Science Minus Details

Why Does Old Ice Cream Get Crunchy?

noreply@blogger.com (LeeBee) — Tue, 19 Feb 2013 21:54:00 +0000

This was originally posted on Sustainable Nano, which is my new project. You should go check it out! Science Minus Details will live on though! Poop posts will come, have faith!!!!

As with all good meals of information, let's start this one off with ice cream!

In an effort to grow out of my "slim fit" clothes, I've begun an ice-cream-after-every-dinner diet.

Even the cat likes my diet!

An added bonus is that I go through jugs of ice cream so quickly that I NEVER have to deal with old, gross, crunchy ice cream! You know what I'm talking about. You reach into the back of your freezer, find that jug of 6-month-old ice cream, only to discover that it tastes like the perfect mixture of sugar, fat, and sand.

In order to understand this gritty phenomenon, let's talk first about what gives freshly purchased ice cream that wonderfully non-gritty texture. The ice cream manufacturing process is controlled very carefully, such that the ice in ice cream comes in the form of lots of super-tiny ice crystals. These ice crystals are usually around 10 to 100 micrometers in size, which is so small that our tongues can't even detect them as crystals, which is one reason ice cream is so smooth! However, if their size increases significantly, our tongue notices the crystals and the ice cream tastes gritty. But how do the crystals get bigger? Well, as we talked about in the previous post, small crystals have more surface area compared to an equal mass of large crystals. This means that lots of the atoms that make up small crystals are stuck out on the surface of those crystals, instead of being nestled on the inside. Those surface atoms would much rather be on the inside of the crystal, surrounded by other identical atoms. We scientists would say the surfaces of crystals have extra energy, relative to the insides of crystals.

Water molecules on the surface of ice crystals have extra "surface energy" because they aren't fully surrounded by other water molecules.

As a consequence of this, small crystals are always looking for a way to grow larger so that a smaller percentage of their atoms will have to live on the crystal surface. That is exactly what happens over time as ice cream sits in the freezer—the ice crystals find a way to grow larger—leading to that oh-so-disappointing gritty texture. One way this crystal size growth can happen is when small crystals clump together to make larger crystals. This turns some of the unhappy surface atoms into happy interior atoms.

An even cooler way crystals can grow larger is by stealing individual unhappy surface atoms from other crystals. Basically, the surface atoms are so unhappy, they simply "abandon ship" and wash up on the shores of another crystal, making that second crystal larger. This process results in larger crystals growing and smaller crystals shrinking. This can continue to happen until the small crystals disappear completely! Cool!

Ostwald ripening. Surface molecules move from one crystal to another. This results in the growth of larger crystals because they have less surface area per unit volume.

What in the world does this have to do with nanotechnology? Well, if we shrunk the smooth-tasting ice crystals to be around 1,000 to 100,000 times smaller, they would be nano-ice crystals. We scientists would then call them "nanoparticles," and we can make them from lots of different materials. Nanoparticles are so tiny that their surfaces have WAY MORE extra energy, and this energy can be harnessed to do some amazing things! To choose one example of many—big chunks of gold can't do much for a chemist except buy her lots of late-night meals and maybe a new ~~car~~ bike (we're sustainable here, remember!). However, nano-sized chunks of gold have such energetic surfaces that they can link two different chemicals together—where nothing at all happens without the nano-gold.

Gold nanoparticles can act as "catalysts" in chemical reactions.

The surfaces of nanoparticles can also be harnessed to degrade pollutants, turn fuels into electricity in fuel cells, and tons of other great stuff! Their surfaces are also largely responsible for how these materials behave in the environment and in organisms' bodies (more on that soon!). So, the more we understand about these special surfaces, the better we can predict where nano-pollutants might end up and how toxic or non-toxic they might be. We can then hopefully use this information to design nanoparticles that are "benign by design." So, to stretch the ice cream analogy to its limits, it's best to understand as much as we can about nanoparticle surfaces in order to avoid any gritty-tasting negatives, but there are still plenty of smooth-tasting positives!

References & Further Reading (subscription/purchase required for some):
Clark, C. The Science of Ice Cream; Royal Society of Chemistry: Cambridge, 2004.
Halford, B. Ice Cream. Chem. Eng. News, 2004, 82, 51.
Corma, A.; Garcia, H. Supported gold nanoparticles as catalysts for organic reactions. Chem. Soc. Rev., 2008, 37, 2096.
An, K.; Somorjai, G. A. Size and Shape Control of Metal Nanoparticles for Reaction Selectivity in Catalysis. ChemCatChem, 2012, 4, 1512.
Zhong, C.J; Luo, J.; Fang, B.; Wanjala, B. N.; Njoki, P. N. Loukrakpam, R.; Yin, J. Nanostructured catalysts in fuel cells. Nanotechnology, 2010, 21, 1.
Mudunkotuwa, I. A. and Grassian, V. H. The Devil is in the Details (or the Surface): Impact of Surface Structure and Surface Energetics on Understanding the Behavior of Nanomaterials in the Environment. J. Environ. Monit. 2011, 13, 1135.

Why Are Olympic Medals Gold, Silver, and Bronze

noreply@blogger.com (LeeBee) — Thu, 09 Aug 2012 06:21:00 +0000

Check out these divers, trying super-hard to dive the best dive that has ever been dived:

These faces don't lie. Image via.

Incredible feats of strength, dedication, and squished faces are on prominent display at the London 2012 Olympics. I won't pretend to understand what drives Olympic athletes to be so zany, but I do know that if they squish their faces hard enough they will be rewarded with one of these beautiful Olympic medals.

2012 Olympic Medals

There they are...silver, gold, and bronze...from left to right. But why are those medals made out of those metals????? AND, why is bronze good, silver better, and gold the best??

INTERESTING TIDBIT: The gold medal is really gold-plated silver--just 1.34% gold. The last Olympic gold medals made entirely of gold were given out in the 1912 Stockholm games.

Let's tackle the first question first. Why those three metals? To start with, bronze can be made by mixing copper with tiny amounts of other metals such as tin. Humans figured this out around 5000 years ago and it changed everything. So instead of bronze, silver, and gold, let's talk about copper, silver, and gold. Those who know their periodic table will know that copper, silver, and gold all come in the same column.

Elements in the same column generally have many similar properties. In this case, the most important property these metals share is the fact that they can be found naturally in their pure, "native" form. Most other metals are only found in their mineral form, and can only be obtained in pure form by producing them in crazy chemical reactions.

Native gold. Image via.

As a result, copper, silver, and gold were three of the first metals that early humans could get their dirty little hands on. While gold is almost always found in pure form, silver and copper are more commonly found bonded to other atoms such as sulfur and oxygen in mineral deposits. Eventually we clever humans figured out how to make pure silver and copper (then bronze) from those mineral deposits, which led to the metals' widespread use as money, decorative things, and eventually Olympic medals. Another property that makes those metals especially awesome is their resistance to bonding with oxygen and sulfur in a process known as tarnishing. It happens, but slowly enough that products made from the metals are still useful.

Tarnished silver (left) vs untarnished silver (right). Image via.

But why is bronze good, silver better, and gold the best? This story starts way earlier than the bronze age. Let's take a mental walk back in time to before the first Olympic games, before humans walked the earth, before the dinosaurs died out, before any life existed on earth, even before the earth or the sun existed! Nearly all the non-hydrogen atoms on earth were formed inside a star that existed over 5 billion years ago. That star smashed protons and neutrons together forming elements heavier than hydrogen such as carbon and oxygen, in a process that releases the energy required to keep the atom-crunching star in business. However, as the atoms get heavier, less and less energy is released, such that making any element heavier than iron requires an energy input. Here's a cool graph that shows that:

The result of this is that elements heavier than iron are less abundant than those lighter than iron. So, when that element-producing star reached the end of its life and exploded, it paved the way for the formation of our solar system in which elements towards the bottom of the periodic table (including copper, silver, and gold) are rare.

Copper is the lightest of the three Olympic medal metals, and so is the most abundant, making up 0.0068% of the earth's crust. Silver is heavier than copper, lies just below it in the periodic table, and makes up 0.000008% of the earth's crust. Gold is the heaviest, lies near the bottom of the periodic table, and makes up only 0.0000004% of the earth's crust. So, the order of awesomeness of the Olympic medals is simply a function of their rarity relative to one another, which is caused by crazy stuff that happened billions of years ago inside a now long-dead star!!!

FINAL THOUGHT: Next time you see Michael Phelps holding his billionth gold medal, think about how he is a hunk of atoms of abundant elements from high on the periodic table (oxygen, carbon, hydrogen) holding a hunk of atoms of a rare elements from low on the periodic table.

The periodic table is so awesome!!!!!!!!

References & Further Reading:
Chemistry of the Elements by Greenwood
The Evolution of Matter by Tolstikhin and Kramers

Is the solar system tilted sideways??

noreply@blogger.com (LeeBee) — Tue, 26 Jun 2012 13:58:00 +0000

Do you ever think about how cool it is that someone on the opposite side of the earth from you is standing "upside down"--your feet facing their feet?

Or even when you travel from one US coast to another, you are standing at a ~45 degree tilt relative to how you were standing before.

I had thoughts like this swirling in my head during one moonless night on the pacific coast, as the campfire died down and our very own milky way galaxy came into view.

Us, our planet, and our solar system...we all live in the "suburbs" of our milky way galaxy, in one of its spiral arms.

So, when we see the milky way in the sky we can gaze toward the shiny lights "downtown," near the center of our galaxy. We can also gaze at other suburbs of our galaxy, getting an edge-on view of the spiral arms.

Image adapted from William Castleman.

The campfire was now completely gone, and as the earth continued to turn, the milky way moved higher and higher in the sky. Pretty soon it was straight overhead--the spiral arms stretched above my head toward the northern horizon and the galactic center at my feet toward the southern horizon.

"The milky way and I sure are aligned tonight," I thought. Pondering this a bit longer, I realized that I was laying down parallel to the plane of our galaxy.

The milky way was huge and cosmically more significant than me, but my body was still oriented in a particular direction with respect to it. Crazy! Had I been laying on the ground oriented west-to-east I would have been floating in space perpendicular instead of parallel to the plane of our galaxy. Think about it!

Me, floating parallel to the plane of the milky way galaxy. Not to scale.
Actually this is the nearby Andromeda Galaxy. Adapted from UniverseToday.

My sense of north-south-east-west was not exact, but hopefully you get the idea. I was lying roughly north-to-south...I was parallel to the plane of the galaxy...therefore the orbit of the earth and its north-south axis must also be parallel to the plane of the galaxy.

In order for this to be possible, we--us, our solar system--must be oriented perpendicular-ish to the plane of the galaxy. Something like this:

The solar system and the milky way, tilted. Note: SUPER not to scale.

It turns out I'm not totally bonkers, and the solar system is "tilted" with respect to our galaxy. You can see that in this 360 degree panoramic picture of the sky.

Click to see in full glory!!! via APOD.

In addition to the familiar band of light from our milky way galaxy in this image, you might also notice the dimmer band of light running left-to-right. This is known as zodiacal light, and is caused by sunlight being reflected off tiny dust particles scattered like a pancake in the plane of our solar system. Zodiacal light can be used to literally see into the plane of our solar system. So here you can visibly see the plane of the milky way vs the plane of our solar system, and as you can see they are tilted with respect to one another by about 60 degrees.

You can see this even better in this image of the sky that was made by looking at infrared light (shifted here into the visible spectrum so we can see it, of course).

Infrared image of the sky. Click it! via APOD.

The mega-bright line from left-to-right is the milky way galaxy. It looks more bright here than in the image above because infrared light can pass through the dust that normally blocks part of our view of the milky way. The more diffuse blue-ish light is the zodiacal light from our solar system. See, we are tilted by 60 degrees!

WOAH!!!!

*note: The tilt of the earth's axis of rotation with respect to the plane of the solar system and earth's orbit around the sun greatly complicate this whole issue. So, to avoid entering a quagmire of celestial-mechanical-insanity, I'm ignoring it entirely. Please forgive me. If you'd like to learn more, check this confusing stuff out. Also for a different explanation of all this, go here.

What is Lichen? Why is it so cool??

noreply@blogger.com (LeeBee) — Tue, 15 May 2012 04:10:00 +0000

On a recent bike trip to the shore of Lake Waubesa near Madison, WI I saw this awesome tree covered in this crazy greenish stuff.

Summer has returned to the northern hemisphere and I'm SO PSYCHED.

That greenish stuff on the trunk of the tree are lichens. Lichens are the coolest fungi! Lichens are also the coolest plants and the coolest bacteria! Wait... how is that possible????

Lichens are composite organisms! Lichens are composed of a fungus along with some sort of photosynthetic organism such as an algae or cyanobacterium. One reason that this is totally insane is that fungi, plants (algae), and bacteria come from three totally different kingdoms of life. Their last common ancestor existed around 2 billion years ago (ref1 ref2), yet somehow they are able to live in harmony! Behold one of the greatest wonders of the natural world!!!!

Lichens, reason #420 that the world is awesome. image via kindofcurious.com

The awesomeness, however, has only begun. It's neat when lichens grow on trees, but its even more neat when they grow on rocks. Lichens come in all shapes, sizes, and colors. The yellow-greenish stuff covering these rocks are lichens.

The ability to grow on rocks is a great example of why the organisms that compose lichens need one another. The algae and cyanobacteria are able to photosynthesize. To do that they need light and carbon dioxide, both of which are readily available on any exposed rock surface. However, the other thing they need is water, which is hard to come by on the surface of a rock. Water may be plentiful during rainfall, but rocks do a horrible job of helping that water stick around afterwards. This is where the fungi come in. They are able to form the "body" of the lichen within which the photosynthetic organisms can grow, and these fungal "bodies" help retain the much-needed water. In return, the fungi simply take a share of the tasty sugars the photosynthetic organisms are able to make. What a deal!!!

Lichen Formation. The top image shows an algal cell being enveloped by fungal filaments. The bottom image shows an algal cell that has been almost completely covered in fungal filaments. images via Ahmadjian & Jacobs.

Lichens get even cooler though. On newly exposed rock faces, lichens are often the first organisms to move in, and are known as "pioneer colonizers." During their existence on life's frontier, they actually help create soil (ref)!!! Soil is super-complex, but is composed primarily of minerals and organic (carbon-containing) matter. Lichen help create soil by sticking their numerous little appendages into cracks in the rocks, which speeds up the erosion of those rocks. They also excrete molecules such as oxalic acid that can help dissolve the rocks in a process known as weathering. The above two things contribute to the mineral component of the soon-to-be soil. Lichen contribute the organic matter component by dying, returning their photosynthetically derived bodies to the environment. This organic component performs the function that the lichen once did, helping retain water so it is available between rainfalls.

Here's the really crazy part. The presence of soil paves the way for plants to grow and replace the lichen. Plants depend on soil in part to retain water between rainfalls. So, those poor hard-working lichens actually create the conditions for their own destruction!

You'd better believe the lichens was there before the plants. image via mamluke.

Let's hear it for lichen!!!!

Yoe the Scientist's Nano-Sized Brain

noreply@blogger.com (LeeBee) — Tue, 17 Apr 2012 03:19:00 +0000

Deep in the heart of south-central Wisconsin, there lives a scientist who would prefer to remain nameless and (nearly) faceless. We will call him Yoe.

Yoe the Scientist

Yoe is a graduate student at the University of Wisconsin, Madison. He is interested in transforming the nature of matter. Yoe is also interested in things that are very small. He combines these interests by researching nanowires made of the element silicon. Before we dive any deeper, let's talk about what the heck "nano" means. "Nano" usually refers to things that have one dimension (height, width, etc) of 1-100 nanometers. This is around 100 to 100,000 times smaller than the width of a human hair. SMALL! A nanowire is simply a wire whose diameter is around 100 nanometers or less. A human hair could be called a "microwire," since its average diameter is around 100 micrometers.

Scanning electron micrograph of a human hair. Via The University of Wales Bioimaging Laboratory.

Yoe makes his silicon nanowires by a method that seems truly crazy to me. Not crazy in the "extremely dangerous" sense of the word (though his method is not without danger), but crazy in the "extremely awesome" sense of the word. First, he takes a chemical called silicon oxide and puts it in a long ceramic tube. He then heats the tube up to 1200 degrees Celsius (2,200 degrees Fahrenheit!) and flows a steady stream of hydrogen gas (4% in argon) through the tube. The machine he uses is called a tube furnace (clever huh?), and looks like this:

A red hote tube furnace. Image via Yoe the Scientist.

The box in the center is what creates the heat. The tube goes right through its center and is glowing red hot due to blackbody radiation. This is a cool-looking experiment!!!

Holy Crapola!!! Image via Yoe the Scientist

It's not completely clear what happens next, but here is a guess. These insanely hot conditions cause some of the solid silicon oxide molecules to jump from the bottom of the tube, into the hydrogen gas stream. During their journey down the tube the silicon oxide and hydrogen can react with one another and be transformed into the pure element silicon. Towards the edge of the furnace the temperature in the tube drops, and this causes the newly formed silicon to fall onto tiny stainless steel disks that Yoe placed there. In his first experiment he put a bunch of disks in the tube, because the disks towards the outer edge of the tube would be cooler and the disks towards the inside of the tube would be hotter. Yoe wanted to find the "sweet spot" where the temperature was just right to allow his nanowires to form.

Nanowire experimental setup. Image adapted from one created by Yoe the Scientist

After Yoe stopped the reaction and the disks cooled down, they looked totally flat and boring aside from being slightly different colors than before. Just by looking at them, Yoe had no idea whether he had made his nanowires. So, Yoe looked at the disks with a super-powered microscope called a scanning electron microscope. These microscopes are WAY more powerful than normal visible-light microscopes, and they look like this on the inside.

Super high tech!!!!

Not all of the steel disks had nanowires on them, but one of them had millions and millions of them! They were everywhere!! Yoe was super-psyched!!! The nanowires looked like this at 1,500 times magnification (click to look at high-res version, seriously! Click!!!):

One of the steel disks that was hotter than the one shown above looked like total insanity!!! There were nano-sized wires, ribbons, spheres, and (if you look closely) corkscrews!! CLICK THIS IMAGE!!!

Yoe zoomed in on another portion of this disk and even found a nanoBRAIN! This nanobrain is 300,000 times smaller than your brain!! Check it out!!!

Yoe the Scientist's Nanobrain.

Yoe thinks the nanobrain started out as a nanodroplet of liquid silicon. He thinks that as the silicon cooled down, the outside surface solidified first. Then as the inside of the nanodroplet cooled and shrunk further, the solid silicon shell crinkled up--kind of like how the surface of a grape shrivels up when it is dried out to become a raisin. This is also similar to how your fingers prune up when they're in water, though the mechanism for that is a bit different.

Here's what is kind of surprising. Yoe thinks the nanobrain and the insane jumble of wires and ribbons are really cool, but he is more interested in doing experiments using the nanowires shown in the first image. You may ask, "Is Yoe some sort of dummy? Why isn't he more interested in the awesomer-looking image and the nanoBRAIN??!?" Yoe is no dummy. He is making these nanowires to study how they will work in the batteries of the future, and he prefers the nanowires in the first image for two main reasons.

#1) There are a lot of them. Their abundance, in addition to their tiny size, will make for a more powerful battery. #2) They are all pretty much the same size and shape, which makes them easier to study. If he saw something awesome happen using the insanity in the second image, it would be difficult to determine whether it was caused by the nano-sized wires, ribbons, spheres, or corkscrews. Scientists love cool-looking stuff, but they also want to know answers--and these interests don't always overlap.

The moral of the story is, Yoe the scientist had successfully made his nanowires! Here he is, celebrating his success at science!!

This post also appeared on Chemistry-Blog.com.

Rosetta: Languages and Space Probes

noreply@blogger.com (LeeBee) — Tue, 03 Apr 2012 05:42:00 +0000

Linguists estimate that around 50% of the worlds languages will go extinct by the end of this century (ref). Just as John Hammond used the the DNA preserved in ancient dino-hungry mosquitoes to revive extinct dinosaurs in Jurassic Park...

...future generations may use the information encoded on a three inch disk, known as a Rosetta disk, to bring long-dead languages back to life. At least that's the idea. The Rosetta disk project was hatched by people at the Long Now Foundation, who used technology developed at Los Alomos National labs to miniaturize 13,500 pages of text from over 1,500 human languages onto a three inch disk of nickel. I like to think about these disks as language time capsules.

The teaser-side of a Rosetta disk. via the Long Now Foundation.

Shown above is the "teaser-side" of a Rosetta disk, which reads "Languages of the World: This is an archive of over 1,500 human languages assembled in the year 02008 C.E. Magnify 1,000 times to find over 13,000 pages of language documentation" in eight languages. This graphical teaser is necessary because the tiny writing on the opposite face is so small that it is nearly invisible to the naked eye!

The library of Alexandria, the largest collection of human knowledge of its time, burned to the ground around 48 BC. This was a HUGE bummer. If only the librarians had made duplicates!! With that in mind, the Long Now Foundation people have created multiple Rosetta disks. It is more likely that humanity's linguistic past will be preserved with multiple disks scattered across the globe, in the event that one country decides to go on a disk-smashing-binge.

In an abundance of caution, or perhaps because it is totally awesome, they have even sent a Rosetta disk into space!!! In February 2004 the European Space Agency (ESA) launched the aptly named Rosetta spacecraft, with a Rosetta disk on board. Wicked!!

However, the spacecraft's primary mission is not to carry this nickel disk into space, but instead to go visit a comet named 67P/Churyumov-Gerasimenko. Scheduled to arrive in May 2014, the Rosetta spacecraft will not only make the first long-term observations of a comet, but it will even send down a lander to get humanity's first up-close-and-personal glimpse! As you can see from the image below, we have a lot to learn!!!

But what about the disk? Why not just upload a file with the Rosetta disk information onto the spacecraft's computer? Before I answer that question, ask yourself how long you expect the hard-drive on your current computer to last. A few more years if you're lucky. Not long! Digital stuff breaks and its information is almost inevitably corrupted. Perhaps more troubling is the fact that digital formats change, making information stored in a previous format unreadable. How long do you think it would take you to access the information on this 5.25" floppy disk? Pretty long, and they've only been obsolete since the 1990s!

So, the idea is that information physically written out has the best chance of surviving the test of time. Miniaturization was necessary due to the incredible amount of information the Long Now people wanted to preserve. Unfortunately the information written on the Rosetta disk also has an expiration date. It is only expected to last around 2,000-10,000 years, according to the Long Now people. As the nickel atoms obey the 2nd law of thermodynamics and ever-so-slowly shift around in random directions on the disk surface, the letters they comprise will lose their shape. Bummer!! The disk will get to tour the solar system 300-1,500 times along the comet's 6.6 year orbit of the sun before becoming unreadable.

Regardless of its legibility, the Rosetta disk, that relic of our curiosity, our sense of posterity, and our very existence, will probably be flying through space for a very, very long time. A likely scenario for its demise would begin with the comet making a close encounter with a planet or other huge object. This could knock the comet off its orbit and send it careening into the sun where it and its Rosetta buddies will be turned into a plasma. That kind of thing happens all the time, and was even recently captured on video (source)!!!

I'm going to be a downer here at the end and point out that the odds of human or non-human people finding this disk on the orbiting comet are astronomically small. But it is still awesome!!

If you would like to know a bit more about the Rosetta space mission, check out this awesome video:

Also, I first learned that this space mission carries a Rosetta disk on the Long Now Foundation's podcast, which you should DEFINITELY check out.

Lemurs! Aye-ayes! Mammal woodpeckers!????!

noreply@blogger.com (LeeBee) — Tue, 13 Mar 2012 05:42:00 +0000

Prepare to be assaulted by cute pictures and amazing discoveries! By the end of this post you will never look at the mammal world in the same way.

As I walked into the lemur enclosure during my discovery-filled visit to the Duke Lemur Center as part of the Science Online 2012 conference, I was impressed not only with the lemurs' musky odor but also with their piercing eyes. So intense, so seemingly interested!

Coquerel's Sifaka (mother and child) living large at the Duke Lemur Center. via their Blog.

I was privileged with such an up-close view because the lemurs were in their indoor/outdoor enclosures to escape the chilly North Carolina winters. Lemurs are accustomed to the warmer tropical climate of their home island Madagascar.

The Duke Lemur Center houses the largest colony of lemurs outside of this island nation, and as part of their research and conservation efforts they make sure their lemurs have ample opportunity to "make the sex" (procreate). In fact, I visited in January at the very heart of Coquerel's Sifaka birth season. This unstoppably cute Coquerel's Sifaka baby was born just days before I visited.

I dare you to find a cuter pro-simian primate picture!! via Duke Lemur Center Blog.

Understandably, they wouldn't let me anywhere near the babies, but they did show me these two photos. The puffball of adorableness on the left is a pygmy slow loris (not a lemur, but related) and the craziness on the right is my favorite lemur, an aye-aye. Can you believe the contrast?!

Baby Battle: Pygmy Slow Loris vs. Aye-aye

Cute/crazy-looking babies are only the beginning of the wonders of the lemur world. By studying lemurs' DNA and that of other primates, scientists can tell that lemurs and other African primates parted evolutionary ways around 65 million years ago. Here is what earth looked like back then. No Himalayas!

This was long after Madagascar split off from mainland Africa around 160 million years ago. This fact along with some fossil evidence from Madagascar means that lemurs must have somehow traveled to the island from eastern Africa. The current best guess for how that happened is on rafts of floating vegetation (ref). That's right! Imagine relaxing one sunny day on a luxurious but tenuously attached riverside vegetation mat and BAM, you're off to Madagascar where your DNA will help form a brand new primate suborder.

Madagascar's isolation, diverse range of habitats, and lack of big scary predators have allowed lemurs to evolve into a crazy variety of ecological niches--some not typically associated with mammals. This is why the aye-aye is my favorite lemur, because it is the woodpecker of the mammal world.

Not a mammal. via WrenWorks.

The main adaptations it has developed in order to fill this niche are its crazy big ears...

57-day old baby aye-aye. via Duke Lemur Center Blog.

...crazy big teeth...

Aye-aye skeleton. Crazy big teeth. Aye-ayes are the only primate whose teeth continue to grow throughout their lives. This caused scientists to initially misclassify them as rodents instead of primates. via Mammalian Species.

...and crazy long thin fingers.

Look at those fingers! via David Haring.

Notice the extra creep-tacular middle finger! The aye-aye uses this terrific trio of adaptations to tap on trees and listen/feel for the hollow tunnels made underneath the bark by wood-boring beetle larvae. Once located, they gnaw their way in...

Intently gnawing aye-aye. via David Haring.

...and extract their meal with their extra spooky finger (extra spooky stare optional).

Aye-ayes! Woodpeckers of the mammal world! They're AMAZING! In case you remain unconvinced of their awesomeness, I leave you with this:

Clams' Insane Molecular Diversity

noreply@blogger.com (LeeBee) — Tue, 28 Feb 2012 17:53:00 +0000

When I tell people I am a chemist the most common response is, “Oh man, I hated that in school, especially organic chemistry!” That's an unfortunate but reasonable response. Trying to understand these tiny things called molecules that are impossible to see can be kind of like learning about a never-to-be-seen dimension in which up is down and left is orange.

Thinking about chemicals can be very disorienting. Image via Andrew Lipson.

I love chemistry though because the shapes of these molecules scribbled on the chalk board actually have consequences that we can see in the world. The changing color of leaves on the approach of winter is caused by actual changes in the structure of the matter of which those leaves are made. The effects of the diversity of molecular shapes in the world around us can actually be SEEN with our eyes!

Green and yellow leaves on the Katsura tree with the chemicals responsible for those colors (chlorophyll a and yellow-chlorophyll-catabolite, respectively). Image and knowledge via Krautler et. al.

When someone tells me they are a biologist my most common response is, “Oh man, biology is so complicated!” It seems so daunting to me to move beyond a simplistic description of aspects of life such as "chemical X results in color Y" and actually try to understand the nearly unfathomable diversity of chemicals that come together to make each living thing unique.

Not to scale. Clams are way bigger than DNA, which is way bigger than water.

I am certainly not capable of crafting a simple yet complete description of how the shapes of the molecules that make up living things contributes to those things' visible shapes, sizes, and colors.

Fortunately, where my scientific brain fails, an artistic brain succeeds. Video artist and experimental animator David C. Montgomery has created a beautiful video capturing the diversity of shapes, patterns, and colors that are present within several different species of life. When watching this video (full screen it!!), try and think about how all of the differences you see are caused by differences in the shape, arrangement, and composition of the unimaginably tiny and diverse molecules of which the living things are composed.

LIFE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Experiments at Home #2 - "Skillet Control Oven"

noreply@blogger.com (LeeBee) — Tue, 14 Feb 2012 03:14:00 +0000

In my last post I showed how my skillet was coated in liquid after a short stay in my pre-heating oven. I guessed that the liquid was water and that it came from the burning of natural gas. Though I was quite confident in my guess, I admitted I hadn't done any other experiments to show that the liquid actually was water.

Thankfully, The Second Criterion blogger Jenny pointed out that while my oven produces heat by burning natural gas...

This is my oven! Definitely try this at home!!!
If you want to know why the flame is blue, check out this post.

...hers works by running electricity through a metal wire. This heats the wire in a process known as resistive heating, first made famous by the incandescent light bulb.

Here is what the resistive heating coil looks like in Jenny's oven. Look at that color!

Importantly, electric ovens do not produce any water. Jenny proposed simply repeating my skillet experiment in her electric oven. If the skillet is covered in liquid after a trip into her oven, this would be pretty strong evidence against my water-from-combustion hypothesis. If there is no liquid, then my hypothesis still stands.

Fast forward to Jenny's apartment--here is a picture of the initial appearance of the skillet:

Here is Jenny putting the skillet into her oven:

Jenny gets super psyched about experiments too!!!!

We turned the temperature up to 350 degrees Fahrenheit,

and set the timer for 3 minutes.

After 3 minutes we opened the oven and were quite alarmed to find a black cat trying to put a hex on our experiment.

"Who gave you permission to do science in my kitchen??"

Being good scientists though, we put our superstitions at bay and observed the appearance of the skillet.

Behold! No liquid on the skillet!

The liquid from the gas oven experiment was probably water from burning natural gas! I'm sure there are more experiments we could do though. Any ideas?

Finally, even though these experiments covered something relatively trivial, I think the process provides a good example of how science actually works. I observed liquid on the skillet and proposed the hypothesis that the liquid was water from combustion. I shared this hypothesis and other people suggested some followup experiments. You may have a vision of a scientist being alone in her lab spewing out discovery after discovery, but science works much better and is much more fun when you share your results and thoughts with other people.

In my experience, four very useful things happen when scientists talk:

1 - Immature jokes are told (most often about farts).

2 - Scientist A suggests why Scientist B is wrong about something.

3 - Scientist A proposes followup experiments or possible interpretations for Scientist B's results.

4 - More fart jokes.

This is what it looks like when scientists hang out! Hi pals!

Related Link: This is What A Scientist Looks Like

Experiments at Home #1 - "The Skillet Mystery"

noreply@blogger.com (LeeBee) — Tue, 31 Jan 2012 05:22:00 +0000

In my ever-continuing quest to become an actual adult, I have recently begun to cook. I use a real oven and everything!

In my usual encounter with the oven it takes just a few minutes of pre-heating before I realize that I have yet again left the big skillet inside. Panicked, I pull it out of the oven, and notice something weird! Finally I decided to repeat the skillet-in-the-oven experiment and document my findings. Here we go!

Step #1--observe the condition of the skillet before its trip into the oven.

Step #2--place the skillet in the oven.

Conducting experiments gets me super psyched!

Step #3--turn the oven temperature up to 350 degrees Fahrenheit and set the kitchen timer to 3 minutes. Note: experimental conditions chosen semi-arbitrarily.

Step #4--remove the skillet from the oven and observe its condition.

Observation #1: The skillet is cool to the touch.
Observation #2: It's covered in water!!!!

If you're not convinced, here is a before and after shot.

Water has clearly condensed on the pan after its 3 minute trip into the pre-heating oven.

After a few times seeing this same thing, I finally stopped to ask myself, "Why in the hell is this skillet covered in water???" Got any guesses for what's going on?

Here's my hypothesis. Ovens create heat by burning natural gas, which is composed primarily of methane. When methane is burned it produces carbon dioxide and WATER:

The same thing happens when any other hydrocarbon (gasoline, diesel, propane, etc) is burned. This is why you sometimes see water coming out of the exhaust pipe of cars.

So the oven flame was producing water, but why does it coat the skillet? Well, after only 3 minutes in a pre-heating oven the skillet was still cool to the touch. So, when the water vapor from the hot hot flame came into contact with the cool skillet, it lost enough heat to turn back into liquid water. Kapow! Wet skillet!

Mind you this is just my hypothesis, but I'm fairly certain its correct. Actually proving something in a scientifically rigorous manner is my day job and is painstaking work, so I prefer to spend my free time in "hypothesis wonderland." Welcome to my secret place!

Any skeptics out there, feel free to offer alternative hypotheses (dragon juice? unicorn blood?).

Related Post: Experiments at Home #2 - "Skillet Control Oven"

I Am a Scientist! - part 2

noreply@blogger.com (LeeBee) — Tue, 17 Jan 2012 04:02:00 +0000

I am a scientist. Here is me pretending that life in lab is just as I had imagined it as a child...lab coat, frizzy hair, flasks of colored solutions, smoke, and all:

Erlenmeyer flasks are my favorite piece of laboratory glassware.

Here is what lab is actually like most of the time...hunched over a desk, reading papers, trying to understand what the results of my experiments mean and what I should do next:

Sitting like this at your desk will destroy your back. Trust me!

Realizing that a scientific life only occasionally involves crazy explosions and bright lights was initially disheartening. However, I have enjoyed making discoveries and doing things nobody else has done before. For example, I was the first person on the planet to make this molecule. Wild, right?!

This didn't exist before I made it!!

The best thing about being trained as a scientist is that it has allowed me to more fully understand and appreciate the world around me. I started this blog in part to share that sense of wonder, and it has allowed me to learn-about/write/share all sorts of stories about pee, fire, helium, nuclear radiation, etc.

Another amazement-sharing outlet is giving science demonstrations in elementary school classrooms. The kids get most excited (as do I) about the demonstration at the end involving orange, green, and pink flames.

A solution of lithium chloride in methanol sprayed into a flame. Try this at home only after growing a big beard that your girlfriend hates. Just kidding, don't try this at home.

As time has gone by I have become less interested in pushing the boundaries of knowledge through research and more interested (perhaps selfishly?) in pushing the boundaries of my own knowledge by reading about other people's research.

Knowledge feels good.

My problem is that research, not learning/communication, currently pays the bills. How do I switch this around? Perhaps I could be blogging differently, or using another medium...the possibilities are endless!

With the goal of starting to figure this out, I am attending a conference in North Carolina for like-minded science enthusiasts/communicators this week called ScienceOnline2012. I am SUPER psyched! I hope I will learn how to improve what I do on this blog, discover new media/venues, meet buttloads of people/collaborators, and maybe even figure out how to get paid someday! We'll see what happens!!

Stay tuned for ScienceMinusDetails2012 upon my return. Topics covered will include fart/poop science, experiments you can do at home, and nano brains. Get psyched!

Any topics you want to learn more about or suggestions for what to do with my life?? Please leave them as comments! :-)

Related/Rehashed Post:

I Am a Scientist! - part 1

Feynman on Flowers

noreply@blogger.com (LeeBee) — Tue, 13 Dec 2011 14:00:00 +0000

I had planned to post my favorite quote from one of my favorite scientists, Richard Feynman, when I discovered that the fine folks at the Sagan Series had already set it to images and music. Its the first passage in the video, and it communicates way better than I could one of the main reasons I love science. Enjoy!

And for those script-lovers in the audience:

I have a friend who’s an artist and he’s sometimes taken a view which I don’t agree with very well. He’ll hold up a flower and say, “Look how beautiful it is,” and I’ll agree, I think. And he says—“you see, I as an artist can see how beautiful this is, but you as a scientist, oh, take this all apart and it becomes a dull thing.” And I think that he’s kind of nutty. First of all, the beauty that he sees is available to other people and to me, too, I believe, although I might not be quite as refined aesthetically as he is; but I can appreciate the beauty of a flower. At the same time I see much more about the flower than he sees. I can imagine the cells in there, the complicated actions inside which also have a beauty. I mean it’s not just beauty at this dimension of one centimeter, there is also beauty at a smaller dimension, the inner structure. Also the processes, the fact that the colors in the flower evolved in order to attract insects to pollinate it is interesting—it means that the insects can see the color. It adds a question: Does this aesthetic sense also exist in the lower forms? Why is it aesthetic? All kinds of interesting questions which shows that science knowledge only adds to the excitement and mystery and the awe of a flower. It only adds; I don’t understand how it subtracts.

Richard P. Feynman (1918-1988)

P.S. Do yourself a favor and go read "Surely You're Joking Mr. Feynman!" Adventures of a Curious Character.

"The Shape of It All" or "Dr. Licorice Explains Why Bisphenol-A is Scary"

noreply@blogger.com (LeeBee) — Tue, 22 Nov 2011 12:00:00 +0000

I recently made a chemical that smelled extremely familiar, but after numerous wafts, I couldn't quite tell what it reminded me of.

Me wafting the chemical I made. The chemical is the tiny bit of brown oil in that small clear jar in my left hand.

This puzzle went unsolved for days until my labmate Michelle used some of the chemical and was like, "Lee, have you noticed how that chemical you made smells just like licorice?"

I was like, "OMG, you solved it!!!!"

Victory Licorice!!!

Of course, the next thing I did was find out what chemical gives licorice its smell. That is when I became super psyched. The chemical in licorice is called anethole, which is shaped super-similarly to the chemical I made!

Even though they are made of different atoms, the similar shape of these two chemicals is almost certainly why they smell the same. DISCLAIMER: I have done no experiments to prove this, so this is just my hypothesis. However, the validity of my hypothesis is supported by one of the pillars of modern biology, often described as form follows function. Namely, the way things act in biological systems is directly related to their shape. This is of course an oversimplification, but a powerful one nonetheless. To make matters a bit more complicated (but more amazing!!), many scientists think our sense of smell not only senses chemicals' shapes but also how they vibrate! See comments section below for more details.

How does this "form follows function" thing actually work though?? One of the primary ways is when tiny molecules (like those drawn above) fit snugly into tiny pockets of big proteins (like the smell receptors in your nose). When this molecule-protein match is made all sorts of crazy things can happen. In addition to smell, this is how adrenaline makes peoples' hearts go crazy and viagra makes dudes' penises go crazy.

Adrenaline or viagra? You be the judge.

Pharmaceutical companies spend much of their time making differently shaped molecules until they find one that fits just right into the desired protein. Below is an image of that happening. In this case, the molecule squeezing into a pocket of the protein causes cancer cells to age and die--all because of the relative shapes of the molecule and protein. Amazing!

Image of a drug called nutlin (the small green stick-looking thing) fitting into a pocket of a protein called MDM2 (the big blobby-looking thing). via bioscience.org.

Sometimes companies make new molecules and they just accidentally happen to be the right shape to fit into certain proteins. This is the case with the chemical Bisphenol-A, or BPA. BPA is similar in shape to estrogen molecules, so it fits into proteins in your body into which estrogens also fit. Here is BPA side by side with the estrogen known as estradiol.

They may not look too similar, but 3D models make the similarities more clear. Also it turns out the portions highlighted in blue are the ones that interact most strongly with estrogen-related proteins in the body, and those blue portions are pretty much exactly alike. This is why BPA is known as an estrogen mimic, because its shape allows it to act very similarly to estrogen in the body.

Estradiol and other estrogen molecules are known as hormones, because they interact with our bodies' endocrine system. Our endocrine system is super-duper fundamental to our existence and is responsible for a wide variety of extremely important bodily functions. When something is wrong with our endocrine system it can cause crazy things to happen like the development of diabetes, obesity, buttloads of cancers, and tons of sexually-related changes, just to name a few.

Endocrine system organs.
Also, first nudity on Science Minus Details ever! You are witnessing it!

Our endocrine system is exquisitely sensitive to tiny amounts of hormones. This is one reason why BPA acting like a hormone is so scary, because you don't have to be exposed to much of it for it to have an effect. This is especially so during early development (fetuses, babies, children). One team of researchers found that pregnant women with higher levels of BPA in their urine during pregnancy were more likely to have children that were hyperactive and aggressive (ref). BPA can potentially change the way your children act for life!!!!* Call me alarmist, but come on, that is super intense! Adults are not immune either, as male workers in a factory producing BPA were found to have reduced sexual desire, reduced satisfaction with their sex life, and increased risk of erectile and ejaculation difficulty, relative to a non-BPA-exposed control group (ref). Erectile dysfunction! Mega bummer!

But you don't have to be a factory worker to be exposed to BPA. Aside from being found in those polycarbonate bottles from which everyone has (hopefully) stopped drinking, BPA can also be found in canned foods and even cash-register receipts! (ref, ref, ref) This chemical is everywhere, including in your body! Studies have shown that up to 95% of people in the united states have BPA in their body (ref).

"Would you like paper, plastic, or a messed up endocrine system?"

I could go on and on about this, but I'll stop by saying that BPA is just one in a class of chemicals known as endocrine disruptors. These are in all sorts of consumer products, from rubber duckies (!!!) to couches and other furniture. Wowza!

Instead of ending on a down-note, let's talk about how crazy, confusing, and amazing the universe is. THC (the chemical in weed, duh) fits snugly into proteins in your body known as cannabinoid receptors, and this results in the sensation of being "high."

mmmmmmmm, activated cannabinoid receptors...

Your body makes its own chemical that fits snugly into your cannabinoid receptors too. Based on what I've told you so far, you would predict that this chemical would be shaped kind of like THC. However, in 1992 researchers discovered that it looks waaaaaay different (ref). So, sometimes things of different shape can end up acting in a similar way in your body. Biology is pretty complicated!!! Here are the two molecules side-by-side.

The "anand" in anandamide is the sanskrit word for bliss. Scientists are cool!

In summary, the shape of molecules is super-duper important to how they behave in your body. However, just when you think you have things figured out, life throws you a weed-laced curve ball to remind you how how awesome the universe is. That's all folks!

Further reading on endocrine disruptors:

Awesome book, great for non-scientists and scientists alike:

Our Stolen Future: Are We Threatening our Fertility, Intelligence, and Survival?--A Scientific Detective Story

Awesome technical literature reviews:

Epigenetics, Evolution, Endocrine Disruption, Health, and Disease

Bisphenol-A and the Great Divide: A Review of Controversies in the Field of Endocrine Disruption

Endocrine Disrupting Chemicals Targeting Estrogen Receptor Signaling: Identification and Mechanisms of Action

Large Effects from Small Exposures. I. Mechanisms for Endocrine-Disrupting Chemicals with Estrogenic Activity

The Steroid Hormone Biosynthesis Pathway as a Target for Endocrine-Disrupting Chemicals

*This study is still ongoing. Data only exists for the children at two years of age. Also, this study only shows a correlation, but data exists in lab mice that shows causation. So come on.

Asteroid Particles

noreply@blogger.com (LeeBee) — Tue, 08 Nov 2011 13:20:00 +0000

Recently the Japanese Aerospace Exploration Agency sent a spaceship to an asteroid named Itokawa. A spaceship to an asteroid!! As if that wasn't awesome enough, the spaceship landed on the asteroid, collected material, and returned home to earth! These are images of tiny particles collected from the surface of that asteroid.

These particles are around half the diameter of a human hair. Click to make them HUGE!

Here are three views of Itokawa, which is about 630 meters x 250 meters. Assuming a spacesuit didn't slow you down, and the surface of the asteroid were boulder-free and easy to walk on, it would only take you ~20 minutes to walk around the whole thing the long-way. Pretty small!!

Click to make them HUGER!

Even though the asteroid is small and the asteroid particles are tiny, there are still some cool orders-of-magnitude involved in humans' study of these objects. Check it out. Holy crapola!

Relative to bottom image, the middle is a ~100x zoom, the bottom is a 100,000x zoom.

Think about it!!

Aside from that coolness, this is cool because it is the first time humans have collected material from an asteroid. First time, ever! The last time something similar was done was during the Apollo program four decades ago! About time!

Why go through all this trouble for these tiny asteroid particles, you ask? Well for one thing the more we know about asteroids, the more well-equipped we are to avoid a getting hit by one and in the process becoming extremely dead (as a species). This may seem far-fetched, but we're pretty sure it has happened before, and there is no reason it can't happen again.

T-rex, really pissed off about his imminent demise. Triceratops, resigned to his/her fate (or maybe already dead from the T-rex).

An image of the chicxulub crater, thought to have been caused by the asteroid that brought about the demise of the dinosaurs. This is not a visible image, but an image of the gravity distortions caused by the asteroid impact.

By measuring the density of Itokawa, this Japanese mission showed us that this asteroid is more of a rubble pile than a solid object. If you were trying to deflect a 600 meter-long rubble pile or a 600 meter-long solid mass from hitting earth, you would probably use slightly different tactics. Now we know with more certainty what these types of asteroids are and can start planning!

Aside from saving earth, here's what gets me psyched about the mission to study Itokawa. Most of the objects in the asteroid belt are leftovers from the very beginning of the solar system. They have never reached sizes large enough to cause them to melt and allow their heavier elements to sink to their cores, as happened with earth and the other planets. These asteroids really are the leftovers of the cosmic soup from which the solar system was born. How cool that this stuff is still around and that humans went and brought some back to earth! For more on what scientists are learning from these asteroid particles, go here and here.

Here's what gets me MEGA psyched: Space particles -- brought back to earth so we earth particles (aka humans) can use our eye/brain particles (aka eyes) to learn more about the nature of our solar system and how we got here! Earth particles investigating space particles in order to better understand themselves! And there are pictures!!!

I'll leave you with this video of the Japanese Hayabusa probe bringing these asteroid particles back to earth. You will see the probe slamming into our atmosphere, whereupon most of the spacecraft was vaporized, leaving the heat-shielded capsule (which is hard to see since its not burning up) to land safely in the australian outback.

Also here's a photo of the scientists documenting their recovery of the capsule. That capsule was on an asteroid!!!

Science!!!!!!!!!!!!

Why Pee is Cool - entry #6 - "Pee, Our Connection with the Earth's Metabolic Cycle"

noreply@blogger.com (LeeBee) — Tue, 25 Oct 2011 12:38:00 +0000

Here, in the final PeePeePost, is where we bring all we have learned together and find out how the act of peeing unites us with our planet.

Any form of life that we know of needs two basic things. The first is matter, as life has to be made of something. The second is energy, so life can do something with that matter (e.g., move around, reproduce, watch trailer park boys). Most life on earth gets its energy from the sun. All life on earth gets its matter from...from earth, duh!

As we learned in the last PeePost, the atoms in your body are no different from the atoms in rocks/oceans/air/etc. Additionally, the composition of our bodies is close-ish to that of the earth's crust!!

Graph of abundances of chemical elements in the earths' upper continental crust. We are made mostly of the really abundant stuff in the upper left (e.g., oxygen, carbon, hydrogen, etc.)

Because of those two facts, I like to think of any kind of earth life as little tiny earth particles--walking, talking, peeing, sometimes neighborly little chunks of the earth's crust.

Humans are earth particles.

These earth particles are constantly using earth's atoms, moving them around, changing them from one chemical to another. This, with a lot of help from non-living things like evaporation and gravity, results in atoms moving all around the earth. In this process, the atoms will spend time in all sorts of lifeforms, and they will even spend time in non-living things like rocks, the oceans, and our atmosphere. The movement of a molecule or chemical element in this way is known as a biogeochemical cycle. The most well-known biogeochemical cycle is probably the water cycle:

One thing this image doesn't capture is plants and animals changing water into oxygen and back again.

The water cycle is super-complicated, but basically involves water evaporating from the oceans, falling out of the atmosphere as rain, and letting gravity pull it back to the ocean through rivers and groundwater. I like to think of this as the continents' way of taking showers.

The coolest thing about biogeochemical cycles like the water cycle is that WE participate in them! Every time you pee you are putting yourself somewhere in that cycle. So if you live in a place like California, where people drink water pretty directly from precipitation, when you pee the water goes via the waste-water treatment plant to lakes and streams and eventually into the ocean. That looks like this:

So we know that water is in our pee, but what else is there? In PeePee Posts 2, 3, and 5 we talked about nitrogen being in our pee. The nitrogen cycle is really cool! It starts with nitrogen atoms in the atmosphere in the form of N₂. Plants need nitrogen atoms to survive, but they can't use the abundant N₂ from the air. So, these awesome earth particles called nitrogen-fixing bacteria take electrons from chemicals like sugars, dump them into N₂, throw in some protons and energy, and form the ammonium ion (NH₄⁺). Other organisms then change the ammonium ion into the nitrate ion (NO₃^-).

Now those things (NH₄⁺ and NO₃^- ions), plants can use. They take either ion and incorporate them into proteins and other parts of their body. We then eat plants' bodies and pee their nitrogen back out as urea, which gets turned back into ammonium ions. Eventually the nitrogen goes back into the atmosphere, completing the cycle. Here is the nitrogen cycle. Check us out!! Peeing!!! We're part of it!

Notice the big factory on the right. In the early 1900s, we humans figured out how to turn N₂ into NH₄⁺, just like the nitrogen-fixing bacteria do! This was a STUPENDOUS discovery! Today this process accounts for 1-2% of all the worlds energy usage!! Its use on such a gigantic scale has altered the nitrogen cycle in ways that could take centuries to calm back down to a steady state. (awesome article here) What effects this will have on life on earth are not at all clear. Scary!

Humans imitating plants in this fertilizer factory in Billingham, England. Photo courtesy addictive picasso.

In PeePee Post 4 we learned that phosphorus is also in our pee. The phosphorus cycle is cool because it is MEGA MEGA slow. As opposed to the nitrogen and water cycles, which can move through the atmosphere, the phosphorus cycle moves through the earth!!!!

Here's how it happens. Mountains containing phosphorus in the form of chemicals called phosphates are slowly eroded by rain and wind. On the way down the mountain the phosphates are used by plants and animals in things like their DNA or bones. The phosphorus atoms continue their slide down the mountain, eventually reaching the ocean where organisms use them some more. However, eventually the phosphorus atoms fall all the way down to the bottom of the ocean! You might be thinking that this pathway from mountains down to the bottom of oceans seems more like a one-way trip and less like a cycle. So what completes the cycle? Mountain formation!!!! This brings the phosphorus from the bottom of the ocean back up onto land, and as you might imagine it takes a LONG TIME! (awesome review here)

There we are, participating in the cycle by eating plants and other animals, and peeing out their phosphorus atoms. Just as with the nitrogen cycle, we humans have discovered ways to drastically change the way this cycle works. We do this by mining huge phosphate deposits for use as fertilizer. There are enough phosphate deposits for us to keep doing this for a long time, but if we want to keep going like this eventually we are going to have to mine the bottoms of the ocean or wait for mountain formation to catch up. As with many of our experiments on what earth systems can handle, the long-term consequences of our actions are unclear, but the preliminary data is enough to freak me out.

Anyway, check out this insanely huge phosphate mine in India.

Phosphate mine in Jhamar Kotra, India. Apparently it is common in the mine to find fossils of the mega-ancient stromatolites that helped form this phosphate deposit. Photo via Geology Rocks!

This mine is so big you can actually see it on google maps!

View Larger Map

It's not all doom and gloom though. Even though I find it scary how significantly our industrial practices are affecting earth's biogeochemical cycles, I still think it is awesome that when we pee we are naturally participating in these cycles. We participate in all sorts of other biogeochemical cycles when we pee (potassium, sulfur, etc). All life on earth is connected via these cycles in one way or another. Give that some thought next time you're peeing. You are participating in the earth's metabolic system!

Related Posts:

PeePeePost #1: "Why Is Pee Yellow?" or "Rainbow of Urine"
PeePeePost #2: "Why Does Pee Smell?" or "Aroma of Life"
PeePeePost #3: "Explosive Urination" or "Gunpowder Comes from Pee!!!"
PeePeePost #4: "PeePee Portal to Phosphorus" or "What the Alchemists Did Right"
PeePeePost #5: "How Pee Unites You With Rocks"

Why Pee is Cool - entry #5 - "How Pee Unites You With Rocks"

noreply@blogger.com (LeeBee) — Tue, 11 Oct 2011 12:45:00 +0000

From around the 2nd century onwards, many people subscribed to the doctrine of vitalism. For alchemists, vitalism primarily meant that matter from the inorganic, inanimate world (crystals, rocks, etc) was fundamentally different from matter from the organic, living world (us, kittens, pee, etc). Specifically, they believed that that non-living matter could not be transformed into living matter. Vitalists held that the matter of life, the chemicals that compose living things, could be synthesized only by living things themselves.

In 1828 a German chemist named Friedrich Wöhler made a discovery that bridged the divide between living and non-living matter, and the story of how he did this starts of course with pee.

Friedrich Wöhler. German chemist/peepee enthusiast and 1828 blower of minds.

One liter of human pee contains about 20 grams of a nitrogen-containing chemical called urea. Where does all this nitrogen come from? Well, from the plants and animals we eat of course! Their bodies contain nitrogen atoms mainly in the form of proteins, which they use for all sorts of things. We pee out urea in order to dispose of all these nitrogen atoms--atoms that go in must come out.

We eat nitrogen atoms mainly in the form of protein, use them for various things, then eventually pee them out in the form of urea.

This may seem very simple now, but let's travel back in time to the 18th century when people knew waaaay less. Sometime around 1727, Dutch scientist Herman Boerhaave was playing around with pee and became the first person to isolate urea. His recipe called for boiling off all the water from "fresh, well-concocted urine of persons in perfect health" until it reaches the consistency of "fresh cream". After squeezing out every last drop of liquid from this fresh-cream-of-urine, he put it "into a tall cylindrical vessel...for the space of a year". Such patience! After that year, the paste had turned into a solid mass on the bottom of the cylinder with some sort of mysterious oily substance on top. He discarded the oil and rinsed the crystals with cold water to remove all the salts (NaCl, etc), leaving nearly pure urea that he then recrystallized from hot water to give the pure stuff.

Boerhaave's insane recipe for the isolation of urea from urine. Please do try this at home. On the right is a wicked microscope image from this recent publication in which they grew their crystals from water just like Boerhaave did almost 300 years ago!!!

So now people knew about urea, a pure substance that had something to do with animal life. Still no philosopher's stone though, bummer. Over the years people re-discovered urea and came up with better ways of isolating it from urine, so that any reasonably well-trained (al)chemist had access to the stuff.

Now what? Well, as I said in 1828 Friedrich Wöhler came along and blew peoples' minds, that's what!!! Instead of playing around with chemicals from the organic, living world, he was playing around with chemicals from the inorganic, dead world. One day he was trying to do a simple reaction known as a salt metathesis between two chemicals known as inorganic salts. He expected the ions in these inorganic salts to simply change places:

To his great surprise however, he isolated a chemical that behaved suspiciously like urea.

After doing a few experiments on his synthetic urea side by side with urea isolated from animals, he concluded he had indeed made a chemical from the living world out of a chemical from the non-living world.

After this discovery, Wöhler wrote to his mega-famous mentor Jöns Jacob Berzelius (1779-1848) and said:

I must tell you that I can make urea without the use of kidneys, either man or dog.

So understated! Ultra-famous, mega-old chemist Justus von Liebig (1803-1873) struck a more momentous tone:

[The] extraordinary, and to some extent inexplicable, production of this substance without the assistance of the vital functions, for which we are indebted to Wöhler, must be considered one of the discoveries with which a new era in science has commenced.

The living and non-living worlds had been bridged for the first time in human history. Our atoms are indistinguishable from the atoms of the rest of the earth. WOAH!!!

This discovery did not however cause vitalists to completely give up and admit that living beings can in principle be fully explained through an understanding of their physical nature. Instead vitalism itself gradually morphed into something that is more recognizable to us today. Though many different people think many different things on this subject, Kurt Vonnegut summed up a view that seems pretty reasonable to me in his book "Breakfast of Champions":

Our awareness is all that is alive and maybe sacred in any of us. Everything else about us is dead machinery.

References & further reading: here, here, here, & here.

Related Posts:

PeePeePost #1: "Why Is Pee Yellow?" or "Rainbow of Urine"
PeePeePost #2: "Why Does Pee Smell?" or "Aroma of Life"
PeePeePost #3: "Explosive Urination" or "Gunpowder Comes from Pee!!!"
PeePeePost #4: "PeePee Portal to Phosphorus" or "What the Alchemists Did Right"
PeePeePost #6: "Pee, Our Connection with the Earth's Metabolic Cycle"

Why Pee is Cool - entry #4 - "PeePee Portal to Phosphorus" or "What the Alchemists Did Right"

noreply@blogger.com (LeeBee) — Tue, 27 Sep 2011 12:44:00 +0000

Travel with me back in time, when humans were first beginning to wonder things like "What the hell is the world around me made of anyhow!?" Picture yourself as an ancient alchemist, repeatedly trying in vain to figure out a way to turn anything into gold. You pretty much suck at doing science, but as a result of all your fool-hearty work you do know how to do things like mix, heat, and distill stuff. The first problem you face as an alchemist is that you need some substance to do experiments on.

Pee

It turns out that a pissload of alchemists spent centuries doing crazy experiments on PEE! They boiled it, they added stuff to it, they let it rot, they distilled it, etc. Finally, in 1669 one dude used pee to discover one of the most poisonous substances then known, a new glow-in-the-dark element he called phosphorus. Here is a dramatized picture of the alchemist/chemist/scientist (the distinction has never really been clear to me) Hennig Brand, attempting to discover the philosopher's stone, but actually discovering the chemical element phosphorus. What a good day in the lab!!!

The Alchemist in Search of the Philosophers Stone by Joseph Wright. Depiction is of Hennig Brand discovering the element phosphorus. The glow of phosphorus shown is 4sure exaggerated.

Nobody knew what a chemical element was at the time, but phosphorus turned out to be the 13th one ever discovered. Since then we have discovered 105 more! Phosphorus caused quite a stir upon its discovery in part because it glows (!!!), which I'm sure blew everyone's post-medieval mind! The light-producing mechanism is just like that from glow-sticks, and is known as chemiluminescence (not phosphorescence...confusing, huh?). In the case of phosphorus, it glows when it comes into contact with oxygen. It spontaneously combusts!

Phosphorus' love affair with oxygen explains why it primarily occurs in nature combined with four oxygen atoms, in a species known as a phosphate ion (PO₄^3-), which is pictured below. The negative charges on the oxygen atoms are balanced in our urine by positively charged ions like protons, sodium and ammonium to make things like disodium hydrogen phosphate (Na₂HPO₄).

The Phosphate Ion (not actual size).

Though we need phosphates in our bodies (for bones, DNA, and cellular communication), we pee them out simply because any atoms that enter our bodies (via eggs, milk, beans, etc) eventually have to leave (via pee, duh).

Why are we talking about phosphate ions in pee? Because it was the PeePee Phosphate ions that Brand turned into phosphorus.

Though Brand kept his recipe hidden for as long as he could, we now know that it required 121 gallons of urine (imagine 121 pee-filled milk jugs!!) to produce a single gram of phosphorus (1 small paper clip = 1 gram). So inefficient, but still a pretty good start! Brand's recipe was inefficient because it called for a number of steps we now know are unnecessary and/or wasteful. One of these steps called for letting the urine "lie steeping in one or more tubs til it putrify and breed worms". Worms!!!!

I will skip the details of Brand's insane method and summarize the simplified method that was developed by those who came after him. First, you gather all 121 gallons of urine and boil away all the water, leaving behind a thick syrup. You then combine that syrup with some sand in an old-school container known as a retort. At the end of the retort is usually some sort of collection flask, like the one you see glowing in the above painting and also in the scheme below.

Contraption to turn pee into phosphorus. Fully-assembled apparatuses like this are known as alembics, and are classic alchemical tools.

You then heat the crap out of the syrup/sand mixture, which performs two important reactions. The first is to turn the organic molecules in the pee syrup (amino acids, creatine, etc) into charcoal, which is basically pure carbon. This is just like burning a marshmallow on a campfire, and it happens in this case because of the high heat and low oxygen content inside the retort. In the second reaction the newly-formed carbon atoms steal the oxygen atoms from the phosphate ions, in turn forming elemental phosphorus! Other stuff happens with the sodium ions and sand, in an overall reaction that looks something like this.

Shout out to the chemists in the audience who spent more than 0.25 seconds on this graphic! :-)

Amazingly, this is essentially the same process used to produce phosphorus today, except calcium phosphate ore is used in place of pee and the carbon comes from coke instead of decomposed pee molecules.

Phosphorus then went on to have quite an impact on human history. Its toxicity and spontaneous-combustion properties led to its widespread use in weapons during World War I and later wars. Those same spontaneous-combustion properties also allowed phosphorus to revolutionize the match-making industry. Unfortunately, at the time of its discovery, phosphorus was the most toxic substance ever synthesized by humans. This meant that countless people in the public and especially the match-making industry died or were injured due to phosphorus exposure. Phosphorus exposure causes a horrible disease known as "phossy jaw" in which the afflicted person's jaw rots away. If the jaw is not removed quickly this condition leads eventually to death from organ failure. DARK! Chemicals can be dangerous, so we should all be careful when we create new ones!

Mega phossy jaw, housed in London's Hunterian Museum. via londonist.

As more and more people died from phosphorus matches, match makers went on strike and countries started banning them. New matches were invented that used the less toxic form of phosphorus known as red phosphorus. We have been talking about white phosphorus up until now. The only difference between the two is that the atoms are arranged in a different way, which among other things causes red phosphorus to be way less toxic than white phosphorus. Match technology marched on, read more here.

SUMMARY of INSANITY!!!: Alchemists, though they have a bad reputation now (undeservedly, imho), are responsible for the discovery of the element phosphorus through their weird experiments with pee. The way they figured out to make it is essentially the same way we make phosphorus today, and the manufacture of phosphorus went on to revolutionize the way we fought wars and started fires. All because of curiosity and pee!!!

Further reading: The 13th Element: The Sordid Tale of Murder, Fire, and Phosphorus by John Emsley

Related Posts:

PeePeePost #1: "Why Is Pee Yellow?" or "Rainbow of Urine"
PeePeePost #2: "Why Does Pee Smell?" or "Aroma of Life"
PeePeePost #3: "Explosive Urination" or "Gunpowder Comes from Pee!!!"
PeePeePost #5: "How Pee United You With Rocks"
PeePeePost #6: "Pee, Our Connection with the Earth's Metabolic Cycle"

Why Pee is Cool - entry #3 - "Explosive Urination" or "Gunpowder Comes from Pee!!!"

noreply@blogger.com (LeeBee) — Tue, 13 Sep 2011 12:45:00 +0000

So far we have learned what gives pee its color and smell, and now we will delve into the explosive way pee has changed the course of history. That's right, pee can be turned into an explosive!

To find out how we have to travel in our minds back to the beginning of human civilization--specifically, the domestication of animals. One thing that large domesticated animals like horses and cows produce in bulk is urine (pee pee!). When these animals are kept inside some sort of shelter, their pee seeps into the dry plant-less ground beneath their feet, where microorganisms turn urea into ammonia. The little pee-digesting organisms don't stop there though, they combine the ammonia with oxygen, eventually giving rise to the nitrate ion, in a process known as nitrification.

Nitrification:

Ammonia + Oxygen → Nitrates

NH₃ + 2 O₂ → NO₃^- + H⁺ + H₂O

Nitrification of Ammonia. Note: animals pee out urea, but microbes turn urea into ammonia, which then undergoes nitrification.

Those nitrate ions combine with other minerals in the soil (metal carbonates, for example) to make a mixture of calcium, magnesium, and potassium nitrates (I will refer to these as "metal nitrates"). More and more of these metal nitrates can accumulate over time due to the absence of nitrate-ion-consuming life such as plants in the soil of the animals' stables. Eventually the soil can become so saturated with metal nitrates that crystals of these substances grow beneath stable floorboards or along the walls of adjacent cellars.

Metal nitrates (a.k.a. saltpeter) being extracted from underneath stable floorboards by a "saltpeter man" or "peterman"

Metal nitrates (in this case 95% potassium nitrate) growing from the cellar wall of an old mill. source

You might ask "What does all this have to do with explosives?". We're getting there, trust me. Before humans could use the metal nitrates for really big and reliable explosives, they had to figure out how to purify them. The problem with the mixture of metal nitrates produced by nitrification of urine is that it gives a mixture of metal nitrates, when what you really want is potassium nitrate. The calcium and magnesium nitrates soak up too much water from the air, which diminishes their explosive potential. Arab scientist Hassan Al-Rammah (inventor of the torpedo) was one of the first people in history to leave a clear record of how to isolate pure potassium nitrate in his epically-titled 13th century text "The Book of Military Horsemanship and Ingenious War Devices" (!!!!). He described dissolving the metal nitrate mixture in water, mixing the resulting solution with wood ash (which has lots of potassium carbonate, as we discovered in this fire post), then filtering and crystallizing. Using wood ash serves to swap out all the undesirable calcium and magnesium ions from the crude metal nitrate mixture for desirable potassium ions from the wood ash, resulting in pure potassium nitrate. 13th-century chemistry used pee-breakdown products and wood ash! Insane!

People eventually figured out how to combine all the above processes into one, by setting up so-called "niter beds" (could not find a photo, interwebs please provide!!!!). These are beds of straw and wood ash, kept out of the sun to avoid plant growth, onto which buckets of urine are dumped periodically. The bacteria do their work, the wood-ash provides the potassium, and after a year or so, tiny crystals of relatively pure potassium nitrate can be seen growing from the top of the niter bed! Or, as Joseph LeConte put it:

As the heap ripens, the nitre is brought to the surface by evaporation, and appears as a whitish efflorescence, detectible by the taste.

What ingenuity humans have! Amazing! Also, tasting crystals that grew off a pee/straw mixture is pretty surprising!

Now that we have pure potassium nitrate, let's continue our trek towards understanding its use in explosions. The picture below is another way to think about nitrification, and it shows the HUGE volume of oxygen gas that it takes to make a tiny volume of nitrates. For this reason, you can think of potassium nitrate as if it is solidified oxygen. This is very important to why it is good for use in explosives.

A comparison of the volumes of reactants and products in the nitrification process. Roughly 200:1, if you want numbers. Nitrates can be though of as an extremely dense form of oxygen.

So why does "solidified oxygen" help with explosions? Most explosions are simply combustion reactions that happen really really fast. In normal combustion reactions, the rate at which something burns is limited by how fast the oxygen molecules can reach the flame. That is why blowing on kindling of a campfire helps it burn faster and brighter, because you are increasing the rate at which oxygen molecules reach the fire.

Young dude, increasing the rate at which oxygen molecules reach his nascent fire.

So, when you mix potassium nitrate ("solidified oxygen") with some sort of fuel (charcoal, for example) and set the mixture ablaze, the resulting reaction doesn't have to wait for the lazy lumbering oxygen gas molecules to arrive, because it has all the oxygen it needs right there in the form of the potassium nitrate. Therefore, the combustion occurs nearly instantaneously. Imagine taking all the energy that is released from a campfire throughout the course of an evening and releasing it all at once. That's right...KAPOW!!!!

Now this discovery didn't really revolutionize human civilization until we figured out how to use it to kill each other. Gunpowder is made by mixing potassium nitrate with two fuels (i.e. atoms that can combine with oxygen atoms and release energy), carbon (charcoal) and sulfur. The oxygen atoms leave the nitrates and move onto the carbon and sulfur atoms, releasing a buttload of energy. This process is so explosive because the "solidified oxygen" is turned into products that are mostly gases (carbon dioxide, etc). The gaseous products take up lots more room than the solid starting materials...which explains the KAPOW.

In order for this oxygen exchange reaction (aka explosion) to happen as quickly as possible (aka biggest explosion possible), you need to make sure each carbon and sulfur atom is very near a potassium nitrate molecule. This is why people who make gunpowder use these crazy ultra-mixing contraptions called ball mills:

This ultra-mixture is then so primed to undergo the oxygen exchange reaction that a small spark, amount of heat, or mechanical shock will set it off. The thing that sets off this reaction in modern guns is called a percussion cap.

MIND-MELT-RECAP: the dawn of agriculture gave us animal stables, which gave us LOTS of pee, which gave us metal nitrates, which we somehow learned how to purify, which eventually gave us the worlds' first explosives, which we eventually turned into gunpowder! Agriculture to cow pee to guns! Who knew?!!

Cool references:
"Some History of Nitrates" J. Chem. Ed. 2003, 80, 1393. link
"The Chemistry of Fireworks" RSC Publishing, 2000 link
"Chemical Technology in Arabic Military Treatises" Ann. N.Y. Acad. Sci. 2006, 500, 153. link
"The Nitrifying Bacteria: a review" J. Soil Sci. 2006, 4, 59. link

Related Posts:

PeePeePost #1: "Why Is Pee Yellow?" or "Rainbow of Urine"
PeePeePost #2: "Why Does Pee Smell?" or "Aroma of Life"
PeePeePost #4: "PeePee Portal to Phosphorus" or "What the Alchemists Did Right"
PeePeePost #5: "How Pee United You With Rocks"
PeePeePost #6: "Pee, Our Connection with the Earth's Metabolic Cycle"

I blame my lack of productivity on the earth's axial tilt!

noreply@blogger.com (LeeBee) — Wed, 27 Jul 2011 04:12:00 +0000

The axis of the rotation of the earth relative to that of its rotation around the sun is tilted by 23.5 degrees. This causes some pretty extreme changes in the climate here at 43 degrees N latitude:

For example, here is what Wisconsin looks like in the winter:

This leads to very productive weekends of staying inside and barfing blog posts out of my brain and into the computer.

Here is what Wisconsin looks like in the summer:

This leads to extreme levels of outdoor awesomeness, but very low levels of indoor blog-post-barfing productivity.

Never fear, Science Minus Details will return to full glory soon. For now I will leave you with Mike Flores' awesome summer 2010 time-lapse montage.

Have fun in the sun, I will see you soon!

Why Pee is Cool - entry #2 - "Why Does Pee Smell?" or "Aroma of Life"

noreply@blogger.com (LeeBee) — Tue, 10 May 2011 02:09:00 +0000

In Germany, nothing marks the beginning of spring like asparagus! Running from April through the end of June, asparagus season (spargelzeit) is a big deal in Germany. Here is me happily participating in this wonderful German tradition:

Me, about to have an asparagus aneurysm

As you may know, after eating asparagus, your pee can smell pretty gross.

Bathroom Safety Tip #1: never inhale bathroom-related vapors directly, always gently waft them

If you are confused by the above statement about asparagus-pee, fear not, there is a genetic basis for your confusion! Some people can smell asparagus-pee, while others can't, and this difference is caused by a difference in your DNA! This issue is not quite that simple, as not everyone produces smelly asparagus-pee after eating asparagus (awesome article here, awesomer article here).

Regardless, if you can smell asparagus-pee, it smells because there are asparagus-pee molecules making their way into your nose! It's exactly like when you smell people's farts, molecules that were once inside their butts have made their way inside your nose! Gross! The asparagus-pee molecules that you smell come mostly from the breakdown of a molecule known as asparagusic acid, which is present naturally in asparagus. When your body breaks down asparagusic acid it forms a wide variety of chemicals, all of which contain sulfur!

One dude eating asparagusic acid from asparagus and peeing out smelly asparagus-pee molecules (left). Another dude directly inhaling (not wafting, cuz he is unsafe!) those asparagus-pee molecules (right). Notice all the sulfur atoms!

Many chemicals that contain sulfur atoms smell horrible in similar ways, and I have no idea why this is. This is one chemical/biological mystery that, much to my chagrin, remains unsolved in my head (internet people, if the reason is known, please help!!!). Aside from sulfur, the thing that all these smelly asparagus-pee chemicals have in common is that they are "light" enough (a.k.a. they are "volatile", which means they have a relatively low boiling point) that they can float up into the air and into your nose. That is partly why asparagus doesn't smell like asparagus-pee, because asparagusic acid is not volatile (remember that word). In fact, asparagusic acid boils above 300 °C (>600 °F), so there is no way any of it gets into your nose!

Other nasty sulfur-chemical smells you may have encountered include rotten eggs, skunk spray, garlic bad breath, and natural gas.

While there is no known advantage for humans to pee out volatile and smelly asparagus molecules, many other animals have harnessed the power of stinky sulfur chemicals for their own benefit. For example, cats pee out a sulfur-containing chemical known as felinine, which breaks down into a more volatile (and therefore more stinky) sulfur chemical. It is this more volatile chemical that gives cat urine its distinctive odor.

Felinine and/or its smelly breakdown products are thought to play a role in attracting female cats to male cats so they can hook up and make babies. Many other animals use their pee in a similar fashion. In order to avoid different species getting their pee mixed up, different animals use slightly different chemicals, which causes their urine to smell pretty different! So simple!

Side Note: Cat prey, such as rats, have caught onto this urine-related chemical signaling and run away when they smell these cat pee chemicals. The parasite known as T. gondii has in turn caught onto this. When this parasite infects a rat, it causes the rat to be attracted to instead of repelled by the smell of cat pee chemicals, and the rat is therefore more likely to get eaten by a cat!! This allows T. gondii to infect the cat, which is great for T. gondii because it needs to infect cats in order to reproduce sexually. Nature is amazing! If this interests you, definitely check out this radiolab podcast on parasites.

Let's get back 2 basics though... let's talk about human pee and what we all have in common. The primary reason animals pee is to get rid of nitrogen atoms (more on this in future posts). We humans primarily use the nitrogen-containing chemical urea for this, though we also directly excrete small amounts of the very simple nitrogen-containing chemical called ammonia. Urea has no odor, mostly because it is not volatile enough to float into your nose. However, ammonia has a very strong odor, as this molecule is smaller and therefore more volatile than urea. This is one reason why everyone's pee smells pretty much the same--because of ammonia. This is also why lant (aged pee, gross!!) smells worse than brand new pee, because the odorless urea molecules have over time combined with water to produce more smelly ammonia molecules. This happens on its own when urea sits around in water, but it can also be sped up by microbes that have an enzyme called a urease.

New smelly pee can become old smellier pee over time due to urea turning into ammonia

However, even though everyone's normal, non-asparagus pee contains smelly ammonia, that doesn't mean it all smells exactly the same. The full answer to why pee smell varies slightly between people involves tons of details, but the simple answer is that everyone's body deals with chemicals slightly differently. This causes tiny variations in the volatile chemicals that are peed out, which leads to slightly different "pee bouquets". Some examples of the kinds of smelly chemicals we pee out in varying amounts include acetone (nail polish remover), benzaldehyde (almond flavor), acetic acid (vinegar), dimethylfuran, pyrrole, and even toluene (paint thinner)!

Because subtle, ambiguous answers can sometimes be unsatisfying, we'll finish this post with two insane human biological disorders that are anything but subtle.

Some people have the misfortune of urinating out a nitrogen-containing chemical called trimethylamine, which is the same chemical that gives dead fish its smell. Gross! This disorder is known as trimethylaminuria or "fish-odor syndrome", and is caused by the person's body not being able to turn trimethylamine into the less volatile (and way less smelly) chemical trimethylamine N-oxide. Trimethylamine therefore builds up in the fish-odor syndrome victim's body and comes out in his/her urine, sweat, and breath. What a bummer!

Double Bummer!!!

We'll finish off today's peepee talk with a sweet tale. Instead of having dead-fish-smelling-pee, some people's pee can smell like maple syrup! This is caused by a genetic defect that causes a buildup in certain kinds of amino acids in people's bodies. Those amino acids have to go somewhere, and some of them end up turning into a chemical called sotolon (proposed mechanism here), which then gets peed out. This is the same chemical that gives maple syrup its distinctive awesome smell, hence the maple-syrup-smelling-pee-pee! Unfortunately this disease can be fatal if left untreated (mega sad), however with proper treatment people are able to live healthy lives (mega happy).

CT scan of infant with maple-syrup urine disease. More info about and source of image: pediatricneuro.com

For the purpose of making artificial maple syrup, companies isolate sotolone from the herb fenugreek. So, since most sotolone molecules pass through your body unchanged, if you ever want your pee to smell like maple syrup, just eat lots of fenugreek. But remember, never directly inhale pee vapors, always waft!

Alternative caption: Correct way of wafting pee with a severed hand.

Stay tuned for more peepee posts! Leave comments if you have more questions about pee!

Related Posts:

PeePeePost #1: "Why Is Pee Yellow?" or "Rainbow of Urine"
PeePeePost #3: "Explosive Urination" or "Gunpowder Comes from Pee!!!"
PeePeePost #4: "PeePee Portal to Phosphorus" or "What the Alchemists Did Right"
PeePeePost #5: "How Pee United You With Rocks"
PeePeePost #6: "Pee, Our Connection with the Earth's Metabolic Cycle"

Why Pee is Cool - entry #1 - "Why Is Pee Yellow?" or "Rainbow of Urine"

noreply@blogger.com (LeeBee) — Tue, 26 Apr 2011 03:00:00 +0000

PeePee! Jokes about it will never stop being funny, and facts about it will never stop being interesting!

Do not try this at home. via phasezero

In this series of posts we will learn what pee is and discover how it connects us with the rest of life on earth and how humans have used it to learn more about the nature of the universe. Get ready for a wild ride!

To begin with, what is pee anyway? Well, like most things associated with life, it is mostly water (>95% in fact). The other primary constituents of pee are various nitrogen-containing chemicals (mainly urea for us and other mammals) that are the result of your body breaking down protein.

We will talk more about urea in future entries, but to start with let's talk pee color! The yellow color of your pee comes mostly from the breakdown of chemicals in your blood! Crazy right?!! Your body is constantly making new chemicals and breaking down old ones, and your blood chemicals are no exception.

The chemical in your blood that makes it red is called heme. Heme is the molecule to which oxygen molecules bind to be distributed throughout your body. The red color of heme is primarily due to electrons in its iron atom but also to electrons in its cool ringed structure (the ringed structure is called a porphyrin, and is found in plants' chlorophyll as well as in the ground's crude oil!). Your body turns the heme molecule from red to yellow by ejecting the iron atom out of the center and breaking the ringed molecule open using oxygen.

This is how your body gets rid of old heme molecules.

The ring-opened product is known as urobilin, and is one of the primary reasons your pee is yellow. Your pee tends to be more yellow in the morning than in the evening simply because there is a higher concentration of urobilin in morning pee since you've been breaking down old blood molecules all night.

Notice all the alternating single and double bonds (highlighted in blue) in both molecules and that metal (Fe = iron) in heme. Those are the two reasons they absorb visible light and are colored! This is a common theme for all colored molecules anywhere!

There are lots of jobs available in health care!

Any peepee aficionados out there may know that yellow is not the only color that your peepee can beebee. The pee of people who have a disorder called porphyria (derived from the greek porphyra, meaning "purple pigment") can be purple, brown, or even red! This is due to a malfunction in one of their enzymes responsible for manufacturing heme, which results in a log-jam of heme-molecule precursors that end up being urinated out.

Brownish urine can be caused by the buildup of porphyrin precursors. This peepee image and those below were taken from lifeinthefastlane.com.

Your pee can be intensely yellow- or orange-colored if you take excess B vitamins, specifically vitamins B2 and B12. Your body deals with this excess by just peeing them out. Notice how vitamin B12 looks similar to heme.

Look at all those alternating single and double bonds and that metal atom (Co = cobalt)! Chemistry is easy and fun!

Orange- or even red-colored urine can be caused by certain pharmaceutical drugs (e.g. rifampicin and phenazopyridine) or by beets (which contain cool betalain pigments such as betanin and indicaxanthin)(ref, ref).

Orange urine can be caused by excess B vitamins, a variety of medications, and bunches of other stuff.

Perhaps best of all, the anti-malarial drug methylene blue (and lots of other drugs) can actually turn your urine green (blue drug + yellow pee = green crazy pee)!

Green urine can be caused by a variety of medications, or even foods such as asparagus.

I spoke too soon about the best pee of all. Purple (!!!) urine can result from bacteria smashing two light yellow molecules together to make the mega purple dye indigo (ref). Incidentally, indigo was one of the first dyes ever produced by humans, dating back to 7th century BC Mesopotamia. It was produced in a nearly identical process to the one that happens in purple-peeing-people.

The bacterial transformation of indoxyl sulfate to indigo. Indigo changed the world, I'm not kidding, look it up.

Purple pee can be caused by the production of a mega famous dye by bacteria in your urine.

All these awesome colors are created by molecules that have either a single metal atom or alternating double and single bonds, which allows their electrons to move in such a way that they absorb visible light. It's that simple! When you pee the chemicals out they can make up less than 1% of your urine, yet they absorb so much light they can completely change the color of your pee!! Amazing!

Related Posts:

PeePeePost #2: "Why Does Pee Smell?" or "Aroma of Life"
PeePeePost #3: "Explosive Urination" or "Gunpowder Comes from Pee!!!"
PeePeePost #4: "PeePee Portal to Phosphorus" or "What the Alchemists Did Right"
PeePeePost #5: "How Pee United You With Rocks"
PeePeePost #6: "Pee, Our Connection with the Earth's Metabolic Cycle"

"Barely Bad Bananas" or "Where Does Background Radiation Come From???"

noreply@blogger.com (LeeBee) — Tue, 12 Apr 2011 12:09:00 +0000

The totally normal banana that this totally normal monkey is eating is radioactive, but so is the monkey!

Radioactive Monkey Eating Radioactive Banana, from Arne Bevaart

But that is so confusing! If radioactivity/radiation = scary, and bananas/monkeys = not scary, how can bananas/monkeys = radioactivity/radiation????? Well, it turns out that whether we like it or not, we live in a radioactive world, as xkcd.com so wonderfully illustrated:

via xkcd, click image to enlarge

For a brief reminder about what nuclear radiation is and its relationship to other kinds of radiation, see this previous post. In this post I will describe how/why living on earth means we are necessarily exposed to (small amounts of) high energy radiation, starting with bananas and monkeys. I won't keep repeating it throughout, but keep in mind that just because something is radioactive or emits radiation does not necessarily mean it is harmful.

Bananas are known for their high concentrations of potassium, an element that monkeys, humans, and almost all other living things require for the normal functioning of their cells. Most potassium on earth is not radioactive, but 0.01% of it is! This radioactive potassium was around when the solar system formed out of ancient starstuff. It is still around today because it releases its radiation very slowly, with a half life of over one billion years. As the solar system is ~4.6 billion years old, that means that when the earth was formed only around 0.08% of the potassium on it was radioactive.

Another element that has been around since the beginning of our solar system is uranium--the same stuff that is used in nuclear power plants. Uranium is found in low concentrations throughout the earth's crust, and this is the reason that living in or visiting stone, brick, or concrete buildings exposes you to radioactivity. In fact, the concentration of uranium is so high in the granite walls of the US capitol building, that they release more radiation than is legally allowed for the walls of a nuclear power plant! We are also exposed to radiation from uranium (and thorium) released into the environment by coal-fired power plants (though that is among the least worrisome of the health risks posed by these plants). Uranium and thorium occur naturally in coal.

Mega huge granite mine, in Graniteville, Vermont (definitely click to see high-res). Check out that insane staircase!!!

When a uranium atom undergoes radioactive decay, it becomes an atom of a different element, which is usually also radioactive. One of those elements is radon, which seeps out of the ground and into our atmosphere (or our basements) then into our lungs. Another radioactive uranium-decay product is the element radium. We encounter radium when we eat brazil nuts, which have the dubious distinction of being the most radioactive food in the world. These nuts contain 1000x more radium than most other foods of their size.

A Brazil Nut Tree, which due to the HUGE size of its root system, is able to concentrate relatively high levels of radium in its nuts (tee hee).

All of the background radiation sources described so far come from radioactive elements naturally present on earth since the very beginning. The other type of background radiation we are exposed to comes from space!!! Most of the energy hitting earth from space comes from the sun, and most of that energy is in the form of electromagnetic radiation in the visible range (that's why we evolved to see it!!!). The sun also sends us some higher energy electromagnetic radiation (i.e. gamma rays and X-rays), but lucky for us, that radiation is blocked by our atmosphere. The cool picture below shows what kinds of electromagnetic radiation make it through our atmosphere.

Only visible light and radio waves make it through our atmosphere very well. click image to enlarge.

Even though our atmosphere blocks most of the harmful (ionizing) electromagnetic radiation coming from the sun, that's not the only thing the sun sends our way. It also bombards us with very fast moving tiny particles known as cosmic rays. Cosmic rays are essentially little parts of the sun, as they consist primarily of protons and alpha particles (a.k.a. hydrogen and helium atoms without their electrons). Some of the energy released when these particles slam full speed into our atmosphere can be seen near the northern and southern poles of earth in the Aurora Borealis and Aurora Australis:

Aurora Australis. Created when charged cosmic rays are funneled to the south pole by the earth's magnetic field where they slam into oxygen and nitrogen atoms in our atmosphere.

Even though the cosmic rays are slamming into our atmosphere (and not our bodies), we are still exposed to the energy that results from this collision. When a single cosmic ray hits our atmosphere, as many as a billion (!!!!) other particles can be created (including radioactive carbon atoms, which is why carbon dating works). In addition, high energy electromagnetic radiation like gamma rays can be created by these collisions low enough in our atmosphere that the gamma rays actually reach us down on the surface of the earth. It's these particles and gamma rays that contribute to a significant portion of the background radiation to which we are exposed.

Brief nerd-out: in fact some cosmic rays are sooooo energetic, traveling at near the speed of light, that there is no way they came from our sun, and scientists aren't yet sure exactly where they come from at all!

When you go higher in the atmosphere, there is less of its protective oxygen and nitrogen atoms to block the radiation coming from space. Therefore you receive radiation at faster rates when you are in the mountains (~2x compared to sea level), flying on planes (~10x), or in the international space station (~100x). In fact, it was first established that cosmic rays were coming from space by bad-ass scientist Victor Hess, who in 1912 carried a radiation counter up in a balloon and detected increasing levels of radiation as he rose to over 17,000 feet. Now that's what I call science!

Victor Hess, bad-ass scientist.

Bananas, brick houses, brazil nuts, bedmates, and our beautiful sun... they all expose us to radiation. Again, not generally enough to worry about, but that doesn't mean its not totally crazy!!!

Baby ape going ape about how cool background radiation is.

Related Post:

What is Nuclear Radiation and How Can It Hurt Me?

What is Nuclear Radiation and How Can It Hurt Me?

noreply@blogger.com (LeeBee) — Tue, 29 Mar 2011 12:00:00 +0000

People get really freaked out about nuclear radiation.

Dude with Awesome Beard, Freaking Out

Since we are all really freaked out by the ongoing trouble with Japan's Fukushima nuclear power plant and the hazards posed to the Japanese population by escaped nuclear radiation, let's figure out what nuclear radiation is, and let's begin by talking about radiation in general. The word radiation is used to describe any type of particle or wave that is moving through space really fast, which encompasses lots of things. The kind of radiation that will be most familiar to you is LIGHT, which is a kind of electromagnetic radiation.

Electromagnetic Radiation, so-named because it consists of electric and magnetic waves that fly through space together.

Electromagnetic radiation can have a tiny amount of energy, a huge amount of energy, or anything in between. Visible light, the kind you use to see, is electromagnetic radiation that has a medium amount of energy. Here is a picture of all the different kinds of electromagnetic radiation.

We're talking about electromagnetic radiation because nuclear radiation gives off the highest-energy form of electromagnetic radiation, known as gamma rays. These are the type of nuclear radiation that pose the greatest health risk to life. Gamma rays are dangerous because they can penetrate deep into your body, and shielding yourself from them takes lots of matter (the element lead is commonly used for this simply because it is very dense). Once in your body gamma rays can knock electrons out of your atoms, which in the short term results in symptoms of "radiation poisoning" (nausea, vomiting, bleeding, death) due to large numbers of cells in your body dying. In the long-term, gamma rays knocking electrons out of your atoms can cause changes in your DNA that lead to cancer.

In order to understand where gamma rays come from, let's take a brief detour to talk about nuclear energy. Here is an atom:

If too many protons, neutrons, or both are crammed into the nucleus of an atom, the nucleus will be unhappy and will reduce its size in a number of different ways, giving off LOADS of energy in a process known as radioactive decay. Nuclear power plants use the elements uranium and/or plutonium and capture the energy of their radioactive decay in the form of heat (Clear Science! has three nice posts about nuclear power that you should check out sometime). When uranium or plutonium undergo radioactive decay, they transform into a wide variety of elements with smaller nuclei (for more go here). In this process of becoming smaller, three main types of radiation are emitted, known as alpha (a), beta (b), and gamma (g) radiation.

Gamma radiation we have already discussed. It is released when the nucleus of an atom doesn't change size at all, but instead just rearranges how its protons and neutrons are packed together.

Gamma Decay, the rearrangement of nuclear structure.

Alpha radiation we learned about in the last post about helium because it occurs when a radioactive nucleus gets smaller by spitting out a helium nucleus. The resulting helium nucleus has lots of energy and is also known as an alpha particle.

Alpha Decay, ejections of a helium nucleus, also known as an alpha particle.

Beta radiation occurs when a neutron turns into a proton by spitting out an electron, which in this instance is known as a beta particle. Oh, and a neutrino is also ejected (neutrinos are really cool, trust me, read more here).

Beta Decay, neutrons turn into protons by spitting out high energy electrons and neutrinos.

The main thing distinguishing the danger posed by these three types of radiation is how far they can travel into your body.

Radiation Penetration

We already talked about how gamma radiation is dangerous because it is a form of electromagnetic radiation that can hit and damage any part of your body, inside or out. Beta particles however, having more particle-like properties than gamma rays, can penetrate only small distances into your body, and can even be stopped by thick layers of clothing. Alpha particles are relatively large and can't travel any further than the outer layers of dead skin on your body, so external exposure is relatively benign.

Alpha and beta particles aren't sounding scary at all, huh?? Well, here's where nuclear radiation differentiates itself from electromagnetic radiation in a really bad way. Gamma radiation may be able to penetrate your skin and organs, but alpha and beta particles can be released inside your body when you breathe in tiny amounts of radioactive material or eat foods to which they are stuck. The intensity of normal cancer-causing electromagnetic radiation like x-rays drops dramatically the farther away you travel from the source. Radioactive materials however, can travel great distances by being blown around in the wind and eventually settling back down to the ground (a.k.a. nuclear fallout) or by contaminating waterways and food chains. In the case of the Chernobyl disaster, radioactive particles were detected over 700 miles away at a nuclear power plant in Forsmark, Sweden.

A = Chernobyl, Ukraine; B = Forsmarsk, Sweden. Radioactive material traveled atleast this far.

Once inside your body, the radioactive materials are free to emit alpha and beta particles, which cause large amounts of damage much in the same way as gamma rays--messing with the atoms in your DNA, leading to a wide variety of cancers. One particularly insidious example is a radioactive form of the element strontium, which if inside your body can substitute itself for the calcium atoms in your bones and release beta particles, causing bone cancer and leukemia. Another example is radon gas, which is so dangerous because you can easily and unknowingly breathe it into your lungs, where it stays and emits alpha particles, leading to lung cancer. Radon gas is produced naturally by the decay of uranium in the earth's crust, and it can seep out of the ground and reach dangerous levels inside your home, so watch out! My parents had a radon problem in their basement once, but they took care of it. Finally, radioactive iodine atoms are produced when uranium atoms split apart, and if inside your body, those iodine atoms concentrate in the iodine-containing hormones in your thyroid gland and give you thyroid cancer. This is why people are instructed to take potassium iodide pills when uranium-decay products are released into the atmosphere, in an effort to swamp your body with non-radioactive iodine atoms to out-compete the radioactive iodine atoms for space in your thyroid gland chemicals.

In summary, nuclear radiation contains LOTS of energy in the form of both light waves and particles. The properties of nuclear radiation make it great for use as an energy source (good), but those same properties mean it can cause lots of damage to life if released into the environment (bad).

Related Post:

"Barely Bad Bananas" or "Where Does Background Radiation Come From???"

"Where Did Helium Come From?" or "Jupiter & Saturn, Helium Hoarders"

noreply@blogger.com (LeeBee) — Tue, 15 Mar 2011 13:58:00 +0000

All matter in the Universe is made up of three-quarters hydrogen and one-quarter helium (by weight), with relatively insignificant amounts of all the other elements (not including dark matter, whatever that is). This crazy abundance of hydrogen and helium has been around in nearly the same ratio from minutes after the big bang over 13 billion years ago. Wowza!

Hydrogen

Helium. (see story of Larry Walters)

Partial evidence for the incredible abundance of hydrogen and helium in the universe can be seen right here in our own solar system, in the form of the "gas giant" planets Jupiter and Saturn, which are both composed primarily of hydrogen and helium, with small but significant amounts of carbon, oxygen, nitrogen, and other elements. The composition of these planets is thought to be similar to that of the "primordial solar nebula" from which the solar system was formed. Woah!!

Jupiter, as imaged by Voyager 1 in 1979. Mesmerizing!!!! You can see a few of Jupiter's 63 moons too!

Saturn, as imaged by the Hubble Space Telescope. Saturn has aurora too, just like earth!

Earth on the other hand, is composed primarily of iron, oxygen, and silicon, with only minuscule amounts of helium. As you can see in this awesome chart that compares the compositions of the planets in the solar system, the composition of Earth is waaaaay different than that of Jupiter and Saturn (click to enlarge)(thanks to researchers at the Australian National University):

Densities and Elemental Compositions of the Planets. Earth is divided into two sections, with Earth on the left and our moon on the right.

Why the huge difference between the gas giants and Earth? Where did all our helium go?

Well, as helium loves to do, it floated away! Even though scientists believe that Earth began with a pretty decent amount of helium in its atmosphere, Earth is not massive enough to gravitationally hold on to this extremely light element, so the helium just rose to the top of our atmosphere and never stopped rising. Jupiter and Saturn however are 300- and 100-times (respectively) more massive than the earth, and they have plenty of gravity to hold on to their helium. So sweet.

BUT: If helium in our atmosphere just floats away, and you are still able to buy helium for birthday balloons or to float you and your lawn chair, where did that helium come from? Well, if it can't be up above in the atmosphere, that leaves us with only one option, down below in the earth. It's true! We get all our helium from underground! It gets trapped in pockets along with natural gas, and is piped out of the ground by energy companies, who then separate the helium from the other natural gas chemicals (i.e. methane, ethane, nitrogen, etc).

Here is the craziest part: That helium was not around when Earth formed. So where did it come from??? Well, it is constantly being produced by the radioactive decay (like in a nuclear reactor) of the elements thorium and uranium (images courtesy Theodore Gray).

The radioactive decay of these elements ejects alpha particles, which are pretty much the same thing as helium atoms. This produces around 3000 metric tons of helium per year in the earth's crust! That is where almost all our helium comes from!

Alpha-Decay

These ejected helium atoms travel at thousands of miles/hour, and are slowed down by bouncing off other atoms, producing heat in the process. That is one of the primary reasons the core of the earth is still molten, even after 5 billion years! This "geothermal" heat eventually radiates from the earth and can be captured in places where the heat flow is high, like Iceland, which gets one quarter of their energy from geothermal sources.

Global Heat Flow (source). Notice Iceland is in a yellow zone.

So crazy!!!

Cool Chameleons, Cool Carotenoids, Cool Colors

noreply@blogger.com (LeeBee) — Tue, 08 Mar 2011 20:31:00 +0000

Check out what this chameleon can do! Understanding how chameleons do this will help you to understand how all life on earth is connected.

Chameleons change color by expanding and contracting little balls of pigment in their skin, thereby increasing and decreasing the amount of that color that we see. They have a number of different kinds of color-making cells (called chromatophores) that contain different pigments, and they can make a variety of colors by turning these cells on or off in different combinations (i.e. blue + yellow = green) (for more, see here).

The pigments in these chromatophore cells are composed of different chemicals that absorb different colors of light. An example of one of those chemicals is beta-carotene, which due to all the double bonds in its cool chemical structure, absorbs blue-green light:

Chemicals with lots of alternating double and single bonds usually absorb light in the visible range, which means the light that bounces off them will be colorful.

When sunlight hits a chameleon that has its beta-carotene-containing pigment balls expanded, the beta-carotene will subtract out the blue-green light making the resulting light appear orange-ish.

The color wheel. When you subtract blue-green light from sunlight, the resulting light will be the color on the opposite side of the color wheel, in this case orange-ish. Plants absorb mainly red-orange and blue light, leaving the green light on the opposite side of the color wheel to hit our eyes--that's why plants are green!!

Chameleons are not the only animals that contain beta-carotene and other molecules like it (known collectively as carotenoids). These molecules are also the reason that lobsters are red and flamingos are pink:

Lobsters are red.

Flamingos are pink.

This story starts to get more amazing here... Our (and other animals') ability to visually detect the pink of pink flamingos is dependent on carotenoids. Before we use them in vision, we split carotenoid molecules in half, creating the chemical known as retinal:

Animals use oxygen to split beta-carotene molecules in half, making two retinal molecules that they use to see stuff (see here).

Retinal then finds its way into our eyes, where it combines itself with a protein. Just like beta-carotene above, retinal absorbs light in the visible range, and when that happens, the cells in our eyes send a signal to our brain. Our brain receives similar signals from retinal-containing cells all over our eyes, and combines them to make an image (for more go here). Just like chameleons use different carotenoid-derived colored chemicals to make their bodies beautifully-colored, we use different carotenoid-derived colored chemicals to detect those beautiful bodies. Amazing! Nature has taken advantage of the light-absorbing structure of carotenoids for such different purposes!

UNITY OF LIFE CONCLUSION IMMINENT:

Animals generally can't make their own carotenoids, so they rely on eating plants as a source of these molecules (in fact, flamingos turn white if they are fed a carotenoid-free diet). BTW: this is why carrots are supposed to be good for your vision, because they contain large amounts of beta-carotene.

But plants don't make carotenoids just so we animals can steal them, plants make them so they can use them in photosynthesis. When carotenoids absorb light, they are absorbing energy from the sun, and plants use that energy to turn carbon dioxide and water into sugar and oxygen. Nature takes advantage of the light-absorbing structure of carotenoids for yet another purpose!

CONCLUSION:

Animals like chameleons use carotenoids to change the color of their bodies, animals like us humans use carotenoids in our eyes to see these colors, and plants make it all possible by making the carotenoids which they use to capture solar energy! All life on earth is connected!