DrTechniko

Train Young Innovators Anywhere Anytime

biology

By

Story 3 – Discussion (part 2)

The second part of Story 3 explores more aspects of the DNA molecule both when used as a message and when used to create new organisms. Also, we take a look into biological processes that are defined in terms of positive and negative feedback loops.Here are some questions you might want to discuss with your kids:

Q: What happens when we change a sequence in the DNA or we start messing with the DNA strand and we cut and paste pieces from other DNA strands into it?
A: We get an engineered DNA strand that may or may not exist in nature. The change can be as small as changing the color of your hair or as big as transforming you into a new type of organism altogether, like a mutant.

Q: What do you think is Daena’s best quality that makes her a great DNA detective?
A: First, she knows her biology. Second, she is inventive and tries to find solutions based on her knowledge. Third, her solutions are not complicated. They are simple and they work.

Q: How did Daena beat the Ugga Ugga virus at the end?
A: First she changed the DNA of the Ugga Ugga virus to create a stronger (and not evil) virus, the Gaga Gaga virus, and then used the Gaga Gaga virus to kill the Ugga Ugga virus by creating a negative-positive feedback loop.

Q: How does a negative feedback loop work? Can you show an example of a negative feedback loop at your home?
A: A negative feedback loop works by regulating the amount of something. The more of the “something” we have, the feedback loop will try to make this “something” less. The less of the “something” we have, the feedback loop will try to make this “something” more.
This is for example how we maintain temperature in a house using a thermostat. In this case the “something” is the “heat”. The more heat we have, the thermostat will tell the A/C to blow cool air into the house to bring down the heat.

I hope we learned something useful today,
Dr. Techniko

By

Story 3.5 – Daena the DNA Detective And The Ugga Ugga Virus (The Final Battle)

“We need to catch one of these viruses and …” but before Daena could form a plan, the big hungry monkey head with the twisted sharp teeth started approaching them.

“DannyBot, this Ugga Ugga seems to take an interest in us. We should head back and reevaluate. I’m not in the mood for drama.”

They turned around but another Ugga Ugga virus blocked the exit.

“Dannybot, without being too dramatic I think we are …”

The virus zoomed at them, mouth wide open.

“DOOMED!”

But the next instant the virus was caught by a lasso made of DNA coming out of … DannyBot’s body. The lasso wrapped the virus around the mouth and body tight as a squeezing tentacle. Once Daena realized they were safe she headed to the exit, DannyBot and their new prisoner behind her.

“If I were not under the shock of a near-death experience, I would be impressed. Dannybot, I didn’t know you could do that.”

“It’s quite a basic function I’ve been designed for. My lasso makes bonds at the molecular level with the object so the object is unlikely to escape,” said DannyBot as if he had lassoed a harmless-looking water molecule.

They dragged the Ugga Ugga prisoner to the closest White Cell headquarters, at the tonsils.

DannyBot constructed a message from DNA, asking for permission to see the Warden and gave it to the nearest guard. It felt like a lifetime until the gate opened. When they found the Warden he was floating around his office, eating random proteins. He looked quite well-fed in fact.

“What can I do you for, Miss Daena?” asked the Warden.

“First of all, it’s DNA Detective Daena. Second, you ‘ve been infected by a genetically engineered virus. As proof, I brought a sample right here into your office.”

“He don’t look so dangerous to me. Just a monkey face. We ‘ll take the prisoner from here. Off you go now.”

The guards escorted them out of the headquarters.

“I assume the mission has been completed. Shall I set course for the extraction point?” asked DannyBot.

“Nothing would cheer me up more, but I have a depressing feeling about this. Let’s just wait out here. How much time left?”

“There are three hours left to total infection.”

It felt like forever until finally the gates opened. At first, it looked like the Warden coming out of the gates. But as he moved out of the gate and into the light, he didn’t look as white as before. He looked dark and ugly and had twisted sharp teeth. Like an Ugga Ugga virus!

The two guards at the gates tried to swim away, but before they could escape, a hoard of hungry monkey faces stormed out of the gates and brought an end to them.

“Eat my children. Eat and multiply!” said the Warden as the monkey heads swarmed the area. Then his eyes fell on Daena. He started eating his way towards her in a steady pace.

“This doesn’t look good. DannyBot, let’s hide before more of these monsters realize we are here!”

“Don’t go Missy. Come and feed me,” said the Warden, and then gulped down a couple of his children.

They zoomed away from the tonsils and went into hiding behind the nose. “The Warden might be slow, but his children are multiplying. How much time left, DannyBot?”

“We have entered the last hour.”

Daena sighed. This was all very stressful. She wished she was back inside her vial even if it was not near a window, even if had to look at the same sticker all day:

-The recipe of life and death lies in the DNA-
The recipe lies in the DNA, she thought. Her mind drifted off to her first class at the detective academy and the principle-of-life rule they all had to memorize:

The DNA recipe is written with 4 letters.

What are they?

T, G, C and A.

And when DNA splits in two

Each half is called RNA

And every letter T is replaced by a U.

“That’s it!” Daena jumped with excitement. “I figured out how to kill the Ugga Ugga virus! The recipe of life and death lies in the DNA. Get it, DannyBot?”

DannyBot blinked.

Daena sighed. “Ugga Ugga’s DNA contains the recipe for making an Ugga Ugga virus. It’s like when you read a message written in DNA language using the T, G, C and A 4-letter alphabet. Only the message is also the recipe. Do you see?”

“I don’t see how this helps us defeat the Ugga Ugga virus,” said DannyBot.

“Well, here is the missing puzzle piece. DNA doesn’t make the Ugga Ugga directly. It has to first split into two RNA strands, and in the RNA alphabet T is replaced by a U.”

“I don’t see how this helps us defeat the Ugga Ugga virus,” repeated DannyBot.

“Don’t you get it? What’s the code name of the Ugga Ugga virus in RNA alphabet?” said Daena as if explaining the concept to a hydrogen atom.

“U-G-G-A-U-G-G-A,” said DannyBot.

“Can you search your data for the U-G-G-A-U-G-G-A sequence in the Ugga Ugga virus’s RNA?”

A few moments later DannyBot said “I searched. I found the pattern.”

“Great. I want you to synthesize the same RNA strand but replace the U-G-G-A-U-G-G-A pattern with the G-A-G-A-G-A-G-A pattern.”

DannyBot synthesized the mutated Ugga Ugga virus strand. One by one he glued together A’s and C’s and G’s and U’s until he had a full RNA strand.

“The sequence is ready. But I don’t see how this helps us defeat the Ugga Ugga virus,” said DannyBot.

Daena closed her eyes. She wished she had a hydrogen atom for a partner.

“Because if we get the Warden to eat this mutated Ugga Ugga strand, then he will use the wrong recipe to make children. His children will be Gaga Gaga viruses instead. Then the Gaga Gaga viruses can fight the Ugga Ugga viruses. I think it’s time to pay a visit to these depressing monkey faces.”

They zoomed back to the tonsils with the Gaga Gaga strand in hand. The Warden eyed them with a hungry look.

“Bring them to me, my children!”

Before Daena and DannyBot realized what was going on, they found themselves wrapped by DNA lassos from a bunch of Ugga Ugga viruses.

“My calculations tell me he means to eat us,” said DannyBot.

“You depress me.”

“Miss Daena. Why so gloomy? You should be happy, because you’ll make a tasty snack,” said the Warden and opened his mouth.

“Wait, wait! You don’t want to eat me like that. I’m more tasty if you eat this first as an appetizer,” Daena waved the Gaga Gaga virus strand in his face.

“You ‘re a real lady,” said the Warden and he gulped down the Gaga Gaga strand. He burped and said “Missy, that was really yummy. Remind me to get the recipe after I eat you.”

He came closer to Daena, opened his mouth and was about to close it over her head, but instead he grew and grew and grew until he… burst and a bunch of Gaga Gaga viruses came out of his body.

Soon a war begun between the Ugga Ugga and the Gaga Gaga as they started eating each other. Whenever an Ugga Ugga ate a Gaga Gaga, it gave birth to Gaga Gagas.

But, whenever a Gaga Gaga ate an Ugga Ugga, it gave birth to Gaga Gagas. Soon the Ugga Ugga’s were wiped out.

“He should not have eaten the Gaga Gaga strand before checking it, but I didn’t think it was a good idea to tell him,” said DannyBot.

“DannyBot, you are learning. Yet you still have ways to go to before you understand the genius of my scheme that killed the Ugga Ugga virus.”

“There was nothing to understand. It was based on a pair of positive and negative feedback loops. It is quite a very elementary and primitive principle of life,” said DannyBot.

“You really depress me.”

By

Story 3 (part 1) – Discussion

Story 3 hopes to demonstrate some of the latest advances in biotechnology, nanotechnology and biological computing.

All these sciences leverage the unique properties of the DNA molecule that can be used to build molecular structures and to encode and decode information using the A, C, G, T alphabet. The key is to think of DNA as both a message and a recipe. You can read a recipe like any other text. But if you also buy the ingredients and then follow what the recipe says then you are actually “building” something: a dish that can be served.

Here are some questions you might like to discuss with your children.

Q: How does a virus infect a cell?
A: http://www.youtube.com/watch?v=Rpj0emEGShQ

Q: What is a bioengineered virus?
A: It’s a virus that is synthesized in a laboratory. Typically scientists start with a real virus found in nature. They study the virus in a safe environment inside a laboratory and then they try to modify some of its properties by manipulating the DNA code.

Q: Aren’t viruses supposed to be evil?
A: Viruses are typically labeled as “evil” or “harmful” because they can harm a human cell. However, if a virus is engineered it might have a positive effect on a human body. For example, scientists have engineered a virus that infects bacteria in the human body and prevents them from being resistant to antibiotics. This helps the human body recover faster from a bacterial infection.

Q: How is DannyBot a robot?
A: Not all robots are made from metal and wires. Nano-robots (also known as nanobots) are made from molecules like DNA. There is a whole field called Nanorobotics, which studies how we combine molecules into little machines. Check out this walking nanorobot for example:

http://www.youtube.com/watch?v=GVqJdAqTD4Q

Q: How can DannyBot read and decode DNA?
A: DannyBot does this using a method known as DNA sequencing, which is a fancy term for “figure out the sequence of A’s, C’s, G’s, and T’s in the DNA if we read it from start to end”. We know that A binds to T and C to G. So, the way to read the sequence of the A’s, C’s, G’s, and T’s, is to try to bind to them with all possible letters in the DNA alphabet and see which one sticks. So if we use a T and we see that it binds to the DNA then we know that we have an A in the sequence.
So, here is an easy exercise for you: what will the DNA sequence be if we see that GAGAGAGA matches? (answer: CTCTCTCT).

Here is a video that explains this in detail (the video is advanced):
http://www.youtube.com/watch?v=91294ZAG2hg

I hope we learned something useful today,
Dr. Techniko

By

Story 3 – Daena the DNA Detective And The Ugga Ugga Virus

-The recipe of life and death lies in the DNA-

Daena sulked as she looked at the message on the sticker of her vial.

“I’m depressed. I haven’t been assigned anything interesting since I graduated from the Detective Nanoengineering Academy and placed into this horrible tube in this horrible lab. I was voted the most beautiful nanoengineered virus in the Nature Journal. They could have at least placed us near a window to get some sun. Don’t you think, DannyBot?”


“I don’t see the importance of sunlight radiation,” said DannyBot.

“Are all nanobots as entertaining as you are?”

“Nanobots are robots made of DNA strands. We are not made to entertain. We are made to decode DNA, to synthesize DNA, to take apart DNA…” DannyBot went on and on about his functions.

“Booooriiiing. What’s the point of using DNA, if you can’t build something to have fun? Look at the humans in the lab. They are made from DNA like us, but they get to work on interesting things and laugh and go out. Why not us?”

“Because we are not humans,” said DannyBot.

“You depress me.”

Daena decided to swim around. She was kicking a bunch of floating aminoacids, when a human moved towards the vial and squeezed a drop of liquid into it. A DNA strand appeared into view.

“Looks like we got a message. Another boring mission I bet,” said Daena.

DannyBot swam towards the floating DNA strand, hooked himself onto it and started reading it base by base like a tape: A, T, G, A… Then he decoded the message.

“Message Start. Detective Daena. The chairman has been infected with a genetically engineered Ugga Ugga virus. The chairman will turn into a monkey in the next 12 hours. If word gets out, the government will close the lab and destroy all genetically engineered viruses including you. Your mission is to locate and neutralize the virus. You and DannyBot will be injected into the chairman’s body. Extraction coordinates have been provided. Extraction will commence once the virus has been neutralized.”

DannyBot spit out the last base of the DNA strand. “Message Stop.”

“I really hope we take care of this virus. I don’t want to end up inside the body of a dumb monkey forever.”

The lights went out as the vial was put into a box. When Daena saw the light again it was at a great speed as she was injected into the body of the chairman.

“We are into the blood stream,” said DannyBot. “Cell analysis shows our location to be the chairman’s butt.”


“That is so humiliating,” said Daena.

“Actually, humility is considered a virtue in some human cultures,” said DannyBot.

“You depress me.”

Daena tightened up. “Let’s go catch this Ugga Ugga virus and feed him to the white blood cells before he spreads. What is the most likely infection scenario?”

“Most likely scenario is airborne infection through the throat,” said DannyBot.

“I’m not looking forward to getting coughed at, but let’s head for the throat.”

They floated inside the bloodstream through the digestive track to the stomach and from there climbed all the way to the lungs and then the throat. When they arrived, the throat seemed normal.

“I do not detect any viral activity in the proximity,” said DannyBot.

“Great. We are back to nothing. DannyBot, how much time do we have left?”

“10 hours.”

“And how long will it take us to search the entire body?”

“21 hours. The math indicates we have less than 50% chance to find the Ugga Ugga virus in the next 10 hours,” said DannyBot.

“Simple math won’t get you anywhere, DannyBot. Set course for the brain’s thalamus, the pain processing center. If the chairman didn’t breathe in the virus then someone forced it into him. We can figure out where if we follow the pain. I should be working with humans. I should be named the greatest DNA detective in the world.”

Daena stretched proudly.

“Actually, you are the only DNA detective in the world, so by definition you are both the best and the worst detective,” said DannyBot.

“You depress me.”

They jumped into the blood stream next to the spinal cord and followed all the way up to the brain. DannyBot mounted on top of a nerve center and waited for pain signals. After a few minutes, they heard one of the nerves scream “Ay!” “Ay!” “Ay!”

“The pain signal appears to be originating from the left eye,” said DannyBot.

“I’m not looking forward to meeting this Ugga Ugga virus, but let’s head for the left eyeball.”

And so they floated from the brain to the nose and from there to the eye. As they entered the eyeball they shook from their horror. Thousands of big fat viruses that looked like hungry monkey heads with twisted sharp teeth swam inside the eyeball. Some would attack and try to eat each other, but most of them attacked the chairman’s cells. Their jaws would grab onto a cell and eat their way into it. Once they disappeared into the cell, there would be a moment of silence. But only a moment. The cell would then grow and grow and grow like a balloon and then explode.

“Bang!” a cell exploded near Daena and out of it came a hoard of ugly twisted monkey heads. They swam towards a bunch of eyeball cells nearby. But one of them, a really big one, turned and looked at Daena…


To be continued…