W is for Wasps

It’s summer time. ¬†And you know what that means? Sure, summer means picnics, barbecues, and sun.

But it also means the coming of the most dreaded outdoor villains: wasps.

Some people freeze up when they see the stripey serial stingers, others try to wave them away. ¬†I prefer the stoic strategy of a short, sharp yelp followed by a crazed hand-waving motion. ¬†It’s not a conscious decision, nor one that I am proud of, but the wasps seem to get the idea that I don’t want them around.

What is a wasp?

Image by Stannered

In taxonomic terms, a “wasp” is any member of the suborder¬†Apocrita¬†that isn’t a bee or an ant. ¬†While that may help useful for biologists, it doesn’t really tell us anything about the creatures.

Wasps are a varied group of hairless, six-legged flying insects that measure anywhere from to 1mm (Fairy Wasp) to 4.5cm (Japanese Hornet).  There are thousands of species of wasp, many of which are specially adapted to feed on and parasitize insects we would regard as pests.


And the way they parasitize those pests can be cruel indeed.  Some parasitoid wasps lay their eggs inside their prey, only to have the eggs hatch a few weeks later, letting their young eat their way out of the unsuspecting caterpillar that has been feeling a strange itch recently.

Other wasps lay their eggs inside plants, genetically modifying a plant’s¬†seeds to suit the wasp’s¬†needs.

Still other inventive wasps have figured out that they can lay their eggs in the nests of other wasps and trick another queen into raising their young.

It seems there is nothing a wasp won’t lay its eggs in.

Fighting Wasps

Not all wasps are content merely laying eggs in unusual places.  Some have acquired a taste for honey.

Meet the Japanese Giant Hornet.

While European honeybees haven’t developed defenses, asian honeybees have discovered a way to fry invaders.

So while you may just think of them as a nuisance when you’re trying to enjoy your picnic, remember that with wasps, there is more than meets the eye.

T is for Tardigrade

By Jonathan Farrow from the Thoughtful Pharaoh 

Boil ’em, mash ’em, stick ’em in a stew.¬† They’re versatile!

No, I’m not talking about taters. ¬†I’m talking about tardigrades: quite possibly the most durable¬†creatures on Earth.

They might also be the strangest combination of cute and terrifying anybody has ever seen looking through a microscope.

Cute and terrifying.  Image by Abribus
Meet the water bear.  Strange combination of cute and terrifying. Image by Abribus

Tardigrades, also known as water bears, evolved 500 million years ago. ¬†They have survived on a diet of moss and lichen since around the time¬†the first fish evolved and shortly after animals evolved at all. ¬†While their basic body plan hasn’t changed much, they haven’t been evolutionarily idle. ¬†They’ve developed some pretty neat¬†adaptations (some of which will be discussed below) and diversified into over 1000 unique species. One thing all¬†of these species¬†has in common is size: all species of tardigrade¬†measure¬†between 0.1-1 millimetre (comparable to the size of a single salt crystal).

The amazing thing about these itty-bitty balls of chitinous cuticle is that they can withstand pretty much every type of extreme we can cook up. ¬†They’ve been boiled to over 150 degrees celsius without breaking a sweat. ¬†They’ve been frozen to -250C and didn’t need tiny parkas. ¬†They’ve been dipped in acid, shot into space, dried out, and zapped with thousands of times the lethal radiation dose for a human and they just kept chugging.

Why won't you die!? Image by Frank Fox
Why won’t you die!? Image by Frank Fox

Why are we being so cruel to these tiny creatures?  Because they keep surviving.  Things that terrify us and would kill almost any lifeform barely even faze them.  Tardigrades have expanded the notion of habitable environments and understanding their indestructibility has profound implications for both earthbound medicine and for life on other worlds.

I think tardigrades are pretty darn cool.  This is likely due in no small part to the fact that the lab where I did my thesis in undergrad was home to a healthy colony of moss-eating tardigrades.  Up on the third floor of the Life Science Building at McMaster University, my former supervisor, Dr. Stone (or Doc Roc as he likes to be called) has been testing tardigrade tolerances with Taru, his PhD student.

“Ewww, you can see all of its insidey bits” – Me, the first time I looked at a tardigrade through a microscope. Image by Daniel Adrian Ciobanu, Krzysztof Zawierucha, Ioan Moglan, and ŇĀukasz Kaczmarek.

I got in touch with Doc Roc this week to ask him a few questions about tardigrades. ¬†To give you an idea of the kind of (awesome) professor he is, one of his research goals was to publish a one-sentence paper. ¬†He accomplished that goal with the help of quite a number of semi-colons. ¬†As you’ll see below, I think he likes that useful but oft-forgotten punctuation mark.

Thoughtful Pharaoh (TP): Where do you find tardigrades?

Doc Roc (DR): Tardigrades are found the world over, literally on all continents and in all bodies of water; they inhabit all systems, marine, freshwater, terrestrial; they occur terrestrially on moss.

[They’re everywhere!]

TP: What have you done to test the limits of tardigrades?

DR:  We have tested their tolerance to temperature (cold), radiation, desiccation, pH, g-forces (simulated), and red food dye (I think that you know the tale); we have witnessed complete revival from -80 degrees Celsius for up to 6 months (but they can tolerate -250 K); 4000 Gy radiation (6 Gy kills humans); completely drying out inside an evaporating water droplet (tales in the literature purport over 100 years in a desiccated state); over 16000 g (Earth atmosphere being 1 g Рmeteoritic impact being an order-of-magnitude greater, however); and sensitivity to red food dye.

[The tale of the red food dye: In one of many discussions of tardigrades in that lab, I was asking if these incredible creatures had any weaknesses.  Doc Roc told me about a curious incident that happened when he tried to stain tardigrades to see them better.  He tried putting some red food colouring onto the plate and they changed colour and were easy to spot, but they also all died. Green and blue food colouring did nothing, but red colouring stressed the tardigrades to death.  Strange that such an indestructible creature could be undone by food colouring.]

TP: What is the most interesting thing about tardigrades, in your opinion?

DR: I think that understanding how their tolerance and reproductive modes (e.g., parthenogenesis) evolved are the most interesting topics for tardigrade research.

[Tardigrades don’t need males to reproduce. ¬†Females can lay unfertilized eggs which will hatch as clones, genetically identical to the mother. ¬†The advantage of this is that they don’t need to waste time looking for mates. The disadvantage is low genetic diversity.]

TP: What do you want to do next?

DR: We plan to investigate how they tolerate the high radiation doses (e.g., their DNA repair mechanisms).

[McMaster has a small nuclear reactor on campus, which has been used in recent years to expose tardigrades to high levels of radiation.  After thousands of times a lethal radiation dose for humans, the tardigrades were fine and in some cases the irradiated ones did better than their lab-housed control counterparts.  How they can survive and continue to reproduce remains a mystery but it almost certainly involves some incredible DNA repair.]

TP: Do you ever name the tardigrades?

DR: The student who studies them is named Taru, which seems an appropriate name for one; given that we work with a parthenogenetic species, I would name them Tarugrade 1, Tarugrade 2, …

[Seems reasonable to me.]

TP: If they’re so invincible, why haven’t tardigrades taken over the world?

DR: Organisms are limited in their resources, so populations can grow unchecked only to the extent that living materials are available (populations crash thereafter); predators additionally can reduce population sizes.

[In other words, tardigrades can still starve and get eaten.  Just like every other creature.]

TP: What can studying tardigrades tell us about life on other planets?

DR: Studying tardigrades can inform us about the limits to which organisms can survive, helping researchers to identify which extreme environments are viable and whether organisms could be transported between planets.

[The theory that life arrived here from another planet (called panspermia) is not as crazy as it sounds.  I wrote a bit about it a while ago.]

Thanks Doc Roc!

If you have any other tardigrade questions, feel free to comment below and be sure to share this with your friends. Spread the water bear word and let us not be frightened of our tardigrade overlords!

Tardigrade 1
This guy looks like he’s ready to partygrade. Image by the Goldstein lab.

If you want to learn more:

  • The BBC recently published a pretty comprehensive article about these resilient little critters here
  • TARDIS was a European mission in 2007 to see how well they survived in space
  • A (bearded!?) Hank Green produced a video about them for SciShow in 2012.

S is for Simple Rules

By Jonathan Farrow from the Thoughtful Pharaoh

Consider the following: schooling fish, roundabouts, segregation, and human consciousness are all examples of the same fundamental property of the world.  It may seem crazy to suggest that roundabouts may be interesting in some sense, but bear with me.

The property in question, and this week’s topic, is emergence. ¬†In each case individual entities, by following simple rules, can create complex patterns of behaviour. ¬†What makes these patterns special is that they can’t be predicted based on the simple rules alone.


If you’ve ever seen a murmuration of starlings, you have probably found yourself wondering how that many birds (upwards of 100,000) can all fly so quickly in such close proximity without hitting each other. ¬†For those of you uninterested in ornithology (the study of birds), there are also plenty of examples of swarms in entomology (the study of insects) and ichthyology (the study of fish), and even¬†chiropterology (study of bats).

Image by SteveD
Image by SteveD

In each case, the animals are unaware (and frankly, uncaring) of the beautiful shapes their swarms make. ¬†They aren’t even trying to swarm. ¬†They are trying to survive and their instinct tells them to follow a few simple rules. ¬†Since the advent of computers, scientists have been trying to find out what those rules are.

One of the most famous computational models of swarming behaviour was proposed by Craig Reynolds in 1986.  In his Boids program, simulated birds had to follow three rules:

  1. Separation:¬†Don’t crash (steer away from nearby boids).
  2. Alignment: Get with the program (steer towards the average heading of nearby boids)
  3. Cohesion:¬†Don’t get lost (steer towards the average location of nearby boids)

This model is actually a really good model for the behaviour we observe in birds and fish.  Recent studies have also shown this alignment rule is especially important for bats.

Locusts, on the other hand, seem to have a much simpler set of rules.  Locusts just want to avoid getting their backsides eaten.  When approached from behind, locusts will tend to fly forward for fear of cannibalism.  This creates an overall tendency to move forward and can lead to giant swarms.

Image by CSIRO
Image by CSIRO


If you’ve ever been to Swindon (and, from what I hear, you’re not missing much if you haven’t), you might have come across quite possibly the most offensive piece of civil engineering in the UK.

That's right.  A giant roundabout.  Image in the public domain
That’s right. A giant roundabout. Image in the public domain

As a North American, I cringe at the thought of even a tiny roundabout but Swindonians apparently hate everything that is good in this world.

They built the Magic Roundabout. ¬†A terrifying series of 6 small roundabouts encircling a larger roundabout that goes the other way. ¬†If that sounds confusing, it’s because it is.

The more confusing part, however, is that hundreds of thousands of cars pass through it unscathed.  While there is certainly a lot of anxiety about it, there have been only 14 major accidents in 25 years.

Hell for North Americans.  Image from the BBC
Hell for North Americans. Image from the BBC

The vast majority of people pass through fine, despite there being 5 different entry and exit points and many conflict points (places where streams of traffic cross).  This happens because of a few simple rules:

  1. Follow the lines
  2. Give way to cars coming from the right
  3. Drive to where you want to go
  4. Don’t crash

Apparently it’s actually an effective way to move cars through an intersection, but my North American sensibilities just can’t handle it.

For more information on this piece of crazy road engineering, visit this explanatory page and watch this video.


Choosing¬†who you associate with based on a singular trait has been known to lead to a lot of issues in the past. ¬†As a dog person, I’ve lost a lot of friends to cats (and their parasites). ¬†Despite my friendly demeanour and my ability to put up with a fairly large proportion of cat-lovers in my immediate vicinity, at a certain point I start to feel uncomfortable and want more fellow dog-lovers.

Tensions flare.  Image by Peretz Partensky
Tensions flare. Image by Peretz Partensky

In 1971, Thomas Schelling set out to model this behaviour and came out with a somewhat surprising and scary result. ¬†Even when people are fine with being in the minority, if they are dissatisfied when surrounded by a large majority of “others”, they will tend towards segregation. ¬†The model followed a few simple¬†rules:

  1. If you are surrounded by a certain percentage (e.g. 30%) of similar people, you are satisfied
  2. If you are surrounded by a certain percentage of different people (e.g. 70%), you are dissatisfied
  3. If you are dissatisfied, move to somewhere where you are satisfied.

Within a few rounds, there is very little diversity left as people¬†tend to move towards those who are similar. ¬†This, despite the fact that no individual is saying they outright dislike the other group or couldn’t live with members of the¬†other group. ¬†This model helps to explain why segregation is so hard to eliminate.

Interestingly, this tendency towards segregation can be reversed if a maximum of similar people rule is added:

4. If you are surrounded by a certain percentage of similar people (e.g. 90%) you are dissatisfied

Again, complex patterns and simple rules.

To learn more about the model, go here.


There are approximately 100 billion neurons in an adult human brain.  These neurons are connected in intricate ways to create an estimated 100 trillion connections.

Now that's a lot of connections!  Image from Wikimedia
Now that’s an impressive set of connections! Image from Wikimedia

Somehow (and to be honest we’re not really sure how yet), these connections lead to all of our brains’ activities from thought to imagination and¬†memory. ¬†The abilities of the system (the brain) couldn’t possibly be known from the rules that neurons abide by. ¬†All that a neuron does is pass on its signal according to a set of rules. ¬†We still don’t know what those rules are.

We do know that when a neuron is activated (whether by electrical or chemical stimulation), it activates other neurons.  The precise number and location of these other neurons is still a big mystery in neuroscience, but it must be activating both nearby neurons and neurons on the other side of the brain.  This dual activation of long- and short-distance connections is what creates the sustained patterns we observe in fMRI scans.

Human Connectome Project
The¬†Human Connectome Project, kind of like the Human Genome Project before it, is setting out to map all of the brain’s 100 trillion connections to better understand how it works. ¬†Image by Xavier Gigandet et al.

While I don’t mean to suggest that everything in life can be boiled down to simple rules, I think it’s pretty incredible the patterns¬†that emerge from individual actors all playing their parts.

R is for Ratzilla

An excerpt from my favourite scene in the 1987 film, the Princess Bride:

Westley:¬†Rodents of Unusual Size? I don’t think they exist. [R.O.U.S.¬†attacks Westley] Westley:¬†Ahhhh!!!

Why is that my favourite scene?  Because I laugh every time I watch it. The R.O.U.S. is just so ridiculous-looking and shows up right after Westley disbelieves its existence.

For the devoted readers out there, you’re maybe wondering what my obsession with R.O.U.S.es is, because I’ve written about them¬†before, but somehow they capture my imagination unlike any other strangely-proportioned creature. ¬†I think it has something to do with the comedic effect of reversing¬†the expectation of something cute.

Rodents of Unusual Size: They do exist. Image from the Princess Bride
Rodents of Unusual Size: They do exist. They are definitely not cute.  Image from the Princess Bride

The R.O.U.Ses from the Princess Bride have come to set the standard for overgrown rodents, but sometimes reality is stranger than fiction.

The largest discovered member of the rodent family (membership to which depends on having a pair of razor-sharp, ever-growing incisors), Josephoartigasia monesi is estimated to have been the size of a bull.


Reconstruction of head
A reconstruction of J. monesi’s¬†skull based on the bones that were recovered. Image by Andres Rinderknecht & Ernesto Blanco

Since only its skull was discovered, the¬†¬†weight of this creature has been debated. ¬†The original discovery paper pegged the mass of the monstrous mulch muncher at 1211kg on average with a maximum of 2584kg. To put that into perspective, that’s anywhere from 1 to 4 dairy cows. ¬†A more recent study, however, showed that depending on the part of the skull you use to predict the mass of the full creature, J. monesi¬†could have weighed from as low as 356kg (half a cow) to 1534kg (back up to the 2-cow range). ¬†Even if the creature was as small as 356kg, that still makes it nearly 6 times heavier than the current rodent heavyweight champion of the world, Floyd Mayweather the capybara.

In any case, it’s definitely big enough for a recent¬†Science Magazine article¬†to correctly use¬†the term “Ratzilla”.

Rodents of Unusual Size: They do exist.  Image from the Princess Bride
RATZILLA!!!  Image by James Gurney

Ratzilla’s bite force was recently estimated up to 4000N, enough to outperform modern crocodiles and tigers. ¬†It was definitely a herbivore though, and is thought to have used its teeth as elephants use their tusks: to dig around for tasty treats.

Luckily for us, Ratzillas (Ratzillae?) no longer roam the plains of South America.  They went extinct about 2 million years ago, after 2 million years of rodent dominance.  Interestingly, that makes them the contemporaries of terror birds, sabre-toothed cats, and giant ground sloths. Their size and sharp teeth probably made them tough prey items.

Just like the R.O.U.Ses in the Princess Bride though, they were probably susceptible to fire jets and swords.

And with this rodent rant written, I promise to not write about any more Rodents of Unusual Size for the remainder of this ABCs series.

Q is for Quokka

What’s half a metre long, weighs 3-4kg, and has the cutest face you ever did see?

Image by Gaurav Pandit

Nope, cuter.

Image by Garrett 222

Even cuter.

Quokka Cute
Image by Jin Xiang

Yup, there it is! ¬†This, dear readers, is a quokka. ¬†A native of South west Australia, this marsupial has recently skyrocketed to fame because of the way¬†its mouth seems to rest in an adorable little smile. ¬†A quick Google image search will reveal hundreds of awesome pictures (that aren’t licensed under creative commons) and a growing number of quokka selfies. ¬†It looks so happy that it has even been dubbed the mortal enemy of Grumpy Cat.

So, what’s the deal?

The quokka is a vegetarian (one of those darn salad-eaters) that prefers leaves and stems.  Since its habitat is so dry, it will swallow its food whole only to regurgitate it later, chew it up, and swallow again in order to make sure it sucks out all of the moisture.  Their digestive systems are tuned to allow survival in the dry climate of Western Australia.  This means that when humans try to feed the quokkas with bread or give them water, the poor animals can go into toxic shock and die.  For the love of all that is cute in this world, do not feed quokkas.

I'm fine with my flower.  I don't need your charity! Image by Vicsandtheworld
I’m fine with my flower. I don’t need your charity!
Image by Vicsandtheworld

Like other marsupials, quokkas have a very short pregnancy¬†of only one month, followed by five¬†or six¬†months of pouch-time. ¬†Unlike most other marsupials, quokkas have the ability to double down on their reproduction. ¬†The day after giving birth and moving the joey to their stomach pouch, female quokkas will mate again and will pause the development of the new foetus in a process known as embryonic diapause. ¬†If the joey in the pouch doesn’t make it (quokka-god forbid), the female can resume the embryo and still call the season a reproductive win.

One thing the quokka’s PR people (who have done an excellent job so far, by the way) might not want you to know is that female quokkas, when threatened by predators, will quite literally throw their babies under the bus. ¬†They will eject their joey and head for the hills, hoping that the predator takes the easy prey and they get to live another day.

Image by Hesperian
A nice, happy quokka family. ¬†That obviously didn’t resort to infanticide in the case of this joey. ¬†Doesn’t Nature just suck sometimes? ¬†Image by Hesperian

For the readers out there still keen to snap the perfect selfie, the best place to find quokkas is¬†on Rottnest Island, a tiny, 19km2 bit of land off the coast of Perth. ¬†[Non sequitur –¬†I can’t help but hear “Purse” said with a lisp whenever I come across Perth.] ¬†The island was named Rottnest (Rat’s Nest) by a dutch explorer who thought the resident quokkas looked like “a kind of rat as big as a common cat”.

Just like the selfie stick we know is lurking out of the frame of all those hilarious pictures,¬†disaster may be around the corner for the quokka. ¬†The¬†Australian Government¬†rates the Rottnest Island population as stable, but the quokka’s mainland habitats are under threat from foxes (an invasive species) and forest clearing. ¬†These threatened mainland populations are especially important because they contain much more genetic diversity than the island groups. ¬†The IUCN classifies the quokka as Vulnerable, one step above Endangered. ¬†This is due not to the population size (upwards of 10 000), but rather to the extremely small range and susceptibility to environmental change.

The quokka's range is quite limited.
The quokka’s range is quite limited.

The quokka is a species of very cute and biologically strange marsupial whose Australian home is under a myriad of threats.  Why the internet is currently abuzz with it remains a mystery, but there are certainly some adorable pictures to be taken and some interesting things to be learned.

P is for Plant Defences

By Jonathan Farrow of the Thoughtful Pharaoh

As the great glam metal band Poison sang in 1988, “Every Rose Has Its Thorn“.

Like so many glam metal bands to grace the world’s stages before them,¬†none of Poison’s members were botanists. If they were, they might have known that roses actually have prickles, not thorns.

It’s an easy enough mistake to make. ¬†But because I am a pedant at heart, I want Poison to know that, technically, thorns¬†are¬†modified branches, spines are modified leaves, and prickles are modified skin. That means roses have prickles. I therefore petition that the lyrics of the chorus of the song be changed from:

Every rose has its thorn
Just like every night has its dawn
Just like every cowboy sings his sad, sad song
Every rose has its thorn

to the more scientifically accurate:

Every rose has its prickle
Just like brine turns veggies to pickles
Just like every cowboy is really quite fickle
Every rose has its prickle

Thorn (modified branch) from a citrus plant.
Thorn (modified branch) from a citrus plant. Image by Edgovan22
Spines (modified leaves) from a Pereskia grandifolia (aka rose cactus) plant
Spines (modified leaves) from a Pereskia grandifolia (aka rose cactus) plant  Image by Frank Vincentz
Prickles (modified skin) from a rose bush.  Image by JJ Harrison

But how did plants come to develop¬†all of these different ways to impale gardeners’ fingers in the first place?

To answer that question, let’s imagine a world without thorns, spines, or prickles. No toxins, sap, poisons, or deterrents of any kind. ¬†In a world like that, as long as there were herbivores, plants wouldn’t last long. ¬†They’d get eaten up pretty quick and getting eaten generally isn’t good for your reproductive health (with a few noticeable exceptions *cough* black widow spider¬†*cough*). ¬†So there’s a lot of evolutionary pressure on plants to develop ways to avoid becoming lunch.

Predation from salad-eaters¬†isn’t the only pressure on plants, though. ¬†They also need to compete with other plants around them by growing to capture more sunlight and they need to devote resources to reproducing. ¬†This is called the growth-differentiation balance. ¬†Plants, with limited resources, must choose between straightforward growth and developing specialized defences. ¬†If this theory is¬†true, we would expect plants that didn’t have to worry about getting eaten would be less thorny. ¬†In October 2014, an international team of researchers showed that in an herbivore-free zone, like the favourite hangouts of leopards on an African savanna,¬†non-thorny plants thrive, whereas the thorny plants do best in the favourite hangouts of salad-eating impalas.

Salad-eaters (aka herbivores) don’t just take an evolutionary backseat to this escalation¬†of plant defences. ¬†Ever since the first animals¬†started emerging from the sea and started choosing¬†salad, plants have been trying¬†to send them back and animals have kept coming. ¬†It’s an evolutionary arms race.

And if the Cold War taught us anything, its that arms races lead to some pretty ridiculous specializations.  Here are a few of my favourites on the plant side of things:

Sorcerer Corn

Behold! Sorcerer Corn!  Image by Silverije
Behold! Sorcerer Corn! Image by Silverije

It looks like regular corn. ¬†And that’s because it is.

Regular corn seedlings, when exposed to a chemical in the saliva of beet armyworms, will release a chemical that summons a cloud (or, less dramatically, attracts) parasitoid wasps which will lay eggs inside of the armyworms.  These eggs will hatch after two days and eat their way through the armyworm from inside out.

Corn isn’t the only plant that releases signals like¬†this. ¬†In fact, you know the smell of freshly-cut grass? ¬†That turns out to be the plant equivalent of¬†screaming out to any relatives in the area to “GET READY! THERE’S SOMETHING THAT WILL HURT YOU NEARBY!”

Flinching Flowers

We normally think of plants as stationary things, unable to move.  This is usually true, but there are some plants which have the ability to quickly shut their flowers or droop on contact.  The most famous example of this is the Venus Flytrap, but that is more of an offensive flinch.

Image by Mnolf
Image by Mnolf

Mimosa pudica, or the sensitive plant, also has this flinching (thigmonastic) ability.  When touched, this species will close its flowers and fold away its leaves, thus decreasing its surface area and making it harder to see and eat.

I'm just going to fold away now...
I’m just going to fold away now… ¬†Image by Hrushikesh

Whether its by developing thorns, spines, prickles, the ability to fold up, or the ability to call helpful predators, plants have not been idle in the fight against salad-eaters. ¬†Every rose has its¬†prickles (not thorns!)¬†because of this ancient struggle and while they may be annoying, I guess we should be happy roses¬†haven’t evolved to attract parasitoid bears that will leave cubs inside of our stomachs to gnaw their way out over the course of a week.


O is for Ocean Acidification

By Jonathan Farrow from the Thoughtful Pharaoh

We all know that CO2¬†emissions are warming the planet. ¬†Or at least,¬†most of us¬†do. ¬†What often goes unreported is the effect of carbon dioxide on the worlds’ oceans. ¬†A lot of the CO2¬† that we pump into the air makes its way to the water and is making it more and more difficult for shelled creatures like sea urchins, lobsters, and coral to survive.

This is Bob the lobster. This is his “I’m sad because of the increased levels of anthropogenic carbon dioxide that are making my life harder” face. ¬†Image by Pedrosanch

In order to understand why this happens, we need to go back to secondary school chemistry.

Don’t worry, I’ll make sure Jared doesn’t pick on you.

No Jared! No!     Image public domain

The first lesson we need to recall is about acids.  What is an acid?

Something that bubbles in a flask?  Image by Joe Sullivan
Something that bubbles in a flask? Image by Joe Sullivan

Acids are compounds that have free hydrogen ions floating around. ¬†These hydrogen atoms are quite reactive, so it means the more free hydrogen you have floating around, the more reactive your compound. Acidity is usually measured in pH, which stands for the “power of hydrogen”. ¬†pH is measured on a scale (creatively named the “pH scale”) that ranges from 0 to 14.

Compounds that get a 0 on the scale are exceedingly acidic, meaning they are made up of pretty much just free-floating Hydrogen ions. Compounds that rate 7 are perfectly neutral, like distilled water. Compounds on the other end, near 14, are called “basic” or “alkaline” and instead of having lots of hydrogen ions to give away, they have all sorts of space for hydrogen atoms. ¬†This makes them reactive because they can strip hydrogen from things that don’t usually want to give it away (like Edward Norton’s hand in Fight Club).

The other confusing bit to remember is that the pH scale is logarithmic, meaning that each number you jump actually indicates a multiplication by 10. For example, something with pH 3 (like soda) is 100 times more acidic than something with pH 5 (like coffee).  This means if a large body of water (like the ocean) shifts by even a small pH number, the effect can be very large.

Image by OpenStaxCollege
Image by OpenStaxCollege

The second lesson we need to recall is about equilibrium.

In chemistry, everything tends towards balance. If you combine equally strong acids and bases, they will react together until the result has a pH that is in between.  You might also get a volcano-themed science fair demonstration.

When CO2 combines with water (H2O), they form carbonic acid (H2CO3).  The carbonic acid will break up (dissociate) into bicarbonate (HCO3) and a hydrogen ion (H+).  In a basic environment, the bicarbonate will dissociate further into carbonate (CO32-) and the result will be two hydrogen ions (2H+).

We can visualize this path with a chemical equation:

H2CO3¬† —- ¬† H+ + HCO3– ¬†¬†—- ¬† 2H+ + CO32-

Where this path stops depends on the environment it is in.  In an acidic environment, the balance will tend towards the left, with more hydrogen bound up with the carbonate (because there is no space in the solution for more free hydrogen).  In a basic environment, the balance will tip to the right, releasing more hydrogen and freeing up the carbonate.

Currently, the pH of the ocean sits at about 8.1 (slightly alkaline). ¬†Because of this, there is plenty of carbonate available for creepy-crawly-shellfish to use to build their homes. ¬†Crustaceans and corals combine the free carbonate with calcium to form calcium carbonate (aka limestone, chalk, and Tums). They can’t use bicarbonate (HCO3) or carbonic acid¬†(H2CO3) and find it hard to form anything at all in an acidic environment.

This means that as we add CO2 to the water, we create more carbonic acid and contribute to the acidity of the ocean, dropping its pH.  Not only does this make it hard for the little guys down there trying to make a living, but it also endangers the big chompers that eat the little guys.

The ultimate big chomper.  This is what happens when you jokingly search for
The ultimate big chomper. This is what happens when you jokingly search for “chomper” on wikimedia.

A recent review¬†found that even under the most optimistic emissions scenario, the ocean’s pH is likely to drop to 7.95, affecting 7-12% of marine species that build shells. Under a high emissions scenario, the pH will go down to 7.8, affecting 21-32% of those species.

In order to keep track of the progress of this acidification, researchers from Exeter have proposed using satellites to monitor hard-to-reach bits of the ocean.

Regardless of the pace of the change, scientists agree one thing is certain: the oceans will become less hospitable for shell-builders.  The superficial impact of this for humans will be rising prices on shellfish, but there will be much deeper ramifications throughout marine ecosystems.

And I think we all know who is to blame.


Thanks Jared.

L is for Loch Ness

By Jonathan Farrow from The Thoughtful Pharaoh

Loch Ness, in the middle of the Scottish Highlands, has more fresh water in it than all the lakes and rivers in England and Wales combined.  It is neither the deepest lake in Britain nor the largest by surface area, but since it comes a close second in both categories, it claims the top spot for volume.  The loch is home to eels, salmon, and char and its shores support a healthy population of deer and waterfowl.  The area has historical significance as well, with Urquhart castle being instrumental in the war of Scottish independence.

Loch Ness, in all of its Google Map glory.  Not pictured: the monster.
Loch Ness, in all of its Google Map glory. Not pictured: the monster.

Despite all of this, when people read or hear “Loch Ness”, the next word they think of is almost always “monster”. ¬†This is a shame, because sadly, Nessie does not exist.

We know this for sure. ¬†There have been numerous, comprehensive reviews of the ‘evidence’ and a recent sonar survey of the entire loch failed to turn up anything even close to a giant sea monster. ¬†If Nessie is supposed to be a plesiosaur, you might think a population of giant, carnivorous sea creatures that somehow survived extinction and has been living in the same lake for 65 million years would make more of an impact on people in the region. ¬†There would be lots of stories about sea monsters, and old ones too. ¬†There aren’t really any credible mentions of this monster until the 1930s. ¬†No songs, folk tales, or myths, despite the area¬†being populated for thousands of years.

Not a sea monster, 1934.  Photo by Robert Wilson, published in the Daily Mail
Not a sea monster, 1934. Photo by Robert Wilson, published in the Daily Mail
Also not a sea monster, 1977.  Photo by Anthony Shiels
Also not a sea monster, 1977. Photo by Anthony Shiels
Still not a sea monster, 2012.  Photo by George Edwards
Still not a sea monster, 2012. Photo by George Edwards

My favourite little tidbit from my reading into the series of Nessie¬†hoax photographs is a photo of a supposed flipper which was used to name a new species in¬†Nature¬†in 1975. ¬†The scientific name of the Loch Ness Monster, according to Profs. Peter Scott and Robert Rines, is¬†Nessiteras rhombopteryx. ¬†I leave it up to the reader to decide if it is a coincidence that the name is an anagram for “monster hoax by Sir Peter S”.

The 1972 'flippers' in question.  Hard to see much at all, I think. Photo by Academy of Applied Science/Loch Ness Investigation Bureau
The 1972 ‘flippers’ in question. Hard to see much at all, I think. Photo by Academy of Applied Science/Loch Ness Investigation Bureau

While it is undoubtedly good fun to trash pseudoscience, the focus on the monsters of Loch Ness (or lack thereof) takes attention away from what I think is much more interesting: Loch Ness is part of the very same geological feature as the fjords in Norway, the hills in Newfoundland, the Gulf of St. Lawrence, and the Appalachian mountains in the southern USA.

Loch Ness is part of the Great Glen Fault, a crack in the Earth’s crust that runs in a straight line across Scotland, through the Irish Sea, and into Northern Ireland. ¬†This crack is very old, pre-dating even Pangea.

When two pieces of the Earth's crust slide against each other like this, it is called a transcurrent, or strike-slip, fault.  Image by Hellinterface
When two pieces of the Earth’s crust slide against each other like this, it is called a transcurrent, or strike-slip, fault. Image by Hellinterface

In fact, the process that brought the continents together into¬†the supercontinent of Pangea is the very same one that created mountains along this fault line. ¬†Back in those days, over 400 million years ago, the Atlantic ocean didn’t exist. ¬†As the plates of Baltica (modern-day Scandinavia and North-Eastern Europe) collided with Laurentia (modern-day North America and Greenland) and the small microcontinent of Avalonia (modern-day England, Wales, and parts of Northern France), bits of the crust were pushed up. ¬†This formed mountains.

As the plates collided, the highlighted area became raised.  The grey lines in this image are the current coastlines.  Image by Woudloper.
As the plates collided, the highlighted area became raised. The grey lines in this image are the current coastlines. Image by Woudloper.

Over time, the plates continued to move, and the Mid-Atlantic Ridge pushed Europe and North America apart, forming the Atlantic Ocean.  While Laurentia and Baltica are still around as the bases of the North American and Eurasian Plates, Avalonia was essentially spread to the winds.

Avalonia definitely got the roughest deal out of the three colliding plates. Image by Woudloper
Avalonia definitely got the roughest deal out of the three colliding plates.
Image by Woudloper

This is why, if you walk the Highlands of Scotland or the Appalachians, you will find the same rock types.  They were born in the same place in the same way, and have become separated by an ocean.

Loch Ness is an incredibly poignant way to visualize this separation because, just by looking at a map, you can see a crack in the earth.  If you look at the Northeastern part of Newfoundland, you can see the same crack with the same angle.

[For another explanation of this 400 million year old connection, watch this video by Tom Scott.]

Loch Ness is a wonderful place, not only for its natural beauty, but also for its geology. ¬†So do go visit, but don’t expect to find a monster.

I is for Island Evolution

By Jonathan Farrow from The Thoughtful Pharaoh

Unbeknownst to the rest of us, a debate has been raging in the world of biogeography.¬†¬†The debate stems from a simple observation made by a young Canadian scientist in 1964: island animals are weird. ¬†Sometimes they’re way bigger than normal, like the Tenerife Giant Rat, and other times they are way smaller than normal, like the Elephas falconeri, a tiny species of elephant.

A Rodent of Unusual Size, the (now extinct) Tenerife Giant Rat.  Image by Wikimedia user M0rph
A Rodent Of Unusual Size, the (now extinct) Tenerife Giant Rat. It reached sizes of up to 1.14m  Image by Wikimedia user M0rph
An itty-bitty extinct elephant thought to have weighed only 200kg. Image by Ninjatacoshell at the North American Musueum of Ancient Life

J.B. Foster published a short, two-page paper in the April 1964 edition of Nature positing that rodents get bigger and lapidomorphs (rabbits), carnivores, and artiodactyls (deer/goats) get smaller on islands.  This, he thought, was because small animals found the isolation of islands to be liberating.  They no longer had to worry about predators and could grow to fill their new space.  Larger animals, however, might be restricted by the relative paucity of resources on islands and would have immense evolutionary pressure to become smaller.

This led to Foster’s Rule, also known as the Island Rule. ¬†It states that in general, big animals get small on islands and small animals get big. ¬†They also do so very quickly (in evolutionary terms). ¬†For instance, red deer on Jersey, an island in the English Channel, were shown to have shrunk to to 1/6th their original size in only 6000 years.

There’s a problem, though. ¬†Like pretty much every rule in biology, there are lots of exceptions. ¬†Sometimes small animals get smaller (like Brookesia micra, the world’s tiniest chameleon) and relatively big animals get bigger (like Haast’s eagles).

So cute, right!?  Image by Frank Glaw, Jörn Köhler, Ted M. Townsend, Miguel Vences
You’ve heard of angels on the head of pin, but what about chameleons on the head of a match. So cute, right!? Image by Frank Glaw, J√∂rn K√∂hler, Ted M. Townsend, Miguel Vences
The giant, moa-hunting Haast's Eagle of New Zealand.  Almost as scary as terror birds.
The giant, moa-hunting Haast’s Eagle of New Zealand. Almost as scary as terror birds. ¬†Image by John Megahan

A 2011¬†article by a joint Israeli-Italian-British team of researchers calls the whole theory into question, showing that the smallest species in any given group is no more likely to be from an island than would be expected by chance. Size extremes, they say, exist everywhere. ¬†Islands don’t have some sort of monopoly. ¬†They do concede that large mammals tend to get smaller, but they think the idea that small animals get bigger only seems like common sense because they are easier to notice.

A British paper from 2008 throws even more confusion into the mix, showing that depending on the kinds of statistical tests you use, you can show that the island rule either exists or doesn’t. ¬†They suggest that the island rule should be looked at¬†in “taxonomically restricted studies” – biologist-speak for “case-by-case basis”. ¬†That seems to kind of defeat the purpose of a nice heuristic, though.

One thing we know for sure is that islands isolate organisms.  This isolation means that evolution can work differently for the island population and might lead to all sorts of interesting changes.  This type of evolutionary change is also called allopatric speciation and is responsible for the variation that Darwin saw in Galapagos finches.  Whether islands always create a particular kind of change is still up for discussion, but nobody can doubt that when organisms of unusual size appear, they deserve attention.

Darwin's famous finches.  He observed that some beaks were better suited for cracking seeds and others for tearing fruit.
Darwin’s famous finches. ¬†Image from The Voyage of the Beagle

D is for Dinosaur Evolution

By Jonathan Farrow from The Thoughtful Pharaoh

When was the last time you ate dinosaur?  I had some just the other day, next to my peas and carrots.

File:Washing peas and carrots.jpg

Shocking as it may seem, dinosaurs are all around us and we interact with them on a fairly regular basis. ¬†If you’re sitting there saying to yourself, “No, dinosaurs went extinct millions of years ago!”, let me remind you of one critical and oft-forgotten fact: all modern birds (including chickens, turkeys, toucans, and cuckoos) are dinosaurs. ¬†That’s right, the mascot for Froot Loops is a dinosaur. ¬†KFC can change it’s name to Kentucky Fried Dinosaur and still be scientifically accurate.

How can this be? ¬†¬†It all has to do with how biologists name and classify organisms (the technical term for this is taxonomy). ¬†Scientists, being very much into order and rationality, made up a few¬†systems for naming organisms and describing¬†their evolutionary relationships. ¬†The system I’m going to focus on today, cladistics, has only a few basic rules and is incredibly helpful for understanding the history of life on our planet. ¬†Unfortunately it can be a bit daunting because there is some pretty scary-looking jargon. ¬†Let’s unpack some of that jargon and apply it to dinosaurs in order to find out how the heck the same word can be used to (correctly) describe animals as different as stegosauruses and canaries.

File:Stegosaurus Struct.jpg
Dinosaur, Photo by Yosemite
File:Serinus canaria -Parque Rural del Nublo, Gran Canaria, Spain -male-8a.jpg
Also a dinosaur, Photo by Juan Emilio

Two of the most important concepts for cladistics are that:

  1. All life on Earth evolved from a single common ancestor.
  2. Organisms should be classified based on last common ancestors, with organisms that share recent common ancestors being interpreted to be more closely related than organisms with more distant common ancestors.

Think of your family.  Everyone is descended from your grandparents (premise #1 above) and you are more closely related to your siblings (last common ancestor is your parents) than your cousins (last common ancestor is your grandparents; premise #2 above).

Screen Shot 2015-01-22 at 7.12.48 PM

Those are the basic rules of cladistics.  Pretty simple in theory, right?  The problem is that with organisms that have been dead for millions of years and only leave behind fragments of bone, deciding where they fit in to the family tree gets difficult.

File:House of ROMANOV-tree-fr.png
Like fitting Rasputin into this Romanov family tree.

Now let’s look at some of¬†that jargon I promised.

The first word¬†we need to understand is monophyletic. ¬†A¬†monophyletic group is a set of organisms that all share a common ancestor. ¬†You, your siblings, and your mum make a monophyletic group. ¬†You, your siblings, your mum, and your dad are not monophyletic because (hopefully) your mom and dad are not related. ¬†Some scientists¬†call¬†monophyletic¬†groups clades¬†and they are the bedrock of cladistics. ¬†A “proper” group must be monophyletic.

Screen Shot 2015-01-22 at 7.15.04 PM
A nice pink monophyletic group with you right in the middle.  Examples from nature include birds and primates.

If the group you’re looking at isn’t monophyletic, it might be¬†paraphyletic¬†or¬†polyphyletic. ¬†These are two types of almost-groups that can¬†confuse a lot of people. ¬†Paraphyletic groups choose¬†a section of the family tree, ignoring a large chunk. ¬†Polyphyletic groups choose a few individuals throughout the tree without regard for common ancestors. ¬†In the family analogy, a paraphyletic group could¬†include your mom and two of your siblings but not you. ¬†A polyphyletic group might include you and your cousin.

A nice purple monophyletic group.  Some examples from nature: bacteria and birds.
A less-nice purple paraphyletic group. Some examples from nature: Reptiles, Fish
Screen Shot 2015-01-22 at 7.18.34 PM
A rather arbitrary blue polyphyletic group.  Examples from nature: flightless birds, warm-blooded animals.

Phylogenetic trees are the most common tool used by biologists to depict evolutionary relationships.  Generally the root of the tree is interpreted to be the oldest and the branches are the newest.  Every branching point is called a node.

So far we’ve been looking at phylogenetic trees of your hypothetical family, but now that we have a primer in cladistics under our belts, we can start to look at a dinosaur phylogenetic tree.

Image from an article by Matt Wendel at UC Berkeley

The way to interpret this diagram is to think of time increasing as you read up. At the bottom there are the most recent common ancestor of all crocodiles, pterosaurs, and dinosaurs: Archosaurs.  Just as with all of the other terms on this diagram, everything up from any given node belongs to the group labelled at the node.  This means that all dinosaurs are archosaurs (but not all archosaurs are dinosaurs).

Archosaurs evolved in the late Permian or early Triassic period, about 250 million years ago.  The most familiar archosaurs from that time are probably sail-backed beasts like Ctenosauriscus koeneni.

File:Ctenosauriscus BW.jpg
Image by Nobu Tamara

At the next node, you see ornithodirans, a word which refers to dinosaurs and pterosaurs. The interesting part to note here is that pterosaurs (like pterodactyls and Quetzalcoatlus) aren’t dinosaurs. ¬†They are the closest relatives to dinosaurs without actually being dinosaurs.

Those are some big flying non-dinosaurs!
Those are some big flying non-dinosaurs!

The next node on that diagram is the one we’ve been waiting for: Dinosaurs! As you can see, dinosaurs are a monophyletic group. ¬†If you want to refer to the dinosaurs that were wiped out by an asteroid 65 million years ago, you have to make a paraphyletic group and exclude birds. ¬†You can do this by saying “non-avian dinosaurs”. ¬†Let the pedantry begin!

A picture I took at the Oxford Museum of Natural History.  Can you spot what's wrong with this panel?  High horses feel nice, don't they?
A picture I took at the Oxford Museum of Natural History. Can you spot what’s wrong with this panel? High horses feel nice, don’t they?

As the diagram shows, the dinosaur lineage splits at this point and we find one of the most important features that helps scientists classify dinosaurs.  It all comes down to the hip.  One group, the ornithischians, have backwards-facing pubises in line with their ischia, while saurischians have down-and-forwards facing pubises at an angle to their ischia.  This will become much clearer with some labelled images:

ornithischpelvis saurpelvis

Once you know to look for it, this difference becomes glaringly obvious whenever you look at a dinosaur skeleton.  Here, have a look at a few different images of dinosaurs and see if you can tell if its ornithischian or saurischian (I often just think of these as OРand SРbecause even when I say them in my head I trip over the -ischi-).


You are well on your way to being a dinosaur expert!

The last node we are going to discuss in the evolution of dinosaurs is the theropods.  The word itself means beast feet and it is the last taxonomic word you can use to accurately describe both T-Rex and turkey.  Theropods are a terrifying group of creatures, laying claim to speedy velociraptors, vicious ceratosaurs, and of course, the King, Tyrannosaurus Rex.  They evolved fairly early on (~230 million years ago) and include most carnivorous dinosaurs and their descendants.

My favourite extinct dinosaur is Ankylosaurus magniventris, an armoured tank of a creature with a club-tail that definitely meant business.  On the other hand, my favourite non-extinct dinosaur is probably Meleagris gallopavo, a colourful but mean-looking dino best served with potatoes and cranberry sauce.