MbShea@PWP@English@UMCP

Day 1 (Monday but I posted on Saturday, August 24). 

Good (soggy) morning.

Do not forget to complete the ER Reviewing Task that is divided between the two trains DUE TONIGHT.  At the point in the semester, please endeavor to respect and support colleagues into managing their schedules. Here is a train song for today! Trixie Smith (1895?-1943), blueswoman, with her Freight Train Blues-->

At the end of class, we will chat about "boomer," which appears in this Trixie rendition and the change from the late 1800s to now. The opening lyrics are:

I was born in Dixie in a boomer shack
Just a little shanty by the railroad track

I want to warm up today, but looking at something I posted recently on a Friday: comic ethos in sci illustration. This three-slide set is simply for your contemplation and enjoyment.

Now, to pick up the Google doc guidance sheet you have see before.  Let's look at a few items today and Wednesday, including numbers in science prose, conventions on titles for wholes (italics) and parts (double quotation marks), etc.  On Wednesday, we will look at dangling modifiers, which are clauses at the beginning of sentences that when read grammatically are wrong and often funny.  

I am seeing lots of empty subjects, like It is/was and There is/are.  Use your search function to avoid these weak constructions that are often at the beginning of sentences and/or main clauses.

Now, onto word choice/word evolution (including de-evolution with some ideas from thoughtful U Michigan dean and English professor/linguist: Anne Curzan.

Kinder, funner?

registers of formality and occasion

code switching/audience accommodation

many Englishes (airplane English, for one!)

More science is written/promulgated globally by non native English speakers than native speakers

Critical thinking v. perfect grammar and diction

December, 2021 Washington Post opinion "Why Words in English Die Out" by Curzan. Link is NOT paywalled if you are on campus technology.

Good morning. 

I will talk about Friday's Eli Review task where I will post TWO DIFFERENT LINKS where you begin your 

• Train Ride to Atlanta, planning to wrap up between the last day of class and the first weekend of finals
• Train Ride to Boulder, planning to wrap up after the first weekend and before/on the last day of finals.

Ok, craft lessons, re Theme and Variations, you have seen before!

BEGINNING with Definitions.  You can consider bullets.  These work well when the concepts are closely related. For example,

Let's review PCR types before we look at Guerro's modifications in her study:  

1. Polymer chain reaction (PCR) tests for....
2. Quantitative PCR (qPRC)...
3. Pyro sequencing ....

The treatment studies for Patel's rice productivity work examine subtle soil pH variability in spring crops typical of terraced fields in SE Asia.  The soil categories, based on surveys of Thailand posted at the UN FAO (Food and Agriculture Organization) data base:

podulized categories 3-8: blah blah....

spodosoil category 6:  blah blah....

hydropodosoils (two)  designed for this experiment but based on FAO emerging research linked here.

More complex definitions might need their own paragraphs. Consider defining what a highly conserved gene is and how that work helps scientists use animals for human disease. Do not forget the idea of bolds, here. However, we can also use nested definitions. Example from my work-->

In my work with farmers and nitrogen scientists, i need to define Q method, which tests subjectivity rather than objectively.  Farmers get this but scientists tend not to. For a short video definition of Q-methods, see this four-minute video and related pages hosted by Q-method expert Tim Deignan. Mb here: curated referal links are an option for your definitions, which are nearly always common knowledge.

Train ATLANTA: Here is our video inspiration from Edward Kennedy, aka Duke, Ellington--> 

We change up this metaphor a bit with the idea that we are traveling to Atlanta, GA, down the East Coast from DC.  A train to Atlanta will arrive at the destination faster than a train to Boulder, CO starting in the same place.

Train BOULDER: Our inspiration now is Emmy Lou Harris-->

Later today, I will send you an ELMS email with dates for both Trains with the associated ER Writing and Reviewing Tasks. And, similarly, I will adjust your ELMS Calendar.

Next up, for craft lesson: Voice to distinguish between researchers work (show cased by you in the body paragraphs) --> USE THIRD PERSON.  Related, in your two analysis tasks (one general; one stats/logos of numbers focused), signal that this is YOU commenting --> USE FIRST PERSON.

Examples you can model after (mentor text is our friend)-->

Postel also sees this genomic study as offering a way to visualize which oncogenes are turned on, likely by environmental factors. (add rest of para)

I see that Postel uses both R-squared and p values to vet some of this genomic analysis.  As a computational biologist, Postel understand the scale-effects of p values that, while low, might be more of an artifact of size rather than a check against randomness.  She speaks about this in a note to Figures 8 and 9, as well as in the analysis section.  I think this means that the R-squared test and associated visuals are a better statistical test for this genomic study.

Pacquin's inference about this study on words that carry emotional import comes from his used of survey instruments from 2018 through 2020.  He excluded 2021 forward in an abundance of caution concerning the pandemic context, which might skew results to the negative.  He ganged three surveys together -- all used same questions -- to test five words......

Survey analysis relies on t-tests and calculation of a critical value. I agree with Pcquin that the one-tailed sample t-test is correct because the identical surveys are ganged together. This test looks at whether the mean (aka average) of data from one group (in this case the differences in identified emotional content) is different from the critical value.  I also noticed that he included within supplementary tables all the ways the five words differed in survey responses by age (quintiles), gender (two variables), and self identified liberalism or conservatism (two variables). The math here involved permutations to yield desired sub categories.  Pacquin discussed primarily.....However, I would be interested in the Q categories and plan to study those datasets more closely.

• Lemon and Pear flow chart, aka the Theme+Variations visual

Newish: text-based guidance/checklist, I have references before(long Google doc but worthy!) But first, let's think about new language for our body points in the document middle.  I give you 

Happy Monday.

DO NOT FORGET MONDAY"S ER Reviewing Task. Doing this on time helps, generally, all your colleagues. You can be especially courtesous to those students in their week of Passover, too.

Let's talk about definitions choices.  One way to manage this helpful background for your reader is to divide the primary or main actor definitions from the secondary or supporting actor definitions. You can arrange these in two waysl. The first way is to use two paragraphs in your cognitive wedge, starting with the primary ones. Then transition to the secondary ones in the next paragraph.  Here is some language in your openings and closing of these linked paragraphs (sharing the job of defining terms for readers):

Before we look at Kaspari's ethnography study, let's review briefly these essential terms:

You can use bullets, if you like; equally fine is a paragraph where you devote a sentence to each definition.

Expert readers in arboriculture may skip or skim these definitions:

Having established key arboriculture terms, let's turn now to method definitions about Kaspari's use of ethnography in this agro-ecology work. 

Ethnography studies typically....

Mixed methods from sociology combines both quantitative and qualitative data sets....

Having described Kaspari's methods that combine rigorous science with thoughtful social science descriptions, we turn to three important take-aways from this innovative 2010 study.

Now you can begin your "thick and rich descriptive" body paragraphs.

A second way to handle these definitions would be to devote one paragraph to the primary or main actor definitions and use nested definitions within the body paragraphs.  To make this work, you should be extremely concise.  And, use appositives as a good technique (introducing short, helpful information, here, definitions).

For example-->

Patel and Shen used pyrosequencing --  detects pyrophosphate release and light generation on nucleotides  -- in their microbiome study of naked mole rats.

For the qualitative data set -- categorical values are qualitative -- Kaspari later used chi-square to assess the presence of a relationship....

Readers will find helpful to recall that chronic wasting disease (a prion "infection") in deer is similar to bovine encephalopathy (aka mad cow disease)....

Both of these definition choices (prefacing paragraphs and nested definitions) are location-dependent. 

• smaller definitions set off by punctuation in an appositive -- think bunny ears, paws, and hind feet.

Now, to analysis paragraphs (the hardest you write, for most). Like definitions, these paragraphs are also location-dependant. You have two choices:

• Using one paragraph, you note one or, say two or three, critique(s) AFTER your three or four body paragraphs. This is the arrangement depicted in the celery flow chart. THINK PEARL NECKLACE; of course, Mb uses a metaphor.
• ANOTHER arrangement is that you locate a critique paragraph in between one or more of your body paragraphs. Make them small paragraphs as a way to signal the critique is not the same as the body paragraphs you are presenting from the research article.  PEARLs with GOLD BEADS. To be specific-->
• 
  
  • small analysis paragraphs between your body paragraphs of cool points -- think gold beads between larger pearls.

Voice helps, too, in analysis.  Use first person in your analysis "moves" aka paragraphs and third person when presenting more generally the points of your author.

We will also look at a Google Doc from an earlier semester where we took on questions the week before the one-article review was due.  Can be instructive, I think.

Ok: how do I critique? You have two strategies that will help you work through this critical thinking. First, most researchers conduct self critique!  See what they say and adapt that "science humility" into your critiqu. Then, you can use language to acknowledge this-->

Bove and Dearborn acknowledge that their experiment may be under powered....

Yu and Feliz, anticipating push back about mixed methods, note the chi squared technique that they also retest with a correction for smaller sample sizes: Fisher's exact t-test   . In the supplemental notes, the authors note an additional test, the Monte Carlo mathematetial approach, that is, a chi-squared test with a simulated p value.

Let's also look at language helpers from the Manchester University Academic Phrasebank and a few other places.  Critique and counter argument for junior scientists is hard.  Having some phrases to prime the pump can be helpful. Here, the pump is your brain.  These sentence starters will help you think critically and write with some confidence.

Wikimedia Common, under Creative Commons license

Manchester University academic writing phrase bank. Look at all these sections:

I will post Friday's Writing Task on Tuesday morning.  To prep for Wednesday, look at the stats or number logos that your authors use.  Read about these tests. Wikipedia is a good start. Review your stats notes. You might search on the term in a resource called Stack Exchange. Here is a link to the statisics-search there.

Morning!

Articles have beginnings, middles, and ends. Think Lemon-shaped. Interestingly, beginnings and ends have similarities. We have a number of options; look at these seven strategies for opening (Google doc based on CAIN, Rice University). Some rough thoughts about formality and audience type:

News article openings are good for the lay audience.  Why?  Several strategies:

• highly visual
• interesting case
• hook with tidbit of interesting information
• topic (timely)

For technical audiences, open with

• review of logos (detail of costs, population size, enormity of problem)
• controversy
• new application or breaking news

We hook the reader at the beginning. Being successful here relies on thinking about our readers. Science and technical readers are not leisure readers! Let's look at this recent article in PloS One about writing scientific prose. In Science, two scientists talk about how they read articles. Ruben writes with a somewhat lighthearted approach while Pain responds to his piece with her approach. Read the comments. Peek into the strategies of technical readers.

Arrangement matters in the IMRAD article. Here is one "bible" of writing (and reading) scientific prose:  Mayfield Guide (open access courtesy of MIT). Now, let's look/review at the basic parts of the IMRAD article using these elements from Mayfield. (Take-away? Your opening will be different from the IMRAD opening but looking at these links will help you improve as a reader): 

• • 3.4.1 Introduction
    • 3.4.1.1 Problem Statement
    • 3.4.1.2 Purpose
    • 3.4.1.3 Scope

(In-class, brief discussion about the ETHOS paragraph.  Please ask or type questions.)

1. If you cannot find a first author author bio, focus on the last author. Let's review the conventions on order in authors. Here is a thoughtful NCBI/NIH article on first author conventions. Two additional resources are this 2010 open access piece at Science and this 2012 Nature short guidance article.
2. You can also rely on the process of peer review and the journal ethos. One way is to consider the journal's impact factor. This is a crude tool and is like a baseball bat driving a safety pin into fabric. 
3. You can look at citations BUT consider the boundaries between scientific publisher ecosystems.
4. Look up article in PubMed (a National Library of Medicine project, part of NIH).
5. For tech/data sci pieces, you can explore the GitHub and/or Stack Exchange activity.
6. Try the last name at Science Daily or Phys.org.

Writing craft lesson on article titles and journal names. Italics sourround article titles, while journal titles are italicized.  as carrying the ethos of peer review. USE ITALICS! Do NOT put the long title of this article in your paragraph.) Let's discuss these two samples, familiar to you from last week-->

Kaspari s work on traditional, plant-based pigments in Romania, "A ethnographic field study approach to farmer accounts of their Morello cherry arboculture: the difference in local cherry liquors begins with horticultral sections stemming from the laste middle ages." This research article appears in the Journal of Food Science. Her 2010 ethnographic study is based on interviews with 250 families in ten villages.  

In a 2010 study on Morello (sour cherry tree) cultivars, ethnographic researcher Kaspari found a number of genetic subtypes,  some in use for hundreds of years.  Appearing in the Journal of Food Science (July, 2012), this ethnographic analysis …..