Problem-solving research

(Response to “Hypothesis-Overdrive”

While I agree with the critique of “hypothesis” by Glass and by Glass & Hall, I believe that basing research funded by the public dollar on “questions” misses the point. What intriques a researcher in the form of a question may be very hard to explain to a layperson, or even a colleague in the same field. I prefer to explain to my students that research proposals must be “problem-solving”. These are typically mechanistic or design/engineering or targeted description (essentially the same as Freedman’s taxonomy of research problems -Freedman, P. (1960). The Principles of Scientific Research. Oxford, Pergamon Press. ), but inevitably the solution to scientific problems involves all three modes of research. Problems are solved by proposed design, hypotheses or search strategies, all of three of which can be collected under the rubric of ‘testable solutions”. Hypotheses are tools for solving problems; and we should dispense with any hypothesis as soon as it no longer is helping us solve the problem. I would suggest that “questions” and “models” (more or elss as described by Glass and Hall) are also tools for problem solving. Scientists should love hypotheses or questions no more than a journeyman loves her hammer.
Now, I suggest, that anyone can come to understand a problem, even if they never understand the hypothesis. Now, problems can be posed as questions, but not all questions identify problems. “How does Toxoplasma infection cause mice to lose their fear of cats?,” refers to a problem but “Does Toxoplasma damage fear-processing neurons in the amygdala” refers to an hypothesis that MIGHT solve the problem. Similarly, we can identify a design-engineering problem as a question (“How can we send humans to Mars and bring them back alive”) or as a statement (“The problem is to send humans to Mars and bring them back alive”). Similarly, we can express the targetted description of the human genome as a questions (“What is the sequence of the human genome?”) or as a mechanistic question (“How can we explain the genetic basis of human disease?) or as search stragety (“Sequencing the human genome should reveals details critical to explaining the genetic basis of human disease”).

On using a wiki: one month’s experience

We’ve used the The Methodological Annex wiki through for six weeks, a total of 22 articles relating to methods used in our weekly Immunology journal club. Here are some preliminary observations:

  • It takes me (as administrator) about 30-45′ each week to set up the wiki structure.  I do this to maintain a certain structure and because I have the categories in mind as I write the questions. (So far I retained administrator control over the “entry” point page that lists all the articles  and their questions.  )
  • Few students have made use of the wiki to write up their answers (which are given orally each week in a seminar following the journal club). Since TMA itself is voluntary, there is no way to require student entries to the wiki and there is so far little incentive to do so.
  • The wiki is straightforward with standard wiki features.  There’s a minor odd feature that if you highlight a text to make a link, the wikia will replace it automatically with other text, so that you have to go back and edit it back to what you want. It should accept the highlighted text as default.
  • The chief impediment to getting students to write to the wiki I think is that it takes additional time to write up and edit a wiki.
  • A second impediment has to do with copyright issues.  Under the doctrine of fair use, it is appropriate to take tables and figures from copyrighted works for display in a one-time teaching seminar, but not for repeated use or in a stable public forum. This means that figures would have to be redrawn. In most cases, students actually use the whiteboard for diagrams- so is is non-trivial to post them to the wiki.
  • One solution to the copyright issue would be to take the wiki private, using the wiki feature of Blackboard, for example.

Stanley Fish on “Plagiarism is not a big moral deal”

need to comment on this opinion piece by Stanley Fish

Stanley Fish

: brought to my attention by Jim Good.

Immunology is non-linear/Immunology from the bedrock/

A draft prezi on building a course in immunology that builds on prior knowledge. I think we also need to consider efficiency, efficacy and motivation. Highly motivated students might learn more effectively under a ‘logical’ or linear mode; less motivated or highly burdened students might benefit more from a non-linear, prior-knowledge approach. Finally, learning styles might also make a difference. Global learners for example might benefit better from a “bottom-up” or logical/linear mode of teaching, while concrete learners might learn better using a “top-down” approach based on prior knowledge. Then again we might see the former as theory based, the second as problem-oriented.
So, crudely, perhaps:
linear non-linear
bottom-up top-down
logical prior knowledge
global concrete
theory-based problem-based

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Math is non-linear

Here’s an argument that Math need/should not be taught in a (logically) linear fashion, either: a prezi by Allison Blank:

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Teaching Immunology from the Bedrock

Recently I had the opportunity to ß test an introductory lecture for an Immunology course using the guiding principle that students learn by constructing new knowledge (constructivism)  on a bedrock of prior knowledge.  This general notion is supported by studies of long-term potentiation which indicate that new synaptic connections create the substratum for long-term memory best when learning is repeated with rest times between stimulations.  Moreover, long-term memory seems to be firmest when

  • learning is intermittent
  • learning times are relatively short (<15′ per “segment”)
  • learning modes are varied
  • reinforcement requires using knowledge in different ways
  • reinforcement accesses higher order thinking (eg. Bloom models)

The problem for classroom teaching  of the subject of Immunology is, then: how to identify the prior knowledge of students, and how to teach in such a way that new knowledge is constructed so that it is ready as prior knowledge for the next teaching session.

Traditional approaches have used mixed learning strategies such as readings and homework to supplement didactic learning.  Most if not all current textbooks use a similar sequence of chapters, starting with “fundamental immunology” in the first part of the course and ending with “clinical immunology” in the latter part.  A first chapter summarizes the cell types and anatomical structures of the immune system, followed by a chapter on “innate immunity” (moving from the last chapter of the book to the first about 6 years ago).  Then follows a series of chapters which purport to construct knowledge of immunity on the basis of fundamental knowledge: MHC molecules and antigen presentation; T cells and their receptors; B cells and their receptors and so forth. This strategy develops a sequence of topics based on logical categories that more-or-less follow the presumed ontology of the immune response: the sequence of presentation  seeks to  mimic a presumed sequence of events or processes in nature.  Thus we learn that cells respond via innate responses to antigens to stimulate T cells to stimulate B cells to make antibodies, resulting in a variety of functional and dysfunctional effects.

The theoretical advantage of a course built on ontology or on logic is that it is independent of the prior knowledge of students: all we have to do is ensure that students have a minimum competency in the area (using placement strategies, remediation) and then build on the minimum competency.

The disadvantage of this course is that is forces someone else to provide the remediation, or blocks student access to the course.

But ontology has nothing to do with prior knowledge, which is knowledge that we (or our students) happen to have before entering the classroom.  It is like starting a course in macromolecular design with a discussion of quarks, charm and spin.

Can we design a course around “prior epistemology” rather than ontology?    To construct a course of immunity on the basis of prior knowledge, we’d start with what student already know about, which is not likely to be the various types of white cells, anatomy, innate immunity, MHC and antigen presentation, and so forth.  In fact, prior knowledge of immunology is likely to reflect things that the general public knows about: vaccines, transplantation, allergy and autoimmunity, HIV. These are the topics typically taught at the end of a course in immunology.

The proposal:  start the course with clinical cases, examples, things that students already know about and are interested in.  A large fraction of applicants to our PhD program, for example, claim they want a PhD in immunology because a family member has autoimmune disease.   Then, why not start with autoimmunity? Or, most students have or know someone with allergy or asthma.  Then, why not start with allergy?

Here’s the new sequence that might evolve:

Concept map of Immunology (using Tuft University's Visual Understanding Environment). Green: exogenous factors. Pink: human interventions. Blue: endogenous processes.

We might start with any of these major areas, but Type I allergy provides a convenient path that builds on prior knowledge, because it relies to a large degree on a single class of antibody, IgE, with a relatively simple mechanism. Most students will have heard of antibodies and know vaguely what they do. Most students will have heard of anti-histamines. Most students will have heard of anaphylactic shock.

Allergy =>description of mechanism of allergic manifestations (down-stream causation) and treatments of Type I disease (which provides the basis of nearly all other immune pharmacologicals), then efficient causes of allergy (chiefly, IgE). =>treatment of IgE structure and function; B cells, mast cells, anti-inflammatory drugs.

Then generalize from IgE to Ig and the full array of antibody functions: opsonization, complement, neutralization, autoimmune disease,Types II and III hypersensitivity and the efficient causes of class switching. Granulocytes and macrophages.  This is where we first learn about cell trafficking.

This leads to discussion of antigen/antibody diversity => VDJ recombination, somatic hypermutation and affinity maturation,  AID, germinal center reaction, T cell help, CD40.  Hapten-carrier phenomenon.

This leads to discussion of  T cell help: signal 1 vs signal 2, cytokines, TCR and nature of T cell antigens. Th1 vs Th2.  T cell trafficking.

This leads to concept of antigen presentation by MHC molecules and processing; MHC-restriction in the molecular sense.

This leads to concept of MHC polymorphism and MHC-restriction in the genetic sense,  transplantation, matching.

This leads to bone marrow transplantation, thymic education, self tolerance; cytotoxic T cells and virus-resistance.

Finally, we need to understand how T cells are activated, so we reach the end of the course with a discussion of dendritic cells, revisiting antigen presentation, bringing in co-stimulation of T cells, and introducing Toll-like receptors and other innate mechanisms.

The Methodological Annex: A wiki and a teaching tool

About a year we created a “methodological annex” to our weekly departmental journal club which all of our graduate students attend.  This was a voluntary meeting, for one hour immediately after the journal club, for students who haven’t yet passed their Qualifying Exam; two to three faculty members also attend. Faculty assign a question about the methods of the paper to each of four students each week; these are responsible for explaining the method and responding to questions in Qualifying Exam-style.

The outcome- after one year we have spent over 40 hours in The Methodological Annex, covering roughly 160 methods.

This year we will begin posting these topics in a new  public wiki,

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