{"id":500,"date":"2010-06-14T16:40:37","date_gmt":"2010-06-14T21:40:37","guid":{"rendered":"https:\/\/www.pbs.org\/wnet\/humanspark\/?p=500"},"modified":"2011-03-03T14:39:17","modified_gmt":"2011-03-03T19:39:17","slug":"freak-genomics-lesson-activities","status":"publish","type":"post","link":"https:\/\/www.pbs.org\/wnet\/humanspark\/uncategorized\/freak-genomics-lesson-activities\/500\/","title":{"rendered":"Lesson Activities"},"content":{"rendered":"<p><strong>Introductory Activity<\/strong><\/p>\n<ol>\n<li>Start class with a brief      review of the structure of DNA, genes, and the human      genome.\u00a0 Ask students to log on to      the <a href=\"http:\/\/www.pbs.org\/wgbh\/nova\/genome\/dna_flash.html\">Journey      Into DNA<\/a> interactive in pairs or groups, depending on how many      computers are available.\u00a0 As      students click through the interactive, ask them to look for the answers      to the following questions and write the answers in their notebooks.\u00a0 (You can ask these questions aloud as      the students click through the screens, or project them on a screen or      write them on the board for the class to see.)<\/li>\n<\/ol>\n<ul>\n<li>How many cells are in the       human body? (<em>100 trillion<\/em>)<\/li>\n<li>How many bases are in the       human genome? (<em>3 billion<\/em>)<\/li>\n<li>Where is the genome located       in the cell? (<em>in the nucleus,       except for the red blood cell<\/em>)<\/li>\n<li>How many chromosomes are in       the genome? (<em>46 \u2013 23 pairs<\/em>)<\/li>\n<li>How much of the DNA in the genome has a known       function? (<em>3% &#8211; 97% of the <\/em><em>DNA<\/em><em> sequence does not code for proteins<\/em>)<\/li>\n<li>How many bases are in a       gene? (<em>anywhere from 100 \u2013 several       million<\/em>)<\/li>\n<li>Identify the four bases and       how they pair with each other. (<em>Adenine       pairs with thymine, cytosine pairs with guanine<\/em>)<\/li>\n<li>What makes up a nucleotide       molecule? (<em>sugar, phosphate, and       base<\/em>)<\/li>\n<\/ul>\n<p>Give students approximately 10 minutes to complete the interactive.\u00a0 When everyone is finished, review the answers with the class.<\/p>\n<ol>\n<li>Ask class, based on their      prior knowledge and what they saw in the interactive, to come up with a      working definition for \u201cgene.\u201d\u00a0 (<em>Answers may vary, but should include      something like \u201ca unit of <\/em><em>DNA<\/em><em> that determines a specific trait or specific genetic      information.\u201d<\/em>)\u00a0 Ask students to come up with a class      definition of \u201cgenome.\u201d (<em>Again,      answers may vary, but should include \u201call of the genetic material in an      organism.\u201d<\/em>)<\/li>\n<li>Explain to students that much      of what we know about the human genome comes from the Human Genome      Project.\u00a0 Tell students that the      Human Genome Project was an international effort, sponsored by the U.S.      Department of Energy and the National Institutes of Health that ran from      October 1990 to April 2003.\u00a0 Goals      of the project included identifying all of the approximately 25,000 genes      in human DNA and determining the sequence of the 3 billion base      pairs that make up human DNA.\u00a0 To accomplish these goals, samples of      genetic material were collected from volunteers all over the world and      sent to Human Genome Project collection centers, where scientists worked on      sequencing and analyzing the DNA.\u00a0 The full sequence was first published in      April 2003.\u00a0 Ask students what they      think some of the benefits might be to conducting this kind of large scale      project?\u00a0 (<em>Accept all student answers.)<\/em> Explain that by mapping the genome,      scientists are hoping to better understand genetic predispositions to      diseases such as breast cancer, cystic fibrosis, and liver disease. The      mapping of the genome will also make it easier for scientists and doctors      to share information and discoveries about particular genes and genetic      disorders.<\/li>\n<li>Tell students that the human      genome is not the only genome that has been sequenced.\u00a0 In fact, as part of the original Human      Genome Project, genomes of other organisms, such as mice and the <em>e. coli<\/em> bacteria were sequenced and      analyzed both to help develop the gene mapping technology and to learn      more about interpreting gene function.\u00a0      Now that the technology for sequencing and interpreting the genome      is in place, scientists are studying the genomes of organisms that can      help us to learn more about human ancestry and evolution \u2013 chimpanzees and      Neanderthals.\u00a0 By viewing and      comparing the results of the Human, Chimpanzee, and Neanderthal Genome      Projects, scientists can piece together a sort of \u201cRosetta Stone\u201d of      genetic changes and evolution since humans last shared a common ancestor      with chimps six million years ago.<\/li>\n<\/ol>\n<p><strong>Learning Activity 1<\/strong><\/p>\n<ol>\n<li>Tell students that the      majority of work on the Neanderthal Genome Project was done at the Max      Planck Institute in Leipzig, Germany, where a team of scientists      and biologists extracted DNA samples from Neanderthal      remains found in Vindija Cave, Croatia.\u00a0 Tell students that you are going to show      them a video clip explaining some of this team\u2019s work.\u00a0 Ask students to note, ask they watch the      clip, the major genetic differences between Neanderthals and modern      humans.\u00a0 Play clip, \u201c<a href=\"wnet\/humanspark\/files\/2011\/02\/Ratty-Old-Genes-.mov\" target=\"_blank\">Ratty Old      Genes<\/a>.\u201d\u00a0 When clip is finished, ask      students to share their answers to the question, \u201cWhat are the major      genetic differences between Neanderthals and modern humans?\u201d (<em>It\u2019s a trick question \u2013 according to      the clip, there are <\/em>NO<em> major      genetic differences!<\/em>)<\/li>\n<li>The genomes of modern humans      and Neanderthals, as well as chimpanzees, are overwhelmingly similar.\u00a0 Draw the following table on the board,      or project it on a screen for the class to show the similarities between      the three genomes:<\/li>\n<\/ol>\n<table border=\"1\" cellspacing=\"0\" cellpadding=\"0\">\n<tbody>\n<tr>\n<td width=\"197\">\n<p align=\"center\"><strong>Species<\/strong><\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\"><strong>Chromosomes<\/strong><\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\"><strong>Base Pairs<\/strong><\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"197\">\n<p align=\"center\">Human<\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\">46 (23 pairs)<\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\">approx. 3 billion<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"197\">\n<p align=\"center\">Neanderthal<\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\">46 (23 pairs)<\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\">approx. 3.2 billion<\/p>\n<\/td>\n<\/tr>\n<tr>\n<td width=\"197\">\n<p align=\"center\">Chimpanzee<\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\">48 (24 pairs)<\/p>\n<\/td>\n<td width=\"197\">\n<p align=\"center\">approx. 2.8 billion<\/p>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>Tell students that when comparing genome sequences, humans and Neanderthals share 99.7% of base pairs, and humans and chimpanzees share 98.5% of base pairs.<\/p>\n<ol>\n<li>Comparison of the human      genome to the chimpanzee and Neanderthal genomes may help to identify      features that set anatomically modern humans apart from\u00a0\u00a0\u00a0 other      hominins.\u00a0 It may also be helpful in      tracing the path of human evolution.\u00a0      By comparing modern human DNA and Neanderthal DNA scientists can identify      genes that may have changed or evolved since humans and Neanderthals      diverged from their common ancestor approximately 500,000 years ago.\u00a0 We know from the video clip that there      are very few genetic differences between humans and Neanderthals, but just      how few?\u00a0 According to the published      report from the Neanderthal Genome Project, which can be found <a href=\"http:\/\/www.sciencemag.org\/content\/328\/5979\/710.full\">here<\/a>, if      students are interested, there are only 78 \u2013 out of three billion! \u2013      instances of single letter nucleotide changes between present day human DNA and Neanderthal DNA.\u00a0 In these instances, the Neanderthal      genome was in the same state as the chimpanzee genome, called the      \u201cancestral state,\u201d whereas the present-day human genome had changed.<\/li>\n<li>Although scientists can      identify the single-letter nucleotide changes between Neanderthal DNA and modern human DNA, they have not yet been able      to identify how these minute genetic difference translate to physical      differences between Neanderthals and humans. In studying and making      comparisons between Neanderthal DNA and human DNA, scientists did find evidence      of gene flow from Neanderthals to humans, meaning that traces of      Neanderthal DNA and sequences found in the Neanderthal genome      are also found in modern human DNA.\u00a0 However, the gene flow only occurs in      one direction \u2013 no evidence of human DNA has ever been found in any      Neanderthal DNA samples.\u00a0      Again, it is unclear how this contributes to our modern human      physical characteristics or knowledge about human evolution.\u00a0 The traces of Neanderthal DNA that do appear in the human      genome occur randomly rather than consistently, which does not indicate      any sort of evolutionary pattern or benefit.<\/li>\n<li>Human and chimpanzee genomes      are compared in different ways but still display striking similarities.      When looking at the two genomes scientists don\u2019t just compare the single      letter sequences but take into account all of the insertions, deletions,      duplications, and rearrangements in the sequences. Even with all of this      information the two genomes are close to 96% identical, and 29% of the      genes found in the two genomes are completely identical.\u00a0 There are signs of evolution over time      from the chimpanzee genome to the human genome \u2013 over 50 genes from the      modern human genome are completely or partially missing or deleted from      the chimpanzee genome, suggesting the development or evolution of new      genes and traits over time \u2013 but scientists have yet to pinpoint the exact      significance of many of these changes.<\/li>\n<\/ol>\n<p><strong>Learning Activity 2<\/strong><\/p>\n<ol>\n<li>Explain to students that one      of the anticipated benefits of the Human Genome Project, as well as having      the Neanderthal and chimpanzee genomes for comparison, is that we can isolate      specific genes and through them learn about human evolution and      development, behavior patterns, and response to diseases and environmental      stimuli.<\/li>\n<li>Review the concept of gene      regulation with class: certain genes in a cell can be turned on or off \u2013      expressed or repressed \u2013 in order to carry out a particular purpose or      function.\u00a0 For example, in humans,      each cell in the body contains all of the same genes and the same genome,      but different genes are expressed in each cell, which is why we have      different types of cells in our body \u2013 some cells \u201cturn on\u201d the genes to      be skin cells, some are brain cells, some are stomach cells, etc.\u00a0 Gene expression is regulated by both      signals from inside the cell and external factors such as interaction with      other cells, proteins, temperature and other environmental      conditions.\u00a0 This interaction      between the genome and the internal and external cues dictates everything      that happens during a cell\u2019s life.\u00a0      Scientists know that gene regulation is an essential function, but      are not sure what makes the process happen.<\/li>\n<li>Explain that while we know      that genes turn themselves on and off in different parts of the body \u2013 the      gene that gives you freckles in your skin cells has no need to turn itself      on in your pancreas \u2013 scientists are exploring how genes express      themselves differently in different species.\u00a0 The differences in how a gene expresses      in a chimpanzee, Neanderthal, and a human may explain significant evolutionary      differences and changes between the three species.\u00a0 Tell students that you are going to show      them a video clip focusing on one such gene that expresses very      differently in different animals, unofficially known as the \u201clanguage      gene.\u201d\u00a0 Write the following      questions on the board or project them on a screen and ask students to      write the answers in their notebooks as they watch the clip:<\/li>\n<\/ol>\n<ul>\n<li>What is the \u201clanguage gene\u201d       called? (<em>Foxp2<\/em>)<\/li>\n<li>Name at least three animals       that have this gene. (<em>fish, mice,       chimps, humans<\/em>)<\/li>\n<li>What happened to the mice       with the human form of this gene? (<em>they       had a lower-pitched squeak<\/em>)<\/li>\n<li>Is the chimp version of this       gene more similar to the human version or the mouse version? (<em>the mouse version<\/em>)<\/li>\n<\/ul>\n<p>Play clip, \u201c<a href=\"wnet\/humanspark\/files\/2011\/02\/Talk-of-Life-.mov\" target=\"_blank\">Talk of Life<\/a>.\u201d\u00a0 When clip is finished, review questions and answers with class. Explain that scientists are still trying to determine what internal and external factors turn the Foxp2 gene on, and how it affects speech once it is turned on.<\/p>\n<ol>\n<li>The Foxp2 gene is of special      interest to scientists for several reasons \u2013 language may be what sets us      apart from our earlier hominin ancestors, and has allowed us to      communicate and organize as a society \u2013 but it is not certain yet it the      gene is essential to \u201cthe human spark.\u201d\u00a0      Tell students that while the Foxp2 gene is different in humans and      chimpanzees, as they saw in the video clip, recent research indicates that      the Neanderthals possessed the same version of the Foxp2 gene that modern      humans have today.\u00a0 Tell students      that scientists are trying to figure out if this means that Neanderthals      had the same capacity for speech as modern humans.\u00a0 Split the class into two groups,      assigning one group to argue for Neanderthal speech capabilities, and the      other group to argue against Neanderthal speech capabilities.\u00a0 Based on what students have learned      about the minor genetic differences between humans and Neanderthals, as      well as what they know about how genes express differently based on      internal and external factors, ask each group to formulate a basic thesis      supporting their assigned argument.\u00a0      Give each group 10 \u2013 15 minutes to discuss, and then present to the      class.\u00a0 (<em>Sample arguments <\/em> <em>FOR: the genetic differences between      the two species are so minor that we could speculate that the gene would      \u201cturn on\u201d the same way as in humans, anatomy is so similar that the same      genetic expression would likely result in the same physical      expression.\u00a0 AGAINST: Since the      repercussions of the genetic differences are unknown we can\u2019t know if the      Foxp2 gene would express in the same way, just because the gene is the      same doesn\u2019t mean the expression would be the same \u2013 the mice in the video      clip didn\u2019t start talking just because they had the same gene.<\/em>)\u00a0 Depending on the time and resources      available to you and your class, you may wish to extend this activity, and      have students spend more time researching this topic in the computer lab      or library, and present their arguments in a debate setting.<\/li>\n<\/ol>\n<p><strong>Culminating Activity<\/strong><\/p>\n<ol>\n<li>Tell students that information      from the genome can also help us track the spread of human populations      across the globe as well as biological evolution.\u00a0 The prevailing theory for the spread of      modern humans, called the \u201cOut of Africa\u201d or the \u201cRecent Single Origin\u201d      theory, states that anatomically modern humans evolved solely in Africa      between 200,000 and 100,000 years ago, and members of one branch of the      population eventually left Africa and spread out across the world,      replacing earlier hominid populations (such as Neanderthals).\u00a0 Scientists and genealogists are able to      track the movement of this group, as well as splinter groups and      populations through information found in the genome.<\/li>\n<li>By using this information,      many scientists and genealogists believe that all modern humans can trace      their lineage back to a single common ancestor (or group of common      ancestors) in Africa that lived between 100,000 and 200,000 years ago. \u00a0\u00a0They are able to do this by tracking two      specific types of DNA that do not combine with any other DNA, thus passing from      generation to generation virtually unchanged, with the exception of random      mutations.\u00a0 These types of DNA are Y-chromosome DNA (yDNA), found in the sperm      cell and passed down from father to son, and mitochondrial DNA (mtDNA), found outside of      the cell nucleus and passed from mother to daughter.\u00a0 As time goes on, the random mutations      are passed down over several generations and become inheritable genetic      markers.\u00a0 This combination of      genetic markers in an individual is called a <em>haplotype<\/em>, and population groups that all share the same      haplotype are called <em>haplogroups<\/em>.<\/li>\n<li>Ask students, in pairs or      groups, to log on to the <a href=\"https:\/\/genographic.nationalgeographic.com\/genographic\/lan\/en\/atlas.html\">Atlas      of the Human Journey<\/a> interactive at the National Geographic      website.\u00a0 Explain that several years      ago National Geographic launched a project, similar to the Human Genome      Project, collecting samples from volunteers all over the world, collecting      genetic information to identify genetic markers and track human migration      throughout history.\u00a0 Ask students to      click on the \u201c60 \u2013 55,000 B.C.\u201d section of the timeline.\u00a0 Ask each pair or group to click on one      of the six lines on the map: L0, L1, L2, L3, M*, or M1, read the      information about their line, and answer these three questions:<\/li>\n<\/ol>\n<ul>\n<li>When did this haplogroup       first appear?<\/li>\n<li>Where did this haplogroup       first appear?<\/li>\n<li>Where members of this       haplogroup now?<\/li>\n<\/ul>\n<p>Give students approximately ten minutes to complete the activity, and then tell them they can have another five to ten minute to explore the interactive on their own.\u00a0 Ask them to think about the \u201cOut of Africa\u201d theory in mind as they click through the interactive, and think about how the growing and spreading human populations might have encountered Neanderthals or other early hominids as they migrated to other areas of the globe.\u00a0 Do students think the human populations would have faced challenges or difficulties?\u00a0 Do they agree with the \u201cOut of Africa\u201d theory?<\/p>\n<ol>\n<li>If the \u201cOut of Africa\u201d theory      is indeed accurate, and the modern humans did replace the early hominid      populations\u2026how did they do it?\u00a0      This brings up an uncomfortable subject for many scientists who are      opposed to the idea of any interbreeding between anatomically modern      humans and Neanderthals.\u00a0 However,      many other scientists believe that genetic evidence indicated that      interbreeding must have occurred.\u00a0      Comparisons of Neanderthal and modern human mitochondrial DNA does not appear to indicate      interbreeding, while regular nuclear DNA analysis indicates the      opposite \u2013 it\u2019s easy to see why scientists disagree!<\/li>\n<li>The Neanderthal Genome      Project team at the Max Planck Institute found what they consider to be      evidence on the side of at least some interbreeding between Neanderthals      and modern humans.\u00a0 When      Neanderthals existed, they lived exclusively in Europe, Asia, and the Middle East.\u00a0 In studying and comparing Neanderthal      and human DNA, the scientists found that any present day      human whose ancestral group originated in one of those geographic regions      shared between one and four percent of the Neanderthal genome, which would      seem to indicate some interbreeding.\u00a0      At the same time, no present day humans of African ancestry shared      any percentage of the Neanderthal genome \u2013 as their ancestors never would      have come into contact with the Neanderthals. \u00a0If, indeed, there was interbreeding, as      the Max Planck Institute scientists suggest, they believe it would have      happened at least 45,000 years ago, in the Middle East, before the      divergence of the human populations across the Eurasian regions.<\/li>\n<li>For homework, ask students to      select one of the following three writing prompts, and write a one-to-two      page essay:<\/li>\n<\/ol>\n<ul>\n<li>Consider the Human Genome       Project and its efforts to understand genetic disorders, diseases, and       other intricacies and peculiarities of human DNA.\u00a0 What do you think scientists could       learn by studying the DNA of specific haplogroups or       population groups?\u00a0 What are the       potential implications of scientists using genetic information to       classify people based on ethnic heritage?<\/li>\n<li>Presently, scientists       disagree on whether or not Neanderthals and modern humans interbred       during the time they co-existed in Europe, Asia, and the Middle East.\u00a0 Do you believe the there was       interbreeding between the two species?\u00a0       Why or why not?\u00a0 How might       this have affected the way modern human populations spread across the       globe?<\/li>\n<li>In the Genographic Project,       scientists isolated specific genes to trace human evolution through paths       of migration from one location to another.\u00a0 At the Max Planck Institute, scientists       isolated the Foxp2 gene to trace hominin evolution through the       development of language.\u00a0 Imagine       you are a scientists, and you can choose a specific type of gene to help       you trace the path of human evolution over millions of years.\u00a0 What would you choose?\u00a0 Why?<\/li>\n<\/ul>\n<p>Proceed to <a href=\"https:\/\/www.pbs.org\/wnet\/humanspark\/lessons\/freak-genomics\/video-segments\/501\/\">Video Segments<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Introductory Activity Start class with a brief review of the structure of DNA, genes, and the human genome.\u00a0 Ask students to log on to the Journey Into DNA interactive in pairs or groups, depending on how many computers are available.\u00a0 As students click through the interactive, ask them to look for the answers to the [&hellip;]<\/p>\n","protected":false},"author":42,"featured_media":0,"comment_status":"open","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4376,1],"tags":[],"class_list":["post-500","post","type-post","status-publish","format-standard","hentry","category-no-home-page","category-uncategorized"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.1.1 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Freak-Genomics ~ Lesson Activities | The Human Spark | PBS<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.pbs.org\/wnet\/humanspark\/uncategorized\/freak-genomics-lesson-activities\/500\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Freak-Genomics ~ Lesson Activities | 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