The DNA Tube Discussed

Governor Tommy Thompson's Jan. 2000 Speech

Story of the Development of the DNA Tube.

DNA Tube used in a University of Wisconsin-Madison Science Class.

The Paradox of the DNA Tube: A Parable for Science as Exploring the Unknown
Based on an Interview of Tom Zinnen by Thomas Gauds, June 4, 2004, at Milwaukee's Discovery World Museum.
TG:	What's in the DNA tube?
TZ:	DNA. We hand these samples out to young people. Most have learned that DNA is too small to be seen—which is not true, but that is what most people learn. This sets up a contradiction: we hand them this tube and say that it contains purified DNA. They say it can't be, because DNA's too small to be seen and this looks like cotton. From their prior experience they say it looks like cotton. So we take advantage of this paradox to make it into a parable about how we test ideas in science: how science tries to figure out what we don't know yet.
	You have three big ideas here. It's either DNA or it's not DNA—hypothesis and null-hypothesis—or could it be cotton, which is the competing alternative hypothesis. A hypothesis is what I call a testable idea.
	So the next question is how do you test if this is DNA or cotton?
	That's interesting because you get to watch how people think about DNA and cotton--and testing. A lot of people think they need a microscope. That tells me those people think that seeing is believing, and seeing closer means bigger insight. There's a certain implication there that "to see is to know," which implies if you can't see you can't know. That's not really true. And besides even if you used a really good microscope, you'd be able to see it better but you wouldn't know if it was DNA or whether it's cotton.
	Some kids are pretty sharp and they say they need some known DNA and some known cotton. Then the next step we tell people after they've gone around this microscope route is we tell them DNA dissolves in water. So how can we test if its DNA or cotton? Their thinking goes along these lines: "Let's pour water in there and see if it dissolves. If it won't dissolve, then it's cotton; if it dissolves, then it's DNA.?
TG:	Is that where coaching comes in?
TZ:	Yes. We ask them to back off from the idea of just pouring water in the tube because if the white stuff in the tube is DNA and it dissolves, how many tests can you run? One. Is that a very good number of tests to run? No. So now what are you going to do? Well, you can pinch off some and put it on the table. Now you introduce them to the idea that sampling is a good idea in science.
	The key question about a sample is: does the sample fairly represent that from which it was taken?
	You have to think about what makes a good sample, and what makes a good sample better. So now they have a little of this DNA on their table top and they can save the rest for a souvenir. We ask them to take some cotton lint out of their pants pocket, a piece of lint about the same size as their sample of DNA. Now you have two samples, side by side, in a fair compare. To put water on both samples, we suggest you use both index fingers dipped in a glass of water to move a drop of water onto each sample, and rub each sample with an index finger. Do the samples dissolve? Then we get to see how people construct meaning out of the evidence. What have you proven?
	Some people will say, "DNA dissolves in water. You told me that. This stuff dissolves in water. I tested it. Therefore this is DNA."
	Other people will scratch their head and say, "Well, it's not cotton."
	One logical syllogism or logical thinking says "DNA dissolves in water; this stuff dissolves in water; therefore, this stuff is DNA." But this is flawed: the white stuff could be cotton candy. The better logical syllogism says, "Cotton does not dissolve in water; this stuff does dissolve in water; therefore, this stuff is not cotton." I don't know if you can prove that it's DNA, but you can sure disprove that it's cotton.
	So with this itty bitty parable you've introduced the distinction between proof and disproof, experiment versus experience, the power of controlled comparisons, and the power of competing ideas. And then you test the hypotheses. The funny thing about the paradox of the DNA tube is that it's not about DNA; it's a parable about science as exploring the unknown, and science as challenging and testing ideas that compete with what we think we know.
TG:	How did you get involved working with Discovery World?
TZ:	In September 2002, I was contact by Discovery World asking for help with the Digital Literacy Accelerator program. I met with the students in that program and introduced the idea of the ways science has of knowing, and the idea of genomics, which is a descriptive science a little bit different than genetics, as an analytic or experimental science.
	The students visited the Biotechnology Center in Madison, Wisconsin in the Fall of 2002 and Spring 2003 to do a couple of video shoots for descriptive educational videos the students were preparing to make. My job was to work with the educators at Discovery World and figure out what the students had in mind, and figure out how we could help the students learn more about their areas of interest.
	In the first year they came over during the work week, which meant I could line up faculty and staff researchers to be in the lab. Also I could set up for the different video teams to go and shoot B roll of equipment in the labs during the week when most of the workers were there.
	(Interviewer's note: B roll is the secondary or "safety" footage for a film. In order to string together two interview clips that were not shot consecutively, an editor will cut away from A Roll to B Roll, while the audio from the A Roll shot plays under.)
	Out of that work by the students was the final product completed last year during the Digital Literacy Accelerator Program.
	For the PIC program, the emphasis has been on a 60 Minutes/CNN-like news type stories that are 2-4 minutes videos on different areas (of genomics). The program is working with students from one school instead of five on Saturdays instead of during the week.
	The students again came to the Biotechnology Center in Madison twice, both on Saturdays. I set up an agenda based on what the educators were looking for. The first group (all sixty participants in the PIC program) visited to see what UW-Madison looked like as a research campus, as a community of scientists who see science not as what we already know, but figuring out what we don't know yet. One goal was giving the students a feel for how the buildings are what the people look like in the buildings, and what the labs are like.
	I call it the Star Trek versus Star Wars mind-set. Most movies give you the idea that people in science are — well, everything's very neat and clean in the labs and people wear lab coats. Like in Star Trek, everything's very neat and people wear uniforms. But in Star Wars you have Han Solo in dirty clothes banging on the Millennium Falcon and trying to get this piece of junk to fly. That's one of the things I try to get across to people: lot of different labs look a lot of different ways, and the ways that people look and dress in labs is a wide range.
	The only way to defeat those simplistic views is to give people a real alternative by walking around for an hour or two. The objective for the first visit was to give the participants a chance to visit the campus, give them a chance to see research labs and to do some hands on experimentation, and to be able to talk to some scientists.
	The second time the group came (a subset of the larger group who made a choice to follow the biotechnology track) they had a much more concrete objective. There were five video crews. Within each crew there was a director, a camera person, a sound person, etc. We had a pretty tight schedule. Each team had to be able to shoot an interview, shoot B roll, and go out and interview a person they ran into outside our building. There were logistics issues and a feeling of "let's get down to brass tacks" which wasn't the case in the first visit.
	Regarding the subjects suggested (genomic mapping, DNA synthesis, DNA sequencing, DNA microarrays, DNA optical mapping, protein analysis through mass spectroscopy), we gave them some research subjects based on our signature research. Part of this collaboration is that not only do we do research at the University, but one of our missions is also sharing that science with the public. The science that we can share best is that which is based on our research. What we do in our BioTrek outreach program is a series of activities called Doing DNA: DeCode of Life. We start off with a series of analogies and activities to get kids to think about DNA and how people imagine and envision DNA both molecularly and functionally over the years.
TG:	What are some of the analogies?
TZ:	One of the parables is to ask the students, "If I gave you choice between having a plate of cookies or a recipe card for cookies, which would you take and why— It's not like there's a right answer and a wrong answer. There are advantages and disadvantages to both. We're trying to get them to think creatively and analytically so that when it comes to making a choice or decision they've thought about it in a sophisticated, deep way.
	A recipe is a very interesting thing to have, especially if you say recipe card because of the difference between a recipe, which may or may not be written, and a recipe card which is a record. So now you have a record, and you're introducing more and more the idea of why is a record of information important. There's another "in-" word which is ingredients because often kids will say "I'll take the recipe because the recipe card because the ingredients are on it. Are the ingredients really on the card? Is there a pile of flour and sugar on the card? The students will often clarify by saying, "What I mean is, the ingredients are listed." I try to get them to clarify what it is to have a record, and what it means to say, there are ingredients there, as compared to saying that there's a list of ingredients there.
	It's a powerful thing to be able to store, retrieve, edit and copy and share recorded information. DNA is something that we study because it's a genetic recipe card. We don't write on DNA, we write in DNA. The information is embedded in the sequence of the A's and T's and G's and C's.
	(Interviewer's note: DNA is composed of four nucleotides, or building blocks call A, T, G and C. A nucleotide consists of three molecules; a sugar, a phosphate group, and a molecule called a base. If the double helix is a twisted ladder, the sugar and phosphates form the sides of the ladder and pairs of bases form the rungs. There are four different bases, usually abbreviated A, C, G, and T for adenine, cytosine, guanine, and thymine).
TG:	What's another analogy you use?
TZ:	Well, we can have the students build The Human DNA Model. The title is intentionally ambiguous. This is like two teams shaking hands after a baseball game. Each kid is one letter in this DNA and the most important thing about this is that it gets across that the two strands are facing in opposite directions. The fancy word for that is anti-parallel. But if you say anti-parallel to people, they get completely lost. But if you say. "What does it look like when two baseball teams shake hands after a game— they can imagine one team is facing one way and the other team is facing the other way. The idea that DNA can be pulled apart from two complementary strands is really important technological tool because the one strand becomes a probe for its opposite complement or mate.
TG:	Why is that important?
TZ:	That's important because when we go to talk about DNA microarrays, or DNA chips, they are basically a whole bunch of single strands of DNA spotted on a small piece of glass (see example).
	When I say a whole bunch I mean 262,000 different spots or dots all of single-stranded DNA and on a glass slide the size of a dime you have 262,000 different assays of genes. This is one of the best examples we have of being able to align with Discovery World's themes of Dream Big, Think Small. This goes back to Richard Feynman's statement, "There's plenty of room at the bottom." In other words, as you get smaller and smaller and smaller and get to the nano-level, things behave differently. The kinds of insights you can get are going to be different, and the kinds of ingenuity and inventions you can create are going to be very different, and I think this is a good example of that. You see this little piece of glass is hardly the size of a dime. You think that there's 262,000 dots on there, all built from single-stranded of DNA, waiting to stick to its complement.
	(Interviewer's note: Richard P. Feynman, scientist, teacher, raconteur, and musician. He assisted in the development of the atomic bomb, expanded the understanding of quantum electrodynamics, translated Mayan hieroglyphics, and cut to the heart of the Challenger disaster. Nobel Prize for Physics 1965.) (Feynman website)	Feynman
TG:	How can you get people to imagine working at the nano level?
TZ:	We try to do things at the whole body level and then let the learners begin to project on to the single molecule level. I don't know if that works, but what I personally aspire to is to listen to people, find out what kind of analogies they already have in their mind, see if you can coach, coax and cajole them towards models or visions closer to the best available scientific ideas that we have right now.
	If I have a specialty, it's in non-formal learners. One of the things I get to do is to focus on individuals who have an interest that they want to investigate and inquire at their individual space and pace. Can we give people, whether they are grandparents or grandchildren, a chance to wrestle with puzzles, paradoxes and parables so that what we are building is the ability to do science so that we can learn how to figure out what we don't know yet?" As the proverb goes, we're trying to give people a chance to learn how to fish. That's one of the great things about Discovery World: it gives kids who are organized through school — the "formal learning system"— extra tools and opportunities to do this informal, high-end inquiry.
TG:	How will your work with the PIC students prepare them for the future?
TZ:	We use a "Logic Model" approach to the assessment for this work. With a Logic Model you start with your vision. What do we want out of ourselves, what do we want out of the students we work with, what are the outcomes? You back up and take a look at the outputs. Do we want them to produce demonstrations that they have actually gotten to these outcomes? And in order for them to get those outcomes, what type of inputs do we have to provide?
	For me one of the biggest outcomes is the idea of science savvy and entrepreneurial ingenuity. Besides Discovery World, I don't know of any other place that emphasizes enterprise, ingenuity, creation of wealth for the commonweal they way that Discovery World does. That's important for Milwaukee because it gets at the idea that "to know is a good thing, but to know how is also a good thing (maybe even better)." When you know and know how to invent and create and then put the economics in, that's a big deal. It's a good thing to be able to use ingenuity to create new ideas or process that help people without harm to others. It's great to be able to work with a place that also has a focus on the idea that "the value of an idea is in its application."

Governor Tommy Thompson's State of the State Speech

January 25, 2000

When I look in to the eyes of my dear little granddaughter, Sophie, I see the eyes of the future of Wisconsin.

A new generation with endless potential, as we begin a new journey with eager anticipation--- confident that new achievements lie ahead.

For this century offers deeper valleys to explore, wider rivers to swim, taller mountains to climb.

Wisconsin is prepared to conquer them all. Ladies and Gentlemen, I say to you tonight at the dawn of a glorious new century that the state of the state is revolutionary.

See quicktime movie of Governor Thompson's remarks

Wisconsin is where the future begins. The next fifty years will look different.

The University of Wisconsin-Madison research will be able to decode the human genome and allow for your personal genetic profile to be traced encoded on a chip so that it can be downloaded by a doctor so your illness can be diagnosed and treated.

This research is going to help us solve the mysteries of cystic fibrosis, cancer and Alzheimer's disease.

Ladies and Gentlemen, the face of the future economy lies in this little tube and many others like it in laboratories all across Wisconsin.

Unlocking the mysteries of this small strand of DNA is just one way we're going to ignite a new industrial revolution through the unlimited potential the bioscience and high technology industries.

New discoveries in science and technology will create high skilled, high paying jobs in Wisconsin. Those jobs will provide a higher quality of life for our families and brain gains for our state.

A driving force behind this new economy will be the new Wisconsin Idea, a partnership between the University of Wisconsin and the private sector.

In the early 1900s, the scientific pioneers at the University of Wisconsin revolutionized the state's agriculture industry with new ways to measure milk quality, reduce food spoilage and eliminate disease in dairy herds.

Today, the science being done our university laboratories is literally spawning new companies that make the technology and products to bring to the marketplace.

The DNA Tube Handout

Click icon to see full-size .jpg handout

Most people have never seen purified DNA.

And when they do, they often think it's just string.

In doing so, they've been both skeptical and creative: They look at the label, they look at the stuff, and they come up with an alternative idea.

We encourage people to test their alternative idea.

The Puzzle

Is there an easy way to test if the white stuff is string or DNA?

What happens if you put cotton string in water? Most people know the string gets wet, but doesn't dissolve.

What happens if you put DNA in water? Most people don't know, but they'll guess that it dissolves (and in fact DNA does dissolve in water).

So water becomes the tester.

We encourage people to take a small snippet of the white stuff in the DNA tube and put it on a tabletop.

We ask them also to find a piece of lint or thread from a cotton garment so they have a known piece of cotton, and put that on a tabletop near the snippet of white stuff.

Then we ask people to put a drop of water on each piece, and ask: Does either dissolve?

If the white stuff dissolves, is this proof that it's DNA? Many people will at first say yes.

But some will point out that if the white stuff dissolves, it's not really proof that it's DNA, it's only proof that it's not cotton.

In this way, the DNA Tube can be more than Show and Tell.

The DNA Tube can be a "Think and Test"Tube. It illustrates the power of experiment and a difference between proof and disproof.

Developing Science Savvy: Transforming How We View and Do Science.

The Puzzle of the DNA Tube is a good parable for how we know what we know and how science probes the unknown. Here are some themes illustrated by the DNA Tube.

The label tells us the white stuff is DNA. The label is an appeal to authority.

People often doubt that it's DNA. Skepticism is a cherished trait to scientists.

This doubt also indicates that people have some inkling or nape theory of what DNA should look like. The suggestion that the white stuff is actually cotton is an example of making connections. New ideas must compete to displace existing ideas: so learning often depends first on unlearning.

Now the puzzler has a hypothesis (the white stuff is DNA) and a null hypothesis (it is not DNA) and an alternative hypothesis (it's cotton string).

Different hypotheses need to be constructed so that they make different predictions. Now the challenge is to have the creativity and ingenuity to come up with a way to test or discern between those ideas. Water is the tester and gives the Logic Fork: if the white stuff is DNA, then it is expected to dissolve. If the white stuff is cotton, then it is expected to not dissolve.

This is the Archimedes Eureka Point: not when you know the answer, but you know how you're going to get the answer.

Now comes the challenge of designing the experiment. First, the scientist plans ahead and realizes that it's better to take a sample of the white stuff, rather than using all of it. That leaves some white stuff for repeating the tests to confirm.

Second, the sleuth can anticipate alternative interpretations and add fair comparisons to exclude those. For example, if the white stuff dissolves, a skeptic could say, "How do you know that your tapwater doesn't dissolve cotton?" Rather than argue about it, the scientist tests it. The scientist takes some known cotton (from clothes, for example) and tests whether it dissolves in water side by side with the white stuff.

Now comes the Prometheus Thinking. Prometheus can be translated as "Knowledge Aforethought."Scientists can anticipate the possible results and lay out the conclusions they'll make for each possible result. If the white stuff is DNA, and the cotton is cotton, and the water is water, then scientists would expect that the white stuff will dissolve and the cotton will not. If both the white stuff and the cotton were to dissolve, then this would not be evidence that the white stuff is DNA. If the cotton were to dissolve, then something would be amiss — either the "cotton"isn't really cotton, or the "water"isn't really water, and the scientist knows the test would not be valid and so the scientist would make no conclusions about the white stuff.

Scientists know they can keep it simple: just put the white stuff on a tabletop, and some cotton near it. And drop some water on each. Then the scientist watches and records.

In drawing the conclusion the scientist is careful to distinguish between proof and disproof. If the white stuff dissolves in water and cotton does not, this does not prove that the white stuff is DNA. It only proves that it is not cotton. As one fifth-grader pointed out, the white stuff could just be cotton candy.

Evolution of the DNA Tube

(images not to scale)

Example of original version of DNA tube in microfuge tube with label wrapped around the tube.

Second-generation DNA tube upgraded with one-sided pennant label.

Third-generation DNA tube with cylindrical tube, red screw cap, and two-sided pennant label.

Fourth-generation DNA tube with revised messages and toll-free phone number

DNA tubes are made by Paul Pierick

Story of the Development of the DNA Tube.

By Tom Zinnen

I first saw DNA in tubes used as souvenirs when I worked at Agrigenetics on the east side of Madison during 1985-86. As part of the Open House at Agrigenetics in the summer of 1985, Mike Murray, leader of the corn genetics group, had prepared several dozen plastic test tubes with screw top lids and containing alcohol with corn DNA suspended in it.

The Lawrence Hall of Science at the University of California, Berkeley, also used tubes of DNA in alcohol as souvenirs. In the mid 1990's, my friend Mike Grasmick asked me if I would make some DNA tubes as souvenirs for a group of visitors to the Frito-Lay Research Lab in Rhinelander. I thought the alcohol-filled tubes had several drawbacks: the alcohol could leak, the DNA couldn't be easily handled, and the tubes were too big to put in a pocket. So I decided to use dry DNA placed in a small, clear plastic tube (a standard 1.5 ml Eppendorf-type microcentrifuge tube).

The dry DNA is a standard product extracted from salmon testis and purchased from the Sigma chemical company. (link to .pdf from Sigma describing the DNA product) The DNA is used routinely in labs as a non-specific "blocking" agent in Southern blots. The DNA comes in a white plastic bottle and looks like cotton fibers.

The DNA tube needed a label, and the first approach was to wrap a label around the tube; but this blocked the view of the DNA. I tried a label on a string, which did not obstruct the view of the DNA, but could get tangled when several tubes were piled together.

Next I tried a "pennant" approach by attaching the label abutting the tube, rather than around the tube, with cellophane tape that wrapped around the tube and laminated the label. Because the cellophane is clear, it didn't block the view of the DNA in the tube, and the pennant label doubled the size of the label surface so we could double the space for our messages. The microcentrifuge tubes were clear the conical shape distorted the view of the DNA, so we soon switched to a clear and colorless cylndrical tube and chose to pay extra for the bright red screw-top lids. This gave us a white label with black print and a red lid, a colorful combination.

Tamara Towns in my lab developed a printable form containing many copies of the same label. I began discussions with a representative of a label-printing company and Cheryl Redman worked with a rep to produce the custom-made labels with clear adhesive wings.

The parable of the DNA tube developed out of the unexpected response I often received when I handed a tube to adults on campus: "Wow, cool. But what is this really? Cotton?"

The tubes are hand made, and keeping a ready supply on hand was a challenge until Cheryl Redman contacted a local agency that provides job training for people with disabilities. Paul Pierick has been making the DNA tubes for us since about 1998.

DNA Tube used in a University of Wisconsin-Madison Science Class.

Thanks again for letting me use the DNA tubes (with the students in Plant Pathology 123).

The tubes were a big hit! We had the students isolate DNA from the fruit smoothie, and gave them a protocol that told them what the individual steps of the extraction procedure did. So they knew that the DNA precipitated because it was soluble in water but not in ethanol.

Then we asked them what they would need to run an experiment to determine if what they had isolated was really DNA. Right away they said that they would need a positive control of "pure DNA", so it was really fun to be able to say "I just happen to have that right here" and to bring out little tubes labeled DNA.

They all came up with an experiment that involved resuspending their putative DNA in water and using the pure DNA as a control. Their prep was so dirty, that it only partially dissolved. I was worried that this would be a problem, but they were fine with it. They concluded that their sample partially dissolved, so it must be partially DNA. There was a lot of great discussion, and they thought that it was really fun.

Thanks again!

Elizabeth Rosen