Managing the Flow of
Information in Scientific
Writing
1 April 2015
Scientific writing is bad writing.
Characters and actions
Once upon a time....
SO: Choose a manageable
set of characters, and stick
with them.
In fact, don’t just stick with them: use them to organize and control the flow of
information in your sentences and at the paragraph level.
In fact, don’t just stick with them: use them to organize and control the flow of
information in your sentences and at the paragraph level.
Some terminology: all sentences contain a topic position and
a stress position. They’re unmoveable, and they do precisely
what their names suggest: the first states your topic, and the
second contains the info you want to stress. (This is generally
info that is unfamiliar to your reader: it’s almost always best to
move from familiar to unfamiliar.)
Topic position
All sentences contain
Stress position
a topic position and a stress
position.
In fact, don’t just stick with them: use them to organize and control the flow of
information in your sentences and at the paragraph level. Your character should
almost always appear in the topic position, so that your reader has something
familiar to orient herself.
Topic position
All sentences contain
Stress position
a topic position and a stress
position.
In this presentation (so far), sentences have been my main
character, so it makes sense that “all sentences” would be in
the topic position here.
An Astro-ph example: “On Detecting Biospheres from
Thermodynamic Disequilibrium in Planetary Atmospheres”
Atmospheric chemical disequilibrium has been proposed as a method for detecting extraterrestrial biospheres from exoplanet
observations. Chemical disequilibrium is potentially a generalized biosignature since it makes no assumptions about particular
biogenic gases or metabolisms. Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium
in the atmospheres of Solar System planets, in which we quantify the difference in Gibbs free energy of an observed
atmosphere compared to that of all the atmospheric gases reacted to equilibrium. The purely gas phase disequilibrium in
Earth's atmosphere, as measured by this available Gibbs free energy, is not unusual by Solar System standards and smaller
than that of Mars. However, Earth's atmosphere is in contact with a surface ocean, which means that gases can react with
water, and so a multiphase calculation that includes aqueous species is required. We find that the disequilibrium in Earth's
atmosphere-ocean system (in joules per mole of atmosphere) ranges from ~20 to 2E6 times larger than the disequilibria of
other atmospheres in the Solar System depending on the celestial body being compared. Disequilibrium in other Solar System
atmospheres is driven by abiotic processes, and we identify the key disequilibria in each atmosphere. Earth's thermodynamic
disequilibrium is biogenic in origin, and the main contribution is the coexistence of N2, O2 and liquid water instead of more
stable nitrate. In comparison, the disequilibrium between O2 and methane constitutes a negligible contribution to Earth's
disequilibrium with this metric. Our metric requires minimal assumptions and could potentially be calculated using observations
of exoplanet atmospheres. Our Matlab source code and associated databases for these calculations are available as open
source software.
An Astro-ph example: “On Detecting Biospheres from
Thermodynamic Disequilibrium in Planetary Atmospheres”
This abstract contains four main characters (and their variants):
●
●
●
●
Atmospheric chemical disequilibrium
Earth’s atmosphere
Disequilibrium in earth’s atmosphere
The group’s metrics and software
An Astro-ph example: “On Detecting Biospheres from
Thermodynamic Disequilibrium in Planetary Atmospheres”
Atmospheric chemical disequilibrium has been proposed as a method for detecting extraterrestrial biospheres from exoplanet
observations. Chemical disequilibrium is potentially a generalized biosignature since it makes no assumptions about particular
biogenic gases or metabolisms. Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium
in the atmospheres of Solar System planets, in which we quantify the difference in Gibbs free energy of an observed
atmosphere compared to that of all the atmospheric gases reacted to equilibrium. The purely gas phase disequilibrium in
Earth's atmosphere, as measured by this available Gibbs free energy, is not unusual by Solar System standards and smaller
than that of Mars. However, Earth's atmosphere is in contact with a surface ocean, which means that gases can react with
water, and so a multiphase calculation that includes aqueous species is required. We find that the disequilibrium in Earth's
atmosphere-ocean system (in joules per mole of atmosphere) ranges from ~20 to 2E6 times larger than the disequilibria of
other atmospheres in the Solar System depending on the celestial body being compared. Disequilibrium in other Solar System
atmospheres is driven by abiotic processes, and we identify the key disequilibria in each atmosphere. Earth's thermodynamic
disequilibrium is biogenic in origin, and the main contribution is the coexistence of N2, O2 and liquid water instead of more
stable nitrate. In comparison, the disequilibrium between O2 and methane constitutes a negligible contribution to Earth's
disequilibrium with this metric. Our metric requires minimal assumptions and could potentially be calculated using observations
of exoplanet atmospheres. Our Matlab source code and associated databases for these calculations are available as open
source software.
An Astro-ph example: “On Detecting Biospheres from
Thermodynamic Disequilibrium in Planetary Atmospheres”
Each of the sentences in this abstract contains one of the main characters in the
topic positions, and uses that character to introduce new material in the stress
position:
An Astro-ph example: “On Detecting Biospheres from
Thermodynamic Disequilibrium in Planetary Atmospheres”
Atmospheric chemical disequilibrium has been proposed…
Chemical disequilibrium is…
Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium... in which we
quantify the difference in Gibbs free energy of an observed atmosphere.
The purely gas phase disequilibrium in Earth's atmosphere…
However, Earth's atmosphere is in contact…
We find that the disequilibrium in Earth's atmosphere-ocean system…
Disequilibrium in other Solar System atmospheres is driven…
we identify the key disequilibria in each atmosphere…
Earth's thermodynamic disequilibrium is biogenic…
In comparison, the disequilibrium between O2 and methane constitutes a negligible contribution to Earth's
disequilibrium with this metric.
Our metric requires minimal assumptions…
Our Matlab source code and associated databases for these calculations are available as open source
software.
From sentence to paragraph: topic strings
Topic strings help you organize old and new information at the level of
paragraphs. There are *three types of topic strings:
Focused topic strings: Use the same character in the topic position of
several consecutive sentences. These are effective for defining or
characterizing a concept, but can become tedious if used too
consistently.
Chained topic strings: Move the information in the stress position of
one sentence to the topic position of the next sentence. Chained topic
strings let you cover a lot of information quickly, but if used for too many
consecutive sentences, may threaten to lose your reader.
Mixed topic strings: Combine these two.
*A paragraph can also have incoherent topic strings, in which there is no discernible organization among topics. As
“incoherent” implies, this makes for difficult reading.
From sentence to paragraph: topic strings
Focused topic strings (use the same character in the topic position of
several consecutive sentences):
Atmospheric chemical disequilibrium has been proposed…
Chemical disequilibrium is…
Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium... in
which we quantify the difference in Gibbs free energy of an observed atmosphere.
The purely gas phase disequilibrium in Earth's atmosphere…
From sentence to paragraph: topic strings
Chained topic strings (move the information in the stress position of one
sentence to the topic position of the next sentence):
Here, we present the first rigorous calculations of the thermodynamic chemical disequilibrium in the atmospheres of Solar
System planets, in which we quantify the difference in Gibbs free energy of an observed atmosphere compared to that of all
the atmospheric gases reacted to equilibrium. The purely gas phase disequilibrium in Earth's atmosphere, as measured by
this available Gibbs free energy, is not unusual by Solar System standards and smaller than that of Mars. However, Earth's
atmosphere is in contact with a surface ocean, which means that gases can react with water, and so a multiphase calculation
that includes aqueous species is required. We find that the disequilibrium in Earth's atmosphere-ocean system (in joules per
mole of atmosphere) ranges from ~20 to 2E6 times larger than the disequilibria of other atmospheres in the Solar System
depending on the celestial body being compared.
Topic position
Stress position
calculations of the thermodynamic disequilibrium
observed atmosphere (Earth’s)
gas phase disequilibrium in Earth’s atmosphere
is not unusual
Earth’s atmosphere
Earth’s atmosphere ocean system
disequilibrium in Earth’s atmosphere ocean system
From sentence to paragraph: topic strings
Mixed topic strings (combine these two):
Character 1
Character 1
Character 1 is related to character 2. Character 2
Character 2
Character 2 introduces Character 3
Character 3…
Concluding sentence that recaps the relationship between Character 1, 2,
and 3, or collapses the middle term and posits a direct relationship between
character 1 and character 3