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Developing an Invertebrate Zoology college course (Read 10264 times)
Jeffery Smith
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Developing an Invertebrate Zoology college course
Dec 06th, 2012, 1:44pm
 


General biology or anatomy and physiology are fairly easy to organize as most textbooks have the same order of topics, and much of the basic information hasn't changed much. I'm putting together a course on invertebrate zoology, and Tinderbox is the only program that seems to fit the task. These are my challenges:
(1) there are many different groups (phyla and classes) of invertebrate animals.
(2) each group has characteristics that I need to identify (how the embryonic egg divides, whether it has a true body cavity, no body cavity, or a false body cavity, whether the first opening in the embryo is the mouth or the anus, etc.).  I am using attributes for those.
(3) the evolutionary history of these has become both clearer and more complicated now that we can compare the DNA or RNA of different animals.
(4) some information is too long for attributes (such as the geographic distribution, normal habitat, etc.).

Right now, I am putting the phyla and classes (classes are smaller groups within phyla) into a Tinderbox outline, and have attributes defined for type of embryonic cleavage, number of species alive today, body cavity type, etc.

Does this seem like a logical approach to the situation? When the database nears completion, I should be able to go to the phylum container titled "Porifera" and get all of the information I gathered on sponges before assembling my Porifera lecture.

Feedback please.  Smiley
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Mark Bernstein
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Re: Developing an Invertebrate Zoology college course
Reply #1 - Dec 6th, 2012, 2:22pm
 
This makes sense -- Tinderbox's hierarchy fits nicely into the hierarchical classification system of species, and so into your course's systematic organization.

Don't forget to use links for cross-references.  This is especially important when you want to distinguish similar traits among distant species. For example, skunks and zebras both have stripes, but they're not very close to each other!  Similarly, you might want to use a different link type to connect species that might conjecturally be lumped: the Eastern and Western Meadowlark, say.

I'd also be sure to include a section for issues that you'll want to cover but that don't have an obvious place in the taxonomy.  You might, for example, want to have some discussion of the history of science -- how we know about these relationships, what older theories looked like.  You might not know just where to put this in the course yet, but if you're jotting notes about Wilson's Worm, you might want to remember to discuss your story about meeting Wilson that time in Woonsocket....
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Jeffery Smith
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Re: Developing an Invertebrate Zoology college course
Reply #2 - Dec 6th, 2012, 3:24pm
 
Thanks for the input, Mark. I'm reading and highlighting "The Tinderbox Way" 2nd ed., and it is answering many of my questions regarding prototypes, inheritance, and how best to use attributes. As you indicate, there are many levels of taxonomy (Kingdom ↔ Phylum ↔ Class ↔ Order Family ↔ Genus ↔ Species are just the major taxa), and using OmniOutliner just buries things too far to the right for me. And I do get little exceptions that I need to track (such as a tiny group within a large group that is freshwater rather than marine, or a sponge that is actually carnivorous).

I looked at DevonThink Pro, Eaglefiler, etc., but they seem to be repositories for files, not organizers of notes. Tinderbox is the only program that reminds me of Ashton-Tate's Framework of the 1980's. I remember nesting things inside of things inside of things inside of things. Cool!
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Mark Anderson
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Re: Developing an Invertebrate Zoology college course
Reply #3 - Dec 6th, 2012, 4:20pm
 
If your outline builds notes in taxological order (Kingdom, Phylum, etc.) then you can get the list via this action:

collect(ancestors,$Name).sort($OutlineOrder)

The collect() returns a list though not necessarily in the order you want. So using List.sort(attribute) gives you the order from top to bottom.  Add '.reverse' on the end of the above to flip the order. Want to format the list for output? Use List.format().

The code above could be used in a Display Expression or Hover Expression or to populate a user String attribute.

How you arrange the data in TB depends partly on how you want to use it. Only read it in long form in TB, or when exported to HTML or some other format? The appropriate device rather depends on such choices.

(edit: typo)
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« Last Edit: Dec 7th, 2012, 6:27am by Mark Anderson »  

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Jeffery Smith
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Re: Developing an Invertebrate Zoology college course
Reply #4 - Dec 6th, 2012, 5:37pm
 
Thanks much for the sorting tip. I will also be able to use that with geological time periods (Cambrium, etc.)
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Re: Developing an Invertebrate Zoology college course
Reply #5 - Dec 6th, 2012, 5:47pm
 
Absolutely!  Tip, until you're happy you've got the hang of some of these more complex actions, don't be afraid to run up a quick test in a new Tinderbox document so you can concentrate in the code without too much data getting in the way. You're welcome to use my 'Starter' TBX (get it here) as it has lots of attributes of various data types, and prototypes, etc., preconfigured for rapid testing. You can easily add it as a favourite too, see how.
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Jeffery Smith
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Re: Developing an Invertebrate Zoology college course
Reply #6 - Dec 6th, 2012, 6:27pm
 
Thanks a bunch, Mark. I downloaded the starter and will add it to my database.  Smiley
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Jeffery Smith
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Re: Developing an Invertebrate Zoology college course
Reply #7 - Dec 7th, 2012, 8:22pm
 
The more I work on this project, the more I realize that I can be dumping information into the database first, and organizing later. That is sobering, in that most databases require careful design first or risk having to start over again from scratch. The more information I plug into the database, the more insight I get into how to classify it.
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Mark Bernstein
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Re: Developing an Invertebrate Zoology college course
Reply #8 - Dec 7th, 2012, 10:47pm
 
Imagine how much easier we'd have made things for the early naturalists!

But, yes, that's the main point of Tinderbox: a way to use the power of the computer to help organize your information, even though you can't know in advance how best to design the organization.

Documents that learn over time!
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Jeffery Smith
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Re: Developing an Invertebrate Zoology college course
Reply #9 - Dec 10th, 2012, 9:16pm
 
Another benefit is that the level of indentation isn't tied to the level of taxonomic rank. Most of the phyla have classes as their next level, but some of the larger phyla have subphyla between phylum and class. I have prototypes for phylum, subphylum, class, order, and family. As long as I attach the note to the proper prototype, I can have multiple levels of taxa and keep them all straight. The annoying thing about most (if not all) outline processors is that you can't do multiple indents (>1 indent from a parent).
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Mark Anderson
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Re: Developing an Invertebrate Zoology college course
Reply #10 - Dec 11th, 2012, 4:31am
 
With hierarchy based prototypes, don't forget to consider $OnAdd to help set your prototypes. Thus the $OnAdd for Order might be:

$Prototype="pFamily";

Where 'pFamily' would be the name of the prototype for a Family object (use whatever prototype name you like, as long as it''s unique to the doc).

For Phylum you could either use no $OnAdd or go with a default of Class and reset as Sub-Phyulm where required. The $OnAdd only fires when a note is moved into a container or is newly created within it. Therefore, manually changing the prototype after it is initially set by the parent's $OnAdd is perfectly possible.

Agents will help if, say, you want to consider several orders and how the species within them fulfil the same niche roles. You agent query for orders X and Y is:

(descendedFrom("X") |descendedFrom("Y")) & $Prototype=="pSpecies"

That might seem back to front. We want to filter out Family objects but why not start the query with the prototype test? Well, there are more species notes in the whole TBX than the combined descendants of Orders X and Y. so we first collect the latter and from that set we drawn only the species notes.

Now, if you set the agent's $CleanupAction you can open a map of the agent (the items will of course be aliases) and you can arrange them as you wish to help explore relationships. If creating links, be aware of the fact aliases and originals have separate links.
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Jeffery Smith
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Re: Developing an Invertebrate Zoology college course
Reply #11 - Dec 11th, 2012, 11:19am
 
Thanks Mark. I'll fiddle with that in a test file. Still getting my sea legs here.  Wink
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