PhET/C3/Natural-Selection/English - Revision history

Snehalathak at 07:33, 16 October 2018

2018-10-16T07:33:48Z

Snehalathak at 07:18, 16 October 2018

2018-10-16T07:18:27Z

Snehalathak at 07:03, 16 October 2018

2018-10-16T07:03:10Z

Madhurig at 09:31, 12 October 2018

2018-10-12T09:31:59Z

Madhurig at 09:01, 12 October 2018

2018-10-12T09:01:47Z

Madhurig at 07:27, 28 September 2018

2018-09-28T07:27:29Z

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Vidhya at 10:16, 24 September 2018

2018-09-24T10:16:38Z

Vidhya: Created page with " {|border=1 | | '''Visual Cue''' | | '''Narration''' |- | | '''Slide Number 1''' '''Title Slide''' | | Welcome to this tutorial on '''Natural Selection''', an '''interactive..."

2018-09-06T05:37:24Z

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
| | '''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 may arise due to errors in '''DNA''' replication or due to '''DNA''' damage.

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/ http://phet.colorado.edu]
| | Use the given link to download the '''simulation'''.

[http://phet.colorado.edu/ 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'''.

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'''.

'''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'''.
|-
| |
| | 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 plotted on 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 on '''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 colored lines appearing in the graph after mutation and food selection.
| | Observe how differently colored 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 colors 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 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.
| | 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.
|-
|}

@@ Line 173: / Line 173: @@
 ||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'''.

@@ Line 16: / Line 16: @@
 '''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'''

@@ Line 140: / Line 140: @@
 '''Graph'''
-'''Time until next generation progress bar'''
+'''Time until next generation''' progress bar
 '''Play/Pause button, Step button'''
@@ Line 213: / Line 213: @@
 |-
 ||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.
@@ Line 220: / Line 220: @@
 ||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.

@@ Line 26: / Line 26: @@
 '''Java ''' version 1.8.0
-'''Firefox Web Browser ''' version 60.0.2
+'''Firefox Web Browser''' version 60.0.2
 ||Here I am using,
 '''Ubuntu Linux OS''' version 16.04
-'''Java ''' version 1.8.0
+'''Java''' version 1.8.0
 '''Firefox Web Browser''' version 60.0.2
@@ Line 126: / Line 126: @@
 Point to the '''Reset All button'''.
-||The '''interface''' has :
+||The '''interface''' has:
 '''Simulation''' panel
@@ Line 168: / Line 168: @@
 |-
 ||Point to the '''Population vs 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 plotted on the y axis and time on the x axis.
 |-
 ||Click '''Play button''' at the bottom of the '''interface'''.

← Older revision		Revision as of 10:16, 24 September 2018
Line 80:		Line 80:

	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 100: / Line 100: @@
 Type '''java space hyphen jar space Natural-Selection_en.jar'''.
 Point to the '''browser''' address.
@@ Line 107: / Line 108: @@
 Type '''java space hyphen jar space natural-selection_en.jar'''.
 '''File''' opens in the '''browser''' in '''html format'''.