Tuesday, December 21, 2010

Of Bread Molds, Bacteriophages, and Bug Brains: The Fight Against Infection

On a quiet morning in September of 1928, a brilliant but absent-minded microbiologist found that one of his Petri dishes containing colonies of bacteria had been contaminated with a fairly common mold that is usually found on bread and fruit. Rather than simply throw out the plate, the scientist noticed that there were no bacterial colonies growing around the mold—instead there was a clear zone around the mold that was completely absent of growth. Upon further investigation, he realized that the mold, called Penicillium notatum, was secreting a substance that inhibited growth of certain bacteria. This microbiologist, Alexander Fleming, had just discovered one of the most important substances of the twentieth century: penicillin.

Over the next few decades, several scientists worked on better understanding, purifying, and mass-producing penicillin. In fact, penicillin was an important force in World War II, saving as many as 15% of Allied troops with severe infections from battle injuries. Penicillin was, and continues to be, very important in handling bacterial infections. It was the first effective drug used to treat diseases such as gonorrhea, syphilis, or gangrene. However, penicillin cannot inhibit the growth of many types of bacteria and sometimes causes problematic side effects. As a result, there has been an assortment of semi-synthetic derivatives of penicillin produced (such as ampicillin and amoxicillin) that have a similar mechanism of action but can treat a wider variety of infections with fewer complications. Over the years, other antibacterials with different modes of action, such as erythromycin, mupirocin, and tetracycline, have been discovered, developed, and have saved countless lives.

However, all antibacterials have the same problem: bacteria can develop resistance. This means that a drug employed to treat an infection, especially if it is overused, is no longer effective. All antibiotics work by interfering with some aspect of the pathogen’s metabolism that is different from the host’s. But if a bacterium evolves so that some aspect of its metabolism is altered, a drug no longer works. The matter is further complicated because many bacteria can share genetic information, so that resistance can be passed from one species to another. The resulting bacteria can wreak havoc, since treatments are either ineffective, extremely expensive, or toxic to the patient.

This problem has propelled a search for the next generation of antibiotics. Many drugs so far have been found in nature, from common molds to plants to bacteria themselves. A great number are slightly altered versions of these natural compounds that somehow improve the original. But many of the most promising new antibacterials are being found in the strangest of places, most notably, cockroach and locust brains. Though an initially strange idea, it makes sense to look inside of insect brains for highly effective antibiotics with few side effects. Bugs tend to live in nasty environments teaming with all sorts of bacteria, so in order to protect themselves from infection, they produce substances that will kill off invaders and protect their delicate little nervous systems. Scientists have also turned to the seas for new antibacterials. Some marine invertebrates, such as the hydra or sponge, produce antibacterials that attack bacteria in completely new ways. Instead of using a regular molecule, they can use proteins to kill off pathogens.

Another unique strategy is the use of viruses to inhibit bacterial growth. Bacteriophages, which are viruses that infect bacteria, are perfectly safe in the human body and are very effective in killing off pathogens. Furthermore, they are highly specific and thus will not affect the “good bacteria” that are found in our bodies, which has been a problem with some commonly used antibacterials. Phage therapy is certainly not a new strategy, having been used for decades in eastern Europe, but it is only now being investigated for use in the United States. Research on phage therapy has been looking promising for treatment of highly problematic infections, such as those caused by methicillin-resistant Staphylococcus aureus (MRSA).

The twentieth century brought us the ultimate answer to Louis Pasteur’s Germ Theory (which states that many diseases are caused by microbes): antibiotics. Antibacterial drugs, from the mold-derived penicillin to the extremely toxic chloramphenicol, have revolutionized medicine and turned diseases that were originally a death sentence to completely treatable conditions. Hopefully, the twenty-first century will bring a new host of strategies that will fight pathogenic bacteria and keep us healthy.

Note: Though they are often used interchangeably, there is an important difference between antibacterials and antibiotics. Antibacterials specifically handle bacteria, whereas antibiotics take on any microbe (a better term is “antimicrobial”). In this article, I have opted to use both words, but never synonymously. See this Venn diagram for my completely unnecessary and by no means thorough explanation:

Sunday, December 5, 2010

Quick Pasta!

One thing I have had to learn over the past year is to make protein-ish, cheap, and filling meals quickly--I mean, when you're studying for finals or have three tests and two papers due in the span of four days, you do have to eat (clarification: you SHOULD eat, even if you don't HAVE to). Strategies have included canned food, cooking and freezing food on weekends, scrambled eggs, microwaved potatoes, and slow cooker meals. This week, I discovered a new one: pasta on the fly.

The basic idea is this: combine easy-to-make protein with frozen vegetables and rice-cooker pasta. It turns out that making pasta in the rice cooker takes very little time and effort. I have, on other occasions, used real pasta sauce, cooked garlic and onions, and added ground beef. But if I don't have the time for that, bacon (microwaved), garlic powder, butter, and shredded mozzarella are quite delicious! And for veggies, some defrosted broccoli or peas do just fine.

Making pasta in a dorm is pretty easy. Put water in the rice cooker, and when it boils, add pasta. Once the pasta is cooked, dump it into a strainer and rinse with cold water. Add crumbled bits of bacon, tons of shredded cheese, some butter, plenty of salt, frozen veggies, pepper, and garlic powder. Nuke to get the cheese to melt and the veggies to defrost, and you've got enough pasta to last you for at least a whole day.

Oh, and as for gluten-free pasta: it turns out that Wal-Mart now carries it, and a little goes a looong way. Win.

Study break over. Time to go back to micro and the second draft of my thesis...

Tuesday, November 9, 2010

Benoit Mandelbrot, Father of the Fractal

Last month, the world lost one of the most brilliant mathematical minds of the past few decades: Benoit Mandelbrot. This mathematician was born November 20, 1924, in Poland, grew up in France, and spent most of his adult life working in the United States. Mandelbrot made contributions to numerous fields, including economics, information theory, and fluid dynamics, but he is perhaps best known for his work in theoretical mathematics, specifically, fractal geometry. A fractal is a shape that possesses the property of self-similarity——zooming in reveals that the border forms patterns similar to the whole, making the shape never-endingly complex. Computer programs can be used to generate fractals that have color-coded areas, giving rise to beautiful, trippy images.

However, a fractal is more than just a pretty picture. The equations that give rise to these fractals can actually be used to describe various phenomena in nature.

In fact, Mandelbrot was first inspired to explore the concept of fractals when pondering how best to measure the coast of Britain. This seemingly easy endeavor is actually quite difficult. The more precise the measurements are, the longer the coast becomes. Mandelbrot realized that these complex borders can be described according to simple formulas. For instance, the mathematician’s eponymous fractal, the Mandelbrot set, is defined by a very simple equation: z → z^2 + c. But zooming into the border of the fractal reveals consistent, infinite complexity.

Fractal geometry can be applied to a variety of fields. Fractals have been used for image analysis software, musical compositions, image compression, and even computer games. They can also be used in more scientific fields, such as seismology or medicine. Perhaps most importantly, fractals have shown that seemingly random and confusing things can actually be described and predicted very precisely with elegant formulas. Thanks to Mandelbrot, it is now understood that all sorts of phenomena, from occurrences in nature to the stock market, are full of intricate patterns that reveal a hidden order and beauty in the world.

Rest in peace, Benoit Mandelbrot. You will be missed.

Benoit Mandelbrot, 11/20/1924-10/14/2010

Watch this TED talk by Mandelbrot himself a few months ago:

Fractal wrongness

Saturday, November 6, 2010

Global Warming Meets Turing Test!

I don't normally visit twitter pages (don't have a twitter account to begin with), but this one is pretty awesome. It's a bot that scans twitter for the latest global warming denialist tweets and automatically generates a rebuttal with links for support! Of course, it's a PROGRAM so it's not always spot-on, but still, the idea is pretty cool. Ah, the wonders of repetitive, poorly researched claims...


So this is a lame post, whatever. "New" recipe coming soon!

Sunday, October 3, 2010

Star Trek Technology: When Science Boldly Goes Where Fiction Has Gone Before

The post below is based on an article I recently wrote for the science/tech page of the school newspaper (I haven't posted for a while, so I figure something extremely geeky and of mediocre quality is better than nothing...). Enjoy!

Also, I have a new blog design! Isn't it neat?

For decades, the genre of science fiction has enthralled and even inspired generations of nerds, and perhaps one of the most-loved science fiction franchises is Star Trek. Yes, this show may call to mind geeky conventions and socially-awkward individuals, but after the 2009 film caused more widespread acceptance, it’s official: it is now okay to like Star Trek. Part of the franchise’s appeal lies in the awesome technology, and interestingly, the geeks who first liked the series have brought some of the gadgets out of science fiction and into the real world.

Set phasers on stun
Perhaps the most well-known Star Trek gadget is the phaser. The phaser is a device that shoots a beam of energy, which, depending on the setting will “stun,” “kill,” or “vaporize” the target. While there still aren’t weapons in use that will actually stun or vaporize, it is possible to make something similar to the fictional device, using only a blue-ray player and a few assorted materials you can find at any hardware store. The army is also toying with a few less sleek (read: bulky and expensive) weapons that could someday be useful for crowd control, since they are equipped to paralyze people with ultra-sonic waves and similar apparatuses.

The Ship
Without a doubt, the most powerful devices are found on the Star Trek ships themselves. Unfortunately, most of the technology is not yet developed, or is barely even conceptualized.

For instance, some experiments with transporters have been done, but nothing with human beings. Theoretically, a transporter would convert somebody into an energy pattern then convert that energy back into matter at a different location. The amount of information coded by only one person is nearly impossible to even imagine, and the ethical issues abound—is a person still the same person if they’ve been re-created in a different place?

However, the coolest trekkie ship technology being developed is the tractor beam. In the Star Trek world, the ships have devices that can literally pick something up and move it without touching it—for instance, if the Enterprise came across a ship that needed repair, it could “tow” it to a nearby station. Scientists have found ways to shift small objects around using lasers and hot gas. Of course, this means that the tractor beam could not be used in outer space, since space is a vacuum and thus does not contain air. But the potential applications are quite exciting.

I’m a doctor, not an engineer
Some of the coolest gadgets in the Star Trek universe are found in sickbay. Patients are regularly diagnosed or treated with small devices that do not break the skin, calling to mind our modern-day super-fast thermometers or jet injectors used to inject substances intramuscularly without needles.

Perhaps a more well-known device is the VISOR worn by Geordi La Forge in Star Trek: The Next Generation. The VISOR, a small device worn around the eyes that hooked above the ears, enabled the blind La Forge, to see the world through most of the electromagnetic spectrum (although he could not see visible light). While we still don’t have a device as powerful as the VISOR, researchers have begun to find ways to give people back some degree of vision. Like the VISOR, some of these devices use tiny machines that feed information directly to the brain or retina, allowing someone who cannot see with their eyes to pick up some degree of visual stimuli.

In Star Trek, procedures are almost always performed on people without even having to cut them open. While we still have to go into the body in some way, many modern surgeries are performed with minimal invasiveness—or, even better, by ROBOTS. And of course, there is now something that can act like the electronic pad the doctors so often used to read and analyze patient information: the iPad.

We may not have all the amazing technology from Star Trek yet—holodecks, androids, warp drives, true cloaking devices, photon torpedoes, deflector shields, and (fortunately) the Borg are still to come—but we do have a slew of other sci-fi-esque contraptions that will become, if they haven’t already, a staple of modern life.

Wednesday, September 1, 2010

Chicken Satay-ish

Probably one of the awesomest things about living in an apartment this year (besides my WONDERFUL roommates) is that I can constantly make food and have people over. Today, I did both (sort of)--so much fun! My friend J came over early this afternoon, and helped me make the rice and adjust the ingredients for the sauce, since I know absolutely nothing about cooking with curry and he is apparently familiar with Thai cuisine. R (one of my roommates) set the table, L (another roommate) dropped by, and we had a lovely time eating dinner!

    Main ingredients:
  • 5 chicken breasts, cut into bite-sized chunks
  • 2 cups long-grain rice + 4 cups water (in rice cooker)
  • Extra-virgin olive oil for skillet

  • 5 gigantic spoonfuls of apple sauce
  • 3 gigantic spoonfuls of chunky peanut butter
  • 1 spoonful curry
  • 1/2 spoonful chili powder
    (Microwave until the ingredients mix together smoothly, or ~3 minutes.)

Cook chicken in skillet. Add sauce and push around until well mixed. Serve on rice, with additional curry and chili sprinkled on top if desired. Absolutely delicious, and SO filling.

I will definitely have to try more "different" recipes. It's easy to shy away from the odd ones, since they're a bit intimidating, but this shows that they can be very WIN!

Recipe ripped off from foodnetwork.com. Thanks to my awesome mother for finding it for me!

Monday, August 2, 2010

Terapia de Tilapia

A bit less than a month ago, I had one of the most terrible weeks this year. It was absolutely AWFUL. My medication ran out, experiments didn't work, my lab presentation was a total fail, etc. I decided to take action, and spent Thursday lunch break cooking. This recipe was sort of improvised, using another recipe as a starting point. I had been craving fish, so I settled on tilapia, which I happened to have in the freezer.

  • 5 tilapia filets
  • ~3/4 stick butter
  • black pepper
  • lemon juice
  • chili powder
  • thyme
  • salt

I started by melting the butter and mixing in the spices. Then, I dipped each filet into the mixture. Using my brand new skillet, Oscar, I cooked each filet for 2-3 minutes per side, pouring extra seasoning mix on top.

After they looked reasonably cooked, I moved them to a tupperware and added 1/2 onion, thinly sliced. After the onions were thoroughly done, I added them to the tupperware then put in 1 white potato, sliced. I occasionally poured any extra butter mixture on top. These then went into the tupperware as well.

Though I was planning on eating the tilapia for lunch the following day, my roommate L and I ended up eating this for dinner, along with some broccoli. Delicious--and therapeutic!