Archive for the ‘chemistry’ Category

Cold, damn cold.

May 1, 2010 Leave a comment

After writing much of these posts and then showing off my work, my wife, more often than not, will ask questions of stuff that I never even considered. In telling her about water bears, she just had to ask how they managed to freeze the water bears to near absolute zero. This eventually led to me looking up how liquid nitrogen is made (it’s actually a really cool process, just you wait) and then I started looking at other stuff related to the cold. Which, unfortunately is going to lead to a meandering totally disorganized post. So strap yourselves in because in the words of Martin Lawrence, “Shit just got real.”

When looking stuff up about water bears, I wanted to learn more specifically about how they are able to survive being frozen. It turns out that when temperatures drop water bears and other cold-blooded animals make chemicals known as cryoprotectants. These cryprotectants lower the freezing temperature of cells to prevent the damage caused when cells freeze and crystallize. It’s crazy that these animals can go so far as changing their body’s chemical make up to survive.

Along with cryoprotectants many cold-blooded animals will bury themselves during winter months. Many will do this in the mud at the bottom of rivers or lakes. Cold water is more oxygenated than warm water and the animals actually get all the oxygen they need through their skin.

Cryoprotectants are actually administered to those who choose to be cryogenically frozen. This is to avoid cell damage when the water in the body freezes and crystallizes. Despite the widespread knowledge of the process of cryogenic freezing, only about 200 Americans have actually gone through the process in the forty years that its been around. Instead of being frozen before death occurs in hopes that future medicine will be able to cure whatever ailment the patient has, a person has to phyisically die in order to be preserved. The hope is that later science will be able to not only cure the ailment but also reverse the death. The theory behind all of this is that the brain may be able to retain long term memories for a short time after the body has died.

Unfortunately, one of the big problems with cryonic freezing, is that the cryoprotectants can protect the body from freezing, at the cost of essentially poisoning it. However, it’s assumed that the poisoning effect will be easier to undo than the cell damage that would otherwise occur.

Oddly enough, the best way to pay for the staggering costs of the initial freezing, not to mention the ongoing cost of storage, is to use life insurance to cover it. Apparently if you set up a plan when you’re young, freezing can actually be quite affordable. I’m setting up an account for my daughter first thing Monday. I can’t wait to see the look on my insurance agent’s face when I ask her about it.

Morbidly, I wanted to find out more about what happens to cells when they get frozen. it turns out that when people get frostbite, it’s actually the result of a defensive measure taken by the body. When the extremities are subjected to very cold conditions, the body will dilate the blood vessels going to those extremities. Hence, the extremities slowly undergo cell death due to a lack of oxygen and also freeze. The body will choose to kill off a portion of itself in order to keep the rest alive. While not exactly the same, this reminds me of the way that the body will sometimes cause a person to faint. If blood vessels dilate for some reason (say a dashing young southern gentleman chooses to call upon me and kisses my wrist), blood pressure will happen to drop. The brain will sense this and choose to cause the body to pass out so that the head (and the brain encased so deliciously within that head) will drop down. Less pressure is then required to drive blood to brain. The brain therefore saves itself by shutting down part of the body.

If the body is subjected to extremem cold for too long, the blood vessels will eventually tire out. This causes a surge of blood flow to the extremeties which makes people believe that they’re warmer than they actually are. This is combined with the hypothalamus shorting out. The hypothalamus usually regulates body temperature, and when it shorts out people think that they’re warmer than they are. A number of people who die of hypothermia are found having shed their clothes because of this.

So in much less depressing SCIENCE!, the way they make liquid nitrogen is awesome. If you like sauce it’s also awesomesauce.  First, they have to liquid air. You can do that by taking air air and cooling it down a bunch. The easiest way to do that is to compress it down a lot. But according to PVT, by lowering the volume, the pressure and temperatures have to go up. To counteract this, the air is cooled in a heat exchanger and then vented into another chamber to begin the process again. It’s repeated again and again until droplets are formed.

Once you have liquid air, all you have to do is distill off the other elements that make up air, and any hillbilly worth his moonshine knows how to distill. What you are left with is about 20% liquid oxygen and 79% liquid nitrogen and 1% other stuff. Once made, liquid nitrogen has to be kept in a special container that lets it vent occasionally. Liquid nitrogen will generally stay a liquid for quite a while if pressurized correctly. However, unless kept at -331 F, ambient temperature will slowly cause some of it to revert to its gaseous form. This can cause a bit of a problem since gaseous exerts a tremendous amount of pressure (nearly 700 times as much as liquid kind). Unless liquid nitrogen is kept in a ventable container, it can rapidly decompress and cause the container it’s in to explode, like a monkey in space.

Bonus! In searching for the answer to how liquid nitrogen is made, I found this neat little website which lets you run an applet that shows PVT in action. Go ahead and start wasting time with it.


See eff effin sees

March 21, 2010 Leave a comment

As my wife will attest, I have a horrible, horrible memory. This isn’t just important dates and anniversaries, which with the exception of my mother’s birthday I always seem to remember, but encompasses a lot of stuff that I supposedly have learned throughout the years. Case in point, I was rereading Carl Sagan’s Billions and Billions the other day and couldn’t remember a great portion of a chapter that I know I’ve already read. The chapter talks about the hole in the ozone layer, how it was formed, and what the effects of it are. Despite being wholly depressing, it was also extremely interesting to find out more details about something that has become much more prevalent and part of the collective psyche of the world in the last few years.

Get your hard hats out for this one, Skippy, because I’m about to drop some chemistry on you.

Most of the time, when we talk about oxygen, we’re referring to oxygen the molecule versus oxygen the atom. The molecule oxygen is made up of two oxygen atoms (O2); ozone is made up of three oxygen atoms (O3). Oxygen molecules are fairly stable but will break apart into two separate oxygen atoms when reacting with some form of energy.  Ozone is less stable than oxygen molecules but more stable than oxygen atoms. When a lone oxygen atom meets up with an oxygen molecule, they will pair up and form ozone.

O2 + Energy -> 2O

O2 + O + M -> O3 + M

The M stands for some sort of catalyst and is necessary to bind the O2 and  O together. This is why the smell of ozone is often associated with electrical devices. Electricity passing through the air will provide the energy necessary to break apart the oxygen.

This seems like good news for the ozone layer. The energy from UV rays provided by the sun is more than enough to break up the O2 so we should be constantly generating O3 in the upper atmosphere, since O3 becomes more stable at lower temperatures and pressures. The problem with this is that ozone can be broken up far easier than it can be created. All you need is another catalyst, like chlorine, and the upper atmosphere is filled with chlorine.

CFC is a generic term for a chemical compound involving carbon (that’s the last C) fluorine (that’s the F) and/or chlorine (that’s the first C), it stands for chlorofluorocarbon. When CFCs were first used, they were seen as a miracle compound. They had a number of important uses; the most prevalent use was in refrigerators, replacing the toxic ammonia or sulfur dioxide that was previously used, but were also eventually used in aerosols, cleaning agents and Styrofoam. There was no noticeable downside to them. They weren’t dangerous to humans in any way, shape or form. At least that they knew about at the time. The problem is that when CFCs are released into the atmosphere, they hang around for quite a while before reaching the upper stratosphere and the ozone layer.

Once they reach the upper atmosphere, the CFCs hang around for a couple of dozen years before good old Mr.Sun tears them into pieces. This results in lots of Cl atoms floating around. As I said before, chlorine is a great catalyst to break up O3, so once wrenched apart from its carbon and fluorine brethren it becomes a veritable home wrecker to the happy little ozone family. It goes down like this:

O2 + Energy (in the form of UV light) -> 2O

2CL + 2 O3 -> 2ClO + 2 O2

2ClO + 2O -> 2Cl + 2 O2

The net result of this is:

2 O3 -> 3 O2

Once it’s done with its business, the chlorine is left unchanged and is free to repeat the process again and again. And again and again and again and again.  Eventually the Cl will drift down from the upper atmosphere and make its way back to the surface of the Earth, but not before going through this whole process about 100,000 times.

If one chlorine atom can do that much damage, imagine what a large chunk of it can do. How large of a chunk, you may ask, well, at peak production, we were doling out CFCs at the rate of a million tons per year. Luckily, we’ve since cut back enormously on our CFC production.

You’ve got to hand it to DuPont for a big portion of that. At the start of the whole ‘depletion of the ozone layer’ debate, they were gearing up to be the evil nature hating conglomerate a la Giovanni Ribisi in Avatar, and with good reason. They were making $600 million per year on CFCs. They wanted to run their own tests to determine what exactly the danger was. No doubt, their finding s would turn up no ill effects. Once they were faced with the facts and a number of nations agreed to reduce the emissions of CFCs, DuPont became an industry leader and vowed to stop production far earlier than the deadline that was being enforced. Good on them.

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Categories: chemistry Tags: , , , , ,

Apparently A through W were taken

February 13, 2010 Leave a comment

I’m around X-rays all of the time at the hospital. They’re a common instrument used by the docs, so common that I don’t think that many people how appreciate them. I mean, every school kid learns about X-rays when they match objects to a corresponding letter, unless your teach is weird and makes you use xylophone. No one ever seems to uses xenon, our noble friend. It’s not like they’re new and exciting, though. They’ve been around for over 100 years. Still, it’s amazing that through a relatively safe, quick and  inexpensive method we can get a picture of a person’s skeleton and find problems with major organs.

One day when I was about 20, I developed chest pressure. It felt like there was a boulder on my chest. My mom took me to the ER, we got an X-ray and were told by the doctor that I had probably  an inflammation of the lining surrounding the lungs. I was sent home and told to take some ibuprofen (if I’m remembering things correctly, it turns out the doctor who told me this really doesn’t know his stuff because this is a symptom of a bigger problem, at least according to this). The next day we were called back to the hospital. The radiologist discovered something. He showed us the x-ray and told me to look at the top of my left lung. It looked exactly like the right one to me, then he pointed to a little black smudge at the top of the lung, which I couldn’t find distinguishable from any of the other black smudges on the x-ray. Two percent of my lung had deflated or collapsed. TWO PERCENT! The little smudge that he was pointing out was the “flat” part. No wonder the OR doc didn’t pick up on it.

But how do X-rays see what they see and why can they show through some things better than others? It turns out that X-rays work because of atomic energy states, kinda. When atoms are hit by photons (like from visible light) the electrons can absorb the energy from the photon and jump to a higher energy state. If the photon then drops to a lower energy state it has to give off the same amount of energy in the form of a photon. This is what happens when it’s said that light reflects off of objects, and explains how we see things. We’re not seeing the light wave bouncing off the object, we’re seeing the light given off by the object after the energy from the light source moves the electrons to a higher state. The larger an atom is, the more energy that’s required to move the electron to a higher state.

X-rays have a higher energy than visible light. When they hit atoms, instead of knocking an electron into a higher energy state, X-rays tend to knock the electrons completely away from the atom.  However, since electrons have such a high energy, they have a hard time hitting smaller atoms. Most of the rays pass right by smaller atoms while hitting larger ones. The soft tissue of the body is mostly made up of smaller atoms. Bones are made up of calcium which are big enough to absorb some of the x-rays. This also explains why lead is used to shield people from X-rays; it’s one of the largest atoms and absorbs x-rays like the sham-wow absorbs stains. When we look at an X-ray image, we’re actually looking at the negative. This is why the soft tissues, which most X-rays just pass through, appear darker than bones.

Categories: chemistry, Science Tags: , ,

The sicko experiment: part three

January 26, 2010 Leave a comment


Biotin sounds like a robot. In fact, it even looks like a robot.

A robot with a little carboxylic acid tail. This guy should be making meals for me, cleaning up after me and cracking wise, not floating around my body. What gives?

Like most B vitamins, Biotin is necessary for cell growth and metabolism. It also helps with transferring carbon dioxide, you know, so you don’t DIE. Apparently I don’t really need to take it because bacteria in my intestines produces more biotin than I actually need.

A deficiency of biotin would cause hair loss and and scaly rashes. However, to induce such a deficiency the bacteria would have to stop working, which could be caused by eating raw egg whites, a total of twenty per day would probably do it. I don’t really plan on doing that anytime soon, so I consider myself pretty safe. Cool vitamin, but ultimately unnecessary to take anymore.

Vitamin B6

This one can’t be too important, it doesn’t even get a proper name. Turns out it’s important for histamine synthesis. I’m assuming that the antihistamines I take daily are meeting up with B6 almost constantly and creating the most wonderful explosions. It also helps in creating hemoglobin, which I suppose is important. A deficiency of B6 results in confusion and neoropathy. So while I’m not sure what it really does, I know what it doesn’t do when it’s not there, which is pretty scary.

Vitamin B12

For how important it is, B12 gets hosed in the name category. You automatically associate with B6, but B12 actually helps out with all of the bodies functions, but most importantly the brain and nervous system.You can actually absorb it through the mucus membranes in the mouth. Not getting enough B12 actually causes anemia and a number of psychological maladies including depression, forgetfulness, mania and psychosis. This explains why I draw so many vitamin B12 blood samples in the psych ward of the hospital. It’s also crazy complex looking.

Categories: Biology, chemistry Tags:

Whoopsie daisy

January 9, 2010 2 comments

In my last post I mentioned how I thought that nitroglycerin the medicine and the explosive were given the same name, but were different substances. I then compared that to how alcohol and rubbing alcohol are different, because you don’t want to drink rubbing alcohol. As it turns out, this was a completely bogus analogy. It turns out that I should’ve been comparing the similarities between the two kinds of alcohol and the two kinds of nitroglycerin instead of trying to show how they were different.

As it turns out, rubbing alcohol and the alcohol we drink are the same thing, it just has to do with the concentration. Most of the alcohol that we drink is between 5 percent and 50 percent ethyl alcohol (the proof is in the proof, with beer/wine being on the lower end and ‘hard’ liquors being on the higher end), whereas rubbing alcohol is about 75 to 90 percent ethyl alcohol. Kind of the way that nitroglycerin the medicine is much more diluted and less concentrated than the explosive.

So why isn’t rubbing alcohol safe for us to drink? Besides the high toxicity of the alcohol levels, methyl alcohol and other poisons are added to rubbing alcohol. This is done so that it can be sold as a disinfectant without the high taxes and restrictions associated with other alcohols. There are also poisons added to give rubbing alcohol its unique smell, which is used as a warning sign to avoid unintentional consumption.

Along with learning new things, I sometimes really enjoy finding out that I’m wrong about something. When I’ve made a mistake and learn about it, I’m much less likely to make the same mistake. It’s an effective learning tool since I have a vested interest in finding out how I screwed up so that I can avoid it in the future. Learning something new by making a mistake ensures that I’ll remember something much better than I would by just learning the same material on its own.

Nitroglycerin is crazy awesome

January 8, 2010 3 comments

I always knew that nitroglycerin was an explosive and a kind of heart medication, but I didn’t realize that they were the same thing. They’re not usually talked about at the same time, so I figured that one was nitro-glycerin and the other nitroglycerin or that one was nitroglycerine. Like the way that alcohol and rubbing alcohol are both alcohol, but you don’t want to drink rubbing alcohol (trust me on this one). Or that one of the nitros stood for nitrite while the other was nitrate. In short, I thought they were different.

Nope, same thing. Same exact thing. The medicine they give people for heart attacks is identical to the stuff they use to make stuff explode, the only difference is the concentration.  When it was first produced in the 1800s nitroglycerin accidentally blew up quite a few people. It’s an extremely volatile compound and until safer ways were invented to produce it there were numerous, shall we say, incidents. Since there were numerous deaths associated with these incidents, they became quite the news items and nitroglycerin became known as something to avoid. When it was discovered to be a good vasodilator (vaso meaning vein and dilator meaning dilator) and doctors started giving it to people exhibiting symptoms of chest pain, they needed to call it by a different name so as to not panic the patient.

Alfred Nobel (the Nobel prizes Alfred Noble) discovered that if you mix nitroglycerin with silica, it forms a much more stable paste. Stick that in a tube with some sawdust and a blasting cap and you have dynamite. This is different from TNT (trinitrotoluene) which means that AC/DC lied! Nitroglycerin causes veins to dilate. While this alleviates heart pain, it can cause migraines. If exposed to too much of it, the body becomes accustomed to it and nitroglycerin loses some of its effects. This wears off over time, and people who work in nitroglycerin processing often suffer from ‘Monday morning headaches’. During the week, they’re exposed to so much nitroglycerin (since it can be absorbed through the skin), that their bodies become accustomed to it. Over the weekend this wears off and when they return to work Monday morning, the nitroglycerin is effective again, which causes the workers blood vessels to dilate and creates headaches.

Nitroglycerin is uses nearly every day where I work (the medicine, not the explosive), and I never realized how long it had been around for. I tend to think that anything that is used so effectively would have to be relatively recent.  The same thing that doctors give to patients as a little pill in stronger concentrations and greater quantities is a highly volatile explosive. How awesome is that?

Running for the shelter of everyone’s little helper.

November 23, 2009 Leave a comment

This weekend while laid up with a cough, I experienced two of the different effects of caffeine. One of the effects was very welcome, as the caffeine in an excedrin helped to relieve my headache. The other effect wasn’t as welcome, when the same caffeine kept me awake for the next four hours. While I lay there, trying to fall asleep, I started to wonder how caffeine did what it did, and whether the reaction that reduced my headache was the same thing that kept me awake. Part, but not all, of what kept me awake also relieved my headache.

As we digest caffeine, it enters the bloodstream, because of it’s relatively small size caffeine is also able to pass through the blood-brain barrier. While in the brain, caffeine binds itself to adenosine receptors. Adenosine is found everywhere in the body and is important in ATP metabolism. In the simplest terms it is the last stage of turning the food that we eat into the energy that we use to function. In the brain, adenosine has a slightly different role by protecting the brain by suppressing neural activity, by doing this adenosine makes us drowsy. When caffeine binds to the adenosine receptors, which it’s able to do because of caffeine’s similar chemical structure to adenosine, it blocks adenosine from doing the same and prevents us from becoming drowsy. This is one of the ways in which caffeine works.

Since adenosine is naturally created by the body, when it’s not able to function as it normally does the body reacts. When caffeine takes the place of adenosine and block adenosine receptors, it doesn’t suppress neural activity like adenosine does. The body is used to this suppression, and when it doesn’t occur, the body reacts. The relative increase in neural activity, makes the pituitary gland believe that the body is in some sort of danger and activates the adrenal glands to release adrenaline. So caffeine delivers a one-two punch by first inhibiting drowsiness and then by releasing adrenaline which makes us more alert, along with several other side effects. One of the more important side effects is that the liver releases sugar to give the body extra energy.

This explains why caffeine makes us more alert, but doesn’t explains why it relieves headaches. One of the functions of adnenosine in the brain is to dilate blood vessels.  This is so that when we’re sleeping, and our breathing slows, the body is still able to get all the oxygen that it needs. Unfortunately, dilated blood vessels in the brain can become inflamed and create headaches. When caffeine binds to the adenosine receptors, they inhibit blood vessels from dilating. One of the other effects of adrenaline is that it constricts blood vessels, which further reduces headaches.