G is for Gravity Waves

By Jonathan Farrow from the Thoughtful Pharaoh

Deep in Antarctica, right on top of the geographic South Pole, there is a research station that peers back in time to the very beginning of our universe. Named the Amundsen-Scott Station, it is home to instruments such as the creatively named South Pole Telescope (SPT), the Keck Array, and the BICEP experiments.

The temperature is currently sitting at about -30C and it’s the height of summer. ¬†The sun won’t set at the station until March 23rd and once it sets, it won’t rise again until September. ¬†So why the heck (or, one might say…Keck)¬†would we build an observatory there?

Because the temperature is so low and the altitude is so high (2743m) at the South Pole, the air is thin and dry, reducing blurriness normally caused by¬†the atmosphere. ¬†There are no cities nearby to cause light pollution and there are months of nonstop night, allowing for¬†continuous observation. ¬†It’s an astronomer’s dream. ¬†Except the nearly-constant -30C temperatures. ¬†And the remoteness. ¬†But otherwise, dreamlike.

Damn that looks cold! Photo from 2003
The perfect place to set up a top-secret laboratory from which to take over the world!… I mean… uh… from which to observe the beginnings of the universe. ¬†Yeah, that’s what we’re doing. ¬†Definitely that. ¬†Image credit: NASA

So what are astronomers looking for all the way down there at the end of the world? ¬†They are searching for clues as to how the universe started. ¬†Ever heard of the Big Bang Theory? ¬†No, not these clowns, the theory about the beginnings of the universe. Although, come to think of it, the theory is actually pretty well summed up by the first line of the Barenaked Ladies’ theme song to the Big Bang Theory (yes, those clowns):

Our whole universe was in a hot dense state,
Then nearly fourteen billion years ago expansion started. Wait…

That’s really the core of the¬†theory: ¬†everything used to be really hot and dense and now its¬†not. ¬†What happened in between is what the astronomers at the South Pole are trying to figure out.

History of Universe
For a bit of a primer on this diagram, check out A Short History of (The Universe), an essay I wrote which introduces the origins of the universe.  Image by NASA

Astronomy is awesome because when we look up, we are actually looking back in time. ¬†The distances involved are so great that it can take years (or billions of years) for light to reach us. ¬†So, what if we just looked as far as we could, wouldn’t we be able to see the Big Bang happening? ¬†What would that even look like?

Unfortunately, because everything was so hot and dense right at the start of the universe, nothing could stick together so the universe was just a soup of energetic particles.  Any light that was emitted was bounced around like the light from a flashlight in thick fog.  About 380 000 years after the Big Bang , the universe had cooled and expanded enough to let atoms form and collect electrons.  Atoms are mostly empty space, which means that unless they are packed very close together like in a solid or liquid, they are transparent.  What resulted was light spreading pretty evenly throughout the universe, starting 13.7996 billion years ago.  This is what is called the Cosmic Microwave Background Radiation (CMBR).  Cosmic because it comes from space, Microwave because it has lost a lot of energy since the Big Bang and is now only 2.7 degrees above absolute zero, Background because it is there no matter which direction you look, and Radiation because it is light.

WMAP
A map of the Cosmic Microwave Background Radiation. The different colours represent slight anomalies (about 10^-5 degrees C difference). Red is a little bit hotter, dark blue is a little bit colder.  Image by NASA

So, no matter how far you try to look, this map is all that you see.  It is all that can be seen because it is the oldest light that escaped.  Sounds kind of disappointing, but astronomers think that that image (what some refer to as the baby picture of the universe) holds clues to what happened before.

If there was inflation, faster-than-light expansion of space and time (again, check out my essay on the history of the universe¬†if you’re confused), that process should have produced gravitational waves.

“Woah, woah, woah. ¬†Hold up. ¬†I understand gravity, apples falling on heads, etc etc… ¬†How the Keck could there be gravity¬†waves?”

One of Einstein’s key contributions to science was the understanding that space and time are¬†linked and that they are¬†influenced by mass. ¬†He described space-time as a fabric that could be warped by the presence of mass. ¬†All that¬†gravity is, he said, is the curvature of space-time around mass. ¬†A simplified way to understand this is by thinking of¬†space-time as a trampoline. ¬†If you put a mass on the trampoline, it will create a depression. ¬†The heavier the mass, the more extreme the depression. ¬†Now, if you have an extreme depression and move it very quickly back and forth, it will create waves in the same way that a moving hand in a pool will create waves. ¬†Astronomers think that inflation must have created gravity waves with a very specific signature. They also think that very heavy stars moving quickly, like binary neutrino stars, would create these gravitational waves.

Loooook into my gravity waaaaves.  You are not getting sleepy.  You are paying attention, commenting below, and sharing this with your friends.
Loooook into my gravity waaaaves. You are not getting sleepy. You are paying attention, commenting below, and sharing this with your friends.  Image by NASA

If (or, once they are discovered for sure, when) gravity waves pass through you, it is space itself which is expanding and contracting.  You are not moving, but as the wave passes through your arm, your arm will be closer to your body than it was before and time for it will move slower.

The thing about gravity, though, is that it is by far the weakest of the fundamental interactions (Electromagnetic, Weak, Strong being the other, stronger ones).  By a factor of about a nonillion (1 with 30 zeroes after it).  This makes the waves it creates very difficult to detect.  While your arm is probably having a taste of timelordery as you read this, there is no way you could possibly feel it.  Gravity waves are not interesting for how they make us feel, but rather for the challenge they present in detecting, for the possible confirmation of our current physical model, and for what they can tell us about the origin of the universe.

So let’s come back¬†back to the barren, frigid wasteland of Antarctica and the astronomers freezing their buns off for science. ¬†BICEP2, the second iteration of the¬†Background Imaging of Cosmic Extragalactic Polarization experiment, looked at the¬†CMBR and looked for patterns in the light. ¬†These patterns, called b-mode polarization, can be produced by gravity waves, but also by interstellar dust.

In order to cancel out the effect of dust, the BICEP2 team used data from Planck, a European satellite launched in 2009 with a very similar mission: to study the early universe. ¬†Whereas BICEP2 could only look at one particular wavelength with high sensitivity, Planck could look in a few different wavelengths but didn’t have quite as much sensitivity for these b-modes. ¬†Dust doesn’t leave the same polarization patterns in¬†light in¬†different wavelengths, so by comparing the results from different wavelengths from Planck, the BICEP2 team was able to show that the b-modes weren’t from dust and so had to be from gravity waves from the early universe. ¬†Proof of inflation! ¬†Proof of the standard model! A possible Nobel Prize!

./b_over_b_rect.eps
Those swirls are the b-mode polarization that astronomers were looking for. ¬†This diagram, while confusing as Keck (it’s going to catch on!) and quite complicated, was EVERYWHERE when the announcement was made. ¬†Image by BICEP2 team

So, understandably excited and with a positive result in hand, there was a big announcement at the Harvard-Smithsonian in March of last year.  Unfortunately, the data they used was preliminary.  In September, new data was released and the effect of dust seems to have been larger than they thought.  The team reduced the confidence in their findings but still stood by a significant result.  Just last month, in January 2015, another set of data was released that makes the BICEP2 findings inconclusive.

It seems the team jumped the gun a little bit, were blinded by the impact of their apparent discovery, and had too much confidence in preliminary data. The result of all this is that there is still no direct evidence of inflation or of gravitational waves and the teams at Planck and BICEP are going to work together now with the strengths of their instruments.  Within a few years, the effect of dust should be able to be cancelled out and we will be able to see whether we were right about the beginning of the universe.  And all the frostbite will have been worth it.

F is for Faraday

By Jonathan Farrow from The Thoughtful Pharoah

The year is 1791. ¬†On a crisp autumn morning in South London, Margaret Hastwell, a blackmith’s apprentice, gives birth to her third son. ¬†With her husband, son, and daughter crowded around, she decides to name the newborn¬†Michael. ¬†Michael Faraday.

Margaret had a lot on her plate, what with two young children, a husband who was often sick, and quite a few bills to pay. ¬†She probably didn’t have much time or energy for idle thought or daydreaming. ¬†I doubt if she much considered what Michael might do with his life other than get by. ¬†There is no way it occurred to her that Michael would grow up to revolutionize the world of physics, make electricity a viable source of mechanical energy, and inspire countless scientists, engineers, and young people (including but not limited to Einstein, Rutherford, and this young science communicator, 223 years later). But that is exactly what he would do.

Faraday went to elementary school and learned to read and write, but by the time he turned 13, he had to start work in order to help his parents make ends meet. ¬†He was apprenticed to a local bookbinder and spent the next 7 years diligently mending books. ¬†But that wasn’t all he was doing. ¬†He was also reading. ¬†Over those 7 years, Faraday read voraciously and became interested in science, particularly the topics of Chemistry and Electricity. Luckily for him, George Riebau, the bookbinder to whom he was apprenticed, took an interest in young Faraday’s education and bought him tickets to lectures by¬†Humphry Davy¬†at the Royal Institution in 1812. ¬†This was only¬†shortly after Davy had¬†discovered calcium and chlorine through electrolysis. ¬†Davy was a big name in science¬†at the time, comparable to today’s Stephen Hawking, Neil Degrasse-Tyson, or Jane Gooddall, so it was with wide eyes that young Faraday attended. ¬†He was so blown away by what he saw and heard that he faithfully wrote notes and drew diagrams. ¬†These meticulous notes would prove to be his ticket into Davy’s lab.

Davy Notes
“I got a golden ticket!” Image from the Royal Society of Chemistry

Later that year, Faraday sent a letter to¬†Davy asking for a job¬†and attached a few of his notes. ¬†Davy was impressed and so interviewed young Faraday, but ultimately rejected the eager young fellow, saying “Science [is] a harsh mistress, and in a pecuniary point of view but poorly rewarding those who devote themselves to her service.” ¬†Translation: ¬†“Sorry, I don’t have space for you in my lab, but just to let you know… Science really isn’t very profitable.” ¬†A few months later, one of Davy’s assistants got in a fight and was fired, so guess who got a call? ¬†That’s right, Mikey F.

Not only did Faraday get a spot in Davy’s lab, but he also got to go on a European¬†tour with Mr. and Mrs. Davy. ¬†Pretty sweet deal, right? ¬†On the eighteen month journey, Faraday got to meet the likes of Amp√®re and Volta. ¬†If those names are ringing distant bells, it should be no surprise. ¬†Those eminent continental scientists give their names to standard units of electrical current¬†(Ampere)¬†and potential difference¬†(Volt). ¬†Re-invigorated, 22-year-old Faraday returned to London and took up a¬†post at the Royal Institution as Davy’s assistant.

The next two decades saw Faraday make great advances in chemistry, including discovering benzene, liquefying gases, and exploring the properties of chlorine. ¬†He didn’t get much chance to focus on electricity, however, until 1821. ¬†In that year, Faraday started experimenting with chemical batteries, copper wire, and magnets. ¬†Building on the work of¬†Hans Christian √ėrsted, Faraday’s¬†work was some of the first to show that light, electricity, and magnetism are all inextricably linked (we now know that they are all manifestations of the electromagnetic force). He was a dedicated experimentalist and between 1821 and 1831, he effectively invented the first electric motor and, later, the first electric generator. ¬†These two inventions form the basis for much of today’s modern power system. ¬†The electric motor that opens your garage door as well as wind and hydro-electric generators work on the exact same principle that was discovered by Faraday back in 1831: electromagnetic induction.

Faraday’s insight was that when connected¬†by conductive material, an electric¬†current could make¬†a magnet move. ¬†He also found that the reverse was true: a moving magnet can¬†create a flow of electrons: an electric current.¬†The experiment is actually quite simple and you can even¬†try it at home. Induction enables the transformation of energy between¬†mechanical, electrical, and magnetic states. ¬†Before Faraday, electricity was seen simply as a novelty. ¬†Since Faraday, we’ve been able to use it for all sorts of things. ¬†Like writing science blogs!

The famous iron ring experiment.  Two insulated coils of wire are wrapped around an iron ring but kept separate.  Attaching one to a battery will create a momentary current in the other.  Induction!
The famous iron ring experiment. Two insulated coils of wire are wrapped around an iron ring but kept separate. Attaching one to a battery will create a momentary current in the other. Induction!   Image by Eviatar Bach

[While he was definitely a gifted scientist, Faraday knew next to nothing about mathematics. ¬†He observed, took careful notes, and had an intuition for how to design experiments, but could not formalize his theories in mathematical language. ¬†He would have to wait for James Clerk Maxwell, a young Scottish¬†prodigy, to do the math and formalize¬†Faraday’s Law¬†in the 1860s.]

Faraday continued his work on electricity and gained all sorts of recognition, including medals, honorary degrees, and prestigious positions.  This increased pressure may have been to blame for a nervous breakdown in 1839.  He took a few years off, but by 1845 he was back at it, trying to bend light with strong magnets.  He discovered little else after the 1850s, but continued to lecture and participate in the scientific community.

Older Faraday with glass bar
While that does look remarkably like a cigar, Faraday is actually holding a glass tube in his hand. A glass tube… of Science! ¬† ¬†Public Domain image from Wikimedia

So not only can Faraday be considered to be one of the fathers of the modern world because of his breakthroughs in electricity, but he can¬†also be considered to be one of the fathers of modern popular science communication. ¬†In 1825, he decided to give a series of Christmas lectures at the Royal Institution, specifically aimed at children and non-specialists. ¬†He gave these lectures every year until his death in 1867 and was renowned as a charismatic, engaging speaker. ¬†He tried to explain the science behind everyday phenomena and in 1860 gave a famous lecture on the candle, something which everyone had used but which few actually understood. ¬†The¬†Christmas lectures continue to this day and, continuing with Faraday’s legacy, the Royal Institution is one of the UK’s leading science communication organizations.

Doesn't that look fun!?
Doesn’t that look fun!? ¬† ¬†Public Domain image from Wikimedia

It is not simply that Faraday was a great scientist and lecturer, nor that he managed to escape poverty in 19th century England to become world-renowned. ¬†Michael Faraday’s story is so¬†great¬†because by all accounts, he deserved every bit of success he gained. ¬†One biographer, Thomas Martin, wrote in 1934:

He was by any sense and by any standard a good man; and yet his goodness was not of the kind that make others uncomfortable in his presence. His strong personal sense of duty did not take the gaiety out of his life. … his virtues were those of action, not of mere abstention

It’s no wonder that Einstein had a picture of him up in his office. ¬†I think I might just print one off myself.

Faraday painting 1842
Still pretty handsome considering this painting is from 1842, making Faraday 51 years old.   Public Domain image from Wikimedia

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-).

Tyrannosaurus_skeletonStego-marsh-1896-US_geological_surveyBrontosaurus_skeleton_1880s

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.

C is for Cat Feces

By Jonathan Farrow from The Thoughtful Pharaoh

I’ve never been a cat person, myself. ¬†They just seem a bit too contemptuous as a species.

Cats, aside from being aloof, clawed, and kind of mean, also form a necessary part in the life cycle of a single-celled protozoan called¬†Toxoplasma gondii. ¬†This sneaky parasite can only reproduce in¬†feline intestines¬†but also finds its way into the tissues of pretty much all warm-blooded mammals. ¬†Its reach seems almost limitless and extends to more than half of the world’s bears, birds, cattle, cats, domestic chickens, deer, dogs, domestic geese, goats, mice, pigs, rabbits, rats, sea otters, sheep, and humans. ¬†And those are only the populations that were studied. ¬†Ever heard the expression that glitter is the herpes of the craft world because it gets everywhere? ¬†More accurately, glitter is the T. gondii of the craft world.

The life cycle of Toxoplasma gondii.  Humans are on the left side of this diagram along with the rodents and small birds.  Image from
The life cycle of Toxoplasma gondii. Humans, along with the rest of Noah’s menagerie,¬†would be on the left side of this diagram. Felines, aka devilspawn, are on the right. ¬†Image from Wikipedia

I call it sneaky because T. gondii¬†has been shown to alter the behaviour of its rodent¬†hosts in order to make it more likely to be ingested. ¬†The physical mechanism for this is still under investigation and largely unknown but¬†there are¬†two interesting experiments¬†worth noting. ¬†The first found that¬†rodents infected with T. gondii are more active and more excited about new places, making them¬†more likely to be noticed¬†(and eaten) by cats. ¬†The second purports that rodent brain chemistry is altered so that the unfortunate rats¬†finds the scent of cat pee sexually attractive. ¬†The scientific paper which explains this second theory is even titled “Fatal attraction in rats infected with Toxoplasma gondii”.

A lesson for rodents:  don't listen to the parasite in your brain.  Cat pee IS NOT ATTRACTIVE! Image from Wikimedia
A lesson for rodents: don’t listen to the parasite in your brain. Cat pee IS NOT ATTRACTIVE!
Image from Wikimedia user Lxowle

So we’re pretty confident that T. gondii can alter the behaviour of rodents, but what does it do to¬†humans?

We’re not sure…

For those with weak immune systems or for the pregnant, a T. gondii infection can cause acute toxoplasmosis, a potentially fatal disease characterised by swelling lymph nodes, sore muscles, and flu-like symptoms. ¬†I wouldn’t worry about that too much because it’s about as lethal as the flu for those with regular immune systems.

For the rest of us, infection with this parasite is largely¬†asymptomatic. ¬†There’s no way to tell whether you’re infected or not without a blood test. ¬†Unless you ask Czech researcher Jaroslav Flegr. ¬†He, along with a growing number of scientists, believes there is enough evidence to show that latent toxoplasmosis makes humans more thrill-seeking. ¬†According to a 2012 paper in the Journal of Experimental Biology, infected individuals are more likely to get into traffic¬†accidents, score differently on personality tests than un-infected individuals, and infected men are taller on average with more masculine facial features.

Rodent and human brains are not so different, it turns out.

Japanese_litter_box_in_use
Patient Zero. From Wikimedia user Ocdp

If your cat got infected and you happened to get exposed while cleaning out its litter box, chances are that you are infected. ¬†Your cat’s poo is likely changing your personality. ¬†If, like me, you don’t and have never owned a cat, that doesn’t mean you’re safe from infection. ¬†T. gondii is really good at getting into your body and making its way to the central nervous system, where it acts the puppetmaster and, expecting you to be a rodent, makes¬†you excited about¬†new environments. ¬†All this¬†so that you can be eaten and it can reproduce.

Pretty interesting, eh?

B is for Bat Echolocation

By Jonathan Farrow from The Thoughtful Pharaoh

Ever wish you could see in the dark?  It would make life a bit easier.  No more tripping over clutter on the ground or feeling walls for a switch.  Humans rely quite heavily on their sight, but some animals can make do by illuminating their surroundings with sound.

Bats are just such an animal. ¬†They belong to a privileged group of organisms including toothed whales (like sperm whales, dolphins, and killer whales) and shrews that use sound to see the world. ¬†By listening for the reflections of their¬†high-frequency clicks, bats¬†are able to build up an accurate picture of the world around them. ¬†The clicks are often too high for humans to hear, sometimes reaching as high as 110 kHz (human hearing generally goes¬†from 20Hz-20kHz). ¬†This amazing superpower is called echolocation but not all bats have it. ¬†Most microbats (usually small, insect-eating, with proportionally large ears) can echolocate using their throat to produce clicks, while megabats (larger, fruit-eating, with large eyes) usually can’t. ¬†Like most rules in biology, though, these distinctions aren’t¬†universal. ¬†Some megabats have evolved¬†echolocation by way of specialized nose structures and others are smaller than big microbats.

An example of a Megabat, waiting for Comissioner Gordon to turn on the signal. Photo by Gerwin Sturm
An example of a megabat, waiting for Comissioner Gordon to turn on the signal.
Photo by Gerwin Sturm
This little microbat can't wait to be free! Photo by Neal Foster
This little microbat can’t wait to be free!
Photo by Neal Foster

So now that you’ve been acquainted with the notion of echolocation and the bat family tree, let’s start talking about some neat things that bats can do with their special ability.

Jamming

Since echolocation is dependent on a bat receiving and interpreting the reflections of sound, it is particularly¬†susceptible to interference. ¬†The biggest source of interference is the bat itself. ¬†Bats produce some of the loudest sounds in nature and have some of the most sensitive ears to register the reflections that come back hundreds of times quieter. ¬†Imagine revving up¬†a Harley Davidson and putting a traffic cone on your ear to hear someone whispering across the room. ¬†It would probably hurt if you did those things at the same time. ¬†You’d be too rattled by the revving to be able to listen to the whisper. ¬†Bats avoid this by temporarily disconnecting their ears as they shriek, then quickly reconnecting them in time to hear the echo.

One particular species of bat, the Mexican free-tailed bat (Tadarida brasiliensis), has been recently observed messing with its competitors’ signals. ¬†By emitting a special signal right when another bat is about to catch an insect, the bats make each other miss. ¬†It’s the bat equivalent of yelling “PSYCH!” when someone is about to shoot a free-throw. ¬†Unlike the obnoxious friend though, the bat version¬†actually works. ¬†The bats’ success rate drops by about 80%. ¬†It’s such an effective strategy that two bats will even hang out near each other, jamming each others’ signals every time one swoops in for a bug, until someone gives up.

Adapting

The same species of bat that jams also lives in close proximity to natural gas fields in New Mexico.  Some of the rigs have compressors that emit a constant, loud noise that can interfere with echolocation calls.  For the Mexican free-tailed bats, whose normal calls fall within the same frequency range as the compressors, the loud wells are avoided when possible.  The bats have also begun to change their calls, making them longer and in a more restricted range of frequencies.  This strategy would make the calls more easily distinguishable from the background din and marks the first time human-made noise has been shown to interfere with bat life.

Sneaking

We know that humans can’t hear a lot of what the bats are “saying” when they are building up a sonar picture because our ears aren’t sensitive to the right frequencies. ¬†This makes sense because, for the vast majority of humans, it really doesn’t matter what the bats are saying. ¬†It’s a whole¬†other issue if you’re a moth about to be eaten. ¬†There’s a lot of (evolutionary) pressure to hear the bats coming in order to avoid getting eaten. ¬†Some noctuids, a rather large family of moths, have evolved bat-sensing ears that warn the insect of impending disaster. ¬†If the bat is far enough away, the moth will make a break for it, otherwise it will just start flying erratically in random directions to try and make the bat miss. ¬†The Pallas long-tongue bat (Glossophaga soricina) still manages to get a meal by using only ultra-high-frequency, low intensity calls to find moths and by going silent on approach. ¬†This stealth mode doesn’t trip the moth’s defences.

Stealth bats.  Also happen to have the fastest metabolism of any known mammal. Photo by Ryan Somma
Stealth bats. Also happen to have the fastest metabolism of any known mammal.
Photo by Ryan Somma

For more information on echolocation and bats, check out:

The Bat Conservation Trust, a UK charity devoted to all things bat

This Scientific American article about how echolocation works

This study about Mexican free-tailed bat jamming

This study about Mexican free-tailed bat adapting

This study about Pallas long-tongue bat sneaking

A is for Axolotl

By Jonathan Farrow from The Thoughtful Pharaoh

Imagine a creature that never grows up, can regenerate limbs without scars, and has a sort of slimy, alien-like cuteness. ¬†Sounds like a critter you’d like to meet, right? ¬†Ambystoma mexicanum, the axolotl, lives all over the world in aquaria but their only wild habitat is under severe threat. ¬†Chances are that neither of us will ever meet a wild one and that is a shame.

This fascinating amphibian, through a quirk of evolution, is neotenous.  This means that it never really leaves the tadpole stage.  Where most salamanders and frogs will leave behind external gills and develop lungs to breathe on land, the axolotl decides it is perfectly happy and stays put underwater with beautiful gill fans collecting the oxygen it needs.

Image by Faldrian
This axolotl is a strong, independent amphibian that don’t need no lungs or terrestrial environment. ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† ¬† Image Creddit:¬†Faldrian

Not only does this incredible creature never grow up, but it can also totally regenerate lost limbs.  This makes it a valuable model organism for scientists to study in the lab.  The exact mechanism behind this regeneration is still being investigated, in hopes that one day a technique for human regeneration will be discovered, but there are some interesting findings that have already come out.

The generally accepted theory was that when a limb was cut off, the axolotl would send a signal to the stump that would turn the cells at the end to pluripotent stem cells. ¬†These cells would be able to duplicate and grow into any tissue and are similar to the cells found in embryos. ¬†Recent research out of Germany, however, showed that¬†the cells at the end of the stump don’t revert to a totally embryonic state. ¬†They are still able to grow into tissues, but only certain kinds of tissue. ¬†The part of the stump that was muscle¬†remembers that it needs to grow muscle, whereas the part that was nerve remembers that it needs to grow nerve.

Step-by-step limb regeneration.  From the lab of James Monaghan
Step-by-step limb axolotl limb regeneration.      From the lab of James Monaghan

Lake Xochimilco in Mexico City is the only place in the world the axolotl can be found in the wild, making them critically endangered according to the IUCN.  They used to live in another nearby lake named Chalco, until that was drained for fear of flooding.  For hundreds of years the axolotl was abundant enough to be a staple in the diet of locals, but now they are nearly impossible to find.  In a 2002-2003 survey where over 1800 nets were cast over the entirety of Lake Xochimilco, scientists could only find 42 of the little amphibians.  The first thing to understand about axolotl decline is that calling Xochimilco a lake is kind of a stretch.

"Lake" Xochimilco.  Basically a network of canals surrounded by farms.
“Lake” Xochimilco. Basically a network of canals surrounded by farms.

This small, restricted environment is a closed system, meaning it does not drain anywhere.  It is also surrounded by farms which provide much of the food needed to feed Mexico City.  Agricultural runoff from the farms and pollution from the nearby megacity accumulate, causing severe damage to the ecosystem and endangering the few axolotls that remain.

The axolotl is an incredible animal at severe risk of extinction in the wild. ¬†It is the Peter Pan of the animal kingdom, refusing to¬†grow up and hiding from hooks. ¬†It’s most amazing power, regeneration, is still being studied and one day may prove the key to human limb regrowth. ¬†For all this and more, the¬†axolotl is most definitely an interesting thing.

Some captive axolotls, like this one, are leucistic (a condition similar to albinism that causes animals to become white).  Aren't they cute? Image by Henry M√ľhlpfordt
Some captive axolotls, like this one, are leucistic (a condition similar to albinism that causes animals to become white). Aren’t they cute?
Image by Henry M√ľhlpfordt

For more information on this beautiful creature, follow the links below

Weird Creatures with Nick Baker did a great documentary on axolotls which is available on Youtube.

The IUCN has put the axolotl on its red list of endangered animals

The German team who study axolotl limb regeneration

Want to adopt a bat with Avon Bat Group?

A BIG thank you to Kiri and Stuart from the Avon Bat Group for coming to Enter the Bat Cave and showing off the beautiful little animals they have in their care. Everyone really enjoyed getting up close and personal with an animal that is so rarely seen by the general public.

Stuart and Kiri with their bats and Bish the bear from Bristol Improv Theatre
Stuart and Kiri with their bats and Bish the Bear from Bristol Improv Theatre

If you are interested in supporting Avon Bat Group, adopting a bat, or just want to know more about your new favourite mammal; you can find more information on their website at www.avonbatgroup.org.uk, or like their facebook page for regular updates. We hope that after all you learnt during the evening, you can really appreciate how important their work is.

Thank you to everyone who came last night, we hope you had a great evening! Keep an eye on the website for more information about our next event and for another of Antony’s excellent infographics about Enter the Bat Cave.

Not Such a Slippery Slope

“It is important that legislation keeps pace with scientific progress.”¬†Robert Winston

A little breakthrough for medical research happened last week, not in the lab, but in the House of Commons. By a huge majority the commons voted to allow a new IVF technique called mitochondrial donation, which can be used to stop babies from inheriting mitochondrial DNA diseases. Most mitochondrial DNA diseases are passed from mother to child and can cause debilitating symptoms such as muscle weakness, diabetes, heart problems, movement problems, epilepsy or even death. With a 1 in 4,000 prevalence, apparently Charles Darwin even had a form of the disease, which caused continuous vomiting and terrible headaches.

Image Credit: Michiel1972
Image Credit: Michiel1972

Even though scientists, politicians and most of the public seem to be in a rare state of agreement over this topic, it has of course had its opponents. Before we take a look at the arguments of those who worry about its safety, let’s first take a tentative dip into fertilisation to find out how this new technique works.

The mitochondria are the power house of cells in the body and provide energy to carry out different cellular function. Each mitochondria actually has its own DNA, separate from the DNA that makes you who you are, which it uses for controlling its own function and energy production. When this mitochondrial DNA becomes faulty, usually a trait passed down from the mother, the mitochondria could malfunction, causing all sort of trouble.

This new technique takes the nuclear DNA, the DNA that really makes you you, from a patient’s egg and places it into an egg from a healthy donor which has already had its own nuclear DNA removed. The healthy egg is then inserted back into the mother to develop. As the donor egg contains healthy mitochondrial DNA, you’ve now got yourself a healthy little baby growing.

Image Credit: 44444 UAE
Image Credit: 44444 UAE

The main concerns that have been expressed are worries over safety, and the ever slippery slippery slope towards designer babies. Personally, this is something I have never understood. In today’s health and safety dominated, slightly science-sceptical, government a discovery that has gained so much media interest would never have­­ been allowed to be used by the public without endless supporting evidence and safeguards. As to those who see the children as three-parent babies, technically only 0.1% of the DNA is not from the parents so perhaps they should be called 2.0001 parent babies. I agree it doesn’t quite have the same ring to it, though.

It’s been unusual to see such major media coverage for a subject that could be viewed as too complicated for the public to get behind. Hopefully this is a welcome look into a future where new scientific breakthroughs are more broadly accepted.

ENTER THE BAT CAVE Ft. Batwoman Heather Nichol

Plunge into the depths of one of Bristol‚Äôs darkest bat caves ‚Äď a place where the echoes of lost souls linger and haunt the footsteps of all those who enter. Fleeting silhouettes of winged creatures lay claim to these walls, and the stench of guano weighs heavy on the air‚Ķ

OK, so in reality we just turned off all the lights in the Bristol Improv Theatre, and the Rising Ape team forgot to wash, but bear with us for a moment. Rising Ape returns with a night of bat-themed madness. Bring a team and stretch your wings in the quiz. You better know your long ears from your short snouts, your Dracula from your Orlok, and your Slazenger from your Gunn & Moore. But as bat researchers stuck in a terrifying cave, we don’t expect you to just sit there all night. Be prepared to get up close and personal, untangling these creature’s fascinating secrets for yourselves with help from some special guests. To conclude the night’s eerie proceedings, real-life Batwoman Heather Nichol will share her personal journey into the world of bats.

Tickets available at http://improvtheatre.net/calendar/enter-the-bat-cave/

Tickets also available on the door.

Enter the Bat Cave... there is no exit.
Enter the Bat Cave… there is no exit.

More about Heather Nichol: Heather has been involved in bat conservation for the past 5 years. She was first introduced to the world of bats during her undergraduate degree at the University of Leeds, and has since taken part in various conservation projects, including a project that discovered the first know breeding colony of Alcathoe bats in the UK. Heather has just completed a Masters by Research at the University of Bristol studying one of the hot topics in ecology at moment: bat fatalities in wind farms in Britain.

Welcome to the new age of antibiotics

By Alex Hale

“I have been trying to point out that in our lives chance may have an astonishing influence and, if I may offer advice to the young laboratory worker, it would be this – never to neglect an extraordinary appearance or happening.”¬†Alexander Fleming

Nearly 30 years after the discovery of the last antibiotic, a new bacterial culturing technique may end the drought of new medicines.

Scientists have discovered 25 new antibiotics using a new lab technique which will hopefully discover many more. One of these new antibiotics, called teixobactin, has shown promising results in treating gram-positive bacteria such as MRSA and bacterial tuberculosis. The researchers are also hoping that harmful bacteria won’t gain resistance to teixobactin for at least another 30 years, as it uses an unusual multi-pronged attack that will be much harder for any germs to combat. It hasn’t been trialled on humans yet, but the test mice have responded very well. If human trials also go well, it may finally be possible to treat some of the nasty multi-drug resistant superbugs that have been troubling doctors for many years.

Although it’s fantastic news that a new antibiotic has been discovered, the main

Traditional testing of antibiotics in vitro. Image credit: Graham Beards
Traditional testing of antibiotics in vitro. Image credit: Graham Beards

story here is the new technique.  Traditionally, bacteria are grown on agar plates in a lab, but this new technique uses soil as the culture medium where bacteria feel at home and are happy to grow. This may not sound as interesting as a new superbug-killing drug, but teixobactin comes from the 99% of bacteria that have never been cultured, and without this technique it would never have been! This 99% is an untapped treasure trove that researchers were unable to culture in a lab environment until now, and this unexplored group could hold the secret to treating any number of infectious diseases.

If these new antibiotics are everything that they appear to be then it’s an easy bet that the team from Northeastern University in Boston, Massachusetts, will be up for a Nobel Prize. Perhaps they will have a more positive message than Alexander Fleming, who in his Nobel Prize speech for the discovery of Penicillin, couldn’t resist presciently warning everyone of the dangers of over use.

It has all come just in the nick of time as well, as we were all starting to prepare for the worst. A horrid future of antibiotics slowly becoming useless as more and more bacteria became resistant to them. Hopefully, that is no longer the case.