doc w/ Pen

journalist + medical student + artist

Category: Uncategorized

The Mirror Image Of Life

I was talking to a dear friend on the phone this morning (you know who you are!). She is a very intelligent, wonderful, beautiful, and insightful woman, and we got talking about the basis and origins of life. Yes, the basis and origins of life … at 6:30 a.m. This is what the two of us do. We are a bit nuts. We come at these conversations (which happen with great frequency) from very different perspectives. She is a Muslim, I am an atheist. She is a future chemist, I am a future geneticist/physician. But the fact that we have different backgrounds enriches our dialogues, and brings us both to a greater understanding of the world around us, each other, and ourselves. It is an amazing tango of science and philosophy.

Back to the origins of life. In biochemistry, which I took last semester, we learned various theories about how life *may* have begun. Theories about RNA, DNA, and various other macromolecules coming into existence due to environmental and atmospheric changes. My friend and I were talking about those theories this morning. She, who also took biochemistry (although in a different section), then said something very interesting. She said that science cannot explain life. It just can’t. It’s not about whether God does or does not exist. (She knows my views on that subject, and respects them.) Science simply cannot explain how molecules went from nonliving to living. That transformation eludes explanation. In one of her most brilliant future-chemist moments, she then went on to say that one difference between life and non-life, one way to understand this difference, is related to chirality.

To quote my dear friend: There is an inherent relationship between chirality and life.

Two examples of chirality: a hand, and the amino acid alanine.

Two examples of chirality: a hand, and the amino acid alanine.

For those of you who have never suffered through organic chemistry, allow me to explain the concept of chirality. An object that is chiral is non-superimposable on its mirror image. An object that is achiral is superimposable on its mirror image. Here is an example. Take your hand. Hold it up to a mirror. The mirror image of your hand cannot be placed exactly over your actual hand, with the physical features of your hands aligning properly. Therefore, your hand is chiral. (According to Wikipedia, the word “chiral” is actually derived from the Greek word for hand, kheir.)

In chemistry, as well as in the pharmaceutical industry, chirality has profound implications. For example, one version (called an “enantiomer”) of a chiral molecule may be an active pain-relieving drug, while the other “enantiomer” may be very toxic to the body. The simple spatial rearrangement of the atoms can cause this dramatic shift in effect.

But what my dear friend was talking about is much more profound. I will explain. Take amino acids, the building blocks of proteins. In living organisms, amino acids are found in only one of their two enantiomeric forms. In the picture above, there are images of both L-alanine and D-alanine. These are the two enantiomeric versions of alanine, the simplest amino acid that exists. They contain the exact same atoms, but arranged differently in space around the central carbon atom. As we learned in biochemistry, “L” means “life.” In other words, living organisms contain the “L” enantiomer of amino acids. Not the “D.” This seemingly simple spatial rearrangement is literally the difference between a molecule that supports life and one that does not. If that isn’t profound, I don’t know what is.

A Publication! (and other news)

I know I haven’t posted in a while; things have been pretty crazy lately. This semester, my last semester as a post-baccalaureate pre-medical student, has definitely been my most difficult. Statistics is a breeze thus far, but biochemistry and organic chemistry II are definitely keeping me on my toes.

We had our first biochem exam a couple of weeks ago, and I was not looking forward to it. (That’s putting it lightly.) We had covered a lot of complex material about enzyme kinetics, and other protein-related information, and my professor had not covered it effectively, in my view. So there was much confusion about what would actually be tested on the exam. But I made out like a bandit (albeit a very hard-working bandit) – 94%, the highest grade in the class! I was quite pleased, but also felt I quite deserved the grade because I worked my butt off studying for that test.

I have an organic chemistry exam this coming Thursday, and so that will be my focus this week. We are currently studying techniques that help you determine the formula and structure of a compound (mass spec, IR, and NMR). It’s quite interesting, honestly, and a nice break from all of the reactions. But I know all of those reactions will be tested on our upcoming exam – my professor (whom I adore; she is a fantastic teacher) is an organic chemist, and highly emphasizes synthesis. I have made charts with all the reactions we have learned thus far, both by starting material (i.e., all the reactions you can do with an alkene) and by final product (i.e., all the ways to make an alcohol). We have, literally, studied dozens of reactions across the two semesters of this class! It is definitely a challenge to keep them straight in my head, especially when there are three or four reagents you have to use in a reaction, and when the synthesis requires more than three steps.

But there is light at the end of the tunnel! My spring break is next week, which will be a nice reprieve. As I mentioned in a previous post, I am going to a Drosophila genetic conference over break, which will be a nice change of pace from school.

And as the title of this current blog post suggests, I will soon have a publication! The professor with whom I am working on the Drosophila larvae research is presenting a poster at the genetics conference next week. Last Thursday, he told me that my name will be on the poster! I was quite pleasantly surprised, because in no way did I expect to get a publication of any sort out of my work with him this semester. But he told me that I absolutely deserved it, with all of the great data I have generated (which will be presented on the poster). It will be a proud moment when I am at the conference next week and I tell people I meet, “Oh yes, I am working on Drosophila research this semester related to the genetics of odor receptors and larval behavior. My professor and I have a poster here at the conference. You should go see it, it’s quite interesting.”

While it’s quite exciting, in and of itself, to have a publication, it will also be quite helpful for my medical school application efforts. MD / PhD admissions committees really want applicants to have some sort of publication, so being able to put this on my application will be quite wonderful. The fact that the poster is being presented at an international conference doesn’t hurt!

I’m also quite excited about the possibility of whom I might meet at the conference. At the suggestion of the conference organizers, I have even printed up business cards for myself so that I’m not scrawling my name and e-mail address on scratch paper in the event that I meet someone I want to contact later.

Well, that’s all the news for now. Back to studying …

The Unsilencing of a Gene

Rat neuron

Rat neuron

As many of you know, I love genetics. So when I was perusing Nature on my iPad this morning (working on my New Year’s resolution), I went straight for the article with the word “allele” in the title. (An allele is a version of a gene; we all inherit two alleles of each gene — one from our mother and one from our father. This concept is very important for the article I read.)

The article was about a drug that was found to “unsilence” an allele in mice, serving as treatment for a disease called Angelman syndrome, a severe neurodevelopmental disorder.

Normally, we have two potentially active alleles of each gene. However, in a particular gene called Ube3a, only the maternal allele “works” due to a process called imprinting. The paternal allele is effectively silenced. So if the maternal gene is mutated or dysfunctional in some way, then the gene product of Ube3a doesn’t get made — there is no functional paternal allele to take over. The result is Angelman syndrome, according to this article.

So researchers looked at 2,306 different molecules (yes, that number is right) to see whether any of them would “unsilence” the paternal allele. One — an anticancer drug called a topoisomerase inhibitor — did. The scientists eventually found another topoisomerase inhibitor that worked even better, and tested it in vitro (in culture) and in vivo (in living mice). In both cases, the Ube3a gene was activated in the target neurons.

While this type of treatment has a long way to go before it is approved for use in humans, this research study does offer hope to some people. (Angelman syndrome is estimated to affect 1 in 15,000 births, according to the Nature article.)

This article also contains many concepts that I learned in my genetics course. Which made it easier to understand, of course, and also reminded me that what we learned was significant and will be important in my future as a physician-scientist.

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!


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!


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.