Algorithms, Abstractions, and Iterations: Teaching

Computational Thinking Using Protein Synthesis

Translation

Authors: Peel, Amanda, and Friedrichsen, Patricia

Source: The American Biology Teacher, 80(1) : 21-28
Published By: National Association of Biology Teachers
URL: https://doi.org/10.1525/abt.2018.80.1.21

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 INQUIRY & Algorithms, Abstractions, and
INVESTIGATION Iterations: Teaching
Computational Thinking Using
Protein Synthesis Translation

• AMANDA PEEL, PATRICIA FRIEDRICHSEN

ABSTRACT its solution in a way that a computer—human or machine—can

One of the eight Next Generation Science Standards (NGSS) scientific practices effectively carry out” (p. 7). This definition is widely held in the engi-
is using mathematics and computational thinking (CT). CT is not merely a data neering and computer science fields. CT is not merely a data analysis
analysis tool, but also a problem-solving tool. By utilizing computing concepts, tool, but also a problem-solving tool. By utilizing computing con-
people can sequentially and logically solve complex science and engineering cepts, people can sequentially and logically solve complex science
problems. In this article, we share a successful lesson using protein synthesis and engineering problems. In this article, we share a successful lesson
to teach CT. This lesson focuses primarily on modeling and simulation
using protein synthesis to teach CT.
practices with an extension activity focusing on the computational problem-
solving practices of CT. We identify and define five CT concepts within the
aforementioned practices that form the foundation of CT: algorithm, abstraction,
iteration, branching, and variable. In this lesson, we utilize a game to familiarize Computational Thinking: Algorithms
students with CT basics, and then use their new CT foundation to design,
construct, and evaluate algorithms within the context of protein synthesis. As an Weintrop et al. (2016) place computational thinking in science and
optional extension to the lesson, students enter the problem-solving environment mathematics into four taxa: data practices, modeling and simulation
to create a program that translates mRNA triplet codons to an amino acid chain. practices, computational problem-solving practices, and systems
We argue that biology classrooms are ideal contexts for CT learning because thinking practices. Although there is overlap among the taxa, this
biological processes function as a system, and understanding how the system
lesson focuses primarily on modeling and simulation practices with
functions requires algorithmic thinking and problem-solving skills.
an extension activity focusing on computational problem-solving
practices of CT. Modeling and simulation practices include assess-
Key Words: computational thinking; genetics; heredity; molecular genetics; protein ing, designing, and constructing computational models; using
synthesis.
computational models to understand a concept; and finding and
testing solutions. Problem-solving practices include programming,
troubleshooting and debugging, preparing problems for computa-
tional solutions, choosing effective computational tools, assessing
Introduction different approaches or solutions to a problem, developing modular
The Next Generation Science Standards computational solutions, and creating computa-
(NGSS) call for engaging students in science tional abstractions.
and engineering practices (NGSS Lead States, CT is an essential In Table 1, we identify and define five CT con-
2013). One of the eight practices is using cepts within the aforementioned practices that
mathematics and computational thinking,
skill for navigating form the foundation of CT: algorithm, abstraction,
defined as tools for evaluating data and creat- today’s complex iteration, branching, and variable. In this lesson,
ing simulations (Schweingruber et al., 2012). we utilize a game to familiarize students with CT
However, experts in the field of computer technological world. basics, and then use their new CT foundation to
science, such as Jeannette Wing, the corpo- design, construct, and evaluate algorithms within
rate vice president of Microsoft Research, have an expanded defini- the context of protein synthesis. As an optional extension to the les-
tion. Wing (2006) defines computational thinking (CT) as “the son, students enter the problem-solving environment to create a pro-
thought processes involved in formulating a problem and expressing gram that translates mRNA triplet codons to an amino acid chain.

The American Biology Teacher, Vol. 80, No 1, pages. 21–28, ISSN 0002-7685, electronic ISSN 1938-4211. © 2018 National Association of Biology Teachers. All rights
reserved. Please direct all requests for permission to photocopy or reproduce article content through the University of California Press’s Reprints and Permissions web page,
www.ucpress.edu/journals.php?p=reprints. DOI: https://doi.org/10.1525/abt.2018.80.1.21.

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 Table 1. CT concept definitions.
CT Concept Definition Example
Algorithm A sequence of steps to solve a problem A recipe is an algorithm for how to make a particular food.
Abstraction Simplifying information; displaying only When someone asks you what you did yesterday, you tell
the information that is needed them you stayed at home and watched Netflix, not that you
woke up, took a shower, got dresses, ate breakfast, fed your
dog . . . , etc.
Iteration Repeating a sequence of steps until a When you eat a meal, you put food in your mouth, chew,
condition is met swallow, and repeat until the food is gone.
Branching Choosing a path, if/then/else statements Driving through traffic lights: IF the light is green, THEN you
go, ELSE you slow down and stop.
Variable A value that can change; used in If you were writing an algorithm for your morning routine, you
programming to make programs would write: wake up, get out of bed, shower, put on clothes,
universal eat breakfast. In this algorithm, “clothes” is a variable, and its
value (what you actually wear each day) changes. Maybe on
Monday, clothes = a dress, and on Tuesday, clothes = a shirt
and jeans.

CT is an essential skill for navigating today’s complex techno- Table 2. Lesson outline.
logical world. Students will need to be technologically literate to
Day Learning Activity Objective
become contributing members of society, and many scholars
believe that CT is a key component of technological literacy (Barr 1 Introduction to CT Using Students will problem-
& Stephenson, 2011; NRC, 2010; Sanford & Naidu, 2016; Wing, Lightbot solve in a programming
2006). Additionally, scholars believe that students need to learn game to explore basic
CT as a problem–solving skill to be utilized across disciplines (Barr CT concepts.
& Stephenson, 2011; Bundy, 2007; Mishra et al., 2013). As such, 2 Applying CT: Writing Students will write an
CT should be integrated into K-12 curricula to familiarize students Translation Algorithms algorithm to simulate
with its problem-solving power. We argue that biology classrooms how the system of the
are ideal contexts for CT learning because biological processes translation process
function as a system, and understanding how the system functions functions.
requires algorithmic thinking and problem-solving skills.
Many biological processes can be represented as algorithms to 3 Extending CT: Students will design a
complete a task, which is a form of a computational model. For Programming program to simulate the
example, in protein synthesis, the problem is that the body needs Translation with Scratch patterns associated with
to make proteins from DNA code; the solution is transcription, (optional) the translation process.
translation, and protein folding, which are steps to create an active
protein from DNA. As such, biological processes are perfect contexts
for CT integration through algorithmic modeling. In this lesson, stu- their CT skills to programming. This lesson can be shortened and
dents begin learning CT through writing algorithms for familiar pro- completed in fewer class periods, if desired. Students can be tasked
cesses, and then these CT basics can scaffold future learning about with playing Lightbot as homework, and Day 3 is an optional exten-
complex processes. Once students have a CT foundation, they can sion. The Lightbot game was chosen because it was successfully used
utilize these computational modeling skills to understand new bio- to introduce CT to undergraduate students in a small pilot imple-
logical processes. The following lesson is designed to be an introduc- mentation carried out by the authors.
tion to CT through protein synthesis, but this lesson can be altered
to fit many biological processes.
Materials
A Classroom Implementation The following materials are needed: computers or iPads/tablets,
The following protein synthesis and CT lesson was piloted in two Internet access, translation video: https://www.youtube.com/
high school Advanced Placement (AP) biology classes at the end of watch?v=TfYf_rPWUdY, LightBot app for tablets or https://light-
the year, after students had taken their AP exams. Three 90-minute bot.com/hocflash.html, whiteboards, markers, erasers, and sticky
class periods were needed to implement the full lesson, which is out- notes.
lined in Table 2. This lesson was designed to scaffold CT experiences Optional materials for Day 3 include: Scratch program: https://
by first introducing students to CT, then asking students to apply CT scratch.mit.edu/projects/100898229/#editor, and a Scratch Account:
skills to protein translation, and finally asking students to extend www.scratch.mit.edu

22 THE AMERICAN BIOLOGY TEACHER VOLUME. 80, NO. 1, JANUARY 2018

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 Day 1: Introduction to CT Using Lightbot The right-hand side of Figure 2 depicts an iteration level in the
Students begin by either downloading the Lightbot: Code Hour app Lightbot game. While abstraction is still being utilized with the P1
or going to this URL: https://lightbot.com/hocflash.html. This game command and PROC1 blocks, this level adds iteration by introduc-
introduces students to computational thinking basics (algorithms, ing repetition. In this program, PROC1 calls itself in the last step of
iterations, and abstractions), and we suggest that teachers become the algorithm, which results in the PROC1 steps being on a contin-
familiar with the game before using it. Rather than writing code, users uous loop and repeating until all of the dark squares have been lit by
engage in drag-and-drop programming where they click and drag the robot. Without the use of iteration in this level, the main
blocks to create a program. Students should work through the chal-
lenges in the first level either individually or in pairs. The objective
of the game is to light all of the dark squares using the robot, and in Table 3. CT concept examples for student notes.
order to do so, the player combines different block commands to CT Concept Examples
make the robot move and light the squares (Figure 1). After complet-
Algorithm Game example (MAIN blocks): In every
ing all the challenges in the first level, students share their strategies for
level you build an algorithm to light the
each challenge.
colored squares.
The combination of blocks placed inside the MAIN box on the
Real life example: When someone asks you
right side of the screen is the algorithm the robot follows. Students
for directions to your house, you give them
build their algorithm by dragging blocks from the lower portion of
an algorithm.
the screen. Once students create an algorithm that lights all the dark
squares, they can go to the next challenge. Students will create differ- Abstraction Game example (Procedure): The
ent algorithmic solutions to each game level, which is a great oppor- procedures were abstractions of the steps in
tunity to discuss the creativity needed to design solutions and the main program
problem-solve. The game saves the students’ programs, so they can Real life example: When someone asks you
go back and look at their algorithms at any time. After the students what you are doing tonight, you tell them
play a few levels, the teacher leads a discussion on algorithms, giving you’re going to eat spaghetti, not that you
definitions and examples. The CT concept definitions and examples are going to boil water, put the noodles in
discussed in the implementation are found in Tables 1 and 3. We for 10 minutes, heat the sauce, brown the
continue to play the different levels of the Lightbot game, pausing meat . . . , etc.
to discuss and take notes on abstraction and iteration. Throughout Iteration Game example (loops): The loops in the
this lesson, students experience and discover the CT concept as they games were examples of iteration. They
play the game, and then the teacher provides the technical term and repeated the sequence until all the squares
definition as part of a discussion of the tasks in the game. As seen in were lit.
Figure 2, the main program has only three blocks, which calls the Real life example: Each day is an iteration,
PROC1 program three times. This is an abstraction because the P1 each week, each month, each year.
is a simplification of the PROC1 blocks, and without this abstrac-
tion, the main program would have 15 blocks instead of three. This Branching Real life example: Choosing what to wear
abstraction simplifies the main program and reduces the program- each day: if it is cold outside, then wear a
ming time as well as the main program space. sweater, else don’t wear a sweater.
Variable Real life example:
Set variable1 = 5 (program user decides
each time they run the program)
Set variable2 = 6 (program user decides
each time they run the program)
Program: variable1 + variable2 = 11 (the
sum of the two values set by the program
user)

Figure 1. Lightbot game. Figure 2. Abstraction (left) and Iteration (right).

THE AMERICAN BIOLOGY TEACHER COMPUTATIONAL THINKING 23

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 program would be six blocks long because it would have to call the algorithms created by the students in the AP biology class. Each algo-
PROC1 blocks six times to light all of the blocks, thus iteration also rithm looks different, but both have abstraction, iteration, branching,
saves time and space. Experiencing these CT basics in a game envi- and variables, and contain correct translation processes.
ronment helps students engage in programming logic without hav- In Figure 3, Example 1, P1 (the second box) is an abstraction of
ing to learn any code. The last levels of procedures and loops are the main program (the first box), and the last command of P1 calls
challenging, and students and teachers might struggle with complet- itself (P1) until the stop codon, which is iteration. Example 2 also
ing the algorithm. If this is the case, the solutions can be looked up shows abstractions of the main program with P1 and P2 steps and iter-
on Youtube. ation when P1 calls itself in Step 3. To show branching, Example 1
Next we discuss branching and variable usage in algorithms. utilized multiple if/then/else statements in both the main program
Although branching and variables are not part of the Lightbot game, and the P1 program. In Example 2, there are multiple branching
they are essential CT components that are less complex than the pre- exemplars with if/then/else statements in Step 3 of P1 and Step 1 of
vious concepts. Branching is an if/then/else operation that allows the P2. Both examples use codon and anticodon as variables within the
algorithm to check a condition and choose a path to follow based on algorithm.
that condition. For example, IF the weather says it will rain today, The depth of this activity is flexible, and can be adapted for any
THEN I will carry my umbrella, ELSE I will leave my umbrella at level of biology. It can also be applied to any biological process and
home. Branching allows flexibility in algorithms, so students can can be used to scaffold body modeling and/or paper modeling.
adjust the steps based on important conditions. With body modeling, students act out processes utilizing props.
Variables are used in algorithms to make the steps universal. For paper modeling, students will need paper cutouts of the neces-
For example, if we write a program that adds 5 and 6, that program sary components (ribosome, mRNA, amino acids, tRNA), and they
will only be useful to someone who needs to add those two specific perform the process with the cutouts. Utilizing these modeling
numbers. We can make it universal by making the program add any strategies, students can test the correctness of the algorithms by
two numbers together, utilizing variables. The program will say: var- performing the steps of their algorithms. This particular instantia-
iable1 + variable2, and the user will set the values to any numbers tion was used to review the translation material. We recommend
they choose. Then the user can enter the two values they need added that when introducing CT and writing algorithms for the first time,
and the program will calculate it. Once students have this CT foun- it should be connected with a process students already know.
dation, we engage them in a transfer task of writing a translation Under these conditions, students can use their knowledge of the
algorithm, allowing students to apply the skills developed in the biological process to make sense of CT. This review activity is also
Lightbot game to the biological process of protein synthesis. a great formative assessment because it is easy to see where stu-
dents struggle with the biological process and where they have an
Day 2: Applying CT by Writing Translation accurate grasp of the process. Students can use their knowledge
Algorithms of CT to make sense of most biological processes, so CT is a pow-
Once students have learned about CT in LightBot, we then apply erful sense-making technique in biology classrooms.
these concepts to the translation process of protein synthesis. Stu-
dents watch the translation video and, working in groups of two Day 3: Extending CT By Programming Translation
to four, write a translation algorithm (see http://www.hhmi.org/ with Scratch (optional)
biointeractive/translation-basic-detail). We urge students to use When implementing this lesson, teachers can continue with apply-
all of the CT principles discussed in the previous activity in their ing CT concepts through computational modeling, or they can
translation algorithms. We use whiteboards and dry erase markers extend the application into problem solving in a visual programming
to construct the algorithms, but other materials can be used, such environment. In this classroom implementation, we continued the
as poster board or butcher paper. Students should refer back to lesson with the visual programming extension. We review triplet
the video to create their algorithms. Algorithms can take many codons and their corresponding amino acids by showing students
forms. They can be paragraphs, flow charts, pictures, lists, or any the triplet codon table, and reviewing how to read it. In the next
combination of these. It is important to make sure students remem- activity, students will create a program that reads triplet codons
ber that this is a creative process, and there is no right or wrong and returns the corresponding amino acid sequence to the user.
algorithm as long as the steps make sense and result in the correct To do this, students use a visual programming tool, Scratch at
product, which, in this case, is a polypeptide chain. www.scratch.mit.edu. We use one Scratch account per class section
After the groups finish constructing their algorithms, we engage and have students save their programs with their names in the title.
students in a gallery walk so they can evaluate each other’s algorithms. To become familiar with Scratch, teachers are encouraged to watch
In the gallery walk, students walk to other groups’ algorithms, read video tutorials and explore Scratch guides (https://scratch.mit.edu/
them, and provide constructive feedback on sticky notes. This allows help/). Instructors may find it useful to go through tutorials with stu-
students to see how other groups constructed their algorithms and dents before the activity as well.
gives them the opportunity to think about ways to improve other Once students have logged into their Scratch accounts, we intro-
groups’ algorithms and their own algorithms. Next, students read duce the various aspects and vocabulary of the program and practice
the feedback they received and make adjustments to their algorithms. using it (Figure 4). To program using Scratch, the user clicks on
Students in this pilot struggled with variables more than the other CT blocks and drags them into the script screen, where the blocks are
concepts, and we had to pause before the gallery walk to scaffold their attached to make an algorithm. The blocks are color-coded in the
variable understandings by discussing how codons and anticodons tool box under motion, looks, sound, pen, data (variables), events,
can be used as variables in their programs. Figure 3 shows two final control, sensing, operators, and more blocks. Scratch is commonly

24 THE AMERICAN BIOLOGY TEACHER VOLUME. 80, NO. 1, JANUARY 2018

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 Figure 3. Two examples of student-generated algorithms.

used to program animations and game-like environments, but in this #editor for the complete Scratch program used in this lesson. The
lesson we will use Scratch to compute an output utilizing logic and amino acids in this program are grouped by the first two nucleoti-
variables. des in the triplet codon, but there are multiple ways to program
Next, we build the first few sets of blocks together with the stu- this information, and the grouping of amino acids is not necessary
dents (while projecting the computer screen) and talk through all for correct code.
of the blocks used. Figure 5 demonstrates how to create the blocks Next, students work in pairs or individually to finish the codon
necessary for the program. We tie the blocks to CT concepts when- algorithm. We tell students that when they encounter a problem, they
ever possible (Figure 6). For example, using the if/then block is uti- should do their best to solve the problem on their own by trying dif-
lizing branching, and utilizing the data blocks, or orange blocks, is ferent blocks. When we do help students, we refrain from giving them
applying variables. See https://scratch.mit.edu/projects/100898229/ the answer, and attempt to lead them to the solution by asking leading

THE AMERICAN BIOLOGY TEACHER COMPUTATIONAL THINKING 25

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 Figure 4. Scratch layout and vocabulary.

Figure 5. How to create blocks. Figure 6. Scratch and CT connections.

26 THE AMERICAN BIOLOGY TEACHER VOLUME. 80, NO. 1, JANUARY 2018

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 questions and giving suggestions, such as, “What do you want to hap- and attainable. “I liked how simple and approachable each activity
pen? Tell me what you want your program to do.” Often, if we can get was. The activities were games that I found easy to do, yet chal-
the student to say the right code, they can find the corresponding lenging like a game on my phone. Each activity was something
blocks. As such, we often ask them to explain what they are trying that I could do outside of class by myself” (Student 1). One stu-
to do, and lead them to using the language on the blocks so they dent did indicate that they did not enjoy the Scratch activity
can figure it out on their own. because of “personal interest reasons” (Student 8), and other stu-
If the teacher chooses not to use the Scratch programming exten- dents said that the Scratch program was repetitive and tedious,
sion, the same content can be covered utilizing computational model- which can be a very common programming trait.
ing. In accordance with the procedures from Day 2, students can write When asked if the activities helped them review and under-
an algorithm that takes in mRNA codons and translates them into stand translation, students responded positively. Some students felt
amino acids, resulting in an amino acid sequence. In this activity, stu- like the activities were a good review of the process, and others said
dents would be modeling the Scratch program without having to use it helped them solidify some of the process details. “[There] was so
computers or program. Figure 7 depicts an example algorithm for much stuff that was [occurring] in translation, when [I] first learned
translating mRNA to amino acids (AA). about it 2 years ago, the process was murky, couldn’t really touch
base on what happened in what order and the scale of everything”
(Student 6). “[It’s] easier to see translation when you work through
it and have to apply it to programming. It helps you see the pat-
Student Feedback
terns and the bigger picture so that you can get past the basic idea
After implementation, nine of the ten participating students filled of translation and focus on the smaller detailed things” (Student 4).
out a short survey about their experiences during the lesson. Prior Students also said that programming with Scratch helped them
to this lesson, only one student had experience with CT. When understand the codon to amino acid translation.
asked what they liked about these activities, students said they When asked if the activities helped them understand CT, stu-
enjoyed playing Lightbot and “liked that it allowed creativity in dents also responded positively. “I’ve never had much experience
the process and there was not one single right answer to how to with programming or computation thinking, so I found this very
solve the problems” (Student 3). Another student liked that the interesting. The activities were simple and easy to grasp as well,
activities “let you see that there are connections between each so I understood the basics of computational thinking pretty well”
activity and how they tie and apply into translation. It also helps (Student 1). Students thought the scaffolding that Lightbot pro-
you see translation in a bigger picture” (Student 2). Although vided aided them in their foundational CT understanding. “The
these activities were rigorous and new to the students, most app helped a lot. It made it not intimidating and the knowledge
enjoyed the challenge and thought the activities were appropriate transferred well to the whiteboard activity” (Student 5).

Figure 7. Example mRNA to amino acid sequence algorithm.

THE AMERICAN BIOLOGY TEACHER COMPUTATIONAL THINKING 27

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 In addition to CT understandings, we wanted to know if stu-
dents could identify CT applications and usefulness. When asked References
if they thought CT was useful, students responded with a variety
Barr, V., & Stephenson, C. (2011). Bringing Computational Thinking to K-12:
of applications. Students mentioned programming and making
What is Involved and What is the Role of the Computer Science
programming more efficient, data analysis applications, and various Education Community? Acm Inroads, 2(1), 48–54.
problem-solving applications. “Computational thinking helps one Bundy, A. (2007). Computational Thinking is Pervasive. Journal of Scientific
see the significance of all possible outcomes and be a more acute and Practical Computing, 1(2), 67–69.
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programming-like skills will become more useful” (Student 1). CT Technology and Creativity in the 21st Century: Of Art and Algorithms.
“organizes things so that a student isn’t seeing everything as one TechTrends, 57, 10–14.
step, but can see operations that have patterns” (Student 2). CT National Research Council (NRC). (2010). Report of a Workshop on the
“forces us to think about the cause and effects of all events. Some- Scope and Nature of Computational Thinking. Washington, DC: National
times, in a lot of businesses even, the steps are overlooked and then Academies Press.
a problem or an error results” (Student 9). NGSS Lead States. (2013). Next Generation Science Standards: For States, by
States. Washington, DC: National Academies Press.
Sanford, J. F., & Naidu, J. T. (2016). Computational Thinking Concepts for
Conclusion Grade School. Contemporary Issues in Education Research, 9(1), 23–32.
Schweingruber, H., Keller, T., & Quinn, H. (Eds.). (2012). A Framework for
This implementation was a successful pilot of a series of lessons that K-12 Science Education: Practices, Crosscutting Concepts, and Core
introduced students to CT through engagement with the protein Ideas. Washington, DC: National Academies Press.
synthesis translation process. Students played the Lightbot game to Weintrop, D., Beheshti, E., Horn, M., Orton, K., Jona, K., Trouille, L., &
develop a foundation in CT concepts. These skills were transferred Wilensky, U. (2016). Defining Computational Thinking for Mathematics
to the translation process as students designed, constructed, and and Science Classrooms. Journal of Science Education and Technology,
25(1), 127–147.
evaluated translation algorithms. Finally, students engaged in visual
Wing, J. M. (2006). Computational thinking. Communications of the ACM,
programming to create a program that translated an mRNA strand to
49(3), 33–35.
an amino acid chain. We also introduced an alternative activity to
the Scratch extension that continued with algorithmic modeling of
translation. Throughout the lesson, students learn about and apply
algorithms, abstraction, iteration, branching, and variables. Students AMANDA PEEL is a PhD student in science education in the Department of
who experienced the three-day lesson responded very positively and Learning, Teaching, and Curriculum at the University of Missouri; email:
self-reported CT learning and a deeper understanding of translation. [email protected]. PATRICIA FRIEDRICHSEN is an associate
After this lesson students were also able to see the varied applications professor jointly appointed in the Department of Learning, Teaching, and
and usefulness of CT. We argue that biological processes are ideal Curriculum and the Division of Biological Sciences at the University of
Missouri; email: [email protected]
contexts for CT integration, and this lesson is an example. As biology
teachers consider incorporating CT into their classrooms, we
encourage them to share this article with their computer science
teachers and collaborate on other projects using CT in biology.

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28 THE AMERICAN BIOLOGY TEACHER VOLUME. 80, NO. 1, JANUARY 2018

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