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I Teach Evolution, Do You? – Part II

February 26, 2011 in KABT News

Two weeks ago, I was struck by the information on biology teachers that I read in the article On Evolution, Biology Teachers Stray From Lesson Plan (duplicate post that you don’t have to login in to read) by Nicholas Bakalar.  At that time, I decided that I would share some of my thoughts and lessons that I used to teach evolution in my freshman Biology course. 

This particular lesson is the second of a series of activities that was conducted at the very end of the school year at the end of my unit on genetics after having covered standard Mendelian genetics and content associated with inheritance in humans.

The Biology of Race and Inequality

Lesson 1 - Comparing Chimpanzees using mtDNA Sequences (previous post)

Lesson 2 – Comparing Humans using mtDNA Sequences

Background – In the early summer of 2002, I attended a Dolan DNA Learning Center workshop at the Stowers Institute where a group of biology instructors were introduced to one wet lab and a number of bioinformatics activities associated with their new educational program called Genetic Origins.  Scott Bronson and Ewe Hilgert ran the workshop that specifically introduced us to the study of mitochondrial (mt) DNA and Alu genomic elements.

Objective- For students to apply what they learned in the previous activitiy on comparing chimpanzee mtDNA seqeunces to the analysis to human mtDNA sequences, and to realize that mtDNA comparisons do not support the concept of distinct human races.  

Because the previous activity demonstrated that mtDNA sequences were supportive of their being geographic subspecies of chimpanzees, many students will assume that the data for human mtDNA sequences will be just as supportive of geographic categorization of humans into races (they may even remember that Linneaus had segregated humans into distinct categories as well, although I would not reminded them of this directly). 

In the end, students should notice that the human mtDNA data is different than the chimpanzee mtDNA data, in that there is more variation within groups of humans than there is between those same groups.  In chimps there is significantly more variation between groups than within groups.  The main question that arises from this observation, is “Why is this so?”

Introducing the Activity - I do little introduction for this activity.  Since they would have just complete the comparison of chimpanzee mtDNA sequences, they know what to do and appreciate being allow to just get started.

Potential Supplemental Items

Although I haven’t used these resouces in conjunction with this specific activity, they may be nice additions that would provide students with background on the diaspora of modern human.

1. Spencer Well is Building a Family Tree for All Humanity (20:51)

I would now consider having students view this video for homework, although it is short enough that it could be viewed after they finished the activity above.  Here are some comments about Spencer Wells’ research on the TED website where this video is located.

By analyzing DNA from people in all regions of the world, Spencer Wells has concluded that all humans alive today are descended from a single man who lived in Africa around 60,000 to 90,000 years ago. Now, Wells is working on the follow-up question: How did this man, sometimes called “Y chromosomal Adam,” become the multicultural, globe-spanning body of life known as humanity?

Wells was recently named project director of the National Geographic Society’s multiyear Genographic Project, which uses DNA samples to trace human migration out of Africa. In his 2002 book The Journey of Man: A Genetic Odyssey, he shows how genetic data can trace human migrations over the past 50,000 years, as our ancestors wandered out of Africa to fill up the continents of the globe.

2. Humans May Have Left Africa Earlier Than Thought

Here are two NPR audio stories from this year that may be interesting as well, An Earlier Departure Out of Africa? (9:48) and Tools Suggest Humans Left Africa Earlier via Arabia (4:23).

3. Mr. Wallace’s Line by Jared Diamond (August 1997)

This is a great general introduction to Alfred Wallace and biogeography.  It mainly discusses non-human animal life in the Malay Archipelago, but there is a reference to  Tim Flannary and Jonathon Kingdon’ hypothesis that successful island hopping is responsible for making modern humans modern.  This thought takes a more interesting twist with the more recentdiscovery of Homo floreseinsis on one of these Indonesian Islands.

4. Luigi-Luca Cavalli-Sforza’s book, Genes, Peoples, and Languages (207 pages)

This is a great book that contains relevant background information on population genetics.

NPR Science: February 14

February 19, 2011 in Teaching Resources

Week of February 14, 2011

Click on the logo above to go the the NPR Science site, or use the links below to navigate to one of the stories that I thought may interest you.

Last week, I showed my students my most recent NPR post and allowed them to pick the story title that most interested them to watch and talk about at the beginning of class.  They picked the video on the Meat-Eating Furniture and were quite intrigued.  Then, I showed them James Randi’s video on Homeopathy.  None of them had heard of homeopathic treatments but they appreciated being educated regarding the difference between these treatments and drugs that have been through FDA approval.

Happy listening!

Becoming Naked and Clothed

February 17, 2011 in Teaching Resources

Exploring Human Evolution and Culture through the Study of Lice.

Yesterday evening I took the time to watch Nova Science NOW hosted by Neil DeGrasse Tyson.  Although I enjoyed the entire program, I was especially intrigued by the segment on the research of David Reed at the University of Florida’s Natural History Museum.

This segment discusses how molecular comparisons of our clothing, head, and pubic lice with the head and pubic lice found in chimpanzees and gorillas, respectively were used to infer the time when modern humans began wearing clothing, and when ancestral humans lost most of our hair.  With so much in the news lately about the diversity of human microbe flora, etc… this research could provide a clear example of the distinct niches that are found on the human body.

Watch the 11 minute segment at the Nova ScienceNOW, and then read the summary article In Lice, Clues to Human Origin and Attire from the New York Times, or download and read pdf’s of the scientific research below.

  1. Origin of Clothing Lice Indicates Early Clothing Use by Anatomically Modern Humans in Africa from the journal of Molecular Biology and Evolution.
  2. Pair of lice lost or parasites regained: the evolutionary history of anthropoid primate licefrom BioMed Central
  3. A list and some links to other publications can be found at Dr. Reed’s website.

I think this would make a great bioinformatics/molecular clock activity as well.

I Teach Evolution! Do You?

February 12, 2011 in Teaching Resources

Earlier this week, I scrolled upon the above post on my twitter account, followed the link to the New York Times article On Evolution, Biology Teachers Stray From Lesson Plan (duplicate post that you don’t have to login in to read) by Nicholas Bakalar, and read… 

Here’s was struck by…

  • “Only 28% of biology teachers consistently describe straightforwardly the evidence for evolution and explain the ways in which it is a unifying theme in all of biology.”   So, 72% of biology teachers don’t do this?  Could this be true?
  • “13 percent explicitly advocate creationism.”  So, 59% may accept evolution in some manner but just don’t teach it?  Wow!
  • It’s hard to be optimistic, but Eric Plutzer, one of the authors of Defeating Creationism in the Courtroom, But Not in the Classroom (the research being cited in the NY Times article) stated that, “We think the ‘cautious 60 percent’ represent a group of educators who, if they were better trained in science in general and in evolution in particular, would be more confident in their ability to explain controversial topics to their students, to parents, and to school board members.”

… this sad commentary reported during the week of Charles Darwin’s 202nd birthday! 

So, is there anything that we can do as a KABT community to help “better train” biology teachers in science and evolution? 

I really don’t know, but I thought I could at least share some of what I have done to teach evolution during my 18 years in the freshman biology classroom.

Below, I relate the general structure of the freshman biology courses that I have taught, and the introductory setting that I tried to establish.  These brief comments are followed by the first of a series of activities (other will be presented in future posts) which I have used to provoke a thoughtful and respectful discussion of the biological concept of race.  After I finish with the series of posts on biological race, I will think about backing up and filling you in on some of the other activities, discussion, homework assignments, etc… that I used to teach the fundamental concepts of natural selection and speciation.

Course Perspective

I don’t claim to have expert knowledge of evolution, nor do I have special abilities when it comes to teaching evolution, but I can demonstrate that at least 25% of my class time in freshman biology was spent learning about evolution.   Two of my 8 units, over the course of the year, were devoted to the topic, and I integrated the evolutionary perspective into some course work during my previous units on classification, ecology, as well as subsequent units on cell biology, cell energetics, molecular biology, and genetics.  The activities that I will be presenting in this, and subsequent posts, were some of the culminating activites my students completed at the end of my unit on genetics second semester. 

Thus, it is safe to say that I generally accept Theodosius Dobzhansky’s claim that, “Nothing in biology makes sense except in the light of evolution.”

Introductory Setting for Teaching Evolutionary Biology

Like many biology teachers, I began the school year establishing the difference between science and non-science through a few lessons where we covered concepts including empirical and rational epistemologies, observation, discovery-based and hypothesis-based science, and theory.  One of my lessons was motivated by Brad Williamson, who introduced me to the Secret of the Psychics Nova video and the accompanying con he used to perform on his students (more on that later). 

One important goal of this introductory material was to set the appropriate tenor in the classroom.  Although I have never had a single significant distracting classroom experience involving creationism with students or their parents, I thought it was important to develop a standard for what constitutes science from the beginning so that if later issues popped-up, they could be judged against this pre-established standard.

The Biology of Race and Inequality

This first of a series of activities was conducted at the very end of the school year at the end of my unit on genetics after having covered standard Mendelian genetics and content associated with inheritance in humans.

Lesson 1 - Comparing Chimpanzees using mtDNA Sequences

Background – In the early summer of 2002, I attended a Dolan DNA Learning Center workshop at the Stowers Institute where a group of biology instructors were introduced to one wet lab and a number of bioinformatics activities associated with their new educational program called Genetic Origins.  Scott Bronson and Ewe Hilgert ran the workshop that specifically introduced us to the study of mitochondrial (mt) DNA and Alu genomic elements.

Objective- To introduce students to the concept of subspecies through study of the geographic distribution of chimpanzee populations and a comparison of  mtDNA from some of these isolated populations, in an effort to prime them for a discrepant event with regard to a similar activity involving humans (they may even remember that Linneaus had segregated humans into distinct categories as well, although I would not have reminded them of this directly).

Introducing the Activity - When starting things off, I most would commonly show a map of the ranges of the subspecies of chimpanzee found in Africa (above).  I would prompt the students to remember what we learned about scientific names from first semester (we had only learned about bionomials not trinomials), and proceed in having them hypothesize why these populations of chimpanzees were given distinct three word names.  It was pretty clear to most students that the trinomials may represent a single species that has recently begun to develop geographically isolated populations.  I would likewise prompt them to remember what we had discovered about processes of speciation (we had already learned about allopatric speciation and pre and post-zygotic isolating mechanisms), and have then hypothesize differences that may exist within mitochondrial DNA samples taken from three of the subspecies (see the activity below). 

Once some thoughts had been generated, I would model the procedure in the activity that follows, making sure that students understood how to cut the mtDNA sequences from the supplemental document below and successfully paste them into the appropriate online sequence alignment tools.  Realize 1) that other alignment tools could be used (I always had problems with the Dolan Center’s online tools and googled this one up years ago) and 2) one can actually speed things up by pasting all the sequences at once.  I usually showed the students the short cut later when we discussed their answers at the end of the class period or the following day.  I imagine that using the slower process actually gave them time to think about the data as it was processed resulting in more thoughtful answers.  In a subsequent activity with human mtDNA sequences, I would allow them to use the short cut because they would then have a good enough understanding of significance of what they were doing.

Let everyone know if you have any questions or general words of advice in response to things said.  Otherwise, thanks for your attention, and I will be talking to you again soon!

Happy Birthday Chuck!

How Evolution Gave Us The Human Edge

January 22, 2011 in Teaching Resources, Technology

Click on the image above to access this unique NPR Resources containing

  • 4 Interactives on Brewing a Human, An Upright Primer, Lost Cousins and Fossil Forensics (the last two are a small portion of the Smithsonian Human Origins Initiative)
  • A collection of 20 NPR audio stories previously broadcast on Morning Edition or All Things Considered that provide an eclectic and pretty comprehensive prespective on human evolution.  Topics include, skin color, walking and running, tools and weapons, diet, brain development, talking and language, culuture and belief systems.

I have not used this resource in class having just noticed it while preparing my previous post on the NPR Science site.  If you have used it before and have particular suggestions on its integration please share your experiences with a comment.

Energizing Evolution

January 1, 2010 in Teaching Resources

it, as well as our understanding of it, just keeps going and growing and going…

During the holiday break, I have come across a number of valuable resources (video, audio, and paper) for demonstrating to students that the processes of natural selection and speciation, that Darwin made us aware of 150 years ago this past year, are actually occuring before our very eyes.  

Instead of hypothetical just-so-stories, these resources are user friendly and thought provoking real world examples with organisms and adaptations that students can relate to.  These examples also highlight the work of the people, and the personalities, behind the acquisition of new scientific knowledge.  I commend these scientists and numerous others who understand the importance of communicating science to a sometimes skeptical public and whose efforts have provided us with these wonderful resources and springboards for learning.

 Lizards

Read on to find out about these 7 resources…

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Avida-Ed: Exploring Evolution in Silico

October 8, 2009 in Labs, Student Research Ideas, Teaching Resources, Technology

At the NABT Conference in Atlanta in the fall of 2007, Brad Williamson talked me and a few others who were loitering around to come to a workshop presentation on Avida-Ed software as a means of fostering inquiry of evolutionary processes.  After the presentation, Brad suggested that I write a post about the experience.  At the time, I didn’t have much to say.

Having had time to play around with Avid-Ed and to make my way through most of the unedited model lessons downloadable from the Avida-Ed website, I have decided to make the post.  The best place to start is to download the software developed by Robert T. Pennock from the Avida-Ed website at Michigan State University, and to read the Discover magazine article written by Carl Zimmer highlighting Robert Pennock’s development and use of the research version of the software to study the process of evolution (The first activity below has pre-activity questions that require students to read this article).  The links below will get you that far.

  1. Avida-Ed Website
  2. Testing Darwin by Carl Zimmer in February 2005 edition of Discover magazine.

If you are a self learner, after downloading the Avida-Ed, open it, drag the @ancestor into the black area of the Petri Dish window to the right, select the play button, and have fun.  Otherwise, keep reading…

Well, as I said, I have had the time to make my way through the unedited model lessons posted on the Avida-Ed website.  In effort to prepare to introduce my freshman honors biology and AP Biology student for the software, I have cut and pasted, edited, and created (in some cases) more detailed step-by-step instructions for the activities presented in their models lesson.  In a few cases, I have even collected and attached data in a teachers section at the end of the student friendly documents that help you understand what the students will be doing prior to your own exploration of the software.

Explorations in Evolution Series

  1. I – Introduction to Avida-Ed
  2. II – Observing an Instance of Evolution in Avida-Ed
  3. III – How do Resource Availability & Mutation Rate influence Avidian Fitness?
  4. IV – Observing Mutations in the Genomes of Evolving Avidians
  5. V – Common Misconceptions of Evolution

I look forward to your comments and criticism of the activities but realize that I am just beginning to use these activities in my class for a second time.

As a justification for activities such as these, if you take the time to read the Bio2010 published by the National Academies as well as the most recent bulletin from HHMI (read Thinking like an Engineer and Add 56), you will quickly learn that we should be doing more to motivate our keen biology students to appreciate the importance of other scientific perspectives (mathematics, computer science, physic and engineering).  Similarly, we should be reaching out equally to those that are already bent toward study in these other fields and show them that they can fulfill there interests while helping to make new discoveries in the biological sciences.

Download the non-education version of Avida.

Enjoy!

Facebook and Frameshift

September 5, 2009 in KABT News, Teaching Resources, Technology

Facebook
I don’t know about you, but I timidly joined facebook last fall to begin my journey in learning how this social networking resource might be of use both personally and professionally.  

Happily, I have discovered that there are educational relevant uses for facebook!  I will write a extended blog post on how I use it with students in the near future but today I read something on my facebook home page that I thought I should pass along.

As a member of facebook, one can join groups and follow updates on other people’s pages.  Some of these people happen to be practicing scientists or others on the periphery of the science community.  One individual I happen to follow is Carl Zimmer.  Most of you are familiar with Carl’s collection of quality books.   If you aren’t a member of facebook, you can follow his blog via his website (which links to the Discover’s blogsite – my how connected things are – if you have your own website you can add it with an RSS feed – maybe KABT should consider this).  

Well, the cool thing about reading Carl’s blog is that you are kept up-to-date on his insights into the active world of science, and don’t have to wait a year or two for such insights to be integrated into his next book.

Frameshift

journal[1].pgen.1000634.g005
In one of his posts from yesterday, Losing Teeth, but Keeping Genes, he reviews a recently published article Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals from the online journal PLOS Genetics.    Here is the gist of the story from Carl:

Their results were pretty much what they expected, but they’re still pretty amazing. There were no frameshift mutations in ENAM among the mammals with teeth. But 17 out of 20 species without teeth or enamel had at least one. In all 20 enamel-free species, a stop command (known as a stop codon) was present. These genes are shot.

I am certain that you all teach about “frameshift” mutations.  The two resources above could become additions to your bag of supplemental tricks that make such concepts come alive for your students.  They can also help in your integration of evolutionary biology throughout the curriculum, and to supplement topics like “adaptation, pseudogenes, purifying and neutral selection, molecular clocks, and radiation and convergent evolution”. 

Enjoy reading, and maybe I’ll see meet you in facebook someday soon!

Nature’s Evolutionary Gems

January 3, 2009 in KABT News, Nature, Teaching Resources

A pdf Resource for Teachers wishing to spread Awareness of Evolution by Natural Selection

darwinnatureimage1
www.nature.com/evolutiongems

In this celebratory year of the Birth of Charles Darwin and the publication of his On the Origin of Species, it is fitting that the January 1 issue of the journal Nature announces a document “for teachers and others wishing to spread awareness of evolution by natural selection.”  The document is accessible at the link above, which forwards one to a seventeen page pdf file

The document includes student-friendly ”editorial introductions” to 15 papers that have been published in Nature during the past decade.  These papers were selected “to illustrate the breadth, depth and power of evolutionary thinking”, and cover natural selection from the perspectives of the Fossil Record, Habitats, and Molecular Processes.  The specific titles are given by clicking the more link at the end of this post. 

Each abstract is formatted to a single page, and is followed by a link to the orginal paper, links to additional resources (which may not be accessible), and a link to the website(s) of the author(s).  For those that don’t have a subscription to the journal, many of the links to abstracts of the original research papers provide access to the full text and a freely downloadable pdf .  Happy readings!

Nature, thanks for compiling this fitting and freely available educational resource!  It is a wonderful New Years Gift!

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Darwin and Wallace: Books Reviewed (in part)

January 21, 2008 in Labs, Teaching Resources

A few years ago one of my more accomplished students was kind enough to give me a parting gift of David Quammen’s The Song of the Dodo, and even though the book is more generally about the scientific development of Island Biogeography (as the subtitle states), the authors historical accounts of the concept inspired an interest in Alfred Wallace. More recently, I have read David Quammen’s The Reluctant Mr. Darwin and Peter Raby’s biography Alfred Russel Wallace: A Life both of which contain information relevant to understanding the relationship between the icons of evolutionary biology, Darwin and Wallace.

In the first of Quammen’s books mentioned, he suggests a conspiracy, of sorts, that Darwin used to maintain his priority over the concept of natural selection.

“Then one day Darwin received a manuscript in the mail from a young, obscure naturalist named Wallace – and the Wallace manuscript, to Darwin’s horror, contained his own precious concept. Wallace had found his way to it independently. For a brief heartsick period, Darwin believed that the younger man had eclipsed him and preempted his life’s work by staking a just claim to priority. As things developed, however, with Joseph Hooker’s collusion, Wallace and Darwin announced the concept simultaneously. For a variety of reasons, some good and some shabby, Darwin received most of the recognition; and Wallace, in consequence, is famous for being obscured.” p 20-21 of Song of the Dodo

Quammen more fully develops this potential conspiracy in a detailed discussion of the correspondence that occurred between Darwin, Lyell, Hooker, and Wallace that informed the later of the now famous arrangement presenting an excerpt of Darwin’s 1844 essay along with Wallace’s paper to the Linnean Society of London on July 1, 1858.

“Darwin was understandably abashed and tried to portray himself as a passive party swept along by events… a claim that is weaselly at best and arguably untrue, given his strong hints and lamentations to both men (Hooker and Lyell).” p 168 of The Reluctant Mr. Darwin

Quammen does reference the known correspondence to build his case, and does concede that the actual letters to Wallace have been lost and that Darwin was dealing with the loss of one of his children during this period (which I imagine was quite important in his leaving things to Lyell and Hooker).

Obviously, Quammen’s words and evidence made me contemplate and question the motives, honor, etc… of this great man, a human all the same. But, I was happy to read Raby’s biography of Wallace where he presents another perspective on the relationship between these two great men. In contrast, some of his accounts rescued Darwin’s qualities from Quammen argument.

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