Title: Cathy Codon on RNA Transcription (as witnessed by Yolanda Gil) NOTE: There are comments in the notes view of these powerpoint slides
1Cathy Codonon RNA Transcription(as witnessed
by Yolanda Gil)NOTE There are comments in the
notes view of these powerpoint slides
2Executive Summary
- Entered RNA transcription 6 times (6 trials)
- 3 times because of software problems
- Never entered it correctly or completely
- No Transcription subevent in 6 trials, added when
YG hand-generated KANALs output - In trial 1 subject decided not to follow
guidelines in training material - Trial 6 is the most representative (slides 36-55)
3Trial 1Transcription
4- Defined top-level node Transcription as a kind
of Transcribe (I think) - Brings in DNA and RNA-polym
- Clicks on Transcription, gets arrow
direct-object-of-change (YG is this a bug?) - Brings in Promoter
- Tries to unify Promoter with DNA
- Reads the handout with components
5- Collapses all roles of Transcription
- Draws arrow between Transcription and RNA
Polymerase calls it subevent - Brings in Terminator
- Goes back to RNA Transcription text description
6Screenshot
Direct-object- of-change
subevent
Transcription
RNA Polymerase
DNA
Terminator
Promoter
Make Contact
Break Contact
Move
7Screenshot
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
DNA
Terminator
RNA
Promoter
Make Contact
Break Contact
Move
8Screenshot
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
DNA
TerminatorAction
subevent
RNA
PromoterAction
Make Contact
Break Contact
Move
9Specifies Participants in Make Contact
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
DNA
TerminatorAction
subevent
Things Making contact
RNA
PromoterAction
Move
Make Contact
Break Contact
Leaves location empty
location
10Specifies Participants in Break Contact
Subevent arrow is hidden behind
instrument
Transcription
RNA Polymerase
Direct-object- of-change
TerminatorAction
DNA
subevent
PromoterAction
RNA
Things breaking contact
Move
Make Contact
Break Contact
Leaves location empty
location
11- Saves it, keeps editing
- Collapses everything, uncollapses
- Reorganizes things
121140 Collapses everything, uncollapses,
reorganizes
Transcription
DNA
Direct-object- of-change
subevent
Move
RNA
RNA Polymerase
Break Contact
TerminatorAction
PromoterAction
Make Contact
13- We stopped for 10min
- User admits to NOT have followed the steps we had
specified earlier, on purpose. User just thought
about all the processes and all the objects, then
connected them. User prefers to do things that
way. - When using the tool, user feels as if doing a
puzzle and not the transcription process held in
mind
14- Notices PromoterAction
- User says its an error, it should not be there,
user just wants the label to read Promoter - User is happy that it is a subevent, as stated
Because the promoter is doing things
151157
Transcription
instrument
Direct-object- of-change
DNA
RNA RNA Polymerase
RNA Polymerase
User wonders what it is and where it came from I
said (user) dragged it user says didnt mean
to
16Trial 2Transcription-1
17- User waits for me for 15 min, during that time
user browses through the training material - Underlines verbs in the text
- Defines Transcription-1 as a kind of action
- Brings in RNA, DNA, Promoter, Term, RNA-Polym
- Brings in Make-contact, Move, and Break-contact
18Screenshot
Direct-object- of-change
instrument
Transcription-1
RNA Polymerase
DNA
Terminator
RNA
subevent
Promoter
Make Contact
Break Contact
Move
19- Make-contact disappears (bug)
- Saved
- Edited
- Everything not connected to Transcription-1
disappeared - Abort trial because of software problems ?
20Trial 3Transcription-2
21- Define transcription as action, bring in all
relevant components (steps 3,4,5 of previous
trial)
22Transcription-2
DNA
I notice that Make Contact and Transcription are
now unified (user probably does not know), So
Transcription-2 has all the roles of Make-contact
Wanted to define DNA as the object of
Transcription, Drew the arrow wrong, so object
was not in menu. I explain why
23Make-contact and transcription-2 were somehow
unified, thus the roles
Transcription
The objects Making contact
DNA
TerminatorAction
subevent
RNA
PromoterAction
RNA Polymerase
Break Contact
Move
24- User clicks to simplify
- System freezes
- Abort trial because of software problems ?
- User makes comment about liking to collapse
things and simplify only likes to see the detail
at times, I dont need it, but I like to see it
25Trial 4Transcription-3
26- Define transcription as action, bring in all
relevant components (steps 3,4,5 of previous
trial) - User makes Move a subevent of Transcription-3
- User collapses Transcription-3, Move is lost and
cannot get it back - Abort trial
- I explain again arrows in detail
27Trial 5Transcription-4
28- Define transcription as action, bring in all
relevant components (steps 3,4,5 of previous
trial)
29Transcription
RNA Polymerase
DNA
RNA
subevent
TerminatorAction
Move seems to always end up at the left hand side
(I.e., coming first)
PromoterAction
Make Contact
Break Contact
Move
30Direct-object- of-change
instrument
Transcription
RNA Polymerase
DNA
RNA
subevent
TerminatorAction
PromoterAction
Make Contact
Break Contact
Move
31Direct-object- of-change
instrument
Transcription
RNA Polymerase
DNA
RNA
subevent
TerminatorAction
PromoterAction
Thing moved
Make Contact
Break Contact
Move
32- Subject collapses Move to get rid of detail
- For each subevent (Make-Contact, Break-Contact)
assigns roles and then collapses - goes too fast to take notes
- Looks at the screen, says Shall I test it?
- The screen is as in next slide
33Cmap
instrument
All the participants in the subevents are
specified
Transcription
RNA Polymerase
Direct-object- of-change
DNA
subevent
RNA
Move
Make Contact
Break Contact
TerminatorAction
PromoterAction
34- Instead of asking questions, subject decides to
check knowledge by uncollapsing nodes - Move the thing moved-gt RNA polimerase
- Make-contact the things mkg ctc-gt DNA and RNA
polym - Break-contact the things brkg ctc-gt DNA and
RNA-polym - Says actually DNA and RNA break contact,
- Since there is no delete fn in software, wants to
abort and make another one where Move has RNA and
DNA as objects because RNA moves away, actually - Says another mistake in Break-contact, should say
RNA and DNA
35- Decides to ask some questions before discarding
this - Asks two questions really fast (I cannot see)
- Says very confident I know everything I did is
right, because the picture was the answer
36Trial 6Transcription-5NOTE Organized in
episodes. In newer versions of powerpoint, you
can see the bullets numbered (statements made by
user, YG, or comments)
37Define Overall Process
- Define Transcription-5 as action, bring in all
relevant components (steps 3,4,5 of Trial 2) - Defines Transcription-5 as a kind of action
- Brings in RNA, DNA, Promoter, Term, RNA-Polym
- Brings in Make-contact, Move, and Break-contact
38- User specifies participants in substeps
- Move- the thing moved RNA
- User says wait, RNA polym moves
- YG says it is ok to add two moves
- User says ok but didnt do that (user forgot?)
- Collapses everything and then expands
- Has the same thing as in Trial 5, but has no
participants specified for Make-contact and
Break-Contact (see next slide)
39Screenshot
instrument
Transcription-5
RNA Polymerase
Direct-object- of-change
DNA
subevent
RNA
Move
Make Contact
Break Contact
TerminatorAction
PromoterAction
40User is Ready to Test Knowledge
- User saves and wants to ask questions
- User re-reads text description of RNA
Transcription before asking questions to SHAKEN
41Ask Questions
- What is the instrument of Transcription-5?
- Ans RNA-polymerase User says it is correct
- During Tr-5, what role does the polymerase play?
User notes it is an important question - Ans In Tr-5, RNA poly plays the role
- BUG nothing shown!
- User tries the last item (to ask questions
through cmaps) - BUG doesnt seem to work.
42Ask Questions (cont)
- How many instruments are in Tr-5?
- Ans only 1 (yg notesystem does not say which
one) - How may objects are in Tr-5?
- Ans 2
- Which objects are in Tr-5?
- AnsRNA and DNA User says thats correct
- User says what is the point of asking questions,
it is the same as the graph. - YG explains
43User Wants to Continue Asking
- User says there is a lot of details that she
would normally teach - User says she/he is done with the scenario and
she wants to continue asking more questions
44Ask Questions (cont)
- Explain Tr-5?
- Ans object
- instrument
- Subevents Move, Make-Contact, Break-Contact,
Promoter, Terminator - User reads this and finds it perfectly
- normal!!
- She wants to bring back Transcription-1 and ask
questions about it. - YG suggests to stick with Tr-5
BUG It does not say Promoter Action Terminator
Action as it did in the cmap
45Running KANAL (YG notes the interface rendering
is unclear)
- Summary of alternative paths in simulation
- Move
- Step Move
- Checking Precondition object musnt be
restrained succeed - Warning no effect was produced
- Step Make-Contact
- Checking Preconditions the location of O1 must
be the location of Make Contact Failed - Click here for suggestions
- Checking Preconditions the location of O2 must
be the location of Make-Contact Failed
46User Says It is Done!
- YG notes the simulation is not giving useful
output because of a software problem - User says the scenario is done
- YG says some things not working in software, but
she will simulate what the system would say if it
was working ok
47Hand-Generated KANAL-Style Output is Presented to
User
- YG shows Move
- Conditions RNA is unrestrained Succeed
- Effect no effect! ERROR
- suggested fix specify destination of RNA
User says cytoplasm - User goes to editor, adds
RNA
location
place
Here is where the user wants to say cytoplasm!!
48User confused about Fluents
- User brings in Cell
- User saysthis is interesting, the system is
asking me to edit to add more details - Tries to connect RNA to Cell in order to say that
RNA moves to Cell (i.e., cell is the destination
of Move)
RNA
location
Cell
BUG it says Place Cell
49Adding another Move
- User Adds another Move for RNA polym
- Bug the two moves got disconnected somehow
- YG said to pretend this
Transcription
subevent
Move
Move
50Hand-Generated KANAL-Style Output is Presented to
User
- Move
- Conditions RNA is unrestrained Succeed
- Effect RNA is in cytoplasm
- YG decides to move to another error at this
point since locations are messed up, and since
the RNA has not been created anyway - YG decides to see if user realizes Transcribe
substep is missing, i.e., there are no substeps
to create the RNA
51Hand-Generated KANALConfusion about Expected
Effects
- YG asks
- What are the expected effects of Transcription?
- User does not understand, YG tries again
- what is true after transcription that was not
true before? - What is the expected state of the world after
transcription? - User says
- RNA is taking the message and moving to the
location where it needs to be delivered/used - RNA has transferred the message from where it is
to where it needs to be used
52Hand-Generated KANALUser understands step is
needed to create the RNA
- YG tries again
- Is the DNA same? Yes
- Is the Polymerase same? Yes
- Is the RNA same?
- User says RNA didnt exist before
- ?User specifies that expected effect is RNA is
created - Suggested fixes add subevent that creates RNA
- User says RNA is created by Break-contact
53User finally adds Transcribe substep!
- User looks back the paper material and say maybe
one subevent needs to be Transcribe - User adds Transcribe as subevent
- direct-object DNA
- thing-created RNA
- instrument RNA-Polym
- source location
- destination location
54Transcribe Source and Destination
- YG asked to fill out source and destination
- User says it is where the collision happens
- User confused that the overall process is called
transcribe and that the actual copy is also
called transcribe
Source is collision site
Source is promoter
55An Example Analogy that Did not Seem to Help
- YG tries an analogy
- YG says start at is promoter. User gets it
- User explains that when we say source it seems
to mean where the info comes from, e.g., the
book, the DNA
- Transcribe DNA
- What chapter 2
- Start at page 2
- End at page 7
- Location copy room
analogy
- Transcribe DNA
- What gene
- Start at DNA
- Location cell