Difference between revisions of "PhET/C3/Natural-Selection/English"

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(Created page with " {|border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide''' | | Welcome to this tutorial on '''Natural Selection''', an '''interactive...")
 
 
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−
 
 
{|border=1
 
{|border=1
−
| | '''Visual Cue'''
+
||'''Visual Cue'''
−
| | '''Narration'''
+
||'''Narration'''
  
 
|-
 
|-
−
| | '''Slide Number 1'''
+
||'''Slide Number 1'''
  
 
'''Title Slide'''
 
'''Title Slide'''
−
| | Welcome to this tutorial on '''Natural Selection''', an '''interactive PhET simulation'''.
+
||Welcome to this tutorial on '''Natural Selection''', an '''interactive PhET simulation'''.
 
|-
 
|-
−
| | '''Slide Number 2'''
+
||'''Slide Number 2'''
  
 
'''Learning Objectives'''
 
'''Learning Objectives'''
Line 17: Line 16:
  
 
'''Natural Selection PhET simulation'''
 
'''Natural Selection PhET simulation'''
−
| | In this '''tutorial''', we will demonstrate, '''Natural Selection, an '''interactive PhET simulation'''.
+
||In this '''tutorial''', we will demonstrate, '''Natural Selection''', an '''interactive PhET simulation'''.
 
|-
 
|-
−
| | '''Slide Number 3'''
+
||'''Slide Number 3'''
  
 
'''System Requirements'''
 
'''System Requirements'''
  
−
'''Ubuntu Linux 'OS ''' version 16.04
+
'''Ubuntu Linux 'OS ''' version 16.04
  
−
'''Java ''' version 1.8.0
+
'''Java ''' version 1.8.0
  
−
'''Firefox Web Browser ''' version 60.0.2
+
'''Firefox Web Browser''' version 60.0.2
−
| | Here I am using,
+
||Here I am using,
  
−
'''Ubuntu Linux OS''' version 16.04
+
'''Ubuntu Linux OS''' version 16.04
  
−
'''Java ''' version 1.8.0
+
'''Java''' version 1.8.0
  
−
'''Firefox Web Browser''' version 60.0.2
+
'''Firefox Web Browser''' version 60.0.2
 
|-
 
|-
−
| | '''Slide Number 4'''
+
||'''Slide Number 4'''
  
 
'''Pre-requisites'''
 
'''Pre-requisites'''
−
| | Learners should be familiar with biology and ecology.
+
||Learners should be familiar with biology and ecology.
 
|-
 
|-
−
| | '''Slide Number 5'''
+
||'''Slide Number 5'''
  
 
'''Learning Goals'''
 
'''Learning Goals'''
Line 52: Line 51:
  
 
On pedigree
 
On pedigree
−
| |  
+
||Using this '''simulation''', we will look at a population of rabbits for effects,
−
Using this '''simulation''', we will look at a population of rabbits for effects,
+
  
 
Of mutations and selection factors
 
Of mutations and selection factors
Line 61: Line 59:
 
On pedigree
 
On pedigree
 
|-
 
|-
−
| |  
+
||
−
| | Let us begin.
+
||Let us begin.
 
|-
 
|-
−
| | '''Slide Number 6'''
+
||'''Slide Number 6'''
  
 
'''Mutations'''
 
'''Mutations'''
Line 75: Line 73:
  
 
Recessive
 
Recessive
−
| |  
+
||'''Mutations'''
−
 
+
−
'''Mutations'''
+
  
 
Mutations are alterations in the '''nucleotide''' sequence of any genetic element.  
 
Mutations are alterations in the '''nucleotide''' sequence of any genetic element.  
−
 
−
They may arise due to errors in '''DNA''' replication or due to '''DNA''' damage.
 
  
 
They are passed onto offspring.  
 
They are passed onto offspring.  
Line 89: Line 83:
 
Inheritance of mutations can be dominant or recessive.  
 
Inheritance of mutations can be dominant or recessive.  
 
|-
 
|-
−
| | '''Slide Number 7'''
+
||'''Slide Number 7'''
  
 
'''Link for PhET simulation'''
 
'''Link for PhET simulation'''
  
 
[http://phet.colorado.edu/ http://phet.colorado.edu]
 
[http://phet.colorado.edu/ http://phet.colorado.edu]
−
| | Use the given link to download the '''simulation'''.
+
||Use the given link to download the '''simulation'''.
  
−
[http://phet.colorado.edu/ http://phet.colorado.edu]
+
[http://phet.colorado.edu/ http://phet.colorado.edu]
 
|-
 
|-
−
| | Point to the '''file''' in '''Downloads folder'''.
+
||Point to the '''file''' in '''Downloads folder'''.
−
| | I have already downloaded the '''Natural Selection simulation''' to my '''Downloads folder'''.
+
||I have already downloaded the '''Natural Selection simulation''' to my '''Downloads folder'''.
 
|-
 
|-
−
| | Open the '''terminal''' by pressing '''Ctrl+Alt+T simultaneously'''.
+
||Open the '''terminal''' by pressing '''Ctrl+Alt+T simultaneously'''.
  
 
At the '''terminal prompt''', type '''cd Downloads''' and press '''Enter'''.
 
At the '''terminal prompt''', type '''cd Downloads''' and press '''Enter'''.
  
 
Type '''java space hyphen jar space Natural-Selection_en.jar'''.
 
Type '''java space hyphen jar space Natural-Selection_en.jar'''.
 +
Press Enter.
  
 
Point to the '''browser''' address.
 
Point to the '''browser''' address.
−
| | To open the '''jar file''', open the '''terminal'''.
+
||To open the '''jar file''', open the '''terminal'''.
  
 
At the '''terminal prompt''', type '''cd Downloads''' and press '''Enter'''.
 
At the '''terminal prompt''', type '''cd Downloads''' and press '''Enter'''.
  
 
Type '''java space hyphen jar space natural-selection_en.jar'''.
 
Type '''java space hyphen jar space natural-selection_en.jar'''.
 +
 +
Press '''Enter'''.
  
 
'''File''' opens in the '''browser''' in '''html format'''.
 
'''File''' opens in the '''browser''' in '''html format'''.
 
|-
 
|-
−
| | Cursor on the '''interface'''.
+
||Cursor on the '''interface'''.
−
| | This is the '''interface''' for the '''Natural Selection simulation'''.
+
||This is the '''interface''' for the '''Natural Selection simulation'''.
 
|-
 
|-
−
| | Point to the rabbit hopping in the '''simulation''' panel.  
+
||Point to the rabbit hopping in the '''simulation''' panel.  
  
 
Click '''Pause button''' at the bottom of the '''interface'''.
 
Click '''Pause button''' at the bottom of the '''interface'''.
−
| | Observe the rabbit hopping in the '''simulation''' panel.  
+
||Observe the rabbit hopping in the '''simulation''' panel.  
  
−
Click the '''Pause button''' at the bottom of the '''interface'''.
+
Click the '''Pause''' button at the bottom of the '''interface'''.
 
|-
 
|-
−
| |  
+
||Point to the interface.
−
| | Now we will explore the '''interface'''.  
+
||Now we will explore the '''interface'''.  
 
|-
 
|-
−
| | Point to each section in the '''interface'''.
+
||Point to each section in the '''interface'''.
  
 
Point to the '''Reset All button'''.
 
Point to the '''Reset All button'''.
−
| | The '''interface''' has :
+
||The '''interface''' has:
  
 
'''Simulation''' panel
 
'''Simulation''' panel
Line 140: Line 137:
 
'''Add Mutation'''
 
'''Add Mutation'''
  
−
'''Edit Genes'''
+
'''Edit Genes'''
  
 
In the middle,
 
In the middle,
Line 146: Line 143:
 
'''Graph'''
 
'''Graph'''
  
−
'''Time until next generation progress bar'''
+
'''Time until next generation''' progress bar
  
 
'''Play/Pause button, Step button'''
 
'''Play/Pause button, Step button'''
Line 156: Line 153:
 
'''Environment'''
 
'''Environment'''
  
−
'''Chart'''
+
'''Chart'''
  
 
Clicking on the '''Reset All button''' takes you back to the starting point.  
 
Clicking on the '''Reset All button''' takes you back to the starting point.  
 
|-
 
|-
−
| | Under '''Selection Factor''', point to the default selection '''None'''.  
+
||Under '''Selection Factor''', point to the default selection '''None'''.  
  
 
Under '''Environment''', point to the default selection of '''Equator'''.  
 
Under '''Environment''', point to the default selection of '''Equator'''.  
  
 
Under '''Chart''', point to the default selection of '''Population'''.  
 
Under '''Chart''', point to the default selection of '''Population'''.  
−
| | Let us keep the default settings:
+
||Let us keep the default settings:
  
 
'''None''' for '''Selection Factor'''
 
'''None''' for '''Selection Factor'''
Line 173: Line 170:
 
'''Population''' for '''Chart'''
 
'''Population''' for '''Chart'''
 
|-
 
|-
−
| | Point to the '''Population vs Time''' graph.
+
||Point to the '''Population vs Time''' graph.
−
 
+
||Observe the '''Population versus Time''' graph.
−
| | Observe the '''Population versus Time''' graph.
+
  
−
It shows the number of rabbits plotted on the '''y axis''' and time on the '''x axis'''.  
+
It shows the number of rabbits along the y axis and time on the x axis.  
 
|-
 
|-
−
| | Click '''Play button''' at the bottom of the '''interface'''.  
+
||Click '''Play button''' at the bottom of the '''interface'''.  
−
| | Click '''Play button''' at the bottom of the '''interface'''.  
+
||Click '''Play button''' at the bottom of the '''interface'''.  
 
|-
 
|-
−
| | Point to the black line in the '''Population''' graph.  
+
||Point to the black line in the '''Population''' graph.  
−
| | In the graph, observe how the black line moves to the right.  
+
||In the graph, observe how the black line moves to the right.  
 
|-
 
|-
−
| | Keep clicking on '''Step button'''.  
+
||Keep clicking '''Step button'''.  
−
| | Keep clicking on the '''Step button''' to move the '''simulation''' along faster.  
+
||Keep clicking on the '''Step button''' to move the '''simulation''' along faster.  
 
|-
 
|-
−
| | Point to the '''simulation''' panel and the '''Game Over pop-up box'''.
+
||Point to the '''simulation''' panel and the '''Game Over pop-up box'''.
  
 
Point to the text “'''All of the bunnies died!'''
 
Point to the text “'''All of the bunnies died!'''
−
| | If there are no rabbits left, you will see a '''Game Over pop-up box''' like this.  
+
||If there are no rabbits left, you will see a '''Game Over pop-up box''' like this.  
  
 
The text will read “'''All of the bunnies died!”'''
 
The text will read “'''All of the bunnies died!”'''
 
|-
 
|-
−
| | Click on '''Play Again button'''.  
+
||Click on '''Play Again button'''.  
−
| | Click on the '''Play Again button''' to resume the '''simulation'''.  
+
||Click on the '''Play Again button''' to resume the '''simulation'''.  
 
|-
 
|-
−
| | Click on '''Add a Friend''' to add another rabbit to the '''simulation'''.  
+
||Click on '''Add a Friend''' to add another rabbit to the '''simulation'''.  
−
| | Click on '''Add a Friend''' to add another rabbit to the '''simulation'''.  
+
||Click on '''Add a Friend''' to add another rabbit to the '''simulation'''.  
 
|-
 
|-
−
| | Click on '''Pause''' at the bottom of the interface.
+
||Click on '''Pause''' at the bottom of the interface.
−
| | Click on '''Pause''' at the bottom of the interface.
+
||Click on '''Pause''' at the bottom of the interface.
 
|-
 
|-
−
| | '''Slide Number 8'''
+
||'''Slide Number 8'''
  
 
'''Generations of Progeny'''
 
'''Generations of Progeny'''
  
 
[[Image:]]
 
[[Image:]]
−
| | '''Generations of Progeny'''
+
||'''Generations of Progeny'''
  
 
Observe the labels on the right and roman numerals on the left of each row.
 
Observe the labels on the right and roman numerals on the left of each row.
Line 219: Line 215:
 
And so on until row V (five).  
 
And so on until row V (five).  
 
|-
 
|-
−
| | Point to the graph.  
+
||Point to the graph.  
−
| | We will allow the population to grow until F3.  
+
||We will allow the population to grow until '''F3'''.  
  
 
This would be three steps after the mating pair.
 
This would be three steps after the mating pair.
 
|-
 
|-
−
| | Click '''Play''' at the bottom of the interface.  
+
||Click '''Play''' at the bottom of the interface.  
−
| | Click '''Play''' at the bottom of the interface.  
+
||Click '''Play''' at the bottom of the interface.  
 
|-
 
|-
−
| | Point to the '''progress bar'''.
+
||Point to the progress bar.
−
| | Note how the '''progress bar''' is full when a new generation begins.  
+
||Note how the progress bar is full when a new generation begins.  
  
 
The '''progress bar''' starts moving to the left as a generation starts growing.  
 
The '''progress bar''' starts moving to the left as a generation starts growing.  
 
|-
 
|-
−
| | Click '''Pause button'''.
+
||Click '''Pause''' button.
−
| | Click '''Pause button'''.  
+
||Click '''Pause''' button.  
 
|-
 
|-
−
| | Click the second button at the top left corner of the graph to '''zoom out'''.  
+
||Click the second button at the top left corner of the graph to '''zoom out'''.  
−
| | Click the second button at the top left corner of the graph to '''zoom out'''.  
+
||Click the second button at the top left corner of the graph to '''zoom out'''.  
  
 
You can now see the height of the next step.  
 
You can now see the height of the next step.  
 
|-
 
|-
−
| | Point to the black line showing the total number of rabbits.  
+
||Point to the black line showing the total number of rabbits.  
−
| | The black line shows the total number of rabbits in the graph.
+
||The black line shows the total number of rabbits in the graph.
 
|-
 
|-
−
| | Under '''Selection Factor''', click the '''Food radio button'''.  
+
||Under '''Selection Factor''', click the '''Food radio button'''.  
−
| | Under '''Selection Factor''', click the '''Food radio button'''.  
+
||Under '''Selection Factor''', click the '''Food radio button'''.  
 
|-
 
|-
−
| | Under '''Add Mutation''', click the '''Long Teeth button'''.  
+
||Under '''Add Mutation''', click the '''Long Teeth button'''.  
−
| | Under '''Add Mutation''', click the '''Long Teeth button'''.  
+
||Under '''Add Mutation''', click the '''Long Teeth button'''.  
 
|-
 
|-
−
| | Point to the '''text-box''', “'''Mutation coming'''” at the bottom of the '''simulation''' panel.  
+
||Point to the '''text-box''', “'''Mutation coming'''” at the bottom of the '''simulation''' panel.  
  
 
Point to the yellow triangle with the lightning to the left of the text.  
 
Point to the yellow triangle with the lightning to the left of the text.  
  
 
Point to the picture of long teeth in the text-box.  
 
Point to the picture of long teeth in the text-box.  
−
| | A '''text-box''', “'''Mutation coming'''” appears at the bottom of the '''simulation''' panel.  
+
||A '''text-box''', “'''Mutation coming'''” appears at the bottom of the '''simulation''' panel.  
  
 
Note the yellow triangle with the lightning inside.  
 
Note the yellow triangle with the lightning inside.  
Line 262: Line 258:
 
You can see a picture of long teeth in the text-box.  
 
You can see a picture of long teeth in the text-box.  
 
|-
 
|-
−
| | Under '''Edit Genes''', point to the rows next to the '''Teeth''' label.  
+
||Under '''Edit Genes''', point to the rows next to the '''Teeth''' label.  
−
| | Under '''Edit Genes''', the rows next to the '''Teeth''' label have become active.
+
||Under '''Edit Genes''', the rows next to the '''Teeth''' label have become active.
  
 
The '''radio buttons''' can now be clicked.  
 
The '''radio buttons''' can now be clicked.  
 
|-
 
|-
−
| | Point to each row with two options appearing under the '''Dominant''' and '''Recessive''' columns.  
+
||Point to each row with two options appearing under the '''Dominant''' and '''Recessive''' columns.  
  
 
Point to the upper row with a picture of short teeth to the left.  
 
Point to the upper row with a picture of short teeth to the left.  
  
 
Point to the lower row with a picture of long teeth to the left.  
 
Point to the lower row with a picture of long teeth to the left.  
−
| | For each row, two options appear under the '''Dominant''' and '''Recessive columns'''.  
+
||For each row, two options appear under the '''Dominant''' and '''Recessive columns'''.  
  
 
To the left of each row are the pictures of long and short teeth.  
 
To the left of each row are the pictures of long and short teeth.  
 
|-
 
|-
−
| | Point to default selections of dominant mutation for long teeth and recessive for short teeth.  
+
||Point to default selections of dominant mutation for long teeth and recessive for short teeth.  
−
| | Default selections are dominant mutation for long teeth and recessive for short teeth.  
+
||Default selections are dominant mutation for long teeth and recessive for short teeth.  
 
|-
 
|-
−
| | Point to the '''progress bar''' and the graph.  
+
||Point to the '''progress bar''' and the graph.  
−
| | Observe the '''progress bar''' and the graph after the mutation has been added.  
+
||Observe the '''progress bar''' and the graph after the mutation has been added.  
 
|-
 
|-
−
| | Point to the graph.
+
||Point to the graph.
  
 
Keep clicking on the '''Step button'''.  
 
Keep clicking on the '''Step button'''.  
  
 
Point to the interval between two narrow steps after the mutation in the graph.  
 
Point to the interval between two narrow steps after the mutation in the graph.  
−
| | Let us allow the population to grow for another three generations after the mutation.
+
||Let us allow the population to grow for another three generations after the mutation.
  
 
Keep clicking on the '''Step button'''.  
 
Keep clicking on the '''Step button'''.  
Line 293: Line 289:
 
The interval between two narrow steps in the graph corresponds to a generation.  
 
The interval between two narrow steps in the graph corresponds to a generation.  
 
|-
 
|-
−
| | Click on the second '''Zoom Out button''' until you see the steps.  
+
||Click on the second '''Zoom Out button''' until you see the steps.  
−
| | Click on the second '''Zoom Out button''' in the graph until you see the steps.  
+
||Click on the second '''Zoom Out button''' in the graph until you see the steps.  
 
|-
 
|-
−
| | Point to differently colored lines appearing in the graph after mutation and food selection.  
+
||Point to differently coloured lines appearing in the graph after mutation and food selection.  
−
| | Observe how differently colored lines appear in the graph after mutation and food selection.  
+
||Observe how differently coloured lines appear in the graph after mutation and food selection.  
 
|-
 
|-
−
| |  
+
||Point to the legend below the graph.  
−
Point to the legend below the graph.  
+
||Note that the timing of mutations and selection factors will affect population growth.  
−
| | Note that the timing of mutations and selection factors will affect population growth.  
+
  
−
The legend below the graph gives the different colors and what they mean.  
+
The legend below the graph gives the different colours and what they mean.  
 
|-
 
|-
−
| | Point to dominant '''radio button''' selection next to long teeth.  
+
||Point to dominant '''radio button''' selection next to long teeth.  
  
 
Point to the magenta line for long teeth, the olive line for short teeth.  
 
Point to the magenta line for long teeth, the olive line for short teeth.  
−
| | We introduced a dominant mutation for long teeth.  
+
||We introduced a dominant mutation for long teeth.  
  
 
Let us look at the magenta line for long teeth, the olive line for short teeth.  
 
Let us look at the magenta line for long teeth, the olive line for short teeth.  
 
|-
 
|-
−
| | Point to upper olive line and a lower magenta line.
+
||Point to upper olive line and a lower magenta line.
−
| | Initially, the olive line is above the magenta line.  
+
||Initially, the olive line is above the magenta line.  
  
 
The number of short-toothed rabbits is higher than that of the long-toothed rabbits.  
 
The number of short-toothed rabbits is higher than that of the long-toothed rabbits.  
 
|-
 
|-
−
| | Point to upper magenta line and a lower olive line.  
+
||Point to upper magenta line and a lower olive line.  
−
| | Later, the magenta line is above the olive line.  
+
||Later, the magenta line is above the olive line.  
  
 
The number of long-toothed rabbits has increased relative to the short-toothed ones.  
 
The number of long-toothed rabbits has increased relative to the short-toothed ones.  
 
|-
 
|-
−
| |  
+
||
−
| | This means that long teeth help rabbits survive by eating the available food.  
+
||This means that long teeth help rabbits survive by eating the available food.  
 
|-
 
|-
−
| | '''Slide Number 9'''
+
||'''Slide Number 9'''
  
 
'''Fur Mutation'''
 
'''Fur Mutation'''
Line 336: Line 331:
  
 
Three generations after mutation
 
Three generations after mutation
−
| | '''Fur Mutation'''
+
||'''Fur Mutation'''
  
 
Set up conditions to study effects of a fur mutation on survival of rabbits.  
 
Set up conditions to study effects of a fur mutation on survival of rabbits.  
Line 346: Line 341:
 
Allow the population to grow for another 3 generations after the mutation.  
 
Allow the population to grow for another 3 generations after the mutation.  
 
|-
 
|-
−
| | Show the wolves move in and out killing the rabbits.  
+
||Show the wolves move in and out killing the rabbits.  
  
 
Show the brown rabbits that begin to appear after the mutation.  
 
Show the brown rabbits that begin to appear after the mutation.  
−
| | Observe how the wolves move in and out, killing the rabbits.  
+
||Observe how the wolves move in and out, killing the rabbits.  
  
 
Brown rabbits begin to appear after the mutation was introduced.  
 
Brown rabbits begin to appear after the mutation was introduced.  
 
|-
 
|-
−
| | Show the '''radio button''' selections for dominant mutations for long teeth and brown fur.
+
||Show the '''radio button''' selections for dominant mutations for long teeth and brown fur.
  
 
Show the graph.  
 
Show the graph.  
−
| | Note that we are still looking at effects of the dominant long teeth mutation besides brown fur.
+
||Note that we are still looking at effects of the dominant long teeth mutation besides brown fur.
 
|-
 
|-
−
| | Point to the graph and '''simulation''' panel.  
+
||Point to the graph and '''simulation''' panel.  
−
| | Compare numbers of rabbits having white and brown fur in the graph and '''simulation''' panel.  
+
||Compare numbers of rabbits having white and brown fur in the graph and '''simulation''' panel.  
 
|-
 
|-
−
| | Point to the red line above the cyan one.  
+
||Point to the red line above the cyan one.  
−
| | Initially, there are more white rabbits than brown rabbits.
+
||Initially, there are more white rabbits than brown rabbits.
 
|-
 
|-
−
| | Point to later steps showing the cyan line above the red one.  
+
||Point to later steps showing the cyan line above the red one.  
−
| | Later, the number of brown rabbits has increased relative to white ones.  
+
||Later, the number of brown rabbits has increased relative to white ones.  
 
|-
 
|-
−
| |  
+
||
−
| | At the equator, with wolves killing the rabbits, brown fur is an advantage for survival.  
+
||At the equator, with wolves killing the rabbits, brown fur is an advantage for survival.  
  
 
This strategy to blend with the environment is called '''camouflage'''.  
 
This strategy to blend with the environment is called '''camouflage'''.  
 
|-
 
|-
−
| |  
+
||
−
| | What can you say about the numbers of long- and short-toothed rabbits?
+
||What can you say about the numbers of long- and short-toothed rabbits?
  
 
Sometimes a mutation changes the phenotype of all rabbits.
 
Sometimes a mutation changes the phenotype of all rabbits.
Line 381: Line 376:
 
Here, there are more long-toothed rabbits than short-toothed ones.  
 
Here, there are more long-toothed rabbits than short-toothed ones.  
 
|-
 
|-
−
| | '''Slide Number 10'''
+
||'''Slide Number 10'''
  
 
'''Tail Mutation'''
 
'''Tail Mutation'''
Line 392: Line 387:
  
 
Three generations after mutation
 
Three generations after mutation
−
| | '''Tail Mutation'''
+
||'''Tail Mutation'''
  
 
Set up conditions to study effects of a tail mutation on survival of rabbits.  
 
Set up conditions to study effects of a tail mutation on survival of rabbits.  
Line 402: Line 397:
 
Allow the population to grow for another 3 generations after the mutation.  
 
Allow the population to grow for another 3 generations after the mutation.  
 
|-
 
|-
−
| | Keep clicking on the '''Step button''' to move the '''simulation''' along faster.  
+
||Keep clicking on the '''Step button''' to move the '''simulation''' along faster.  
−
| | Keep clicking on the '''Step button''' to move the '''simulation''' along faster.  
+
||Keep clicking on the '''Step button''' to move the '''simulation''' along faster.  
 
|-
 
|-
−
| | Click on the 2<sup>nd</sup> '''Zoom Out button'''.  
+
||Click on the 2<sup>nd</sup> '''Zoom Out button'''.  
−
| | Click on the 2<sup>nd</sup> '''Zoom Out button'''.  
+
||Click on the 2<sup>nd</sup> '''Zoom Out button'''.  
 
|-
 
|-
−
| | Point to the differently colored lines in the graph.  
+
||Point to the differently colored lines in the graph.  
−
| | Note the number of rabbits with brown fur, long teeth and short tails.  
+
||Note the number of rabbits with brown fur, long teeth and short tails.  
  
 
It is higher than that of rabbits with white fur, short teeth and long tails.  
 
It is higher than that of rabbits with white fur, short teeth and long tails.  
 
|-
 
|-
−
| |  
+
||
−
| | Brown fur and short tails help escape from wolves.
+
||Brown fur and short tails help escape from wolves.
  
 
Long teeth help survival by making it easier to eat vegetation.  
 
Long teeth help survival by making it easier to eat vegetation.  
 
|-
 
|-
−
| | Under '''Chart''', select '''Pedigree'''.  
+
||Under '''Chart''', select '''Pedigree'''.  
−
| | Under '''Chart''', click '''Pedigree'''.  
+
||Under '''Chart''', click '''Pedigree'''.  
 
|-
 
|-
−
| | Point to the text, “'''Click a Bunny'''” at the top.  
+
||Point to the text, “'''Click a Bunny'''” at the top.  
  
 
Click on the rabbit at the left bottom corner of the '''simulation''' panel.  
 
Click on the rabbit at the left bottom corner of the '''simulation''' panel.  
  
 
Point to the rabbit framed inside a blue rectangle.  
 
Point to the rabbit framed inside a blue rectangle.  
−
| | Note the text, “'''Click a Bunny'''” at the top.  
+
||Note the text, “'''Click a Bunny'''” at the top.  
  
 
Let us click on the rabbit at the left bottom corner of the '''simulation''' panel.  
 
Let us click on the rabbit at the left bottom corner of the '''simulation''' panel.  
Line 432: Line 427:
 
Observe how the selected rabbit is framed inside a blue rectangle.  
 
Observe how the selected rabbit is framed inside a blue rectangle.  
 
|-
 
|-
−
| | Point to the '''pedigree chart''' for the rabbit framed in the blue rectangle.  
+
||Point to the '''pedigree chart''' for the rabbit framed in the blue rectangle.  
−
| | The '''pedigree chart''' appears for the rabbit framed in the blue rectangle.  
+
||The '''pedigree chart''' appears for the rabbit framed in the blue rectangle.  
 
|-
 
|-
−
| | Click on the top right '''button''' in the '''Pedigree''' window.  
+
||Click on the top right '''button''' in the '''Pedigree''' window.  
−
| | Click on the top right '''button''' in the '''Pedigree''' window.  
+
||Click on the top right '''button''' in the '''Pedigree''' window.  
 
|-
 
|-
−
| | Point to the '''Pedigree''' window that has separated.  
+
||Point to the '''Pedigree''' window that has separated.  
  
 
Point to the '''Population''' chart behind it.  
 
Point to the '''Population''' chart behind it.  
  
 
Resize the '''Pedigree''' window.
 
Resize the '''Pedigree''' window.
−
| | The '''Pedigree''' window is separated and the '''Population''' chart appears behind it.  
+
||The '''Pedigree''' window is separated and the '''Population''' chart appears behind it.  
  
 
We can now resize the '''Pedigree''' window.
 
We can now resize the '''Pedigree''' window.
 
|-
 
|-
−
| | Point to the color of the previous generations of rabbits.  
+
||Point to the color of the previous generations of rabbits.  
  
 
Point to the red crosses on the rabbits.  
 
Point to the red crosses on the rabbits.  
  
 
Point to the yellow triangle with the lightning symbol inside.  
 
Point to the yellow triangle with the lightning symbol inside.  
−
| | Note the color of the previous four generations of rabbits above the selected rabbit.  
+
||Note the color of the previous four generations of rabbits above the selected rabbit.  
  
 
Red crosses on the rabbits indicate that they are dead.  
 
Red crosses on the rabbits indicate that they are dead.  
Line 460: Line 455:
 
It shows that that rabbit underwent a mutation so its genotype and phenotype changed.  
 
It shows that that rabbit underwent a mutation so its genotype and phenotype changed.  
 
|-
 
|-
−
| |  
+
||
−
| | '''Pedigree''' analysis allows study of inheritance of genes based on data about phenotypes.  
+
||'''Pedigree''' analysis allows study of inheritance of genes based on data about phenotypes.  
 
|-
 
|-
−
| | Click repeatedly on the '''Step button'''.  
+
||Click repeatedly on the '''Step''' button.  
  
 
Show the window where rabbits can be seen all over the planet Earth.  
 
Show the window where rabbits can be seen all over the planet Earth.  
−
| | Click repeatedly on the '''Step button'''.  
+
||Click repeatedly on the '''Step''' button.  
  
 
Rabbits can be seen all over the continents on the planet Earth.  
 
Rabbits can be seen all over the continents on the planet Earth.  
 
|-
 
|-
−
| | Point to the caption, “'''Bunnies have taken over the world!'''”  
+
||Point to the caption, “'''Bunnies have taken over the world!'''”  
−
| | Observe the caption, “'''Bunnies have taken over the world!'''”  
+
||Observe the caption, “'''Bunnies have taken over the world!'''”  
  
 
These are the long-term effects of the '''simulation''' under these conditions.  
 
These are the long-term effects of the '''simulation''' under these conditions.  
 
|-
 
|-
−
| |  
+
||
−
| | Do refer to '''Additional material''' provided with this '''tutorial'''.  
+
||Do refer to '''Additional material''' provided with this '''tutorial'''.  
 
|-
 
|-
−
| |  
+
||
−
| | Let us summarize.
+
||Let us summarize.
 
|-
 
|-
−
| | '''Slide Number 11'''
+
||'''Slide Number 11'''
  
 
'''Summary'''
 
'''Summary'''
Line 488: Line 483:
  
 
'''Natural Selection PhET simulation'''
 
'''Natural Selection PhET simulation'''
−
| | In this '''tutorial''', we have demonstrated how to use the '''Natural Selection PhET simulation'''.  
+
||In this '''tutorial''', we have demonstrated how to use the '''Natural Selection PhET simulation'''.  
 
|-
 
|-
−
| | '''Slide Number 12'''
+
||'''Slide Number 12'''
  
 
'''Summary'''
 
'''Summary'''
Line 501: Line 496:
  
 
On pedigree
 
On pedigree
−
| | Using this '''simulation''', we looked at a population of rabbits for effects:
+
||Using this '''simulation''', we looked at a population of rabbits for effects:
  
 
Of mutations and selection factors
 
Of mutations and selection factors
Line 509: Line 504:
 
On pedigree
 
On pedigree
 
|-
 
|-
−
| | '''Slide Number 13'''
+
||'''Slide Number 13'''
  
 
'''Assignment'''
 
'''Assignment'''
Line 520: Line 515:
  
 
For changes in '''pedigree''' under different conditions
 
For changes in '''pedigree''' under different conditions
−
| | As an '''assignment''', observe the rabbits:
+
||As an '''assignment''', observe the rabbits:
  
 
For effects of mutations and selection factors in '''Arctic''' environment
 
For effects of mutations and selection factors in '''Arctic''' environment
Line 528: Line 523:
 
For changes in '''pedigree''' under different conditions
 
For changes in '''pedigree''' under different conditions
 
|-
 
|-
−
| | '''Slide Number 14'''
+
||'''Slide Number 14'''
  
 
'''About the Spoken Tutorial Project'''
 
'''About the Spoken Tutorial Project'''
Line 537: Line 532:
  
 
If you do not have good bandwidth, you can download and watch it
 
If you do not have good bandwidth, you can download and watch it
−
| | The video at the following link summarizes the '''Spoken Tutorial project'''.
+
||The video at the following link summarizes the '''Spoken Tutorial project'''.
  
 
Please download and watch it
 
Please download and watch it
 
|-
 
|-
−
| | '''Slide Number 15'''
+
||'''Slide Number 15'''
  
 
'''Spoken Tutorial workshops'''
 
'''Spoken Tutorial workshops'''
−
| | The '''Spoken Tutorial Project '''team conducts workshops using '''spoken tutorials''' and gives certificates on passing online tests.  
+
||The '''Spoken Tutorial Project '''team conducts workshops using '''spoken tutorials''' and gives certificates on passing online tests.  
  
 
For more details, please write to us.
 
For more details, please write to us.
 
|-
 
|-
−
| | '''Slide Number 16'''
+
||'''Slide Number 16'''
  
 
'''Forum for specific questions:'''
 
'''Forum for specific questions:'''
Line 561: Line 556:
  
 
Someone from our team will answer them
 
Someone from our team will answer them
−
| | Please post your timed queries in this forum.
+
||Please post your timed queries in this forum.
 
|-
 
|-
−
| | '''Slide Number 17'''
+
||'''Slide Number 17'''
  
 
'''Acknowledgement'''
 
'''Acknowledgement'''
−
| | This project is partially funded by '''Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching'''.
+
||This project is partially funded by '''Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching'''.
 
|-
 
|-
−
| | '''Slide Number 18'''
+
||'''Slide Number 18'''
  
 
'''Acknowledgement'''
 
'''Acknowledgement'''
−
| | '''Spoken Tutorial Project''' is funded by '''NMEICT, MHRD''', Government of India.
+
||'''Spoken Tutorial Project''' is funded by '''NMEICT, MHRD''', Government of India.
  
 
More information on this mission is available at this link.
 
More information on this mission is available at this link.
 
|-
 
|-
−
| |  
+
||
−
| | This is '''Vidhya Iyer''' from '''IIT Bombay''', signing off.  
+
||This is '''Vidhya Iyer''' from '''IIT Bombay''', signing off.  
  
 
Thank you for joining.  
 
Thank you for joining.  
 
|-
 
|-
 
|}
 
|}

Latest revision as of 13:03, 16 October 2018

Visual Cue Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Natural Selection, an interactive PhET simulation.
Slide Number 2

Learning Objectives

We will demonstrate,

Natural Selection PhET simulation

In this tutorial, we will demonstrate, Natural Selection, an interactive PhET simulation.
Slide Number 3

System Requirements

Ubuntu Linux 'OS version 16.04

Java version 1.8.0

Firefox Web Browser version 60.0.2

Here I am using,

Ubuntu Linux OS version 16.04

Java version 1.8.0

Firefox Web Browser version 60.0.2

Slide Number 4

Pre-requisites

Learners should be familiar with biology and ecology.
Slide Number 5

Learning Goals

We will look at a population of rabbits for effects:

Of mutations and selection factors

Of environment

On pedigree

Using this simulation, we will look at a population of rabbits for effects,

Of mutations and selection factors

Of environment

On pedigree

Let us begin.
Slide Number 6

Mutations

Mutations

Changes in phenotype may be visible

Dominant

Recessive

Mutations

Mutations are alterations in the nucleotide sequence of any genetic element.

They are passed onto offspring.

Mutations may or may not change the observable traits or phenotype of an organism.

Inheritance of mutations can be dominant or recessive.

Slide Number 7

Link for PhET simulation

http://phet.colorado.edu

Use the given link to download the simulation.

http://phet.colorado.edu

Point to the file in Downloads folder. I have already downloaded the Natural Selection simulation to my Downloads folder.
Open the terminal by pressing Ctrl+Alt+T simultaneously.

At the terminal prompt, type cd Downloads and press Enter.

Type java space hyphen jar space Natural-Selection_en.jar. Press Enter.

Point to the browser address.

To open the jar file, open the terminal.

At the terminal prompt, type cd Downloads and press Enter.

Type java space hyphen jar space natural-selection_en.jar.

Press Enter.

File opens in the browser in html format.

Cursor on the interface. This is the interface for the Natural Selection simulation.
Point to the rabbit hopping in the simulation panel.

Click Pause button at the bottom of the interface.

Observe the rabbit hopping in the simulation panel.

Click the Pause button at the bottom of the interface.

Point to the interface. Now we will explore the interface.
Point to each section in the interface.

Point to the Reset All button.

The interface has:

Simulation panel

On the left side,

Add Mutation

Edit Genes

In the middle,

Graph

Time until next generation progress bar

Play/Pause button, Step button

On the right side,

Selection Factor

Environment

Chart

Clicking on the Reset All button takes you back to the starting point.

Under Selection Factor, point to the default selection None.

Under Environment, point to the default selection of Equator.

Under Chart, point to the default selection of Population.

Let us keep the default settings:

None for Selection Factor

Equator for Environment

Population for Chart

Point to the Population vs Time graph. Observe the Population versus Time graph.

It shows the number of rabbits along the y axis and time on the x axis.

Click Play button at the bottom of the interface. Click Play button at the bottom of the interface.
Point to the black line in the Population graph. In the graph, observe how the black line moves to the right.
Keep clicking Step button. Keep clicking on the Step button to move the simulation along faster.
Point to the simulation panel and the Game Over pop-up box.

Point to the text “All of the bunnies died!

If there are no rabbits left, you will see a Game Over pop-up box like this.

The text will read “All of the bunnies died!”

Click on Play Again button. Click on the Play Again button to resume the simulation.
Click on Add a Friend to add another rabbit to the simulation. Click on Add a Friend to add another rabbit to the simulation.
Click on Pause at the bottom of the interface. Click on Pause at the bottom of the interface.
Slide Number 8

Generations of Progeny

[[Image:]]

Generations of Progeny

Observe the labels on the right and roman numerals on the left of each row.

Generation P is shown in row I (one).

The F1 generation in row II (two) is made up of the progeny or children of generation P.

And so on until row V (five).

Point to the graph. We will allow the population to grow until F3.

This would be three steps after the mating pair.

Click Play at the bottom of the interface. Click Play at the bottom of the interface.
Point to the progress bar. Note how the progress bar is full when a new generation begins.

The progress bar starts moving to the left as a generation starts growing.

Click Pause button. Click Pause button.
Click the second button at the top left corner of the graph to zoom out. Click the second button at the top left corner of the graph to zoom out.

You can now see the height of the next step.

Point to the black line showing the total number of rabbits. The black line shows the total number of rabbits in the graph.
Under Selection Factor, click the Food radio button. Under Selection Factor, click the Food radio button.
Under Add Mutation, click the Long Teeth button. Under Add Mutation, click the Long Teeth button.
Point to the text-box, “Mutation coming” at the bottom of the simulation panel.

Point to the yellow triangle with the lightning to the left of the text.

Point to the picture of long teeth in the text-box.

A text-box, “Mutation coming” appears at the bottom of the simulation panel.

Note the yellow triangle with the lightning inside.

This indicates a mutation.

You can see a picture of long teeth in the text-box.

Under Edit Genes, point to the rows next to the Teeth label. Under Edit Genes, the rows next to the Teeth label have become active.

The radio buttons can now be clicked.

Point to each row with two options appearing under the Dominant and Recessive columns.

Point to the upper row with a picture of short teeth to the left.

Point to the lower row with a picture of long teeth to the left.

For each row, two options appear under the Dominant and Recessive columns.

To the left of each row are the pictures of long and short teeth.

Point to default selections of dominant mutation for long teeth and recessive for short teeth. Default selections are dominant mutation for long teeth and recessive for short teeth.
Point to the progress bar and the graph. Observe the progress bar and the graph after the mutation has been added.
Point to the graph.

Keep clicking on the Step button.

Point to the interval between two narrow steps after the mutation in the graph.

Let us allow the population to grow for another three generations after the mutation.

Keep clicking on the Step button.

The interval between two narrow steps in the graph corresponds to a generation.

Click on the second Zoom Out button until you see the steps. Click on the second Zoom Out button in the graph until you see the steps.
Point to differently coloured lines appearing in the graph after mutation and food selection. Observe how differently coloured lines appear in the graph after mutation and food selection.
Point to the legend below the graph. Note that the timing of mutations and selection factors will affect population growth.

The legend below the graph gives the different colours and what they mean.

Point to dominant radio button selection next to long teeth.

Point to the magenta line for long teeth, the olive line for short teeth.

We introduced a dominant mutation for long teeth.

Let us look at the magenta line for long teeth, the olive line for short teeth.

Point to upper olive line and a lower magenta line. Initially, the olive line is above the magenta line.

The number of short-toothed rabbits is higher than that of the long-toothed rabbits.

Point to upper magenta line and a lower olive line. Later, the magenta line is above the olive line.

The number of long-toothed rabbits has increased relative to the short-toothed ones.

This means that long teeth help rabbits survive by eating the available food.
Slide Number 9

Fur Mutation

Set up conditions to study effects of a fur mutation on survival

Brown fur dominant, white fur recessive

Selection factor = Wolves

Three generations after mutation

Fur Mutation

Set up conditions to study effects of a fur mutation on survival of rabbits.

Keep brown fur as the dominant mutation and white fur as the recessive mutation.

Choose wolves as the selection factor.

Allow the population to grow for another 3 generations after the mutation.

Show the wolves move in and out killing the rabbits.

Show the brown rabbits that begin to appear after the mutation.

Observe how the wolves move in and out, killing the rabbits.

Brown rabbits begin to appear after the mutation was introduced.

Show the radio button selections for dominant mutations for long teeth and brown fur.

Show the graph.

Note that we are still looking at effects of the dominant long teeth mutation besides brown fur.
Point to the graph and simulation panel. Compare numbers of rabbits having white and brown fur in the graph and simulation panel.
Point to the red line above the cyan one. Initially, there are more white rabbits than brown rabbits.
Point to later steps showing the cyan line above the red one. Later, the number of brown rabbits has increased relative to white ones.
At the equator, with wolves killing the rabbits, brown fur is an advantage for survival.

This strategy to blend with the environment is called camouflage.

What can you say about the numbers of long- and short-toothed rabbits?

Sometimes a mutation changes the phenotype of all rabbits.

If so, the graph will not compare the mutation versus the wild type (unmutated) phenotypes.

Here, there are more long-toothed rabbits than short-toothed ones.

Slide Number 10

Tail Mutation

Set up conditions to study effects of a tail mutation on survival

Long tail dominant, short tail recessive

Selection factor = Wolves

Three generations after mutation

Tail Mutation

Set up conditions to study effects of a tail mutation on survival of rabbits.

Keep long tail as the dominant mutation and short tail as the recessive mutation.

Choose wolves as the selection factor.

Allow the population to grow for another 3 generations after the mutation.

Keep clicking on the Step button to move the simulation along faster. Keep clicking on the Step button to move the simulation along faster.
Click on the 2nd Zoom Out button. Click on the 2nd Zoom Out button.
Point to the differently colored lines in the graph. Note the number of rabbits with brown fur, long teeth and short tails.

It is higher than that of rabbits with white fur, short teeth and long tails.

Brown fur and short tails help escape from wolves.

Long teeth help survival by making it easier to eat vegetation.

Under Chart, select Pedigree. Under Chart, click Pedigree.
Point to the text, “Click a Bunny” at the top.

Click on the rabbit at the left bottom corner of the simulation panel.

Point to the rabbit framed inside a blue rectangle.

Note the text, “Click a Bunny” at the top.

Let us click on the rabbit at the left bottom corner of the simulation panel.

Observe how the selected rabbit is framed inside a blue rectangle.

Point to the pedigree chart for the rabbit framed in the blue rectangle. The pedigree chart appears for the rabbit framed in the blue rectangle.
Click on the top right button in the Pedigree window. Click on the top right button in the Pedigree window.
Point to the Pedigree window that has separated.

Point to the Population chart behind it.

Resize the Pedigree window.

The Pedigree window is separated and the Population chart appears behind it.

We can now resize the Pedigree window.

Point to the color of the previous generations of rabbits.

Point to the red crosses on the rabbits.

Point to the yellow triangle with the lightning symbol inside.

Note the color of the previous four generations of rabbits above the selected rabbit.

Red crosses on the rabbits indicate that they are dead.

The yellow triangle with the lightning symbol inside indicates a mutation.

It shows that that rabbit underwent a mutation so its genotype and phenotype changed.

Pedigree analysis allows study of inheritance of genes based on data about phenotypes.
Click repeatedly on the Step button.

Show the window where rabbits can be seen all over the planet Earth.

Click repeatedly on the Step button.

Rabbits can be seen all over the continents on the planet Earth.

Point to the caption, “Bunnies have taken over the world!” Observe the caption, “Bunnies have taken over the world!”

These are the long-term effects of the simulation under these conditions.

Do refer to Additional material provided with this tutorial.
Let us summarize.
Slide Number 11

Summary

We have demonstrated,

Natural Selection PhET simulation

In this tutorial, we have demonstrated how to use the Natural Selection PhET simulation.
Slide Number 12

Summary

We looked at a population of rabbits for effects:

Of mutations and selection factors

Of environment

On pedigree

Using this simulation, we looked at a population of rabbits for effects:

Of mutations and selection factors

Of environment

On pedigree

Slide Number 13

Assignment

Observe the rabbits:

For effects of mutations and selection factors in Arctic environment

After switching mutations from dominant to recessive and vice versa

For changes in pedigree under different conditions

As an assignment, observe the rabbits:

For effects of mutations and selection factors in Arctic environment

After switching mutations from dominant to recessive and vice versa.

For changes in pedigree under different conditions

Slide Number 14

About the Spoken Tutorial Project

Watch the video available at http://spoken-tutorial.org/ What_is_a_Spoken_Tutorial

It summarizes the Spoken Tutorial project

If you do not have good bandwidth, you can download and watch it

The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it

Slide Number 15

Spoken Tutorial workshops

The Spoken Tutorial Project team conducts workshops using spoken tutorials and gives certificates on passing online tests.

For more details, please write to us.

Slide Number 16

Forum for specific questions:

Do you have questions in THIS Spoken Tutorial?

Please visit this site

Choose the minute and second where you have the question

Explain your question briefly

Someone from our team will answer them

Please post your timed queries in this forum.
Slide Number 17

Acknowledgement

This project is partially funded by Pandit Madan Mohan Malaviya National Mission on Teachers and Teaching.
Slide Number 18

Acknowledgement

Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at this link.

This is Vidhya Iyer from IIT Bombay, signing off.

Thank you for joining.

Contributors and Content Editors

Madhurig, Snehalathak, Vidhya

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