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Q1 – Week 10- 11/1 – 11/5

                                                                                                                                Jump to:  Tuesday,   Wednesday,  Thursday,   Friday                                                                                                                                   ___________________________________________________________

11/1 – Monday –  B Day – 

Main focus –                                                                                                                                                          
a)  Connect the concepts of Evolution, Speciation, Extinction, and Adaptive radiation
1.    60 Minutes sits down with historian and author Yuval Noah Harari

2.    Class lecture through Evolution 2 to Origin of life Presentation.

           Genetic Drift/Natural Selection/Gene Flow —-> Speciation ——>  Extinction ——> Adaptive radiation  

*used this phylogenetic tree to discuss gene flow: 

Evolution 2 Presentation: 

Origin of life Presentation: 

Todays Lecture:


11/1 – Monday’s Homework: –

1)  Please complete the Evolution of Oxygen Form  form using the videos listed below: 

Prokaryotes vs. Eukaryotes: The entire video

Oxygen & Life Evolution: (1:30 – 3:00)

Breathless Through Time: 0nly up to about 14 min

Evolution: The entire video

1: Evolution of Oxygen Form 21-22

End of Monday!


11/2 – Tuesday –  A Day – 

Main focus –                                                                                                                                                          
a) To complete the Data collection of Lab 1 – 
                                                                                                                                                                                                        b)  To Review Mendelian Genetics through a dihybrid Cross                                                              
1. We will use our lab Notebooks to identify the 4 possible phenotypes that resulted from the F1 cross of the dihybrids.
2.  We will use our lab notebooks to draw a punnet square to determine the expected ratios of the phenotypes of the cross.


WE actually completed a dihybrid cross (F1). Your lab needs to show this information:
P1: (this was the parents of our original seeds)  :                         ANL/ANL  YGR/YGR              x                anl/anl  ygr/ygr
                                                                                                  Purple Stems   Green Leaves            Non-purple stems   yellow leaves
F1: (this was the genotype of the seeds we first planted) :               ANL/anl  YGR/ygr   x   ANL/anl  YGR/ygr                                                                                                                                 Purple Stems   Green Leaves     Purple Stems   Green Leaves
F2: (this was the generation of the seeds from the cross above (OUR second planting):  There will be 4 different phenotypes:                                             
Today we determined the expected phenotypical ratio of the offspring of the F1 generation by completing a punnet square of the dihybrid cross. 


This is what I modeled on the board today (actually this is what I did a couple of years ago):
From the Punnet square:
Purple Stem/Green Leaf              :  9
Purple Stem/Yellow Leaf             :  3
Non-purple stem/ Green Leaf    :  3
    Non-purple stem/ Yellow Leaf   :  1    

Fast Plants Presentation: 

Today’s Lesson – well it as last year – we will use data that I will post above but the concepts are the same.


11/2 – Tuesday’s Homework: –

                                                                                                                                                                                                                                    1.  Please read the article about Stanley Miller below:

Be prepared to to have a RAT Quiz on this article tomorrow.

I will explain the Rat Quiz tomorrow.

Would you rather have a form tonight??

It might help to make a NORT of the article. 🙂



11/3 – Wednesday –  B Day – 

Main focus –                                                                                                                                                       
a)  To complete the Data collection of Lab 1 – 
b)  To Link our Lab 1 data to Microevolution                                              
1. We will use our lab Notebooks to identify the 4 possible phenotypes that resulted from the F1 cross of the dihybrids. We will do it a second time to see if there is any changes from yesterday and confirm other students data.  Sometimes the alleles we are investigating take longer to develop than others (another allele) and thus it might be easier to identify them a day later.                                                                                                                                                                                    
Please add your data to the correct column in the link to the Google Sheet below:                                                                                                                                                                             
2.  We will use this data to evaluate if microevolution is occurring.                                                                                                                                            This will update as you update your individual data   

                                                                                                                                                                                                                              Today we looked at the second generation of the of our Fast Plants and we discovered and calculated the frequency of the Non-purple Stem Color allele (q) which is a recessive allele.  We did this by recognizing that our F1 population were 100% heterozygotes,  thus every individual had the recessive (q) AND the Dominant allele (p).  
Have all heterozygote individuals thus ensures that our:  F1 generation =   q = . 5  and  q = .5 
We wanted to see if there was micro evolution at the Stem Color allele in the second generation.
Remember the the Hypocotyl – (stem below the cotyledons) was
                                                               Purple                        Or                  Non- purple (green)
                                 ANL/anl or ANL/ANL                                        anl/anl
                                                            ANL is the p                                                               anl is the q
The codlydon (baby leaves) was 
                                                                Green                       Or                          Yellow
                                 YGR/YGR or YGR/ygr                                     ygr/ygr
Because Baby leaf color was easier to identify we will use only the baby leaf allele to test for EVOLUTION. 
                                                              p = YGR                                     q = ygr
Now we are after the q for the second generation to see if there was EVOLUTION but we had some work to do calculate the q.  
NOW the jumping off point is the homozygous individuals BECAUSE WE KNOW THEIR DEFINITE GENOTYPE (q2) if we identify the expressed recessive phenotype.  Homozygous and Heterozygous genotypes share the same phenotype so we cannot get allele frequencies directly from those individuals.
This was our class data for the F2 generation from our FAST PLANTS:
 purple green: 173

purple yellow: 52
non-purple green: 98
non-purple yellow: 23
                                   = 346 total individuals

                =  52 + 23 = 75 individuals that are homozygous recessive

 Yellow baby leaf
 *Individuals/ total
q2 =   75/ 346  q2= .22 q2= √.22

    q =  .47

p = .53

1 – .47

q =  .47


 Lets compare the 2 generations:
                                                                                      F1            F2
                                                                          q=      .5             .47
The second generation q changed?? We are NOT in Hardy-Weinberg Equilibrium and thus there is evolution! 
Only 3 things that will cause evolution.  Gene Flow, Natural Selections and Genetic Drift
Clearly  there were no pollinators (bees) that had pollen from other FAST Plants from other AP CLASSES THus Gene Flow is not a factor.
We only had 2 generations occur and natural selection requires a significant selective pressure to demonstrate changes in allele frequency. We only gave some plants LED lights which we found in Lab 2 NOT to have a significant difference in health or fitness of the LED plants and thus natural selection is not a factor.
NOW because we had a small population we most definitely had Genetic Drift occurring.  Small populations can make chance events occur that can result in the change in the frequency of the alleles and possibly lead to the “death of an allele”.
Play the AlleleA1 simulation


Using the AlleleA1 simulation, Genetic Drift of allele A1 (p) or the dominant allele LEAD to the “death of A1 alelle” after 300 generations of 346 individuals. This is due to random events in producing gametes in meiosis AND in Random fertilization.

This what is meant by the drift! With no other forces working, No Natural Selection, Gene Flow, or inbreeding an allele is lost from the population.  Remember we are tracking only 1 allele and that is very possible that this happening at other alleles in the genome of the species.

Genetic diversity is decreasing and this population is becoming less like the populuation it once belonged to.

Genetic Drift can lead to loss of alleles as I have shown you in the Excel Spreadsheet or the simulation that I have demonstrated for you.  If these alleles are connected to ANY part of the reproductive genes then Speciation can occur as reproductive isolation will occur between different populations  of the same species.
Natural Selection, Gene flow, and Genetic Drift can all lead to decreased genetic diversity in a population.  These forces that cause relative allele frequencies to change at the population level can also influence the selection forces that shape them over successive generations.  Remember that Evolution is not perfect and reproductive success is determined by alleles that are best favored for the current environmental conditions.  These best favored alleles which are selected for due to the selective pressure by the environment of are ones that ARE THE BEST AVAILABLE alleles that the population currently has to choose from.  Remember that only Natural Selection is adaptive but this adaptation occurs from what alleles are available and these available alleles are subject to change by the action of Gene Flow and Genetic Drift.  So Gene Flow and Genetic Drift are not adaptive but they shape Natural Selection by providing the choices!!!!
Speciation, or reproductive isolation that occurs from the loss of alleles in the reproductive process, almost always occurs from small groups 
AND the forces that make Speciation possible are the forces that make a species susceptible to extinction.  
Lowering the genetic diversity through Stabilizing Selections or through Genetic Flow and Genetic Drift essentially decreases the variety of alleles that could potentially give the population the ability to survive when environmental conditions change.
FOR EXAMPLE:  The current 3 elephant species that inhabits Africa and Asia have a distant relative in the  
                                     Manatee which is its the closest living ancestor.
What forces are at work?
Let us revisit a phylogenetic tree of  Evolution of Humans (Hominids):
Why are the Chimpanzee still with us?
Why have so many of our early ancestors gone extinct?
Notice that bipedalism was an adaption that occurred long before large brains?
What possible selective pressures made bipedalism an advantage OR do you think that bipedalism was just a non adaptive form of evolution?
A very interesting article on this last question:                                                   


11/3 – Wednesday’s Homework: –

1) Read article on the RNA world Hypothesis :               

     Skip the  Self-Replicating Molecules Undergo Natural Selection                                                                                                                    

2) Watch video : It is important to read the article first.  You will haver another RAT quiz on this reading!

RNA World Hypothesis: The entire video

End of Wednesday..



11/4 – Thursday –  A Day – 

Main focus –                                                                                                                                                       
a)  To review the Stanley Miller experiment from Yesterday’s RAT
b)  To Take a RAT on the RNA World Hypothesis                                                                                      
C)  To review carbon dating or radioactive dating (concepts of protons, electrons, neutrons)
1. Give back yesterday’s graded RAT and Review
                                                                                                                                                                                                                                          Origin of Life – Stanley Miller RAT                                                                                                                                                                       View Download                                                                                                                                                                                                                                                                                                                                                                                                                                  2.  Take a RAT on the RNA World Hypothesis
3. Complete yesterday’s discussion with :
Speciation, or reproductive isolation that occurs from the loss of alleles in the reproductive process, almost always occurs from small groups 
AND the forces that make Speciation possible are the forces that make a species susceptible to extinction.  
Lowering the genetic diversity through Stabilizing Selections or through Genetic Flow and Genetic Drift essentially decreases the variety of alleles that could potentially give the population the ability to survive when environmental conditions change.
FOR EXAMPLE:  The current 3 elephant species that inhabits Africa and Asia have a distant relative in the  
2:  Review  Speciation to Origin of Life Form, endosymbiosis of chloroplast and mitochondria 
When did eukaryotes begin?  Endosymbiosis of mitochondria – 
From the form did cyanobacteria evolve into plants??? 
Endosymbiosis – 
Symbiogenesis, or endosymbiotic theory, is an evolutionary theory that explains the origin of eukaryotic cells from prokaryotes. It states that several key organelles of eukaryotes originated as a symbiosis between separate single-celled organisms

The Origin of living systems is explained by natural processes.

The process of evolution explains the diversity and unity of life. A number of experimental investigations have provided evidence that the conditions early in the Earth’s history provided an environment capable of generating complex organic molecules and simple cell-like structures. For example, in the “organic soup” model, the hypothesized primitive atmosphere contained inorganic precursors from which organic molecules could have been synthesized through natural chemical reactions catalyzed by the input of energy. In turn, these molecules served as monomers (building blocks) for the formation of more complex molecules, including amino acids and nucleotides. Some models suggest that primitive life developed on biogenic surfaces, such as clay, that served as templates and catalysts for assembly of macromolecules. Under laboratory conditions, complex polymers and self-replicating molecules can spontaneously assemble. It remains an open question whether the first genetic and self-replicating material was DNA or RNA.


Evolution Presentation: 


11/4 – Thursday’s Homework: –


*Today’s best out of 2 RAT quiz will become extra credit on the next test.

If your best grade out of the 2 was an 80 then  take the 80 / 10 = 8 / 2 = 4 points on the next test.                                                                                                                                                                                                                          

1:  Please begin your write-up of the Brine Shrimp Lab.  It is a EVOLUTION LAB!!!!!!!!                                                                         I will share with you a link to work on the lab.  WE have already gathered data and made a table and a graph with error bars. You should complete the Background, Question, Hypothesis, materials, Procedure tonight. 

Please use all the concepts that we learned from Evolution into this lab.

The lab is due Monday 11/8 and the format of the formal write-up is as follows:                                                                                                                   

1:  Write up of Brine Shrimp.
 HERE IS AN EXAMPLE (link to one of my previous AP BIO student’s work)
Using the general rubric below and the one explained in the Lab Report Rubric link I gave out I would like to see the following sections in your Lab write up.
There is another example posted in the Lab Report Rubric.  I am requiring these sections below to be titled and included in your lab report but you are making this lab your own.  Although we did the same data collection and experiment, you are to make your lab unique in the lab write-up.  You will spin this lab to your interests by writing a unique background that will cover a least a page single spaced or 2 pages double spaced.  Use this opportunity to research something about Brine Shrimp that may relate to your experiment.  This is something that you will bring back into your discussion in your conclusion.  This could really be anything related to your experiment or the Brine Shrimp BUT you must direct your discussion to your Question and then Hypothesis. 
1: Title Page – Your name, Date, Title of experiment
2:  Background – Your background is like a literary review of the topic in a published study. I am not asking you to write a term paper on the Brine Shrimp but I am asking you to write an essay on the ANYTHING that is remotely related to this investigation.  Develop your Background so that your discussion eventually LEADS to a Questionthat you will test with your Hypothesis.  I know this is open ended but this is how you make this lab your own.  Do make this a cohesive piece of writing and you may probably need to investigate this information.  At the end of the lab I will ask for your resources, so make note of where you are gathering information. DO NOT MAKE THIS a bunch of unrelated ideas or facts.  I gave you some example below from past students of mine so take a look to get a feel of what I am asking. This part of your lab should be 1 page single spaced or 2 pages double spaced.
3: Question – testable  question that relates to your hypothesis
4:  Hypothesis:  Use the correct format: If the Independent variable is modified…
5.  Materials:
6: Procedure:  Step by step instructions on how you would complete this experiment.
7:  Data:   Graphs, Data Tables, etc.
8: Results:  Summarize your data, but do not make conclusion statements. “the trend of the data is that as the salinity increases the … Do not state that Brine Shrimp prefer this or that (those inferences are conclusion statements).  THis will be a short section.  A couple sentences will usually suffice.
9: Conclusion:  This section will be heavily scrutinized. What does the data tell us about the Brine Shrimp?  Here is where you get dirty with the data. What is the data inferring about the Brine Shrimp?  Was your hypothesis supported or not and Why?  What are the implications or possibilities because of your outcomes.  What could be further investigated?  
If you get vague you will lose points. You must fully develop your points and support them with logic! Remember that many experiments are built from the conclusions of other labs.  This means your points in your discussion will not be facts but just very good possible explanations.  Another experiment would be needed to test the validity of these statements. However,  if you support your statements with solid logic from evidence collected in the lab then you are addressing all the possible implications from YOUR WORK or experiment.  In this point of your conclusion you will be MAKING A LEAP from your work based on data analysis to a POSSIBLE implication BIOLOGICALLY for the Brine Shrimp.  If you do this by tying the Background discussion with your discussion here it will result in very will impressive lab write – up! 
The second part of your conclusion must discuss the limitation of the lab. What are the errors in the lab that may affected your outcomes. You need to be specific and heavily detailed here.
10. Sources – Just give me web address of the sites that you got information from.
End of Thursday..


11/5 – Friday –  B Day – 

Main focus –                                                                                                                                                       
a)  To Review the RNA world Hypothesis.
b)  To build and make a vocabulary study guide for Test 2 Monday.                                                 
1.  We will review yesterday’s RAT and important concepts                                                                                                                     
      RNA world Hypothesis RAT
      View Download       
2. We will review the Origin of life form   
3.  You will have a vocabulary section on your next test (Monday) You will have to match definitions given to the correct vocabulary word. From the list of Vocabulary words below that could be on the test, please define them using the class textbook.  Try to put them in your own words because you will be using my definitions which I will not share.
 You will need to make definitions for these words FROM the book.  Do not Google them as the online definition may not be different from the biological definition.                                                                                                                                                               
Textbook link                                                                                                                                                                                                         

 I may some of these, all of these or not any..

Vocabulary words  Text   Vocabulary words  Text
 Homologous structure  pg 463  sexual dimorphism  pg 482
 Analogous Structure  pg 465   heterozygote advantage  pg 484
 Convergent Evolution  pg 464  Prezygotic barrier  pg 489
 Divergent Evolution  postzygotic barriers  pg 489
 vestigial structures  pg 463  polyploidy  pg 495
 biogeography  pg 466  punctuated equilibria  pg 502
 founder effect  pg 477  endosymbiosis  pg 516
 bottleneck effect  pg 478  adaptive radiation  pg 524
 gene flow  pg 479  mass extinction  pg 521
 genetic drift  pg 477 aerobic
 fitness  pg 480 anaerobic
 Directional selection
 pg 481   eukaryotes
 Disruptive selection  pg 481   prokaryotes
 stabilizing selection  pg 481   phragmoplast
allopatric speciation pg 493 Mothers against decapentaplegic
Test 2 – Topics – 
Every topic on test 1 (you have the key linked in power school):
 Item  Key   Concept

 Chapters text/Review videos – Links are to my youtube videos.

 chi squared practice problem.pdf
View Download
 Chi-squared practice problem

 Evolution of homo sapiens form


 This was emailed   Morphology (difference in the structure) of organisms from fossils is used to determine how close organisms are related in terms of when they evolved and which organisms share a common ancestor.
Cladograms and Evolutionary Trees are built from this evidence

Text: 460 – 467

Text: 542 – 547
(general concepts here, if I did not cover something that you are reading then you are not responsible for it.)

Classwork practice with a cladogram:                                  Cladogram Classwork 2122.pdf
View Download          
 Evolution 1 – Cladograms of Minions.pdf
View Download
 Evolution 1 – Cladograms of Minions key p.pdf
View Download
 Build Cladograms from observable differences in traits.
 Evolution 2 – Cladograms and biotech.pdf
View Download
 Evolution 2 – Cladograms and biotech key p.pdf
View Download
 Build Cladograms based on genetic evidence (nucleotides, protein differences).
 Cladogram Practice Problem new.pdf
View Download
 A more difficult cladogram problem
 Evolution 3- Hardy-Weinberg Principle 1 Student .pdf
View Download
 Evolution 3- Hardy-Weinberg Principle 1 complete key .pdf
View Download
 Based on 5 conditions: No mutations, large population size, no gene flow, random mating, and no natural selection, the frequency of allelles for a train will stay constant.  The equation:
(p + q) = 1 (For total alleles in population)
p2 + 2pq  + q= 1 ( For the individuals)
IN Reference Table:

 Evolution 4- Hardy-Weinberg Principle 2 .pdf

 Evolution 4- Hardy-Weinberg Principle 2 Key p.pdf
View Download
 Hardy-Wienberg Principle 

Text: 474-476

 Hardy – Weinberg Equilibrium practice problem new.pdf
View Download
 Hardy-Wienberg Practice problem

 Evolution 5 – Pocket Mouse Activity.pdf

 Evolution 5 – Pocket Mouse Activity key p.pdf
View Download
 Hardy-Wienberg Principle take home quiz
 Genetic drift/Gene flow/types of Natural selection  Text 477 – 482
 Speciation-  Text 493 – 498
 Types of reproductive isolation  Text 490 – 491

Origin of Life – Stanley Miller RAT   

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 will be reviewed in class

 Origin of life – Stanley Miller


 Link to article
RNA world Hypothesis RAT
 will be reviewed in class  RNA World Hypothesis  Link to article
Google Slide presentations (these are links to the presentations I used in class):


11/5 – Friday’s Homework: –

*Please use the following link to view a protein resource. 

The protein resource is not for Test 2 and is not part of OUR homework.


1:  Please complete the Brine Shrimp lab using the guidelines posted above in Thursday’s post.                                                                                                                                                                                                                                                                                    
2. Study for Test 2 – vocabulary and all concepts learned throughout the year. The focus will be on evolution principle 
     but everything is game. I will link the key to the last test if you want to take a look on the items on the last test.
3. Complete the form below for extra credit.   If you get a 100 after 3 submissions I will replace a quiz grade (*single weight*) that is not a 100 with this grade.  It would be a great review of Hardy Weinberg.                                                                                                                                                                        

3: Extra Credit Hardy Weinberg form Form 2

End of Week 10!