Welcome to the 2012 Biology I Honors Project - Pingry School

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Dec 3, 2012 (4 years and 6 months ago)

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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 s
tay 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 student
s

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 support
ing test
s

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 th
e 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 o
f 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 tr
y to recreate the experiment to
shoot it
down. Oddly, some
times

these are
good friends of the publishing scientist
, but it is the nature of s
cience; 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 yo
u 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 p
ublic. These generally fall in
to 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 s
econdary 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? Whi
le 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 wer
e 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 o
n
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,
W
hen

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
up
on 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 l
ater time
at which there was, then t
here 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 th
at 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 the
ir

theories are bas
ed 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.
T
his 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
resu
lting 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 env
ironment 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 can
no
t change their
genetics during their life time, then traits
are acquired f
rom parents. Y
ou
,

as an
individual
,

receive
all the instructions

necessary to make you from your parents.

You get one
set
from your mot
her 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, t
he 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 mu
tation 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 repro
ductive 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 o
rgans 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.
T
he story of the stretching
giraffe

helps to explain thi
s further. So, there is a short necked ancestor of a giraffe

named Gertrude. Gertrude
reaches fo
r 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 woul
dn’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 k
id, but works out all
his life. The result; Charles gets buff
. H
e falls in love, gets
marrie
d to Rosalind, mov
es 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 wa
s 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
c
haracteristics

, 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 pr
ojects
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 wh
ich 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

. P
erhaps 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 the
ories 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 physi
cs, 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

Mat
t
hew (

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 severa
l programs. You will be using Atom Smith and Fold I
t first.


Generating Electronegativity and Molecular motion.


Molecules are made of atoms
.


T
hus
,

we
n
eed 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 w
ith 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 Lamar
c
k’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 H
2
. 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 p
otential 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 t
o
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 R
unner, more than an an
vil 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 fo
r 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 molecul
ar bonding is slightly different than the
one before it. Please notice that the horizontal axis on this graph is
label
ed 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”, c
lick on the Simulation
Menu Bar

4.

Select “Open the gas lab”


You should be looking at something
simi
lar to the window on the right.
Potential Energy of
two bonding
molecules

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 wi
th 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 mol
ecule

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 as
k

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 conce
pt 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 movemen
t 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 “Neo
pentane” 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.


Biolo
gical systems

generally differ from

the system you just looked at b
y
one major characteristic; si
ze. 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 I
t


should give you some idea about how
a certain class of the
biolo
gical
molecules, proteins, fold
. The score and a couple other features
actually highlight a few key molecular ideas.


10.

What does the score act
ually 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 y
o
u 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 mol
ecules 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 sh
ould
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 p
lease 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 p
artner 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 a
ny

PINGRY SCIENCE TEACHER

or
PINGRY LIBRARIAN

for help.

9.

YOU MAY NOT ASK ANYONE ELSE FO
R
HELP UNLESS
SPECIFICALLY AUTHO
RIZED BY A PINGRY BIOLOGY
TEACHER.



ALFANO

DE

FUNG
-
KEE
-
FUNG

MAXWELL

OMARA

TORRES





Special Thanks:


Deanna Russell

Agensys Pharmaceuticals


Dr. Jeremy Parsons

University of New Mexico, Alberquerque


Edward Scovell

Rockefeller University


Tim Herman

Milwaukee School of Engineering


Dr. Charlotte Appleton Shealy

United States Air Force


Dr. Troy Hibbard

DCU University
Glasnevin (Dublin, Ireland)


Jedediah Daniel Shields

Black Hawk, Michigan Technical University


Dr.
Randall Seeley

University of Cincinnati College of Medicine


Kathi Smith

University of Cincinnati College of Medicine


Dr. Kivanc Birsoy

Massuchessettes Institute of Technology



Works Cited

1.

Nature Publishing Group, Nature.Com, Available at
www.nature.com

(2011).

2.

American Association for the Advancement of Science, Science (AAAS), Available at
www.sciencemag.org

(2011).

3.

American Society for Biochemistry and Molecular Biology, Home, Available at
http://www.jbc.org/

(2011).

4.

Society, M
. M., The New England Journal of Medicine: Research & Review Articles on Disease & Clinical
Practice, Available at
http://www.nejm.org/

(2012).

5.

Rockefeller University Press, The Journal of Cell Biology, Available at

http://JCB.rupress.org

(2012).

6.

National Center for Biotechnology Information, Pubmed
-
Home, Available at
http://www.ncbi.nlm.nih.gov/pubmed/

(2012).

7.

WGBH, NO
VA PBS, Available at
http://www.pbs.org/wgbh/nova/

(2011).

8.

The New York Times Company, WikiLeaks, Available at
http://topics.nytimes.com/top/reference/timestopics/organizations/w/wikileaks/index.html

(2011 (April 25)).

9.

Koloata, G., Glimipsing a Scientific Future as Fields Heat Up, Available at
http://www.nytimes.com/2010/11/09/health/09stem.html

(2010 (Nov 8)).

10.

Nature Publishing Group, Getting Published in Nature: The Editorial Process, Available at
http://www.nature.com/nature/authors/get_published/

(2011).

11.

Collins, J., Darwin's Impact on Philosophy.
Thought

34
, 185
-
248 (1959).

12.

Lodish H, B. A. Z. S. e. a., in
Molecular Cell B
iology

(W. H. Freeman, New York, 2000), Vol. 4th Edition, p.
Section 1.2.

13.

WGBH, RNAi, Available at
http://www.pbs.org/wgbh/nova/body/rnai.html

(2011).

14.

WGBH , Available at
www.pbs.org/wgbh/nova/body/rnai.html
.

15.

Futuyama, D. J.,
Evolution
, 2nd ed. (Sinauer Associates, Inc., Sunderland, 2009).

16.

Thompson, K., Huxley, Wilberforce and the Oxford Museum, Available at
http://www.americanscientist.org/issues/pub/2000/5/huxley
-
wilberforce
-
and
-
the
-
oxford
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