APPENDICES[UPLOAD INTO SUPPLEMENTARY ...ddamelin/My Documents/C… · Web viewParameters of the electric field can be set in a dialog box, which can be opened from the model container's

A P P E N D I C E S

I. Models Available as of August 2002II. Enhancement Modules and Associated Textbook ChaptersIII. Meeting National Standards (NSES and Benchmarks)IV. Sample Module: Exchange of Materials between Living Organisms and the

EnvironmentV. Software Structure (Diagram)VI. Models in Thematic ModulesVII. Classroom ScenarioVIII. Evaluation StudiesIX. Advisory Board Short BiosX. Letters of Support

Dr. Jacqueline S. Miller Dr. Mark BloomDr. Stephen CaseDr. Alexei Semenov Dr. Joe HarrisDr. Sigmund AbelesDr. M. Patricia MorseBrad Williamson

XI. Resume of External Evaluator, Dr. Sigmund AbelesXII. Sample Screen Shots of ModelsXIII. Timeline

Concord Consortium Molecular Logic Appendix page 1

A P P E N D I X I . M O D E L S A V A I L A B L E A S O F A U G U S T 2 0 0 2A . M O D E L S I N M O L E C U L A R W O R K B E N C H 2 D ( M W 2 D )

These models were developed to support research units in the Molecular Workbench project. As they were built with the Concord Modeler using MW2D, they are all constructed using the basic scientific principles of and are all interactive. The Concord Modeler is capable of quickly generating a large number of additional models. Later versions of the Concord Modeler will produce more options for student interaction. These models illustrate the range of topics that can be addressed with MW2D and the ease with which specific models can be made using the Concord Modeler from MW2D.

1. Elastic collision between two particles 2. Observing Newton's 3rd Law through simple particle dynamics 3. Interatomic interactions: Towards state of matter (I) 4. Interatomic interactions: Towards state of matter (II) 5. The mass effect on diffusion6. Equipotential contour plot of force fields7. Brownian motion 8. Deep impact: Critical condition9. Deep impact II: Slow mode10. Particles in a gravitational field11. Effect of the Lorentz force on a charged particle12. Hexagonal close-packed lattice structure for Lennard-Jones particles 13. Using periodic boundary conditions14. Soft and hard obstacles15. Use of obstacles 16. Simple osmosis model17. The effect of heat bath18. Icon transport in an electric field19. Molecular dynamics simulation of electrolysis20. Comparison of gas and liquid states21. Comparison of liquid and solid states22. Phase separation of two species23. Hydrogen loading24. Constant-pressure simulations25. Construct a chemical bond network26. Molecular dynamics simulation of bullet-proof27. Interaction of two benzene molecules under periodic boundary conditions28. The bead model of polymers29. Ensemble of molecules 30. Architecture of 2D micelle 31. Folding and unfolding: The conformational dynamics of a polymer32. Folding and unfolding: The solvent effect33. Cartoonized cell model34. Molecular ladders35. Validity of the Gay-Berne model on modeling molecular motion36. Dipole-dipole and dipole-field interactions37. Charge-dipole interaction


38. Merging dynamics of two clusters 39. Dynamics of liquid crystal molecules40. Electrophoresis

B . M O D E L S C O M B I N I N G P E D A G O G I C A W I T H M W 2 D These are models that combine a basic MW2D model with Pedagogica controls, in order to provide students with a sequence of sophisticated pages that include models (effective August 2002). These are particularly effective for contextualized models than might include graphics depicting macroscopic phenomena linked to the model.

S T A T E S O F M A T T E RMolecular states of matterPhase changesSpace filling properties of matter

A T O M S I N M O T I O NModeling an atom (Superball)Two atoms in a box- (collisions and transfer of energy)Modeling a gasGas diffusionGas lawsHeat versus temperature

N A T U R E O F W A T E RWater and charged particlesDiscovering the charged nature of waterMerging water drops

D I S S O L V I N GSalt crystals and temperatureThe response of water to charged particles

W A T E R P U L L S S A L T I O N S A P A R TWater shells EvaporationDissolving sugar and oil in waterDissolving salt in oil

O S M O S I SSimple diffusion across a membrane with one pore.Particle pressure on membrane wallThe role of pores (adjustable)

C . M O D E L S C O M B I N I N G P E D A G O G I C A W I T H B I O L O G I C A Interactive models available for most of the areas of Mendelian genetics as taught in high school biology.


M E N D E L ’ S L A W O F D O M I N A N C EDominant and recessive alleles

M E N D E L ’ S L A W O F S E G R E G A T I O NMeiosis and fertilizationMonohybrid inheritanceProbability (2 x 2 Punnett square)Pedigree

Test crossesM E N D E L ’ S L A W O F I N D E P E N D E N T A S S O R T M E N T

Dihybrid inheritanceProbability (4 x 4 Punnett square)

E X C E P T I O N S T O M E N D E L ’ S L A W SIncomplete dominancePolygenic traitsLethal traitsSex determinationSex-linkageDNA and mutations


A P P E N D I X I I . E N H A N C E M E N T M O D U L E S A N D A S S O C I A T E D T E X T B O O K C H A P T E R S

Modules and Model-based Activities

Alignment with texts

Module Titles

Model-based activities, included in each module

BSCS. Biology. A molecular Approach Everyday Learning Corporation

Biology: The Web of Life. Addison Wesley Longman

Essentials of Biology. Holt, Rinehart and Winston

I. Molecules and Life

Monomers & Polymers

Water is SpecialPhases of MatterMolecules of Life

The Chemistry of Life

General Chemistry

Reactions in Living Cells

Biochemistry Genetic Coding

Chemical basis of Life

MacromoleculesWater, Solutions

A Closer Look at Life

Macromolecules

II. Energy Transfer in Biology

Molecular Kinetic Motion

Reactions and Photons

PhotosynthesisOxygen to ATPEnergy Conversion

and Storage

Energy, Life, and the Biosphere

Organism and Energy

Energy Flow Metabolisms

and Energy Transfer

Photosynthesis and cellular respiration

Energy and ATP Photosynthesis Cellular

respiration Energy Flow in

the Biosphere

Energy and Life

CatalysisCells and

Energy Photosynthesis Cellular

respiration

III. Materials Exchange in Biology

Solutions and Solubility

Diffusion and Osmosis

Passive diffusion and active transport

Oxygen and CO2 Transport

Diffusion & Equilibrium

Osmosis and Dialysis

Exchanging Materials with the environment

Living Systems as Compartments

Exchanged Materials

Membrane as Barrier

How Cells Exchange Materials


Passive and Active Transport

Exchange in Multicellular Organisms

Gas Exchange in

Digestive and Excretory System

Cell Structure and Function

• Membrane• Diffusion &

Osmosis

• Transport in Plants

• Circulatory and respiratory systems

Digestion and Excretion

Cells and their Environment

• Membrane• Diffusion & Os

Movement of water and nutrients in plants

• Circulation and respiration


WaterAdaptation on

LandWaste removalHuman Urinary

SystemIV. Reacting

to the Environment

Pumps and Electrical Potential

Proteins as Molecular Machines

Nerve impulse propagation

Synapses and diffusion

Muscle contraction

Responding to the Environment

Organization of Nervous System

Cellular communication

Transmission of impulses

SynapsesIntegrationDrug and Brain Evolution of

Nervous System

Nervous System

Sensing and control

Nerves at Work

Skin, Skeletal and Muscular System

Muscles in Action

Movement

The Nervous System and drugs

The Central Nervous System

The Sense Organs

DrugsHuman Body Cells, Tissues,

Organs Skin Bones Muscles

V. Copying and Expressing Genetic Information

Protein FoldingCatalysis &

EnzymesTemplate-based

SynthesisSynthesis of DNA and

RNAD

Protein Functions

Expressing Genetic Information

Genetic code: using information

TranscriptionProtein SynthesisViruses

DNA, Genes and Chromosomes

Molecule of Heredity

DNA Structure and Replication

Protein Synthesis

DNA and Gene Expression

DNA Gene

Expression

VI. Repro-duction and Heredity

Genes and Chromosomes

Meiosis and reproduction

Patterns and probability in genetics

Reproduction Cell Division

and Reproduction

Sexual reproduction

Reproduction in Human

Patterns of Inheritance


Mendelian Patterns of Inheritance

Other Pattern of Inheritance

Fundamentals of Genetics

Patterns of Inheritance

Principles of Inheritance

Genetics and Predictions

Predictions and People

Difficult Prediction

Genetics and Inheritance

Genetics Inheritance Genetics

disorder

VII. Mutations, Populations and Evolution

Molecular Basis of Evolution

DNA, Genes and Mutations

Genetic Variations in Populations

Applications and Issues in Molecular Genetics

Mutations and DNA repair

Genetic

Populations and Communities

Populations Growth

Limits to Populations

Principles of Evolution

Evolution Natural

Selection


SpeciationH disorder and gene therapy

Population Genetics

Genetic variation in Populations

Changes in Gene Pool

Microevolution in small populations

GrowthEcosystem

Dynamics

VIII. Molecular Origins of Life

Self-assembly The probability of

improbable events Reactions in pre-biotic

conditions

The Origin of Life

The Origin of Earth

Evolution of Life on Earth

Chemical Evolution

Biological Evolution

The record of the Rocks

The History of Life

Earth Early History

The First Organism

History of Living Things

The Origin of Life

The Early Earth Life in the

Ocean Life on Land


A P P E N D I X I I I . M E E T I N G N A T I O N A L S T A N D A R D S

A . R E P L A C E M E N T M O D U L E S , A S S O C I A T E D B S C S C H A P T E R S A N D N A T I O N A L S T A N D A R D S

Work with our models can deepen understanding of core content areas found in the national standards. Work with models can also meet the more profound standard of helping students to become active learners, constructing and revising their own mental models of the world "in the same way that scientists develop their knowledge and understanding." (NSES).

Modules and Model-based Activities

Alignment with text

National Standards

Module Titles

Model-based activities, included in each module

BSCS Biology. A Molecular Approach Everyday Learning Corporation

NRC: NationalScience Education Standards

Benchmarks for All Americans

I. Molecules and Life

Monomers & Polymers

Water is SpecialPhases of MatterMolecules of Life

The Chemistry of Life

General Chemistry Reactions in Living

Cells Biochemistry Genetic Coding

Matter, energy and organization in living systems

Cell: “The work of the cell is carried out by the many different types of molecules it assembles, mostly proteins.”

II. Energy Transfer in Biology

Molecular Kinetic Motion

Reactions and Photons

PhotosynthesisOxygen to ATPEnergy Conversion

and Storage

Energy, Life, and the Biosphere

Organism and Energy

Energy Flow Metabolisms and

Energy Transfer

Matter, energy and organization in living systems

“Most cell functions involve chemical reactions.”

”Plants capture energy by absorbing light and using it to form strong (covalent) bonds”

Cell: Most cells function best within a narrow range of temperature …”

“At each link in a food web, some energy is stored in newly made structures but much is dissipated into the environment as heat. Continual input of energy from sunlight keeps the process going

III.Materials Exchange in



Passive diffusion

Exchanging Materials with the environment

Living Systems as

The Cell“The complexity

and organization of organisms accommodate

Cell: “Every cell is covered by a membrane that controls what can enter and leave the cell.


Biology and active transport.

Oxygen and CO2 Transport

Diffusion & Equilibrium

Osmosis and Dialysis

Compartments Exchanged

Materials Membrane as

Barrier How Cell Exchange

Materials Diffusion and

Osmosis Passive and Active

Transport Exchange in

Multicellualr Organisms

Gas Exchange in Water

Adaptation on Land Waste removal Human Urinary

System

the need for obtaining, transforming, transporting, releasing, and eliminating the matter …

CellsFlow of Matter

and Energy

IV. Reacting to the Environment

Pumps and Electrical Potential Proteins as Molecular Machines

Nerve impulse propagation

Synapses and diffusion

Muscle contraction

Responding to the Environment

Organization of Nervous System

Cellular communication

Transmission of impulsesSynapsesIntegrationDrug and Brain

Evolution of Nervous System

Behavior of organisms

“ Nervous systems are formed from specialized cells that conduct signals… nerve cells communicate …by secreting specific excitatory and inhibitory molecules”

Basic Function:

“The nervous system works by electrochemical signals in the nerves and from one nerve to the next. “

V. Copying and Expressing Genetic Information

Protein FoldingCatalysis &

EnzymesTemplate-based

SynthesisSynthesis of DNA

and RNAProtein Functions

Expressing Genetic Information

Genetic code: using information

Transcription Protein Synthesis Viruses

Molecular Basis of heredity

“The genetic formation stored in DNA is used to direct the synthesis of the thousands of proteins that each cell requires”

Cell: The function of each protein molecule depends on its specific sequence of amino acids and the shape the chain takes is a consequence of attractions between the chain's parts.

VI. Repro-duction and Heredity


Meiosis and reproduction

Patterns and probability in

ReproductionCell Division and ReproductionSexual reproductionReproduction in Human

Molecular Basis of heredity

HeredityDiversity of

life


genetics Patterns of Inheritance

Genes and ChromosomesMendelian Patterns of InheritanceOther Pattern of Inheritance

VII. MutationsPopulations and Evolution

Molecular Basis of Evolution

DNA, Genes and Mutations

Genetic Variations in Populations

Speciation

Applications and issues in Molecular genetics

Mutations and DNA repairGenetic disorder and gene therapy

Population Genetics

Genetic variation in PopulationsChanges in Gene PoolMicroevolution in small populations


Interdependence of Life

Evolution of Life

Cell: Exposure of cells to certain chemicals and radiation increases mutations and thus increases the chance of cancer.

VIII. Molecular Origin of Life

Self-assembly The probability of

improbable events Reactions in pre-

biotic conditions

The Origin of Life

The Origin of EarthEvolution of Life on EarthChemical EvolutionBiological EvolutionThe record of the Rocks


Evolution of Life:

” Molecular evidence substantiates the anatomical evidence for evolution and provides additional detail about the sequence in which various lines of descent branched off from one another.”

B . T H E M O D E L S A N D N A T I O N A L S T A N D A R D S I N L I F E S C I E N C E

Following is a sample of the way the standards are met with several of the models. Molecular Kinetic Motion

* All matter tends toward more disorganized states. Living systems require a continuous input of energy to maintain their chemical and physical organizations. With death, and the cessation of energy input, living systems rapidly disintegrate. (NSES)


Molecular Construction Kit* The work of the cell is carried out by the many different types of molecules it assembles, mostly proteins.

Protein molecules are long, usually folded chains made from 20 different kinds of amino-acid molecules. The function of each protein molecule depends on its specific sequence of amino acids and the shape the chain takes is a consequence of attractions between the chain's parts. (Benchmarks)

A living cell is composed of a small number of chemical elements mainly carbon, hydrogen, nitrogen, oxygen, phosphorous, and sulfur. Carbon atoms can easily bond to several other carbon atoms in chains and rings to form large and complex molecules. (Benchmarks)

Cells have particular structures that underlie their functions. Every cell is surrounded by a membrane that separates it from the outside world. Inside the cell is a concentrated mixture of thousands of different molecules which form a variety of specialized structures that carry out such cell functions as energy production, transport of molecules, waste disposal, synthesis of new molecules, and the storage of genetic material. (NSES)

* The energy for life primarily derives from the sun. Plants capture energy by absorbing light and using it to form strong (covalent) chemical bonds between the atoms of carbon-containing (organic) molecules. These molecules can be used to assemble larger molecules with biological activity (including proteins, DNA, sugars, and fats). In addition, the energy stored in bonds between the atoms (chemical energy) can be used as sources of energy for life processes. (NSES)

* The chemical bonds of food molecules contain energy. Energy is released when the bonds of food molecules are broken and new compounds with lower energy bonds are formed. Cells usually store this energy temporarily in phosphate bonds of a small high-energy compound called ATP. (NSESCatalysts and enzymes

Most cells function best within a narrow range of temperature and acidity. At very low temperatures, reaction rates are too slow. High temperatures and/or extremes of acidity can irreversibly change the structure of most protein molecules. Even small changes in acidity can alter the molecules and how they interact. Both single cells and multicellular organisms have molecules that help to keep the cell's acidity within a narrow range. (Benchmarks)

Most cell functions involve chemical reactions. Food molecules taken into cells react to provide the chemical constituents needed to synthesize other molecules. Both breakdown and synthesis are made possible by a large set of protein catalysts, called enzymes. The breakdown of some of the food molecules enables the cell to store energy in specific chemicals that are used to carry out the many functions of the cell. (NSES)Aquatic Solutions; Solubility, Diffusion and Osmosis

* Every cell is covered by a membrane that controls what can enter and leave the cell. In all but quite primitive cells, a complex network of proteins provides organization and shape and, for animal cells, movement. (Benchmarks)

Cells have particular structures that underlie their functions. Every cell is surrounded by a membrane that separates it from the outside world. Inside the cell is a concentrated mixture of thousands of different molecules which form a variety of specialized structures that carry out such cell functions as energy production, transport of molecules, waste disposal, synthesis of new molecules, and the storage of genetic material. (NSES)

Protein Folding ("Charged Strings")* The work of the cell is carried out by the many different types of molecules it assembles, mostly proteins.

Protein molecules are long, usually folded chains made from 20 different kinds of amino-acid molecules. The function of each protein molecule depends on its specific sequence of amino acids and the shape the chain takes is a consequence of attractions between the chain's parts. (Benchmarks)


Genes are segments of DNA molecules. Inserting, deleting, or substituting DNA segments can alter genes. An altered gene may be passed on to every cell that develops from it. The resulting features may help, harm, or have little or no effect on the offspring's success in its environment. (Benchmarks)

* The genetic information encoded in DNA molecules provides instructions for assembling protein molecules. The code used is virtually the same for all life forms. Before a cell divides, the instructions are duplicated so that each of the two new cells gets all the necessary information for carrying on. (Benchmarks)

Heritable characteristics can be observed at molecular and whole-organism levels—in structure, chemistry, or behavior. These characteristics strongly influence what capabilities an organism will have and how it will react, and therefore influence how likely it is to survive and reproduce. (Benchmarks)

* Cells store and use information to guide their functions. The genetic information stored in DNA is used to direct the synthesis of the thousands of proteins that each cell requires. (NSES)

In all organisms, the instructions for specifying the characteristics of the organism are carried in DNA, a large polymer formed from subunits of four kinds (A, G, C, and T). The chemical and structural properties of DNA explain how the genetic information that underlies heredity is both encoded in genes (as a string of molecular "letters") and replicated (by a templating mechanism). Each DNA molecule in a cell forms a single chromosome. (NSES)

Changes in DNA (mutations) occur spontaneously at low rates. Some of these changes make no difference to the organism, whereas others can change cells and organisms. Only mutations in germ cells can create the variation that changes an organism's offspring. (NSES)

Biologica* The sorting and recombination of genes in sexual reproduction results in a great variety of possible gene

combinations from the offspring of any two parents. The information passed from parents to offspring is coded in DNA molecules. (Benchmarks)

* The sorting and recombination of genes in sexual reproduction results in a great variety of possible gene combinations from the offspring of any two parents. (Benchmarks)

* Most of the cells in a human contain two copies of each of 22 different chromosomes. In addition, there is a pair of chromosomes that determines sex: a female contains two X chromosomes and a male contains one X and one Y chromosome. Transmission of genetic information to offspring occurs through egg and sperm cells that contain only one representative from each chromosome pair. An egg and a sperm unite to form a new individual. The fact that the human body is formed from cells that contain two copies of each chromosome--and therefore two copies of each gene--explains many features of human heredity, such as how variations that are hidden in one generation can be expressed in the next. (NSES)


A P P E N D I X I V . S A M P L E M O D U L E : E X C H A N G E O F M A T E R I A L S B E T W E E N L I V I N G O R G A N I S M S A N D T H E E N V I R O N M E N T

M O D U L E O V E R V I E W

The “Exchange of Materials” is one of the central themes in a Biology course. It includes a wide range of topics that are either concentrated in one section of a textbook (e.g., BSCS’s Biology. A Molecular Approach), or spread over separate chapters (e.g. Holt, Essential of Biology, or Addison-Wesley’s Biology. The Web of Life.), including Cells and Their Environment; Transport in Plants; Circulatory, Respiratory, Digestive & Excretory Systems chapters. We suggest that despite the variety of covering topics, there are several cornerstone molecular concepts that, if internalized, can make student learning mindful and effective. Below is an excerpt from a proposed Model-based Instructional Module.

Module Objectives: Students will be able to reason about the ways “life processes in a cell are based on molecular interactions” and “the role of cell membranes as a highly selective barrier (diffusion, osmosis, and active transport),”... “that controls what can enter and leave the cell”. They also will be able to explain “how the functional units of excetory and respiratory systems systems in humans (nephron, alveoli) perform their activities.” [Quotations are from the National Science Education Standards and Massachusetts Science Technology and Engeneering Curriculum Framework, 2001]

Step 1. Introduction to the Module and Overview. (Duration 1-2 periods)Using available text and support materials, a teacher introduces students to variety of ways organisms exchange materials with the environment. The overview includes single cells and multicellular organismsm, from plants, to simple animals, to vertebrates and humans. Depending on the individual teaching strategy, it also can include a more detailed excursion into morphology and anatomy of respiratory, circulatory & excretory sytems.

Step 2. Solutions and Solubility Model-based Activities. (Duration 1 period)

After the introductory activities, students work with models of water and aquatic solutions to explore the solubility of sodium chloride (ionic bonds), glucose (polar covalent bonds) and fat (non-polar covalent bonds). Students interact with the model by changing the strength of ionic bonds, thus develop understanding why some salts are more soluble than the others (Fig 1, 2). They also explore the formation of water shells around ions (Fig. 3) – an effect that explains why some ions, whose size does not exceed the size of a water molecule, can not go through the pores in a membrane, while water can; and compare solubility of hydrophilic and hydrophobic compounds (Fig 4)


Fig 1. NaCl in Water: Initial Stage

Fig 2. NaCl in Water: Process of Dissolving

Fig 3. NaCl in Water: Formation of a Water Shell

Fig 4. Oil in Water

Step 3. Membranes as Selective Barriers. (Duration: 1 period)In this lesson, students apply molecular concepts to understand the functioning of cell membranes. They study diffusion and osmosis, and reason about the role of the membrane in the exchange between the cell and environment.

3.1. MACRO -TO-MI CRO CON NECTIO N . To link the models with cell’s structural compnents, students start with Zoom It activity to “travel” from a cell a Plasma Membrane. They learn the size, structure and functions of the Membrane (Fig 5)

3.2. Diffusion & Osmosis. To explore what drives molecules to cross the membrane, students work with interactive Diffusion and Osmosis Modeling Activity (Fig. 5-8). After changing levels of chemical on both sides of the membrane, they discover that chemicals diffuse only when a concentration gradient exists across the cell membrane (Fig. 6, 7). They reason why such diffusion is called passive transport, discuss the role of temperature and grasp sophisticated concepts, such as passive transport; facilitated diffusion and active transport of chemicals across cellular membrane.


Fig. 5. “Zoom ” into the membrane of a red blood cell

Fig. 6. Diffusion of water through a pore in a membrane

Fig.7. Students control pore size and concentration gradients on both sides of the membrane

Fig. 8. “Micro-to-Macro Connection. As students vary osmotic pressure inside the erythrocyte, the cell responds by swelling or shrinking

They discover that like other molecules, water diffuses down its concentration gradient (Fig. 6). By controlling the size of the pores, students make the membrane semipermeable: water crosses the membrane, but dissolved substance cannot Fig.7). The model shows in real time the changes in the pressure developed on both sides of the membrane (Fig. 6, 7: bar-graphs). Students find that when water crosses the membrane, it increases the pressure on the other side, observe conditions for the equilibrium being established, and reason about the nature of osmotic pressure.So far, they were working with a model presented by a container with rigid walls. Cells have flexible walls. Micro-to-Macro connection helps students to transfer the knowledge acquired in the model-based activities, to real world situations. Fig.8 shows molecular model linked to the dynamic macroscopic representation of an erythrocyte. When water crosses the membrane, cell volume increases and the cell swells. This virtual model-based experiment allows students to grasp the relationship between osmotic pressure across the plasma membrane and the final volume of a cell.

Step 4. Model-based activities and Respiration: (Duration 1 period)Using modifications of the above models, students explore how diffusion of gases, O2 and CO2, depends on the difference in pressure of these gases on both sides of the membrane. They change the surface/volume ratio and observe how with the increase of the surface area diffusion rate grows, and connect this finding to what they have learned about the development and adaptation of respiratory system (gills, alveoli). They also explore how binding of oxygen on one side of the membrane increases the diffusion rate of this gas into liquid, thus understand the role of hemoglobin. Step 5. Model-based activities and Excretion. (Duration 1 period)Students link the finding made during the exploration of the diffusion and osmosis models, with what they have learned about structure and function of a nephrons. To develop an “atomic view” on the working of a nephron, they explore a model of a nephron, comprised of many containers, similar to those they have been introduced in the Diffusion and Osmosis modeling activities (Fig 9).


Fig. 9. Model of a Nephron


Module 2. Exchanging Materials Between Organisms and their Environment

Contextualized ModelOsmosis &Dialysis

Contextualized ModelRespiration

Contextualized ModelTransport Across Cell

Membrane

Teacher’s part:Instructional GoalImplementation StrategiesRubricsLink to textStandards

Student’s View

Learning Goals

Macro-to-Micro Connection Adaptations of the model

Embedded Assessment

Text References

Key Concepts

Connections

Model-Based Activities

MW2D Engine

G E N E R I C M O D E L

Diffusion & Osmosis


DNA-to-Proteins


Collisions, reactions &catalysis


Properties of Matter




Monomers-to-Polymers

APPENDIX V. Software Structure

A P P E N D I X V I . M O D E L S I N T H E M A T I C M O D U L E S

Module I. Molecules and LifeMonomers & Polymers Many complex bio-molecules are built from identical or similar parts. Examples include polysaccharides, DNA, RNA, proteins, and lipids. (Uses MW3D as a construction kit.)Water is Special Water molecules are unusually sticky. This makes it hold together and hold on to other polar and charged molecules.

Module II. Transferring Energy in Living Organisms Molecular Kinetic Motion Molecules are made from atoms. Atoms and molecules interact through various forces. This gives rise to temperature, phases, mixtures, and diffusion. Temperature is proportional to the average kinetic energy of the molecules. Pressure is the result of large numbers of collisions between the molecules and the container walls. Reactions and Photons Atoms can react to form covalent bonds. Energy is gained or lost in reactions. Sometimes light in the form of photons is absorbed or emitted in a reaction. Reactions reach an equilibrium that depends on concentrations and energy changes.

Module III. Exchanging Materials with the Environment: Transport, Digestion and Excretion.

Solutions and Solubility. Dissolving gases in liquids. The role of temperature and pressure. Water can dissolve other polar or charged molecules and ions. Mixtures and suspensions.Diffusion and Osmosis. The basis of pressure. Pressure of two species--partial pressures. Diffusion across semi-permeable membranes. Diffusion rate and surface to volume ratio

Module IV. Reacting to the Environment: Stimulus and Response. Nervous and Muscular Systems in Action

Pumps and Electrical Potential neurons as batteries; electric potential; transfer of ions across the membrane; formation and transmission of nervous impulse.Proteins as Molecular Machines: Proteins are assembled in large complexes that work as molecular machines. Muscular contractionSynapses, neurotransmitters and action potential. Neurons as computers. Effects of drugs.

Module V. Copying and Expressing Genetic InformationCatalysis and Enzymes. Different ways an enzyme speed reactions. Shape and charge determine enzyme fit. Metabolism as a sequence of enzyme-catalyzed reactions.Protein Folding - The shape of a protein molecule is determined by its amino acid sequence Protein as Molecular Machines. Proteins conformation determines its propertiesTemplate-bases synthesis of polymers: replication and transcription of polynucleotides


Module VI. Reproduction and HeredityGenes and ChromosomesMeiosis and reproductionPatterns and probability in genetics

Module VII. Mutations, Populations and Evolution: Molecular Basis of Evolution

DNA, Genes and MutationsGenetic Variations in PopulationsSpeciation

Module VIII. Molecular History of Life:Self-Assembly. Molecules can assemble into larger structures. Students will be challenged to create 2D molecules that can self-assemble. Self-Assembly of membranes. Hydrophobic and hydrophilic parts of molecules. Lipid bi-layers.


A P P E N D I X V I I : S C E N A R I O - U N D E R S T A N D I N G S I C K L E C E L L A N E M I A It’s February and the class is studying Gene Expression, in the context of Sickle Cell Anemia. The Molecular Logic models were easily installed on their computers in September using the Concord Modeler. The discussion now revolves around the point mutation, a change in one nucleotide pair, in one of the beta chains in the hemoglobin.

In the beginning of the year, students in her class have learned the basic structure of proteins in the Molecules and Life Module. Working with the Monomers & Polymers model-based activity, they assembled polypeptide chains from various amino acids, and learned what functional groups participate in the formation of the chain. They also explored the tertiary and quaternary structures of hemoglobin and learned that there are four polypeptide chains, two alpha and two beta in the molecule.

The teacher has described to her students that the point mutation that leads to the disease, results in the inclusion of the ‘wrong’ amino acid in the beta chain, that is, a Valine is substituted for a glutamic acid. The class is now engaged in the discussion why such a relatively “small” change – replacement of just one of the hundreds of amino acids that makes the hemoglobin, results in such a dramatic effect.

To help students develop better understanding of the relationship between the primary structure (sequence of amino acids) of a protein and its shape and function, the teacher asks her students to work with to the model-based activity Protein Folding, included in the Molecular Logic software. She invites her students to compare the chemical structure of glutamic acid and Valine. Together, they conclude that while glutamic acid has a strong negative charge, Valine is nonpolar. With this in mind, her students work with the “Charged Strings” model, that is part of the Protein Folding Model-based Activity. (Fig 1, 2). When students replaced in a short string of amino acids, represented as circles, a negatively charged molecule (pointed to with an arrow) to a neutral, they observed a dramatic change in the shape of the resulting chain.

Students discuss how similar change in a tertiary structure can affects the way the hemoglobin acts when exposed to low oxygen levels. They explore a more sophisticated protein folding models to see how a longer polypeptide chain will behave in water (Fig.3).

Working with the models helps students understand why a mutated molecule clumps and forms fibers, which make the sickle cells get stuck in the capillaries.


Fig 1 – Initial Charged String Fig 2. Negative monomer is replaced with one that is neutral

To understand the role of the respiratory pigments in carrying oxygen to the cells, students vary the concentration of hemoglobin, pressure, oxygen and carbon dioxide concentrations using the Solutions and Solubility Model. The model helps them understand the oxygen dissociation curves, graphs that show how much oxygen a respiratory pigment carries when it is in equilibrium with air or water containing various amounts of oxygen. (See Appendix IV). From the Model, the student can determine the pigment’s loading tension (the oxygen pressure at which the hemoglobin reaches saturation) and the unloading pressure (the oxygen pressure at which the pigment carries only half as much oxygen as it can hold when saturated.) The extent to which oxyhemoglobin dissociates is determined primarily by the oxygen pressure in the fluid around the red blood cell, and the pH, which depends on how much carbon dioxide is in the blood where it forms carbonic acid. The oxygen released by the hemoglobin diffuses through the cell membrane where it is involved in the metabolic mechanisms of the cell.

The ‘Protein Folding’ Model-based activity allows the student to investigate the changes in the shape of a protein. With the ‘Solution and Solubility’ Modeling activity, they can investigate how gases dissolve and diffuse in water and pass through membranes. With BioLogica, they could not only actually make the point mutation at the DNA level but also trace the inheritance patterns of the co-dominant gene through a family. We want to stress that this software and the use of the computer are not intended to replace the teacher in the classroom. Quite the contrary—the teacher is indispensable. Not only is a great deal of scaffolding necessary, but also the traditional homework/discussion/feedback takes on greater importance when we ask students to work


Fig.3 Dynamic Molecular Model: Folding of a Polypeptide Chain in Water

APPENDIX VIII. Evaluation StudiesThis appendix describes the questions, methods, and analysis used in the three studies that will make up the formative and summative evaluations.

E V A L U A T I N G S T U D E N T L E A R N I N G

Both formative and summative evaluation will address the following questions concerning student learning:

When using replacement modules, what gains in student learning are observed of traditional biology and new molecular biology concepts including the use of models?

Is their evidence that students reach the learning objectives for each activity-based model? Can the materials eliminate common misconceptions?

Are there differences in student learning by gender, ethnicity, learning style, prior courses, or other factors?

How does the learning of traditional content when using the new material compare to learning with the material it replaced?

What implementation factors effect student learning? Does the approach enhance students' scientific and critical reasoning skills?

This study will evaluate student success and achievement of the learning goals as measured by gains in the end-of-module student assessments described above. These assessments will consist of pairs of approximately equivalent tasks. One member of each pair will be randomly assigned for each student to the pre-test while the other item will be used for the post-test. This will give the same number of students responding in each order for each pair of tasks. This method allows us to compensate for any difference in difficulty between members of each pair and then determine student gains for each item without needing to repeat an item. Each participating student will be asked to complete a short confidential questionnaire concerning ethnicity, gender, educational history, grade, educational expectations, and attitudes toward science.

F O R M A T I V E M A T E R I A L A S S E S S M E N T

In addition to evaluating student learning, the formative assessment will have a materials evaluation part designed to inform revisions of the activity-based models, modules, student assessments, and teacher professional development strategies. This part of the formative assessment will address the following questions:

Are teachers able to integrate project materials effectively into their instruction? Do they select appropriate modules and use them to complement traditional content?

Are teachers able to implement project materials effectively? Are sufficient numbers of appropriate computers available at the right times?

Can students access the model-based activities efficiently and effectively? Are there technical or operational barriers to the use of these activities? Do students understand the instructions for the use of the models?

Do students use each model-based activity as planned? Do they explore relevant parts of the model, seek and receive appropriate scaffolding, and spend appropriate time using the model?

Are the student assessment strategies effective? Are the items and tasks clear? Is evaluation too intrusive? Can teachers use the scoring rubrics effectively? Do teachers and students obtain timely and effective feedback?


After use, are teachers comfortable with the curriculum decisions they made? Do they believe that molecular biology concepts were learned along with traditional content?

Will teachers continue or expand their use of Molecular Logic resources in the future? Data will be gathered from student and teacher questionnaires, classroom observations, student log files, and teacher records. Prior to the start of each module teaches will be asked about their planning process. Each teacher will be asked to keep a daily record in the form of annotations of the teacher’s materials. An end-of-module teacher questionnaire will seek opinions about needed changes in the materials. Spot visits to local classrooms will provide additional data about the materials. Student log files will be generated automatically that record the models each student used, the time spent on each page, the options used, saved states of the model, and any responses requested. This huge source of data will be mined to give us data concerning implementation and embedded assessment. The logs will tell us whether students used the models, explored relevant aspects of each model, and spent a reasonable amount of time exploring their options.

S U M M A T I V E I M P L E M E N T A T I O N S T U D Y

The implementation part of the summative assessment will be designed to answer the following questions:

How are implementation decisions made? Is the need for networked computers a barrier to implementation?

What modules do teachers implement in what kinds of courses? What texts, if any, are used?

Do teachers prefer whole modules, model-based activities, or the underlying models? Are the online TPD materials used? Were they effective in providing needed content,

pedagogy, and technical background? Are the materials for the community effective? How do teacher variables, such as academic background and attitudes about

technology, relate to the implementation of the materials? How do school variables, such as community wealth, focus on science, commitment

to student-centered learning, effect the degree and effectiveness of implementation?

Does the project alter teacher understanding and use of improved teaching and assessment strategies?

Does the amount of project resources teachers use increase over time? This study will be based on responses from the 40 field test teachers and teachers who obtain our materials online and implement them during the period of funding. Online users obtain the material free, but must register and agree to participate in this study. All participating teachers will be asked to complete a questionnaire before and after each semester the materials are in use. All field test teachers and at least ten others will be interview by phone. The initial survey will focus on what modules the teachers plan to implement, the reasoning for their selection of modules, how they treated the material in the past, their instructional practices, and their assessment strategies. Basic background data on each respondent’s education and teaching context will be collected. New users will be asked how they heard about the project and how they decided to participate. Teachers will be asked to self-assess their understanding of biology, molecular biology, computers, the use of models,


instructional strategies, and alternative assessment techniques. This survey will also elicit expectations for the new materials and anticipated difficulties.


A P P E N D I X I X : A D V I S O R Y B O A R D S H O R T B I O SDr. Mark Bloom Staff Biologist, Biological Sciences Curriculum Study (BSCS) Mark currently is Project Director for the development of middle school and high school curriculum supplements under contract from the Office of Science Education at the National Institutes of Health. Before that he helped coordinate DNA Science, Advanced DNA Science, and Genomic Biology Workshop Programs for the DNA Learning Center. He was the first author of college lab manual, Laboratory DNA Science, Benjamin/Cummings, 1996. Scientific editor for DNA Science lab/text, Carolina Biological Supply Company and Cold Spring Harbor Laboratory Press, 1990. Principal investigator of training programs for precollege/college faculty and public opinion leaders funded by the National Science Foundation, Department of Education, Department of Energy, and the Howard Hughes Medical Institute. His PhD was from Rensselaer Polytechnic Institute, Troy, New York, and his post-doc work at the Roche Institute of Molecular Biology, Nutley, New Jersey, where he studied the regulation of heat shock gene expression in E. coli and of chloroplast gene expression in higher plants.Dr. Stephen B. Case is a Research Assistant Professor at the University of Kansas where he also serves as the Assistant director of the Center for Science Education. He is also the cofounder and CEO of Pathfinder Science L.L.C. At the University of Kansas, Dr. Case has taught the Elementary and Secondary Science Methods classes and was PI on the KanCRN Collaborative Research Network ( U.S. Department of Education) and CO-PI and project director of an NSF sponsored project, “Extending Scientific Investigations with GIS”. Prior to coming to the University of Kansas, Dr. Case was an awarding winning high school science teacher for over twenty years. Dr. Case has worked extensively on curriculum development ranging from textbook writing teams on online course development for teachers. Dr. Case’s work has lead to invited presentations at the National Conference on Teaching Evolution, the NSF sponsored Student-Scientist Partnership Conference, and the first Educational Applications of Geographic Information Systems.

Dr. Joseph R. Harris, Director of Systemic Improvement and Educational Reform with The McKenzie Group, has an extensive background in educational technology policies and applications and more than two decades of experience as an administrator and teacher in an urban public school environment. Currently, Dr. Harris serves as the Project Manager for a technical assistance contract in support of a multi-year effort funded by the National Science Foundation designed to promote improved mathematics, science, and technology (SMT) education throughout the nation’s K through 12 public schools. A recent focus of this contract has been to help with the establishment of the Superintendents Coalition, a national membership organization that promotes collaboration among urban school districts engaged in SMT reform.

Dr. Harris served as Project Director for the multi-year development and implementation of the Automated Accountability System (AAS), an on-line, longitudinal school improvement monitoring system for the 9,000+ member schools of the North Central Association. His previous experience includes senior research analyst in the design, administration, and analysis of quantitative and qualitative data collected through written surveys, focus groups, and telephone and in-person interviews for both national and local research studies. Prior to joining The McKenzie Group, Dr. Harris served as an administrator and teacher in the District of Columbia Public Schools. For more than a decade, he coordinated the development, implementation, and operation of an automated instructional management system and played a major role in the development and implementation of the district's Five-Year Computer Literacy Plan. Dr. Harris holds a B.A. in Mathematical Statistics from the


University of Florida, a M.A. in Secondary Education from the Catholic University of America and a Ph.D. in Education Policy from the University of Maryland, College Park.Dr. Jacqueline S. Miller is a senior scientist and principal investigator of two NSF-funded projects in the Center for Science Education at the Educational Development Center (EDC). “Reform-Based Science Curricula: Developing Methods to Determine How They Are Used in High School; Classrooms”, involves designing materials to compare how teachers use reform-based curricula with the intentions of the developers. She has previously served as the principal investigator in the development of Insights in Biology, an NSF-funded introductory biology curriculum for the secondary level. Prior to joining EDC, Jackie carried out basic research in the molecular biology of tumor viruses and parasites as an instructor in the Department of Biological Chemistry, Harvard Medical School and as a senior scientist with Matritech, Inc., a small biotechnology company in Cambridge, MA. Jackie received her B.A. and M.A. in biology from Wellesley College, her Ph.D. in oncology from the University of Wisconsin, and was a postdoctoral fellow at Harvard University.Dr. M. Patricia Morse is a marine biologist and science educator at the University of Washington. For thirty four years, she was Professor of Biology at Northeastern University, the last four of those years she spent as a Program Director at the National Science Foundation in the Division of Elementary, Secondary and Informal Education, Dr. Morse served as a specialist in biology and environmental science in Instructional Materials Development. She holds a BS degree from Bates College, an MS and PhD. from the University of New Hampshire, and an honorary D.Sc. from Plymouth State College. Dr. Morse has published extensively in molluscan biology and more recently in science education (over 50 papers and 34 abstracts). Her work in functional morphology involves microscopic analysis (transmission and scanning electron and confocal microscopy) with an experimental approach, as well as molluscan meiofaunal ecology and systematics studies. She currently serves on the advisory committee of BioProbe at Purdue University (Robinson, PI), a high school curriculum in CD-ROM microscopic technology, a resource for teachers to connect the microscopic world to biology in instructional materials. Dr. Morse is a past president of Sigma Xi, the Scientific Research Society and the American Society of Zoologist. She is currently a trustee at Bates College, serves on the editorial boards of Acta Zoologica and American Zoologist, and is vice-chair of the International Union of Biological Sciences’ Commission for Biological Education. She is currently an Acting Professor on the Faculty of the Zoology Department at the University of WashingtonDr. Judah Schwartz, PhD is Emeritus Professor of Engineering Science and Education at the MIT and Professor of Education and Co-Director of the Educational Technology Center at Harvard. He was trained in theoretical physics and mathematics and did research for some years in the area of atomic physics. His current research interests include the design of microcomputer software environments to improve the teaching and learning of science and mathematics and the application of cognitive science techniques to the study of mathematics and science education. He has a long standing interest in alternative modes of assessment. His most recent major publications are a book-length case study of educational reform entitled "The Geometric Supposer; What Is It A Case Of?" and, with colleagues at Harvard, "Software Goes to School: Teaching for Understanding in the Age of Technology".Dr. Alexei Semenov Rector, Moscow Institute of Open Education, Dr. Semenov was the organizer and co-author of the first all-country curriculum, text-book and software that was based on computer science and technology implemented in all Soviet schools. For the last 8 years he has acted as the Rector (CEO) of the Moscow Institute of Open Education (formerly – the Moscow Institute for Teacher Development) – the state organization responsible for in-service training, guidance and methodical support of all Moscow teachers.


Dr. Dagmar Ringe, Ph.D. Professor of Biochemistry and Chemistry, Rosenstiel Basic Medical Sciences Research Center, Protein Crystallography and Head, Petsko/Ringe Lab at Brandeis University. She is an internationally recognized expert in the areas of protein crystallography, structural biology, and protein structure and function. Dr. Ringe is a past recipient of the Biophysical Society Margaret Oakley Dayhoff Award for Outstanding Performance in Research and a Guggenheim Fellowship award. She has authored 175 scientific publications and is currently the Lucille P. Markey Professor of Chemistry and Biochemistry at Brandeis University. Previously, she was Chairperson of the Graduate Program in Biophysics at Brandeis and Director and Senior Lecturer of the Undergraduate Chemistry Laboratories at MIT.Dr. Ringe's research interests are in the areas of structure and function of proteins, protein-drug interactions, protein crystallography and functional genomic. She leads a laboratory at Brandeis that is analyzing the relationship between proteins' three-dimensional structure and their chemical function. Dr. Mikhail Sitkovsky, Chief, Biochemistry and Immunopharmacology Section, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, the National Institute of Health. Dr. M. Sitkovsky combines an unusual mix of experience and scientific knowledge in several areas of basic biochemical and immunological research with interest in applying basic discoveries into molecular medicine. His recent accomplishment in discovery of physiological mechanism that terminates inflammation in vivo is widely considered a breakthrough with major implications for cancer immunotherapy and autoimmune diseases.Brad Williamson, Currently President of the National Association of Biology Teachers (NABT), Brad is an award-winning Biology teacher at Olathe High School in Olathe, Kansas. He has been consistently on the forefront of innovations in high school Biology education, has participated in numerous national programs, and helped to co-author a coming Biology textbook (Prentice-Hall).


A P P E N D I X X . L E T T E R S O F S U P P O R T Dr. Stephen Case Dr. Joe Harris Dr. Jacqueline S. MillerDr. M. Patricia MorseDr. Alexei SemenovBrad Williamson


Boris BerenfeldThe Concord Consortium Inc.10 Concord Crossing, Suite 300Concord, MA 01742August 15, 2001Dear Boris,I am pleased to have been invited to participate in your project Molecular Logic: The Power of Molecular Models to Classroom Biology and I write this letter of support with great enthusiasm for the work. One of the greatest difficulties in having students develop deep understanding of fundamental principles in biology is in helping them move from the concrete to the abstract, from the macroscopic world they can observe to the microscopic, molecular level which determines how and why things happen. During our development of Insights in Biology, we struggled to help students make this transition through experimentation, model building, and readings. We looked in vain for computer programs that would allow students to take the next step into a molecular world in which they could manipulate models, visualize what was happening at the molecular level and apply principles by making hypotheses and then testing them. For example, students sprinkle salt on a slice of zucchini and observe water leaching out. To explore what was happening at the cellular level students had to envision a cell, salt ions and a membrane and its molecular components. With a computer model they could visualize this, experiment with different conditions, and transfer their understanding by relating this to how a toxin can cause a cell to lose water. Students could explore protein structure beyond pipe cleaners and beads by working with amino acids; they could “mutate” DNA, demonstrate changes in protein structure and show how this small change manifests itself at the level of traits of an organism. The possibilities are endless. Computer modeling coupled with hands-on experiences offer students powerful and complete learning opportunities.Concord Consortium has made significant inroads into developing molecular models for the physical sciences. We are anxious to incorporate the work that you have done as well as the proposed work into our latest NSF-funded curriculum project “Foundation Science: A Comprehensive Middle Grades Curriculum”. Just knowing that such computer modeling programs exist and are available makes our work as developers of curriculum involving abstract, molecular concepts easier and a lot more exciting.I look forward to working with you and your groupSincerely

Jacqueline S. MillerSenior Scientist


Boris BerenfeldThe Concord Consortium Inc.10 Concord Crossing, Suite 300Concord, MA 01742

August 22, 2002

Dear Boris, Thank you for your invitation to serve on the Advisory Board of the Molecular Logic project, now being submitted to NSF. I would be delighted to accept.

One of my more recent projects, done for the American Institute of Biological Sciences (AIBS) in collaboration with the University of Washington in Seattle, was to review ten of the most popular Biology textbooks for secondary education. As had the TIMMS project, we found that most biology curriculum has become ‘overstuffed’ with concepts and facts.” To cite our reviewers, "Most books are just too large, still too encyclopedic, and leave too much responsibility on the teachers to figure out how to use them.” Even when the material was linked to standards, it was often not "accessible, extractable and coherent." (pp. 11-12) We also found that, while topics of importance in biology are well represented in nine of the ten textbooks reviewed, much more attention is needed in creating environments that foster learning, meeting "other content standards", and "pedagogy" standards of the NSES." Biology for high school students must include a meaningful approach to understanding the roles of molecules! Molecular Logic’s ability to infuse these textbooks with meaningful supplementary activities with molecular models is just right. Without an emphasis on molecular biology, students using these texts will fail to understand the most dynamic areas of modern biology. The modeling approach is anideal way to add this dimension to their learning.

The high quality of the Molecular Workbench materials, as well as Biologica, will be a significant asset to the project. The proposed educational strategy of having students learn through guided exploration is the appropriate pedagogical approach for these materials, as the proposing team has shown in prior projects. As a research biologist, I am always concerned that educational projects accurately convey both the process of science and current research topics. I am confident that Molecular Logic will do both. I look forward to working with you on this fine project.

Sincerely,TrishM. Patricia MorseProfessor of Zoology



MOSCOW CITY GOVERNMENTMOSCOW INSTITUTE of OPEN EDUCATION125167, Moscow, Aviatsiony Ln., 6Tel: 151-44-11

Dear Sirs,This letter is to confirm my acceptance of membership in the Board of Advisors of the Molecular Logic project. I consider the expected outcomes of the project as exceptionally beneficial for Russian (as well as international) science education. For more then 15 years I have been involved in introducing ICT in Russian (formerly – Soviet) education. (I was the organizer and co-author of the first all-country curriculum, text-book and software that was based on computer science and technology implemented in all Soviet schools.) For the last 8 years I have acted as the Rector (CEO) of the Moscow Institute of Open Education (formerly – the Moscow Institute for Teacher Development) – the state organization responsible for in-service training, guidance and methodical support of all Moscow teachers. One the functions of our institute is the identification of best educational practices, especially those that involve the use of computers, for the implementation in the school system in the Russian Federation. Last year I was appointed by the Russian Ministry of Education as the head of a working group to survey all educational software titles available in Russian, with the goal of choosing products to be supplied to all state secondary schools of Russian Federation. We considered more then 400 items and chose 25 of them. A few of them were Russian adaptations of American products, namely, Geometer’s Sketchpad and Interactive Physics that are used in hundreds of Russian secondary schools and are highly evaluated by teachers. An opportunity to have a similar (in educational philosophy sense) product – a virtual lab in Biology seems very desirable. One of our immediate goals is to integrate Biology curricula with fundamental sciences using advances in computer science. We expect that the use of dynamic models can facilitate such integration. Now we are in the stage of preparation of a World Bank loan, which will support teacher training, digital educational resources supply and dissemination of high quality educational materials, and launch a set of resource centers for the whole country. I would appreciate an opportunity of piloting in these Centers materials, including the current pilot models, content units or curricular links of the Molecular Logic.Since we have a national biology curriculum, we can engage significant number of teachers with diverse background and perspectives in testing the materials. In exchange for their use, we would be willing to share with American educators some of the best implementation strategies practiced by Russian teachers, including the links from the models to our curriculum.


Professor Alexei Semenov (Dr. Sci.)The Rector


University of KansasCenter for Science Education

1122 West Campus RoadLawrence, Kansas 66045

_________________________August 16, 2002

Dr. Boris Berenfeld,

Concord Consortium

Dear Dr. Berenfeld,

I am delighted to work with the Concord Consortium as a member of the advisory board on Molecular Logic" project. I believe that with careful development that the application of molecular dynamics models to biology could be an extremely powerful instructional/learning tool. Bringing together a team of scientists, science educators, and science teachers has tremendous potential for shared learning as they collaboratively work on the development of these tools.

The proposed structure of the models is a real strength of your proposal. By tying the models to concepts for the National Science Education Content Standards and to widely adopted textbooks allows that classroom teacher the flexibility to adopt and uses these models as appropriate to their classroom. The web-based teacher course will also be an important component to the project. Teachers will need this support to make the changes required in their instructional program.

This is a difficult area for students to work in. The level of abstract necessary to understand simple atomic models let alone molecular interactions stretches many students’ cognitive levels. This proposal concept of “zooming in” from macro to micro levels of organization should provide powerful scaffolding. It is a challenge to all teachers to help students make the jump from abstract representations to observing patterns in the natural world. Concord Consortium has tremendous experience the abstraction jump from model to reality from both Genscope and Biologica. This experience should help Molecular Logic become a powerful and effective instructional tool.

I look forward to working together.

Sincerely,

Steven B. Case

Center for Science Education


A P P E N D I X X I : R E S U M E O F D R . S I G M U N D A B E L E S , E X T E R N A L E V A L U A T O R

RÉSUMÉSigmund Abeles163 Trinity AvenueGlastonbury, CT 06033-1337(860) 633-8054; FAX (860) 633-8054; Email [email protected]

ACADEMIC TRAINING

New York University - University College of Arts and Science, B.A.; Major: Chemistry, Minor: Mathematics. School of Education, Ph.D., Science EducationYale University - National Science Foundation Fellowship - Physics and Chemistry.Columbia University - National Science Foundation Fellowship - Physics.Boston University - Graduate School of Education - Education ResearchRussell Sage College - Elementary School CurriculumOhio University - General Electric Fellowship - Career EducationUniversity of Rhode Island - graduate work in physics.

PROFESSIONAL EXPERIENCE

Teacher of General Science. Central High School. Bridgeport, CT.Physical Chemist. Infrared Spectroscopic Analysis. U.S. Army.Physical Chemist and Ballistician. AVCO Corporation.Teacher of Chemistry, Physics and Electronics. Warren Harding High School, Bridgeport, CT.Teacher of Electronics. Dictaphone Corporation. Bridgeport, CT.Teacher of Electronics, Summer Institute for High Ability Secondary Students. University of Bridgeport. Sponsored by the National Science Foundation.Associate Supervisor. Bureau of Science Education. New York State Education Department. Albany, NY. Physics curriculum and Physics Regents Exams specialist. Elementary school science specialist.Supervisor of Education for the Gifted. New York State Education Department. Albany, NY.Testing Consultant, Educational Testing Service, Princeton, N.J.; IOX Los Angeles, CAConsultant, Science Education. Connecticut State Department of Education. Hartford, CT.Adjunct Faculties: Russell Sage College. Albany, NY; State University of New York-Brockport, Brockport, NY; Rhode Island College. Providence, RI; Eastern Connecticut State University. Windham, CT.; Central Connecticut State University. New Britain, CT.; St. Joseph College. West Hartford, CT.


Faculty, Connecticut State Board of Higher Education. Alternate Route to Certification ProgramDirector, Nine State Consortium on Metric Education. Funded by U.S. Department of Education.Program Administrator, Title II of the Education for Economic Security Act and the Dwight D. Eisenhower Mathematics and Science Education Act. (Math/Science Bill)Principal Investigator, Project CONNSTRUCT, a $7.8 million SSI grant from the National Science Foundation.Science Consultant, Talcott Mountain Science Center. Avon, CT.Evaluation Consultant, National Science Foundation, Statewide Systemic Initiatives; Talcott Mountain Science Center; Technical Education Research Center, and various public school systems.Technical Consultant, Connecticut Academy for Education in Mathematics, Science and Technology, Inc.Project Director, Connecticut Academy Science Assessment Project, Connecticut Academy for Education in Mathematics, Science and Technology, Inc.Senior Science Advisor, Triarchic Intelligence Theory Grant. National Science Foundation. Yale University.External Evaluator for National Science Foundation. Global Lab and Astrobiology Projects. TERC. Cambridge, MA.External Evaluator for National Science Foundation. TEEMSS Project. Concord Consortium. Concord, MA.

AWARDS

American Chemical Society. Western Connecticut Section. Science Education Award.New York University - Founders Day AwardTalcott Mountain Science Center. Outstanding Science Educator AwardConnecticut Science Teachers Association. Lifetime Membership Award.U.S. Office of Education. Certificate of Recognition for Metric Education.U.S. Department of Energy. Special Award for Student Honors Program.EDPRESS. Distinguished Achievement Award for Excellence in Educational Journalism.National Aeronautics and Space Administration. Certificate of Recognition for Service to the Space Shuttle Student Involvement Program.PIMMS (Program to Increase Mastery in Mathematics and Science) Fellow and Vanguard Fellows AwardsConnecticut Science Teachers Association. Connecticut Science Education Fellow.Connecticut Academy for Education in Mathematics, Science and Technology, Inc. First Fellow Award.


Connecticut Academy for Education in Mathematics, Science and Technology, Inc. Certificate of Excellence.

PUBLICATIONS

Coauthor Tips and Techniques in Elementary Science. New York State Education Department. Albany, N.Y. 1966.

Author A Simple and Inexpensive Method to Obtain 'g'. Connecticut Journal of Science Teaching. New Haven, CT. 1966

Editor Forces at Work. Block I of the Experimental Junior High School Syllabus.New York State Education Department. Albany, N.Y. 1966

Co-author Dunning-Abeles Physics Test. The Psychological Corporation. New York. NY. 1967.

Guest Editor Apparatus Section. The Physics Teacher. New York. NY. March 1967.Editor Physics-A Course for Secondary Schools. New York State Education

Department. Albany, N.Y. 1967.Editor and Physics Supplement. New York State Education Department. Albany, NYCo-author 1967.Member Science Testing Board. Harcourt Brace Javonovich. New York, NY 1967-1977.Editor Solar System Media Guide, Grades 4 - 6. New York State Education

Department. Albany, NY. 1968.Editor Electricity and Magnetism Media Guide. New York State Education

Department. Albany, NY. 1968.Editor Atomic Physics Media Guide. New York State Education Department. Albany,

NY 1968Editor Advanced Placement Series, English and Mathematics. New York State

Education Department. Albany, NY 1968.Editor andCo-author Physics Handbook. New York State Education Department. Albany, NY 1970.Editor Man and His Environment. Connecticut State Department of Education.

Hartford. CT 1970Author Writing Behavioral Objectives in Science. Connecticut State Department of

Education. Hartford. CT 1970Editor and Science Educator's Guide. Connecticut State Department of Education.

Hartford.Co-author CT 1970 Author Selecting a Science Program. Learning Magazine. 1977Author Consultant's Corner and State of Science. Connecticut Journal of Science

Teaching. 1978 - 1982.Author Science and the Gifted Child. The Gifted Child Quarterly. 1978


Author Connecticut Report on Inservice Education. "Inservice" Council of States on Inservice Education. February 1980.

Editor Energy Resources Inventory. Connecticut State Department of Education. Hartford. CT 1980.

Editor Energywatch K-6 and Energywatch 7-12. Connecticut State Department of Education. Hartford. CT 1980.

Editor and A Guide to Curriculum Development in Science. Connecticut State Department

Co-author of Education. Hartford. CT 1981.EditorialConsultant Concepts in Physics. Harcourt Brace Jovanovich. New York. NY. 1980.Advisory Challenge Update. Connecticut State Department of Education. Hartford. CTBoard 1984-1991.Author Foundations in Physical Science - Experiences. Coronado Publishers. San

Diego. CA. 1985.Editor Foundations in Earth Science - Experiences. Coronado Publishers. San Diego.

CA. 1985.Author A new era for the science lab? Connecticut Journal of Science Education.

Fall/Winter 38-40. 1985Consultant Scientific Publications. Briarcliff Manor. N.Y. 1985-1986.Writer and Middle School Science. Educational Systems Corporation/Jostens LearningReviewer Corporation. 1987 - 1992.Author and Chapters 10 and 16. Gifted Young in Science. Paul F. Brandwein and HarryCo-author Pasow, editors. National Science Teachers Association. Washington. DC

1989.Editorial Consultant Grey Castle Press. Pocket Knife Square. Lakeville. CT 1991-1992Editor and A Guide to Curriculum Development in Science. Connecticut State

DepartmentCo-author of Education. Hartford. CT 1991.Consultant Science Program Evaluation Guide. Connecticut Academy for Education In

Mathematics, Science and Technology, Inc. Middletown, CT. 1998Editor and Connecticut Academy Science Assessment Project - Teacher Manual. Co-author Connecticut Academy for Education in Mathematics, Science and Technology,

Inc. Middletown, CT. 2000.Principal So You're Trying to Assess Your Elementary and Middle School ScienceAuthor Program. Connecticut Journal of Science Education. Volume 38 No. 2. Spring-

Summer 2001. 20-23.


A P P E N D I X X I I . S A M P L E S C R E E N S H O T S O F M O D E L SThe screen shot below is taken from an activity designed to allow students to explore the effect of concentration on pressure at a constant temperature. The activity was generated with the scripting language Pedagogica interfaced with the MW2D engine. Pedagogica controls the start and run conditions, links to the pressure display from model data, and to generates the instructional supports such as a text box for reflection and an interactive control (open or close pore).


The following screen from BioLogica controlled by Pedagogica includes a popular animation of meiosis that can be run like a movie. The magnifying glass shows a single gamete with its chromosomes labeled with the various genes. The software can record whether students did look at the screens that are necessary to make an accurate prediction.


The following shows parts of the DNA that controls the appearance of the dragon’s tail. Students can edit the DNA to produce other kinds of tails.


This image shows the Concord Modeler in the process of constructing a Web page with embedded models and pedagogical controls. This functionality allows a user (developer or teacher) to make easy-to-use interface for a model, as well as set up questions and feedback zones.


This screen shot shows a Molecular Dynamics model in the Concord Modeler for electrophoresis embedded in a Web page. Parameters of the electric field can be set in a dialog box, which can be opened from the model container's menu. Running this model, students will see particles with different colors and charges (representing different proteins) will move at different speeds, and consequently form layered structures on opposite side walls.


A P P E N D I X X I I I . P R O J E C T T I M E L I N E
