Day…)

Remember to keep the hand sanitizer close and wear a scarf or necktube (which apparently is also called a neck gaiter). They are your best means for protection against respiratory viruses, which are sure to be as prevalent as the incredible deals.

Happy Holidays everyone!


An Open Call For Science Communication…

It’s insane how time flies when you are travelling. One moment it’s the middle of November and next thing you know, it’s almost Christmas…

heywhahappened(You said it…)

Over the last weeks, I have had the honour of attending several conferences. In the middle of November, I was at the Society for Neuroscience meeting in San Diego, which attracted over 30,000 people. It was mainly an advocacy trip although I did gain insight into the field. As a microbiology & immunology scientist, my overall impression could be best described as…

fascinating_o_509159(Especially the microbe-gut-brain axis bubble)

From there, I shuffled off to Helsinki, a mere 10 time zones away. Even though I took care of my microbes, there was no way I could prevent the inevitable…

jet-lag(Jet Lag!)

Thankfully, I had a few days to recover before participating in one of the largest conferences in Europe. It’s known as SLUSH and attracts over 17,500 people. It’s also one of the most unique conferences I’ve ever attended. But don’t take my word for it…

slush-header-2(Welcome To SLUSH!)

I had been asked to give a presentation at this incredible conference on the art of science communication. But there were conditions…

  1. It had to be engaging to a wide variety of audiences;
  2. It had to be thought-provoking messages;
  3. It had to have a link back to the conference itself and…
  4. It could only be 16 minutes.

It took several weeks to hone it in collaboration with some of the organizers but eventually, it took shape. I would describe it to you but it’s probably better if you see it for yourself…

(Lab Rats of Disruption!)

As soon as I was off stage, I was sent into a whirlwind of travel as I had to get back to Toronto – via Iceland…HOOH! – and then head up to Ottawa for the next conference, the Society of Toxicology of Canada. I also needed a change of clothes…

stc2016(Why So Serious?)

To be honest, it was anything but serious. The STC team were amazing and we had many a laugh. I even had a chance to present an actual research-focused presentation. It was the first time in years and I have to say, I was more nervous than I was at SLUSH.

Eventually, I made it home although there was no time for…

sleep(Is this TOO cute?)

I had a long list of Emails and other requests in my Inbox. People from all over the world were reaching out to discuss more about the art of science communication and how to share research with the public, policy-makers, and investors. I’ve since set up enough meetings, conferences, and presentations to last until the middle of next year. Let’s just say I’m going to be…

beaver(A Busy Beaver…)

Which brings me to the title of this article. Some of the requests involve practicing science communication with me. People want to be able to find their voice as well as the right format to make science more interesting. While I am happy to help out, I find that giving a bit of a push will increase the chances at success.

In that light, I’ll offer the chance to be a guest contributor on my blog…

maxresdefault(I know…Jackpot, right!)

Okay, maybe it’s not winning a lottery and there is no money involved – I do all of this for free – but it is a chance to work with me and have your article posted on a site where people are truly interested in learning more about science, research, and health. Also, I don’t attract trolls or other unsavoury sorts. Instead, I do my best to ensure a place for honest discussion and of course, a little bit of fun.

As we head into 2017, which I believe will be one of the most critical years for science communication in decades, I hope some of you out there will want to try giving this strange but rewarding occupation a try. I know it’s not for everyone but for anyone who has that inkling, I would love to help you find a voice as unique as your…

fingerprint(You get the idea…)

If you’re interested in posting a piece on this blog, feel free to comment below or, if you wish, send an Email to…

What Brangelexit Can Tell Us About Antibiotic Resistance…

It was quite the week Two historic events happened over the last seven days. They were captured and shared by millions. However,  only one seemingly gained the attention they both deserved.

The first was one of the most important moments in our generation. It happened in New York and involved 193 countries all coming together to act on what might be the greatest threat in our time…

HLM Antimicrobial Resistance_Identifier

You may have heard about this meeting in the news. What you may not know is the result. It’s a political declaration of action to combat this rising threat to our health. You can read more about it here:

If you hadn’t heard about this meeting, I won’t hold it against you. Because the other incredible event stole away any momentum this might have seen. If you haven’t guessed it by now, it was the announcement that Brad Pitt and Angelina Jolie are…as my friend Sean Webb ingeniously coined…

jolie-pitt-cover-435x580Consciously Unmegacoupling

The news overshadowed any attempt to bring the plight of antibiotics into the spotlight. The Brangelexit, as it is now known, completely stole any chance the UN meeting had to increase awareness of the looming crisis. The declaration became little more than a small news story.

You might think I’m upset. I am. But I also know popular culture far outshines any scientific news, except perhaps…

plutodemotedPoor Pluto…

But as it’s the weekend, I didn’t want to go on some rant. Instead, I felt it best to find a positive from the announcement. As I searched my soul and my….

Plutonian Heart

I realized there was a link between the two events. In fact, I came to understand how the separation of these two mega-stars could actually provide perspective on antibiotic resistance. The feeling was so strong that I almost had to break into song. But, alas, that would not be good and so I decided instead on a different, poetic approach.

I present to you…

brangelinaThe End Of An Era May Save Another

 Woe has struck the land as Brangelina is no more;
The divorce papers have officially been put on file;
Now Hollywood is shaken to its innermost core;
The power couple’s love has turned to a rift most vile.

This tale of separation from a most valued friend;
Is happening in medicine and causing an ominous storm;
We are losing antibiotics upon which we so deeply depend;
Without action, living without them will soon be the norm.

Unlike Brad and Angie, there is hope for us still;
There are ways and means to prevent this great divide;
Now the UN has stepped in using its ceremonious quill;
Declaring the world is ready to act and abide.

We all have a role to play if we wish to avoid Brangelina’s fate;
Working in harmony we can beat antibiotic resistance before it’s too late.

Should Germs Accept The Blame For The Decline in Bar Soap Sales?

I received a note earlier this week about a disconcerting trend in hand hygiene. It seems the bar soaps are becoming less popular. While there are many reasons, one has to do with the fear of germs on the bars themselves. You can read the report here: Slippery Sales For Bar Soap.

While I had thought of writing a rant to refute the claims, I realized the long weekend might not be the best timing for a negative vent. So I sought to channel the emotion into something more constructive…and so I present a short, sweet, Shakespearean sonnet…

ivory-bar-soapThe Plight of The Slighted Soap Bar

One day I happened to browse upon the world wide web;
Hoping to read several stories in delight;
But a report from Mintel made my joy sharply ebb;
And I became more and more uptight.

The tale talked of bar soap, our old trusted friend;
But many apparently considered it a troublesome bane;
There were many a reason for this unwelcome trend;
Including a rather malicious and undeserving stain.

Many people now fear these bars are covered in germs;
They believe the risk of infection is high;
Yet a study – see here – reveals in no uncertain terms;
No threat to their health is nigh.

Sadly, I fear, we may not be able to turn back;
For it is hard to change behaviour in the midst of such meritless flak.


Science Communication, Isaac Asimov, and Creativity…

I am asked quite a number of questions when I’m on the road and as you might expect, most deal with germs. But every now and then, someone wonders exactly how to come up with inventive ways to communicate science.

One answer I like to give is…

isaac-asimovHeed the words of Issac Asimov

Dr. Asimov opened the door to widespread scientific communication through his wonderful writings. He also sparked imaginations worldwide bringing science closer to the individual.

During his tenure on this Earth, he wrote numerous essays on the topic of writing and creativity yet one of his most important for anyone interested in communicating science was written in 1959. It was for the United States Defense Advanced Research Projects Agency, better known as DARPA. It was simply titled…


The essay itself wasn’t released until 2014 and so I read it partly as an after thought as I was already well into my tenure as a science communicator. But as I read it, I found some parallels between his words and the work I was doing. Some of these passages included:

“A person willing to fly in the face of reason, authority, and common sense must be a person of considerable self-assurance. Since he occurs only rarely, he must seem eccentric (in at least that respect) to the rest of us. A person eccentric in one respect is often eccentric in others. 

Consequently, the person who is most likely to get new ideas is a person of good background in the field of interest and one who is unconventional in his habits. (To be a crackpot is not, however, enough in itself.)”

This represents the base for anyone interested in science communication. Rather than following standard routes, taking an unconventional – or, as my blog’s name suggests, mercurial – route can bring about both awareness and in some cases action on the part of the audience.

“My feeling is that as far as creativity is concerned, isolation is required. The creative person is, in any case, continually working at it. His mind is shuffling his information at all times, even when he is not conscious of it.”

When I am in the process of developing those parallels, I do it alone. I have tried numerous times to work with others but as Asimov says,

“The presence of others can only inhibit this process, since creation is embarrassing. For every new good idea you have, there are a hundred, ten thousand foolish ones, which you naturally do not care to display.”

It’s absolutely true. Most of my ideas simply do not fit the goal and are tossed aside. Though this may seem unproductive, as a researcher, it’s all part of the process. In the lab, the same trial and error is used to find the right hypothesis, the best experimental design, the most telling band or fluorescence marker, and of course, the most appropriate journal to publish the results.

All scientists go through these motions though I find few seem to realize how the actions of their vocation form the foundation for creativity. By giving oneself the chance to explore, that ability to find what works can arise.

I’ve only quoted a few passages from Asimov’s essay. I would truly recommend reading the entirety as it is a gripping read especially for anyone who has wanted to make a move towards the creative. He also uses the word sinecure in the most fascinating context.

You can find Dr. Asimov’s essay by clicking the link below:

Published for the First Time: a 1959 Essay by Isaac Asimov on Creativity

If you happen to be a science communicator, or are interested in giving it a try, let me know if the words in the essay ring true.



The Curious Case of Cola To Combat Swimmer’s Stomach

A friend sent me a text message asking a very strange question:

“Can cola kill pathogens after swimming?”

It seemed like an easy answer:

Swimmer’s stomach is a rather annoying condition whereby bacteria swallowed from natural waters end up giving people GI distress usually leading to diarrhea and sometimes vomiting. It’s not fun and any means to prevent the symptoms is welcome news.

But drinking cola? For me it seemed highly unlikely.

Yet the swimmer who swears by it also happens to be an Olympian and one of Canada’s better hopes for a medal.

Richard Weinberger, the 2012 bronze medalist in the Olympic 10K

You can read more about Richard and his quest – as well as his belief in cola – here:
Weinberger Predicting An “Epic” Olympic 10K Race In Rio de Janeiro

So, giving the swimmer the benefit of the doubt, I went in search of a possible mechanism behind his assertion. There were no clinical trials so any evidence he gave was purely personal and word of mouth. But that wasn’t a good enough reason to call it bunk. I wanted a mechanism to provide an explanation as to why it didn’t work – and also why people thought it might.

Then something strange happened. I came across an article from over 15 years ago. It was a rather obscure paper about killing E. coli on animal hides. You can see the abstract here:
The mechanism involved using phosphoric acid – just like the stuff found in cola – and mixing it with acidified salt water.

For me, this was an instant:

OSLO 20090612: A-ha med f.v. Paul Waaktaar-Savoy, Morten Harket og Magne Furuholmen inntok fredag Oslo for å markedsføre sitt nye album 'Foot of the mountain» som kommer i salg 15. juni. Foto: Berit Roald / SCANPIXA-HA! (if you don’t get this, ask your parents)

Reading the paper allowed me to see what could be happening in the gastrointestinal tract and why this cola trick might work. If you’re wondering, it goes something like this:

  1. Drink seawater – this is the only reason it works…freshwater won’t have any effect;
  2. Let it get acidified in the stomach – should be at least a few minutes if not more;
  3. Add phosphoric acid – drink the cola;
  4. Bow head for the gold medal – okay, this only applies to Weinberger.

I’m not saying this mechanism is actually occurring or that the technique works in the body. For that to happen, there would have to be clinical trials. Yet, as with many traditional remedies, this medical benchmark may never be reached.

For people like Weinberger and others, the answer comes down to whether they believe the mechanism. He does and if he stays safe, I’m happy for him. I admit I am skeptical. Yet, if I had known this idea when I was in Rio last year (and swallowed all that seawater) I might have given it a try.

As for my friend’s text message asking about cola and swimming, I know the people asking swim in the pool, not in the ocean. So in this case, the only answer is a very simple and emphatic:



Create a free website or blog at

Up ↑

%d bloggers like this: