Author Archives: sammackinnon

The Bacterial Breakdown of Dietary Fibre in the Gut

It has been known for many years that humans consume a type of dietary fibre called xyloglucan; however, how it’s degraded in the human gut has always been unclear. A recent study published in Nature now indicates that xyloglucans (XyGs) are broken down by a specific type of bacteria that we have in our digestive system. Dr. Harry Brumer from the University of British Columbia collaborated with the University of Michigan and University of York to isolate the gene in the bacteria responsible for this process.

XyGs are found in the cell walls of fruits and vegetables such as lettuce, tomatoes, and eggplants. According to Dr. Brumer “it’s [been] known for many years that our gut bacteria could ferment [XyG] and turn it into short chained fatty acids which we can then uptake and get energy from.”

The following video outlines how bacteria help our body digest this specific type of dietary fibre:

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Gene knockouts were performed to isolate the specific set of genes in the bacteria, Bacteroidetes Ovatus (B. ovatus), responsible for degrading XyGs. By doing this, they were able to see how taking out these specific genes would affect the growth of these bacteria.  Dr. Brumer explains the importance of having B.ovatus in our gut: “our own genome only encodes very few dietary enzymes that break down carbohydrates so that’s really the key thing about these gut bacteria.”

To further help him understand how this process works, three-dimensional computer models were built of the enzyme made by B.ovatus. This gave Dr. Brumer a visual understanding of how the degradation of XyGs occurs at the molecular level.

So how is this relevant to the general public?  In the following podcast, Dr. Brumer explains the basics of his research on dietary fibre degradation and its importance for the average human being.

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As Dr. Brumer explains, “we’ve existed for thousands of years not knowing anything about what’s going on in our gut but the more we know, the more we can positively impact that.”  Dr. Brumer goes on to add that “if you go an antibiotic regiment, you actually damage the bacteria population in your gut. When you link that together with what we know about the capacity of these bacteria to break down complex carbohydrate, dietary fibre, you realize that well maybe you want to think a little but about balancing your antibiotic treatment.”

According to Dr. Brumer, “you are much better eating a vegetable rich diet.” Nevertheless, he does not “advocate [one to be a] complete vegetarian” either. “You need meat to provide protein and it can be challenging for people who are on a strictly vegetable based diet to get enough protein” in their body through alternative sources. Therefore, it is essential to keep a balance between both.

In summary, we harbour a symbiotic relationship with the bacteria in our gut. So keep your gut bacteria happy and they will keep you healthy!


Blog post by Ramen Kaur Sandhar, Sean Liu, and Sam MacKinnon

Image by Sam MacKinnon

The (literal) Birds and the Bees

Ok, I’ll give your parents the benefit of the doubt and assume that at one point in your life they sat you down and told you the ins and outs of “the birds and the bees”.  But just in case they failed to raise you properly, here is everything you need to know.

That’s right – The DEFINITIVE guide to bird and bee sex. You’re welcome.

Let’s BEEgin with the bees.

Bee sex happens in mid-air, usually around 10 feet off the ground. In a spectacular display of desperation, agility, and death (I’ll get to that part in a second), hundreds of male drone bees compete for the opportunity to mate with a virgin queen during her once-in-a-lifetime “nuptial flight”.

Drone bees are all male, and are evolved to be good at one thing:  Sex.  They have better eyesight then other bees, no stingers, and large endophalluses (penises).  During the nuptial flight, a dozen drones, on average, will successfully fertilize the queen.

And then things get weird.

Upon ejaculation, the drone’s penis essentially EXPLODES.

It violently ruptures, and is ripped from the drone’s body, remaining inside the queen’s.  The drone falls to the ground, and dies soon after.  The next drone to mount the queen removes the previous drone’s penis, and then proceeds to insert his own.

This kind of expendable-male mating ritual is not unusual in the insect world – female praying mantises, for example, are famous for biting the heads of of males during or following mating.

But that’s enough about insects. On to the birds!

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Our avian friends have evolved some very unique solutions to bringing sperm and eggs together – some of then just as strange as the bees.

Most male birds don’t actually have penises – chickens for example have no protruding sexual appendages.  Instead, they have a hole called a cloaca.  Both male and female chickens have one.  In order to mate, chickens have to press these holes together for a brief time in a behavior described as the “cloacal kiss”.


The cloaca of a bird is multi-puporsed – it is the exit point of a bird’s urinary, digestive, and reproductive tracts. Yes, that means that urine, feces, and eggs all come out THE SAME HOLE.

You can think of it like a water slide with different starts, but the same ending.



Not all birds engage in the cloacal kiss method of copulation; some DO have penis – and not just any penis, ENORMOUS penises.

There are species of duck with some of the largest penises, relative to body size, of any animal alive.  The Argentine Lake Duck for example, has a 16-inch corkscrew-shaped member that exceeds the duck’s own body length when fully extended.

So there you have it! Everything you need to know (and maybe a few things you didn’t).

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My personal take-away from researching this topic is two-fold.  Firstly, my google search-history has gotten significantly more disturbing, as it now includes the search terms “chicken butt hole” and “duck penis”.

Secondly, I’m left with a much greater appreciation for the strange and inventive reproductive strategies found in nature. One thing is certain – mammals don’t have the final say on what defines sex.  Take it from the birds and the bees – there’s more then one way to do it.


Text and graphics by Sam MacKinnon, 2014

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WE ARE THE EGG PEOPLE (Some brief notes on the evolution of live birth)

Here’s a strange thought: You, and all the people you know, were once microscopic bundles of cells, inside of another person’s body (in your case, your mother’s).  You may be all sorts of awesome now, but your life began extremely humbly – an elegant balance of symmetry, simplicity, and chaotic potential.  And it all started inside of an egg. You, like me, are an egg person. Deal with it.

Eggs are beautiful things. They are such an elegant solution to developing new life, that multiple taxa of animals have evolved to produce them, including fish, amphibians, birds, dinosaurs, reptiles and mammals.  For most fish and amphibians, the laying of eggs is the first step in the process of sexual reproduction.  The eggs are then fertilized by the male in water, where they remain until they develop and eventually hatch.

It’s a neat system, but not one that works very well for terrestrial (earth-living) animals like birds, reptiles and mammals. Developing embryos is a delicate business; they need to be kept moist, sheltered, at a relatively stable temperature, and with a steady supply of nutrients. These are all tall orders for any organism to maintain, let alone a defenseless embryo outside of water.

As it so happens, the safest place for many animals to grow their young is inside of their own bodies.

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Humans, as I’m sure you know, don’t lay eggs.  Instead, we retain our eggs, fertilize, and develop them internally; the type of egg we make defines us as Amniotes, along with reptiles and birds.  Amniotic animals have more complex eggs then fish and amphibians, as they have specialized membranes that grow out of the embryo, and preform multiple functions, including providing the growing fetus with nutrients.

Birds grow their eggs internally for a short period of time, then lay them, and then incubate (keep them warm while they develop).  Inside, the  bird embryos are supplied with nutrients from a yolk sac, which supports them as they grow.  Gas exchange also occurs through the membranes and pores of the shell (yes, eggs breathe!).

While many reptiles lay eggs, there are several species of snakes and lizards that give live birth; some snakes even have placentas.  Placentas are something that also define placental mammals – a group to which humans belong.

In placental animals, the membranes of the amniotic egg develop into the placenta and umbilical cord.  Considered in this way, a placenta is essentially a modified egg, and has many analogous features that can be compared to reptile and bird eggs (a couple of which are illustrated below).  Instead of a yolk sac, human fetuses get their nutrients from their mother’s body via the placenta and umbilical cord.

The placenta acts as a bridge between the mother’s body and the growing child’s – allowing the transport of nutrients, but also acting as a barricade against the mother’s immune system (which will naturally want to treat the baby as a hostile “foreign” life-form inside the mother).

There is considerable evidence that live birth has evolved hundreds times, within a diverse spectrum of animal forms – it is certainly not unique to mammals.  The earliest evidence for live birth dates back 380 million years, to the ancient armored fishes the placoderms.

This tells us something interesting about the nature of live birth from an evolutionary perspective – that the difference between live birthing-mammals and egg-laying mammals is not cut and dry (as nothing ever is in evolutionary biology).  Rather, the two methods of developing young have dozens of crossovers and grey areas, and in a more fundamental way, they are really the same thing. For nature, the egg has never truly gone out of style.

Text and illustrations by Sam MacKinnon, 2014



Power, M. L., Schulkin, J., & Project Muse University Press eBooks. (2012). The evolution of the human placenta. Baltimore: Johns Hopkins University Press.

Porous Science: How Does a Developing Chick Breathe Inside Its Egg? 2012 Scientific American.  Retrieved on 02/24/2014 from:

A ROCKY START: James Hutton and the Age of the Earth

It’s easy to mistake rocks as static objects.  You could stare at a rock for a few hours, and generally, it will do nothing interesting.

But the truth is, rocks are anything but static; it’s just that their dynamics are hidden by the long spans of time required for them to transform.  They erode, they shift, they change, and ultimately, they tell stories.  Rocks are the record keeepers of the Earth.  As we look downwards, through layer after dusty layer of sediment, we can, in a sense, travel backwards through time.

Rocks provide an extremely revealing way of examining the history of our planet, but it took until the late 18th century for scientists to fully grasp this concept.

In 1785, Scotland was at the forefront of Western science and philosophy, during a period of time later dubbed the Scottish Enlightment.  Despite recent advances in naturalism, chemistry, and medical science, people still thought that the earth 6000 years old, an estimate derived from the book of Genesis in the Bible.  Most scientists of the time agreed with this.  Even Isaac Newton (who died in 1727) accepted the idea of a young Earth.

But not everyone was convinced.  One man, James Hutton, had a very different idea.

James Hutton was a Scottish farmer, born in Edinburgh.  He had a degree in medicine, but by all accounts, never practiced medicine.   Hutton was an amiable and insatiably curious man, and initially applied his mind to developing and optimizing new farming techniques. At the same time, he had a much more ambitious pet-project on his mind – developing a geological theory of the Earth.

Hutton’s theory was based on observations, and asserted that rocks are constantly being formed, shifted and eroded; Hutton further concluded that these natural process likely behave in the same way now as they did thousands, even millions of years ago.

One of the primary pieces of evidence that Hutton used to support his theory is a rock on the east coast of Scotland called Siccar Point.   Siccar Point has an unusual structure – it is made up of two distinct layers of different types of sedimentary rocks (Devonian red sandstone, and Silurian greywacke) that contact each-other at a definitive angle.

Hutton concluded that Siccar point could only have been formed by a long sequence of sedimentation (formation of sandstone from small particles), folding and uplift (the buckling and lifting of rock masses over time) and erosion (the breakdown of rock surfaces by weathering), requiring extremely vast amounts of time – amounts far exceeding the mere 6000 year timeline proposed by biblical scholars.

Today, scientists have a variety of tools at their disposal for determining the age of the Earth, including the radiometric dating of fossils.  Although Hutton had no access to these types of techniques, he was still able to conclude that the 6000 year idea was incorrect using observations of modern sediments, and deductive reasoning.  It is a powerful example of one person’s curiosity and logic overcoming centuries of well-entrenched religious and scientific dogma.


Text and illustrations by Sam MacKinnon, 2014



Carruthers, M. W.  (2014).  Hutton’s Unconformity.  Natural History.  108(5): 86.

Repcheck, J.  (2003).  The Man Who Found Time:  James Hutton and the Discovery of Earth’s Antiquity.  Boulder, Colorado: Perseus (Basic Books).