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Unformatted text preview: The
Art
of
Writing
a
Scientific
 Paper
 Mark
Garcia
 General
things
to
keep
in
mind
when
 writing
your
scientific
paper
 •  Keep
pronouns
like
“I”
and
“we”
to
a
 minimum
 •  Never
use
“You.”
 •  The
paper
is
being
written
after
you
have
 performed
these
experiments,
keep
it
in
the
 past
tense
 Parts
of
a
Scientific
Paper
 •  •  •  •  •  •  •  Title
 Abstract
 Introduction
 Materials
and
Methods
 Results
 Discussion
 References
 Title
 What
makes
a
title
good? 

 •  Clear
concise
message
that
conveys
the
 experiments
performed
and
your
findings
 •  Captures
the
attention
of
the
reader
 Example
Titles
 Changes
in
Temperature
and
pH,
and
the
 Resulting
Effect
on
the
Enzymatic
Activity
of
 Catechol
Oxidase

 EXCELLENT:
Concise
and
to
the
 point,
but
still
informative
 Environmental
Changes
and
Their
Effect
on
 Catechol
Oxidase

 Good:
Still
informative,
but
vague
in
 terms
of
what
environmental
 changes
were
made
 Enzymes
 Bad:

Doesn’t
describe
what
aspect
 of
enzymes
is
being
analyzed,
or
 what
enzyme
is
being
tested.
 Abstract
 What
makes
an
abstract
good? 

 •  Should
be
no
more
than
250
words
 •  Think
of
it
as
your
“30
second
Super
Bowl
Ad”
 •  1‐2
Sentences
of
intro,
1‐2
of
M&M,
1‐2
of
 Results,
and
1‐2
of
Discussion
 •  Should,
like
your
title,
be
concise
and
 informative,
but
not
overly
superfluous







 (ex.
Don’t
state
the
amount
of
mL
of
a
solution
 that
were
used)
 •  You
should
write
this
and
your
Title
last
 Example
Abstracts
 Catechol
Oxidase
is
an
enzyme
found
plants
that
is
necessary
for
the
 conversion
of
the
molecule
catechol
into
the
product,
benzoquinone.

 Benzoquinone
is
produced
as
a
means
of
protecting
plants
from
 environmental
threats,
and
its
production
is,
therefore,
crucial
to
plant
 survival.

Here
we
describe
a
series
of
experiments
that
were
used
to
 determine
the
optimum
temperature
and
pH
of
this
enzyme.

Additional
 experiments
were
performed
to
determine
its
specificity
for
its
substrate,
 and,
whether
or
not
it
required
cofactors
to
function
efficiently.

Our
 experiments
determined
the
optimum
temperature
and
pH
to
be
40°C
 and
7
respectively.

Furthermore,
the
results
also
suggested
that
Catechol
 Oxidase
is
specific
for
catechol
and
that
copper
a
necessary
cofactor
that
 contributes
to
enzymatic
activity.

Together,
these
results
further
 elucidate
the
conditions
in
which
this
enzyme
will
produce
the
highest
 yield
of
product,
and
validated
our
initial
hypotheses.

While
these
 findings
were
promising,
further
experiments
could
determine
if
other
 cofactors
other
than
copper
may
be
involved
in
the
reaction,
as
well
as
 what
molecules
may
act
as
enzymatic
inhibitors.
 EXCELLENT:
Concise,
<250
Words,
gives
just
enough
 information
to
let
me
know
what
is
going
on
in
these
 experiments
without
going
into
too
much
detail.


 Example
Abstracts
 Catechol
Oxidase
is
an
enzyme
found
plants
that
is
necessary
for
the
 conversion
of
the
molecule
catechol
into
the
product,
benzoquinone.

 Here
we
describe
a
series
of
experiments
that
were
used
to
determine
 the
optimum
temperature
and
pH
of
this
enzyme.

In
the
experiments
we
 added
3mL
of
enzyme
to
2mL
of
substrate,
and
placed
them
at
 temperatures
of
0,
10,
20,
30,
40,
60,
80,
and
100°C.

Additional
 experiments
were
performed
to
determine
its
specificity
for
its
substrate,
 and,
whether
or
not
it
required
cofactors
to
function
efficiently.
Our
 experiments
determined
the
optimum
temperature
and
pH
to
be
40°C
 and
7
respectively.
Activity
was
lower
at
0,
10,
20,
30,
60,
and
80°C,
while
 denaturation
occurred
at
100°C.

The
enzyme
was
specific,
and
it
needed
 cofactors.

Together,
these
results
further
elucidate
the
conditions
in
 which
this
enzyme
will
produce
the
highest
yield
of
product,
and
 validated
our
initial
hypotheses.

Future
experiments
can
be
performed
 to
learn
more
about
this
enzyme.
 Good
 Still
informative.

Relatively
concise.

Some
parts
are
 too
in
depth,
while
other
parts
are
far
too
vague.
 Example
Abstracts
 Enzymes
are
important
to
all
life.

Here
we
performed
experiments
that
 tested
key
aspects
of
enzymes.

The
enzyme
we
used
was
Catechol
 Oxidase.

When
you
use
this
enzyme
it
turns
brown.

This
was
our
 hypothesis.

Our
results
supported
this
hypothesis
and
will
allow
us
to
 perform
other
experiments.

This
was
a
really
cool
lab.
 Bad


 Very
vague,
Scientifically
incorrect,
 Uses
“You,”
and
is
too
personalized
 and
not
professional
enough
 Introduction
 What
makes
an
introduction
good? 

 •  Information:
You
need
to
fill
your
reader
in
on
 everything
that
they
must
know
to
understand
your
 experiments
 •  Citations:
You
must
internally
cite
the
source
material
 that
provided
you
with
information.

This
can
include
 text
books,
journals,
and
websites
 •  Hypotheses:

You
need
to
state
your
hypotheses
at
the
 end
of
your
introduction
so
that
it
naturally
segues
into
 your
M&M
 •  Flow:

This
section
of
your
paper
should
tell
the
 opening
story
of
your
topic,
and
should
therefore
flow
 in
a
logical
manner.

 Example
Introduction
Excerpts
 
 Mealworms
are
larvae
of
the
common
darkling
beetle
classified
in
the
 Arthropoda
Phylum,
Insecta
Class,
and
Coleoptera
Order
(CISEO,
1997).
They
are
 yellow
in
color
and
are
approximately
two
centimeters
long
(FLOSS
WEB,
2008).
 They
are
general
decomposers
that
feast
on
grasses,
leaves,
feces
and
dead
insects
 (CISEO,
1997).
However,
they
often
infest
mills
and
granaries
(Encarta,
2008).

 
 Mealworms
are
holometabolic
insects.
They
undergo
four
life‐stages,
the
first
 being
the
egg
stage
where
they
are
little
white
eggs.
The
next
stage
is
the
larva
stage
 where
they
look
worm
like
with
a
segmented
thorax
and
abdomen.
At
this
point
 their
legs
are
directly
underneath
their
heads.
The
third
stage
is
the
pupa
stage.
 During
this
phase
the
mealworms
curl
up
and
stay
in
a
rigid
cocoon‐like
shell
for
 several
days
to
several
months
depending
on
the
temperature
and
season
of
their
 environment.
The
final
stage,
adulthood
(the
darkling
beetle),
comes
when
they
 emerge
from
their
pupa
stage.
They
wait
several
days
for
their
wings
to
dry,all
the
 while
turning
browner.
The
larva
stage
is
particularly
important
to
our
experiment
 because
it
corresponds
to
the
period
of
the
greatest
increase
in
mass
(Wikipedia,
 2008).


 EXCELLENT
 This
section
of
the
introduction
gives
a
good
amount
of
 information
on
the
topic,
it
flows
in
a
logical
manner,
and
all
 of
the
citations
are
done
appropriately.
 Example
Introduction
Excerpts
 
 Mealworms
are
larvae
of
the
common
darkling
beetle
classified
in
the
 Arthropoda
Phylum,
Insecta
Class,
and
Coleoptera
Order
(CISEO,
1997).
Mealworms
 are
holometabolic
insects.
They
undergo
four
life‐stages,
the
first
being
the
egg
 stage
where
they
are
little
white
eggs.
They
are
yellow
in
color
and
are
 approximately
two
centimeters
long
(FLOSS
WEB,
2008).
They
are
general
 decomposers
that
feast
on
grasses,
leaves,
feces
and
dead
insects.
 
 The
next
stage
is
the
larva
stage
where
they
look
worm
like
with
a
segmented
 thorax
and
abdomen.
At
this
point
their
legs
are
directly
underneath
their
heads.
 The
third
stage
is
the
pupa
stage.
During
this
phase
the
mealworms
curl
up
and
stay
 in
a
rigid
cocoon‐like
shell
for
several
days
to
several
months
depending
on
the
 temperature
and
season
of
their
environment.
The
final
stage,
adulthood
(the
 darkling
beetle),
comes
when
they
emerge
from
their
pupa
stage.
They
wait
several
 days
for
their
wings
to
dry,
all
the
while
turning
browner.
The
larva
stage
is
 particularly
important
to
our
experiment
because
it
corresponds
to
the
period
of
the
 greatest
increase
in
mass
(Wikipedia,
2008).
Mealworms
also
infest
mills
and
 granaries
(Encarta,
2008).

 Good
 Still
scientifically
accurate,
but
the
logical
flow
is
 affected
by
the
placement
of
some
of
the
sentences.

 Additionally
one
of
the
sentences
is
missing
its
 citation
 Example
Introduction
Excerpts
 
 Mealworms
are
not
actually
worms
at
all.

They
are
bugs,
which
is
gross.

 Mealworms
eat
dead
stuff
and
live
in
dark
places.

Sometimes
they
are
found
in
mills
 with
oats
and
grains.

First
mealworms
start
as
eggs.

Then
they
grow
into
larvae.

 While
they
in
this
stage
they
are
eating
large
amounts
of
food
until
they
grow
bigger.

 This
is
the
stage
that
we
used
to
perform
our
experiments.

Once
mealworms
finish
 with
this
stage
they
move
on
to
the
pupa.

When
you
look
at
them
in
this
stage,
you
 will
see
them
have
a
hard
outer
shell.

Finally
they
become
a
beetle
and
this
is
when
 they
eat
your
food.

The
places
that
they
can
live
depend
upon
what
stage
they
are
 in,
and
they
only
eat
at
two
different
stages.
 
 In
our
experiment
we
looked
at
what
mealworms
eat.

Did
they
want
substrate
 A
or
substrate
B
more?

This
is
the
question.
 Bad


 Not
scientifically
sound,
no
 citations,
personalized,
 disorganized,
openly
asks
a
question
 to
the
reader
rather
than
stating
 hypotheses
 Materials
&
Methods
 What
makes
the
M&M
section
good?
 •  Complete
sentences
(don’t
use
bullet
points)
 •  Divide
up
experiments
into
their
own
 paragraphs
 •  Logical
flow
of
steps
and
information
 Example
M&M
Excerpt
 Determining
the
optimum
temperature
of
Catechol
Oxidase.

Four
 tubes
were
labeled,
0,
40,
60,
and
100°C,
and
filled
with
1
mL
of
 Catechol
Oxidase.

These
tubes
were
then
placed
inside
of
water
 bathes
that
corresponded
to
the
temperatures
written
each
tube,
 and
allowed
to
incubate
for
five
minutes.

At
the
end
of
the
 incubation
period,
1
mL
of
catechol
was
added
to
each
tube
and
the
 mixture
was
incubated
for
ten
minutes.

At
the
end
of
the
incubation
 period,
the
tube
was
placed
in
the
spectrophotometer,
and
the
 absorbance
was
calculated
and
recorded
in
Figure
1
(Garcia,
Orr,
et
 al.,
2010).

 EXCELLENT
 Italicized
fragment
to
denote
what
experiment
this
is.

The
 protocol
is
written
in
complete
sentences
with
specific
 temperatures
and
amounts.

It
is
written
in
the
past
tense,
 but
not
as
a
“How
To,”
and
the
manual
is
cited.
 Example
M&M
Excerpt
 Determining
the
optimum
temperature
of
Catechol
Oxidase.

First,
 label
four
tubes
0,
40,
60,
and
100°C,
and
fill
each
with
1
mL
of
 Catechol
Oxidase.

These
tubes
were
then
placed
inside
of
water
 bathes
that
corresponded
to
the
temperatures
written
each
tube,
 and
allowed
to
incubate
for
five
minutes.

You
then
add
catechol
to
 each
tube
and
incubate
the
tubes
for
ten
minutes.

At
the
end
of
the
 incubation
period,
the
tube
was
placed
in
the
spectrophotometer,
 and
the
absorbance
was
calculated
and
recorded
in
Figure
1
(Garcia,
 Orr,
et
al.,
2010).

 Good
 Still
in
paragraph
form,

delivers
a
logical
flow
of
the
 protocol,
however
it
switches
from
the
past
to
the
 present
tense.

It
also
uses
the
pronoun
“you”
and
at
 times
does
not
give
exact
amounts.
 Example
M&M
Excerpt
 • 
Label
4
tubes:
0,
40,
60,
100
 • 
Added
Catechol
Oxidase
to
each
tube
 • 
Placed
the
tubes
in
water
bath
for
5
min
 • 
Add
Catechol
to
tubes
 • 
Incubate
for
10
more
minutes
 • 
Record
data
in
appropriate
table
 Bad


 Bullet
points
instead
of
complete
 sentences.

Switches
between
 tenses.

Leaves
out
important
 details
in
regards
to
amount
added
 or
where
the
data
was
recorded.
 Results
 What
makes
a
results
section
good? 

 •  Raw
data
(statistical
included)
 •  Figures
to
represent
your
data
 •  Description
of
the
data
in
your
figures
written
 in
complete
sentences,
but
no
analysis
of
the
 data
 •  Statistical
data
(p‐value,
whether
or
not
the
 null
hypothesis
was
or
was
not
rejected)
 Example
Results
Excerpt
 Treatment
A
refers
to
the
mealworms
placed
in
 plastic
vials
of
wheat
bran
while
treatment
B
refers
to
 those
placed
in
peat
moss.
Even
though
the
average
 mass
gain
of
the
mealworms
in
treatment
A
was
 0.028
grams,
there
were
some
specimens
in
 treatment
A
that
did
have
mass
loss.
However,
this
 mass
loss
was
inconsequential
overall
because
it
was
 so
small.
The
loss
of
mass
may
have
been
a
result
of
 biological
defects
in
that
particular
mealworm.
 Treatment
B
holds
a
very
different
outcome
with
an
 average
mass
gain
of
‐0.005.
Treatment
B
also
had
 some
positive
mass
gain
but
the
mass
loss
was
much
 larger
than
in
treatment
A
and
also
more
frequent.

 EXCELLENT
 Figure
is
a
reasonable
size
and
is
accompanied
by
a
legend
at
 the
bottom
that
describes
what
is
shown
in
the
figure.

The
 paragraph
next
to
it
describes
what
is
in
the
figure.

(See
 example
paper
to
see
how
these
two
components
are
 arranged
together)
 Example
Results
Excerpt
 Treatment
A
refers
to
the
mealworms
placed
in
 plastic
vials
of
wheat
bran
while
treatment
B
refers
to
 those
placed
in
peat
moss.
Treatment
A
had
a
mean
 gain
of
.028
g,
while
Treatment
B
had
a
mean
loss
of
 0.005
g.


 Good
 Graph
present
and
properly
labeled
with
legend,
but
 the
paragraph
is
missing
some
of
the
additional
data
 that
was
presented
in
the
“Excellent
presentation,”
 like
the
Low
and
High
values
for
each
data
group
 Example
Results
Excerpt
 Treatment
A
mean
was
0.028.

Treatment
B
mean
 was
‐0.005.
 Bad


 No
real
information
is
given
in
the
 paragraph
outside
of
the
means,
 and
the
figure
legend
is
missing

 Discussion
 What
makes
a
discussion
section
 good? 

 •  Logical
progression
of
information
(Don’t
jump
 between
experiments,
explain
them
in
the
order
 in
which
they
were
in
your
materials
and
 methods/results
section)
 •  Analyze
your
data
 –  Were
your
hypotheses
validated/nullified?
 –  Did
you
receive
unexpected
results?
 –  Was
there
a
significant
difference
between
some
of
 your
sets
of
data?
 •  Future
Directions/Alterations
to
Experiments
 Example
Discussions
Excerpt
 The
optimum
temperature
and
pH
conditions
for
production
of
benzoquinone
by
catechol
 oxidase
were
found
to
be
40
°C
and
at
a
pH
of
7.
Biologically,
this
is
a
reasonable
as
these
 results
typically
occur
in
plants
that
are
found
in
environments
ranging
from
approximately
 25°C
‐
40°C.
We
did
not
hypothesize
that
any
benzonquinone
would
be
produced
at
0
°C,
 yet
it
was
nonetheless
present
in
our
testing.
This
could
possibly
be
a
result
of
the
fact
that
 the
catechol/catechol
oxidase
solution
in
the
tube
was
not
instantly
cooled
by
the
ice
bath.
 Once
the
ice
bath
did
cool
the
solution,
there
was
not
enough
activation
energy
available
 to
allow
the
chemical
reaction
to
occur
and
production
of
benzoquinone
ceased.
Also,
in
a
 60
°C
water
bath,
the
temperature
was
enough
to
curb
the
production
of
benzoquinone
 after
a
period
of
time.
In
a
water
bath
at
100
°C
no
benzoquinone
was
produced
at
either
 of
the
time
intervals.

Enzymes
are
proteins
and
will
therefore
denature
when
energy
in
the
 form
of
heat
begins
to
break
bonds
in
the
folding
structure
of
the
protein.
The
heat
from
 the
boiling
water
disrupted
the
bonds
and
attractions
that
defined
the
enzyme’s
 quaternary
and
tertiary
structure
and
as
a
result,
disrupted
the
overall
shape
and
function
 of
the
enzyme.

 EXCELLENT
 Analyzes
results
and
determines
whether
those
results
 support
or
nullify
hypotheses.

Offers
explanations
and
 further
hypotheses
that
would
fuel
future
research.

If
 statistical
data
were
present,
this
would
also
be
the
section
 where
that
data
would
be
analyzed.
 Example
Discussions
Excerpt
 Theoptimum
temperature
and
pH
conditions
for
production
of
benzoquinone
by
catechol
 oxidase
were
found
to
be
40
°C
and
at
a
pH
of
7.

We
did
not
hypothesize
that
any
 benzonquinone
would
be
produced
at
0
°C,
yet
it
was
nonetheless
present
in
our
testing.
 Also,
in
a
60
°C
water
bath,
the
temperature
was
enough
to
curb
the
production
of
 benzoquinone
after
a
period
of
time.
In
a
water
bath
at
100
°C
no
benzoquinone
was
 produced
at
either
of
the
time
intervals.
 Good
 Addresses
and
analyzes
some
of
the
data,
but
does
 not
elaborate
on
why
any
of
these
results
may
have
 been
obtained.

The
flow
of
this
particular
part
of
the
 discussion
is
logical,
but
simply
does
not
contain
the
 information
needed
to
build
a
case
for
future
 research
 Example
Discussions
Excerpt
 The
optimum
temperature
was
40
C.

The
optimum
pH
was
7.

This
proved
our
hypotheses.

 Future
directions
and
experiments
need
to
be
performed
to
ensure
that
the
data
is
good.

 Some
product
was
seen
at
0
C.

This
was
probably
because
of
human
error.
 Bad


 Short.

Does
not
elaborate
at
all
or
attempt
to
analyze
any
 of
the
data.

Vague
about
what
the
future
directions
are.

 Disjointed
composition
of
the
paragraph.

States
that
the
 hypothesis
was
proven
instead
of
supported.

Chalks
any
 error
up
to
human
error
instead
of
attempting
to
provide
 an
additional
scenario
wherein
those
results
could
have
 been
obtained.
 References
 http://www.calvin.edu/library/knightcite/index.php?standard=APA
 ...
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This note was uploaded on 01/06/2012 for the course BIOL 1406 taught by Professor Markgarcia during the Fall '11 term at Collins.

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