MCTP Genetics Capstone

Week 1:

Fourteen students showed up for the first class, four of which were
males.  Most, but not all, were MCTP students.  The classroom is a
rather dreary standard classroom in the engineering building.

We gave out three handouts: a description of the capstone course, a
list of suggested projects, and a book list.  After some initial
general discussion, we gave the students a "Knowledge Probe" classroom
assessment instrument consisting of several questions:

1. Why is it important for future science teachers to learn about
genetics? 2. What opportunities does this topic present for making
connections between math and science and between the sciences? 3. Have
you studied genetics previously? 4. What do you know about genetic
paternity testing and what do you think of its accuracy and ethics?

Student first wrote responses individually for 10 or 15 minutes, then
formed into small groups of 3 or 4 to compare and discuss thir
responses.  Finally, a representative from each group was asked to
stand and report on their groups discussion.  A whole-class discussion
followed. Most of the discussion centered around the last questions
(thanks to Ken Berg).

Ken Berg conducted an interesting hands-on activity in which stacks of
coins were modified by taking one coin from the top of each stack and
combining them to make an new stack, repeating the process over and
over.  The students were asked if they noticed anything.  Ken then
conducted a discussion with the class about dynamical systems, fixed
points, triangular numbers, and how these ideas might relate to
genetics.  I threw in a few comments about John Conway's Game of Life
(a 2-dimensional "cellular" dynamical system) that exhibits "emergent
behavior" (unexpected behavior resulting from the repeated application
of simple rules to a simple underlying system).  A couple of the
students had seem computer implementations of Life.

Students were sent away with instructions to buy and begin reading the
David Suzuki book and any one of the other books on the book list.
(There is no textbook - these are all paperback tradebooks).

------------- 
Week 2:

Part two of the "Knowledge Probe", this part focusing on more technical
issues related to the underlying science.

1.  In what way did Gregor Mendel's work change previously held ideas
about inheritance?

2.  Put the following scientific accomplishments in historical order,
earliest first: a. Genetic factors given the name genes. b. Individual
animal sperm cells observed. c. Microscope invented. d. DNA implicated
as the genetic molecule. e. DNA's complete genetic code deciphered. f.
Scientists discover that all living things are composed of cells. g.
Double-helix structure of DNA proposed. h. DNA isolated from the
nucleus of cells. i. Human Genome Project begun.

3.  Describe in general terms the structure of DNA.  What structural
properties allows this molecule to store genetic information?

4. Colorful anthropomorphic imagery is often used to describe molecular
mechanics.  For example,  on page 38 of Genethics, David Suzuki writes:

Ò...the enzyme swoops in on the DNA double helix like a bird of
prey...and thrusts a shoehorn-like extension between the strands,
prying them apartÓ.

Elsewhere, molecules are said to "embrace", "weld", "fuse", "grip",
"release", "align", "drift", "attach", "recognize", "pass through",
"hover", "slide", "move away".

How to molecules "know" where to go?  What is their method of
propulsion?  Do they have motivation?  In general, when two molecules
react, they most come together: what causes them to come together?

5.  What is the so-called "central dogma" of molecular genetics?

6. DNA stores information that directs the cellular synthesis of
proteins.  Why proteins?  Why are proteins so important?  What about
hormones, carbohydrates, fats and other biological compounds?  How do
they get produced?

7. The Genetic Code of DNA was completely deciphered in 1966.  Here is
a portion of that code:

UUU: Phe    UCU: Ser    UGU: Tyr UGU: Cys    UAA: STOP   AUG: Met and
START

and so on.   What is the meaning of this code?

8. Do all living things have the same Genetic Code, or do lower forms
of life have simpler version of the code or no uniform code at all?

9. What is the difference between meiosis and meitosis and why is this
important for genetics?

10. How does the modern methods of genetic engineering differ from the
classical and ancient method of artificial selection?  ----------
Students wrote responses to these questions individually, then I asked
students to volunteer their answers to the whole class for discussion.
Most students thought the questions were "hard".  I explained that the
purpose of the test was to One student commented "I had all that in
previous classes, but I just couldn't remember the correct answers".
This suggests to me that my questions are not sufficiently conceptual
and are too fact-oriented.

We spent a considerable time discussing these questions.  In
particular, on question 4, I tried to guide the students into making
connections with previous physics and chemistry classes that they had
had by asking them some leading questions: why do humans die when they
get too cold?  Why is our "normal" body temperature range so narrow
when the planet on which we evolved has such a wide temperature range?
What is the physical meaning of temperature?

I will summarize the student's responses (anonymously) at a later time.

In the last hour, we solicited ideas for projects from the class. The
two suggestions we got were: (a) artificial selection, e.g. dog
breeding; and (b) genetic diseases.  We spent some time trying to
"flesh out" these ideas with connections to science and mathematics.

We gave out a handout of "Web sites that teach genetics" and had each
student "sign up" for one of the sites to investigate before the next
class and to make an oral report to the class next week.

------------- 
Week 3:

We began with oral reports from each student on the Web sites that they
had chosen to investigate.  With the exception of a couple of students
who had one excuse or another, each student had visited their site and
had definite opinions about the utility (or lack thereof) of that site.
Some students were impressed by the volume of information, lesson
plans, activities, lab experiments, etc. that were available.  Other
were not so thrilled with their sites - some were found to be too
shallow, some too complex, and some just boring (e.g. MendelWeb).

In the next portion of the class, we worked on project ideas and
fielded questions from the students about the project requirements.  We
then told the students to choose preliminary groups of 2-3 students
each and to pick preliminary project topics for discussion, with the
understanding that these were only preliminary groupings and could be
changed later. This created a period of great tumult as students milled
around an talked in small groups.  Finally, some groups started to
emerge with ideas that they bounced off Ken and myself.  By the end of
the class, all the students had chosen groups and project ideas.  Their
assignment for next class - make a preliminary oral project proposal.
Some of the groups were eager to leave class a little early so they
could stop by the library to get started.

Interestingly, the most popular topic for projects is gene testing -
several groups choose topics related to this theme (e.g. forensic
applications; genetic disease testing, etc).

---------------

Week 4:

We began by continuing the oral reports from each student on the
genetics Web sites that they had chosen to investigate.  Reports on the
"Understanding Gene Testing" and on the "Virtual Flylab" site were
presented.  That still leaves two students to give their reports next
week.

Next, we heard reports from each of the preliminary groups on their
proposed project ideas.  The groups (2 to 4 students each) and project
ideas are beginning to firm up nicely.  One group did in fact change
their project plans after hearing that their first idea overlapped too
much with other projects.  The projects fell into three categories:
animal breeding; genetic diseases; and gene testing (with three
projects related to the gene testing theme).

We followed this with some comments and discussion about what
constitutes a good capstone-level project. To illustrate some of the
ways that basic science and mathematics can be integrated into and
related to genetics topics, I shared some material that I had found
related to the animal breeding and gene testing themes.  First, I
circulated an article from that morning's Washington Post about
"Dolly", the Scottish sheep clone, and passed out copies of a related
article in the Post a year ago (taken from the Post's Web site) that
announced that research group's first experiments with the technique at
the cellular level.  (The big news this year was that the artificial
fertilized eggs had developed into normal fetuses and grown into
seemingly normal adult sheep).  I pointed out the use of an electric
"spark" (in the language of this year's article) or electric "current"
(in the language of last year's article) to force the fusion of two
cells in the process.  I posed several questions for class discussion:
What does electricity have to do with anything?  Electricity is physics
and this is biology, right?  Was it a spark or a current, or is there a
difference?  What could electricity possibly do to help cells fuse?
Are there other instances where electricity is involved in any way with
biology. We spent some time talking about this and before we finished,
students had brought up all sorts of interesting connections that they
has learned about from movies, TV, and other courses: Mary Shelly's
Frankenstein myth and its historical context; Volta's batteries and
twitching frog's legs; electrocardiograms; electrical defibrillators;
the electrical nature of the nervous system.  I mentioned the use of
electrophoresis as a laboratory technique to separate biochemical
molecules.  We didn't answer all our original questions, but we did
illustrate lots of rich connections.

Then I talked a little bit about how one might find out some practical
information about forensic gene testing by doing a Web search using the
the search terms "forensic" and "gene testing". This turned up lots of
interesting sites, and I circulated around the room color printouts of
parts of several of the more interesting sites, including the sites of
companies that do paternity testing as a routine business.  Some of
those pages had examples of "gel scans" of DNA patterns and we
discussed how it might be possible to estimate the maximum number of
possible distinguishable patterns based on the length of the strip, the
width of the bands, and the number of discernible intensities (grey
values).

Their assignment for next time is to make progress reports on their
projects.

---------------

Week 5:

Isn't it nice when the newspapers and magazines are filled with stories
that relate to what we are teaching?  So it is with the cloned sheep
story that seemed to be everywhere this week. I handed out copies of
the science column from Monday's Washington Post (almost always
interesting and well-written anyway) to the class, a transcript of an
interview with the besieged scientist Ian Wilmutt (from the Roslin
Institutes Web site), and an article from the New Scientist
(www.newscientist.com/clone).  I read brief selections dealing with the
idea of cell differentiation and gene expression.  I asked students if
they had learned about these ideas in previous classes; most had not -
or did not remember. One student objected to the new cloning procedure
by saying several times that "It's not a cell" and claiming that
scientist had already cloned monkeys.  I asked the class how previous
cloning experiments (based on undifferentiated embryo donor cells)
differed from the current experiments (based on a differentiated adult
donor cell whose differentiation had been reversed - a real
breakthrough in biology).  I asked the class what practical benefit
using an adult donor cell rather than an embryo donor might have (e.g.
the donor phenotype is observable beforehand in the adult donor
animal).  Throughout all of this discussion that was fairly good
participation from the students - or at least from some students.
There are always those who mostly sit and listen.

The challenge here for all of us is to identify the specific
connections between all this and the basic science and mathematics that
they have learned. If asked about this, student will say something
general like "biology is based on chemistry, which is based on the laws
of physics and described by mathematical patterns" or some such thing.
Getting more specific than that is a challenge. At least in this
cloning business there is an explicit mention of electricity, but where
does temperature and motion and algebra come in?  Students still tend
to keep these fairly separated in their minds - perhaps because they
have mostly been exposed to separate courses taught by instructors who
aren't very much interested in other fields of learning.

Another discussion ensued about the ethical problems of human cloning.
I brought in the Op-Ed section from last Sunday's Post containing an
editorial that claimed that the worry about human cloning was
overwrought because of a "general lack of understanding about what
genes are and how they work".  A few questions for thinking and
discussion: how exactly would a clone differ from an identical twin,
genetically, legally, and theologically?  Why would clones be expected
to have a lower legal or social status (e.g. to be used for harvesting
replacement organs)?  (After all, our history has been that in-vitro
fertilization children have been accorded all human rights). What role
does genetics play in human success?  If you clone a rich or a smart
person, will you get a rich or a smart clone?  What does recent
research say about the role of embryonic development and early
childhood experiences on brain cell and cognitive development?  Why is
normal sexual reproduction, which produces offspring with novel and
untested genetic combinations, considered better than cloning, which
produces offspring with already tested genetic combinations?  Does all
this have anything to do with math and science?

In the second half of the (three-hour) class period, we did a hands-on
classroom exercise on DNA fingerprinting (which I found - where else? -
on the Web at:
http://www.gene.com/ae/AE/AEPC/WWC/1994/dna_fingerprinting.html).
Several of the student projects deal with gene testing, so I thought it
would be useful to learn something about how it works.

The overall question is: how is it possible to develop a reliable and
low-cost way of fingerprinting DNA.  We each constructed models of DNA
for each student from strips of paper labeled with two rows of letters:

G A A T T C G A A T T C G G A A T T C A A G A A T T C A 
A G C T T A A G C C T T A A G T T C T T A A G T G A C T

and so forth - different sets of letters for each student, because
everyone has unique DNA (except for identical twins, of which we had
none in the class).   I asked the students what the letters meant, why
there were two rows, and whether they noted any regularities.  Some
students thought that the letters were amino acids - I suggested they
re-read that section of Suzuki's book.  One student complained that
this was not a good model of DNA because it was too big and we could
see the letters! He also complained that the two rows of letters didn't
match!  (This is a student for whom, sadly, complaining is a higher
personal priority than learning.)

We forged on, creating models for a "restriction enzyme", looking for
"recognition sites" on each student's DNA, and cutting the DNA models
into fragments.  Each student determined the length of each fragment
and counted how many fragments of each length they ended up with.
Finally, each group choose two of the students' results to submit to a
separation process based on fragment length (called "gel
electrophoresis" in the laboratory), which basically comes down to
preparing a "frequency histogram" of the fragment lengths (math
concept?).

Then the idea was to combine all the group results to see if we got an
easily distinguishable patterns for each DNA sample. Here is where
whiteboard would have been handy (unfortunately, we are assigned to a
generic shared classroom with only a blackboard). Indeed, each pattern
was different.

I followed up by asking the student if they had personally learned
anything from this this experiment.  Most said yes (except - guess
who?)  There were several complaints, however, about the written
directions, which several students thought were unclear.  I have to
agree that I struggled with it, too, but is that always bad?  To what
extent should an instructor pre-filter and pre-digest everything that
the students have access to?

It is clear that the students just *love* these instructor-driven
hands-on activities.  I wish, however, I could get them to be more
self-directed, more interested in SEEKING OUT learning, and less
dependent on me to orchestrate all this.

We broke up early to allow the student time to work in their project
groups.

---------------

Week 6:

Today one of the project groups had made some real progress since last
week and was bubbling over with excitement.  Their project is  on the
technology of DNA testing.  They made a little presentation to the rest
of the class, telling how they had made a trip to the NIST to visit a
DNA testing lab, where a scientist there had shown them around,
answered questions, and given them some "handouts".  They were very
excited by this - to see that what we had been talking about in class,
and what they had been reading about, was actually "real".  But the
best part was that their presentation generated all sorts of discussion
and questions from the class (and from the instructors) - in fact, they
were planning to make a return visit to that same lab, armed with some
real questions to ask.

One of the interesting things they discovered in that NIST lab was the
importance of a technique called "thermal cycling" or "temperature
cycling", in which solutions of DNA and protein are cycled through a
carefully-designed temperature program. Another fascinating connection
to concepts that they had dealt with in introductory physics and
chemistry.  Why is temperature so important?  What is temperature,
anyway?  Something you set on a thermostat?  We already covered heat
and temperature in physics - isn't that enough?  Lots of questions.

We followed this with the last two of the Web site reviews.  Allison
had visited the "Morgan Multimedia Genetics Tutorial" site and reported
that it was very good, written in clear language, and embellished with
nice multimedia effects, including rotating DNA molecules and the like.
(The URL is http://morgan.rutgers.edu/).  She said that she learned
quite a bit from the tutorial, even though she had "covered" genetics
in previous courses she had taken.

I then shared with the class some Web sites that I had found related to
their projects.  AltaVista searches on the phrases "dna fingerprinting"
and "cat genetics" had come up with quite a number of very interesting
pages, which I had printed out and distributed to the groups working on
those projects.  Some of the groups had already found some of those
sites, but some were new to them.

After the break, I handed out floppy disks and instructor's manuals for
"GenScope". a multi-level genetics simulation program designed for the
middle-school and high-school levels.  (The URL is
http://copernicus.bbn.com/genscope/index.html).  The instructor's
manual talks a lots about teaching methods and has journal entries from
the teachers who were involved in field testing the program.  It makes
very interesting reading.  Our plan is to spend portions of a class or
two in a computer lab working on this program - but it's turning out to
he hard to find a suitable computer lab that we can reserve and that
has enough of the right computers, etc.  In the meantime the student
were encouraged to get a head start and explore on their own if they
have access to a computer.

I had planned to give a little quiz towards the end of class, but some
of the groups were be this time very anxious to get to work on their
projects, so we broke up early. 

----------------
Week 7:

We started today's class with a little quiz.  Just four questions,
based on the readings, discussions, and activities from the last few
weeks:

1.  Why did the story of Dolly, the cloned sheep, make such big news
this year, when the same research team had published an article in
Nature last year entitled "Sheep Cloned by Nuclear Transfer from a
Cultured Cell Line"? What, if anything, was different and significant
about this year's experiments?

2. Describe the process that was used to clone Dolly. Specifically how
does process differ from the cellular process of normal sexual
reproduction?

3. Describe the process of "DNA fingerprinting" involving the use of
"restriction enzymes" and gel electrophoresis.

4. Dr. Berg made the comment during the last class that DNA
fingerprinting "throws away" lots of data.  Is that true?  Is it
possible from the results of a DNA fingerprinting experiment to obtain
the complete DNA sequence (a list of all the base pairs) of the DNA
tested?  If not, how can DNA fingerprinting be useful for anything?

After the papers were turned in, we had a general discussion about
these questions.

I distributed a handout on locating and evaluating on-line information
(http://www.inform.umd.edu:8080/UMS+State/UMD-Projects/
MCTP/Technology/handouts/Informatics.html) and the table of contents of
the genetics article in the on-line Encyclopedia Britannica, which was
recently subscribed to by the University and is available to all
campus-based accounts.  The on-line Encyclopedia Britannica is quite
up-to-date and is a good "first read" for unfamiliar material, before
tackling more specialized sources.

I also told the students about on-line access to several science
magazines, including Scientific American, Science News, and Discover,
which often have good articles.  I passed out print-outs of some
articles on DNA fingerprinting, genetic diseases, and cat genetics to
the project groups working on those topics.

  The last part of the class was devoted to talking about project
schedules, requirements, and presentation. I explained that each group
will be expected to make their final presentation (20 min + 10 min for
questions) in the last regular class meeting (May 13th, 1-4 pm). I'll
arrange to have their presentations video taped.  I also told them to
submit their project write-ups in machine-readable form. Together with
scanned graphics and digitized video frames, this will be used to put
together a Web-based presentation on each project, which all the MCTP
participant will be invited to view and comment on. 

------------
Week 8

Back after the spring break, we began with a discussion of an article
in yesterday's Washington Post (Monday, March 31) about scientists from
Ohio who had constructed an artificial human chromosome.  The article
even tried to explain what genes, chromosomes and DNA are.

The major topic for the day was a discussion of the question: what do
people need to know about genetics?  We focused on two populations of
people: (1) middle school kids, and (2) college-educated adults.  To
address the first population, we looked at the National Academy of
Sciences "National Science Education Standards", which are on the Web.
I handed out printouts of the following excerpt:

Science Content Standards: 5-8 Life Science
http://www.nap.edu/readingroom/books/nses/html/6d.html#ls

"REPRODUCTION AND HEREDITY

Reproduction is a characteristic of all living systems; because no
individual organism lives forever, reproduction is essential to the
continuation of every species. Some organisms reproduce asexually.
Other organisms reproduce sexually.

In many species, including humans, females produce eggs and males
produce sperm. Plants also reproduce sexually--the egg and sperm are
produced in the flowers of flowering plants. An egg and sperm unite to
begin development of a new individual. That new individual receives
genetic information from its mother (via the egg) and its father (via
the sperm). Sexually produced offspring never are identical to either
of their parents.

Every organism requires a set of instructions for specifying its
traits. Heredity is the passage of these instructions from one
generation to another.

Hereditary information is contained in genes, located in the
chromosomes of each cell. Each gene carries a single unit of
information. An inherited trait of an individual can be determined by
one or by many genes, and a single gene can influence more than one
trait. A human cell contains many thousands of different genes.

The characteristics of an organism can be described in terms of a
combination of traits. Some traits are inherited and others result from
interactions with the environment." 
-------------- 
Dr. Berg challenged the students to consider whether these were
reasonable standards; he urged them to distinguish between what is
really practical in the real world and what is considered ideal by the
scientists who wrote the standards.  This generated much discussion.
Some students felt that middle school students would not really care
about genetics because they wouldn't see how they could use that
information for anything. It was a very free-wheeling discussion.
Some of the student felt that most 8th graders would not know this
material until they got through a high school biology class and that
even many adults don't know these things.

We eventually moved on the second population, college-educated adults.
To address that population, I suggested that we look at a recent
general science textbook intended for non-science majors.  I selected
the work of one of the authors of the "Cultural Literacy" movement,
namely Trefel and Hazen from George Mason University.  We looked at
their textbook "The Sciences: An Integrated Approach", published in
1995.  I explained that this was not being presented as the "the"
answer - just the views of these authors. The book "covers" almost all
of the sciences, as well as some technology and "science and society"
topics.  How much genetics do they cover and exactly what topics?  They
have a few pages on classical single-factor Mendelian genetics, working
out the one-gene (3:1) and two-gene (9:3:3:1) inheritance patterns.
Then they go though a basic overview of molecular genetics, DNA
structure, replication, and transcription, the genetic code, protein
synthesis, ribosomes, mRNA and tRNA, DNA sequencing, viruses, mutation,
DNA fingerprinting, and genetic engineering. There are several very
nice color diagrams.

We discussed whether or not it was reasonable to expect this level of
coverage in such a book, whether college-educated people generally, or
future middle school science and math teachers specifically, should
know this stuff. We found that the material in the chapter corresponded
quite well with the coverage of the "knowledge probe" test I had given
at the second class meeting.  Another good discussion. Some of our
students admitted that most of what they learn in their college courses
they are learning just to pass the courses and get a degree and that
they have no real interest in much of the material.  I assigned this
chapter as reading for the class.

Next week: progress report from the project groups. 

------------- 
Week 9

This week our class was centered around the Science article on page A3
of Monday's Washington Post entitled "Model Demonstrates How Evolution
Obeys Mathematical Laws".  This gave Ken Berg a good opportunity to
focus on some related math topics.  The article is about scaling
relationships and "power laws" and shows a "log-log" plot of the mass
of various mammals (in grams) vs their rate of energy consumption
(expressed in watts).  This relationship is remarkable regular over a
very wide range on animals -  from a mouse to an elephant, 5 decades of
mass.  This is an example of a "power law" in which one variable is
related to another raised to some power (exponent).  In this case the
rate of energy consumption is proportional to the three-forths power of
mass. The article also discussed the relationship between life span and
heart rate vs mass of the animal, which follow other power laws. Ken
had the students measuring the slopes of lines on log-log plots and
relating that to the exponent.

This kicked off a discussion about logs and exponents, and linear and
log and log-log plots, which lead to an even more interesting
discussion about math and math phobia in which several of the students
admitted that they were "turned off" by the articles use of such
"scary" terms as "three-quarter power law" and "log-log" plot.

The article also talked about fractal geometry, in the context of the
fractal nature of vascular (circulatory) systems in plants and animals.
This lead to a discussion, lead by Ken, of the meaning of dimension and
fractal dimension.  We puzzled over such questions as "Is the surface
of the earth two dimensional?"

I felt that the Post article, while interesting and informative, was
not a good model of constructivist learning, as it presented "final
form" results and terminology without the opportunity to discover.  We
agreed that a better way of presenting this material would be to let
students acquire the data and then let them explore the relationships
themselves.

------- 
Week 10/11

Last week (Week 10) we mapped out the plan for the rest of the
semester.  Because the students need more time to work together on
their projects, we decided to define Weeks 10, 12 and 13 as "work
weeks" where the individual project groups would meet to work on their
project rather than having whole-class meetings. The final project
presentations will be done in the last class meeting (May 13. 1-4 pm,
EGR 0135 in the Engineering Classroom Bldg.)

This week was therefore the last formal whole-class activity. We spent
the entire class in a computer lab, working in pairs or individually on
"GenScope". a multi-level genetics simulation program designed for the
middle-school and high-school levels.
(http://copernicus.bbn.com/genscope/index.html).  I handed out an
assignment sheet that gave them several specific tasks to perform using
this program, involving creating "dragons" with specified
characteristics (color, wings, horns, legs, tails) at the chromosomal
level (by directly selecting alleles of the gene(s) responsible for
that characteristic) and at the cellular level (by selecting and
fertilizing gametes of two parent dragons).  They "discovered"
recessive and dominant behavior, polygenic traits, sex linkage,
meiosis, segregation and crossover, and observed the classical
Mendelian inheritance patterns as well as the DNA sequence differences
of different alleles.

It was interesting watching the student take to this.  None of them had
any real trouble with the "computer" part - operating the program
itself.  I could see a lot of excitement in some of the students when
they finally got something to work or discovered some hidden aspect.

As they completed the assigned tasks, some of the students continued to
explore the program, investigating multi-generation color inheritance
patterns in the "pedigree" mode, for example.  Others fired up a Web
browser and did some searches for their projects (this was a
"networked" lab).

During this time, Dr. Curtis Sears, an observer from the National
Science foundation, visited the class and talked to the students,
individually and in small groups, about their project, the Capstone
class, and about their MCTP experiences generally.  Some of the
students enthusiastically showed off their new-found knowledge and
accomplishments with the GenScope program.