Applying to Graduate Programs in STEM, Part 1: The Application Process

I was contacted by fellow blogger Aaron Long of The Doctoral Road to write a series of guest blog posts. The Doctoral Road covers topics on graduate programs in the humanities, and Aaron asked that I give the STEM perspective. To read my post, click here.

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Poetry in the Science Classroom

In school, particularly K-12, students spend a lot of their mental power categorizing themselves.  Which clique do I fit into?  Jocks, nerds, cheerleaders, popular kids, drama dorks, marching band, emos, goths, punks, skateboarders, surfers, or rappers?  AP, gifted, average, or failing?  Team Edward or Team Jacob?

One false dichotomy that was evident during my course on DNA with Duke TIP:  scientist or artist.  Of my 16 middle school students, 14 had very strong opinions that they were clearly scientists and had nothing to do with creative ventures.  The other two students were the types to dabble in a lot of different subjects, so they understood that this is not an either-or situation.

Clearly, this class, like most of the general public, does not get the chance to see the creativity that goes into science.  New technologies and novel ideas are the base materials of high-impact publications.  Interdisciplinary science is defined as taking information or techniques from one field and applying them to another.  Hence, the birth of biochemistry, molecular evolution, and bioinformatics.

Many of the long-shot, crazy-unless-it-works ideas are never published (let alone publicized) and are called negative data.  Even worse, the current tight funding situation has led to fewer innovative grants funded (see Bruce Albert’s comments).  Plus, the way science is often taught in schools makes it seem like scientists spend all their time memorizing books of known facts instead of synthesizing new knowledge and solving problems.

Back to my middle school students, their attitudes about science vs. art became so vehement that they would bad-mouth the neighboring creative writing class.  Creative writing became the slow gazelle of the entire TIP summer camp.  So the creative writing teacher and I did what good teachers do:  conspire against the students.

I gave the students a 30 minute assignment:  write poetry about DNA.  You would have thought I asked them to cut off their right hand.  I had to deal with more whining for this assignment than any other from that entire summer.  To make the assignment a little more student-friendly for students who didn’t want to worry about rhyming, I offered a perennial favorite of student poetry – the haiku (though since haiku are shorter than other poems, they had to write at least 10).  Here are some excerpts of the results:

“…And those pairs are made up of bases
That hold like the knot on your shoe laces.”

“…When they need to make copies there’s no hesitation
They begin a process called replication

The double helix is pulled apart by the helicase
This happens very fast like a race…”

“…Molecule of life
with base pair after base pair

coding my person”

“DNA is the start,
Proteins are the end,

RNA comes in the middle,
A Helicase unbends…”

DNA Haikus #8
“We are being used

Replicators control us
The fittest survive”

The Replication of DNA
“The parent making a child

Like mother & daughter strands
Then daughter becomes mother,
The cycle starts again…”


DNA by Unnamed Teaching Assistant
“It started with Watson and Crick;

Molecules muddled ball-and-stick.
Base pairs, sugars and phosphates too,
hydrogen bonds hold them together like glue.
Double helix is the shape of the strands,
complimentary like left and right hands.
The direction it takes, 5 to 3 prime,
which is how we will end this DNA rhyme.”

Untitled Haiku
“This class isn’t very easy

DNA is very, very hard

Each of these poems was reviewed by the creative writing class, who provided excellent constructive criticism in the style of the “feedback sandwich.”  Many students reported warming up to writing creatively about science.  Plus they had the chance to learn about peer review etiquette.

Does writing creatively have a place in the college classroom?  Absolutely.  If designed well, a creative assignment asks students to break away from traditional modes of assessment (quizzes, tests, calculations, labs, etc.).  Students are forced to synthesize what they know in new combinations.  For the instructor, a creative writing assignment may be more useful in assessing how well students understand the material beyond memorization.  Plus they are far more entertaining to grade.

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TED Talk: Gabe Garcia-Colombo – My DNA Vending Machine

The worlds of science and art do not always see eye to eye.  Many people feel that they are almost mutually exclusive.  If you’re artistic, you don’t understand math and science.  If you’re a science geek, you don’t have an artistic bone in your body (in addition to the other 206).  These fields seem as opposite as protons and electrons or Othello and Iago.

The truth is not so black and white.  Creative folks have to employ a knowledge of their materials.  STEM nerds need creativity to figure out the hows and whys of the world.  One lesson I try to instill in my students is that the scientific method, that dry series of steps we’re forced to memorize since elementary school, is actually how people inherently learn and solve problems.

This post is the first in a series I will write on the subject of creativity in the science classroom.  My goal is for students to explore their own creativity and for instructors to see the utility of these types of lessons.

Many of us have extracted DNA from strawberries.  Gabe Garcia-Colombo, the artist in the video, was inspired by this process to have DNA extraction parties with his friends.  Taking it a step further, he has created a vending machine at which you can purchase a vial of someone else’s DNA.

This video would be a good assignment after a DNA extraction lab, whether from strawberries or from students’ cells.  Once they see how easy it is to obtain DNA, a larger impact discussion can occur about genetic rights.

Questions for students:

  • What did Gabe Garcia-Colombo do after he was inspired by DNA extractions?
  • Describe the DNA vending machine.
  • What are some pros for having DNA vending machines?  For instance, would the public benefit somehow from these machines?
  • What are some cons for having DNA vending machines?  Could these machines somehow harm the people buying the DNA or the donors supplying the DNA?
  • Would you buy someone’s DNA out of the vending machine?  Would you supply your own?  If you would supply your own, would you donate your DNA or ask for some money?
  • Name 3 things you could do with someone else’s DNA?  What resources would you need?
  • How should ownership of DNA work?  Should it be like property or intellectual property?

Students may leap to the possibility of cloning a human from their DNA which may be a discussion for another class.  The big ideas that students should recognize is that owning a person’s genetic code is both intimate and limited.  It is intimate because that code is present in nearly every cell in that person’s body.  But it is also limited in that you have to have access to sequencing technology to decipher the code, and even then our ability to predict phenotypes (traits or medical history) are not very strong at the moment.

Another issue to raise is more nefarious:  framing someone with their DNA as evidence.  Ask students how this may be achieved and what sort of steps could be taken to avoid this problem.

Gabe Garcia-Colombo’s innovative DNA vending machine raises interesting questions in the burgeoning age of personalized genomics.  That’s what a little creativity can do for science.

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De-extinction: Resurrecting Lost Species

A hot topic in biology is the idea that we could resurrect extinct species.  Immediately, most people start to think about Jurassic Park and having a dodo as a pet.  Studying the science and ethics of this type of research can help shape students’ attitudes toward ecology and preservation efforts.

One of the major movements in ecology over the past century has been the preservation of species and their habitats.  In the 60’s and 70’s, the U.S. Congress passed acts to classify species as threatened, endangered, and extinct, which offered specific legal protections.  Many species have been brought back from the edge of extinction through these efforts, such as the bald eagle and grizzly bear.

Image from:  Wikipedia

Image from: Wikipedia

However, these efforts have fallen short for many species including the Pyrenean ibex and the Western black rhinoceros.  Classic examples of species that have been hunted to extinction in the past hundred years are the dodo, the Tasmanian tiger (thylacine), and the passenger pigeon.  Worse still, habitat destruction and global warming currently threaten much of the world’s biodiversity.

Advances in biotechnology may offer a new hope for resurrecting extinct species.  In this first TED Talk, Stewart Brand describes different methods for bringing animals back from the dead.

Some projects use techniques similar to those used to clone Dolly the sheep.  Others try to back-breed extant (living), related species to re-create the lost organisms.  Brand shares many of the ideas that biologists are currently testing.

Similarly, in the following TED Talk, Michael Archer shares his person experiences in trying to resurrect two (currently) extinct species – the gastric brooding grog and the thylacine.  His important successes on the way to bringing these species back make these ideas seem even more real and possible in our lifetimes.

One question that arises from these videos is what will happen to these species once they’ve returned.  Will they act the same as their ancestors if they have no parents to teach them?  If they exhibit the DNA but not the behaviors of the original animal, does that mean they are a different species altogether?  There are no easy answers to these questions, which can make them good fodder for a classroom discussion or a debate.

Another question harkens back to ecology – what impact would reintroducing these species have on their habitats?  While the removal of these species would have profoundly impacted their ecosystems, placing the species back in could also have negative effects.  After students have seen one or both of the previous videos, this last TED Talk by George Monbiot about this very topic can be a natural extension of the conversation.

According to Monbiot, returning these species could also have beneficial effects and lead to a more balanced ecosystem.  Much will depend on the particular species and the context in which it lived, including how it obtained food, what predators it had, and what other species benefited from its existence.

This entire conversation may seem like science fiction, but it is quickly becoming science fact.  Recently extinct species may be revived first, depending on the availability of high-quality frozen tissues.  As our ability to manipulate genomes improves, we could potentially resurrect species from nothing more than their genetic sequence.  Many articles have been published recently about hominid genomes such as Neanderthals.  Even if we did not have viable cell samples from these species, we could eventually see our evolutionary cousins on exhibit at the local zoo.

Work such as this has important ethical questions that students should consider.  Why should we develop these tools and resurrect species?  By that same token, why should we spend time and money to help endangered species?

If you start reviving species, which ones should receive priority?  An idea for an assignment would be to ask students to identify one or a few species that they believe would be important to bring back and to justify their choices.  You may also ask them to consider the difficulty of resurrection in their choices.  A real-life Jurassic Park would be an amazing experience, but it would be extremely difficult to obtain useful biological samples from 65 million-year-old fossilized bones.

What should we do with the species once they have come back?  Should there be an ultimate goal, such as reintroduction into the wild?  Or is anything possible, including zoos, domestication for agriculture, keeping as pets, hybridizing with other species, etc.?

Resurrecting extinct species has the promise of righting some of mankind’s destructive past and helping to preserve biodiversity.  Students can apply their knowledge of biological techniques, genetics, and cell biology to these complex issues.  The real world context should also motivate them to generate ideas, formulate opinions, and start to care about matters of ecology.

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TED Talk: Skylar Tibbits – The Emergence of 4D Printing

In biology, DNA is the blueprint, but it is proteins that are the workhorses of the cell.  For the most part, proteins are the components that actually “do” something.  They catalyze reactions, give the cell structure, communicate information, haul cargo, and help the cell move.

The idea that proteins can assemble themselves is a difficult one for students to grasp.  First, they have to understand that proteins are encoded by a particular sequence of amino acids (genetics, central dogma, cell biology).  Next, they need to know that these amino acids interact in particular, semi-predictable ways (biochemistry).  Then, the students have to learn that structure determines protein function and changes in structure can alter function (more biochemistry).  This combination of details makes proteins a very difficult subject to discuss, particularly with novice students.

Skylar Tibbits gave an excellent TED Talk that can help introduce the idea of “self-assembly” to students.  In this talk, Tibbits shows videos of objects made of plastics, such as ones you would obtain from a 3D printer.  The difference with Tibbits’ objects is that after they are made, they change conformation on their own.  These materials are “pre-programmed” to transform in response to heat, time, or different solutions.  The conformational changes almost look like a trick, but as Arthur C. Clarke said, “any sufficiently advanced technology is indistinguishable from magic.”  That’s exactly what cells are – a 3.7 billion-year-old technology.

I would recommend first introducing students to translation and protein structure (primary, secondary, tertiary, and quaternary).  As you prepare to show the video or assign it for homework, preface it by making the connection to protein self-assembly.  These are some possible guiding and reflection questions for students:

  • What is “self-assembly?”  If all products where manufactured to self-assemble, how would that change how factories work?  Can you think of examples from your everyday life of objects that you would like to see self-assemble?
  • What is a benefit of self-assembly for cells?  What sort of systems would a cell have to possess if proteins did not self-assemble?
  • What about a protein determines how it functions?  Is this true for proteins that act as enzymes?
  • What features of a protein do you think enable it to self-assemble?
  • Would a protein that normally exists embedded in the plasma membrane self-assemble in the same way as a cytosolic protein?

After introducing protein folding and function in this way, you can follow up by showing students this popular video from Harvard:  The Inner Life of the Cell.  In the video, ribosomes produce proteins that self-assemble and later have particular roles in the cell.  Both of these videos can help students understand these complex topics using excellent images of these processes in action.

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The Next-Generation Science Lab

Science fiction has given us many views of what the science labs of the future will look like.  The Star Trek medical bay (depending on the series) features needleless drug delivery, teleportation replacing baby delivery, and non-invasive rewriting of the genetic code in every cell.  Minority Report had an endlessly interactive computer system to interpret predictions of future crimes.  Even the slightly more realistic Contagion showed how science could be performed through automation and coordination of robots.

Star Trek Sickbay

But what will research labs look like in the next 5 to 20 years?  What environment will the next generation of scientists grow up in?  Looking at my graduate mentor’s lab notebooks, I cannot fathom the genetics work of the mid 1990s before the Human Genome Project data was freely available on Ensembl, when genes had to be cloned and sequenced on huge gels.  Graduate students in the next decade will look back at our labs and wonder, “How in the world did they get anything done without *blank*?”

Internet of Things

Enter modern technology.  WiFi networks, smart phones, and the cloud are starting to change the face of science labs.  The Internet of Things is a term for connecting inanimate objects to the local ethernet and world-wide internet.  Everyday examples are TVs, lamps, security systems, and even refrigerators and ovens that can help you save energy, make a grocery list, and protect your house.  Now developers are starting to apply the same model to the parts and equipment of research lab.

Traditionally, each person in a lab maintains a lab notebook as a repository of their experiments, data, and ideas.  But lab notebooks are decidedly analog:  everything is written on paper, nothing is linked, information is easily buried and lost, and important details can be omitted.  Even when using computer files on lab servers, documents and spreadsheets can easily become disarrayed.

Bench Tools

To fill the gap are apps such as ZappyLab’s Bench Tools.  My favorite feature of this app is that you can enter in your step-by-step protocol, and then use it like a checklist for any samples or experiments you are running.  You can even embed timers into particular steps.  If your lab is short on timers, or you want to bring your timer with you to lunch, there is a quadruple timer in this app as well.  You can also add notes and write down your results in the journal feature.  A related service from ZappyLab is PubChase, which purports to be a better search engine for the scientific literature and can help you find more relevant papers to your work.  ZappyLab is currently running a Kickstarter campaign to expand their services.

Paid services offer even more options.  Lab Guru coordinates nearly everything for a lab, including literature libraries, protocols, sample databases and trackers, storage locations, linking experiments, inventory, orders, and much more.  Used well, you’d never forget where that box of specimens is, what concentration of buffer you need, or what the results of the last time you ran that western.

Collaboration and sharing data can have their own problems, especially when your data sets, images, videos, etc. exceed the confines of standard cloud services like Dropbox.  Websites such as figshare are trying to meet the need of the Big Data movement in science.  They also offer a means of publishing your data, though how this type of open publication fits into academia is yet to be determined.

Bucking the traditional publication trend are open access journals such as PeerJ.  PeerJ’s model is to charge users a modest fee to join, and members can publish as many articles for peer review and publication as they like for free.  All articles are then made freely available to the public.

The Future of Labs

From my point of view, the trend in science is that over time, as new technologies make experiments easier and faster, the bar for publication rises.  In 1953 Watson and Crick published their famous paper elucidating the structure of DNA.  This famous article is about one page long with two figures (a drawing and a barely comprehensible X-ray diffraction image).  Doubtlessly, generating these data involved a tremendous amount of dedication, hard-work, and insight.  In the future, as our technologies improve, the expectation may mean that you have to have a genetics screen, sequencing for mutations, crystal structure, animal models, and small molecule inhibition studies just to be sent out for review.

We need to start considering how to apply these changes to undergraduate education.  After all, if we want our current students to be ready to work in a technology-aided laboratory, then they should gain experience in their lab courses.  For instance, undergraduates are expected to maintain lab notebooks.  What if they kept track of their protocols and data on tablets or smart phones instead?  They could include their own pictures and videos, which would also make for a more rewarding lab experience.  Sharing data with classmates is also easily achievable.  Where once lab courses were focused on an individual or group’s data, now sections of 12-24 students can work in concert to generate robust, and potentially useful, data sets.  These rich lab experiences could increase student retention and even entice more students toward careers in research.

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MOOCs: A Pragmatic View

Massive open online courses (MOOCs) have had a tremendous impact on education.  They have been mentioned in many major news outlets, causing controversy and an anti-MOOC backlash.  Prof. Mohamed Noor of Duke University has shared his personal experiences with running his own MOOC on his blog.  My goal with this post is to cut through the controversy by breaking down what a MOOC is and what it is not.

MOOCs are a natural extension of the Internet age.  The World Wide Web was established with an ethos that information is free.  Search engines such as Google and databases such as Wikipedia and IMDB work under the same premise.  Even Youtube provides a platform for free information dissemination, along with adorable cat videos.  Industries such as print media have struggled in the face of this idea.  Now consumers must ask, “Why should I pay for information that I can find for free with a couple of mouse clicks?”

With the advent of freely available information, some teaching scholars saw a looming identity crisis for academic education.  Previously, students would attend school or college in order to gain information.  Pay for tuition, buy the books, attend the classes, and we will certify that you have knowledge in a particular field.  Professors acted as gate keepers of information that was not easily accessible.

Now, though, information is free and abundant.  In some ways, there is too much information available.  But if the Academy no longer has a monopoly on knowledge, what is the purpose of higher education?  The prevailing answer came to be that universities would show students how to sort through the information, identify what was important, and use it effectively.  I believe that the “flipped classroom” came out of this idea: students find and take in the facts outside of class and apply the knowledge to current topics and real world problems.

In that manner, MOOCs almost seem like a social experiment.  Can we scale up a college-style course and make it freely available online?  The sheer numbers have demonstrated that it is possible.  Hundreds of thousands of students around the world have enrolled into classes from major universities.  Professors are bringing knowledge to the masses like Prometheus brought fire from Mt. Olympus to mankind.

With that lofty goal, most of the press surrounding MOOCs have heavily extrapolated their existence as the first sign of a collegiate apocalypse.  If college classes are available online for free, then why should anyone pay for college?  Universities have used their own online courses for more than a decade, and the results are mixed.  Some motivated students excel in the online environment, some eke by, and others simply do not make it.  The same is true for MOOCs:  of the thousands of students enrolled, often only 10-20% complete the requirements of the course.  That low pass rate still represents thousands of students in most classes, which is more than a single professor usually teaches in many years in the classroom.  The other 80-90% don’t finish for their own reasons, myself included.

So what, then, is the purpose of a MOOC?  MOOCs aim to provide students with  new knowledge.  You can learn basic statistics, how to program a computer, neuroscience, art history, genetics, and hundreds of other topics.  Classes attempt to bring students from the basics up to the current controversies.  For example, a genetics course would present information about how parents pass traits to children, what a gene is, how biotechnology works, and how new advances in the field are impacting shaping our lives and changing the face of medicine.

In the first MOOC I took, I used the course as a primer for using the R programming language.  For me, it was basically a workshop to learn a new skill.  I could put the experience on my resume, or just use it for personal benefit.

MOOCs, in their current incarnation, cannot replace the college experience.  As I mentioned before, colleges are moving away from the knowledge transfer model to more of a skill development and professional experience model.  College graduates should be well versed in functional knowledge in their areas of specialization.  Biology majors should be able to design experiments, interpret scientific data, and potentially apply their knowledge to treat disease.  Spanish majors should not only know how to construct a sentence, but should also understand the cultures of Spanish-speaking countries and be able to apply their linguistic and cultural skills to a community (ESOL teacher, translator, international entrepreneur, etc.).  MOOCs can guide you through information and give you perspective, but they cannot fully prepare you in the same manner as earning an undergraduate degree.

Since MOOCs are completely online (except for local meet-ups), students do not benefit from the extracurricular experience.  There are no research labs, internships, hospitals, or student groups.  A college degree states that you completed a certain amount of coursework with competency.  The college experience encompasses the rich personal growth that comes from new opportunities and interactions.

I am a firm believer in the utility of MOOCs.  Information should be free, and one of the obligations of those of us in higher education is to make our work relatable and understandable by the general public.  Much of work is funded by government agencies.  In some ways, we are beholden to taxpayers and they deserve to know where their money goes.  Various groups malign science, art, and the humanities based on a lack of experience.  If we can reach out to more people in a free and approachable manner, we can show the value of our work to the greater good.

In summation, MOOCs are not a threat to colleges.  If anything, they may inspire students to pursue higher education.  MOOCs can be seen as a form of outreach similar to visiting students at a local elementary school.  Teaching a MOOC can inform your work in the physical classroom by identifying common misconceptions and building a community of learners.  Taking a MOOC can help you experience a new field in a low risk manner.  MOOCs may not make colleges obsolete, but they will push colleges to improve the educational experience.

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