doc w/ pen

a journalist becomes a doctor before your eyes

Month: December, 2011

Gene-ious!

Geneticists, and scientists in general, may not exactly have a reputation as having a sense of humor. But, I argue, many of them truly do. I have evidence to prove it, which I will present in this post. I stumbled across this evidence when searching for an appropriate name for my iPad. I simply Googled “funny gene names,” and came up with a list of sometimes hilarious, sometimes poignant, sometimes culturally referenced, names for genes of various organisms (especially my dear Drosophila melanogaster). Here are some of my favorites, taken from a couple of Web sites that I found: jpetrie.myweb.uga.edu/genes.html, http://www.curioustaxonomy.net/gene/fly.html, and tinman.nikunnakki.info/browser. I hope they bring a smile to your face, as they did to mine.

These are all from Drosophila melanogaster:

 Gene name History behind name
 18wheeler This gene is expressed in 18 stripes in developing larvae.
 agnostic Agnostic flies fail to learn odors in certain temperatures. Agnostic people also have problems making up their minds.
 amontillado Mutant larvae do not hatch. In Edgar Allen Poe’s short story “The Cask of Amontillado,” a man who is still alive is walled in.
 brokenheart A mutation in this gene causes a defect in heart development.
 cheap date These mutants are very sensitive to alcohol.
 cleopatra In these mutants, an interaction with the asp gene is lethal. Queen Cleopatra supposedly committed suicide with a poisonous asp.
 clown Mutants’ eyes are red and white.
 coitus interruptus Mutant males literally engage in withdrawal during copulation (it lasts about 60% of the normal 20 minutes).
dachshund Flies have crippled legs, resembling this dog species.
dreadlocks The connections between nerve cells of these flies are not correct, and the result resembles the hairstyle of the same name.
drop dead These mutants’ brains deteriorate rapidly; they begin to walk in an uncoordinated way and then die.
dunce These flies have impaired learning.
glass-bottom boat These flies’ larvae are transparent.
grim, reaper These two genes together mediate programmed cell death (apoptosis) in the fruit fly.
groucho Mutants have a greater-than-normal number of bristles (like Groucho Marx).
icebox Female icebox mutants do not care about courting males.
ken and barbie Both male and female mutants lack external genitalia (like Ken and Barbie).
limo This gene is involved in protein transport.
lot A Biblical reference: mutants like salt more than usual.
lush Mutation causes increased desire for alcohol.
out cold Mutants lose coordination when the temperature falls, and eventually become paralyzed.
sarah Mutants are practically sterile (another Biblical reference, to Sarah, Abraham’s wife).
stuck Mutant flies get stuck in females.
swiss cheese Mutants have holes in their brains that resemble swiss cheese.
van gogh Swirling wing hair patterns resemble van Gogh’s paintings.
yuri Mutants have difficulty with gravity. The gene was found on the 40th anniversary of Yuri Gagarin’s historic space flight.

Thanks to the tinman Web sites I referenced above for these gene names and explanations; visit the site for more. Fun stuff!

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INDY: My Techno Bling

ipad 2Back in January of this year, I wrote a post about things I was looking forward to in 2011. One of those things was an iPad 2. Had my circumstances (i.e., my marriage and living situation) not changed, perhaps I would have pre-ordered one as I suggested in that post. But things did change, in many ways, including financially. So throwing down $1,000 (or so, plus $25/month for a data plan) seemed impossible.

However, as I was wrapping my dad’s gift on Christmas Eve morning, suddenly I began channeling his “if-you-want-it-get-it” attitude. (It didn’t help that a good friend had just bought a new MacBook Pro, and we had only a few days ago been discussing our desire for iPads as well.) I put Dad’s gift down, hopped on my own MacBook Pro, and went to the Apple.com store. I briefly – only briefly – considered having my iPad 2 to-be shipped to me, but then realized that I desperately wanted it then and there. So I reserved it for in-store pick-up. (And yes, I actually went to the Apple store on Christmas Eve. It was not nearly as bad as I expected, especially since I was only there to pick up, and set up, my new device.)

Because it is my family’s tradition to open our gifts on Christmas Eve, I had little time to play with my new (and very expensive) toy that day, other than to import some of my iPhone apps. One of “Santa’s” gifts to me happened to be a $50 iTunes store gift card, which definitely came in handy the next day – Christmas morning – as I researched, imported, and downloaded more apps for both work and play. (One of those apps – BE Write HD – I am using to write this very blog post!)

INDYSo, my dear bloggers, meet INDY: my iPad 2. INDY is a reference to a gene in Drosophila melanogaster (the fruit fly, about whom I have written much), which, when mutated, makes a fly live twice as long. I’m definitely hoping my iPad’s “genes” are good! (But I did buy AppleCare just in case.) The gene is called “INDY” in reference to a line from “Monty Python and the Holy Grail,” in which a person who is being taken to be buried yells out, “I‘m not dead yet!” (See the movie still on this page.) The name is a perfect confluence of my interests: words (and more specifically, acronyms), British humor, genetics, mutations, and Drosophila. I think it’s just darn cute, too.

While the device itself is also quite cute, it is also quite functional, given that there are literally hundreds of thousands of apps available to download. Those apps basically enable this little tablet to do much (though not all) of what a laptop can do, for much less than you’d pay for computer software. The most expensive app I bought (QuickOffice, $14.99) allows you to create and edit Word, Excel, and Powerpoint files. Compare that to $119.99 for Microsoft Office. I also bought a PDF reader app (iAnnotate, $9.99) which allows you to do many of the things that Adobe’s professional program does. This will save me on printing, because I can use my PubMed or Nature Reader apps to look up research articles, download them to my iPad, and then highlight, draw, or take notes on them. Pretty sweet. These apps will also come in handy for school, of course. As will my favorite flashcards app (flashcards++, $3.99), which lets me import flashcards that I’ve made online (I use Quizlet.com) and test myself with my iPad or iPhone. I’ve been using them on my iPhone, but many of the flashcards I’ve made have graphics or diagrams that are hard to see on the small screen. Having an iPad will make it easier to study, clearly!

Along with reading PDFs, I can also read magazines and books on my iPad. I’ve already downloaded a book I’ve had my eye on for some time – “Nature’s Robots: A History of Proteins” – through Amazon’s Kindle app (which also works on the iPad).

Then there are games. And more games. Many of them will run you only a buck or two, although I shelled out a whopping $4.99 for Riven, the sequel to the game Myst I played on my Mac desktop as a kid. (Again, compare to the list price of $29.99.) I’m also currently addicted to Bejewled ($0.99), which has a Tetris-like feel to it. I think that’s the most use I’ve gotten from a single dollar in a LOOONG time.

I’ve only scratched the surface of the apps and features available on the iPad. This is going to be fun …

ADCOM Q&A: Dinner Party

It is understandable that admissions committee members would want to know who has been influential in your life. As such, one question that I’ve seen on a list of medical school interview questions is: If you could invite four people to dinner, who would they be and why? I’ve given this some thought, and have come up with my short list of esteemed dinner guests:

Morgan with his fly drawings.

1. Thomas Hunt Morgan
While “T. H. Morgan” may not be a household name, this man is legendary in the field of genetics. He worked in the early part of the 20th century, shortly after Mendel’s work with pea plants was rediscovered. Morgan worked with Drosophila melanogaster (the same species of fruit fly that we worked with in my genetics class). After much work, he and his students identified a white-eyed mutant fly among the red-eyed wild-type flies. This mutant displayed a distinct pattern of inheritance. Through a series of fly crosses and much analysis, Morgan was able to show that this white-eyed trait is a “sex-linked” trait. That is, the gene responsible for the trait is located on a sex chromosome (specifically, the X chromosome). This was the first direct evidence of the physical basis of inheritance, and it revolutionized the field, leading to scores of other discoveries.

Eleanor Carothers
with Brachystola Magna
(the grasshopper)

2. Eleanor Carothers
The reason I want to meet this woman, who worked around the same time as Morgan, is two-fold. The first reason is that she made a very important contributions to what is called the “chromosome theory of inheritance.” This theory, proposed by two scientists named Boveri and Sutton, said that chromosomes carried the units of Mendelian inheritance (i.e., genes). This was a controversial theory at the time, but Carothers strengthened it by demonstrating the presence of independent assortment (one of Mendel’s theories) of chromosomes in the testes of Brachystola magna (the grasshopper). The second reason I would want to meet Carothers is that she worked as a female geneticist during a time when the field was completely male dominated. I would be very interested to hear her experiences, and to learn from her dedication and determination.

Watson and Crick in the famous
photo with their model of the
DNA double helix.

3. James Watson
4. Francis Crick
I put these two amazing men together because they worked together on their most significant discovery: the discovery of the structure of the DNA double helix. Their work, published as a one-page article in the journal Nature in 1953, paved the way for future work in just about every field of the biological sciences, especially genetics (my own particular interest). While Crick died several years ago, Watson, in fact, is still alive at the age of 83. How I would love to pick his brain!  

ADCOM Q&A: Showing Initiative

Admissions committee members are looking to fill their open medical school seats with leaders, not followers. With that in mind, one question that often gets asked is something to the effect of: What have you done that shows initiative? What did you learn from that experience? 


As a journalist, my entire job was about showing initiative. People rarely handed stories to me; I had to seek them out. Often, I would hear about something in passing, or I would receive a letter to the editor that piqued my interest. But it was up to me to follow up on these tidbits, and to choose an “angle” from which to tell the story.

One story that sticks out in my mind came about because I received a notice from the local state representative’s office that audible crosswalk signals were going to be installed at certain intersections in the town where I worked, thanks to grant money. On its own, that’s not really a story. That’s a bullet-pointed news item among other bullet-pointed news items. This is where my initiative came in: I decided that the way to make this into a worthwhile, newsworthy story was to find someone – someone who was visually impaired – who was going to benefit from these crosswalk signals, and really make it a story about the mobility of a disabled person.

Of course, finding someone who was visually impaired who was willing to talk to me took quite a bit of initiative. I remember it taking a long series of phone calls (and several dead-ends) until someone suggested I talk to a blind woman named Cathy who lived near one of the new crosswalk signals. I set up an interview with her at her apartment. After talking for an hour or so, we ventured outside with her guide dog so that I could get at least an inkling of an idea of what it was like to cross the busy street without being able to see the cars flying by. Cathy told me that while she trusted her guide dog implicitly, the audible signals would make it so much easier and safer for people in her situation to cross the busy intersections where the signals had been installed.

Through my initiative, I took what we in the news business would have called a “news brief” item and put a human face on it. I raised awareness in the local community about why these audible signals had been installed, and who they would benefit – people like Cathy.

I learned from this experience and other similar ones that contextualizing an issue, whatever the issue might be, allows people to relate to it better. When you focus on a person, and how a problem relates to that person, rather than just describe the problem itself, you give your readers the tools to empathize rather than merely intellectualize.

Putting an issue into its context is something that is important in medicine as well. At the clinic where I volunteer, I have seen some physicians describe symptoms, side effects, etc. without connecting them to the actual patient. When this happens, the patient has little frame of reference for what to do with the information. With a diabetes patient, for example, a physician might tell the patient to eat less carbs, but not take the time to figure out what kind of carbs the patient was eating (in order to steer him or her away from those things), or even whether the patient was clear on what types of foods constitute carbohydrates. Other physicians take the same types of information or instructions and put them in the context of the patient’s life, making them more relevant. I translated recently for a physician who was working with a diabetic woman who needed to lose weight. The doctor told the patient that she needed to eat less carbohydrates. She nodded, of course. But the doctor then went the extra step and asked her how many tortillas she was eating every day. His instructions, then, were to cut in half that number as a starting point. This gave the patient something concrete to work with.

Taking initiative – by putting information into a relevant context – was an important part of my job as a journalist, and will continue to be an important part of my future job as a physician. One more reason I am thankful for my past history, and the lessons I have learned.

Spring 2012 Schedule

My lovely schedule for next semester …

The friends with whom I am staying in Nashville are most definitely not morning people (and I most definitely am), so I’ve had some nice quiet time curled up in this awesome, oversized chair that they have. This morning, I decided to enter my schedule for next semester into my Google calendar, and also to figure out when, exactly, classes actually begin. Just so I know how much time I really have off. Turns out classes start Jan. 11, which means I have a little over 3 weeks of vacation. Hooray!

But as I was inputting my schedule into my online calendar (which also syncs to my iPhone, of course), I was also getting excited about the classes I will be taking next semester:

1. Organic Chemistry II (with lab). As much as I was terrified of orgo going into last semester, my fears have abated. Not that it’s an easy class – I most definitely earned my A (yep, an A!) this past semester through hours of hard work at my dry erase board. But for some reason, somehow, orgo makes sense to me. (At least, most of the time, after I have puzzled through it for several hours.) Crazy as this may sound to all of you who have taken or are taking orgo, I actually like drawing reaction mechanisms. And that’s what second semester is all about: more reaction mechanisms and synthesis, which to me is like deciphering a giant puzzle. I’ve always liked puzzles. Plus, Organic Chemistry II is a co-requisite for the next class I’m going to talk about.

Ribbon diagram showing 3-D
structure of a protein. We’ll
be studying these guys in
detail in Biochemistry.

2. Biochemistry. Some people claim they like biology, but not chemistry. In my opinion, this is absolutely impossible. Biology is all about chemistry, when you break it down to the molecular level. That is, if you actually want to understand how things work in a cell, you have to understand chemistry. And I’m definitely a “process” person. By that, I mean I like to understand how/why things work, at a deeper level. Biochemistry, to me, is about unraveling some of the mysteries of biology through chemistry concepts. For example, by learning about the structure and properties of the 20 common amino acids, you can gain a better understanding of how a protein structure develops, why certain mutations (genetics!) cause a loss or alteration of function, etc. In addition, there are so many organic chemistry reactions that are pertinent to biological functions. Life IS organic chemistry, when you get down to it. I know that we will only scratch the surface in this class, but it will be a good preparation for taking biochemistry in medical school/graduate school in the future as well as (hopefully) interesting.

Chi-square distribution graph. This is
the one statistical test I do know; we
covered it in Genetics. I look forward
to learning more such tests in Statistics
this coming spring semester.

3. Statistics. This is another class that, for me, will hopefully be of great utility. Many medical schools (and graduate programs) suggest that pre-medical students take stats; a couple of schools require it. So having taken stats will look good on my application. But that’s not my main reason for taking the course – my real purpose in taking it is to get a foundation in basic statistics so that I can better understand the statistical tests that are used in many of the research articles I read. P tests, T tests … I don’t even know the basics of stats, so I can’t interpret the statistical analysis. (The one bit of stats I know is the chi-square test, which we learned in Genetics.) I know this course won’t give me everything I need – at some point, I’ll have to take a biostatistics course, I think – but it will be a good start.

Drosophila melanogaster, the
subject of the research I will
be doing with Dr. Kreher this
coming spring semester.

4. Research. In addition to my three classroom-classes, I’m going to be doing 2 credit hours of research work with my Genetics professor from fall semester, Dr. Scott Kreher. I will be working with Drosophila melanogaster (fruit flies), most likely doing behavioral assays with the flies related to odor perception. I really enjoyed working with Drosophila in my Genetics lab, so I look forward to this work. It will be nice to be in a research lab again, for sure!

Vacation!

So I made it. I finished the semester. I wasn’t quite sure there for a while how that would happen, but it did (and it always does, doesn’t it?). 

And now I’m on vacation! I mean, really on vacation – I actually took a trip somewhere. My sister Sarah and a dear fellow non-traditional pre-med friend live in Nashville, Tenn., so I decided to head down South to see them for a week or so. I headed out straight after my organic chemistry final, which, considering I’d been up since 2 a.m. studying, made the 8-or-so-hour drive a bit long. But I survived, and here I am, sitting in my favorite oversized chair at my friend’s house, drinking coffee, and absolutely not thinking about homework. Of course, my plan is to begin MCAT prep over break (as you can see on my “ticker,” I take the exam in about 4 months). But I think I need to let my brain rest and recover for at least 24 hours.

Funny Bunnies: Evolution Simulation

Natural Selection

Click to Run

In my last post, I included a link to an online simulation of the lac operon. If you haven’t given it a try, I highly recommend doing so. Today, I want to share another simulation from the same source, the University of Colorado at Boulder. This simulation – entitled Natural Selection – allows you to explore the mechanism of evolution. Again, the premise, graphics, and interface are all very simple, but the lessons are profound.

You start off with one white bunny rabbit that lives at the equator. With the click of a button, you can “add a friend” (start the bunnies propagating), introduce mutations (brown fur, long tail, or long teeth – and decide whether these mutations are going to be dominant or recessive), bring in predators (wolves), give the rabbits food (scrub grass), and change the rabbits’ environment (from the brown equator to the white arctic). Then you watch what happens – do the bunnies die, or survive? And more importantly, the simulation gets you to think about why. There is even a running chart at the bottom that keeps track of your population, both total rabbits and by specific phenotypes (physical traits).

It is a great tool to illustrate how different mutations – for example, brown fur color – can be advantageous in one environment (at the equator, where the ground is brown and the brown rabbits are camouflaged and can better evade the wolves), but not in another (in the arctic, the white fur is more advantageous, for the same reason). You can also watch the effects of changing mutations from dominant to recessive or vice versa, and how that affects your population.

The best part is, if you do a really good job of taking care of your bunnies, they (literally) take over the world. Well, maybe that isn’t so great …

The Joys of Mutation: Manipulating The Lac Operon

Gene Machine: The Lac Operon

Click to Run

When I was homeschooled (preschool – 5th grade), my mom was all about interactive learning. We dissected animals, performed chemistry experiments, baked cookies to learn about adding fractions, all kinds of things. It made learning fun, and it made the learning stick. My love of interactive learning has continued, and it’s one of the reasons I love my science labs – we put into practice the skills and concepts that we have developed in the classroom.

Last week, my Genetics professor, Dr. Kreher, was able to bring that flavor of interactive learning into the classroom as well. We were learning about gene regulation, more specifically, E. coli’s lac operon (the set of genes and other elements that control for the breakdown of lactose, which is a source of energy for the bacteria in certain environments, including our digestive tract). Dr. Kreher had found a lac operon computer simulation program – which is free – that you can manipulate to see what happens when you “mutate” (i.e., remove) certain elements, add lactose, etc. It really made the system come alive, and I now understand the operon in a way that I had not before (in spite of the fact that I have studied it in past courses). I have included a link to the program in this post (just click on the picture above where it says “Click to Run”). While simple in terms of graphics and operation, it really represents how this system works, and what gene regulation means. I highly recommend checking it out. Have fun mutating!

Breakthrough!

This is an example of what I’ve been working on today …
the reaction to the left is called halogenation; the reaction
to the right is called halohydrin formation.

After hours of wrestling through organic chemistry problems (and getting so many wrong) … breakthrough! I think I’m finally getting it. Reaction mechanisms, that is. Well, not ALL reaction mechanisms, just the handful that we’ve studied thus far this semester. (The mechanisms of SN1, SN2, E1, E2, hydrohalogenation, hydration, halogenation, halohydrin formation, and hydroboration-oxidation, to be more specific.)

This morning, when I started studying for my organic chemistry final, it was all a mish-mash to me. Anti addition, syn addition, retention of configuration, racemization, carbocations, bridged halonium ions … I couldn’t keep it all straight. But after making (and reviewing) a huge batch of flashcards and working through gobs of these practice problems, something has clicked. Just now, I found myself looking at a reaction and actually knowing what to do with the bonds, atoms, and electrons. What arrows to draw. What products (including stereoisomers!) would form.

I still have a lot of practicing to do. I don’t have all of these reactions down completely. But I’m getting the hang of it, slowly. Thankfully, my organic chemistry final isn’t until next Friday, so I have plenty of time to cement my understanding. But knowing that I am already on my way is a darn good feeling.

The Art of Orgo

I have my fourth and final regular Organic Chemistry exam tomorrow on reaction mechanisms. In General Chemistry, we studied basic principles of chemistry, and how to mathematically work out many types of problems, but now we’re actually learning how different reactions happen, why, under what conditions, etc. It’s actually pretty interesting. Especially since there are so many pharmaceutical and biological applications for what we’re studying. Given that I want to do a PhD in Genetics, I know that knowing this will be helpful, at least for some of the graduate-level coursework (i.e., Biochemistry) that I will soon be taking.

In the beginning of the year, I used massive amounts of printer paper for doing practice problems. Then as I was cleaning out the basement of my old house, I rediscovered a giant dry erase board that I had bought years ago. I thought to myself, “We do practice problems on the dry erase boards in class; why not do the same at home?” So I lugged the dry erase board to my apartment, bought a big set of colored dry erase markers, and started drawing.

To my surprise, I found that I actually enjoyed doing the problems — drawing things out larger, and using different colors to symbolize bond cleavage and formation (for example) really helped me see the bigger “picture,” so to speak. So that’s how I’ve done my orgo homework ever since.

My drawing board has been especially helpful with reaction mechanisms — these problems have multiple steps, multiple bond breakings/makings, and having a large surface area (and again, many colors to differentiate things) has really made a difference in my learning process.

For kicks and giggles (and to further illustrate my nerdiness, not that that takes much doing), I’ve taken a picture of a practice problem from my textbook that I worked out on my dry erase board.

I know I’m not a doctor (yet), but if looking at this gives you a headache, I recommend taking two Aleve (a.k.a. naproxen sodium) and lying down for about 15 minutes. The blurred vision and pounding will go away soon, I promise.