Friday, September 28, 2007

Time is what you make of it

I have a confession. My confession is slightly embarrassing considering that I work in the Earth Sciences: I don’t know my geologic timescales. When someone tells me a fossil is from the Ordovician or the Precambrian, I have no idea what they are talking about. Was that 10 million years ago? 167 million years ago? 1.92 billion years ago? 569 million years ago? I DON’T KNOW! There’s a reason why I went into Oceanography and not Paleontology – I can’t keep these ages straight. The worst part is that my students have to learn the geologic timescale in their general education class. So while they have everything memorized for midterms, I’m stuck with my finger up my nose trying to remember if the Pleistocene came before or after the Pliocene. That being said, why don’t we take today and learn the geologic timescale together? It’ll be fun!! You get to learn something new and I get to relearn the timescale for the 10th time and pray that my drinking binge this weekend won’t erase my memory. Again.

It would be fair to mention that I DO know some of these Eras and Periods. I know that the Cambrian was the time where all sorts of life appeared on our planet. The Cambrian Explosion was the explosion (!) of life in a very anticlimactic way. It was during this time that we find lots of fossil evidence of worms and sea-bugs and sponges and even more worms, but this time with teeth. Earth sounds like a pretty gross place back in the Cambrian, right?

So the Cambrian explosion occurred around 544 million years ago and I’m going to ignore (for now) the times before the Cambrian which are the Proterozoic, Archean, and Hadean. These 3 are Eras when the Earth was juuust forming. Most Paleontologists ignore these times in Earth history because it’s really really hard to find shit that’s 2-3 billion years old. The life that did exist were things like algae, bacteria, single celled organisms, viruses, and so on. Borrrring.

Moving on, the Cambrian/Precambrian boundary was around 544 million years ago, and then the next exciting thing was the Permian/Triassic boundary which was about 248 million years ago. An aside here: Paleontologists have a pretty clever way of defining the boundary between eras and periods. What they do is look at some sedimentary rock formation that’s got fossils in it, start at the bottom of the formation (where the oldest fossils live), work their way up to the top of the formation (where the youngest fossils live), and wherever older fossilized critters disappear they go “Aha! There must have been some cataclysmic event around this time that wiped out most life on Earth and allowed all these new critters to take over!” I don’t exactly know where they get the numbers from – must be by age dating rocks within the formation using some radioactive isotope. Reason # 122 why I'm not a Paleontologist.

We’ve covered the Boring Era (Precambrian), and then the Gross Period (Cambrian), and then we get into more exciting Eras and Periods like everyone’s favorite the Triassic and Jurassic (248 mya and 206 mya, respectively). Maybe at this point we should create a mnemonic device to help us remember most of these. If we can’t get the dates right, we can at least get the order right. Starting from the oldest first...



Please, …………….Pleistocene

Uh, well. That's a start. You know what? I'm just going to keep this chart handy in case I'm in a life threatening situation where I need to know when the Pennsylvanian was EXACTLY. Yes, that sounds like a good plan.

Happy Friday!

Tuesday, September 25, 2007

Nu(trients) to you

You may have noticed there’s a lot of ocean out there. A lot of ocean that I get to explore while being carted around in big, smelly boats, gathering up hundreds of tiny bottles filled with seawater. My lot in life is as a Chemical Oceanographer. I love what I do, but man there’s a lot of ocean out there. A lot of ocean with a lot of chemicals in it; chemicals which I (and folks like myself) try to make sense of. Specifically, I look at the nutrients in the ocean. Nutrients like silica, phosphorous, and nitrogen. Let’s discuss today about what we might find in the depths of the ocean with respect to these important nutrients.

Let me begin by saying that the best and easiest way to make your point to a room of scientists is to make a graph. Scientists LOVE graphs. They love graphs more than they love New Balance and The North Face, which is a very telling statement if you’ve ever seen a scientist. Scatter plots, bar graphs, pie charts, whathaveyou. If you can put it in a graph, they’ll love you forever. When we plot nutrient concentration vs. depth in the ocean, we end up with a plot like this:It doesn’t matter if this is a graph of phosphate, nitrogen, or silica, most nutrient curves typically have this shape. Why, you ask? Well, let’s start from the top and move our way down.

Oceanic phytoplankton can only live in “The Mixed Layer’. Remember that phytoplankton are plants so they need sunlight to grow and nutrients to be happy. Depending on how murky your water is, sunlight can only penetrate about 60-100 meters down, at the most. The Mixed Layer is phytoplankton Party Time. Such Party Time, in fact, that they tend to use up every last molecule of available nutrients in the surface ocean – that’s why we have a concentration of practically zero in the top 10s of meters on our fancy graph above.

Particles like poo-poo are loaded with avalible nutrients. When that stuff falls through the mixed layer, the nutrients get recycled back into the water column. Below the mixed layer, the nutrients redissolve and are up for grabs again! It’s at this depth that we see a maxima in nutrient concentration.

The rest of our nutrient profile is pretty bland. As you can see, we have a pretty constant concentration except for a wee increase in the deep sea. This increase is no figment of your imagination or analytical error. It was a real head scratcher for ocean chemists for a long, long time because it shows up everywhere in the world and gets bigger as you move from the Atlantic to the Pacific. This, my friends, is evidence of the Thermohaline Circulation. If you were unfortunate enough to have seen “The Day After Tomorrow”, you would have gotten at least the jist of the Thermohaline Circulation – the deepwater “conveyor belt” that moves water from the surface ocean in the North Atlantic all the way around the world until it pops back up in the North Pacific. This current is super slow, but transfers heat all over the world, and apparently deadly storms, and Dennis Quaid, and then we all move to Mexico. The point is that the deep water is really, really old. Because it’s really old, it’s collected tons of particles that have rained down into it as it makes its way around the world. This gives us that slight bump at the very bottom of our graph.

See, now you know how to explain a nutrient profile to your friends! Use this knowledge wisely, as the power of oceanography is unwieldy at best.

Friday, September 21, 2007

Nocturnal Emissions

We talked a little bit earlier in the week about photons and their behavior as waves. Like we said, photons are little packets of energy that behave sometimes like waves and sometimes like particles. They propagate like waves, with different wavelengths having different associated energies. Color, radio waves, gamma rays, x-rays – all of these types of waves (and so many more) make up what’s known as the Electromagnetic Spectrum. But what about the particle behavior of photons? Well, my friends, today we’ll take another look at photons, but this time we examine how they act like particles.

Atoms are very excitable. Atoms and photons interact much like overweight children in a Bouncy Castle. Say your neighbor is having a very rowdy, very annoying party for their 5 year old. For this little thought experiment, imagine that the Bouncy Castle is an atom and all the kids inside are electrons. Everybody is having a good time in the Bouncy Castles, until the chubby kid arrives. The chubbiest kid at the party (who at this moment is outside the Bouncy Castle) represents one photon. He tanks down some cake and ice cream and barrels into the bounce house with a shitload of energy. He’s so energetic, in fact, that one of the other kids (an electron) gets shot out of the Bouncy Castle upon his entrance.

The parents that are loosely chaperoning (drinking at) this party see the commotion and promptly eject the cubby kid, thereby allowing another not-so-chubby kid back into the Bouncy Castle.
This is pretty much what happens to an atom when it gets hit with a photon. The atom starts at Ground State (step 1) – everything relaxed and normal, all of the electrons hanging out in their proper Electron Shells. When a photon hits the atom, the atom absorbs it and in order to conserve its (the atom’s) energy, it has to eject an electron. The atom is now in excited state (step 2). As soon as that electron is fired out of its shell, another electron moves in on the territory and the atom goes back to ground state (step 3). Again, the atom has to conserve energy, so when that electron moves in during step 3, a photon has to be emitted.

How can an atom get excited, you ask? One way is to burn it. Some chemicals burn different colors at juuuust the moment you ignite them. You can see purples and blues and greens, and remember that the difference colors you see represent photons with different energies. Harkening back to the Electromagnetic Spectrum, different colors equal different wavelengths which in turn means different energies. Get it?

This whole burning-with-different-colors thing is how Astrophysicists determine the chemical composition of celestial bodies that are far far away. The fancy name for it is Spectroscopy. As an aside here: my declared major when I transferred to UCLA was Astrophysics. But I hated the undergraduate advisor so much that I switched to Math. Astrophysics is certainly a wonderful field populated with very smart and interesting people, but I’d take a month out at sea over a month trapped in an observatory any day.

Wednesday, September 19, 2007

Do the Wave

We humans can’t see very well when we look far far into outer space. Sure, telescopes give us a glimpse at deep space, but we can only learn so much when we just use our eyes. Luckily there are plenty of other options when it comes to detecting electromagnetic radiation from outer space. Visible light is only one kind of electromagnetic (EM) radiation. We can broaden our view of the universe by using new-fangled instruments that will detect photons with various wavelengths. A photon is basically a little packet of energy. We call photons “packets” because you can’t really call them a particle and you can’t really call them a wave since they behave like both. They can be shot off from an atom the way an electron might be, but we can see them as light, with wavelengths that correspond to different colors. You could say that photons go both ways. They’re swingers, man.

Much like delicious ice cream treats, electromagnetic radiation comes in all kinds of different flavors. We’ve got photons with long wavelengths which make-up things like radio waves, micro waves, and colors like reds and oranges. On the other end of the spectrum we’ve got waves with really short wavelengths like gamma rays, X-rays, and colors like violets and blues. When we talk about wavelengths, we’re talking about the distance from peak to peak OR trough to trough on a wave.

Any wave (EM, ocean, crowd at football stadium) will propagate with a speed that is the product of its wavelength multiplied by its frequency:

velocity = wavelength * frequency

All types of waves in the electromagnetic spectrum travel at the speed of light which is 3 x 10^8 meters per second. That’s 670 MILLION miles per hour (if I did my math right). Crazy fast. So fast, in fact, that nothing travels faster than the speed of light. Yet.

A consequence of this whole traveling-at-the-speed-of-light thing is that the speed of light never changes. For our purposes, it’s a constant. This means that if you increase wavelength you have to decrease frequency and vise versa. So waves like gamma rays that have super small wavelengths have really high frequencies and are super duper energetic. Radio waves and Infrared waves with long wavelengths have lower frequencies. When we talk about frequency, we’re talking about how many waves hit you in a given amount of time. Where gamma rays are like “bam, bam, bam, bam”, Infrared waves are like “bam…………bam…………bam………….bam”.

As an aside here: you ever wondered why your car’s antenna is as long as it is? That’s because the wavelength of radio waves is about 100 centimeters – just about how long your car’s antenna is!

Please excuse me now. I have an appointment to receive a wedgie and be stuffed in a locker.

Tuesday, September 11, 2007

Snell ya later

Snell's law was one of the first physical laws that I learned as a young, fresh faced undergraduate. OH, how time has made me jaded. It’s actually a very simple law that has to do with the behavior of light refraction through various mediums. Let’s explore this law, shall we.

You know how when you stick something like a straw into a glass of water, the straw looks kinda bent? You’re seeing Snell’s law in action. But before we talk about the law itself, we have to make sure everybody is on board with the definition of a “normal”. The normal is just an imaginary line perpendicular to any surface. Perfectly perpendicular at a 90 degree angle to the surface. Easy enough. The only tricky part comes in when you’re dealing with a curved surface like a lens.You can see from the diagram that the normal depends on where you are on the surface of the lens. We’ll come back to this in just a second because this is why lenses are so good at doing what they do.

Back to Snell’s law. Snell’s law says that if a beam of light moves from a medium of high velocity (like air) into lower velocity (like water or glass) the beam is going to be refracted TOWARDS the normal. We can see this in the picture below:
You can see that instead of traveling along its original path, the beam bent up towards the normal. The opposite happens when you move from a medium where the beam has a low velocity to one where the beam has a higher velocity, like moving from glass to air. In this scenario the beam moves AWAY from the normal. Now let’s check out what happens in a lens:
Do this to a lot of beams of light and you’ll be able to focus those beams onto a single point!
Ta-Da! Now that you understand the principles of Snell's law, you can feel good about being a juvenile misfit while you're burning a line of ants with a magnifying glass.

Friday, September 7, 2007

You are incorrect, madam

Well my dears, it seems that I have steered you wrong (as per our discussion earlier in the week). To recap things, I was given some questions in one of my classes and chose to discuss the changing pH in the world’s ocean and how it relates to the uptake of CO2. I was of the opinion that this was a sneaky question seeing as the pH of the ocean is changing as we speak due to how seawater reacts with atmospheric CO2. While this isn’t totally incorrect (you like that double negative?), it’s not the answer that the proff was looking for. Turns out that the correct answer is that the world’s oceans have had a relatively constant pH since the last ocean anoxia event 10s of millions of years ago.

Ocean Anoxia Events (OAEs) are times in the earth’s history where the deep oceans lost most, if not all, of its dissolved oxygen. Lots of very smart people are spending very large amounts of money to figure out why these events occur because nobody has a straight answer just yet.

This is what an OAE is like: You ever been swimming in a lake? Chances are good that if you went in the summer, the upper couple of meters was nice and comfy; but if you swam (swum? swimmed?...oh, forget it) deeper you’d hit a boundary, below which the water gets really really cold. That boundary is called the thermocline and exists not just in lakes, but in oceans too.

thee thermocline

The effects of sunlight can only be felt, at most, 60 to 100 meters deep. We call this layer the surface ocean. Everything below it is considered the deep ocean. The surface ocean and deep ocean don’t transfer water that easily. Upwelling and downwelling are pretty much the only ways the water "communicates". All that warm stuff on top wants nothing to do with the cold and salty stuff on the bottom. The only way to mix them is via ocean currents that move various bodies of water all around the earth through the deep sea.

During Ocean Anoxia Events, the world’s oceans become a lot like that lake. Communication between the surface and the deep is cut off, which limits the input of dissolved oxygen to the deep ocean. Without that input, all the fishes, and jellyfishes, and sharks, and shrimps, and crabs, and microorganisms that live in the deep sea eventually “breathe” up all the available oxygen until there is no more. No more oxygen = no more life = mass extinctions.

The chemistry of deep waters gets really screwy when all the oxygen is gone. Chemicals like hydrogen sulfide appear in the deep sea and we get a condition that is known as “euxinic”. These conditions are bad, bad, bad for the life that we know and love but great for organisms that thrive in low oxygen conditions. So, to bring all this back home to the question of pH, yes, the pH of the world’s oceans has remained relatively constant for a long long time. That being said, I'm going to stand my ground and say that I wasn’t totally wrong. Meh, whatevs. "A" for effort, right?

Wednesday, September 5, 2007


I have lots of things to do lately. New classes to take and teach, bright young minds to nurture with science, and thinking up new and creative ways to put off what I should really be doing. I’m taking a class called “Advanced Biological Oceanography”. Let’s break that down: Advanced – ruh roe. Biological – haven’t taken biology in years (poop sandwich). Oceanography – THIS I got nailed. We’re lookin’ at 1 outta 3. Part of this class is answering a few questions given to us in lecture. We got 3 questions last week:

1.) Why are the chemical properties of water (H2O) different than hydrogen sulfide (H2S)?
2.) How long has the chemical composition of the oceans remained constant? What is the evidence?
3.) How long has the pH of the ocean remained constant? What is the evidence?

Now, I’ll admit that I barely know earth history. I have only absorbed enough to nod at all the right times because I’ve been in close quarters with geologists for the last 2 years, and believe me when I say that close quarters with geologists can get a little rank. The poor microbiologists in this class couldn’t possibly know where to begin, bless their hearts. Can’t say I’m in much better shape, but I guess all I can do is my best. Let’s tackle one of these questions right now, shall we?

#3. Trick question. The pH of the oceans is currently changing due to uptake of CO2. The ocean is an enormous sink for CO2 on the surface of the Earth, taking up approximately 1/3 of anthropogenic (man-made) CO2 (1). As the ocean takes up this CO2, a series of reactions takes place starting with the production of carbonic acid (H2CO3), then bicarbonate (HCO3), then carbonate (CO3). Each reaction frees up a hydrogen ion:

CO2 (g) + H20 (l) <--> H2CO3
H2CO3 <--> H + HCO3
HCO3 <--> H + CO3

The more free hydrogen ions we have floating around, the lower the pH of our oceans. Remember that lower pH means more acidic. The evidence that the pH of the oceans is changing can be gathered from field measurements or by monitoring oceanic calcifiers. As the ocean becomes less alkaline, there is less of the carbonate ion around for these plants and critters to use to make shells and/or skeletons. Bad news for corals.

Well, that’s one down, two to go. Maybe Advanced Biological Oceanography won’t be that bad*.

1: Orr, J. C. et al. (2005). Anthropogenic ocean acidification over the twenty-first century and its impact on calcifying organisms. Nature 437, 681-686.
*Or it will be soul-crushingly hard.