Books Articles amp Online Resources Course Web Site Scientific Writing Books I From Research to Manuscript A Guide to Scientific Writing 2e Michael J Katz Springer New York 2009 ID: 428224
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Slide1
Introduction
Books,
Articles & Online Resources
Course Web SiteSlide2
Scientific
Writing
Books I
From Research to Manuscript: A Guide to Scientific Writing
. 2/e. Michael J. Katz. Springer: New York,
2009
. ($17.95; Amazon, accessed 01/19/10) Slide3
Scientific
Writing
Books II
The ACS Style Guide: Effective Communication of Scientific Information
.
Anne M.
Coghill
and
Lorrin
R. Garson. American Chemical Society: Washington, D.C.,
2006
. ($37.99; Amazon, accessed 01/19/10) Slide4
Scientific
Writing
Books III
Write Like a Chemist: A Guide and Resource.
Marin S. Robinson,
Fredricka
L.
Stoller
, Molly
Costanza
-Robinson, and James K. Jones. Oxford University Press, USA: New York,
2008
. (Paperback: $44.04; Hardcover: $119.38; Amazon, accessed 01/19/10). Slide5
Scientific
Writing
Books IV
SCIENCE RESEARCH WRITING FOR NON-NATIVE SPEAKERS OF ENGLISH, by Hilary
Glasman
-Deal (Imperial College London, UK)Slide6
Scientific Writing: Articles I
Posted at course web site!Slide7
Scientific Writing: Articles II
Posted at course web siteSlide8
Chapter 1
Mind-Mapping & Outlining
Science’s Standard Sequence (SSS)Slide9
Outlining: Mind Mapping ISlide10
Outlining: Mind Mapping II
http://archaea.ucsc.edu/Archaea-23S-tree-Mar07.gifSlide11
Outlining:
Mind
Mapping III
http://www.nature.com/nrmicro/journal/v3/n6/images/nrmicro1159-f1.gifSlide12
Outlining: Mind Mapping IVSlide13
Outlining: Mind Mapping VSlide14
Outlining: Mind Mapping VISlide15
Outlining: Lists ISlide16
Outlining: Lists II
http://livedocs.adobe.com/en_US/InDesign/5.0/images/op_42.png
Numbered Lists
Bulleted Lists
Alphabetic ListsSlide17
Outlining: Lists III
In WordSlide18
Outlining: Lists IV
In WordSlide19
Outlining: Lists V
In WordSlide20
Stereotyped Format
Title 5. Be thoughtful.
Abstract 6. Last item.
Introduction -- As you progress. Materials & Methods 1. Start here!Results 2. What done? How?
Discussion 3. Explain, examine.
Conclusion 4. Think hard!
References -- As you progress.
Here, that’s
a good thing!Slide21
Der Rote Faden
The recurrent theme…
The central theme…
…should be evident in EVERY part of the paper.
What is this about?Slide22
Chapter 1
Words, Numbers & NamesSlide23
Desiderata
Descriptions must be
precise.
Try to be objective.Procedures must be
complete
.
Data must be
exact
(or error bars given).
Logic must be
transparent
.
Conclusions must be
clear & concise (“clean”)
.
Do not leave anything to the reader’s imagination.
I try to leave out the parts that people skip. Elmore LeonardSlide24
Straightforward Message
It may therefore not be unexpected…
These results suggest…
The catalyst probably acts to increase…The catalyst probably increases…
Make your statements explicit. Contrast clearly.
In contrast to the hypothesis by X, we conclude…Slide25
Avoid Vagueness
Avoid relative terms
such as: a lot, somewhat,…
Use “very” very rarely.Avoid emotional judgments such as: beautiful, disappointing, miraculously,… (BUT some of these terms are fine as rhetorical devices, i.e., certainly, of course,
remarkable, obviously,…)
Avoid “filler words”
such as: indeed, in fact, in a sense… (BUT some of these terms are fine as rhetorical devices,
Avoid casual language
such as: bottom line, seat of the pants, cutting edge, …Slide26
Write with Precision: Numbers
Use numbers!
Not “tall”, but “greater than 2 meters”
Not “heavy”, but “greater than 10 kg”Not “brief”, but “less than 1 millisecond”
Use criteria-based scales.
Grade Scale, performance.
Richter Scale, earthquakes.
Mankoski
Scale, pain.Slide27
Numbers II: Richter Scale
The Richter magnitude of an earthquake is determined from the logarithm of the amplitude of waves recorded by seismographs.
A measured number with defined consequences.
Slide28
Numbers III:
Mankoski
Pain Scale
Andrea Mankoski Pain Scale (1995) Numbers characterize well-defined and distinguishable consequence of subjective property.
0 - Pain Free
1 - Very minor annoyance - occasional minor twinges. No medication needed.
2 - Minor Annoyance - occasional strong twinges. No medication needed.
3 - Annoying enough to be distracting. Mild painkillers take care of it. (Aspirin, Ibuprofen.)
4 - Can be ignored if you are really involved in your work, but still distracting. Mild painkillers remove pain for 3-4 hours.
5 - Can't be ignored for more than 30 minutes. Mild painkillers ameliorate pain for 3-4 hours.
6 - Can't be ignored for any length of time, but you can still go to work and participate in social activities. Stronger painkillers (Codeine, narcotics) reduce pain for 3-4 hours.
7 - Makes it difficult to concentrate, interferes with sleep. You can still function with effort. Stronger painkillers are only partially effective.
8 - Physical activity severely limited. You can read and converse with effort. Nausea and dizziness set in as factors of pain.
9 - Unable to speak. Crying out or moaning uncontrollably - near delirium.
10 - Unconscious. Pain makes you pass out.Slide29
Numbers IV: Wong-Baker Scale
Wong-Baker Faces Pain Rating Scale (1995)
Numbers characterize well-defined and distinguishable consequence of subjective property.
Face 0 is very happy because he or she doesn’t hurt at all.
Face 1 hurts just a little bit.
Face 2 hurts a little more.
Face 3 hurts even more.
Face 4 hurts a whole lot.
Face 5 hurts as much as you can imagine, although you don’t have to be crying to feel this bad.Slide30
Write with Precision: Names I
Trivial name.
Example: aspirin
Systematic name. Example: acetylsalicylic acid Be aware of synonyms.
Examples:
Rhodine
(7CI); Salicylic acid acetate (8CI); 2-(Acetyloxy)benzoic acid; 2-Acetoxybenzoic acid; 2-Carboxyphenyl acetate; A.S.A.
Empirin
; AC 5230; ASA;
Acenterine
;
Acesal
;
Acesan
;
Acetard
;
Aceticyl
;
Acetilum
acidulatum
;
Acetisal
;
Acetol
;
Acetonyl
;
Acetophen
;
Acetosal
;
Acetosalic
acid;
Acetosalin
;
Acetylin
;
Acetylsal
; Acetylsalicylic acid;
Acetyonyl
;
Acetysal
;
Acidum
acetylsalicylicum
;
Acimetten
;
Acisal
;
Acylpyrin
;
Adiro
;
Albyl
E;
Asaflow
;
Asagran
;
Asatard
;
Ascoden
30;
Ascolong
;
Ascriptin
;
Aspalon
;
Aspergum
;
Aspirdrops
; Aspirin; Aspirin Protect 100; Aspirin Protect 300; Aspirin-
Direkt
;
Aspirina
03;
Aspro
;
Aspro
Clear;
Aspropharm
;
Asteric
;
Astrix
; Bayer;
Benaspir
; Bialpirina; Bialpirinia; Caprin; Cardioaspirin; Cardioaspirina; Claradin; Colfarit; Colsprin; Contrheuma Retard; Coricidin; Coricidin D; Crystar; Darvon Compound; Dolean pH 8; Dominal; Doril; Duramax; ECM; Easprin; Ecosprin; Ecotrin; Empirin; Endosprin; Endydol; Entericin; Enterophen; Enterosarine; Entrophen; Ewin; Extren; Gelprin; Globentyl; Globoid; Helicon; Idragin; Istopirin; Kapsazal; Lysoprin (pharmaceutical); Magnecyl; Measurin; Medisyl; Melhoral; Micristin; Miniasal; Mycropyrin; NSC 27223; NSC 406186; Neuronika; Novid; Nu-seals; O-Acetylsalicylic acid; Persistin; Polopiryna; Rheumintabletten; Rhodine 2312; Rhodine NC RP; Rhonal; SP 189; Salacetin; Salcetogen; Saletin; Salospir; Salycylacetylsalicylic acid; Solpyron; Supac; Temperal; Toldex; Triple-sal; Trombyl; Xaxa; Yasta; Zorprin; o-(Acetyloxy)benzoic acid; o-Acetoxybenzoic acid; o-Carboxyphenyl acetate
Use Correct NamesSlide31
Names II: Abbreviate / Number
Abbreviations, common. Example: DMSO, aspirin.
Abbreviations, defined by you.
Numbers, defined by you.
Names of chemicals often are long! Often not well-defined either.
Dioxygen
Activation under Ambient Conditions: Cu-Catalyzed Oxidative
Amidation−Diketonization
of Terminal Alkynes Leading to
α-Ketoamides
. Chun Zhang and
Ning
Jiao
J. Am. Chem. Soc.
2010
,
132
, 28-29.Slide32
Names III: IUPACSlide33
Past and Present Tense
Use
PRESENT TENSE for statements which are true now (and have been true in the past as well):
Life is good. Clouds contain water. Everything is made out of atoms.
Use
PAST TENSE
to describe events that have occurred in the past and are no longer happening:
The experiment was performed.
The catalyst was added.Slide34
Use Dictionaries Frequently
ex·e·cu·tion
1.
a.
The act of executing something.
b.
The state of being executed.
2.
The manner, style, or result of performance:
The plan was sound; its execution, faulty.
3.
The act or an instance of putting to death or being put to death as a lawful penalty.
4.
Law
a.
The carrying into effect of a court judgment.
b.
A writ empowering an officer to enforce a judgment.
c.
Validation of a legal document by the performance of all necessary formalities.Slide35Slide36
Chapter 1
Writing a ParagraphSlide37
How to Write Text
Examples & Assignment
Lecture Example:
Aspirin
Textbook Example: Section 2.2
Assignment #1: Handout and online.Slide38Slide39Slide40
How to Write Text I:
Rough Paragraphs
Skeletal Outline
Pile in Ideas
Collect Information from Outside Resources
Form Rough Sentences
Arrange Sentences into Themes (
Temp. Theme Label
)
Turn Lists into Rough Paragraphs
Slide41
Rough §
s
1. Skeletal Outline
Working Title: Aspirin Analogs in Medicine(Heading 1) Introduction (Heading 2) A. General History of Painkillers
(Heading 2) B. General History of Aspirin
(we’ll work on this!)
(Heading 2) C. General History of Aspirin Analogs
(Heading 1) Materials & Methods
(Heading 1) Results
(Heading 1) Discussion
(Heading 1) Conclusion
(Heading 1) ReferencesSlide42
Rough §
s
2. Pile in Initial Ideas
Working Title: Aspirin Analogs in Medicine(Heading 1) Introduction (Heading 2) A. General History of Painkillers
(Heading 2) B. General History of Aspirin
White Tablets
Made by Bayer
Pain Reliever, Painkiller
Antipyretic (lowers fever)
COX Inhibitor
Write a list of
“initial keywords”.
“Initial ideas” provide keywords for your search for information.
1. Brainstorm and list “initial keywords”Slide43
Rough §
s
3. Get Information
Ref. A. Aspirin and Other Non-Steroidal Anti-Inflammatory Drugs as Cyclooxygenase
State of the Art, Barriers and Perspectives.
Avram
, S.;
Duda-Seiman
, D. M.;
Svab
, I.;
Mancas
, S.;
Duda-Seiman
, C.;
Mihailescu
, D. F.
Current Computer-Aided Drug Design
2009
,
5
, 1-12.
Ref. B.
Mechanistic Insights into
Cyclooxygenase
Irreversible Inactivation by Aspirin.
Tosco, P.;
Lazzarato
, L.
ChemMedChem
2009
,
4
, 939-945.
Ref. C.
Aspirin. An
ab
Initio Quantum-Mechanical Study of Conformational Preferences and of Neighboring Group Interactions
. Glaser, R.
J. Org. Chem.
2001,
66,
771-779.
Ref. D.
Synthesis of aspirin : a general chemistry experiment.
Olmsted, John, III
J. Chem. Educ.
1998
,
75
, 1261-1263.
2. Search using “initial keywords”
(We will learn later about “searching”.)Slide44
Rough §
s
3. Study Information
Ref. D. Synthesis of aspirin : a general chemistry experiment. Olmsted, John, III
J. Chem. Educ.
1998
,
75
, 1261-1263.
-- synthesis of aspirin from “oil of wintergreen”
-- two-step reaction, hydrolysis and condensation
-- “oil of wintergreen” is the methyl ester of 2-hydroxybenzoic acid
-- salicylic acid is a synonym of 2-hydroxybenzoic acid
--
acetylation
of salicylic acid with acetic acid anhydride
3. Survey & Study!
Make lists.
Look for key ideas.
Look for leading themes.
Make rough schemes.
Learn the vocabulary!Slide45
Rough §
s
3. Study Information
Ref. C. Aspirin. An ab
Initio Quantum-Mechanical Study of Conformational Preferences and of Neighboring Group Interactions
. Glaser, R.
J. Org. Chem.
2001,
66,
771-779.
-- acetylsalicylic acid is a pro-drug
-- converted into salicylic acid
-- aspirin X-ray structure determined
-- aspirin conformations studied
3. Survey & Study!
Make lists.
Look for key ideas.
Look for leading themes.
Make rough schemes.
Learn the vocabulary!Slide46
Rough §
s
3. Study Information
Ref. B. Mechanistic Insights into Cyclooxygenase
Irreversible Inactivation by Aspirin.
Tosco, P.;
Lazzarato
, L.
ChemMedChem
2009
,
4
, 939-945.
-- aspirin is an NSAID, non-steroidal anti-inflammatory drug
--
cyclooxygenase
(COX) inhibitor
-- aspirin inhibits COX-1 and COX-2
--
acylation
of Ser530
-- aspirin covalently modifies COX
Slide47
Rough §
s
4. Rough Sentences
Ref. B.-- Aspirin is a non-steroidal anti-inflammatory drug (NSAID).
-- Aspirin inhibits both
isoforms
of
cyclooxygenase
.
--
Bromoacetylsalicyclic
acid covalently modifies COX-1 and COX-2 by
acylation
of Ser530.
Ref. C
.
-- Acetylsalicylic functions as a pro-drug for salicylic acid.
-- The structure of aspirin has been studied with experimental and theoretical methods.
Ref. D
-- Aspirin is made by
acetylation
of salicylic acid (2-hydroxybenzoic acid).
4. Collect & Gather.Slide48
Rough §
s
5. Create TTL
Ref. B.-- Aspirin is a
non-steroidal anti-inflammatory drug
(NSAID).
-- Aspirin inhibits both
isoforms
of
cyclooxygenase
.
--
Bromoacetylsalicyclic
acid covalently modifies COX-1 and COX-2 by
acylation
of Ser530.
(
Transesterification
!)
Ref. C
.
-- Acetylsalicylic functions as a pro-drug for
salicylic acid
.
-- The structure of aspirin has been studied with experimental and theoretical methods.
Ref. D
-- Aspirin is made by
acetylation
of salicylic acid (2-hydroxybenzoic acid).
5. Create TTL = Temporary Theme Label
Think of
TTLs
as the
true
keywords!
Are there steroidal
anti-inflammatory drugs?
What does COX
have to do with pain?
Why
acetylation
?Slide49
Rough §
s
6. Rough Paragraphs
-- Aspirin is a non-steroidal anti-inflammatory drug (NSAID) [
Ref. B
]
-- Aspirin inhibits both
isoforms
of
cyclooxygenase
. [
Ref. B
]
--
Bromoacetylsalicyclic
acid covalently modifies COX-1 and COX-2 by
acylation
of Ser530. [
Ref. B
]
-- Acetylsalicylic functions as a pro-drug for
salicylic acid
. [
Ref. C
]
-- The structure of aspirin has been studied with experimental and theoretical methods. [
Ref. C
]
-- Aspirin is made by
acetylation
of salicylic acid (2-hydroxybenzoic acid). [
Ref. D
]
7. Construct the logical flow and rearrange rough sentences accordingly.
6. Source-to-Reference Inversion!Slide50
How to Write Text II:
Working Draft
Deconstruct, clean up, reassemble sentences.
Reexamine the sequential ordering.Reassemble paragraphs.Smooth transitions.
Polish.
Revise. Revise. Revise. Slide51
Source-to-Reference Inversion
Initially: Type the source in the body of your file
Ref. B.
Mechanistic Insights into Cyclooxygenase Irreversible Inactivation by Aspirin.
Tosco, P.;
Lazzarato
, L.
ChemMedChem
2009
,
4
, 939-945.
-- aspirin is an NSAID, non-steroidal anti-inflammatory drug
--
cyclooxygenase
(COX) inhibitor
-- aspirin inhibits COX-1 and COX-2
--
acylation
of Ser530
-- aspirin covalently modifies COX
SRI-1: Create an ENDNOTE at the END OF DOCUMENT
SRI-2: Copy the SOURCE to the ENDNOTE (format now or later)
SRI-3: Insert CROSS-REFERENCE CITATIONS MARKS (as needed)Slide52
SRI-1: Create Endnote
Place cursor here!Slide53
SRI-1: Create Endnote
Endnote!
Then press
“Options…”Slide54
SRI-1: Endnote Mark Inserted
Note that the
reference citation appears.
Endnote section appears. Slide55
SRI-2: Move Source to Endnote Slide56
SRI-3: Insert Cross-Reference Mark
Place cursor here!Slide57
SRI-3: Insert Cross-Reference MarkSlide58
SRI-3: Insert Cross-Reference Mark
Formatted the inserted CR mark to appear as superscript.