MbShea@PWP@English@UMCP

Good morning.  Sunny and somewhat warm, with chance of rain on Wednesday; then, Thursday promises to be chilly. COMPLETE YOUR ER REVIEWING TASK TONIGHT!

Where are we going? We're off to see the wizard, the wonderful wizard of Oz.  But, we have some lions and tigers and bears, oh my, left. 

Let the lions be your body paragraphs.  These are hard.  I am glad to see that most of you are wrestling with that content. Now, the next risk to vanquish-->

Let the tiger (no s, is one paragraph!) be your stats paragraph, which is a combination of you reporting what stats vetting used by your researcher AND your commentary.

Let the bear(s) be your critique paragraph. I ask you to write at least ONE comment (why the bear might be plural) where you critique the findings of your researcher.  Hint: they typcially self critique and you can report that.

You can see that we focus on the end of your review.  Therefore, do a self-check: does your review document look like a lemon? Does the reader slide off through your critique into a few, closely related conclusory ideas?

Does your document look more like a pear? Here, the reader moves through your critique into several caveats about conclusions, complexity about conclusions, policy context etc.

Hint: most people will rely on the lemon shape, as we offer two analysis paragraphs -- stats and generall critique -- then your conclusion paragraph. The order of the stats and general critique are your choice.

Good news:  I do not GRADE THE CONTENT OF YOUR STATS PARA.  Aren't you relieved?

Now, onto the hardest analysis piece: evaluating the statistics used to vet the arguments made about data inference. Statistics overview in class this week.  I urge you to talk about statistics/logos critical thinking with your science and math professors.  To warm up, the ManU Phrasebank includes a "Describe quantities" section. Then, check out the "Reporting results" section, which will help your read your paper's use of statistics or number logos.

You will get better in the future about this critical thinking as you mature as a scientist: Promise! For example, in my field of ecology and environmental science, we are in a quiet riot over frequentist, mutivariate, and Bayesian statistics.  This was an assigned reading for me, in one of my classes. Here is another.

For biomedical researchers, you may appreciate this analysis of the limits of p-values in biomedial research.

Please look at your research articles for Wednesday, noting the type of statistics tool/logos of numbers  (web exhibit with short definitions) used.  Look these up in some way to have a working definition for yourself.  Common tools or tests from student papers over the last 15 years include:

• p-values
• confidence intervals
• Student's t test (and corrections)
• analysis of variance (ANOVA); one-tail, two-tail
• power
• sample size
• type of study/limits -- observational study, case note, double-blind

I recommend using the link above to warm up your brain with a short working definition (remember this critical analysis tool from the rain garden memo?) and then go to Wikipedia or even a text book to read about your selected term(s) for more detail. 

The pre-reading activity will help you enter into the complexity.  Cognitive wedge is also your thinking friend.

I simply want you to know about this area within science articles, even if you do not understand now the statistics. You would not be alone among scientists, if you don't.  I don't, in many cases.  However, I want you to leave this class with an understanding of this important piece of critical thinking for your field. 

One key idea I can wax on about, though, is cautions about the (very limited) definition of significance testing and p-values.  For fun, enjoy this comic.

More generally, your critical analysis can comment on findings, your ideas or your close reading the author critique.  The Manchester University phrasebank is really helpful.  Here are a few selections that I copy/paste here for you. From the "Being critical" section, see these categories-->

We are now mining the complex document for your three points (to make the "fat portion of your review), as well as looking at how to analyse/critique the work (including some stats vetting), and how to close.

First up is Lennart Nacke's useful image of a research article (some of you will need to modify this model to your narrow focus article). I have annotated this visual with some of my approach. Is large/placed in thumbnail form so either click in or open in another browser tab. 

Here is a resource/checklist/gathering spot for Assignment 3. Here, I try to curate the "best hits" of what we talk about, what I place in our class journal.  You may want to look now as you plan how to wrap up the semester.  Please note, that I am planning two paths to finish up:

The A-train to Atlanta (as in first not the grade) to wrap up close to the last day of class (with a parking lot strategy, as ever); AND

The B-train to Boulder (as in second not the grade) to wrap up closer to the end of finals (with a parking lot strategy but shorter).

What this means is that students riding the Boulder train with have one additional ER opportunity to give and receive feedback.

Let's chain back to Week 9 and revisit the "that and which distinction" writing craft lesson. Now, a shorter version of the that-which distinction with science-context samples. Remember: you can always punctuate this correctly. (perhaps a song)

We can also revisit empty subjects.  Why?  I want you to practice this cognitive grammar technique in Assignment 3.  Basically, do NOT USE IT and do NOT USE THERE IS/ARE in your final assignment.  This is a concerted drill on my part to show you how to use other options.  These options are nearly always clearer for the reader, especially in complex prose.

, which was not a healthy situation for the wicked witch

Hello there. (Wrapping up grading/reflecting on the coffee cup memos.  Thank you!).  I want to reflect quickly on a teaching approach that you can use at work and your personal future.  Do not use a deficit model.  Google's AI (cringing a bit about doing this) says (11/4/24):

The deficit model in education is a theory that students' academic performance is due to their own internal deficiencies, rather than the school's structure or other factors. The model assumes that students lack skills, knowledge, or experience, and that the teacher's role is to provide the missing knowledge. 

 

The deficit model can lead to teachers assuming that students are lazy, unmotivated, or underprepared. It can also lead to low expectations for students, and students may not be set up for real-world success. 

 

A more inclusive approach is the asset model, also known as the strengths-based approach. This model focuses on what students already know and their strengths, and can help students feel a sense of belonging and be motivated to succeed. 

Spitballing on the CAIN seven openings:

1. Tell a short story/be visual and clear about characters and actions.
   1. Case that is real (patient)
   2. Composite case that you reveal as not real but highly plausible
   3. Use a widely know lit/media event
2. Use a current event.
   1. Professional meeting
   2. Political event
   3. Cultural event/phenom
3. Capture the size of the problem (very large but sometimes very small works too).
   1. Rate of illness in a population (like diabetes or COVID infection numbers)
   2. Number of Goldilocks planets
   3. Depth of sea flow and number of heat vents
   4. Estimates of insects globally
   5. Financial cost of cod fishery collapse.
4. Open with huge social problem, perhaps a wicked problem.
   1. Can geo-engineering address carbon capture in practical, short-term ways?
   2. Drones may play a role in distributing vaccines in remote areas.
5. Use a smaller question to open a document.
   1. Does ultra high resolution mammography improve the problem of false positives in breast cancer diagnosis?
   2. Can Josh Silver's 2009 TED talk on spectacles be scaled in Amazonia?
6. Quote a respected thinking, related to your problem/research question.
   1. Pick someone you admire.  I suggest looking at Nobel Prize speeches but also the annual cohorts of MacArthur genius winners.
      1. “The power of a theory is exactly proportional to the diversity of situations it can explain.”
         ― Elinor Ostrom, Governing the Commons: The Evolution of Institutions for Collective Action.
      2. ‘As birds form flocks and ants carry food to nests using bottom-up principles of communication and collective action, people can solve their own problems.’
      – Ruth DeFries, 2020. What Would Nature Do?
7. Use statistics (related to number 3).
   1. Protein folding operations are very small and very fast. For example,  very small single-domain proteins ( up to a hundred amino acids) typically fold in one  step. 
   2. Time scales for protein folding are typically at the millisecond level. Indeed, the very fastest known protein folding reactions conclude with one to five microseconds.

How does this help you write paragraphs now?  Try writing am opening paragraph using two of these strategies -- all the while honoring the cognitive wedge. Now, try using those strategies -- with some of the excitement (pathos) about why the article is important -- to close your document.  You can revise later but let's get in there and play ball!

Next paragraph that is very easy to work in concerns establishing the ethos of your first (and perhaps last) author.  Huzzah, we can do this (did with Davis and with either Moore or Hocking). In an author-ethos paragraph (within the first three paragraphs/on the ramp of the cognitive wedge),

• give expertise/specialization and 
• both the PhD/MD or other degree-granting institution AND the current institutional affiliation.

Caution: Do not focus overmuch on undergraduate study.  Note:  PhD are earned, rather than obtained. Sample-->

Kaspari earned a PhD in pharmacognition from the University of Illinois.  He leads an interdisciplinary team at Wexler Institute of Plant Based Technology, which is part of the University of California at Berkeley Plant Science Department.

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.

Tonight PLEASE complete your ER REVIEWING TASK. Help each other move the knowledge and document forward. Be afraid. Very afraid. Comply!

Chilly Monday.  Halloween is Thursday.  Will start grading your coffee cup memos today.  Been reading them, with such pleasure as I prep my responding outline.  

I will post a this week's ER WRITING TASK early Tuesday AM: to ELMS mail and to your ELMS calendar.  You cannot complete this task without having an article.  You MUST HAVE AN ARTICLE NOW (from ealier: copy/download to track your reading)! These shapes guide our work. Can you see the cognitive wedge at the stem end of each fruit?  

What is a research article, anyway?  We will work through this 39 slide Google Presentation.  I am reposting some material from earlier that I provided for context.  I urge you to skim read these links.  You will gain some knowledge that will help you in other classes, in laboratory settings, and your professional future.

Getting clear on technical, scientific prose (in contrast to literature): Let's look at this recent article in PloS One about writing scientific prose (ten step format). Here is a PloS follow-up about writing your first research article. 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.

Writing resources are also reading resources! Here is the open acess "bible" of writing (and reading) scientific prose:  Mayfield Guide. Now, let's look/review at the basic parts of the IMRAD article using this guide. BTW, this book is hosted by MIT.  I follow the MIT ethical practice of teaching openly, so that knowledge is available to all and not just tuition paying students.

As given earlier, a flow-diagram to help you. Open in a new link. Save in a draft document! The lemon and pear document shapes appear here, too.

Happy Monday.  Here is a novel concept for the coffee cup problem by Sardi Design for an Italian coffee company, Lavazza. Is this for real or just an idea meant to shake up our thinking a bit?

Tonight, you have an ER REVIEWING TASK due. A few of you have a Google doc work around to use.  Please be on time for each other.  I will open a parking lot for the to-be-graded coffee cup memo likely early Tuesday AM. You will have a week, as per practice for the rain garden memo.  Be on time for each other.  Take the week for yourself as needed to turn in the memo for a grade. Make sense?

TLDR for next topic: Use the Oxford comma.  Just do it!  Here is explication of this writing craft punctuation choice, with examples-->

To my parents, Ayn Rand and God.

To my parents, J.K. Rowling and God.

To my parents, Stephen Colbert and Jon Stewart.

In a newspaper account of a documentary about Merle Haggard:

Among those interviewed were his two ex-wives, Kris Kristofferson (died last month) and Robert Duvall.

These two preceding examples are from Theresa Hayden, helpfully in a Wikipedia entry. Here is another doosie (courtesy Hayden) that cries out for a serial or Oxford comma.

The Times once published an unintentionally humorous description of a Peter Ustinov documentary, noting that "highlights of his global tour include encounters with Nelson Mandela, an 800-year-old demigod and a dildo collector."

Now, to be clear, the serial comma does not always solve ambiguity problems. Let's look at the Sweet Betsy from Pike (ballad history web exhibt) way to think about the Oxford comma and other options (standard way to teach this in the 60s, 70s; likely regional, as in US west, like Montana).*

They went to Oregon with Betty, a maid and a cook –

• They went to Oregon with Betty, who was a maid and a cook. (One person)
• They went to Oregon with Betty, both a maid and a cook. (One person)
• They went to Oregon with Betty, a maid and cook. (One person)
• They went to Oregon with Betty (a maid) and a cook. (Two people)
• They went to Oregon with Betty, a maid, and with a cook. (Two people)
• They went to Oregon with Betty – a maid – and a cook. (Two people)
• They went to Oregon with the maid Betty and a cook. (Two people)
• They went to Oregon with a cook and Betty, a maid. (Two people)
• They went to Oregon with Betty as well as a maid and a cook. (Three people)
• They went to Oregon with Betty and a maid and a cook. (Three people)
• They went to Oregon with Betty, one maid and a cook. (Three people)
• They went to Oregon with a maid, a cook, and Betty. (Three people)

We can also look at the grocery list problem: 

buying  bread, jam, coffee, cream, juice, eggs, and bacon. VS

eating toast and jam, coffee and cream, juice, and bacon and eggs

Finally, we have a theme song to remember this punctuation convention. Caution: F-bomb in the chorus.

*Mb comments in slight rant about imperfection of Wikipedia as the all-perfect knowledge-pollooza. 

Now, you need short research article for the next assignment!  ASAP. We will speak in class about what works.  Tips:

• topic you care about personally (delight-directed, personal motivation)
• from a class you are taking now (practical, study/write = knowledge uptake)
• from a lab/PI/post doc you know (participate in lab culture; ask researcher)
• from previous position or class (you already know material)
• as part of personal research (for senior thesis, etc.)
• to prep for interviews (grad school; medical school)
  • Care to adopt this "shaman" article? First come/first served.