Genetics and Evolution App

GenEvolApp

Photo from iTunes.

In a biology or genetics course, students are tasked with learning quantitative ideas such as linkage, recombination, and genetic drift.  Up until this point, biology can be heavier on facts and ideas than more numerical subjects such as chemistry and physics.  Then, students have to start grappling with multiple sets of information:  biology in the form of Mendel, chromosomes, mitosis, meiosis, Punnett squares, etc.; mathematics in the form of measurement, algebra, statistics (Chi-square), and probabilities.  Geneticists, like many disciplines, also have their own language and favorite go-to examples.  Problems involve wrinkly peas, dwarf plants, bearded dragons, calico cats, and people with hemophilia; test cross, back cross, parental, and filial.

Like most skills, mastering these complex, interdisciplinary ideas comes through practice, practice, and more practice.  One of the limiting factors for students may be that their instructors only provide so many opportunities to calculate linkage, fitness, and changing allele frequencies.

To fill that need is the iOS app, Genetics and Evolution, developed by Russell Myers of NorthgateArinso Human Resources, and Brandon Millman and Mohamed Noor of Duke University.  They developed an app for iDevices to provide a nearly infinite set of practice problems.  They also published a freely available journal article describing the app:  Myers RB, Millman B, Noor MAF. Genetics and Evolution: an iOS application to supplement introductory courses in transmission and evolutionary genetics. G3 2014; 4: 779-781.

The app contains sample problems and answers for these topics:

  • Mendelian genetics – up to three genes available for Punnett squares in the Cross Simulator
  • Gene/trait mapping – calculating linkage
  • Heritability – using Breeder’s equation
  • Hardy-Weinberg
  • Population genetics
  • Fitness – the Allele Freak feature simulates the possible fates of alleles based on evolutionary influences

Best of all, the app is free!  This app is great for students to practice concepts learned in class.  It can also be an easy way for instructors to generate homework and test questions with the press of a button.  I highly recommend this as a great learning resource.

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Transcription & Translation Practice with the RandomORF Generator

It can be a long and confusing road for students to learn the Central Dogma of Molecular Biology (DNA begets RNA begets protein).  Students have to grapple with specifics such as 5′ to 3′, DNA vs. RNA nucleotides, base pairing, triplets, coding vs. template strand, and using a translation chart.  If you are not very specific with the questions you ask on assignments or exams, you can receive widely varied answers that are the reverse or complement of the “correct” answer.

In the latest issue of CBE – Life Sciences Education, Carr, et al. provide an explanation for their simplified approach to learning the Central Dogma.  Even better, they have created a web application to generate “random” sequences for students to use for practice.  The webapp is called RandomORF Generator, as shown below:

RandomORF generator

 

Figure depicting RandomORF Generator’s interface. Carr, et al. 2014.

The idea is that students will see an oligomer of some number of base pairs and it is up to them to figure out which of the 6 possible reading frames is the one that will encode a protein.  Each of the other 5 reading frames contains a stop codon.  The same is true of researchers looking at novel nucleotide sequences.  You would have to figure out which open reading frame (ORF) is the one with a biological function without multiple stop codons.

Students can practice on their own using this website.  After choosing an oligomer length, the webapp makes a nucleotide sequence.  When the student is finished or needs some help, another click shows the 6 different reading frames and which one lacks any stop codons.  The webapp could also be used to make assignment or exam questions.

As a side note, I want to share my favorite protein translation codon chart (see below).  Many charts are organized into a table, but I find this circular version much easier to handle.  The first RNA nucleotide of the codon is in the innermost circle, the second nucleotide in the middle circle, and the last nucleotide (the wobble base) is in the outermost circle.  With a little practice, students can pick this chart up pretty quickly.

Protein Codon Wheel

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Applying to STEM Graduate School, Parts 2 and 3

The second and third guest posts on applying to STEM graduate school are now up on Aaron Long’s blog, The Doctoral Road: Part II and Part III.  Head over there to learn more!

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TED Talk: Geena Rocero – Why I must come out

Human biology can be a tricky subject.  It takes the world of the abstract, with its nondescript cells, mRNA, membrane structures, etc., and puts it into the context of the human experience.  Trisomy 21 is no longer a factoid to be remembered, but rather a group of real individuals who have the same feelings and desires as the rest of us.  Alzheimer’s starts as a study of neurobiology, but can grow to encompass the difficulties of being a caregiver.  While melanocytes may give your skin pigment, the amount of that pigment has had a profound impact on human history that continues today.

It is in this spirit that I share this TED Talk from Geena Rocero.  Geena was born biologically male, but she identified as a female.  She describes her experiences as a trans woman in this video.  What better way to start a discussion on gender identity than to hear a story from this brave woman.

Topics relevant to this video are:

  • Sex vs. gender
  • Gender identity
  • Gender changes in the biological world
  • Fluidity of human gender and sexuality

Some may say that a video like this is more about social issues and better suited to a humanities classroom.  I wholeheartedly disagree.  Whenever you can engage with a student on an important subject that is directly related to the curriculum, especially one receiving so much current attention in the media, we as educators have an obligation to explore that topic.  We can dispel rumors and create understanding.  We may even have trans students in our classrooms that are struggling with their identity.  By treating the subject fairly and with compassion, you can go a long way to spreading awareness and open-mindedness.

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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:

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

Untitled
“…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…”

DNA oh DNA
“…Molecule of life
with base pair after base pair

coding my person”

Untitled
“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
Refrigerator”

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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