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.”

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

Story 2 – The Dragon’s Treasure Makeover

There was a Dragon in a place far far away and over the thousands of years she had lived, she had gathered almost every known treasure. From gold coins to enchanted weapons, to magical stones and scrolls. The Dragon had it all.

Since she was such a big collector, other dragons often asked her to show them one-of-a-kind artifacts during dinner parties like the Diamond of the Druids or the Sword of the Seven Kings. The Dragon wanted to impress her friends, but her treasure was so vast that she had to search for months and months to find anything. Dragon dinner parties are known to last many days, but even the most patient dragon guests could not wait for a month.

The Dragon  tried to remember spells to help search her treasure faster, but all she knew were dangerous spells used in combat, not in someone’s own dragon lair.

At some point she had hired one thousand and twenty four goblins to do the searching for her. But they turned out to be very unreliable workers (plus they stole treasure). So she breathed fire on them and they ran away (they were not tasty enough to eat).

 

But the Dragon didn’t give up. She decided to post an advertisement on the Magic Network for a wizard. She wanted a wizard smart enough to figure out a way for her to search through her treasure faster.

The next day, a wizard walked into the Dragon’s lair.

“Mighty Dragon, I’m the Great Don Havakloo. I read your ad and I have a very simple solution to your problem. I will perform a My-Treasure-Where-I-Can-See-It Spell.”

“Spellbinding,” said the Dragon. “I’m curious to experience your spell, Don Havakloo.”

And so the Great Don Havakloo opened his copy of Spellopedia Magica, whirled his hands in the air and shouted:

“Treasure oh Treasure piled in far away piles
Move in front of the Great Dragon’s eyes!”

And all the treasure piled up next to the Dragon.

“Now your treasure is closer and you can save time searching for things,” said Don Havakloo.

“Don Havakloo, you really don’t have a clue. It takes me only thirty two steps to get to the treasure but a whole month to search through it. Do you think your spell deserves a reward?”

“Only a hundred gold coins, oh Mighty Dragon. I’m giving discounts today,” said Don Havakloo.

“I’ll give you a hotter reward,” said the Dragon and she blew a red hot flame and burned the wizard to a crisp.
The next day, another wizard walked into the Dragon’s lair.

“Mighty Dragon, I’m the Grand Gobblehalf. I read your ad and I have a very simple solution to your problem. I will perform a Split-My-Treasure-Like-Butter-And-Eat-It Spell.”

“It spells T-a-s-t-y,” said the Dragon. “I’m curious to experience your spell, Gobblehalf.”

And the Grand Gobblehalf opened his copy of Spellopedia Magica, struck his magic staff on the ground and shouted:

“Treasure Pile split in two. One half left and one half right.
And as for my share, I will only take the right.”

The treasure split in two mountains, one stayed near the Dragon, the other next to Gobblehalf.

“Mighty Dragon, now your treasure is half as it used to be, so it will take you half the time to look for things,” said Gobblehalf. “I will take your other half as payment, so no worries.”

“My dear Gobblehalf, since you want to gobble up half my treasure allow me to give you an extra reward,” said the Dragon and blew a red hot flame and burned the wizard to a crisp.
The Dragon was about to give up looking for a fix to her problem, when a young wizard walked into the Dragon’s lair.

The Dragon thought that wizard would be amusing to watch, but she was surprised when the young wizard said “Hi, my name is Thinkalot, what exactly is your problem Mighty Dragon?”

“It’s taking me a long time to find an item in my treasure.”

“Is it because your treasure is too far away?”

“No” said the Dragon. “I burned the last wizard who assumed that was my problem two days ago. It’s because I have too much of it.”

“And what if you gave up some of your treasure to make it smaller? Would that bother you?”

“Yes. I burned the last wizard who tried to take half of my treasure yesterday in fact.”

“And is your treasure organized, Mighty Dragon?”

“No, it’s all randomly piled up.”

The young wizard opened his copy of Spellopedia Magica and searched for the right spell. After a few minutes he said “I think what would help is to use a Sort-My-Treasure-By-Name spell.”


“Sounds like a spelling,” said the Dragon. “I’m curious to experience your spell, Thinkalot.”

So Thinkalot waived his wand and said:

“Amulets and Armors go to A
Bracelets and Broadswords go to B
Charms and Coins go to C”

…and so on and so forth and when he said…

“Zephyrs and Zircons go to Z”

then the treasure divided in 26 piles, one for each letter.

“Now, Mighty Dragon, when you look for the Sword of the Seven Kings all you need to do is look into the pile with the letter S. So, instead of one month, you can find any item in almost one day,” said the young wizard.

“Young Thinkalot, you clearly think a lot. You diagnosed my real problem,” said the Dragon. “You can take anything you like as payment.”

And the young wizard said, “I don’t need a payment, Mighty Dragon. Can I instead come and visit you every week?”

“Sure. Why, Young Thinkalot?” asked the Dragon.

And the yound wizard replied, “Because you have lived a thousand years and I want to learn from your wisdom. Gold is very valuable, but knowledge is invaluable.”