Thesis Proposal: Finding Literature

1st be “quick and dirty”

- Google- Wikipedia

Later, remember Professor Jacoby

Biological Abstracts Medline/Pubmed

(2013)

(1989)

Pub Medbenzodiazepinesfish

Today: Science Writing

Thurs: Begin Data Unit

October 4: Exam

IMRADWhy talk IMRAD in ISR? …

because it’s incredibly fascinating??

NOT REALLY

But …* ISR IMRAD assignment (today)

* YCP lab reports (IMRAD)

* Senior thesis (IMRAD)

* Reading primary lit (IMRAD)

EcologyBiochemistry Journal

THEYCP

STANDARD- know it- embrace it- use it

Introduction

* most readable section (why ??)

* prose is “light” and accessible

Intros should have a great 1st sentence …

IMRAD

A HOOK

Consider 1st sentences from 2 articles_________________________________________

“Organisms receive a wide range of sensory stimuli from their environment.”

Which is abetter hook?

“The often vivid coloration of coral reef fish has led to many hypotheses including camouflage, aposomatism, and warning coloration (Cott 1940, Neudecker 1989).”

What are the functions of any INTRO??

1) Supply background to help reader

Done via CITING LIT

2) Convey why your research is interesting … and worthwhile

Start with general background information …

… but get more specific and relevant …

… introduce your project

… end with specific hypotheses or objectives

Introductions as Funnels

What we know(Lit Citations)

What we don’t knowGaps

Your Study

Hypothesesor

Objectives

The Hook

Historically, blacks in the United States have had a higher incidence of invasive pneumococcal disease than whites, with the widest disparities occurring among children in the first 2 years of life and among adults 18 to 64 years old.1-3 Introduction of a new protein-polysaccharide pneumococcal conjugate vaccine (Prevnar; Wyeth Lederle Vaccines, Madison, NJ) for young children has led to dramatic declines in invasive disease among children younger than 2 years, as well as declines in incidence amongadults and elderly individuals.4 The impact of vaccination on racial disparities in incidence of pneumococcal disease has not been examined.

In October 2000, the Advisory Committee on Immunization Practices (ACIP) recommended vaccination for all children younger than 2 years and for children aged 2 to 4 years with certain chronic illnesses.5 For newborns, the ACIP recommended 3 doses given at 2, 4, and 6 months of age with a fourth dose given between the ages of 12 and 15 months. Fewer doses were recommended for children who began the series later. For unvaccinated children aged 2 to 4 years with certain chronic conditions, the ACIPrecommended 2 doses given 2 months apart. Among healthy unvaccinated children aged 2 to 4 years, the ACIP recommended a single dose of vaccine, with priority given to children of Alaska Native, American Indian, or African American descent.5 The pneumococcal conjugate vaccine is one of a few vaccines for which certain minority populations have been targeted for priority vaccination and was the first to specifically list children of African American descent as a high-risk group.

Eliminating racial disparities in disease incidence is a main objective set forth in Healthy People 2010.6 The goal of eliminating disparities requires meeting Healthy People 2010targets for pneumococcal disease in all racial and ethnic minority populations. The Healthy People 2010 targets for invasive pneumococcal disease are to reduce incidence to 46 cases per 100 000 children younger than 5 years and to 42 per 100 000 adults aged 65 years or older.6 We measured progress toward these goals using data from the US Centers for Disease Control and Prevention (CDC) Active Bacterial Core surveillance (ABCs) system. This analysis examined the impact of childhood vaccination on disease incidence and pneumococcal serotype

Introduction from JAMA

Hook

general

what we

know

thisstudy

GAP

In this study, we used five regional bone and musclephenotypes, including forearm muscle size, forelimb grip strength, forearm bone mineral density (BMD), forearm bone size, and humerus breaking strength, to evaluate the fundamental relationship between bone and muscle systems and to determine the quantitative effect of these regional phenotypes on bone strength among 10 inbred strains of mice. We hypothesized that other regional phenotypes, such as muscle size and muscle strength, would have a considerable contribution to bone strength in addition to bone size and bone density.

Last Paragraph of an Introduction(funnel bottom)

Methods

2 simple (but profound) goals:

* make it clear how you did what you did

* provide sufficient detail for replication

Methods

Ten 250 mL beakersPerkin Elmer UV spectrophotometerBeckman refrigerated centrifugeFifty 100 gram mice250 g NaClTwo hundred 10 mL test tubes-90O C freezerFisher circulating water bathEppendorf pipettes

NO LISTS OF “MATERIALS”

Number 1 Challenge in writing Methods:

getting the right amount of detail

On January 5 I purchased four paper cups, 400.00 g of potting soil, and 12 radish seeds. I carefully labeled the cups A, B, C, and D and then planted three seeds per cup. A plastic spoon obtained from a local hardware store was used to cover each seed with 4 cm of soil.

METHODS

ROUGH DRAFT

Methods: getting the right amount of detail

Same paragraph … revised

Four 200 mL cups contained 100 mL of potting soil (60% peat/40%vermiculite) and were used to germinate “early boy” radish seeds (Park Seed Co.). Each cup contained three seeds covered by 4 cm of soil.

Methods: getting the right amount of detail

The beauty of “Standard Methods”

“ … Surface water samples were collected near the center of each lake in August 1990. Alkalinity, pH, calcium, magnesium, total hardness, conductance, turbidity, secchi transparency, color, tannic acid, chlorophyll a, total phosphorus, and total nitrogen were measured. All analyses and holding times were in accordance with standard methods in USEPA (1983) and APHA et al. (1985).”

Methods … some properties

-Writing is sparse/precise … no fat

- Verb tense: PAST

- Lit citations important … why?

- Subsections useful/appreciated

Subsections

Verb Tense Guidelines

(with exceptions)

Past Tense Mixed Tense

Abstract IntroductionMethods DiscussionResults

The IMRAD Assignment

Today – Introduction Methods

Oct 20 – ResultsDiscussion

Nov 18 – Full IMRAD resubmission

Due Oct 7

Due Nov 3

Option: Work solo or with a partner

WRITING

Recommendation by Jim Jarvis, MDUniversity of OklahomaCollege of Medicine

“It’s not just foreign-born researchers whose lack of English proficiency hurts their careers. Many Americans have the same problem. Every year, I read grant applications from young (and sometimes rather senior) American scientists who MIGHT actually have good ideas. However, the syntax is so fractured, the flow of ideas so random, and the use of jargon and cliché so pervasive, that I am utterly stymied in my attempts to understand the science.

Advice to Undergrad Science Majors

When undergraduates interested in research ask me about the single most important class they should take, I invariably answer, “a rigorous course in English composition”.”

Peer Reviewer ofGrant Proposals

Professional Writing Minor

- WRT210 Writing in Professional Cultures- WRT225 Interdisciplinary Writing- WRT315 Advanced Composition

plus…

9 elective credits selected from WRT courses beyond 102/202

Some people have a natural gift for writing.

For the rest of us ……….

a) THE WRITING CENTER (bottom of HUM –“Creek” entrance)

b) Peer criticism (seek out tough critics)

c) Willingness to revise (ugh)

1) ACTIVE vs PASSIVE VOICES

We’ve all been taught to write with a passive voice

Why?

Passive voicing seems more scientific

pain in reading science …

too much passive voice

SOME SPECIFICS

EXAMPLES

PASSIVE: Nearly half the seedlings were eaten by woodchucks.

ACTIVE: Woodchucks ate nearly half the seedlings.

PASSIVE: Territory size was found to vary with population density.

ACTIVE: Territory size varied with population density.

PASSIVE: Skin extract solution was presented to the fish through a plastic tube.

ACTIVE: I presented skin extract to the fish through a plastic tube. This is OK

Growth rates are positively correlated with rainfall (Jones 1993, Roy and Smith 1988, Williams et al. 1937).

Voice & Citing Literature

Jones (1993) found that growth rates are positively correlated with rainfall. [active voice]

and others

A positive correlation between growth rates and rainfall was found by Jones (1993). [passive voice]

CONCLUSION

* A mix of active and passive works well

* Active voice should always be considered

* OK to use I/we (don’t over-do!)

2) Resist using literary “devices”

Metaphors “the blue whale plows the sea as it migrates north”

“some males struck out during the mating season”

Similes (using “like” or “as”)

“the precipitate was white as snow”

“the heated test tube glowed like the sun”

resist using …

Idiomatic Expressions (peculiar to a user group)

… after anesthesia, the rat was like dead

… the control and experimental groups were significantly different … how cool is that?

… the enriched diet produced ginormous mice.

… the data in Figure 2 are surprising … lol.

3) The abbreviation problem

(especially cell and molecular biology)

4) The NOUN problem

Long Compound Terms

aka “freight-train phrases”

Strings of adjectival nouns modifying a noun

To write densely, scientists use strings of nouns

EXAMPLE:

……. fish urine sodium content.……. sodium content of fish urine.

……. brain tissue culture response rating.……. response rating of brain tissue culture.

……. female blood thyroxin assay results.……. results of the thyroxin assay of female blood.

5) The Temptation of JARGON

Using technical jargon is an ego booster.

mildly “jargony” phrase preferred term

elucidate explainchemotherapeutic agent drugcausal factor causeconceptualization thoughtterminate endutilize use

It is exceedingly unlikely that you can instill in a superannuated canine the capacity to perform novel feats of legerdemain.

You can’t teach an old dog new tricks.

JARGON!!

THEEND

PLAGIARIZE

(from Webster’s 7th New Collegiate Dictionary)

1)To steal and pass off as one’s own (the ideas or words of another)

2)To present as one’s own an idea or product derived from an existing source.

CITE … THEN PARAPHRASE

Exact wording from Whitehouse and Jaffe (1996)

We found that the combat strategy followed by A. laevigata depends upon the specific threat. Atta laevigata mainly recruited soldiers in response to a mechanical disturbance (simulated vertebrate threat), but recruited predominantly small ants in response to a conspecific threat.

Inadequate paraphrasing:

We found that the combat strategy followed by A. laevigata depends upon the exact threat. Atta laevigataprimarily recruited soldiers in response to a physicaldisturbance (simulated vertebrate threat), but recruited predominantly small ants in response to a conspecific threat (Whitehouse and Jaffe 1996).

BE THOROUGH

Q: Is it OK to cite an article that is discussed in the article that you are citing?

A: NO. Citing an article means you have it and have read it.

Exception: It might be “impossible” to obtain an article cited in an article that you possess.

* extremely old* obscure journal* Schmidt librarians can’t locate it* Document Deliver doesn’t work

If so, cite this way:

………. (Jones 1890 in Anderson 2007).

Bonus Points Offer

Find an article that you would like to have for your thesis proposal but cannot get at Schmidt Library.

Use the Interlibrary Loan service at Schmidt to get the article.

To receive 2 bonus points …

1) Forward to Dr. Rehnberg the email sent to you by the library indicating that your article has arrived.

Some sly and crafty writers do something surprising at the very end of the INTRO ...

They briefly state their results!!

Why do this??

In this study we addressed two questions: (1) Is activation of sucrose-sensitive neurons in the chorda tympani nerve sufficient to increase preference? (2) Do all preferred sucrose-like stimuli activate sucrose-sensitive S fibers in the chorda tympani? Our findingssuggest that preferential ingestion of simple or complex stimuli by hamsters can be controlled by sweetness and that activation of S fibers in the chorda tympani nerve may be sufficient but not necessary for preference for sweet stimuli.

A sedimentary conglomerate in motion down a declivity gains no addition of mossy material.

A rolling stone gathers no moss.

Introduce the Research AreaIdentify the research areaEstablish its importanceProvide essential background

Identify the GAP in knowledge

Fill the GAPIntroduce the current workPreview key findings of current work

CiteLit

general

specific

Modified from Robinson et al. 2010

Another INTRODUCTION Model

Do Copper Jacketed Bullets

Auto-Sterilize When Fired?Department of Biological Sciences

York College of Pennsylvania

Gary Petruzzelli

Barrel Cultured

Bullet Cultured

Bullet Cultured Barrel Cultured

Tract Cultured

3) Fired

Cleaned

Bullet Cultured

Bullet Cultured Barrel Cultured

Tract Cultured

3) Fired

Off Shelf

Bullet Cultured Barrel Cultured

Tract Cultured

3) Fired

Inoculated

2) Bullet Treated

1) Barrel Cleaned

Petruzzelli’s Thesis Flow Chart

Avoid Slang(sometimes subtle)

The controversy over the evolutionary origin of the Ascomycetes and Basidiomycetes dates back almost a hundred years, but it has only recently moved to the cutting edge of research.

Recently, scientists have become more interestedin the evolutionary origin of the Ascomycetes and Basidiomycetes, a topic that has been controversial for almost a hundred years.

3) INTROs should end with a …… ??

Statement of Objectives or Hypotheses orQuestions

Qualityof

Document

Poor

Great

Time Spent RevisingRoughDraft

c) Willingness to revise

Slumbering canines are best left in a recumbent position.

Let sleeping dogs lie.

How do we cite articles from online journals?

Paper journal:Martin, E.P. 1996. Phylogenies, spatial autoregression, and the comparative method: a computer simulation test. Evolution 50:1-14.

Online version of the same journalMartin, E.P. 1996. Phylogenies, spatial autoregression, and the comparative method: a computer simulation test. Evolution [serial online] 50:1-14.