Friday, February 29, 2008

Final Exam Review

Below is the list of topics and concepts we have covered this term. Anything on this sheet is fair game for the winter final exam. Pay attention to the percentage amounts, for example: Biotechnology is twenty percent of the exam, therefore you should spend about twenty percent of your study time on this section.

Thanksgiving to Christmas: Genetics

10% of the exam


Mendelian Genetics


Multiple Allelic Traits

Polygenic Traits

Pedigree Chart


Environmental Effects on Phenotypes

Genetic Disorders

Testing for Genetic Disorders

Tracking Genetic Disorders with Pedigree Charts

The Human Genome Project


January: Biotechnology

20% of the exam

How to write a scientific paper

DNA extraction (in particular, uses of specific reagents)

Gel Electrophoresis (materials, how it works)

PCR (materials, how it works)

February: Evolution

You should be able to give a different example or case study for topics as needed. You may only use each example once on the exam.

For example: If this lists says “microevolution” not only do you need to be able to explain what it is, you also need to give a specific example. In this case, you could talk about the Blue Mussels or the mute mutant crickets in Hawaii

Who was Darwin?

Scientific use of the word “theory” v. vernacular use




Speciation Event


Mechanisms of Evolution



Founder Effect / Genetic Drift

Natural Selection

Bottle Neck



Sexual Selection

Males Compete & Female Choice

Intrasexual Selection

Intrasexual Selection

Sexual Dimorphism

Fisher’s Process

Single-Step Selection

Cumulative Selection


Selecting agents

Richard Dawkins

Lamarkism v. Darwinism



Preventing competition


Neutral Theory

Qualifications for Adaptations

Darwin’s Finches

Defining a species


Biological Species Concept

Population Divergence

Causes of speciation

Geographic Isolation

Reduction in Gene Flow

Allopatric population

Peripatric population

Parapatric population

Sympatric population

Defining Macroevolution

Patterns in Macroevolution


Character Change

Lineage Splitting



Punctuated Equilibrium

Diversity in clades (why would one lineage lead to millions of species and another one only lead to a few hundred)

Right place, right time in the environment

Adaptive Radiation

Historical Change in diversity



Trends in Evolution

Random fluctuation v. trends

What causes evolutionary trends


We are wrapping up the unit on evolution by examining macroevolution and watching videos from PBS's series on evolution.

As you prepare to study for the final exam, check out Berkley's Evolution website (which is what I used to put together this unit).


Thank you to those of you who attended the poster session last night and offered critiques on the general biology posters.

Wednesday, February 27, 2008

Extra Credit Opportunity

Yes, it's true. You have two opportunities for extra credit.

Option 1: Go to the ARC on Thursday from 5:30-6:30. ALL the general biology classes are having a poster session on GMO's, the HGP, cloning and stem cells. You will need to fill out a critique sheet for any two posters of your choosing.

Option 2: Create a poster on the mechanisms of evolution (mutation, migration, genetic drift and natural selection, you should also include the bottleneck effect and sexual selection). Your poster should be creative, contain an explanation and an image for each mechanism.

Friday, February 22, 2008

Genetic 'Junk' Could Answer Riddle of Vertebrate Evolution

Wired Magazine
February 21, 2008
"Lampreys, jawless fish closely related to the first vertebrates, possess 41 types of a little-known genetic regulator called microRNA. Some biologists say microRNA answers the mystery of how backbones evolved.
Why aren't you a spineless sack of protoplasm?

Because of a little-known molecule called microRNA, say Dartmouth College biologists.

In a study published this month in the Proceedings of the National Academy of Science, researchers found 41 types of microRNA -- a molecular "off" signal for genes -- that are unique to vertebrates."

Click here to read the full story.

What is a specie?

Today and tomorrow students will take notes on what it takes to classify something as a specie. Why are species important other than for the sake of classification and keeping track of evolution? Defining a specie and conservation are inextricably linked.

An article in Nature, by Rob DeSalle & George Amato details the importance of conservations genetics and speciation.

The 'crisis discipline' of conservation biology has voraciously incorporated many technologies to speed up and increase the accuracy of conservation decision-making. Genetic approaches to characterizing endangered species or areas that contain endangered species are prime examples of this. Technical advances in areas such as high-throughput sequencing, microsatellite analysis and non-invasive DNA sampling have led to a much-expanded role for genetics in conservation. Such expansion will allow for more precise conservation decisions to be made and, more importantly, will allow conservation genetics to contribute to area- and landscape-based decision-making processes Click here to read more.

Thursday, February 21, 2008

Speciation turned classification

We started a lecture on speciation when it came to light that most of the students were pretty shakey on the basics of classification. You should review the powerpoint below as you are responsible for the basics of classification.

Wednesday, February 20, 2008

Darwin's Finches Activity

For Wednesday D block and Thursday B block classes

In this simulation students become birds and are given "beak-types". After completing the activity, students will relate results to adaptations and natural selection.

As students work through this activity, they focused on the following questions

1. What is the relationship between beaks and seed-gathering?

2. Which beak(s) are the favored type(s)?

3. How does natural selection contribute to adaptation(s)?

4. Are the beaks at the end of the simulation the best-adapted ones?


Complete 1/2 page long responses that analyzes or interprets TWO of the following three quotes. TYPE your responses. Each response should be a 1/2 page single spaced.

1. Stephen J. Gould, " Ideal design is a lousy argument for evolution...Odd arrangements and funny solutions are proof of evolution."

2. Richard C. Lewontin, " The relationship between adaptation and natural selection does not go both ways. Whereas greater relative adaptation leads to natural selection, natural selection does not necessarily lead to greater adaptation."

3. Neil Campbell, "Of all the agents of microevolution that change the gene pool, only selection is likely to be adaptive."

Tuesday, February 19, 2008

Sexual Selection & Adaptation

Today B block took notes on sexual selection and learned about various modes of selection. Tomorrow D block will finish notes on adaptation and will experience for themselves what it is like to be one of Darwin's finches.

Monday, February 18, 2008

Sex and the Single Guppy

Sexual Selection:
Why do peacock's have such brightly colored tails? What's a bird's mating dance?

Today D block (and tomorrow B block) learned about sexual selection.

Tonight for homework students will complete the webquest on Sex and the Single Guppy. Complete the worksheet while you go through the activity.

Saturday, February 16, 2008


NOTE: This post is for Saturday's D block class and Monday's B block class

What is it? How does it differ from macroevolution?

Microevolution is evolution on a small scale—within a single population. A population is a group of individuals who reproduce together in the same area at the same time. The neat thing about microevolution is we can see in our life time. Today we looked at two different case studies one about mussels and one about crickets.

Musseling in on Evolution

The Asian shore crab invaded the eastern coast of the U.S. about 15 years ago and began foraging on the native blue mussel, which, at the time, had no defenses against the exotic, aggressive crab. But these days, the blue mussel responds to the crab’s presence by building up a thicker shell over the course of a few months. That extra buttressing helps thwart the crab's attacks — and makes the mussel a harder nut to crack!

blue mussels
Asian shore crab
The blue mussel The Asian shore crab

For the full story, click here.

Quick Evolution Leads to Quiet Crickets

Attack of the flesh-eating parasitoid maggots!! Mutant mute crickets run rampant in tropical paradise!! The headlines may sound like a trailer for a cheap horror flick — but in fact, these sensationalist sound bites accurately describe the situation on the Hawaiian island of Kauai. The "flesh-eating parasitoid maggots" are the offspring of the fly, Ormia ochracea, which invaded Hawaii from North America, and the mutant crickets are the flies' would-be victims. The flies follow the chirps of a calling cricket and then deposit a smattering of wriggling maggots onto the cricket's back. The maggots burrow into the cricket, and emerge, much fatter, a week later — killing the cricket in the process. But this fall, biologists Marlene Zuk, John Rotenberry, and Robin Tinghitella announced a breakdown in business-as-usual in this gruesome interaction: in just a few years, the crickets of Kauai have evolved a strategy to avoid becoming a maggot's lunch — but the strategy comes at a cost...

cricket parasitic maggots inside a cricket
On the left is a typical field crick like those on Kauai, and on the right are the parasitic maggots of Ormia ochracea inside such a cricket.

To read the full story, click here.

Homework: Find an article or case study that discusses microevolution in a specific organism. Be prepared to explain the case to the class as well as answer questions about the case. On Thursday, 2.21, you will have a quiz on evolution, so start studying!

Thursday, February 14, 2008

Student Generated Biomorphs

Today students used the Blind Watchmaker Applet to make their own biomorphs. In addition they finished reading chapter 3 from "The Blind Watchmaker" and answered questions. Click any picture to make it larger.

Each of these represents the 100th generation of an imaginary organism. All of the biomorphs started as a single pixel.

Andrea's Biomorph

Sammy's Biomorph
Dana's Biomorph
Ji's second attempt at Biomorph's

Wednesday, February 13, 2008

Mechanisms of Evolution

Today students took notes on the basic mechanisms of evolution (mutation, migration, genetic drift, bottle necks and of course, natural selection).
Animation on Natural Selection
Overview of the mechanisms of change

Tuesday, February 12, 2008

Rest Day

Enjoy Rest Day, see you tomorrow in class!

Monday, February 11, 2008

Making Cladograms

Objective: Given some groups of organisms and some of their distinguishing characteristics, students will construct a cladogram, and properly interpret and analyze that cladogram in terms of how it shows common ancestry and degrees of evolutionary relationship.

Homework: Sleep in & Enjoy Rest Day!

Saturday, February 9, 2008

Got Milk?

What does Natural Selection have to do with lactose intolerance? Read below to find out!

Medical News Today
9 February 2008

Got Milk?

If you're lactose intolerant, you're not alone most of the world's adults can't digest this sugar found in milk. African tribal people who took up cattle herding thousands of years ago are an interesting exception. Sarah Tishkoff of the University of Maryland discovered that natural selection for lactose tolerance was so strong that it evolved independently in three distinct rural African populations. Lactose tolerance enabled people to drink cow's milk during droughts and survive to produce more offspring who also carried the trait.

Click here for more stories on how evolution impacts us everyday.

Thursday, February 7, 2008

Evolutionary Evidence Takes the Stand

Despite overwhelming evidence attesting to their innocence, last month six medical workers were sentenced to death in a Libyan trial. The crime with which the five Bulgarian nurses and one Palestinian doctor are charged is indeed horrifying. After an outbreak of HIV at the Al-Fateh hospital, the Libyan government accused the defendants of committing an act of bioterrorism by deliberately injecting 426 hospitalized children with HIV-tainted blood. The HIV strain is particularly virulent and has already contributed to the deaths of more than 50 of the infected children. The families of both the victims and the accused are enraged, and the controversy is escalating: the case has already seen one retrial and further appeals are likely. But what about science? What does the scientific evidence have to say? Click here to read the full story.

Students read an article on the Libyan trial and the science behind it, as well as answered the following discussion questions:

This article described a similarity between HIV evolution and fruit fly evolution. What was that similarity? How might the evolution of HIV and the evolution of fruit flies be different?

The HIV viral strains infecting the Libyan children are all slightly different from one another. Explain how they are different and how they got to be that way.

The phylogeny of the children's HIV viruses helped show that the medics did not cause the HIV cluster at the hospital. What aspect of the phylogeny helped show that? Describe how it helped exculpate the accused.

Homework: Read the full story at
Read and take notes on Sections 25.1 and 25.2 for class on Monday.
B Block: please also watch the second video on the post below and answer the questions that follow it.

Tuesday, February 5, 2008

Evolution Unit

What does it mean to evolve? What happens when public opinion and science converge? What do you think about evolution? From now until final exams we will be looking at evolution (both micro & macroevolution).

Today students took a survey to expose their preconceived notions. After the survey we discussed questions which they felt were the most challenging to answer and why. We'll return to these surveys at the end of the unit and see if their responses have changed at all.

We watched the following video clip from PBS's Evolution series and discussed these questions: 1. How does the scientific meaning of a term like theory differ from the way it is used in everyday life?
2. Can the “facts” of science change over time? If so, how?

Homework: Watch this video clip on Darwin (also from the Evolution series) and write down your answers to the questions below. Come prepared for a class discussion.

1. What characteristics made Darwin especially well suited for science?
2. What did Darwin see and do on his five year voyage on the Beagle?
3. Why was the publication of the Origin of Species a courageous act?
4. Why was it simply good science?