Welcome to the 2012 Biology I Honors Project. Our goal for the Honors Projects is to give students an

opportunity to examine the material presented in Biology I in more depth. We also want to present material

that is new to the field of Biology so that it will remain relevant to you, the student, if you decide to pursue a

career in Biology and demonstrate the ever evolving nature of this subject. Remember that I took biology 732

years ago. Truth be told, by writing these projects, I am forced to stay current in Biology and I learn along with

you.

Luke De

This project is collaboration amongst the biology teachers. We have all provided input in this project and we

will all be grading it. You may go to any biology teacher for help on this project. In fact, we encourage you to

go talk to your chemistry or physics teacher about it as well.

Alfano, De, Fung-Kee-Fung, Maxwell, O’Mara, Torres

Scientific Writing: The Levels

This sometimes generates a problem when looking for the information that the project discusses. The most

useful and reliable resource for Biology I students is their text book, though it is not always up to date. In order

for information to make it in to a text book it must pass several highly scrutinized steps. First, the original ideas

are conceived, and then they are tested by a primary scientist. If the scientist is satisfied with the results of the

test she may decide to submit her idea and supporting tests to a journal. Scientists and editors at the journal

will typically generate several questions that the primary scientist must answer by additional experimentation.

Once the scientist has satisfactorily answered all the proposed questions and the accompanying experiments,

the journal may decide to publish the primary scientist’s findings. This is called primary literature. (Click

Hyperlink) Examples include Nature ( 1), Science ( 2), The Journal of Biological Chemistry, Molecular and

Cellular Proteomics ( 3), The New England Journal of Medicine( 4), and The Journal of Cell Biology ( 5). If the

U.S. government, through the National Institutes of Health, funds any of the research that a scientist does, that

research must also be submitted to PubMed (www.pubmed.org) ( 6). After this, scientists in the field ASSUME

that the publication is false and try to recreate the experiment to shoot it down. Oddly, sometimes these are

good friends of the publishing scientist, but it is the nature of science; when given new information, assume it is

false and try to prove it wrong. If a study holds up over time, people become less skeptical about it and other

scientists write reviews of the work. These are probably the best source of information for you as a student.

They are written accurately but with a less informed reader in mind. Please refer to the appendix “A Note on

Sources” to see how to access these. At some point, the media may also come across the journal article and

attempt to summarize for the general public. These generally fall into two categories depending on how much

the author understands and how sensational the author wants her story to be. Some of these are fairly

reliable; I like NOVA ( 7), Scientific American, The Scientist, and oddly enough Wired. I would not trust sources

such popular culture sources as People, Time, and Teen Vogue, which attempt to do the same thing. These are

all secondary sources. As a rule of thumb you can trust a secondary source if it provides links to the original

documents from which they draw their information, and those documents are published in journals. These

sometimes cause a great deal of controversy. ( 8) (Whenever possible you should read and reference primary

literature or reviews of it. If you cannot, make sure that you are dealing with a reliable secondary source.) If

this information sticks around for many years and no one is able to significantly refute it, it may make its way in

to a text book. Thus, the time between original research and inclusion in a text book can be somewhere around

a decade. ( 9, 10) What does this mean to you? While your text book is most likely the safest source of

information for this project, it will not be sufficient.

Background on This Project

“there are no living sciences, human attitudes, or institutional powers that remain unaffected by the ideas that were catalytically

released by Darwin’s work” (Collins 1959) ( 11)

There are two pretty simple, basic questions in biology. The answers to these questions are the theories on

which most of modern Biology is based. So if you aren’t sure about the answers to these questions and all of

Biology is based on them. . .

Questions #1: Did life begin or was it always around?

Question #2: If it did begin, When did life begin?

It is kind of a weird idea, but if life came to be, then there was a time where there was no life. It is also a

generally agreed upon concept that life and non-life are mutually exclusive. This means that something is

either alive or not, it can’t be both. So logically, if there was a time at which there was no life, and a later time

at which there was, then there had to be some creation of life.

How did all the living things that followed this original “lifing” event come about? Basically, how do you

generate new living things.

I am quite pleased to say that neither of these questions is yet answered, but rest assured some people have

some ideas. So technically, you could go to a university and

find people that have been researching something for their

entire life and tell them that their theories are based on the

wrong answer to one of these questions.

Luckily, there are a few ideas, like the central dogma, that

most biologists have agreed on for a very long time. The central dogma of biology states that genetic

information is stored in the molecule DNA. ( 12)

This DNA functions as a cookbook of sorts. The

information here is used to generate a more

versatile molecule with instructions for protein

assembly, RNA. Essentially the information on DNA

is rewritten in RNA. This RNA molecule is then used

to construct a protein. If you want to use the

cookbook analogy, DNA is the cookbook, RNA is a

recipe, and the resulting protein is a food. ( 13, 14)

A Tale of Two Evolutions:

You are probably most familiar with Darwinism, or the Darwinian theory of evolution. It is pretty simple really.

There are instructions that every living organism has, and they got these instructions from the organism from

which they were created. E.g. The instructions to make you came from your parents, and they got their

instructions from their parents and on and on. Somewhere in between one of those transfers of information,

mistakes happened and those mistakes caused a change in the individual. i.e. You descended from your

ancestors with some modifications. These changes allowed you to function differently in your environment.

The environment then selects the trait by allowing an individual to mate more or less. This project deals with a

few of Darwin’s ideas, but most importantly with the idea that an individual does NOT change the information

it passes down to the individual’s children over the course of a life time.

If genes, which are made of DNA, are the

only information passed on from parent

to child, and one cannot change their

genetics during their life time, then traits

are acquired from parents. You, as an

individual, receive all the instructions

necessary to make you from your

parents. You get one set from your

mother and one from your father. Thus,

there are two full copies in each of your

trillion cells. What makes you an

individual (and yes special) is the parts of

the code that you inherit and whether or

not there were any mistakes in copying those codes. ( 15) Though he didn’t understand the mechanism, the

important part of Darwin’s theory of evolution was that changes in these instructions happened by mistake,

mutations. (Your genes do not change over your lifetime.) If a mutation or series of mutations develops

enough of a change in the instructions that a protein functions differently, then environmental pressures will

either cause that organism to increase or decrease its reproductive success. If the trait increases reproductive

success, then the trait gets passed on to more and more offspring.

Lamarckism: In the early 1800s, the most popular theory competing with Darwin’s evolution was Lamarck’s

theory of evolution. (There was a shortage on theory names in 1809) In Lamarck’s theory “a changing

environment alters the needs of the organism, to which the organism responds by changing its behavior, and

consequently uses some organs more than others.” ( 15) Lamarck put forth the idea that organisms change

their genetic makeup over their lifetimes, based on the needs of the organism. The story of the stretching

giraffe helps to explain this further. So, there is a short necked ancestor of a giraffe named Gertrude. Gertrude

reaches for leaves every day. In doing so Gertrude’s neck gets longer, in fact super long. (So far the story is

plausible.) Now the trick comes when Gertrude falls in love, with Wilhelm, and has a child named Gregor.

According to the Darwinian idea, Gregor wouldn’t have a super long neck. According to Lamarck, Gregor’s neck

would actually be super long. Here is another example: Let’s say Charles is a really skinny kid, but works out all

his life. The result; Charles gets buff. He falls in love, gets

married to Rosalind, moves to the suburbs, and has kids.

According to Darwin, those children will not be “buff”

unless they work out as well.

The classic experiment that attempts to shoot down

Lamarckism and, therefore, support Darwinism was done

by August Weissman, who snipped the tails off some mice

and then noted that when those snipped mice had

children, the offspring had intact tails.

Most people remember Lamarck for this idea of “acquired

characteristics” which was eventually disproved, but I believe that he really deserves an amazing amount of

credit for his theory of evolution. Lamarck was one of the first who “fearlessly advocated for evolution and

attempted to provide a mechanism to explain it.” ( 15) I think it is also interesting that for quite some time

Darwin embraced the idea of “acquired characteristics” and actually included this in his ground breaking work,

The Origin of Species. ( 15) Before Lamarck, evolution, and the concept of the “struggle for existence” (Click the

Hyperlink) was not commonly accepted. The main arguments against Lamarck were not his idea of “acquired

characteristics”, but rather the idea of evolution. (There was quite a bit of name calling and people involved in

the debate have been really, really mean to each other. People kept calling Darwin a monkey. True story. )

( 16)

Darwin’s theory, that an organism did not change its genetics over the course of a lifetime, became widely

accepted. As a matter of fact no one for a very, very long time was able to shoot down Darwin’s theory.

Therefore, it is found in most textbooks. (Is it in your text book?) Lamarck’s theory could not explain data that

scientists were providing. It had to be amended to accommodate this data and so it eventually became

Darwin’s theory.

This project:

This series of projects

explores one of the rather

new ideas in the field of

biology. This is the idea of

the “The Dark Genome.” As

explained in the background

of this project, there are two

ideas which are fundamental

to biology. First, that DNA

codes for RNA and that RNA

is read to make proteins.

Second, traits acquired by an

organism over the course of its lifetime are not transmitted to its offspring.

Biological theories are continuously changing to accommodate new data. So the theories we believe to be the

most current will change in the future. A student once remarked that this means that “everything we are

learning is wrong”. Perhaps the case is simply that what you learn now will become more correct in the future.

So yes, it is a near certainty that the theories you learn in biology will become outdated. When there are data

that a theory cannot explain, that theory must either be amended to explain the new data or discarded for a

theory that more effectively explains the new data. Newton’s “laws” of physics, Einstein’s theory of relativity,

Darwin’s theory of evolution, and even modern medicine all face data that they cannot explain. ( 17) Second,

all sciences are connected. Biology is just an extension of Chemistry, Chemistry is an extension of Physics,

Physics is essentially a type of philosophy.

What this means to you, is that in order to truly understand Biology you must learn about its roots in

Chemistry. This brings us to the first part of this project.

Third, no scientist works alone. Any and all modern theories are based off the work of others. William Wells

( 18) and Patrick Matthew ( 19) both described the concept of natural selection before Darwin.

Part I: Molecules and Motion. Biology as we know it is essentially based in how

molecules “act” with each other. It is the chemical nature of these molecules that

determines these actions. In this project you should find themes. Sometimes you will

find that many different questions can be answered with the same basic concept.

In this project you will be asked to play with several programs. You will be using Atom Smith and Fold It first.

Generating Electronegativity and Molecular motion.

Molecules are made of atoms. Thus, we

need to take a look at how they function.

Take a look at this representation of an atom.

You should immediately be able to identify

problems with this picture.

1. Identify 4 things wrong with this

model of the atom and explain why

they are wrong.

The electrons in an atom are problematic.

Specifically figuring out how fast they are

moving and where they are in 3D space may

be far more difficult than it may seem.

Many believe that the exact path of electrons can never be

ascertained. This has to do with the fact that you must know the

position and speed of an electron in order to determine its path.

2. Please explain why it may be impossible for the exact path of

an electron to ever by known. You must use the diagram on

the left , Heisenberg, in your explanation.

Some people say that scientists can’t actually figure anything out.

All they generate are theories, which are simply guesses backed up by some evidence.

3. Concerning Scientific Theories

a. (SQ) Why can scientists not PROVE something to be true? What can they prove?

If there is significant evidence against a certain theory, then the theory must be adapted or replaced by a better

one.

b. Please explain how this applies to Darwin and Lamarck’s theories. Was a theory adapted, or

replaced? Please provide evidence for the current theory and explain how this evidence refutes

the previous one.

You should now be able to answer the question, “Who makes scientific theories in to scientific laws?” and

explain why “Newton’s laws” is not the best name for the ideas that Newton came up with. (Not sure whether

I should run with this idea a little longer)

It Always Comes Down to Energy

Potential energy plays a huge role in determining how molecules and atoms interact. Take a look at the graph

labeled formation of H2. The vertical access is potential energy and the horizontal access is the distance

between two atoms. Potential energy can be a tricky concept. Some people call it stored energy. For example:

Gasoline has a great deal of potential energy and the conversion of this potential energy to kinetic energy

generates the heat you would feel from the fire. You can also think of energy as the ability to change matter.

Something with a great deal of potential energy has the ability to

change many things. There is a classic cartoon scenario that might

help; an anvil being dropped on a cartoon character. The anvil at

10 feet has less potential energy than it does at 20 feet. Thus, the

anvil at 20 feet has the potential to change the cartoon, lets say

the Road Runner, more than an anvil at 10 feet. This also means

that you would have to supply energy to the anvil in order to raise it up. (Don’t tell your physics teacher about

this, it is a bit simplistic) In general it is easiest for things to exist at the lowest potential energy state possible,

we call this “stable” or the ground state. In our anvil example, this would be the anvil on the ground. The

graph describes what happens as the two hydrogen atoms approach eachother.

4. What is the relationship between two hydrogen atoms that are a million miles apart? (How do two

Hydrogen atoms that are a million miles apart affect eachother?) How can you tell from the graph?

5. Notice the left side of the graph. The potential energy is climbing rapidly.

a. Please describe what you think happens when you put two atoms in actual contact with

eachother. Be specific here. Please name the type of reaction.

b. Please explain at the atomic level what is happening when you touch something. Please describe

this in terms of electrons, nucleii, and atoms. (In your answer you may want to adress the

questions, do atoms touch?)

The graph of every reaction will be different. The graph labeled molecular bonding is slightly different than the

one before it. Please notice that the horizontal axis on this graph is

labeled time. This signifies that the reaction goes from left to right.

Note there is an arrow from the starting energy going to the highest

potential energy. This signifies activation energy; it is the energy

that you need to supply to a reaction for it to go forward.

6. (SQ) What is the activation energy being applied to? What

happens at the molecular level that requires this much energy? (In the anvil example, the activation energy

was pushing the anvil up ten feet.)

7. Look at the three rods on the right. You will notice

that each circle is assigned a electrostatic charge.

Draw a graph with a horizontal axis labeled A, B, C,

and a vertical axis labeled Potential Energy. Graph

the “Molecules “ A, B, and C in relation to eachother.

Explain your reasoning. Why have you ranked the

energy of each situation in the order you ranked it?

ATOM SMITH (Molecular Motion)

1. Open the program Atom Smith

2. Close the window labeled “The

Atomsmith Classroom:

Experiments”

3. In the window labeled “The

Atomsmith Classroom: Model

Window”, click on the Simulation

Menu Bar

4. Select “Open the gas lab”

Potential Energy of two bonding molecules

You should be looking at something similar to the window on the right.

Click on “Helium” in the “Gas Molecule” window.

5. Next to the “INSERT” button hit the up arrow until a six is displayed.

6. Hit the “INSERT” button

7. Now look at the top of “The Atomsmith Classroom: Gas Lab” window and select the “Simulation” tab.

8. Near the buttom left of the “Simulation” page click on “START”

9. Play with the buttons at the bottom of the gas box and adjust the

screen

10. Now raise the temperature to 1000 K and just watch.

11. Drop the temperature down to zero and watch for at least a minute.

12. Now click on “STOP”

13. Click on the Box Builder tab and click on “Clear The Box”

14. Build a simulation with six water molecules and run it

15. On the simulation tab, near the bottom, next to the word “Video:” click medium, and zoom in to a

water molecule

16. Raise the temperature back up to 1000k, turn video speed to slow, and watch.

17. Clear the box

18. In the “The Atomsmith: Model Window”, click view Molecule Library, and then Molecular structure

19. Double click on “DNA GC Base Pair”

20. Run a simulation on this at both low temperature and high temperature/slow camera

21. Play with the gas lab. Put whatever you want in there, and run it. Click as many buttons as you can.

22. To drive a point home I am going to ask you to put glucose in the box, , in the “Box Builder” tab click

“Build a Water Layer” in the “Simulation” tab, click “Hydrogen Bonds”

23. Now BEFORE YOU START THE SIMULATION, drop the temperature down to 0

24. Run the simulation for a little bit and then jack the temperature up to 1000K

The previous section should have highlighted something about potential energy, this section has more to do

with kinetic energy and the motion of molecules. As you should’ve figured out by now, temperature is related

to the concept of hot or cold, but is much better described by speed. In fact, temperature is a measure of the

motion of atoms in a given system. But molecular motion is not confined to atoms zooming across the screen

and bouncing off of walls.

8. Consider the movement of helium, water, and DNA. Water exhibits

a type of movement that helium does not. DNA exhibits movement

that water does not. Describe the different types of motion that a

molecule is capable of. If you are having trouble with this question,

put “Neopentane” in the box, it should act like the DNA.

9. Consider the water and the DNA. Both of these systems have a lowest potential energy state.

a. Please describe the lowest potential energy state of the six water molecules and what happens at

the atomic level to generate this lowest potential energy state. Please draw this out and provide

rationale for your drawing.

b. Please draw out the two nucleotides in what you think their lowest energy state will be. Please

provide rationale for your drawing.

Biological systems generally differ from the system you just looked at by

one major characteristic; size. The DNA you observed was actually what is

referred to a monomer unit or single piece. Try to imagine roughly

2,999,999 more of those pieces. That is the size of the human genome. A

genome is the 23 chromosomes that you inherit from either your mom or

your dad. All biological molecules are not quite so large, but most are

considerably larger that the molecules you just looked at. The forces that

govern their motion, however, are the same.

Access the Program Fold It

You may work on the following questions in groups starting on February 15,

2012. Your groups will be assigned.

Fold It™ should give you some idea about how a certain class of the

biological molecules, proteins, fold. The score and a couple other features

actually highlight a few key molecular ideas.

10. What does the score actually represent. Hint: It is actually the inverse

of the score. In the game you can be stuck at a specific score. Using

the wiggle function you can increase your score. If a molecule in the human body is stuck in a certain

conformation, what would need to happen in order for the body to perform a wiggle function?

11. (SQ) In the game you, the player, must get rid of flashing red globes and red mace balls. This actually happens in your body. Molecules act in a way such that they would eliminate mace balls and globes. Using intermolecular forces and macromolecules can you explain why it could be an advantage for molecules to

orient themselves in such a way that they will get rid of the globes and the mace balls? What

does this allow our bodies to do? (A final restatement of the question: Why is it advantageous that molecules in a biological systems follow these rules.)

12. (SQ) This may be the most difficult, yet simple, question on this project. Using the program Foldit. Try to observe a pattern. (When I do X, Y seems to happen.) Succinctly describe the phenomenon you observe and then try to give a reason for your hypothesis. (Because Hydrogen bonds are weaker than covalent bonds in water.) Then create an if/then statement. (If Hydrogen bonds are weaker than covalent bonds in water, then I will see Y happen) You should explain the observations behind your idea. What observations lead you to your idea? (In the end you should have an if/then statement followed by some observations that lead you to create that if then statement)

Note From The Teachers

1. I know that the first part of the project concerning Darwin and Lamarck does not seem to relate to

the ideas of molecular motion covered in the questions. For now, we are using this as an example of a

paradigm shift in biology.

2. When answering questions please refer to the answer checklist. This will be provided on February 15,

2012.

3. Before you hand in your project, please refer to the project check list. This will be provided on

February 15, 2012.

4. You can download atomsmith from the website, www.honorsbiology.com, you can ask your teacher

for it, you can get it from tech, or you can download it on one of the computer lab computers.

5. Make sure that your name is nowhere on your answers.

6. You may only work with a partner on one question!

7. We spend a great deal of time putting these projects together. Please make sure that you do the

same with your answers.

8. You may ALWAYS ask any PINGRY SCIENCE TEACHER or

PINGRY LIBRARIAN for help.

9. YOU MAY NOT ASK ANYONE ELSE FOR HELP UNLESS

SPECIFICALLY AUTHORIZED BY A PINGRY BIOLOGY

TEACHER.

ALFANO

DE

FUNG-KEE-FUNG

MAXWELL

OMARA

TORRES

Special Thanks:

Deanna RussellAgensys Pharmaceuticals

Dr. Jeremy ParsonsUniversity of New Mexico, Alberquerque

Edward ScovellRockefeller University

Tim HermanMilwaukee School of Engineering

Dr. Charlotte Appleton ShealyUnited States Air Force

Dr. Troy HibbardDCU University Glasnevin (Dublin, Ireland)

Jedediah Daniel ShieldsBlack Hawk, Michigan Technical University

Dr. Randall SeeleyUniversity of Cincinnati College of Medicine

Kathi SmithUniversity of Cincinnati College of Medicine

Dr. Kivanc BirsoyMassuchessettes Institute of Technology

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