Rapper’s Delight
There are a lot of different ways to teach biology. You can lecture, give quizzes, hand out worksheets. You can put students into groups and have classroom discussions. Or you can rap to them.
That is what one Standford biology professor, Tom McFadden does. With lessons like “It’s Too Late to Apoptize,” (a parody of Timbaland song “[It's Too Late to] Apologize”) and “I’m Going Back to Plasma Membrane” (from Notorious B.I.G.’s hit “Going Back to Cali”), McFadden makes biology, if not “cool”, then definitely more fun. Check out ”Regulatin’ Genes” (a parody of Jay Z’s “Money Ain’t a Thang”) to see for yourself.
“In the video,” McFadden describes, “they have so much money that they flip through it, throw it up in the air, throw it out of moving vehicles. Since we just had midterms, I’m projecting some wishful thinking in the video – that there are so many A+’s on the midterm that we can just throw them in the air.”
Next up on McFadden’s set list? “You Can Do It” by Ice Cube. He’s planning to rewrite it for his neuroscience class, to teach the biology of the brain. And if his success thus far is any indication—“Regulatin’ Genes” has now received more than 50,000 views on YouTube—McFadden can definitely do it.
One Virus You’ll Actually Want
Credit to Steve Lee, atbatt.com
Back in 2006, MIT researcher Angela Belcher and her team scientists took a nano-sized virus and, by manipulating its genes, made it collect cobalt oxide and gold—thus creating a very small high-energy-dense anode (the negatively charged end of a battery). Recently, Belcher’s team has taken the M13 virus, a common bacteriophage (i.e. it eats bacteria, not humans), and tweaked its genetic code so that it coats itself in iron phosphate—effectively generating nanoparticles of iron phosphate without using an expensive pressure-cooking process. The result? A tiny, powerful, efficient battery.
The most common type of battery used in portable electronic devices (everything from watches, to computers, to pacemakers) is the lithium battery. In order to provide power to these devices, lithium ions and accompanying electrons flow from the negatively charged end of the battery (called the anode), through an electrolyte, to the positively charged end of the battery (called the cathode). The flow of these ions/electrons creates electric current and is what powers our various handheld gadgets.
What engineers, scientists, and manufacturers are working to solve is the challenge of making these batteries store the greatest possible amount of energy while being able to deliver the energy as efficiently as possible. On one hand, certain materials possess greater energy density than others—that is, they can store more energy for their size and weight compared with other materials of equal size/weight. However, efficiency is often sacrificed at the cost of energy density. One such example is the case of iron phosphate, the material of which some rechargeable lithium batteries’ cathodes are composed. Iron phosphate, when it reacts with (or “accepts”) lithium, has a high capacity to store energy. However, iron phosphate is not a very good conductor, and the result is slower ion/electron movement and, therefore, a less efficient battery.
One solution to this problem is to decrease the size of the “passageways” or particles through which the ions and electrons move. However, in cases such as iron phosphate, scaling the material down to nano-sized particles is a laborious, expensive process—or it was until a team of MIT researchers stepped in. Back in 2006, Angela Belcher and her team of MIT scientists manipulated the genes of a nano-sized virus so it would collect cobalt oxide and gold—metal oxides that would increase the energy density of the anode they were creating. Now, Belcher and her team have taken the M13 virus and altered its genetics to a) make it coat itself in iron phosphate and b) cause the virus to bind to carbon nanotubes on one end, thus completing their itty-bitty high-energy-density battery by fashioning the “other end”: the cathode.
Smaller, lighter, more efficient, longer-lasting—these are the qualities needed to make batteries for all of our “take it everywhere” gizmos—including hybrid cars. That is one possible “application goal” for the research, as the lab continues its work on a second generation battery for commercial production.
Articles for further reading:
Join us in New Orleans for Experimental Biology 2009!
New Orleans (frommers.com)
The Experimental Biology 2009 meeting will be held next week (April 18-22) in New Orleans, at the Ernest N. Morial Convention Center.
This annual interdisciplinary meeting is sponsored by multiple societies, including the American Association of Anatomists, the American Physiological Society, and the American Society for Nutrition. Over 15,500 people attended last year’s meeting. There will be symposia, poster presentations, career sessions, lectures and awards, as well as exhibits from scientific suppliers and publishers. Representatives from Wiley will be there to display life sciences books and journals.
If you’ll be attending this meeting, be sure to take advantage of the incredible culture, cuisine and nightlife that New Orleans has to offer. Check out City Park and the Audubon Zoo, lose yourself on Bourbon Street and the French Quarter, and sample some of America’s most flavorful cuisine at Cajun and Creole restaurants. For all the inside information you’ll need to enjoy this fantastic city, refer to Wiley’s Frommer’s Guide to New Orleans.
Experimental Biology 2009 is a great opportunity to network with scientists in many fields of biology, view the latest products and innovations in research technology, and simply enjoy a week in one of the nation’s greatest cities. See you there!
The Acronyms Tell the Story
Can you identify all of the scientific acronyms in this story?
This is a story about MS SNuPE (1) the CP Scientist. MS SNuPE loved animals. In fact, she kept quite a menagerie at her house—she had two Siamese cats, a Black Lab, a parakeet, four FISH (2) and even a hamster. (Fortunately, MS SNuPE was single and had no small children to FRET (3) about.) She was most proud, however, of her newest acquisition: a giant King COBRA (4).
MS SNuPE loved her COBRA. She loved everything about it. She loved the little FLAP (5) of skin that made a hood over its head. She loved its beady black piercing eyes and its little grinning mouth. But what she loved most was the way it moved. All of her other animals trotted or fluttered or skittered, but the COBRA slid and slithered and glided. It was silent and graceful, and she thought that because of this, it must be the smartest animal. She decided that if she could train it to do tricks, she could quit her job as a scientist and join the circus.
Thus, MS SNuPE set out to teach it tricks. First, she tried to make it race the Black Lab and the hamster. This didn’t work, however, because the hamster always got scared and hid under the couch, and as soon as MS SNuPE coaxed the Lab to the starting line, it would realize it was next to a COBRA and start to throw a HisZiFit (6).
Next, MS SNuPE decided to teach her COBRA to do a FLIP (7). She set it on the kitchen table and started flicking its tail, coaxing it toward the edge. Her plan was to make it fall off, tail-over-head, and see how it landed. However, she failed to take into consideration the fact that snakes are all muscle and can wind their bodies into any contortion. Instead of falling off the edge of the table, as she had intended, the COBRA arched over the edge and wound its way around the table leg.
Finally, MS SNuPE tried to teach the COBRA to swim with a FLIPR (8). She bought a little blue one that fit right onto its tail, stuck the COBRA in her partially filled bathtub, and poked at it, thinking that surely its writing would translate into swimming. Unfortunately, it did not move its tail in the direction that would enable the FLIPR to displace water; rather than undulating up and down, the snake wriggled back and forth, slithering along the bottom of the bathtub and coiling into a protective ball at the end by the drain.
Oh bother, thought MS SNuPE, I’ll just send this useless thing back to CircusPets.com. If it doesn’t do any tricks, it doesn’t do me any good. The whole point in her buying a snake, after all, was to quit her job and join the circus. (Even though she loved being a CP Scientist; she had just always dreamt of being in the circus, ever since she was a little girl.) So she went out and bought a big box and some ropes to FRAP (9) it up, so that the COBRA wouldn’t escape. Finally, the package seemed ready to go: the COBRA was safe inside, and MS SNuPE was about to affix the proper postage on the box and call the mailman to pick it up. All of a sudden, though, she became very sad. Sitting down beside the FRAPped up box, she put her head in her hands. What would she do now? She had this big cage in her house, perfectly suited for a COBRA. She had grown accustomed to caring for ten animals, not just nine. There would be a big hole in her life without this COBRA, whether it made for a good circus act or not. How could she ever replace it?
On a whim, MS SNuPE glanced up at her perpetually playing television set. (She is a somewhat typical American after all.) There, broadcast across one particularly garish infomercial, was her answer: a host of small leafy green animals were collected upon a smiling woman’s windowsill. ChIA-PETs (10)!!!
(1) methylation-sensitive singlenucleotide primer extension; Current Protocols in Human Genetics 10.6
(2) fluorescence in situ hybridization; Current Protocols in Cell Biology 22.4
(3) Forster resonance energy transfer, or fluorescence resonance energy transfer; Current Protocols in Microbiology 2A.2
(4) combined bisulfate restriction analysis; Current Protocols in Human Genetics 10.6
(5) Fluorescence Localization After Photobleaching; Current Protocols in Cell Biology 21.1
(6) His6 Zn2+ fluorescent in vivo tag
(7) fluorescence loss in photobleach; Current Protocols in Microbiology 2C.1
(8) fluorometric imaging plate reader; Current Protocols in Pharmacology 9.2
(9) fluorescence recovery after photobleaching; Current Protocols in Microbiology 2A.2
(10) chromatin interaction analysis using paired end ditagging; Current Protocols in Molecular Biology 21.12 for the PET portion
From Online Journals, a New Map of Scientific Research
click to view full sized image (from nytimes.com)
With more journals and new research floating around on the internet than anyone can keep track of, it is more crucial than ever to understand how these overwhelming volumes of information are actually accessed. Now, thanks to new research conducted by scientists at the Los Alamos National Laboratory, we have a visual “map” of academic subjects–both humanities and sciences–constructed mathematically based on online searches where users followed links among categories. The team, led by Dr. Johan Bollen, has published its findings in the latest issue of PLoS One. This research is likely to revolutionize the way we think about academic publishing and how various disciplines are cross-referenced in the real world.
This data may lead to important and unexpected conclusions that a contrived taxonomy, while based on common sense and experience, may fail to capture. We now know that certain subjects are closely associated not because scientists say they are, but because it is statistically shown that linking from one to the other occurs at a high rate of frequency. The map is a much “truer” representation of subject associations than the established method, known as citation analysis, which involves using footnotes and citations to determine how often journals in one field are cited within those of a related field. The reason this method can be misleading, according to the research scientists, is that authors of journal articles may include certain citations for reasons that are personal rather than strictly scientific. After all, scientists are human, too; ultimately a list of citations, while a well-regulated part of the academic process, is still a human construction. That’s where the computers come in.
“What we have is a map of worldwide scientific activity.” –Dr. Johan Bollen
Based on electronic data logged from about one billion user interactions, the scientists used equations to produce a visual map of scholarly subjects represented by online journals. The subjects are color coded based on category, and the lines connecting them show the frequency with which users clicked from one to another in a research session. The proximity of subjects to one another is objectively determined by the strength of these links; similar subjects such as Biochemistry, Analytical Chemistry, and Organic Chemistry appear in a common cluster It is a fascinating visualization of how people actually find data online, and it seems to capture the real activity of scholarly research better than anything else.
It makes perfect sense that there should be such a “road map” of science. After all, the universe of knowledge is like a terrain to be spatially explored; start at one point, follow what interests you, and see where you end up. Isn’t that how all great discoveries are made?
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