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.

Sample Lab Report

Below is a sample lab I wrote for the Eggsperiment. You may use this as a guide for writing your papers. Pay close attention to formatting & use of the past tense.

Ms. Saxe

A Block

Month Day, Year

The Effect of Various Concentrations of Sugar Solutions

on the Percent Change in Mass of a Chicken Egg.

INTRODUCTION

Osmosis and diffusion are essential to maintaining equilibrium of solutes and water in cells. Osmosis is the movement of water across a semi-permeable membrane, where as diffusion is the movement of solutes from an area of high concentration to an area of low concentration¹. Various transport proteins located in the cell membrane assist in moving large solute molecules across the cell membrane. Solutions where the concentration of solutes outside of the cell is less than in the cell are said to be hypotonic. Cells in hypotonic solutions tend to swell as water enters the cell to maintain equilibrium. Solutions where the concentration of solutes outside the cell is greater than inside the cell are hypertonic. In hypertonic solutions, water leaves the cell to try to maintain equilibrium. Lastly, when the concentration of solutes outside and inside the cell is equal the solution is isotonic. Using a chicken egg (without a shell) as a model of the cell membrane, is it possible to observe the effects of osmosis with the naked eye? If an egg without a shell is placed in a sugar solution, then there will be some change in the mass of the egg due to osmosis.

MATERIALS & METHODS

One dozen large white chicken eggs from the Jackson Star supermarket were submerged in Best’s white vinegar for 72 hours in a three liter bowl. During this period, every 24 hours the vinegar was changed to increase the rate at which the shell decomposed. Eggs were moved around in the vinegar once every 24 hours to ensure all sides of the shells were equally submerged. Any time eggs were handled rubber gloves were used to protect the individual from any bacteria that may have been present. After 72 hours, the eggs were ready to be used for the experiment.

The control egg was removed from the vinegar and weighed on an electronic balance to obtain the initial mass. This egg was placed in a 400mL beaker containing 350mL of tap water and labeled as the control. The experimental egg was weighed using an electronic balance and placed aside in a weigh boat while the sugar solution was created. The sugar solution contained 15g of table sugar and 35g of sucrose added to 250mL of tap water, in a 400mL beaker. The sugar solution was stirred thoroughly until all of the grains of sugar were dissolved. The sugar concentrations were recorded in a data table on a lab handout. The beaker was labeled with the last names of group members, class block and placed in a cabinet to sit undisturbed for 48 hours over the weekend. After 48 hours, the secondary observations of the egg were completed including obtaining the final mass of the egg using an electronic balance. Final mass was recorded in the lab handout. Eggs were disposed of by the instructor.

RESULTS

The overall results in E and F block varied greatly: in E block all of the eggs had a negative percent change meaning that they gained mass, where as in F block, all of the eggs had a positive percent change meaning they lost mass.

Figure 1: This graph shows the percent change in mass for all of the eggs tested. Egg number 1 is the control. Eggs 2-5 were from E block and eggs 6-8 were from F block.

DISCUSSION

Perhaps what is most interesting to note about this experiment is that each block experienced the same overall result: E block eggs were all placed in hypotonic solutions and F block eggs were all placed in hypertonic solutions. The results do support the hypothesis that, if an egg is placed in a sugar solution a change in mass will occur. No possible explanation can be found at this current time to explain why the eggs in the various classes reacted so differently to the solutions. Possible sources of error for this experiment include: incorrect labeling of sugar in the large plastic bag; incorrect notation for what and how much was placed in solution and allow the eggs to sit for too long in solution. The table sugar that was used for this lab came from the chem. storage room and had been sitting for an unknown amount of time in a plastic baggy that was loosely secured with a knot. Exposure to fumes and potentially other chemicals may have left residue in the sugar which changed how it reacted in the experiment. If the solutes added to water were incorrectly written down this could certainly have impacted how the eggs reacted. Lastly, since the eggs sat over the weekend, nobody observed them at 24 hours, perhaps the greatest change in mass was visible then, but nobody was able to observe it. Further study would be needed to determine the possible causes of the anomalies in the results.

CONCLUSION

While the data in this experiment is inconsistent between E and F blocks, it does support the hypothesis that if an egg is placed in a sugar solution there will be a change in mass. Further tests using a larger sample size would be needed to establish more consistent events.

ACKNOWLEDGEMENTS

Thanks to Mr. Brummer for supplying the vinegar and Ms. Saxe for soaking the eggs in advance so they could be used in the experiment.

LITERATURE CITED

1. Memorial University of Newfoundland. Principles of Osmosis and Diffusion. [Online]. October 22, 2007 URL: http://www.mun.ca/biology/Osmosis_Diffusion/tutor2.html

Independent DNA extraction

Today students conducted the experiments they wrote over the weekend to extract DNA from various substances. Most students tested the effectiveness of various enzymes on the yield of DNA.

Tonight for homework, please go to the guide for writing scientific papers.
1. Read it, seriously actually read it.
2. You will have a mini quiz on how science papers should be written. If you take notes, you will be able to use them.

Tomorrow in class we will talk about how you will write your papers as well as give out a rubric from paper writing.

Pictures from the DNA extraction

Step 1: Combine spinach, water and salt. Blend for 15 seconds on high and the strain the solution.
Add detergent and then let sit for at least 10 minutes. Pour into test tubes, so the tube is about 1/3 full. Add a pinch of enzymes (in this case meat tenderizer).
Gently stir the enzymes and then at isopropyl alcohol so the test tube is now 2/3 full. Let the magic of chemical reactions and density go to work....and voila! DNA.

If you look closely, you will see a white stringy matter floating the in the tube. That's DNA!

Homework (see the post below). D block class, we will be starting early at 12:15/12:20 so you will have time to complete your experiment.

DNA extraction!

Today (and Saturday) we will be extracting DNA from spinach. You can extract DNA from just about anything. To see how we did this check out the instructions from Utah Genetics.

Homework: Read the 20 Most Frequently Asked Questions about this experiment. You and your partner will be conducting your own version of this lab in class on Monday.

You and your partner should have a procedure written and bring any materials you will need (if they vary from what we used in class).

Article discussions & cloning

Today we finished watching the animation of how a gene is cloned and students presented their biotechnology articles. Below are some of the summaries.

Liver cancer really fatal in China, hard to diagnose, because therapies are limited.

Gel electrophoresis was used to look for proteins whose copies are increased or decreased in patients with the liver cancer. In looking through the variation in proteins, they discovered two proteins that could serve as screening markers for liver cancer.

Towards a faster prenatal test for Down Syndrome

Normal test the results take two weeks, scientists are using a variation of PCR to find out if the child has down syndrome in two hours. The new process is called digital PCR so they are able to see the extra chromosome present. Put on a microfluid chip.

Judges concerns over the smallest of clues

Using PCR tests on crime scene, benefit will require only one nanogram (only 150 cells). Disadvantage, because you only need a little bit of evidence that the sample could become contaminated. Ex: touch an object, pick up some cells, these cells can find their way into the crime scene.

Homework: none

Again, nothing says welcome back like...

a quiz!

Here's our plan for B block today:
1. reading quiz with notes
2. discuss answers
3. hand back papers
4. hand out progress reports
5. discuss homework.

Chapter 20 is all about DNA technology and how techniques such as PCR, gel electrohoresis and southern blot are used. Your homework for tonight is to choose one of those techniques and find a news article from 2007 (or 2008) where your technique of choice is used.
* read the article
* print it out
* come to class prepared to explain why this technique was used.

A good place to look for articles is Science Daily

Work for vacation

Your homework for break is to read chapter 20 and take notes on it; when you return you will have an open notes reading quiz.

Tips for reading and staying focused:

Before reading you should look over the major headings in the chapter and look at the pictures. Read the captions! It costs more money to have a color picture than black text, if publishers are spending money on it, it is there to help you.

Before reading the chapter you should read the section summaries at the end of the chapter to help you keep the big picture in mind.

While reading you should read through an entire paragraph and try not to get hung up on specific details. After reading the paragraph, if you are still confused look to the pictures for clarification.

After reading a section (20.1) close your eyes and try to state 3-4 key points in the section.

While I'm on JUA...

Please sign in with Gina G. (downstairs in Mrs. Berry's office). You should read chapter 20 and take notes. You will have a quiz (and may use any notes you take) when you return from break in January. I suggest you do this before you leave for break so you don't forget.

D block you will have class on Wednesday.

ELSI paper feedback

Lessons Learned:

"I didn't realize that the paper could ONLY be three pages. I had delete the hard work that I did."
"Never trust technology, words are easier to read than squares."
"Footnotes are fun."
"Hard to miss a lot of class and still write a paper."
"Make sure that my own words and my sources are divided."
"Double check your sources...Just because the title says what you need, doesn't mean the paper contains helpful information."

What did we learn through our research?

Genetic Information Nondiscrimination Act is in the process of being passed...Eugenetics is the science of improving a the human genetic population...GM foods have a positive and negative side, for example: GM foods can create new unknown allergens...No laws have been passed about genetic information...Exploring the link between DNA and behavior...

Where are we going from here?

When we return from break we will jumping into chapter 20 (DNA Technology & Genomics) and chapter 21 (the genetic basis of development). We are going to try a new class structure where the first class period will be a lecture, the second period we will go to the ARC and do research and the third period you will present what you learned to your peers.

Working on papers this week

Change of plans, because of tournaments, testing and a variety of other reason, your paper is now due on either Friday or Saturday, depending on when you have class. In the meantime, you will be meeting in the ARC each class period from now until then to work on your papers.

Check out the video below (thanks Mike H.) for more information.

ESLI Research Paper

What is ELSI?

ELSI stands for Ethical, Legal and Social Implications.

What is a research paper?

Look it up. Just kidding. A research paper means you are going to need to gather information from as many sources as possible and then sift through it to find what is helpful to you.

Where can you find information?

There is a link list on the right side bar for some places you can start looking. Many of these pages will have additional links at the bottom of the page which can lead you to more information. You can also check the library catalog.

When is this due?

This is due for all classes on Thursday December 12th.

Write a three page, 1.5 spaced paper (no more, no less) and (quit complaining, this is practically nothing!) addressing one of the following issues:

A. Fairness in the use of genetic information by insurers, employers, courts, schools, adoption agencies, and the military, among others.

A driving question is: Who should have access to personal genetic information, and how will it be used?

B. Privacy and confidentiality of genetic information.

A driving question is: Who owns and controls genetic information?

Use the check list below to make sure your paper meets all the requirements

¨ Three different sources are directly quoted in the paper and cited. For example:

Blah blah blah, “DNA samples can be held indefinitely, there is the added threat that samples will be used for purposes other than those for which they were gathered.”[1]

¨ All of sources are properly cited in the MLA format.

¨ There is an introduction paragraph which gives background of the human genome project (HGP).

¨ The HGP background includes how and why the project was started and when it was completed as well as three major findings that resulted from the project.

¨ If possible find a specific case study that supports your topic and summarize what happened.

¨ Consequences of misuse of genetic information.

¨ The overall paper addresses the Ethical, Legal and Social Implications of the chosen topic.

¨ Paper is proof read, no seriously, please read the paper before you turn it in, and contains no grammatical or spelling errors.

¨ Paper is TYPED.

¨ Paper uses 1.5 spacing, size 12 Times New Roman Font and has 1” margins (yes you will be graded on this.

---

[1] Genetics Legislation. Human Genome Project. Last modified Friday May 25^th, 2007. Accessed 12.6.2007 http://www.ornl.gov/sci/techresources/Human_Genome/elsi/legislat.shtml

Article Discussions

The first half of this week will be spent reading articles from The New Yorker magazine's Annal of Medicine & Annals of Science sections.

Why read articles from The New Yorker?

The New Yorker articles are available to the majority of the public, are well written, well researched narrative essays which have a solid science background. The articles fuse the scientific and emotional sides of debates or issues and therefore provide a unique perspective.

What are we reading?

An Error in the Code: What can a rare human disorder tell us about human behavior.
Individuals with Lesch-Nyhan acutely feel pain but can't stop self mutilating, it is as if their hands and mouths don't belong to them.

Darwin's Surprise: Why are evolutionary biologists bringing back extinct deadly viruses?

"John Coffin 'understand[s] that the idea of bringing something dead back to life is fundamentally frightening,' he went on. 'It’s a power that science has come to possess and it makes us queasy, and it should. But there are many viruses that are more dangerous than these—more infectious, far riskier to work with, and less potentially useful.' Thanks to steady advances in computing power and DNA technology, a talented undergraduate with a decent laptop and access to any university biology lab can assemble a virus with ease." Continue reading...

Homework: Study for a quiz on Thursday on Chapters 13 & 14

Beyond Mendel

This post is for Friday and Saturday (12/1)
We continued with Chapter 14 with the following concepts:

•

•
Codominance

•Multiple Allelic Traits

Polygenic Traits

•Pleiotropy

•Environmental Effects on Phenotypes

•Genetic Disorders

•Testing for Genetic Disorders

•Tracking Genetic Disorders with Pedigree Charts

High blood pressure is a polygenic trait.

The phenotype is an interaction between a person's weight (one or more obesity genes), cholesterol level (one or more genes controlling metabolism), kidney function (salt transporter genes), smoking (a tendency to addiction).

Homework: Complete the rest of the genetics problem set and work on your genetics mini project.

Genetics Mini Project

Read about your assigned topic and do research to present a concise report to your classmates. You will write no more than half a page, typed, single spaced on your topic and give a 2-3 minute presentation during class on Monday. This will be worth a quiz grade. Remember to keep this concise and informative.

You must have a works cited at the bottom of your paper with at least THREE sources referenced.
Wikipedia is NOT an acceptable source. Below are links to potential starting points for your research:

Understanding Genetic Disorders -- Utah Genetics

Human Genome Project

Genetic Disorders from MedLine

Mendelian Genetics (Chapter 14)

Today we reviewed incomplete dominance as well as Mendelian genetics principles (law of independent assortment, law of segregation, dominance, recessiveness). We also learned how the rule of multiplication and addition can help us solve complex genetics problems, rather than write enormous punnett squares.

Would you rather do this to find the probability of getting YYRR:Or this... YY = 1/4 RR = 1/4
1/4 x 1/4 = 1/16, is the probability of getting YYRR

Homework: Genetics Practice Problems, answer the questions at the top of the page (explain...what is...). Write your answers on a separate sheet of paper and use complete sentences. Complete problem numbers 1, 2, 3, 7 and 8.

Meiosis (see below)

For the winter term, all posts from Tuesday's class will apply to Wednesday as well.
In addition, since it was long block today, D block started chapter 14 with the basics in Mendelian genetics.

Homework: read 14.1-14.3 for Thursday. You will not have a quiz, but taking notes would be to your benefit.

Meiosis

So today we learned a valuable lesson: Check your email, especially before you go home for break. Students had a quiz on meiosis today and took notes from a powerpoint. We are only going to spend one day on meiosis because we covered it in detail last year. There are some key points to remember about meiosis:



1. It occurs in gametes
2. It increase genetic variation through crossing over, independent assortment and random fertilization.
3. It creates 4 daughter cells that are NOT identical to the parent cell.

Homework: Read sections 14.1-14.3 for class on Thursday.

Nothing says welcome back like...

a Quiz.

'Tis the season get back to work. Just a reminder that you needed to read chapter 13 over break and that you have a quiz your first class back. Any notes you took on the chapter you will be able to use.

Need to know...

There are 12 questions out of 75 on Chapter 6 on the test.

You should know…

1. in what type of cell you’d find large numbers of ribosomes.
2. what type of RNA and proteins can move through the nuclear envelope
3. the direction of how DNA/proteins move through the endomembrane system
4. the cell part that makes proteins
5. where you would find hydrolytic enzymes
6. the functions of the following cell parts: lysosomes, vacuoles, mitochondria, golgi apparatus, peroxisome.
7. the components of a chloroplast.

Review Sheets

Here's who is doing what review sheet:

Chapter 2: Dana & Andrea
Chapter 3: Jun ALONE
Chapter 4: Nicoya ALONE
Chapter 5: Sammy ALONE
Chapter 6: Ms. Saxe
Chapter 7: Terrance
Chapter 8:Tak and Jae Ro
Chapter 9: Ji
Chapter 11: Rachel and Mike
Chapter 12: David

Your review sheet should at, a minimum, have the vocabulary (and definitions), key concepts and images which help explain concepts.

Final Exam Review

Please sign up for one of the following chapters. 5 people will need to work on their own. If you choose to work on your own, you will get extra credit. Your partner may be from the other class.
You will create a study guide for your peers to use.

This is due Monday in Class. Please make 14 copies of your review sheet, before you come to class.

Chapters 2, 3, 4, 5, 6, 7, 8, 9, 11, 12

Use the post a comment feature to write you First Name and Last Initial and the chapter you will be doing.

Cancer & the Cell Cycle

Today we talked about cancer & the cell cycle. We watched a video clip on the development of tumors from the Howard Hughes Medical Institute and discussed the frequency of various types of cancer around the globe.

Notebook Check & Mitosis

Today B Block had their notebook check and we reviewed the basics of mitosis. Tomorrow we will have visitors to class from the headmaster's council.

Homework: Start studying for the final exam

Reminder: Notebook Check

B block you will have a notebook check on Tuesday.

D block you will have a notebook check on Thursday.

Why have a notebook check?
Your final exam is coming up and if your notebook isn't organized, it's pretty difficult to study. Anything from the first day of class is fair game. I suggest you use the blog to help you get organized. You will only have 20 minutes to complete the notebook check. Questions will be in chronological order.

Mitosis Homework

Mitosis Homework: Read Chapter 12 and please use your own lined paper to complete the following assignment. This activity will count as two homework assignment grades.

Here are some links to help you with the homework:

Review of Mitosis

Cell Cycle and Mitosis Tutorial

Cell Cycle Game

1. How can there be 46 chromosomes in a human cell at metaphase and also 46 chromosomes in each daughter cell?

2. Describe the events in each of the following phases of the cell cycle; G₁, S, G₂, and M.

3. Briefly describe how prokaryote chromosomes differ from those of eukaryotes.

4. Explain the difference between a chromatid and a chromosome, using a diagram with
your explanation.

5. List the stages of mitosis in proper order.

6. Diagram the stages of mitosis and give the major events in each stage.

7. How does cytokinesis differ in plants and animals.

8. How does mitosis ensure that each daughter cell has the same genetic makeup as the parent cell?

9. List and briefly discuss at least two factors that control and regulate cell division

Cyclic AMP disucssions

Today in class we discussed how cyclic AMP can impact how our bodies function at the molecular level. Here's what we learned...

1. Cells of alcoholics have lower levels of cAMP.
2. Researchers have found in that reduced cAMP induction may be an underlying cause of fragile X syndrome, a leading cause of mental retardation.
3. cAMP can effect erythroblasts (which are nucleated red blood cells, found in bone marrow).
4. cAMP responds to liver disease
5. A possible cause of Alzheimer's disease is low levels of cAMP.

Cell signaling continued

Today D block caught up with B block in cell signaling. Also, the chapter 11 PowerPoint is available for download for seven days (until Nov. 8) by clicking here: http://download.yousendit.com/98A18084708E0D7D


Today our goal was to look at the big picture when it comes to cellular communication and signal transduction. Also, there has been a change of plans: You do not have a quiz on chapter 11 tomorrow.

Instead, your homework is to find a disease, condition or poison that is related to the function of cyclic AMP.

What is cyclic AMP (cAMP)? cAMP is a secondary messenger that is produced from ATP by adenylyl cyclase. As a second messenger, cAMP initiates a series of additional reactions in the cell such as phosphorylation and activation of enzymes.Where can you look for information:
Science Daily
PubMed

What should you search for? Try looking up, "genetic disorders cyclic AMP" "toxin cyclic AMP" etc..