In the ongoing saga of my toe, yesterday I got a cortisone shot into the joint. It was neither the least nor the most comfortable experience in my life, but as with any medical incident I end up in, I wanted to know exactly how it worked. So how does a cortisone injection work? What does it do? What is it going to help in my toe?

I was diagnosed with inflammation in the joint as well as a bone contusion. The injection isn’t going to do anything for the contusion, but it will help the inflammation. Cortisone is actually a steroid that the human body produces in the adrenal gland; it gets released, along with adrenaline, when we are stressed. We don’t get injected with human cortisone, however; the stuff that they use is synthetic, and is designed to be longer-acting than natural cortisone.

Cortisone has a lot of usages, as steroids do. There are several ways of taking it; itch cream, for when you get a bug bite, has cortisone in it, but it can also be taken orally or intravenously. I got a small injection right into the joint, myself.

Its function is to suppress the immune system, which ends up reducing inflammation. It does not directly reduce pain (like a numbing agent might). Inflammation is often the cause of pain, because tissue is swelling against itself and causing pressure, which is painful. Now here’s where I’m going to be honest with you: I don’t know how this bit works. I really wanted to find out the chemical processes that make this happen, but type in “cortisone suppressing immune system” into Google and all you get is a ton of woo from acupuncture people saying you shouldn’t use cortisone because YOUR IMMUNE SYSTEM WILL DIEEEEEEEE. I don’t have much patience for that sort of thing, so you’ll have to forgive me.

There is a very, very small grain of truth (that the woo people blow out of proportion) to the immunosuppressant dangers. If you’re immunocompromised in any other way, or have a fungal infection, or another infection, or get a live vaccine (etc), then it is possible that cortisone is going to suppress the immune system further. This is more the case in long-term treatment with cortisone.

To me, the larger danger of cortisone is using it in the wrong situations. There are some things, like overuse injuries, that people get injections for, and continue to get injections for, where the shot doesn’t work. This is mostly because overuse injuries are not always the result of inflammation. Pain is not always the result of inflammation, either, so asking for a cortisone shot whenever you’re in pain is not really the best of ideas, especially if it’s because of something like tendinitis. I would also hypothesize that getting a shot for pain relief without, say, physical therapy to fix the underlying problem would lead to more damage in the long run.

A cortisone injection was a good option for me because at least some of the pain in my toe was due directly to inflammation. The cortisone will reduce that swelling, giving me some pain-free time (during which I am not allowed to immediately go back to my own tricks, damn), and hopefully the inflammation will go away permanently.

The result? Yesterday I was sore from the injection. Today my toe is already feeling a lot better. Hurrah for modern science!

NECESSARY DISCLAIMER: I am NOT A DOCTOR. I have had no medical training. My injection was the result of a discussion with my foot specialist doctor, several imaging sessions, and thought. Talk to your own doctor if you have pain; don’t just go in requesting an injection, even if you think it may be inflammation. Talk with several doctors, if you want. But always make informed decisions within the advice of a professional.

Sources:

http://orthopedics.about.com/cs/paindrugs/a/cortisone.htm

http://en.wikipedia.org/wiki/Cortisone

http://www.drugs.com/mtm/cortisone.html

http://well.blogs.nytimes.com/2010/10/27/do-cortisone-shots-actually-make-things-worse/

• Free geeky pumpkin carving templates: no, it’s not science, but it is nerdy! I think I’m going to do the Pan’s Labyrinth hand-eye creature.
• Computer scientists crack “unbreakable” code and find the minutes of a long-lost secret society: I love stuff like this. So, so much. I took a cryptology course in college and I’ve been hooked ever since. If they could get the Voynich Manuscript…oh my goodness, how exciting that would be!
• This is about the best thing you will read all week, and it’s all about octopuses.

Fish are truly remarkable animals. First off, the question of what a fish is is a pretty tricky one, because fish are defined by what they’re not, namely mammals, reptiles, amphibians, or birds. Secondly, they breathe by doing a direct gas exchange, but only in the region of their gills, unlike water-dwelling amphibians. Anyone who’s had a pet goldfish has watched it swim round, opening its mouth to pass water through, looking like it’s taking big drinks. In all that water, how do fish maintain the proper levels of hydration? After all, everything needs water to survive. How do fish drink?

The answer is: it depends. 

Image by catchesthelight

Let’s talk about our goldfish first (I had one once; his name was Sir Owain Barnabas Ichabod the First. He lived for 6 years and greeted us everyday at feeding time). The first thing we have to understand is the process of osmosis. Most of us heard this term in high school science classes, and since then we’ve only heard it used for non-scientific things. Diffusion is the tendency of molecules to move from an area of high concentration to an area of low concentration, with the “aim” of making everything evenly distributed. Osmosis refers to diffusion in the case of water—because water is so important for life and in so many life processes, it gets its own special name. Basically, water gets into any cell by the process of osmosis: from your stomach into the rest of your body, and so on. A quantity of pure water is always going to have a higher concentration of water molecules than water mixed with other molecules.

This is how freshwater fish get their water. Fish will either absorb or lose water depending on their needs and their surroundings. Being so close to a much higher concentration of water molecules, they do this directly through their skin. Freshwater fish also need salt to survive, and the concentration of salt in their bodies is always going to be higher than the concentration of salt in the surrounding fresh water. So a freshwater fish’s kidneys are always working to expel excess water, so that their salt doesn’t dilute.

But if you live in the ocean, you have no problem with losing salt; in fact, you have a problem with losing water, since the saltwater has way more salt in it than your body. Osmosis here is actually driven by the chemical balancing of salt quantities. Saltwater fish do actually drink water when they open their mouths to let water pass over their gills. Water is processed in much the same way we do, moving from the stomach to the rest of the body. The excess salt is then excreted on their gills, where it goes back into the ocean (or the tank, as the case may be).

So from this, it’s abundantly obvious why saltwater fish can’t live in freshwater, and why freshwater fish can’t live in saltwater. They have very different methods of dealing with water and salt in their bodies, and those methods don’t really adapt well to a different environment. Of course, there are a few fish that can live in both environments: salmon is a great example. Salmon can actually drink freshwater and process it the way a saltwater fish would, which is why they can live in both.

The differences in fish even from just saltwater to freshwater is only the beginning of the huge range of differences found in this group of organisms. No wonder we have trouble defining a fish! But now you don’t have to worry as much about your goldfish getting thirsty; if you’ve cleaned its tank and it has lots of lovely fresh water, it’s probably fine.

Sources:

http://en.wikipedia.org/wiki/Amphibian

http://en.wikipedia.org/wiki/Fish

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_diffusion_works.html

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_osmosis_works.html

http://indianapublicmedia.org/amomentofscience/do-fish-drink/

http://www.aquarium-pond-answers.com/2006/12/how-do-fish-drink.html

Image from SnowCrystals.com

You may or may not know that I work for a Major Outdoor Retailer. Regardless, in the retail world, winter begins in, oh, August. But being a snowboarder, when they start busting out the boards and skis in my store, I start thinking dreamily of days on the slopes, or gliding through quiet forests. I probably won’t be doing much of it for some time, but hey, a girl can dream!

That being said, let’s talk about the thing that makes winter worthwhile: snow. And let’s all take a moment to pray to the snow gods that we get dumped on this season (sorry, Southern Hemisphere friends!).

Done? Good. Oh wait, I’m supposed to be an atheist. Oh well!

Fight Club says it best: “You are not a beautiful and unique snowflake.” But this begs the question: what is so unique and beautiful about snowflakes, anyway? Is it true that each one is unique? And if so, why?

Snowflakes are crystals made of ice. Crystals are solid structures where all the molecules, atoms, or ions within are arranged in an orderly, repeating pattern in all three dimensions. Usually the structure depends upon the structure of the molecule or atom or ion, and snowflakes are no different. Think about your average molecule of water, and its chemical formula: H₂O. This means that there are two hydrogen atoms attached to one oxygen atom, like so:

Image from Wikipedia

Now if you arrange this atom repeatedly in a crystalline structure, the structure is going to be very hexagonal: all snowflakes are, in fact, six-sided (but it’s easier to cut the 8-sided ones out of paper…). Now snowflakes aren’t just frozen raindrops—that’s our favorite weather phenomenon, sleet. Snowflakes are crystals formed when water vapor freezes. The patterns on snowflakes form because corners stick out farther than everything else, making the distance water vapor molecules have to travel less. Then you keep building on those corners, and it becomes, well, all a bit fractal.

Different sizes and shapes of snowflakes form at different temperatures: if you live anywhere where it snows, you’re well aware of this. When it’s very cold out, you get very small snowflakes. The warmer it gets, the larger they get, until it’s right at freezing and you’re getting smacked in the face by wet snowballs falling from the sky (or maybe that was just in Ithaca). This is dependent on the amount of water vapor that can actually exist in the air at a given temperature: the colder it gets, the less water vapor there is.

So we’ve covered the basics of snowflakes now, so what about the ultimate question? How unique is each snowflake? Well, let’s look at it this way: water is a molecule, not an elementary particle. Not every water molecule is alike: some water molecules have a different isotope of oxygen in them, or an atom of deuterium (hydrogen with a neutron). A typical small, basic snowflake contains 10¹⁸ water molecules, which is one quintillion molecules. How much is a quintillion? Well, if you had a quintillion pennies and you laid them out flat, they’d cover the surface of the earth twice. If you put them in a cube, Mt. Everest would only be 1700 feet taller than the cube. A quintillion is a lot.

We’ve already got plenty of potential for difference in that number alone. With that many molecules, the probability that two snowflakes will have the exact same arrangement of the exact same molecules is really, really small. However, there are definitely snowflakes that look alike. The most basic snowflake is just a hexagon, and if you set two of those next to each other, you probably wouldn’t be able to tell the difference without an electron microscope.

For the complex snowflakes, it’s another story entirely. Let’s talk math for a second, and return to a really cool concept you may have learned in high school: combinations and permutations. Say that you have one suit of a deck of cards, the clubs. How many ways can you line up those 13 cards? Well, you have 13 choices for the first slot, and then 12 choices for the next slot, and 11 for the next, and so on down the line. It ends up being 13x12x11x…., or in mathematical notation, 13!, or 13 factorial. 13! comes out to 6,227,020,800. That’s 6 billion. With only 13 cards. So if you have anything like the quintillion molecules described above, and you take that factorial, well, that’s a number that is so far beyond the number of atoms in the universe that it’s incomprehensible. The number of zeros following this number is 249,999,999,999,999,995. That’s a quintillion of zeros. The number of atoms in the observable universe is 10⁸⁰. That’s 80 zeros.

There are nowhere near enough atoms in the universe to create all of the permutations of the snowflake and have a repeat. The odds of two exact snowflakes are so astronomically small that they are effectively zero. Of course, there are only certain patterns that water molecules can combine in, but the order of magnitude is not going to be reduced significantly by taking out the ones that don’t work.

The odds are that we will never see a snowflake that is exactly like another, not in the history of the universe. And if that doesn’t melt your brain, I’m not sure what will.

Sources:

http://www.its.caltech.edu/~atomic/snowcrystals/–SnowCrystals.com is run by CalTech. Amused? Because I am.

http://en.wikipedia.org/wiki/Crystal

http://kokogiak.com/megapenny/eighteen.asp

http://www.mathsisfun.com/combinatorics/combinations-permutations.html

http://en.wikipedia.org/wiki/Observable_universe

http://www.wolframalpha.com/–I did all my calculations for this post using this wonderful computational engine.

• The Ice Age might still be going on inside China’s deepest caves: courtesy of Demosthenes, this is an awesome finding. There are some seriously weird nettles going on in these caves that might be indicative of plant life during the Ice Age. Or they might be completely unique. Either way, nifty nettles!
• Climate shifts sparked 17th century conflict: yay Wired. Turns out conflict in the 17th century (including plagues, wars, famines, etc) can be correlated to climate shifts. Also turns out the authors didn’t extend their argument to today. Oh well. Still cool.
• Early paint making found in Africa: really cool stuff. It turns out there were Homo sapiens making paint from ochre 100,000 years ago, a good 40,000 years before any other discovered workshop. It begs the question why we attribute pyramids and stuff to aliens when our own species has done so many cool things…
• There isn’t an ancient, artistic kraken: at the Geological Society of America meeting this week, Mark McNemanin gave a presentation about how the only explanation for a set of octopus fossils neatly arranged was that an ancient giant kraken artistically arranged them there on purpose. This story got a lot of popular press, but guess what–no plausible evidence. PZ explains it handily, and NatGeo gives credit where credit is due.
• There aren’t enough cuttlefish in your life, and NPR agrees with me.
• Pitchers in baseball retaliate more readily in heat, and while more research is needed, one wonders what’s going to happen with global warming…
• There exists a Dance your Ph.D. Contest, and I’m pretty sure every Ph.D. candidate out there needs to go enter RIGHT NOW.

Humans have lived under the rhythm of the sun for as long as we’ve been around, in whatever shape we’ve been in. Sure, the advances of modern life and the ability to turn on the lights after dark has messed with this a bit, but ask anyone the day after Spring Forward if they’re still affected by circadian rhythms and they’ll give you a sleepy, grumpy “Yes.”

The cool thing is, there is actually a biological reason that we have a circadian rhythm, which is defined as a rhythmic response to light and dark. Light will activate different triggers in your body that will lead you to be more awake; lack of it will shut those triggers down and make you go to sleep. This is why you shouldn’t watch TV before bed.

So what happens when you have an organism that has evolved for millions of years with no light at all? What happens to those triggers, and to the rhythm they engender? Enter the cavefish.

This little guy, Phreatichthys andruzzii, evolved from surface-dwelling ancestors, but has been isolated underneath the Somalian desert for somewhere between 1.4 and 2.6 million years. This fish has no scales, no eyes, and no color—because these things are pretty useless in the complete dark. The authors of this paper compared the cavefish to the zebrafish, Danio rerio, a fish that has a really strong response to light: its genes in its tissues are entrained by direct exposure to light.

To start off with, the authors exposed both the zebrafish and the cavefish to a light-dark cycle of 12 hours on, 12 hours off. Plenty of response from our friend the zebrafish: movement and activity during light, not so much during dark. No response from our friend the cavefish. Okay, so let’s check in larval stages: looking at genes, the zebrafish exhibited a response to light-dark patterns by rhythmic genetic expression, whereas the cavefish had arrhythmic gene expression. So this leads to two possibilities: either the cavefish don’t have clocks at all, or their clocks respond to something other than light.

So let’s test another thing that might make the clock respond: food. If you’ve ever had a pet fish that you’ve fed at the same time everyday, you know as well as I do that they know when you’re coming with the food. Zebrafish behaved this same way, responding (genetically and behaviorally) to both light-dark cycles and food cycles. But the cavefish responded only to food cycles. And when you use bioluminescence and a chemical induction of rhythmic gene expression? Turns out the period of response for cavefish is somewhere around 38 hours, as opposed to 24 for the zebrafish.

Hey, look! Cavefish have clocks! They just don’t respond to light. Interestingly enough, they also respond to temperature: the period length decreased significantly when the temperature went up. Normally, a circadian rhythm is pretty constant over a range of temperatures, but apparently not here. Additionally, zebrafish light-clocks will respond to changes in light, so if you show them a bunch of pulses of light they’ll exhibit a response. Not so with cavefish—their clock is well and truly light-blind.

Genetically, the cavefish genes are not firing in response to light, as they do in zebrafish. Even when you switch the gene promotors between the two fish, cavefish don’t respond to light and zebrafish do. It turns out that a mutation in the photoreceptors might be part of the cause; this mutation in cavefish prevents a chemical from activating to tell the tissue that light has been received. This means that a couple of photoreceptors that were suspected of being the culprits for zebrafish circadian rhythms, Melanopsin and TMT-opsin, have a greater chance of actually being the culprits. We can now look for those compounds in other animals and see if they have a similar effect.

The big question is, why? Why did the clock go all kinds of weird for cavefish? Well, it’s a mechanism that has no selection advantage. If things that eat zebrafish come out at night, it would be beneficial for the zebrafish to get its business done during the day. Similarly, there might be some sort of periodicity in food supply underneath the Somalian desert where the cavefish lives, giving an evolutionary advantage to those fish who respond to the pattern. But this study also points to having a food-entrainable mechanism that is distinct from the light-entrainable mechanism, even though we don’t know what that mechanism does yet.

But perhaps most importantly, this paper teaches us a legitimately awesome word: troglomorphic. It means adapted to an environment without light, but that doesn’t mean it’s not also an excellent obscure insult.

Shine on, you crazy troglomorphs.

Disclaimer: I’m not a geneticist. I read a lot of this paper multiple times, and I can’t promise I understand all of it, but I have done what I can.

Other sources:

http://en.wikipedia.org/wiki/Infradian_rhythm

http://en.wikipedia.org/wiki/Promoter_(biology)

http://en.wikipedia.org/wiki/Transcription_(genetics)

http://en.wikipedia.org/wiki/Chromophore

When you get an x-ray taken, a beam of high-energy photons (x-rays, with wavelengths of .01 to 10 nanometers, much shorter than visible light) is shot at the part of your body you’ve hurt. X-rays penetrate flesh but reflect off bone, making them ideal for imaging broken bones. X-rays can also do damage to your DNA if you’re exposed to too much of them, but the amount used in imaging is perfectly safe.

Sometimes, though, the injury isn’t in the bone: it’s in some part of the soft tissue, which an x-ray can’t show. This is where MRI, or magnetic resonance imaging, comes in.

(Image by US Embassy in Manila)

An MRI machine is comprised of several parts. The whole casing is basically a huge magnet, one strong enough to generate a stable magnetic field. Most MRIs use a superconducting magnet, which is essentially a giant electromagnet. Let’s flash back to high school science for a second: passing a current through a coil of wire will produce a magnetic field (just as passing a magnet through a core of wire will produce an electric current—this is how stoplights know you’re coming). The wires in an MRI are supercooled by liquid helium—the colder the wire, the better the conductivity, and the stronger magnetic field the device can produce. There are also smaller magnets involved, called gradient magnets, which can produce variations in the magnetic field to allow different parts of the body to be scanned. The final component involved are the coils that you put whatever part of your body you’re scanning into; these transmit radiofrequency waves into the body.

Pop quiz: how many protons does a hydrogen atom have?

If you answered one, you’re right. Hydrogen is key in imaging with an MRI. There is a ton of the first element in our bodies, mostly because we’re made of a lot of water and fat. When you put hydrogen in a magnetic field, it aligns with the direction of the magnetic field. Normally, the hydrogen atoms in your body are just chilling, out, spinning whatever way they please. When you’re in an MRI, most of the protons in the hydrogen atoms in your body will align in one way or the other, pointing either up toward your head or down toward your feet. In fact, a huge fraction of them will cancel each other out: for each proton pointing toward your head, there’s one pointing toward your feet, and vice versa. However, there are a few—enough to image with—that don’t get canceled out.

These protons are what we’re looking for. The machine next applies a radio frequency specific to hydrogen, which makes the hydrogen atoms spin in a different direction again. In conjunction with this, the gradient magnets are used to pick out a really specific part of the body—a slice, if you will—by changing the local magnetic field. This allows for really precise imaging, which is super cool. When the radiofrequency pulse is turned off, the hydrogen protons will realign with the rest of the field, and in the process of doing so, they release the energy they absorbed from the pulse. This energy radiates back into the machine, and from this we get an image. The energy the machine receives back tells the machine what type of tissue it was in—any abnormalities are going to put out a different frequency than expected. The signal is received as mathematical data, which is put through a Fourier transform and translated into an image—essentially, frequencies are translated into the picture we see.

And that noise? That comes from the current in the gradient magnets opposing the main magnetic field. Most of the time they give you headphones with music. Hence my Bohemian Rhapsody singalong. I figured the technician couldn’t hear it over the noise, anyway.

If I’m given a copy of my MRI images, I’ll be sure to post them here.

Sources:

http://en.wikipedia.org/wiki/X-ray

http://en.wikipedia.org/wiki/Electromagnet

http://en.wikipedia.org/wiki/Fourier_transform

http://science.howstuffworks.com/mri.htm

Alternate title: children are bear bait (just as we’ve always known).

It turns out you shouldn’t drive a minivan into Yosemite.

Black bears are resourceful animals, and can figure out a great many ways of breaking into things to get the food they want. They forage selectively, picking and choosing their meals to maximize energetic gains and minimize foraging costs. This is a natural behavior, but it’s also one that gets enhanced in proximity to humans.

Black bears also happen to live in Yosemite. Humans have loved coming to Yosemite National Park for over a century, and with little wonder: it’s a beautiful, beautiful place.

(image by K. Moore)

There has been ongoing conflict between humans and bears in Yosemite for as long as humans have been visiting, and it’s a real problem. A big priority for officials in the park is nonlethal management of bears. There are efforts to educate people and penalize them for breaking the rules, of course, but we can all think of instances where this has flat out failed completely.

(image by torhutchins)

Do you see how close that person in the background is to this bear? Not only is this breaking the rules, it’s REALLY, REALLY DANGEROUS.

All bear incidents are documented by the National Park Service. This gives a pretty nice database with which researchers can work. So Breck et al decided to look at selective foraging of vehicles by black bears, to see if one vehicle was preferred over another.

It turns out that over a period of 6 years, minivans were the vehicle of choice for black bears, coming in 1st or 2nd place for break-ins each year. In fact, they sought out minivans moreso than they did other cars, even when minivans weren’t the most available vehicles. The question is, why?

There are lots of possible reasons for why black bears selected for minivans, and it could be a combination of any of them. But here’s my favorite, in the words of the author:

[I]t is possible that minivans were more likely to emit food odors regardless of whether they contained meaningful amounts of food available. This argument is based on the fact that minivans are designed for families with children and small children in particular are notorious for spilling food and drink while riding in vehicles. Thus, vehicles transporting children would emit greater food odors, making them attractive to bears.

This is the point where I wrote “I love this author” in the margin. Of course, as they point out, this would mean that any vehicle transporting children would be targeted more by bears; this would make for a really interesting further study, I think.

Another possibility is that owners of minivans might for some reason be more likely to leave food out, despite rules to the contrary. My theory is that this has to do with them corralling their children and not focusing on what they should be doing. Otherwise, it might be that minivans are easier to break into structurally, or that this might be the learned behavior of a few bears.

Regardless of the reason, the management implications here are really interesting. I’m not suggesting that Yosemite National Park exclude all minivans from entering; on the contrary, that would probably force the bears into choosing their next most selected vehicle, the SUV. But it could focus education efforts more effectively–maybe vehicles carrying families, like minivans do, need extra education and perhaps extra enforcement as well.

I liked this study a great deal: it was very approachable, interesting, a bit humorous, and relevant. The implications for management and further study are strong, and I really look forward to seeing what is done with this information, or at least where it leads.

Then again, child-free days at the park sound pretty good, too.