1. 84 Journal of College Science Teaching
RESEARCH AND TEACHING
Introductory science courses play
a critical role in the recruitment
and retention of undergraduate
science majors. In particular, first-
year courses are opportunities
to engage students in scientific
practices and motivate them to
consider scientific careers. We
developed an introductory course
using a semester-long series of
established laboratory experiments
closely aligned with lecture topics
that allow students to participate
in a cognitive apprenticeship. In
this course, students learn basic
concepts in cell and molecular
biology during lecture and apply
their content knowledge and
acquire research skills in the
laboratory during a series of
related experiments. The ongoing
theme and course structure enable
students to critically analyze their
results each week as they would in
a research laboratory. Assessment
results show that students gain
an understanding of research
and laboratory techniques and
demonstrate evidence of knowledge
transfer from the course to related
scientific journal articles. Students
also learn content equivalent to a
more general molecular biology
course. Centering a course on a
semester-long laboratory project
can provide a solid foundation of
content knowledge and an authentic
introduction to scientific research.
Reenvisioning the Introductory Science
Course as a Cognitive Apprenticeship
By Meredith M. Thompson, Lucia Pastorino, Star Lee, and Paul Lipton
I
ntroductory undergraduate sci-
ence courses are a critical junc-
ture for students considering
STEM (science, technology, en-
gineering, and mathematics) majors
and have been the focal point for
science education reform (Brewer &
Smith, 2011). Ideally, the laboratory
aspect of introductory science cours-
es gives students an opportunity to
learn and practice important skills,
reinforce knowledge of lecture con-
cepts, and understand scientific in-
vestigation (Hofman & Lunetta,
2002); however, many introductory
undergraduate laboratory classes are
a series of “cookbook laboratories”
that are not well integrated into the
course (Handlesman et al., 2004). As
first-year science courses are gate-
ways for potential STEM majors, it
is useful to consider a few key ques-
tions. How can we design first-year
courses to show connections be-
tween the fundamental content cov-
ered in lecture and the process cov-
ered in the laboratory? How can we
structure these courses so students
in them learn and practice important
specific laboratory techniques and
also develop broader scientific think-
ing skills?
Conceptual framework
Induction into the scientific commu-
nity shares many characteristics of
an apprenticeship (Sadler, Burgin,
McKinney, & Ponjuan, 2010). This
apprenticeship engages participants
in authentic activities and practices
in the domain (Lave & Wenger,
1991). A cognitive apprenticeship
is a “learning-through-guided expe-
rience on cognitive and metacogni-
tive, rather than physical, skills and
processes” (Collins, Brown, & New-
man, 1989, as cited in Dennen &
Burner, 2008, p. 427). Students not
only learn what to do, they learn how
to think about what they are doing by
having ongoing feedback from more
experienced instructors. Students
are given multiple opportunities to
engage with the material they are
learning in a context-rich environ-
ment (Hendricks, 2001). Cognitive
apprenticeships begin by modeling
how an expert would approach the
material. Students receive coaching
in the form of feedback and advice,
and the instructor provides scaf-
folding to help students learn, asks
students to articulate their learning
process, and encourages students to
reflect on what they have learned. As
students gain understanding of the
topic, they are given less structure
and more opportunities to explore
and apply their knowledge on their
own (Collins, Brown, & Holum,
1991; Dennen & Burner, 2008). We
designed this course with these ideas
in mind, incorporating the modeling,
coaching, articulation, reflection,
and application of their understand-
ings during the course. The course is
both an actual apprenticeship, in that
students practice laboratory skills
and processes, and a cognitive ap-
prenticeship where students learn

2. 85Vol. 46, No. 1, 2016
how to think metacognitively about
the larger context of the experiment.
Course description
Designed for potential neuroscience
majors, Introduction to Cellular and
Molecular Biology (abbreviated NE
for its focus on neuroscience) covers
such fundamental concepts as DNA
replication; translating genes into pro-
teins; and how the cell regulates key
processes such as mitosis, membrane
synthesis, and transport. The lecture
component of NE covers the standard
complement of cellular and molecu-
lar biology topics seen in the majority
of introductory biology courses (Ta-
ble 1). The syllabus is available in the
supplemental materials (http://www.
nsta.org/college/connections.aspx).
Learning skills in context is an im-
portant aspect of apprenticeships. In
this course, the skills and experiments
in the laboratory are nested within
the context of the series of laboratory
experiments. Lecture and laboratory
are thoroughly intertwined, and lab ex-
ercises are a direct application of each
week’s lecture content. The seamless
integration of lab and lecture has been
linked to student learning of content
and process, and student motivation
(Burrowes & Nazario, 2008). Adding
the cognitive apprenticeship approach
provides a framework that helps
instructors create positive learning
environments for students. Students
are able to learn laboratory skills from
experts by watching them model those
skills and to learn approaches to sci-
entific experimentation that are often
implicit but are made explicit as part
of the cognitive apprenticeship model.
Instructorsareencouragedtomatchthe
difficulty of the material being covered
through scaffolding and to provide
opportunities for students to articulate
what they have learned and to reflect
on their own learning. Each of these
concepts is described briefly below.
Modeling
In modeling, an expert practitioner
demonstrates the skills or tech-
niques to be learned (Collins et al.,
1991). The laboratory component
is designed to mirror a research lab
setting focused on a semester-long
investigation of the mechanisms
of Alzheimer’s disease. Students
read original journal articles and
conduct a series of published ex-
periments (Pastorino, Ikin, Nairn,
Pursnani, & Buxbaum, 2002). This
long-term experiment aligns with
our learning goals of exposing stu-
dents to techniques and aspects of
scientific research by motivating
them to apply information learned
in the lectures much as students do
in problem based learning (PBL)
frameworks (Eberlein et al., 2008;
Pease & Kuhn, 2011; Sungur &
Tekkaya, 2006). Our course adds to
the rich context of PBL with a fo-
cus on modeling scientists’ thought
TABLE 1
Overview of introductory neuroscience course.
Week Theme Lecture Lab
1 DNA DNA structure
DNA replication and repair
Regulation of gene expression
Recombinant DNA technology
Transcription
Students use polymerase chain reaction (PCR)
to replicate BACE DNA.
Students use recombinant DNA techniques by
inserting the BACE DNA into a plasmid.
2
3
4
5
6 Protein Protein structure and function
From DNA to protein: transcription and translation
Students insert BACE DNA into cells and use
SDS-PAGE and Western Blot to test levels of
protein expression.
7
8 Protein
function and
transport in
the cell
Membrane structure
Transport across the cell
Intracellular compartments
Protein transport
Students label wild type and mutant BACE with
specific antibodies to track BACE movement
using a fluorescence microscope.
Students focus on studying the processing of
Amyloid Precursor Protein APP, as a result of
BACE activity on APP, as it occurs in Alzheimer’s
disease pathology.
9
10
11

3. 86 Journal of College Science Teaching
RESEARCH AND TEACHING
processes. The laboratory methods
parallel those discussed in the ar-
ticle as depicted in Table 1.
Coaching
In a cognitive apprenticeship, a ma-
jor part of the coaching occurs when
the instructors make their thinking
explicit, or “visible,” to the students
(Bareiss & Radley, 2010). At the
beginning of each week, a lecture
is dedicated to covering the week’s
experiment to prepare and enable
students to work independently.
The professor models how to read
and interpret journal articles, in-
cluding the importance of reading
figure legends and understanding
the logical flow of the article during
the weekly class session. Students
are challenged to connect lecture
material with the experimental con-
cepts that are emphasized in lab,
where they and graduate teaching
fellows (TFs) actively engage in
discussions about technical details
and rationale. This convergence of
topics between the two parts of the
course allowed the lab instructor
and professor to support students in
developing critical thinking skills
and in transferring ideas from one
context into a different context. A
major challenge of this course was
to remind students that the purpose
of research is to answer the overall
research question, as students often
believed the purpose of the labora-
tory was to learn specific labora-
tory techniques. To ensure that stu-
dents understood why they needed
to clone DNA, graduate TFs and
undergraduate learning assistants
(LAs) revisited this topic repeatedly
as students gained more informa-
tion in lecture. On a weekly basis,
graduate TFs were responsible for
continuously reviewing each as-
pect of the research project with the
students. Students had multiple op-
portunities to understand and revisit
the topics from week to week, and
the lab instructors had multiple op-
portunities to identify and address
areas that were difficult for students
to understand.
Weekly staff meetings included
discussions of pedagogical strate-
gies, such as how to engage students
in active learning, and metacogni-
tive strategies, such as how to help
students interpret journal articles
and troubleshoot anomalous results
(Dotger, 2010).
Scaffolding
Instructors structure learning envi-
ronments by matching the level of
difficulty to students’ abilities, a
process known as scaffolding. By
focusing on challenging yet attain-
able goals, scaffolding reduces the
cognitive load on the learner (Brans-
ford, Brown, & Cocking, 2000). In
this course, the close connection
between the lecture and the labora-
tory allowed the course instructors
to support student learning. The
lecture met three times a week: two
of those lectures provided an over-
view of the foundational concepts
and the third lecture was dedicated
to exploring the specific content
that would be covered in the labo-
ratory. This third lecture included a
preview of the laboratory and time
to review and discuss experimental
results; it also emphasized connec-
tions between that week’s experi-
ment and the larger context covered
in lecture.
Prior to coming to the labora-
tory session, students completed an
online prelab quiz. Quiz questions
emphasized the critical components
and reasoning for the upcoming
experiment. At the start of each lab,
graduate TFs and undergraduate LAs
led a class discussion reviewing the
quiz and linking the purpose of the
current experiment with the overall
research project.
Articulation and reflection
Students demonstrate understand-
ing through articulating their knowl-
edge in discussions and assignments
and through reflection by compar-
ing their own approach with that
of solving problems with an expert
(Collins et al., 1991). Because stu-
dents were following an established
protocol, they were encouraged to
compare their results with those of
their classmates and consider fac-
tors that may have caused their own
experiment to deviate from the ex-
pected results. Failed experiments
were viewed as learning opportu-
nities to deepen the analysis of the
causes and consequences of the ex-
periments.
The assignments in the course also
required students to articulate and
reflect on their learning in the course.
Students read a review article about
molecular mechanisms involved in
Alzheimer’s disease as a first assign-
ment and then more detailed journal
articles as their second and third as-
signments. These assignments were
specific to the field of the research
project, and functioned to (a) in-
troduce the rationale and technical
aspects of the project and (b) help
the students understand how data are
communicated in a research article
with an emphasis on the different
aspects of a research article.
A cumulative final assignment
was focused on writing the lab proj-
ect in the format of a research article,
where students formulated their own
scientific argument and logical pre-
sentation of their data. In this assign-
ment, students described the goals of
the project, the techniques used, and

4. 87Vol. 46, No. 1, 2016
the results in a format that included
the (a) Summary (orAbstract) where
they summarized the objective of the
experiment and the results obtained;
(b) Introduction, where students
reviewed preliminary information
necessary to understand the project;
(c) Materials and Methods, where
students described the methods used;
and (d) Results and Discussion,
where students had to report and
explain their data and also emphasize
their relevance in the context of that
field of research.
Exploration and application
Exploration and application chal-
lenge students to translate their
understanding into a new context
(Collins et al., 1991). In this course,
students were asked to apply scien-
tific thinking skills gained through
the course into a new, yet related
domain through a figure-ordering
assignment. Students assembled a
set of randomly sorted figures from
a research article into a logical order
and provided a rationale for their
chosen sequence. The ordering of
the figures demonstrated students’
level of understanding of the logi-
cal thread of the scientific article, as
well as the ability to use information
from the figure descriptions in their
ordering. Our grading rubric, in-
cluded in the supplemental materials
(http://www.nsta.org/college/con-
nections.aspx), accounts for more
than one possible order based on
the evidence included in the figures.
This exercise was extremely chal-
lenging for the students, providing
a learning opportunity for them and
for the instructors in the course.
Assessment of learning
outcomes
We wanted to know whether struc-
turing the course with a thematic
link between the lecture and lab
with the attributes of a cognitive ap-
prenticeship would provide similar
content coverage compared with
a traditional course, help students
transfer knowledge to different
contexts, and help students’ under-
standings of research in molecular
biology. A pre- and postcourse as-
sessment included content ques-
tions, self-report about students’
goals for the course, and learning
gains as a result of the course. Con-
tent questions were also adminis-
tered to a comparison group of stu-
dents in a more traditional biology
course with a similar range of top-
ics. The figure-ordering assignment
demonstrated students’ understand-
ing of the structure of a scientific ar-
gument and their ability to transfer
knowledge from the laboratory and
lecture to an assignment focused on
a tangentially related scientific arti-
cle. All of these survey instruments
were reviewed and approved by the
Boston University Institutional Re-
view Board.
Content knowledge
The pre- and postcourse assessment
content questions were collected
from existing materials and previ-
ous tests (Shi et al., 2010; Smith et
al., 2005) and past content questions
developed by the authors for other
courses. A comparison group of stu-
dents from a different introductory
biology course (BI) also completed
the pre- and postcourse assessment
for the content questions. Labora-
tory technique questions were de-
veloped by members of the research
team and were only completed by
the students in NE.
The content knowledge questions
were scored 0 for incorrect and 1 for
correct responses and were averaged
together by individual to create a
content pretest and posttest mean.
An average score for each pretest and
posttest was calculated by averaging
the number of correct responses on
the pre- and the posttest, and these
were again averaged to create a grade
pretest mean and posttest mean. The
normalized gain was used to com-
pare scores across different classes
(Singer, Nielsen, & Schweingruber,
2012). The average normalized gain
for each class was calculated using
the following formula:
Normalized = (average post - average pre)
gain (1– average pre)
The results for the content questions
are presented in Table 2. Students in
biology exhibited a normalized gain
of 20%, whereas students in neu-
roscience had a normalized gain of
21%. The effect size of 1.29 for BI
suggests that the mean of the post-
TABLE 2
Average pretest and posttest score and normalized gain for BI and NE.
BI (N = 289) NE (N = 78) BI (SD) NE (SD)
Average pretest score 0.44 0.40 0.13 0.14
Average posttest score 0.55 0.52 0.04 0.13
Normalized gain 0.20 0.21
Effect size 1.29 0.94
Note: BI = introductory biology course; NE = Introduction to Cellular and Molecular
Biology.

5. 88 Journal of College Science Teaching
RESEARCH AND TEACHING
test is at the 88th percentile of the
pretest. The effect size of 0.94 for
NE suggests that the mean of the
posttest was at the 89th percentile of
the pretest. Both are considered to be
large effect sizes. Overall, students
in both NE and BI made similar con-
tent gains related to the questions on
the assessments.
Laboratory skills and techniques
Students in NE answered a set of
questions related to laboratory skills
on the pre- and postcourse assess-
ment. We asked students when they
would use four essential laboratory
techniques (colorimetric assay, trans-
formation, polymerase chain reac-
tion (PCR), and gel electrophoresis)
and when they would use two assays
(green fluorescent protein [GFP]
and immunoblot assays). The aver-
age pre- and postscores as well as
the results of the test of significance
are presented in Table 3. The full
questions and response categories
are listed in the supplemental mate-
rials (http://www.nsta.org/college/
connections.aspx).
NE students made significant
gains in their understanding of all
of the laboratory techniques as a
result of the course. Not surprisingly,
students made the greatest gains in the
questions directly related to course
content: identifying proteins, protein
localization, and using immunoblots.
Evidence of transfer
We measured students’ ability to
transfer knowledge using the figure-
ordering assignment described pre-
viously. During Week 8 of class, we
asked students to complete a version
of the assignment to establish a base-
line. Students organized and provid-
ed a rationale for the figures of the
research article “BACE is Degraded
Via the Lysosomal Pathway” (Koh,
Von Arnim, Hyman, Tanzi, & Tesco,
2005). We gave the postassignment
as a bonus question during the final
exam at the end of the course. In this
case, students had to reorganize only
part of the figures from the article
“Intracellular Itinerary of Internal-
ized β-Secretase, BACE1, and its Po-
tential Impact on β-Amyloid Peptide
Biogenesis” (Chia et al., 2013).
Both the preassignment and post-
assignments were graded by the
professor and teaching fellows. Each
assignment was graded by at least
two people, and students could score
up to 10 points for each assignment:
4 points for the correct order and 6
points for a correct rationale. The
overall results of the assignment ap-
pear in Table 4, and the full assign-
ment description is available in the
supplemental materials (http://www.
nsta.org/college/connections.aspx).
Students made statistically signifi-
cant gains in their ability to provide
a rationale for the ordering of their
figures. However, students did not
improve on the figure-ordering prob-
lem given in the exam compared with
the in-class assignment. The total
score increased from the baseline to
the exam but did not reach statistical
significance. The improvement in
providing a rationale demonstrates
an ability to critically analyze pieces
of evidence into an argument and
provides evidence of students’ability
to transfer the knowledge gained from
NE into a different context.
Understanding of research
Students were asked to report on
their understanding of research on
TABLE 3
Lab skills average pretest and posttest scores, standard deviations, and
significance values.
Lab skills M pre
(SD)
M post
(SD)
p-value
(McNemar)
You’ve selected a 1000μL micropipette to add
a volume of 420μL to your tube. The numbers
on the micropipette window should read:
0.71
(0.46)
0.95
(0.22)
.001
Which technique would you choose to intro-
duce proteins into cells?
0.71
(0.46)
0.94
(0.23)
.001
Which technique would you choose to
separate DNA or proteins by size?
0.31
(0.47)
0.85
(0.36)
.001
Which technique would you choose to
identify which proteins are present in the
sample?
0.3
(0.32)
0.89
(0.32)
.001
Which technique would you choose to
determine where proteins localize in cells?
0.30
(0.46)
0.68
(0.47)
.002
The method scientists use to“tag”GFP to a
protein of interest is
0.36
(0.47)
0.68
(0.47)
.001
An immunoblot assay uses the following
biological molecule
0.55
(0.50)
0.99
(0.11)
.001

6. 89Vol. 46, No. 1, 2016
the final survey. Eighty-five percent
of students (77) reported that they
better understood research as a re-
sult of the course, 14% of students
(13) reported they had the same
understanding as before taking the
course, and only 1% of students (1)
disagreed with the statement that
they learned more about research
from the course. The course experi-
ence influenced 37% of students (33)
to move toward careers in research,
35% of students (27) to move away
from a research career, and 30% of
students (31) were not notably af-
fected by the course.
The course allowed students to
gain insight into different aspects of
scientific research, including a better
understanding of methods, protocols,
and results and an ability to read and
decode scientific articles. After the
course, students better understood
the importance of replicating experi-
ments, sharing results, and the pro-
cess of communicating results to the
scientific community through journal
articles. Students also wrote that the
course demystified the process of
scientific experimentation, allowing
them to “better understand different
scientific techniques,” inspiring them
to be “more excited and interested
in doing research.” In particular, the
students’ comments on the postsur-
vey demonstrated an appreciation of
learning from failure. One student
wrote, “I have gained a lot of respect
for those who develop their experi-
ments and experience trial and error
and still continue with research.”
Another commented, “I have more
respect for researchers because there
is so much that can go wrong.”
Students were asked how much
their experience in NE influenced
their interest in doing future research.
Forty-four students mentioned that
their experience in the course was
a positive influence. Students’ com-
ments demonstrated an appreciation
for the course structure with a closely
related thematic lab, in the context of
Alzheimer’s disease.
“I never had a class where we
dedicated an entire semester to
a research project and I liked it.
I was able to understand better
the concepts then just doing an
entire different lab every week. It
opened my eyes to the world of
research and I am excited to start
this summer.”
“[This course] makes it possible
for me to consider a career in
research rather than pursuing the
premed path. I loved learning
about Alzheimer’s disease and
reaching a point where I could
truly understand scientific writ-
ing.”
Students’ comments specifically
mention how the multiweek examina-
tion in the context of a neurological
disease was beneficial in their learn-
ing. Students participated in a broad
range of scientific practices includ-
ing critically analyzing experiments,
learning how to read and decipher
scientific articles, and applying con-
tent knowledge in the practical realm
of the laboratory.
Discussion
Reform in undergraduate science
laboratories has centered on bringing
research activities to students early in
their undergraduate careers, in par-
ticular on having students engage in
scientific research in the form of ex-
perimentation (Elgin, 2007; Hanauer
et al., 2006; Wei & Woodin, 2011).
Although designing and conducting
experiments is important in science,
it is only one part of what scientists
do (Zimmerman, 2007). This article
demonstrates how crafting an intro-
ductory course around a theme of a
series of laboratory experiments al-
lows for a well-integrated course that
can provide students with founda-
tional knowledge equivalent to tradi-
tional introductory courses and build
students’ scientific thinking skills and
practices.
In addition to providing students
with content knowledge, this course
structure is advantageous to traditional
courses because it allows students
to gain important insights into the
scientific process and develop criti-
cal thinking skills. The alignment of
lecture and laboratory encouraged
students to think about connections
between course content and experi-
mental rationale for the laboratory.
Students evaluated and assessed their
own work in the lab by comparing their
results with the published results and
also with their peers. When students
TABLE 4
Results from the figure-ordering (transfer) assignment.
Prescore Postscore p-value N Pre (SD) Post (SD)
Figure order 3.28 2.81 .037 74 1.30 1.55
Rationale 3.28 4.03 .028 74 2.39 1.98
Total score 6.15 6.77 .181 79 3.37 2.98

7. 90 Journal of College Science Teaching
RESEARCH AND TEACHING
did not obtain the same results as in
the article, the faculty and laboratory
instructors used this difference as an
opportunity to troubleshoot laboratory
techniques and discuss the challenges
of replication studies in science re-
search. This format enabled students
to learn about the research process
through active engagement and criti-
cal reflection as part of a supportive
community. Students also learned
how to evaluate scientific arguments
by observing experts (professors
and graduate TFs) and by practicing
critical reflection during discussions
in class and laboratory. The thematic
approach revisited the material over
a series of weeks, allowing students
many opportunities to understand
challenging material and allowing the
lab instructors to identify and address
areas of difficulty. In many ways, this
laboratory course mirrors the appren-
ticeship that a new graduate student
undertakes when he or she first enters
a graduate lab with the added advan-
tage of having instructors model their
thinking processes in addition to their
physical skills.
This type of course structure has
other advantages. Our class size was
around 100 (only 80% consented to
be included in the study), but such a
course structure could be expanded
to larger classes. Following an estab-
lished protocol enables the students
to pinpoint potential mistakes. It also
enables the graduate TFs to assess
student progress against a standard
and provides a common topic to be
discussed during lecture.The prospect
of managing multiple and different
research projects can create chaos for
instructors and frustration for students
(Crandall, 1997), and concerns about
course management are a barrier
for those considering course reform
(Brown, Abell, Demir, & Schmidt,
2006). This structured approach pro-
vides an alternative for instructors to
consider as they design introductory
courses.
The limitations of this approach
are that the laboratory experiment
cannot cover all of the topics regu-
larly covered in the lecture, leaving
more content for upper level courses.
However, the guidelines in Vision
and Change (Brewer & Smith, 2011)
suggest a focus on concepts rather
than facts and the unification of
learning about content and process.
Although introductory courses can
provide students with a great deal
of foundational content knowledge,
modeling and stimulating critical
thinking on important topics can
provide them with tools they can
use throughout their academic and
personal lives.
Conclusion
The structure of NE provides first-
year students with an introduction
to scientific research processes as
well as a solid foundation in the
fundamental content and skills
in the field of cell and molecular
neurobiology. The semester-long
experiment provides an ongoing
theme for the course and enables
students to reflect and apply their
understanding of course-related ma-
terial from each part of the course.
While learning content equivalent
to a traditionally structured course,
students were actively engaged in
the experiment, understanding the
rationale for each step and critically
evaluating their results against their
peers and the published article. Such
a course structure allowed students
to apply knowledge they gained in
multiple contexts, helped them draw
on that knowledge, and allowed
them to assess their own learning. ■
Acknowledgments
The authors acknowledge Kathryn
Spilios, Elizabeth Co, and Matthew
McIntyre for sharing content questions.
We also thank Eli Shobin and Nathaniel
Kinsky for their assistance scoring
students’responses to the figure-drawing
questions. This work was supported by
an award to Boston University from
the Howard Hughes Medical Institute
through their Undergraduate Science
Education Program.
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MeredithM.Thompson(meredith@mit.
edu) is a research scientist in the Teach-
ing Systems Lab, Department of Urban
Studies, at the Massachusetts Institute
of Technology in Cambridge, Massachu-
setts; Lucia Pastorino (lpastori@bu.edu)
is a lecturer in the Department of Neuro-
science at Boston University in Boston,
Massachusetts; Star Lee is an academic
coordinator in the Department of Biology
at the University of California in Riverside;
and Paul Lipton is director of the Under-
graduatePrograminNeuroscienceatBos-
ton University.