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April 27, 2005
Lab update
How's lab going?
It's fun, really fun :) there's just something about working with your hands, real liquids and proteins at your fingertips. That's not to say that it isn't frustrating... In fact, it's a whole lot more frustrating than computer work because just about everything you deal with in the lab setting is a colorless liquid. If you come across a tube with an unknown liquid inside, you have no easy way of knowing if it has protein, DNA, radioactivity, contaminants, cells... You name it, they're all quite colorless. In fact, it's quite impressive that one of the proteins we're working with is called GFP - green fluorescent protein - which really is green and fluorescent! Tubes of that stuff are pretty neat... they have a real bright green color. Anyway, on the computer you never are in doubt too long as to what you are working with - debuggers are excellent microscopes and can tell you anything and everything you would want to know.
Still, it's fun. I am getting more and more independent which is really nice... sometimes I need a bit of help but the guy I'm working with is very helpful. I feel like I'm learning this stuff very fast. Hopefully some of it will stick when it comes time for me to do my own research!
This week, next week, and the week after is all my crunch time. I've got two projects to finish, plus a problem set and a final exam. Once that is done, though, I'm all finished! Then the life of a graduate student really kicks in (meaning lab, lab, lab...)
Sent from: Karl Gutwin
Posted by kgutwin at 07:55 PM | Comments (1) | TrackBack
April 24, 2005
Osmo-what?
Osmotic pressure? You want me to talk about osmotic pressure? Well, sure... but why do you ask?
Ha, so ok, it was my idea. But I think it's kind of a neat thing.
Aqueous solutions, like many other chemical systems, tend towards equilibrium. Decoded: if you put a chunk of salt in a pot of water, the salt will slowly dissolve, but will spread the saltiness through the whole pot of water rather than all the saltiness just staying where the chunk of salt was. This process happens by diffusion, which we think we understand intuitively because it happens so often (smells spreading through a room, seasonings spreading in a dish) but really there's a chemical basis to it which can have some pretty nifty effects.
Diffusion really works like the following. Imagine a box. Now put some rubber balls in the box that never stop bouncing - the superest super balls you can find. This box is actually a pretty good approximation of what chemists call an ideal gas. OK, so this box is cool, but it's not useful yet. Let's take all the balls out of the box, and put in a divider so that the box is split in two halves. Let's put holes in this divider that are big enough for the balls to fit through but not so big that the divider isn't there any more :) Now, let's put all the balls back in the box, but we'll put them all on one side of the divider. As the balls bounce around, every once in a while one will approach the divider but will be going at just the right angle so that it goes through the hole and on to the other side. The probability that a ball will make this transition across the divider is a function of a few things: the average ball speed, the size of the hole relative to the size of the ball, and the number of balls on one side.
Now you can imagine what would happen over time. First we start with all the balls on one side. Every once in a while a ball would cross over, but it's far more likely at first that a ball will go from the more-balls side to the less-balls side than the other way around. And eventually there will be the same number of balls on both sides, so the probability of transitioning will be equal and the system is said to be at equilibrium.
Ok, fine, this is all good, but what does it have to do with osmotic pressure? And what is osmotic pressure in the first place? Well, osmosis is the diffusion of water across a semipermeable membrane. It is not, as college students think, that mysterious process where you learn things by sleeping with your textbook under your pillow. In fact, if you put "osmosis is sleeping with your textbook under your pillow" on your chemistry exam then you should have at least been paying enough attention in class to know what osmosis means! Ahem, anyway... osmosis is interesting because there are lots of semipermeable membranes out there. By the way, the definition of a semipermable membrane is a lot like that divider I described above. You could imagine that the divider has holes big enough to fit your superballs through but not baseballs. That's a semipermable membrane, and the most common one that we all deal with on a regular basis is the cell membrane, called the "lipid bilayer" by us biogeeks. All cells have at least one of these membranes, and the cool thing about them is that they let water through, but not big molecules like proteins. This is a very good thing! Otherwise, of course, we would just fall to pieces as all our proteins leaked out.
There is something pretty important, though, about the passage of water across these membranes. See, it's a curious chemical fact that aqueous solutions (stuff dissolved in water) tend towards equilibrium. What that really means is that if you take two different solutions, let's say different amounts of regular table salt dissolved in water, and you put them on either side of a semipermeable membrane which lets water molecules through but not salt ions (this is easy because salt ions are relatively big compared to water molecules) the water will move from the lower salt concentration to the higher salt concentration. It does this because the water wants to be in the same concentration everywhere, and it moves through the membrane in order to bring these concentrations to equilibrium.
But wait, you say, this is silly, if the membrane wasn't there the same thing would happen. Yes, of course, it's the same thing that happens when you put a chunk of salt in a pot of water, the area near the salt gets really salty really quickly, but the water moves in to even things out and slowly the salt diffuses through the whole pot. The point of the membrane is that as the water moves, the salt does not! Which means that you end up having different volumes of solution on either side of the membrane. And any time a volume changes, a pressure is involved... hence osmotic pressure.
Osmotic pressure has several important uses and/or connotations. First, you've all probably heard about reverse osmosis water filters. Well, the osmosis is just what I just described. The reverse part is because the filter works by having a semipermeable membrane where one side has a higher solute concentration (a solute is anything dissolved in a solvent, in this case water) compared to the other; water is added to the the high-solute side and pressurized to overcome the backwards osmotic pressure. This produces clean water on the low-solute side since only water can pass through the membrane.
The other important thing about osmotic pressure is related to biology. As I mentioned above, the most common semipermeable membrane is the cell membrane. It's probably also obvious that cells are chocked full packed of nice solutes like proteins and sugars and salt ions and all sorts of other neat molecules. Well, this is all very useful for the cell but there's one slight problem - if the cell ever interacts with pure water with very little dissolved solute, an osmotic flow happens where the water outside the cell rushes into the cell in order to try to equilibrate the solute concentrations. This creates a pressure inside the cell and the cell literally blows up like a balloon. If the pressure is too great, then the cell bursts! This is why, if you're severely dehydrated, they give you a saline IV which has dissolved salts equal to the dissolved salt in the blood. Otherwise, if you got an IV of pure water, your blood cells would explode and you would get very sick very quickly. This is also why people can die from drinking too much water. We don't drink saline water (for some crazy reason I don't really know why) so if you drink lots and lots and lots of water the salt concentration in the blood drops and you get the same problem of blood cells bursting as well as other cells. This only would happen if you drank like gallons of pure water.
So the moral of this story: When running a marathon, take the Gatorade cups (which have dissolved salts! they like to call them 'electrolytes') rather than the water cups.
P.S. Oh yeah, one more thing. It's way past my bedtime but I think this is the coolest osmosis-related thing. So you know how plants get kinda limp and flabby if you don't water them? Or if they die? Well, here's why - it's osmosis related! Every plant cell has a giant water bubble inside it called a vacuole. This bubble is surrounded by a membrane, yes, a semipermeable membrane like all other biomembranes, which has molecular pumps imbedded in it. So when the cell is alive, those pumps pump salt ions (like potassium and chloride) into the vacuole. As this happens, water molecules follow naturally across the membrane, causing the vacuole to pressurize and expand outwards. This causes the whole cell to pressurize and to stiffen up against the cell walls. Hence, nice firm plants, crisp lettuce, etc.! If you forget to water your plant, though, those pumps stop running, the ions leak out and so does the water - which is a good thing for the plant because it keeps it alive at the cost of a little flabbiness. And if the plant dies, the pumps stop completely and all the ions and water leak out and the plant goes completely limp. So water your plants! They thank you.
Posted by kgutwin at 10:03 PM | Comments (4) | TrackBack
Slowing Down
Yeah... my posts are slowing down, slower, slower... I don't know - for some reason, now, having a public journal just doesn't sound all that enthralling to me. It's hard for me to have an excuse to post (tonight I'm only posting because I feel like I ought to, and because I'd rather be doing anything other than my homework) and even when I might have the time, it's hard for me to come up with fun things to talk about.
Let's see, what should I mention?
I fixed my umbrella, again, for what has to be the fifth time. This thing just won't stop breaking but the way it breaks is just too easy for me to keep fixing. Basically the plastic cap at the very top of the umbrella broke off a while ago and I have had various fixes and replacements for it, involving tape, screws, glue, then finally a new, bigger cap and a bigger screw... but this past time the screw came out again! Well, nothing left to do but to JB-weld it. Ayup, that's right, JB-weld works wonders. Well, at least on an umbrella.
I have a concert this Friday. Well, we're only performing one song which is kinda wacky. Our real concert is next Saturday. Here, though, they make the guys wear tuxedos so I had to go out and get decked out. I didn't buy a tuxedo jacket because the jacket I have now is pretty good already and a used tuxedo jacket is at least $60. Other than that, I have all the authentic parts, complete with cheap cuff links. Now I'm all dressed up and I just need somewhere to go...
Another audiobook is in the works, even though Becca's CD player is giving her trouble. She's going to try to clean it which I hope will fix it because it would be kinda silly to spend the time to record an audiobook and have her not be able to listen to it. The title will be withheld until it's finished, which with any luck will be sometime soon.
Lab has been fun although I spent all day Friday doing the same experiment over and over. It's cool that things are working although not quite like we expected but I suppose that's what makes it interesting. It is pretty neat that I'm able to do more and more of this stuff by myself. Maybe by the end I'll be doing it all by myself but for now I'm still basically doing what this guy tells me to do.
We'll leave it there for now. It's been pleasantly rainy here for the past few days and overall things are cheery :)
Posted by kgutwin at 09:49 PM | TrackBack
April 18, 2005
From Earth to Earth
Here it is, the inaugural installment of Science Corner!
All right, enough with the fanfare. Let's get down to business. I'll start with the write-ins.
My father asked three questions, perfectly valid and intellectually intriguing I might add, but since it's my blog I'll respond in the order that I choose :) The first question is really quite amusing...
Why do outhouses have a half-moon on their door?
According to The Straight Dope, a very thorough and reliable online source for information about those funny questions we've always had, the moon on an outhouse door actually has nothing really to do with the highschool definition of "mooning". It actually appears as though the concept of moons on outhouse doors is limited to our imagination, as Cecil rightly points out that it is tough to recall ever actually seeing a real outhouse with a moon on its door. Nevertheless, he has traced the origins of this phenomenon through a few ancient and definitive tomes, and his conclusion is that both the moon and the sun were used in illiterate times to delineate between women and men, respectively. It is also likely that not only is it more difficult to carve a sun out of an outhouse door than a moon, but that women's outhouses were generally better maintained than the men's, and so popular conception has passed the moon as the universal sign of relief when Nature calls.
What is the maximum power output of the human body through muscles?
It's an interesting question, and spans a lot of thought space - everywhere from projects in micro power generation in third world countries to The Matrix (yeah, that's right, Coppertop!) Real numbers are hard to come by, though. Part of the problem is in that definition of maximum. I would guess that very few experiments have actually been done to determine the true maximum - because that would likely kill a person, if not destroy their muscles! Another related point is that the power output depends strongly on the load - i.e. the system is nonlinear. Everybody could agree that to walk across a very shallow incline seems to take much less effort than traveling the same height completely vertically, even if ultimately the potential energy gained is equivalent (Science-speak: potential energy is a state function -- translation: it doesn't matter how you get there, the result is still the same.) What this all means is that you might get different numbers for max power output depending on how hard the person is working (or how hard you're making them work!) Oh yeah, one last point too. You asked about the maximum human power output using muscles, but it's a physical impossibility to have every muscle in our body contributing simultaneously to this hypothetical power measurement, since many muscles pull against each other! So most tests of this kind only really measure leg output since that's where the most powerful muscles in the body are.
A really crummy Figure 1 shows several power curves for "healthy men", "first-class athletes" and estimated maximum. Taking one somewhat clear data point from that graph, Eddy Merckx was able to sustain 440W for one hour, or about 0.6 HP. This is a measure of power, power being energy over time. You asked for this in ergs, ergs being a unit of energy, so the energy expended by Mr. Merckx was 440 watts * 60 minutes in ergs which Google Calculator can easily handle. 1.54 x 1013 ergs is the simple, ballpark answer.
This seems like a lot of ergs, but an erg isn't very much energy. An erg per second is about a tenth of a microwatt. Compared to a lawn mower? Which lawn mower? A push lawnmower has about 4 HP. A riding lawnmower can have up to 12 HP. Energy to energy, this amount of energy would run a 4 HP lawnmower for almost 9 minutes or a 12 HP lawnmower for almost 3 minutes. Of course there are reel-type lawn mowers which a normal human can push for more than 9 minutes so clearly 4 HP is pretty inefficient.
What happens to an onion when it is cooked?
What a tasty question! Onions are such a versatile ingredient, and every food changes chemically when it is cooked, so this is a very important thing to understand. I should point out that the definitive reference for these questions is a book titled On Food and Cooking by Harold McGee. Unfortunately I don't have a copy of this book (hint, hint) so I will have to make do with Internet sources and what I can glean by Amazon's "Search inside the book" (what a useful feature!)
Onions are a member of the genus Allium, which also includes such esteemed members as garlic and chives. The most distinctive thing about the alliums is that they contain compounds which are normally sequestered inside vacuoles (cellular compartments). When these plants are cut or crushed, these compounds combine to form the lachrymators, chemicals which make you teary! Different plants have different levels of these lachrymators, but they are the common compound which give onions through leeks their 'bite'. When cooked, these compounds mostly break down and somewhat react with each other in certain ways depending on the heat and what they are cooked in. This breakdown tends to remove a lot of the sharpness of the onion flavor. Hot fats likely have their strongest effect because they even the heat out significantly and can reach temperatures higher than boiling. One thing not to be taken too lightly is the effect of heat on the sugars that onions contain. We don't often think of onions as sweet (except perhaps the sweet onions like Vidalia) but it turns out that most onions have roughly the same sugar content - the sweet ones simply have less of the lachrymatory chemicals! (This means also that soaking yellow onions in several changes of cool water will tend to remove their sharp flavor and make them taste sweeter.) Those sugars can break down and combine with each other during caramelization, producing a mild, sweet flavor.
Next time, if all goes well, I'll make some mention about the current state of the art in smell chemistry and what makes such a lovely smell or a horrid stink! See you soon!
Posted by kgutwin at 04:13 PM | Comments (2) | TrackBack
April 13, 2005
Rotation Three, Day One
I'm sorry, folks, about last rotation... I know I didn't say a whole lot about it even when I was asked. The truth was that there wasn't a lot there that I could rave about... Mostly it was a lot of sitting at the computer. Part of the problem with computer work is that you don't necessarily feel productive, especially when you're doing searches and trying to figure out how to do something. The other part of the problem is that any computer with a functioning web browser gets me distracted :) (although the SGI that I used only had Netscape 4.7 on it to begin with... Hardly what I would consider functional! I fixed that on short order, though.)
This rotation just began for me today, and already I'm seeing a concrete difference. Mostly because I'm working with concrete things! I'm not going to be doing any computer work this rotation... It's all going to be in the wet lab. I have to admit this made me a bit nervous to start - because I've had very little time in the wet lab, and I feel like my peers have far exceeded me in that area so there's a lot of catching up I have to do. But today went quite smoothly, and I'm remembering things that I learned many months and years ago. What I did today couldn't be considered significant by any scientist who does this stuff on a regular basis -- but for me, each one of these things is important. Even making buffers (which consisted of weighing out various compounds and adding them to water :)
I'm excited, at this point, for this rotation. Maybe later I'll be intimidated but for now I have just the right amount of help that I need, plus the leeway to make mistakes (since, of course, I'm so inexperienced :)
Today I didn't have a whole lot to do so I'm leaving early. I still have a bit of homework to do for tomorrow but I should have enough time to get it all done. Maybe I'll even have some time to do something fun!
Sent from: Karl Gutwin
Posted by kgutwin at 04:50 PM | Comments (1) | TrackBack
April 10, 2005
Been So Busy
Hey all... well, all who's left - I'm sure I've cast off what readership I had remaining at this point. Yes, I know it's been a long time since I've posted. And believe me, I wish I could take the time to do fun stuff like post to this blog... but let me just take a moment to summarize the past week or two:
Work.
Yeah, yeah, we all know and we all get busy. I guess it's just that I never feel like it's ok to take a break, even if it's a really short break. I might have mentioned before that I operate in one of two modes: either laid-back, I have plenty of time, it'll all get done... or panicked, I have no time, damage control I gotta work as hard as possible. I've been in that second mode for the past week - and it's certainly been justified as I was up until midnight at least twice the past week. It's been a little easier now because I'm between rotations and the homework has let up a little bit... but I know it'll crunch even harder in another week, and even harder up to the end of the semester.
If I ever get the chance I'll post to Science Corner. I really really want to, and I actually have the answers to my father's questions, I just haven't had time to write them up in an amusing fashion. Plus I have another half-finished Science Corner article which is waiting for me to spend a few moments on it... it's tough though because you would think I would even have some time to work on it on the train, but many times I can't get a seat on the train and typing while standing on a moving train is tough :)
All I can say is stay tuned. Believe me, nobody wants me to take a break more than myself...
Posted by kgutwin at 07:20 PM | Comments (3) | TrackBack
April 05, 2005
What a great day
Wouldn't it just be the best day for a sail? I can see a couple of little orange buoys (ahem, MARKS) out on the river that they must have been using for racing practice. The wind's blowing pretty well today, must be a warm front coming through.
Too bad I'll be cooped up in class all day. High of 60 degrees, man, it really is spring.
Sent from: Karl Gutwin
Posted by kgutwin at 12:55 PM | Comments (1) | TrackBack
April 04, 2005
Science Corner
So I've been pondering starting a new section of my blog... It would be called Science Corner and would be basically me as Bill Nye the Science Guy. (I would so love to do something like that... But I'm just not funny enough!)
The whole idea would be for me to spend some time explaining a tiny part about how the world works. It could be anything from why ice floats to why we need to eat to how the Internet really works. There's so much that is rattling around in my brain about all this stuff and the honest truth is thay I love explaining it to folks. Sometimes I actually get to explain things to people bit usualy it's just my own mind talking to myself... And that doesn't really help anyone :)
So this means that I'm accepting requests for discussion topics. If nobody responds (which nobody does anymore, tear) then I'll come up with something but then it might end up being something which is interesting only to me. Really, I'll take any question on any science or technology subject.
In the meantime, look forward to Science Corner, coming soon!
Sent from: Karl Gutwin
Posted by kgutwin at 08:35 PM | Comments (4) | TrackBack
April 01, 2005
Lab rotation number two
Here's where I've spent many an hour over the past few weeks. I really have done very little other than working on this computer attempting to build a working model of a protein which the lab prof is trying to crystallize. It's been interesting work but I'm ready for a change....
Sent from: Karl Gutwin
Posted by kgutwin at 02:05 PM | Comments (2) | TrackBack