LS-HHMI Outreach Summer Curriculum Project Classroom Resource Information Form
Title
Recreating the Tree of Life using Bioinformatics
Resource
Type
Lesson Plan
Activity
Other
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Description
Author(s)
Students will classify and create phylogenetic trees using a variety of resources. Initially they will use photographs,
morphological, and ecological information. They will then learn how to use on-line bioinformatics tools to produce a
phylogenetic tree based on short 16S rRNA sequences. The goal of this lesson is for students to gain an understanding of
the history of classification and the way that current molecular evidence and bioinformatics is transforming our
understanding of evolutionary relationships between all living organisms.
Jennifer Regrut and David Form
Author
Institution(s)
Jennifer Regrut, Needham High School
David Form, Nashoba Regional High School
Lab Activity
Homework Assignment
Correlations
Objective
The goal of this lesson is for students to gain an understanding of the history of classification and the way that current
molecular evidence and bioinformatics is transforming our understanding of evolutionary relationships between all living
organisms.
Key
Concepts
History of Classification, Understanding and Creating Phylogenetic Trees, Using On-line Bioinformatics Tools
Student
Prep
Students should have a basic understanding of cell structure and ecological terms such as: autotrophic/heterotrophic,
eukaryote/prokaryote, thermophilic/mesophilic, etc. In addition students should have a basic understanding of the role of
DNA and RNA in central dogma of biology
Materials
Access to the internet
Grade
Level(s)
The lesson can be modified for all grade levels
Teacher
Prep Time
Teacher needs to prepare set of cards for
each group.
National
Standards
Class Time
90 minutes

From time to time, major shifts occur in the scientific view of how things work. More often, however, the
changes that take place in the body of scientific knowledge are small modifications of prior knowledge.
Continuity and change are persistent features of science. 1A/H2*

No matter how well one theory fits observations, a new theory might fit them just as well or better, or might fit a
wider range of observations. 1A/H3a

In science, the testing, revising, and occasional discarding of theories, new and old, never ends. This ongoing
process leads to a better understanding of how things work in the world but not to absolute truth. 1A/H3bc*

In matters that can be investigated in a scientific way, evidence for the value of a scientific approach is given by
the improving ability of scientists to offer reliable explanations and make accurate predictions. 1A/H3d*

Investigations are conducted for different reasons, including to explore new phenomena, to check on previous
results, to test how well a theory predicts, and to compare theories. 1B/H1

Hypotheses are widely used in science for choosing what data to pay attention to and what additional data to
seek, and for guiding the interpretation of the data (both new and previously available). 1B/H2
There are different traditions in science about what is investigated and how, but they all share a commitment to the use
of logical arguments based on empirical evidence. 1B/H4*
Scientists in any one research group tend to see things alike, so even groups of scientists may have trouble being
entirely objective about their methods and findings. For that reason, scientific teams are expected to seek out the
possible sources of bias in the design of their investigations and in their data analysis. Checking each other's
results and explanations helps, but that is no guarantee against bias. 1B/H5
 In the short run, new ideas that do not mesh well with mainstream ideas in science often encounter vigorous criticism.
1B/H6a
 In the long run, theories are judged by the range of observations they explain, how well they explain observations, and
how useful they are in making accurate predictions. 1B/H6b*
State
Standard

New ideas in science are limited by the context in which they are conceived; are often rejected by the scientific
establishment; sometimes spring from unexpected findings; and usually grow slowly, through contributions from
many investigators. 1B/H7

To be useful, a hypothesis should suggest what evidence would support it and what evidence would refute it. A
hypothesis that cannot, in principle, be put to the test of evidence may be interesting, but it may not be
scientifically useful. 1B/H9** (SFAA)
1.2
Describe the basic molecular structures and primary functions of the four major categories of organic
molecules (carbohydrates, lipids, proteins, nucleic acids).
2.2
Compare and contrast, at the cellular level, the general structures and degrees of complexity of
prokaryotes and eukaryotes.
2.3
Use cellular evidence (e.g., cell structure, cell number, cell reproduction) and modes of nutrition to
describe the six kingdoms (Archaebacteria, Eubacteria, Protista, Fungi, Plantae, Animalia).
3.1
Describe the basic structure (double helix, sugar/phosphate backbone, linked by complementary
nucleotide pairs) of DNA, and describe its function in genetic inheritance.
3.2
Describe the basic process of DNA replication and how it relates to the transmission and conservation
of the genetic code. Explain the basic processes of transcription and translation, and how they result in the
expression of genes. Distinguish among the end products of replication, transcription, and translation.
5.1
Explain how evolution is demonstrated by evidence from the fossil record, comparative anatomy,
genetics, molecular biology, and examples of natural selection.
Biotechnology
Biotechnology is a rapidly expanding field of biology that uses a growing set of techniques to derive valuable
products from organisms and their cells. Biotechnology is already commonly used to identify potential
suspects in crimes or exonerate persons wrongly accused, determine paternity, diagnose diseases, make highyield pest-resistant crops, and treat genetic ailments. Educators should recognize the importance of introducing
students to biotechnology as a way of better understanding the molecular basis of heredity. Educators should
also provide students with methods and critical thinking skills to evaluate the benefits and risks of this
technology.
Sources
<If the resource is derived or adapted from previously published material, cite the source(s) here.>
References
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“A Science Primer: Classification and Phylogenetics”
http://www.ncbi.nih.gov/About/primer/phylo.html
Baum, D.A.,et al. “ The Tree Thinking Challenge” Science 310:979-980.
Campbell, N.A. and Reece, J. B. Biology 6th edition. San Francisco: Benjamin
Cummings, 2002.
Clos, L.M. “What is Cladistics?” [6/8/06]
http://www.fossilnews.com/1996/cladistics.htm
Filson, R. “Island Biogeography and Evolution: Solving a Phylogenetic Puzzle with
Molecular Genetics”
http://www.accessexcellence.org/AE/AEPC/WWC/1995/simulation_island.html
Kramer, B. and Flammer, L. “Making Cladograms: Phylogeny, Evolution, and
Comparative Anatomy” Evolution & Nature of Science Institutes (ENSI/SENSI),
University of Indiana. [6/8/06]
http://www.indiana.edu/~ensiweb/lessons/mclad.html
“MicrobeWiki” http://microbewiki.kenyon.edu/index.php/MicrobeWiki
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Assessment
“Microbe Zoo” http://commtechlab.msu.edu/sites/dlc-me/zoo/ “Names & classifying living
things” http://www.backyardnature.net/names.htm
Singer, F., et al “The Comparative Method, Hypothesis Testing & Phylogentic
Analysis” The American Biology Teacher 63(7): 518-523.
Skelton, P. W., A. Smith, et al. (2002). Cladistics a practical primer on CD-ROM.
Cambridge, The Open University; Cambridge University Press.
Shaw, Jonathan. “The Undiscoverd Planet”
http://harvardmagazine.com/2007/11/the-undiscovered-planet.html
“The Tree of Life Web Project” http://www.tolweb.org/tree/
“Tree-thinking Group” http://www.tree-thinking.org
“Understanding Evolution: An Evolution Web Site for Teachers”
http://evolution.berkeley.edu/
“What did Trex taste like? An introduction to how life is related”
http://www.ucmp.berkeley.edu/education/explorations/tours/Trex/guide/index
.html
Dawson, Scott “Creatures from the Black Lagoon: Lessons in the Diversity and Evolution of
Eukaryotes” http://www.ucmp.berkeley.edu/education/events/eukevol.html
The Biology Workbench, a bioinformatics website, hosted by the University of California at
San Diego (workbench.sdsc.edu/)
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