Welcome to the Biology @ SPS Blog

Below are some questions (and answers) you might have about this blog. If you have a question that isn't listed below, feel free to post it as a comment -- just sign your name as "First Name and Last Initial."

Q: Why not just use blackboard instead?

A: Honestly, I'm a lot more familiar with blogging and have been doing this for the past few years. Also, it's easier (for me) to embed videos and pictures. Lastly, if your parents/guardians want to know what's going on in class or see the work you're doing, they don't need to remember a password to log in.

Q: How often am I supposed to check this?

A: You should check it everyday. A summary of what we did in class along with your homework and in some cases links for your homework/projects will be posted here.

Q: Will I ever have to post a comment?

A: Yes, you will. To post a comment you can either create an account or click "anonymous," just make sure that you sign your "First Name and Last

Q: If you don't tell us homework in class will you post something here?

A: Occasionally yes, which is why it is important to check the blog daily. However, to be fair, any assignments posted here that were not presented in class will be posted no later than 5pm.

Q: What if I can't find something that was posted more than a week ago?

A: Try looking in the blog archive, located at the very bottom of the right sidebar. You will be able to search by post title.

Q: What's with all the posts below this one?

A: Those are all posts from last year when I taught Advanced Biology at New Hampton School.

Tsunamis & Supplements

Today Sammy and Jun taught the class about Tsunamis and Supplements, respectively. Sammy had the class participate in a Tsunami simulation to give us the prospective of what it would have been like for individuals in the 2004 Tsunami in Thailand and Sri Lanka to try and escape the wave. After the simulation we headed inside where Sammy impressed us with his vast knowledge of the mechanics of this wave of destruction.

Jun brought in weights for us to use and samples of supplements for us to look at as well as explaining how these work (or don't work for that matter).

Both boys had excellent, engaging and well researched presentations! They certainly set the bar high!

Life in the tall grasses

Today students in B blocked continued to learn about animal behavior in the grasslands, particularly the savannas in Sudan and the plains of the central United States.

B block: Designing an Animal Behavior Experiment

After reviewing the homework from the weekend on animal communication, students designed a detailed experiment to test an animal behavior of their choice.

Students need to keep in mind: how long will the study take, what will be measured, possible sources of error etc.

D block: Lesson Plans

Today students turned in their lesson plans.  Students continued to work on what activity they will do with the class and had time to practice it.

D block lesson plan update

Reminder: D block your lesson plan is due in class on Monday. Make sure you have written down the details of the content you are going to present.

Birds of Prey Cont.

B Block finished watching Birds of Prey and looked out pictures of one of my college buddies trapping lynx in Montana.

Homework: Prepare a short (5 minute) presentation for the class on how your specific organism communicates with those of the same species. Have information on how it communicates to find a mate, food and protect its territory.

Nate...whales (have a specific specie)
Tak...star nosed mole
Rachel...orangutans
Ben...frogs (have a specific specie)
Pat...birds (have a specific specie).

B block: Animal Behavior & Communication

B block had a quiz today on sections 51.1 and 51.2. After the quiz we started to watch the Discovery Channel video Birds of Prey.

D block project information

D block has decided that they are each picking a topic to teach the class about for the remaining class periods. Below are the requirements and due dates for the project.

On Friday May 2nd the notes pages are due. This will count as a homework grade.
On Monday May 5th the lesson plan is due. The lesson must include a pre-assessment, involve everyone in the class and be no more than 25 minutes in length. Students have been emailed a lesson plan template. (click the picture to make it larger).
On Wednesday May 7th the activity or demo that you are doing in class is due.

Presentation Schedule:
Monday: Sammy (Tsunami), Jun (Muscles and Steriods)
Wednesday: Dana (?), Nicoya (Drug Controversy)
Thursday: David (photosynthesis), Mike (Jane Goodall's work)
Friday: Andrea (Human Nutrition), Ji (Brain/Nervous System).

Animal Communication

Today we started some notes on animal communication and even tried to "train" each other to perform basic tasks to get a feel for what it is like when two individuals don't communicate in the same way or have the same knowledge.

Homework for B block: read sections 51.1 and 51.2, you will have a reading quiz tomorrow in class. Any notes you take you can use.

Chapter 53 Project Rubric

Wondering how your project is going to be graded? Well here it is:

Content 62 points: 2 points for each word/concept (one point for each image and one point for each explanation)

Bibliography 10 points: all images and text are cited in the proper MLA format

Creativity & Formatting 14 points: the use of color and text style enhances the presentation.

Spelling & Grammar 14 points: there are no spelling nor grammatical errors.

Chapter 53 project updates

Some changes to the content for the project have been made. Please see the changes below. I will be on duty in Lindsey this evening and around on Sunday if you need help. Please email me to set up a time.

Here are the terms that you need to include AND have collected evidence (pictures or drawings) from the sites we visited:

species richness
relative abundance
predation
secondary succession
interspecific interactions
parasitism
herbivory
community
biogeography
cryptic coloration
ecological niche
ectoparasite
prey
realized niche
exotic/introduced species
disturbances

The terms below you need to include along with images and an explanation, however you can find these in your book or on the web.

individualistic hypothesis
interactive hypothesis
coevolution
aposematic coloration
Batesian mimicry
Mullerian mimicry
endoparasites
interspecific competition
interference competition
exploitative competition
fundamental niche
symbiosis
commensalism
mutualism
primary succession

You no longer need to include the following terms:

parasitoidism
predator
parasite
host
competitive exclusion principal
stability
recruitment
dynamic equalibrium hypothesis

You should get satellite and or terrain images from google. You do not need a separate slide for each term.

Last Day Outside

Today was the last for collecting organisms and Nicoya spotted a great newt as we were leaving. Tomorrow students will have another quiz on the terms and concepts for chapter 53 and we'll talk more about the expectations for the project due on Monday.

Sample Slides for Community Ecology Project

| View | Upload your own

And the results are in...

The quiz that you took on Monday told me that we have some serious work to do in order for you to be prepared for your projects due on Monday April 28th. To recap your projects you need examples of local flora and fauna that fit each of the terms from chapter 53. I will be posting a few slides sample sides later this evening.

Yesterday we had a lot of success catching various organisms (backswimmers, a large newt, a salamander, a tadpole and small fish).

Today we will be going to a new site where yesterday I saw several large frogs and lots of evidence of bacteria.

So what have we been doing this week?

Well, the big news is that you have an additional week to complete your projects, and as such those projects had better FANTASTIC.

Yesterday Nate caught a fish in the Pemi on his first try with the dip nets, we also caught numerous other aquatic insects and learned what not to wear when we go out in the field.

Below are some pictures that Mike took today.

As we pulled up to Burleigh we saw five wild turkeys, some of them were even engaged in displays by ruffling their feathers.

Moose scat (an example of evidence of a herbivore).
Moose Tracks and these were fairly far apart, meaning the moose could be quite large.
Spring is Here! This Red Maple (Acer rubrum) bud burst.

A walk in the woods

Today B block went up to Burleigh Mountain to look for examples of communities, species richness, introduced species and many of the other things for their community ecology project.

Click on the picture below to be taken to the "What Tree is That?" a free website from ArborDay.org

Chapter 53 Project:

Chapter 53 Assignment

Working in groups of 2 or 3, you and your partner(s) will need to become familiar with the following terms and find examples of them in the area around New Hampton School and in the Lakes Region. We will be going up to Burleigh and walking around campus (rain or shine) so that you can collect evidence (drawings, samples and photographs) so make sure that you dress appropriately. Terms marked with an asterisk (*) are ones that you do not need to find evidence for in person, but rather can look up on line or in a textbook. You will have one week to complete this assignment and you will present your findings to your peers in class. You can put together a PowerPoint, webpage, photo/sample album, video or use another form of media.

One of the goals of this project is for you to become more familiar with your surroundings and even to be able to identify various local plant and animal species.

species richness

relative abundance

species diversity

predation

individualistic hypothesis*

interactive hypothesis*

secondary succession

interspecific interactions

coevolution*

parasitism

parasitoidism

herbivory

community

biogeography

cryptic coloration*

aposematic coloration*

mimicry

predator

Batesian mimicry*

Mullerian mimicry*

parasite

hosts

endoparasites*

ectoparasites

interspecific competition

interference competition

exploitative competition

competitive exclusion principle*

ecological niche

fundamental niche

prey

realized niche

resource partitioning

character displacement*

symbiosis

commensalism

mutualism

keystone species

exotic species

stability

disturbances

ecological succession

primary succession

recruitment

dynamic equilibrium hypothesis

intermediate disturbance hypothesis

Cemetery Data Analysis

Today we went to the ARC and many students used excel for the first time (and realized what a nightmare it can be). Rather than use our data we will be using sample data which will be much easier to work with. You should use the paper I gave you in class for the data.

Please make graphs in excel comparing the following populations, all graphs will have age class on the X axis and survivorship on the Y axis. When you select the type of graph, make sure you choose scatter and then you can choose to have the points connected by lines. If you select line graph, it will not work!

Graph 1: Post-1900 females & Post 1900 males (this most closely resembles our cemetery)
Graph 2: Post-1900 females & pre 1820 females
Graph 3: Post 1900 males & pre 1820 males
Graph 4: The summary of both sexes comparing pre-1820 & post 1900.

In addition you will need to analyze this data and write in terms of any patterns or trends that you see. What type of surviorship curve (I,II or III) does each time period most closely resemble etc...

You will be graded on the following:
1. Whether or not the graphs are correct
2. Having a title and labels for each graph
3. How detailed, insightful and accurate your analysis of the graphs is.
4. There should be two graphs per page and your analysis should be no more than one page.

If you have lost the data I gave you in class you can see me tonight when I am on duty in Moore.

Click here for a link on how to make excel graphs

Class in the ARC today

Meet in the ARC today!

Dall Mountain Sheep

Today students learned how to interpret and graph a life table as well as make inferences about a population in a 15 year study. Learning about the Dall Sheep population was the first part of the lab on population ecology, in the second part of the lab students will gather data from a local cemetery to compare life expectancy in modern and historical populations.

The Dall Sheep we learned about in class today were studied on Mt. McKinely (also known as Denali). This summer while hiking in the Healy Range (across from Denali) we ran into several groups of Dall Sheep where we had set up camp. Click on the pictures to below to make them larger and you will be able to get a better look at the sheep.


Katie is in the lower left corner making dinner while the sheep had finally moved on from where we wanted to set up camp.A second group of sheep easily moved along higher on the ridge.

Population Growth

How many people are in the United States? How many people are in the world? Today we started to think about how populations are distributed, what factors limit population growth and various types of survivorship curves.
At the start of class we checked out the U.S. and World Population Clock. The population numbers were written on the board while students worked independently on a summary packet for Chapter 52. At the end of class students predicted how the numbers changed, needless to say there was some surprise. Try it for yourself while you're watching your favorite TV show. Check the clock at the beginning of the hour and then at the end. While you are watching TV so many things are happening in the world that you aren't aware of. Pretty mind blowing.

Homework for both classes:
1. Finish the packet.

2. Find an article that talks about world population growth, the population policy of a country of your choice or something along those lines. Write a summary of your article and your reaction to it.

Test on the Biosphere & Climate Change

Today both classes had a test on the biosphere and climate change.

In Hot Water

Today B block watched the video "In Hot Water" on the impacts of sea water rise and how that impacts not only plants and animals, but humans too.


In addition, students created acted out advertisements for products that can help reduce CO2 levels (like light bulbs, recycling, solar panels etc...)

Reminder: You will have a test on Friday, so study! I am on duty on Thursday night, if you need help.

Climate Change Part II

Today we continued our discussion on climate change and its consequences. On Friday students will have a test on climate change, basic weather patterns and an introduction to the biosphere.

Check out the Goddard Flight and Space Center for amazing satellite images and videos of ice melting, hurricanes, and more.

Click on the picture to see the video we watched in class today of the thermal satellite shots of Katrina. Look closely and you'll see the areas of cool water the hurricane left in its wake (note: this video may take a while to load).

climate change homework

B Block:
We talked about the scientific basis for climate change as well as reviewing climate patterns.

This homework is due Wednesday for both classes.

Part 1: Watch the NASA video clip "Taking the Earth's Temperature."
(This clip can be slow to load, be patient!)

Part 2: Read the article "2007 Was Tied as Earth's Second-Warmest Year" from NASA GISS Research News.

Part 3: Find an article from the popular news media (USA Today, Boston Globe, etc..) that discusses an increase in global temperature. Write a paragraph comparing this article with the one from NASA's website. You may want to compare the scientific methods (if any) that are discussed, any contradictions etc...

Climate Patterns & Ocean Currents

D block took notes on Aquatic Biomes (see post below).

B Block presented their handouts on aquatic biomes and moved ahead with climate and ocean currents.


What is climate? Is it the same as weather? No! Climate is what you expect and weather is what you get. We watched and discussed video clips on what causes the gulf stream and ocean temperatures and climate pattens.

Homework for both B and D block classes DUE MONDAY.

See your email for an analytical question on climate and currents. If you need help, I am on duty on Sunday night in Moore House.

Aquatic Biomes

"I never knew there were so many zones in the ocean...."

B Block:
Today B block had a reading quiz on sections 50.1 and 50.2 as well as took notes on aquatic biomes and stratification.

D block:
Completed the ecosystem brainstorm (see post below). Homework: read and take notes on sections 50.1 and 50.2 for the reading notes quiz on Friday.

Homework for both classes:

•

•For one of the biomes you selected on pages 1094-1097:

•1. Create a handout for your classmates on this biome.

•2. Include at least 2 images (this can be hand drawn or from the web) as well as info from each of the sections in blue (physical environment, chemical…)

•3. You will be giving a brief oral summary to the class on Friday as well as a copy of the handout. Come to class with copies ALREADY made.

Tomorrow I am going to the NSTA Annual Convention in Boston, so hopefully I'll come back with some good stuff.

Welcome Back

This spring we are going to be focusing on ecosystems and the impact humans have on their environment. Today we started off with a brainstorm on what comes to mind when we hear the words "ecology," "sustainability" and "human impact."

Homework: Read sections 50.1 and 50.2, take notes and be prepared for a reading quiz next period.

Study Up!

Finals are this week which means break is next week. Horray! Rather than attempt to have a review session that meets everyone's needs, please email me if you would like to find a time to meet. My schedule is pretty open this week. Good Luck!

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

Meiosis

Mendelian Genetics

Codominance

Multiple Allelic Traits

Polygenic Traits

Pedigree Chart

Pleiotropy

Environmental Effects on Phenotypes

Genetic Disorders

Testing for Genetic Disorders

Tracking Genetic Disorders with Pedigree Charts

The Human Genome Project

ELSI

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

Cladogram

Phylogeny

Clades

Speciation Event

Homology

Mechanisms of Evolution

Mutation

Migration

Founder Effect / Genetic Drift

Natural Selection

Bottle Neck

Fitness

Microevolution

Sexual Selection

Males Compete & Female Choice

Intrasexual Selection

Intrasexual Selection

Sexual Dimorphism

Fisher’s Process

Single-Step Selection

Cumulative Selection

Biomorphs

Selecting agents

Richard Dawkins

Lamarkism v. Darwinism

Adaptation

Mimicry

Preventing competition

Echolocation

Neutral Theory

Qualifications for Adaptations

Darwin’s Finches

Defining a species

Hybrids

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

Stasis

Character Change

Lineage Splitting

Extinction

Gradualism

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

Explosion

Extinction

Trends in Evolution

Random fluctuation v. trends

What causes evolutionary trends

Macroevolution

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).

Thanks!

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

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.

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.

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.

| View | Upload your own

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?

Homework:

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."

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.

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.

Microevolution

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!

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...

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!

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

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

Rest Day

Enjoy Rest Day, see you tomorrow in class!

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.

To check out the activity we did in class, click here.

Homework: Sleep in & Enjoy Rest Day!

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.

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:

n

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 Nature.com
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.

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?

Reminder: Lab Write Up Due Dates

Just a reminder that lab write ups are due in class when you return from break. If you would like me to look over your lab report, please email it to me NO LATER than 48 hours in advance of class.

Have a great midwinter break!

Working on Lab Write Ups

For the rest of the class periods before break (Tuesday and Thursday for B block and Wednesday for D block) students will be working on writing up the lab. For guidelines, click here.

D Block, come to class on Wednesday, if you have a computer bring it, all the computers are already reserved in the ARC. If you don't have a computer, there are some in the science computer lab we can use.

On Thursday B block will be working in the ARC.

PCR based VNTR Human DNA Typing

Below are the guidelines for writing up the experiment. This will be due when you return from midwinter break, IN CLASS. Late write ups will not be accepted. If you would like to email me a draft to read over the break, please do so no later than 48 hours before the write up is due. These guidelines have also been emailed to you as well.

Lab write up guidelines for VNTR on Human DNA

To help you answer these questions, see the lab guidelines, in a pdf, online at: http://www.edvotek.com/pdf/334.pdf You can also look at the blog for many helpful links in the sidebar on the top right of the page.

Title: should adhere to the guidelines (3 points)

Introduction (15 points total)

Background (12 points)

- What is polymorphic DNA? How is it used for identification purposes?

- What is CODIS? How is it used to solve crimes?

- What is an STR? What is VNTR? Which (STR or VNTR) is predominantly used

in law enforcement? Why?

Hypothesis (3 points)

Methods & Materials: (15 points)

Rather than write this section in the conventional way, answer the following questions in paragraph form that is well written. Do not answer the questions in a numbered format.

- Why is the lysis stage of DNA extraction important?

- What are the consequences if any chelex beads remain when PCR takes place?

- What is the purpose of Proteinase K?

- What is the importance of the changes in temperature in conducting PCR?

- What does it mean to “run to red” in gel electrophoresis. Why is this important?

Results (2 points)

Make a statement that summarizes your results. No table or graph is needed.

Discussion (15 points)

Use this space to talk about sources of error. You should have at least five sources of error AND an explanation for each one.

Conclusion: not needed.

Literature Cited (10 points)

You must cite at least five DISTINCT sources. To help you out, you can start with the three sources below. Please use MLA citations.

http://www.edvotek.com/pdf/334.pdf

http://www.dnalc.org/ddnalc/resources/pcr.html

The Textbook

Remember that when you have a quote, it can not

STAND ALONE .
Yes: The animation available from the Gene Almanac¹ demonstrates the importance of temperatures in PCR, “[t]he temperature is lowered to 50⁰-65⁰C…this allows the primers to anneal.”

No: “The temperature is lowered to 50⁰-65⁰C…this allows the primers to anneal.”¹

2 points will be deducted each time a quote is “standing alone.”

Gel Electrophoresis & Staining

In theory, this is what our results would have looked like for the lab we have been working on for the past 3 classes. The image of the gel shows the results of the amplification of the D1S80 loci through VNTR on human DNA. In the first lane is a ladder which can be used to compare the number of base pairs in a segment of DNA. Unfortunately, all you can see (barely) in our gels is the ladder. Despite this setback, I would certainly consider the lab in a success.

Human DNA isolation

Today we started the first of three sections of the experiments using our own DNA. Step one is to isolate the DNA. Similar to the DNA extractions from common foods, we needed an enzyme and detergents; instead of meat tenderizer, we used proteinase K and we substituted a lysis solution for detergent. Tomorrow we will attempt PCR without using a thermocycler (we don't have one, so we will use three water baths). Stay tuned to see if we have any success!

Homework: rewrite the procedure for PCR, remember, you will only be using the procedure you have written, not the procedure in the handout.

Gel Electrophoresis Practice

Today students practiced making their own gels from scratch and pipetting food coloring in the gels.Patrick & Tak pour hot agarose into a gel form.

Using practice pipets to load the gel with food coloring.

Never Say Prove Again!

I just finished grading your lab reports and for the most part they were impressive. However, the word "PROVE" has been officially banned from your scientific vocabulary (it never should have been there in the first place!).

In science you can never really PROVE anything; you can disprove a theory and you can find support for a hypothesis but you can't PROVE it. Hopefully this classy James Bond movie poster will help you remember.

Gel Electrophoresis Lab Instructions

(NOTE: this post is for Friday and Saturday classes)

Objective: go over the procedure for making a gel and conducting gel electrophoresis by taking notes from a powerpoint, watching a short video and doing an online activity.

On Monday we will do a practice run using food coloring and see how it moves through various concentrations of agarose (o.7g, 1.0g and 1.5g)

Because of the special schedule D block will not need to leave lunch early to have enough time for the lab. There is even a video on youtube that shows the steps in gel electrophorsis.

Working on Lab Reports

Today B block worked on writing their lab reports.

B Block's lab reports are due tomorrow (Friday)!

Remember to print off the rubric and complete a self evaluation in the points awarded section. Check out the links at the top of the sidebar on this page for more info on how to write your lab report.

Writing a scientific paper

Today students took a quiz on the guide to writing scientific papers. After completing the quiz, we read a sample paper and answered questions about the information that was (and in some cases was not) presented.

Lab report due dates & nit-picky details.

* B block your lab write up is due Friday in class.
* D block your lab is due Saturday in class.
* Each person will need to write his or her own lab report.
* Please print out the rubric and complete the self evaluation before turning in you lab report.
* 5 points will be deducted if you have not printed out the rubric and completed the self evaluation.

Lab Report Rubric

In addition to being posted here, the lab report rubric has been emailed to students in a chart which includes as self evaluation section, so that they can check and make sure they have all the necessary components. Title 3 points Includes the environmental factors that were manipulated (1 pt). The parameter that was measured (1pt) The specific organism that was studied (1pt). Introduction 12 points Includes the observation (2 pts) Question that led to the hypothesis (2 pts) Relevant background information (5 pts) hypothesis (3pts) Materials and Methods 15 points Describes (not lists) how the experiment was conducted. The equipment used in the experiment is NOT listed, instead is part of the narrative. If well-known methods were used without changes, simply name the methods (e.g., standard microscopic techniques). Results 10 points Here the researcher presents summarized data for inspection using narrative text (4 pts) Tables and/or figures to display summarized data (6pts) ***If Raw data is present 4 points will be subtracted **** Formatting of tables/graphs 7 points All tables and/or graphs have… Title (1pt) A description explaining what is presented (4 pts) X and Y axis are labeled (2 pts) Discussion 13 points Here, the researcher interprets the data in terms of any patterns that were observed (5 pts) An explanation of how the results differed from those hypothesized (5 pts) Include at least 3 sources of error (3 pts) Conclusion 7 points This section simply states what the researcher thinks the data mean, and, as such, should relate directly back to the problem/question stated in the introduction. Acknowledgements 3 points In this section you should give credit to people who have helped you with the research or with writing the paper. If your work has been supported by a grant, you would also give credit for that in this section. Literature Cited (Will vary..max 5 points) This section lists, in alphabetical order by author, all published information that was referred to anywhere in the text of the paper. It provides the readers with the information needed should they want to refer to the original literature on the general problem. Spelling, Grammar & Formatting 5 points

Report is free from spelling and grammatical errors. All section headings are in bold and centered.