"The chymists are a strange class of mortals, impelled by an almost insane impulse to seek their pleasure among smoke and vapour, soot and flame, poisons and poverty; yet among all these evils I seem to live so sweetly that may I die if I would change places with the Persian King."
Johann Joachim Becher (phlogistonist)
Acta Laboratorii Chymica Monacensis, seu Physica Subterranea, (1669).
Monday, March 24, 2008
Apparently, the process by which our olfactory receptors operate is still pretty much unknown, although it is generally suspected that metal based proteins are partially responsible. I know a professor who has his own pet theory about these receptors, assuming that smell can be a good indicator of how well certain chemical compounds might react with metals. In fact he encourages his graduate students to use the smelliest chemicals available when attempting to synthesize new organometallic molecules. Since his group tends to work with chalcogenides, finding smelly compounds isn’t all that difficult.
French researchers have developed a chip which mimics part of the process of smelling to help determine the chemical mechanism. There may be a variety of applications for this technology, but I fully expect that by the time robots are perfected, they will be equipped with a sense of smell.
Using computational techniques, scientists have been able to design an enzyme to catalyse a specific reaction. According to the report "The scientists’ aim was to create an enzyme for a specific chemical reaction whereby a proton (a positively charged hydrogen atom) is removed from carbon – a highly demanding reaction and rate-determining step in numerous processes for which no enzymes currently exist, but which would be beneficial in helping to speed up the reaction." After an extensive screening process, they were successful, but the reaction rate was slower than desired. Not bad, but things became interesting when another research group from Israel stepped in, developing a method which "allowed the synthetic enzymes to undergo 'evolution in a test tube' that mimics natural evolution." After only 7 "generations," the resulting mutated enzyme was 1,000,000 times faster than the original enzyme. In my opinion, this is the cool part. Basically you are letting chemicals perform chemical experiments on themselves. This, of course, means that graduate students are no longer the fastest or cheapest way to develop new chemistry.
This is probably why I find evolution so cool, especially on the molecular level. It’s been basically one looooooong chemistry experiment.
Not chemistry related, but here one fan's top ten list of Jackie Chan stunts. This guy is insane. I know that he performs his own stunts, but I hadn’t realized he had gotten himself hurt so badly so many times.
Sunday, March 23, 2008
Many years ago, I heard about the use of benzene to decaffeinate coffee and I was doubly thankful that I had never been interested in it. The coffee companies had probably stopped using benzene long before I had heard about it, but that didn't stop me from kidding my coffee drinking friends about the health risks. I ran across this article on the decaffeination process the other day and thought it had some interesting chemistry.
I do like honey, although it's used so infrequently around our house that it tends to crystallize into a solid long before we get around to using it. My knowledge of honey is rather limited -- I know it comes from bees and that you shouldn't give it to a child less than a year old. Apparently it also has some medicinal properties of which I was unaware. Most bacteria cannot grow or reproduce in honey and so it can be used on wounds as a topical antibiotic. If you are interested, check out this article on the properties of honey.
Finally, chemists in Italy have created a derivative of aspirin which causes less stomach irritation. I originally thought maybe they had just gotten rid of the acid group, but apparently they generated nitrooxy-acyl derivatives using the acetyl group instead. The derivatives are shown here.
Saturday, March 22, 2008
Friday, March 21, 2008
With that in mind, I'm adding Dan's Data website to my link list and I highly recommend it. The official title of the site is "Dan's Data - PC Hardware and Gadget News," but he covers a lot more ground than that. His specialty is explaining how gadgets work, or in many cases, why they cannot possibly work in the manner described by the manufacturer. He's especially adept at skewering some of the more dubious claims associated with these products and does so in an entertaining fashion. He also appears to be rather familiar with chemistry too, often discussing the chemistry side of products, with more knowledge that I would have thought possible for a gadget guy. He's apparently a reader of Derek Lowe's In The Pipeline chemistry blog. Dan also has a related blog called How to Spot a Psychopath.
Recently Dan has been "discussing" a product promoted by FirePower which purports to be a fuel additive that performs near miracles with fuel economy, exhaust emissions, oil consumption, etc. on cars, trucks, trains, and military tanks (yes, tanks). Apparently, someone from the company was none too pleased with his analysis and apparently forced Dan to remove a link to a presentation which was sent to him by the CEO of FirePower himself. Of course, this resulted in the presentation being mirrored all over the net. You can read Dan's analysis on his website, but after reading over the presentation myself, one item caught my eye. On page 22 of the presentation, the exhaust emissions data for a Toyota Corona Avensis was shown with and without the additive. Here were the results: (Forgive my poor formatting)
Exhaust ______ No Additive ____ With Additive ____ %Difference
CO2 __________ 3.7% ___________ 1.4% _________ -62%
CO __________ 0.027% _________ 0.016% ________ -41%
NOx _________ 39 ppm _________ 16 ppm ________ -59%
FC* __________ 9.8 _____________ 8.1 __________ -17%
FC = fuel consumption in liters/100km
Both CO and NOx levels dropped, which would be a good thing for the environment. However, the amount of CO2 released dropped by 62%! Now this sounds like it would be a good thing, what with all the concern over greenhouse gases and global warming, but there are only 2 ways that the CO2 levels could drop like this. Possibility #1: carbon is being emitted in some other form. It can't be CO since its concentration dropped. The only other possibility would be the release of unburned hydrocarbon. (For unknown reasons, hydrocarbons emissions were not included in the report.) This seems very unlikely as it would have had a catastrophic effect on fuel economy, and the report indicated that the fuel economy actually improved. Not to mention the fact that if this additive really does cause a majority of the CO2 to appear as unburned hydrocarbons, you can be sure the EPA will be knocking on their door very soon. Possibility #2: 62% less fuel was used, which means a fuel economy savings of 62%, which is much larger than the 17% increase in fuel efficiency noted in the report. I do not know exactly how these tests were performed, or under what conditions, but you can be sure that any automotive engineer would immediately catch the low CO2 number. Of course, this product isn't for the automotive industry, it's for the people who don't know much about engines.
Wednesday, March 19, 2008
I stared back at him and asked, "Dude, were you drunk at the time?"
Okay, so I didn't really say that. I don't use the word "dude" at work and despite some eccentricities this person is a nice guy who has helped me out on several occasions. So I bit my tongue and just handed him the book, but I was pretty pissed, and for several reasons. It wasn't just because he had borrowed my book, damaged it, tried to fix it, and then put it back on my bookshelf without saying a damn thing to me. And it wasn't just because I'm overly protective of books, which I am. I'm anal about careful with books -- I don't damage their spines while reading them and I don’t contaminate their pages with food, drink, or bodily fluids. (Hmmm, probably too much information there). When I finish reading paperbacks it's usually hard to tell they were ever opened. I have a really nice hardbound volume of the "Lord of the Rings" which I never open for fear of ruining it, so I read my paperback versions instead, which after 5 or 6 read-throughs do finally show some use.
No, I was upset with the absolutely pathetic repair job. His attempt to repair my book appeared to have been performed during a fire drill, in the dark, and while wearing asbestos gloves. The tape was all over the place, pointing in random directions, and the ends hadn't been cut neatly. Actually the tape hadn't even been torn neatly, appearing more like it had been, well, gnawed off. At least this guy had used transparent tape. Obviously he hadn't considered that this book might have some sentimental value for me, which it does.
The CRC handbook was almost a status symbol for chemists back in the day. No instructor ever asked you to buy one -- but almost every freshmen majoring in chemistry did. This behemoth was 3.5 inches thick, weighed 6 pounds, and contained almost 2300 pages. The only reason it wasn’t heavier was due to the thin vellum-like pages. Considered a lethal weapon in 17 states, this book was often the first place a chemist would look when faced with a chemical question. It held a massive amount of chemical and physical data, but that data was often arcane, sometimes of dubious quality, and referenced using a Byzantine index system that was almost an art form in itself. This was the book you brought to open-book tests for the sole reason of freaking out your competition. Actually using it during the test was unrealistic, as it might take 15 minutes just to find the fact you needed.
So this book does have a lot of sentimental value to me. I don't think I've actually touched it in years -- it's still faster for me to find something on the net than to grab this book -- but it reminds me of those heady days back in college. You can buy this book on a cdrom, but what would be the point? This book is a symbol of my struggles as both an undergraduate and graduate student and represents my academic success more than any diploma ever could.
Hmmm, perhaps I’ll have it buried with me.
In any case, I would like to say goodbye to Mr. Clarke and thank him for many, many wonderful memories.
Tuesday, March 18, 2008
In a subsequent post on the subject, Keim also asks “Could the failure of cable news networks to cover science be a good thing?” Considering some of the problems associated with news reporting, it’s a valid question. If the reporter or journalist has no science background, just managing to get the story correct can be problematic.
Years ago I was a part of an NSF undergraduate research project studying the use of potassium ferrate (K2FeO4) as a water purification agent. Typically, FeCl3 is added to waste water to generate Fe(OH)3 (or FeOOH), which precipitates and sinks to the bottom of the tank, pulling out impurities. This is followed by the addition of chlorine to kill bacteria and other nasty critters. FeO42- also forms Fe(OH)3 but with the added bonus that it oxidizes organic compounds present in the water, removing them prior to the addition of chlorine, which supposedly results in the production of fewer chlorinated organic compounds which may increase the risk of cancer. At one point during that summer, a reporter from a local newspaper came by for an interview, and the advantages of ferrate was explained to him in what we thought were rather simple terms. There was much amusement in the lab a few days later when the newspaper article described how FeO42- destroys cancer causing bacteria.
But even science journalists can miss the boat on a science story. Consider this report on acupuncture in which the author (the health editor) totally missed the point of the results. “Acupuncture is best way to treat back pain, study finds” was the author’s conclusion, although the results clearly demonstrated that random insertion of needles produced just as good of results as traditional acupuncture.
Science will always be playing second fiddle to the rest of the news.
Monday, March 17, 2008
In a sad bit of news, The Chem Blog may be shutting down in the near future. I've only been reading it for a short time, but we need all the chemistry related blogs we can get in this world.
In my last post, I mentioned a little piece of software call Phun. Well, the kids absolutely love it. It's far, far better than I expected and I'm playing around with it myself. You owe it to yourself to watch the video and see what it can do. Design perpetual motion machines, create vehicles that move, and build diabolical death traps to destroy those vehicles. I'm especially impressed with the simulation of liquids. I cannot imagine the programming that went into this thing. The physics is not always perfect and large volumes of water can slow the frame rate, but this is an awesome program. Check out the video here.
Saturday, March 15, 2008
First up is a story about a fire alarm for the deaf. By using an extremely pungent material, this alarm is able to wake someone by smell alone.
Next up is a quick blurb about another example of brain surgery in the ancient world. Unfortunately the patient died during or just after surgery. The reason I even mention this is due to the following quote:
"We interpret the find as a case of complicated surgery which only a trained and specialized doctor could have attempted."
If the patient died, how do they know that a trained doctor performed this procedure? Seems to me even an untrained doctor could have killed the patient. :)
Third, the first sentence of this next story is probably sufficient to let you know immediately whether you wish to pursue it any further.
"Two German air force sergeants are facing a court martial after trying to mass produce sausages made with the blood of their comrades."
Apparently, senior officers got wind of this activity when one of the "comrades" asked if giving blood for sausage-making was against regulations.
Fourth, a link to a list of the top ten signs of the week.
Finally, from Dubious Quality comes news of a computer toy/program called Phun. It reminds me of Crayon Physics. Check out the video and see if you can resist downloading it. My kids will just love playing around with this.
Friday, March 14, 2008
A couple of us looked at each other after that last statement. It didn't seem possible that O2 could diffuse out of us that quickly since it apparently doesn't diffuse in that quickly, hence the need for lungs. And what about holding your breath underwater? Wouldn't that lead to the same sort of problem? Of course this wouldn't be the first time I was wrong about this kind of thing and so I searched the net for information. As of this writing, I have yet to find any mention of this anywhere. However, I did find that breathing an atmosphere of 10% CO2 for a few minutes can produce unconsciousness, so perhaps in a 50% CO2 atmosphere, one or two breaths are sufficient to knock you out. If any of you have an answer to this question, I would love to hear from you. In the meantime, regardless of the answer, you can be sure that when that alarm goes off, I'll be getting my butt out of that room within 20 seconds.
Thursday, March 13, 2008
To the biochemist, however, chirality is everything.
I am just guessing here, but it wouldn’t surprise me to find that 80-90% of the molecules present in a living organism are chiral. After all, amino acids, the building blocks of life, are all chiral (except for glycine). And since they all react with each other, chiral chemistry is very important. Now if all the chiral molecules in our bodies were evenly divided between both mirror images (known as a racemic mixture), this might be a moot point -- but it’s not. For some reason, all life on this planet chose long ago to selectively use only one form of most chiral molecules. For example, we all use the “left-handed” version of amino acids. Their mirror images, known surprisingly as the right-handed versions, are mostly unusable by our bodies.
The big question has always been, “Why (and when and how) did this occur in the first place?” A part of the puzzle has now been answered by researchers at Arizona State University. According to the article, extraterrestrial amino acids found on a meteorite demonstrate the same preponderance of left-handed molecules that we see in biological systems on Earth. Now this doesn’t explain whether the same process which operated in space operated on Earth or if the Earth was merely seeded with organic materials from space, but at least we are one step closer to knowing.
Wednesday, March 12, 2008
I checked out the vending machine today at work and, amazingly, I actually found something I liked -- Raisinets. Lately, finding items I like in this vending machine is cause for celebration. Our building only has about 50 people left as most have already moved into our new, much larger lab. Since vending machine use has slowed down, the vendor isn't bothering to restock it on a regular basis any more. The situation has become dire enough that the mere appearance of the “restocking guy” creates a bit of a frenzy in our building. I suspect the line that forms behind “restocking guy” as he winds his way to the vending machine creeps him out a little. I’m fairly sure he doesn’t care much for the crowd watching as he resupplies the machine. And I’m quite positive he doesn’t take kindly to the stocking suggestions thrown out by the nervous spectators, but that’s what earns him the big bucks.
The process of actually buying something from this machine is somewhat of a ritual. First, you have to overcome the fear that the machine will steal your money, which this particular machine is known for doing. (See note 1) Your outward demeanor is very important. Since a crowd has formed by this time, it’s important to give your co-workers the impression that, hey, you know you might lose money here, but that you’re the kind of person who savors risks. (See note 2) Next, assuming you were successful and the desired snack has appeared, you check the expiration date. This can be difficult since the ink has often faded by the time a snack makes it to this machine. There also remains the possibility that the date consists only of a month and day. If you have to ask “what year?” then you probably have no business touching this machine. And if the expiration date has passed, you have to decide if the date is real or more of a suggestion. Surviving the consumption of the snack will embolden your coworkers into purchasing the same item.
I realized long ago that vending machine operators operate by a different set of rules. I used to think vendors would fill their machines with highly desirable items (Hostess snacks, for example) which would be bought quickly and yield great profits. Vending machines in public places are like that, since the owners can charge insane prices for the right to eat unhealthy snacks. However, vending machines in static locations at the workplace are a different story. Apparently vendors can make more money in these locations by offering crap that nobody wants but which the vendors can get at cutrate prices. Oh, they may occasionally add a few desirable snacks to keep people from abandoning the machine, but they make their money on those people who cannot leave a vending machine empty handed. My vending machine epiphany occurred several years ago when I noticed a recently restocked machine. Before restocking, this vending machine had completely sold out of one item (a Hostess snack) while the item right next to it (some wretched peanut based monstrosity) was completely full. Not a single one had been sold. Not only did "restocking guy" refuse to fill the empty slot with more Hostess snacks, he filled it with more of the wretched peanut based monstrosity that obviously was not selling. Either he had been ordered to push this stuff off on us or he was tired of restocking our facility.
Note #1: This is the same fear parents with young children feel when they are about to put money into an arcade machine at shopping malls, where the machines are poorly serviced, the odds for success are dismally low, and where there really isn’t any recourse available if the machine eats your money.
Note #2: Last weekend, I found myself in just such a situation at a local restaurant – a national chain specializing in buffalo wings. After dropping 2 quarters into a racing game (for my son) requiring a dollar to play, the game rebooted. Yes, I said rebooted -- with hard drive checks and everything. After about 30 seconds, it had finished and, of course, wanted 4 more quarters to play. Now I had to make a choice. If I gave up, my son would disown me. If I lost more money, my wife would dismember me. She was already in a less than happy mood, since our dining experience had been, shall we say, slightly flawed. The portion sizes had been small, it had taken 45 minutes to get our food, they had forgotten to put the proper BBQ sauce on her ribs, and my ribs had been cold – refrigerator cold. So it was with no small trepidation that I dropped in 4 more quarters. Fortunately, fate shone upon me that day.
Saturday, March 8, 2008
The doctor warned me that Orielle might still be in discomfort for a while, and her pain medication would run out by morning. If she looked to be uncomfortable, I was told to come back to the clinic and they would give me a syringe of pain medication. In the morning, although she looked at lot better than when we had brought her in, I could tell she was still a little uncomfortable. So I called the vet and the person I talked to said I could bring her in for the pain medication. I mentioned that the doctor had said I could just get the filled syringe from them and inject her myself. Sure, they said, come on over. After all the pills and injections I’ve given cats over the years, I wasn’t worried about this at all. What’s one more injection anyway? So I get to the vet, they hand me a few syringes and ask if I’ve been told how to use them.
“No problem,” I replied, “I’ve already been shown how to give her insulin.”
“Well, we find it works better if you use her cheek pouch for this.”
“What?” I said, slightly taken aback. “What do you mean by using her cheek pouch?”
“Just open her mouth and place the syringe into her cheek near the back of her mouth and inject the medicine into her cheek.”
After several seconds of picturing this in my mind, I finally managed to say, "That sounds rather...diffcult."
"Oh, it turns out to be fairly easy," the vet said, smiling in a manner that was supposed to be reassuring.
Apparently I wasn't as experienced at this cat stuff as I thought.
"Doesn't that hurt?" I asked.
"Not really. It's better than being poked."
After a few awkward moments of silence, the vet suddenly exclaimed, "Wait a minute. You do realize that these syringes don't have needles in them. You're just squirting the contents onto the inside of her cheeks!"
Relief has never felt so good.
Friday, March 7, 2008
To make my measurements, I was using a styrofoam cup filled with liquid nitrogen to transfer gas samples between various locations within the mass spectrometer vacuum system. Turns out it was actually liquid air (apparently it's less expensive), as evidenced by the bluish color which the liquid would develop as the N2 boiled off preferentially, leaving liquid O2 at the bottom of the cup. I will never understand why that student decided to put out her cigarette into that cup without asking, but she did and the cigarette burst into flame. I push her back out of the way and then turned to watch as the cup itself proceeded to burn fiercely, sending a plume of ashes up to the ceiling where it spread to all corners of the room before settling -- on everything. I spent hours cleaning that lab, but I couldn't clean everything. A month or too later, my advisor noticed the ash, but I was too embarassed to say anything.
In retrospect, there hadn't really been much of a danger, but since that sequence of events had never occurred to me, how can I say that I assessed the hazards properly? How many dangerous situations have any of us been in that we didn't recognize at the time? Chemistry can be a dangerous business, people. Be careful out there!
Thursday, March 6, 2008
Everything apparently turned out fine, but HF is some really nasty stuff. I used some of it once as an undergraduate, but because my advisor had warned me of the danger, I was very careful. Knowing what I know now, he probably could have given me even sterner warnings. With a pKa around 3, it is one of the stronger weak acids, but it's the F- that causes most of the damage. Fluoride ion is quite toxic. It can penetrate deeply into the skin, forming CaF2, which depletes calcium levels in the body. According to one source, skin burns of 25 in2 or greater can result in serious systemic toxicity and death. Calcium gluconate or calcium carbonate gels are the first line of defense in case of skin exposure, precipitating CaF2 before it can work its way into the skin. Fortunately, I do not ever forsee myself using HF again.
This is a reminder that chemistry can be a dangerous business, especially when we start taking things for granted. I've had a few close calls over the years, but I've never been hurt. I wish everyone could be so lucky.
Tuesday, March 4, 2008
A few miscellaneous items today.
First, it has long been known that runners can experience a certain euphoria when running. The generally accepted explanation involved the production of endorphins in the brain. In fact, this assumption has been around so long I assumed it had already been proven. Apparently not. Now a study has indeed shown the existence of the “endorphin driven runner’s high”. I used to run 3 miles a day until my right knee kindly informed me that this was not going to continue. Where were those endorphins then? In all my years of running, I cannot recall ever having felt a feeling of euphoria, except at the end of the run, although the feeling would be more probably more accurately described as "relief". Obviously I was missing out on something there.
Another chemistry blog which I’ve added to my blog list is The Culture of Chemistry. The author, Michelle M. Francl, discusses common facets of chemistry in enjoyable ways. Highly recommended.
You may have seen some of these before, but here is Wired's top 10 amazing chemistry videos.
Finally, you may have seen the Wall Street Journal article which reported the results of a survey in which 70% of people polled found nanotechnology to be morally unacceptable. Since the silliness of this has been covered elsewhere on the net, I won't belabor the point. My question is: Why was that question on the survey in the first place? If the survey hadn't asked if it was morally acceptable, would it have occurred to anyone that it might not be?
Monday, March 3, 2008
There have recently been several articles promoting the use of new porous framework materials for specific gas storage applications. Chemists at UCLA have been working on ZIFs (zeolitic imidazolate frameworks) as a CO2 storage material. Led by Omar Yaghi, who also invented MOFs (metal organic frameworks) in the 1990s, the team has been busy generating as many structurally different variants as possible and measuring their ability to selectively capture different gas molecules. Their latest material, ZIF-69, is particularly good at holding onto CO2, opening up the possibility of using this material to sequester the CO2 released by powerplants. Perhaps even more intriguing, and an area that I expect to see a lot of work in the future, would be the use of these framework materials as fuel storage devices. Both hydrogen and ammonia (an alternative source of hydrogen) have potential as non-hydrocarbon fuels, but their pressurized storage can be tricky. Designing porous materials which allow the storage of these gases at much lower pressures would have huge benefits. Although the potential is there, this is not a slam dunk by any means. You not only have to develop a material that holds on to the gas molecules efficiently, but which also releases those molecules at the appropriate time with a minimum of energy input. I will be interested to see where this research goes.