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MIGUEL JIMENEZ: The
crux of the class

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is really teaching
the students how

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to read the primary literature
and read research papers.

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We wanted it to be
engaging for them,

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so we're kind of
dealing with papers,

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specifically looking
at the microbiome

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and synthetic biology
and drug delivery.

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SARAH HANSEN: So what
are some strategies

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that you use to teach students
how to critically read

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the primary literature?

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MIGUEL JIMENEZ: Yeah, yeah.

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So I mean, first of all, we
choose a variety of papers--

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some that are simpler to
read and some that are--

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with tons of figures.

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But really, we're always
asking them what would

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they do differently if
they were the researchers.

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ALI BEYZAVI: Or maybe, what
are some of the controls that

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are missing or what are
some of the experiments

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that the authors could
do to improve the study?

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We always get started
asking the questions,

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OK, what is the abstract?

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And what is the main
claim of the paper?

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And then, we were guiding
them, figure by figure,

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to understand the article
and explain it in the class.

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MIGUEL JIMENEZ: And so we always
take this kind of step-wise

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approach, where instead of just
taking everything as a given

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when you read a paper, which
is maybe what you would do

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if you're reading a magazine,
here, we're really kind of--

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they first start by
reading the abstract

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and considering what the
authors seem to be suggesting.

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And then, later, they look
at the data just on its own,

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just the figures, and
then think for themselves,

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do the figures actually match
up with what the authors were

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saying in the abstract?

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SARAH HANSEN: So let's talk
a little bit about the role

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of questioning in the course.

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I had the opportunity to sit in
on one of your class sessions.

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And I noticed that
instructor-led questioning

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seemed to be pretty important
throughout the session.

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So talk to us about the
role of questioning.

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How do you select the types
of questions that you do?

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Is there a learning
curve for students,

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in terms of their
confidence and how they

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respond to these questions?

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ALI BEYZAVI: So we try to
challenge them a little bit.

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And we try to ask them, one by
one, to explain each figure.

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And we're trying to keep a
balance between the questions

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we ask and also the
explanations and information

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we provide to students.

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We also study a lot
before each session.

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Maybe for every two
hours of the class,

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we did four or five hours
of reading by ourselves

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to get ready.

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And when we are
asking the students,

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the students were somehow
forced to read in advance.

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And when they read
in advance, then

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they learn much, much faster.

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MIGUEL JIMENEZ: Right.

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And I do think
there was a learning

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curve for the students.

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And Ali, right from
the very beginning,

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had a very cool idea to kind
of pick on students at random.

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And so the first class I
think was a little bit--

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the students were like, whoa--

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[CHUCKLES]

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--we're going to have to answer.

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But I think, very quickly,
the students were great.

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They knew that.

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And so then, they knew
they really had to read.

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And they also learned to read
efficiently with their time,

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so then they can be ready
for any one of the questions.

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And I think, when you
came in, you saw that.

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Like, after several
sessions, they

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could already kind of
on the spot be engaged

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and really reading the paper.

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So I think that was a great
strategy to do it that way.

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And I think another thing
that maybe worked well

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was that the kind of
questions and in the order,

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even, we asked them was almost
very similar from session

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to session.

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So obviously, the paper is
very unique and very different,

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but we always ask like,
what's the main claim;

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which of the figures is
the most important figure

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to support their main claim; and
then, what controls were done?

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What controls could be done?

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And so that was kind of like
these five key questions.

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And we always asked
those questions,

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so I think the
students also were--

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became prepared to answer
those types of questions.

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So I think that probably when
the students were reading

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the papers in the
later sessions,

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they were already
reading the papers

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with those questions in mind.

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So I think that also helped them
in the actual class session.

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ALI BEYZAVI: Absolutely.

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This is a famous
assay microbiologists

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use to see if the bacteria
has been able to penetrate

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the eukaryotic cell.

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So gentamicin kills
everything outside.

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And if the bacteria has
already invaded the cell,

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it's protected inside.

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And then, when you lysed it--

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tumor cells-- you can
extract the bacteria inside.

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MIGUEL JIMENEZ: If you guys
were to do the next figure--

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kind of expand this
paper-- what should

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be kind of the next step?

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AUDIENCE: I would
think they would

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want to combine both the quorum
sensing and the anaerobic.

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MIGUEL JIMENEZ: Yeah,
definitely, right?

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Because their figure
1 shows that they're

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trying to make this system
that only invades tumors.

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And so, that's what the
anaerobic point is for.

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And what is their
argument for why

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they want this quorum
sensing aspect to it?

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AUDIENCE: Because of the
typical density of the bacteria

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at the cancer cells.

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MIGUEL JIMENEZ: Right.

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AUDIENCE: They enjoy
that environment.

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MIGUEL JIMENEZ: Right.

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Right.

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They don't want to
have it just invade

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random cells all by itself.

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They want for them to only
invade the cancer cells

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all in one batch.

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SARAH HANSEN: Let's talk
about the midterm assignment

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in the course.

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What was it all about?

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ALI BEYZAVI: So in the
midterm assignment,

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we tried to give two papers
to students without giving

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the title of the paper.

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We only selected the
figures and tables

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and put it in a PowerPoint
and asked the students

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to look at the figures and
try to connect the dots,

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trying to understand what's
the story of the paper.

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We explained a little bit about
the caption of each figure,

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so that students could see
the figure, read the data,

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and read the caption.

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And then, they were in
charge of understanding

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what the whole paper is
about, what is the main claim,

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and what is the
story of the paper.

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MIGUEL JIMENEZ: And so,
yeah, we were really

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trying to kind of
flip what we normally

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do in a class kind of upside
down, so they were really

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then intended to write an
abstract, based on the figures,

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rather than judge the figures,
based on the abstract.

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And so I think when we
first gave it to them,

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they were a little
bit concerned.

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I think some of the
difficulties they

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had was like how much background
to include in the abstract.

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Or for example,
something that they

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asked a lot of questions about
was how much other readings

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should I do.

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Because it's a little bit like
a quiz, where you give them

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just the figures,
and then they have

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to come up with an abstract.

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So there's always the
intention of trying

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to find which papers the
figures belong to to read

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the original abstract.

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And so we tried to
actually change the legend,

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so that wouldn't be so easy.

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But we also asked
them to not necessary

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directly look up the paper.

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But then, there was
still struggle, though,

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because they still needed
to understand the figures.

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And so there was some amount
of background research

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they had to do.

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And so, if they came upon
some of the background,

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they were like, should
I include that or not,

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and how much to do that.

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But I think, in the end, it
was all OK, because really,

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just even thinking about what
is the main claim without being

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given the main claim, I think
that was really the key aspect

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of the assignment.

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SARAH HANSEN: That's
really interesting.

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ALI BEYZAVI: More
or less, it looked

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like solving a puzzle for them.

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So they had the pieces and
they had to connect them

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in the right order.

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SARAH HANSEN: Students
in this course

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give a final presentation.

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What was that all about?

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MIGUEL JIMENEZ:
Yeah, so now, it's

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kind of giving them
a little bit of--

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allowing them to choose
their own papers.

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So the whole time, we've
been choosing papers for them

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or figures for them to analyze.

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And now, we wanted to see--

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for them to have the
freedom to kind of explore

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a certain aspect of
the microbiome or drug

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delivery of their
choosing, and then,

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for us, also to see kind
of where they took it

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from where we left it off.

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And so the way we
designed this assignment

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was that we asked each student
to choose two papers that they

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would like to present.

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And then, we went
through and chose

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one of those papers
for them to present,

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so at least we would have
all the papers be kind

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of equal length or difficulty.

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And they would
all be matched up,

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but at least, we gave them the
ability to choose the paper.

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And then, they
were meant to just

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do like a 10-minute
presentation to,

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again, go through kind
of the same questions

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we'd go through in every
session, kind of tell all of us

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in the class what is the main
claim, kind of contextualize

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those, and kind of
critique the paper as what

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other experiments
could be done or what

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the researchers do really well.

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ALI BEYZAVI: The
day of presentation,

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I was extremely happy because
I saw that students have really

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learned to go in
to the literature,

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dig into the literature,
find a paper,

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read it, and understand it.

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And I think--

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I and Miguel-- reached one
of the most important goals

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of discourse, which was
teaching students how

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to read and understand paper.

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MIGUEL JIMENEZ: Right.

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And it was really great to
see it in a single session.

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We had eight to nine students,
so we had all these papers

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all presented in
kind of in the way we

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would have presented them.

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So it was really nice--

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affirmation that they had
really kind of understood

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kind of the whole
point of the course.

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SARAH HANSEN: One of
the interesting parts

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of this course is
that students get

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to take visits to working labs.

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Could you tell us a
little bit about that?

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ALI BEYZAVI: Of course.

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We thought that,
besides reading papers,

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it's very good to show
students that things they read

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have some tangible,
real application.

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And Miguel found a
company called Ginkgo Bio.

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They're actively working
on synthetic biology.

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And they're actively
engineering the microbiome

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to get new applications.

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And then, we took the
students over there.

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It was amazing, because they
saw whatever they have learned,

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and they are
learning, and they're

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reading the papers to have
some real-world applications.

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MIGUEL JIMENEZ: So yeah,
from the very beginning,

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when we were developing
the curriculum,

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we heard from
previous instructors

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that rather than taking
them to an MIT lab,

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it would be very kind of
enriching for the students

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to actually go out
off of the campus.

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And so that's why we
chose to go to a company,

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rather than showing them a lab.

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And so interestingly,
we didn't know

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that kind of going into the
semester when we were already

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planning the visit
to Ginkgo Bioworks,

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but most of the students
were actually seniors

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with just a couple of juniors.

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So actually, they were all
very interested in jobs

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and how do you translate some
of this stuff that you learn

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and see here on campus
to the real world.

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And so it was
really interesting,

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I think, for me
and for them to see

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kind of a lab, similar to
where we are right now,

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but what it looks like
really an industry

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kind of on a high level,
very professional.

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And so I think Ginkgo Bioworks
was great for showing them

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they have like these
foundries, or bio foundries,

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where they're doing
synthetic biology

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kind of at a grand scale.

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And so that was really
interesting for the students.

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And we asked them at the end
of the course, and they were--

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that was like one of the
highlights of the course.

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They're really very
excited about that.

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SARAH HANSEN: Why did
you choose to teach

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this course as postdocs?

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And is it something you'd
recommend to other people

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in your position?

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ALI BEYZAVI: Yeah, I
definitely would recommend it.

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As a person who has
done a PhD and has

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been in the graduate school
for a couple of years,

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I was clearly feeling
that, if a researcher wants

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to be successful,
he or she must be

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able to read the literature
almost every day.

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And he or she must be able
to keep up with the speed

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that papers are
generated, at least

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in his or her particular field.

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And we thought that
undergrad students

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should learn these skills
as soon as possible.

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Even if they don't want to do
research or go to grad school,

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even if they want to be
successful in their own career,

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or if they want to go
to industry or whatever,

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it's a great skill
set for them to be

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able to search and learn
from internet and from papers

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and articles.

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So we thought it's
a good opportunity

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to pay back to the
community and teach them

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how to read the papers and
how to think critically.

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MIGUEL JIMENEZ: For
me, personally, it

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seemed like a very interesting
way to look at the literature

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that I already looked at,
but from a different angle.

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When you're trying to teach it
and think about it critically,

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I think I felt like I
also was able to, then,

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look at the literature even
more critically through the eyes

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of the students.

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And you have to
balance both teaching

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and developing the course
with your research,

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but I would really
encourage other postdocs

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to take advantage of
these opportunities.

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Because actually, in
doing so, you actually

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get to kind of look
at your own research

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from a different perspective.

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And so it's good to
have that in mind.

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I would definitely
encourage other people

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to take advantage of
these types of things.