Runaround

I’ve been working with a NMR a lot lately. It generates a reality all its own. Working with it during the past couple of days has taught me a few lessons:

  • You left something down a flight of stairs in the other lab. Figure out what it is.
  • Murphy’s law says as soon as a professor says this needs to be done today, another student will show up with the same urgency, whose sample should take much less time than yours. In theory. His sample is bigger on the inside.
  • After you insert a sample, you will realize that you forgot to remove your metal watch,  which might have messed up the magnetism of the NMR or your watch. No joke, my watch is losing time, though that might be the battery.

    Poor Watch

  • If you’re counting on getting “done” within a set amount of time, you won’t, because…
  • Shimming a sample never works the same way twice!
  • It may be necessary to pray for the equipment to get it to shim properly.
  • If labels can fall off, they will. Color code the caps of NMR tubes in sequences to make things simpler. (I use green-white-blue for incrementally more concentrated solutions.)
  • Make too much solution. Even if you use a volumetric flask, the elves will steal a few tenths of a milliliter.
  • There isn’t enough time to do homework between samples. Well, maybe like one question.
  • Do the dishes. The dish tray is a queue, not a dishwasher.
  • Things often don’t work out as planned. Keep going. 🙂

Tales of This Summer

Room with a View

I’m at MIT this summer! It’s awesome. I can see the Charles River out  my bedroom window. That’s awesome. I’m taking sailing lessons (triply awesome). But I have not written of my adventures yet!

I have a new phobia of pop-top cans. (not awesome.) It was Friday morning and we had just finished a grueling 20-hour journey from Georgia to Massachusetts. Although I only drove a couple of those hours, I was totally worn out. I grabbed a can of Campbell’s soup, pulled the tab…there was blood everywhere. I lost gallons of blood, but knowing I only had mere moments before I lost consciousness to blood-loss, I acted calmly. “Get me a paper towel” I told my younger sister as I washed my wound. “And get Mom, I’m about to faint.” “Joanna, just get a band-aide…” “Shut up! I’m going to faint!” Anywho, I spent the next three weeks feeling faint whenever I changed the band-aid…and the past couple of weeks showing it to anyone who will look. Look at this scar! I can regenerate! It’s awesome!”

I rode public transportation solo for the first time a week ago. I planned to attend a party thrown  by a friend who lives on the other side of Boston. It was out of biking range but I could take the bus and the subway. Unfortunately, I didn’t have a Charlie card, and while I could buy them at Star market, the website claimed the stores closed after 7. (Lies!) “No problem, I’ll just bike over to the subway station to buy a card” I looked for it for a while. After finding the station, I considered giving up the project, but I’d come so far! No, I was going to do this. Getting off the train, I noted that this wasn’t a very nice neighborhood, and I quickly set off in what I thought was the correct direction. “Hey, look! The street just changed names, and I haven’t found the cross-street.” I walked in the other direction. “Heh, heh, heh, now isn’t that funny, the street changed names again!” I then called my friend, who instructed me to walk to the *other* end of the street. After some maneuvering, I eventually found the house. By this time, the party was long since over. But I got ice-cream, and soothing photographs of water, and a summary of the pantheon of Middle-earth gods and genealogy. I also got a bed for the night. But I think I speak reasonably when I say that I am NEVER doing that again.

4th July in Boston

Living in Boston has been an experience. I have heard that Bostonians are rude. I’ll have none of that! Bostonians are kind and considerate…they’re just aggressive. (They invented America! Yah hear?!!) The people at MIT have been very kind and very good at explaining things from first principles. But the nice isn’t exclusive to MIT. The second time I rode the train solo, there were all sorts of tough-looking people on the train. One such person, who was sitting with his own group called over at me. “Hey! I like your shirt!” (Said shirt has “study” written across the chest and has earned me both positive and annoyed comments) “Uh, thanks?” “Yeah!” he said, “I think everyone should find something and just study it.” Yup. Just don’t talk trash about the Red Sox. Don’t do it. (Wearing Yankee’s apparel counts as talking trash.)

As for life in the lab, things have been fairly quiet. Professor Ross’s group, in which I am working, researches how to customize magnetic nano structures. Our research will eventually help to make really tiny memory and logic devices. This is important, because as computers continue to shrink, their components will soon be on the molecular-size level. A very simple example of a memory device in a computer is the electronic flip-flop which is used for counting. You know that computers operate in 0’s and 1’s (or on and off states). If we have a line of magnetic pillars and we turn the magnetic direction of one of the pillars from the “off” to the “on” direction, maybe we can make the next pillar to turn from off to on when the first pillar turns off again. Maybe we can make a third pillar turn from off to on when the second pillar turns off again, which would allow us to count in binary. (001 is 1, 010 is 2, 011 is 3, 100 is four, 101 is five, etc.)

MIT building 10

My project is to figure out how reclined octahedrons’ (diamond-shapes that are lying down so all you see is a triangular face) magnetic dipoles (Magnetic dipoles are like a tiny chunk of magnetism.) behave differently than the magnetic dipoles of standing octahedrons, and how the properties of different materials change the behavior of the magnetic dipoles. In particular, we have been studying what happens to the magnetism when the pillars get squeezed. To do this, we grow the crystals surrounded by a piezoelectric (which expands when current is run through it, and squeezes the pillars) Another thing I, personally, hope to discover is why the octahedrons sometimes lie down and sometimes stand up.

First, I have been modelling these things, I am writing input for an object-oriented micromagnetic framework software and it models the magnetic dipoles. (Translation: I write something that looks like code, and the computer draws me a picture of which way the north and south poles of a magnet are pointing.) So far, I have only drawn a single octahedron. There has been lots of geometry involved. Who knew you could mess up basic geometry so many times? Secondly, I’ve been testing samples of standing octahedrons because the reclined ones do not seem to be growing under the conditions the group thought would work. (For the curious, we have been using a silicon substrate covered with a layer of yttrium doped zirconia, which is covered with a layer of CeO2 which is finally topped with BiFeO3 which acts as piezoelectric and surrounds the pillars which are made of either CoFe2O4, Fe3O4, MgFe2O4, or NiFe2O4.) I’ve been using a vibrating sample magnetometer and a Hi-Res X-Ray Diffractometer.

Currently, I am looking for literature values of saturation magnetization, anisotropy, and exchange energy which I need for computer models. I am also scheming on how to best make an array of these things. (As I use it, an array is a group of objects arranged in rows and columns). I also need to learn how to properly translate the data from the VSM and HRXRD. Yay.

After all that lab work, I visited the Hyannis beach this Saturday. The sea is really salty. I though that perhaps it was a pleasantly salty, but it’s rather disgusting. It really burns when it gets into the eyes. Despite all this, waves are crazy awesome. I love waves. Waves are like wind, only waves can actually bodily move me. I’d take a day at the sea over SixFlags any day. However, I should probably mention that I have not swam at the beach for about fifteen years. I should also mention that I when I went to SixFlags a couple of years ago, I discovered that I don’t like most rollercoasters. The beach is still really awesome.  Kalmus BeachShell Art

The Fighting Chemists

Around 1600, Michał Sędziwój was one of the first to isolate oxygen, a controversial element. He also worked to turn mercury into gold.

Everyone knows that the way we name the members of the periodic table is largely arbitrary. In the beginning, we got fun names based on Latin roots. For example, the name for oxygen, which was discovered around 1772, was derived from the Greek “oxys”, meaning, “sharp” and “genes” meaning “begetter” because it was early believed that all acids contained oxygen. It is interesting to note that oxygen was first known in conjunction with nitrogen, and most other “airs,” as phlogiston, the fire element. When nitrogen was first isolated, as a homonuclear diatomic (two atoms bound together) it was called, “azote,” from the Greek for “lifeless.” Later it was named, “nitrogen” after, “nitre” and the Greek “genes,” for “begetter” because it made nitrate (NO3) compounds. Nowadays the elements we discover are not half as important as those first elements, if by important we mean “useful.” The fights over naming them, however, are ridiculous. In a way, this is a good thing, because it means we have so many scientists in the field that their research overlaps. Science is all about replication of results.

I still think that 10 years is a lot of time to spend in argument over a name after the results have been replicated, only to end up calling element 112, “Copernicium.” Copernicus is a fine scientist to name an element after, even if he was a famous astronomer, rather than a chemist. Did we really need that long to decide on an uncontroversial name like that? I find it ironic that these scientists, who argued as though the world revolved around them, ended up naming the element after the man who proved that it doesn’t. Perhaps someone at IUPAC, the Union of Pure and Applied Chemistry, has a sense of humor. I wanted a 112 to be a name with a back story, like say 66, Dyprosium. There has to be an interesting meaning behind that name. In fact, it means, “hard to get,” a reflection on thirty frustrated attempts to isolate it. More importantly, I want to know how many elements we have officially. When the elements are still in limbo, both in name and in existence, they get names like 118, Ununoctium. This is a fun name to say and a hard one to spell, like many other element names. However, it is so boring and systematic, that it is pretty obvious that IUPAC had a hand in naming it.

At times, I wish the IUPAC had named the entire periodic table the boring way, supplementing traditional names, as they did with their system for naming organic compounds, but I realize that all these names are artifacts of another age. I also realize that trying to instate new names would make elemental names just as confusing and difficult to remember as certain group names. (Curse you, neopentyl!) By the time I am eighty, I predict that we will have developed the technology to confirm the discovery of all 118, but today we are still discovering what the world is made with. That is pretty exciting, even if we do have to manufacture the elements to observe them. Up to the present day, I can date textbooks by which version of the periodic table they contain, and it is truly fascinating to look at my grandfather’s chemistry texts and see how far we have come in fifty years.

Then again, perhaps we have not come so far. In 1811, Courtois was excited about his discovery of new purple substance, and gave a sample to Gay-Lussac. Gay-Lussac proceeded to take the vial of substance Courtois gave him home, study it, and claim the discovery of iodine as an element. (Iodine means, “violet.”) Davy was not happy about that because he had also been working with iodine and identified it as an element. Again, in 1834, Berzelius steamed after Jean-Baptiste Dumas’s lab assistant Laurent offered up a paper discounting his theory dualastic theory of chemical structure (In short, all substances are formed by ionic bonds, but polyatomic ions exist.) with his nucleus theory. (Basically, as long as the geometry of the molecule stays the same, individual atoms may be replaced without changing the nature of the compound.) Berzelius got so upset that Dumas had to write a letter explaining that Laurent had jumped to a conclusion, and that he had nothing to do with his protegé’s theories. If grown men argued over minutiae in the dawn of modern chemistry, then I can rest assured that science, or the scientist, has not changed much over the course of two hundred years. (Is it only that long?)

So IUPAC, you get off the hook for taking 10 years to name 112, “Copernicium,” but could you hurry up with the next batch of names? I want a good story to tell. More importantly, I still can’t spell my name with the elemental symbols.

Science Is Not Exact

I once thought that I liked science because it was so exact. There were rules, and everything turned out exactly the way you expected it to. There is only one problem–it does not. On paper, you can predict exactly what product will form, and maybe even predict our percent yield? (We speak of chemistry here.) In other words, the conventional view of science is that it can quantify everything–and if it cannot, well, then at least it can quantify the exceptions. That is a problem. Science is not exact.

My first experience in a freshman chemistry lab was somewhat harrowing. Do not misunderstand me (or my self-contradictory double-negative construction)–I loved every minute, but I learned a lot about scientific error that I had not learned in our makeshift homeschool laboratory (the kitchen) where I attributed all my errors to things sticking to the pans. The first things I learned in the lab were what a Bunsen burner and hot plate looked like, much to the amusement of my lab partner, but I also learned several other things that the general public could benefit from knowing.

  1. We do not understand chemistry. I was aghast to discover that most of what we know about chemistry was discovered in the 20th century. Before then, it was just carefully experimenting with elements–which may or may not have been pure–in order to classify them by what happened when they reacted with other elements. I have some of my grandfather’s old chemistry textbooks © 1921, 1940, and 1946, and they are primarily descriptive chemistry. What is sulfuric acid? How does it react? How can you make it? They lack the why. Today we know a little bit more, but we are still fumbling to figure things out. I have only just begun organic chemistry–which is rumored to have a lot of memorization of reactions. (Indeed, my father concentrated on chemical mechanisms so he could focus on the why rather than the memorization.) Even so, it seems that in organic chemistry, we are still trying to figure things out. We have classified different kinds of organic compounds and know in general how they react, but the why does not seem widely known.
  2. We have invented several aids to help us, such as the scientific method, but science will never be exact as long as humans (and pieces of equipment) are fallible. The main problem a lot of us have with evolution, and, to a certain degree, global warming is the amount of subjectivity involved. You did an experiment, but did you make an error and does the experiment prove your hypothesis? The temperature of the earth is rising, but is this due to the natural heating and cooling cycles, the placement of your sensors, or even what you want to believe? In the end, it comes down to what the researcher is willing to believe. I routinely researched and wrote my lab reports with the “right” answer in mind (listing the myriad of experimental errors, of course). In addition, science comes down to observation, and thus to the observer. My lab partner would not record deviations from the standard 1 mL release in a titration because he said it was “experimental error.” My partner and I also routinely disagreed on whether the solution was yellow or orange. The scientific method is useful, of course, but as long as the human mind is not a computer, subjective differences will exist.
  3. Sometimes Things Happen. We all remember times where, for some reason, the cookies came out of the oven looking like a smoking heap that had barely escaped the fires of Mordor. We remember times when, despite all our planning, trips just did not work out. Science is like that too sometimes, often because of our own ignorance. I remember my room mate coming home one night and telling me that neither she nor her professor had any idea what their experiment had produced. Whatever it was, it was not what they expected. However, this does not have to be a bad thing. Sometimes it is an opportunity to discover new things. Fleming discovered penicillin this way. My roommate told me another night that by accidentally spilling water into their experiment, they had sped it up and increased the yield. Their only problem was duplicating the results.
  4. Finally, there are always exceptions to the rule, plain and simple. These are not due to human ignorance, error, or the mysterious forces of Things Happening, but because there just are. One thing I have not meant to do in this post is to imply that there are not exact rules in science or that exact truth does not exist. It does, just as it does in every subject and in life, (You may debate that with me in the comments.) but the absolute truth does not have blanket rules, that is all. There is a new rule for each exception. Or  perhaps we do not understand the science well enough to write good rules yet.

Thus, science is not exact, at least not off-paper. I compared science to math before I came to college, but it is not like math; science is more like a cross between math and golf. You can calculate a stroke with mathematical precision to fall into a hole, but the golfer does not necessarily hit it into the hole, although he may come very close. And the more strokes he takes to get to the hole, the more imprecise the experiment gets, or something like that. I do not know anything about golf.

This discussion raises a new question. If science is not exact, and I liked it because I thought it was, then why do I like science now? I suppose I like it because it is a search–a search for truth, an effort to classify what we know, and a study built around discovering new things and helping people. That is why I like science, though my humanity and my lab partner may sometimes annoy me.

Agree? Disagree? Did I miss any other reasons that science isn’t exact? Send me a comment!

Many thanks to jefftaras for making his photo available at stock.xchng. (http://www.sxc.hu/pic/m/j/je/jefftaras/445412_lab_stirrers.jpg)