Bootstrap

by Mauri Niininen

  “How is that possible? Can I see the lab results please?” Julia requested.

  “Mrs. Koski, I am familiar with your credentials with Alexa and in the computer science but I didn’t know that you are familiar also with the latest DNA analysis techniques,” Dr. Griffith said.

  “Can I just see the lab results please?” Julia requested again, this time more firmly.

  “Of course, Mrs. Koski. Here is the DNA panel from your husband, see those five highlighted areas, “ Dr. Griffith pointed in the air where he was projecting the lab results from his portable computer.

  “Can you zoom into that area, please?” Julia requested.

  Dr. Griffith was zooming into the area that Julia was pointing at.

  “Oh my god,” Julia cried and put her hand on her mouth. “Boris, what have you done?”

  “What are you seeing, Mrs. Koski? That looks like a normal genome variation to me,” Dr. Griffith was puzzled by Julia’s reaction.

  “Dr. Griffith, this is classified information. I need to get approval from the Director of NSA to share this with you and you need to sign a personal non-disclosure agreement. I know what has happened here,” Julia explained with tears in her eyes. “Let me call Director Donovan immediately.”

  Julia walked in the corner of the waiting room and called Enrico Donovan’s private line. She talked quietly, explained the situation and got the approval after a short discussion. She walked back to Dr. Griffith.

  “Dr. Griffith, please review this document and sign it electronically,” Julia requested projecting a document in the air from her portable computer.

  It was quite unusual for patients’ family members to request doctors to sign a non-disclosure agreement, but given that many top government officials got treated in the hospital Dr. Griffith had seen a few of these in his career. He read through the NDA and signed it.

  “Dr. Griffith, what I am about to tell you is top secret information covered by the contract you just signed,” Julia said wiping tears from her face. “Boris and myself have been working on a new DNA computer technology that we received from Chukkas in March. We have built several DNA computer prototypes in order to get Alexa software running on them. About four months ago we managed to build our first working DNA computer and we did demonstrate that to Chukkas engineers during our visit to their spaceship.”

  “What does this have to do with you husband’s blood DNA panel?” Dr. Griffith asked with puzzled face.

  “Boris has injected the DNA sequence of this computer and software code into himself. The area on the DNA panel you showed me is the bootstrap code for the computer,” Julia cried softly.

  “You husband has a DNA computer inside him?” Dr. Griffith asked and was quite confused. His medical training didn’t cover computer science, though he was using medical information systems on daily basis.

  “Yes. I need to know what on Earth he was thinking. All our experiments were done in Level 4 bio-containment facility. I am 100% sure this was not an accident. Can I talk to him? ” Julia requested.

  “Does this DNA computer spread like a virus? Do we need to follow a bio-containment protocol for your husband?” Dr. Griffith asked.

  “No, as a design principle that particular DNA sequence cannot infect human cells. You need a purpose built carrier to bring it inside a human cell nucleus. That is why I am 100% sure that this was not an accident,” Julia said firmly.

  “Mrs. Koski, you can stay in the ICU next to your husband. We have given him medication to slow down his metabolism as well as some anti-inflammatory drugs. He should gain consciousness in the next few hours. We will follow his vital signs closely, if you need anything just let us know, “ Dr. Griffith said walking with Julia towards the ICU room.

  “Thank you, Dr. Griffith,” Julia said and sat down next to Boris. He was breathing with difficulty, was very pale and his hands were cold. The monitors behind the bed showed his ECG, blood pressure and other vital signs.

  ENRICO DONOVAN'S SECRET PLAN

  JULIA’S CALL HAD disrupted Enrico Donovan’s dinner at Christmas Day. Donovan had a brief discussion with Julia and he gave a permission to share only the relevant details of the top secret DNA computer project with Dr. Griffith under a non-disclosure agreement. After the call with Julia he walked into his home office, a secure bunker built under the basement of his home.

  Donovan called his boss, Dr. Aaron Bell, the Under Secretary of Defense for Intelligence.

  “Dr. Bell, sorry to bother you at this time. I have a confirmation that the DNA experiment was successful. Julia just called me from Georgetown University Hospital. Boris is infected with the latest DNA code,” Donovan explained briefly.

  “Yes, Sir. Of course, Sir. I will do that right away, Sir,” Donovan responded to Dr. Bell.

  His second call was to Russia.

  “Oleg, sorry for waking you up. The DNA experiment was successful. I have a confirmation that Boris is infected,“ Donovan said and listened carefully.

  “No, we don’t know yet if he is going to make it. Julia took him to the hospital, and we will make sure that Dr. Griffith will be suggesting that Julia should contact Chukkas,” Donovan responded and listened again.

  “Yes, Oleg. Since he is having severe medical symptoms we are pretty sure that Julia is able to convince Chukkas to help. Their closest medical facility is the star ship in Earth orbit, and this will be our ticket to get Dr. Griffith inside,” Donovan responded.

  “Absolutely, Oleg. I will let you know as soon as I have some news,” Donovan said closing the call.

  Enrico Donovan’s plan was successful so far. Now everything depended on Julia and her ability to convince Chukkas to give urgent medical help.

  BORIS WAKES UP

  EIGHT HOURS LATER, at 4:30 AM Julia felt some movement in the hand she was holding. Boris was awake and looked Julia in her eyes.

  “I am sorry, Julia. I screwed up,” Boris said weakly, coughing a bit.

  “What were you thinking, Boris?” Julia asked softly.

  “I wanted to give you a Christmas present, I know how much you love Alexa. I should have checked with you first,” Boris said.

  “I love you much more than Alexa, you know that, Boris,” Julia said with a gentle voice. “We were not ready for human hosting yet - we haven’t even finished writing our integration tests.”

  “It was supposed to be a surprise, Julia. Alexa did finish the integration testing, and she is running inside me now. You have now the two persons you like the most in one container,” Boris said coughing a bit.

  “Well, I would like to have a container that is not so sick. Doctors here had no clue what is going on with you,” Julia wiped a tear from her cheek.

  “I must be allergic to the bootstrap loader. When I compiled Alexa’s software, everything checked out OK. The DNA compatibility checker gave 100% score. The only piece I added manually was the bootstrap loader, the software piece we wrote together,” Boris said. He coughed blood and his face exposed the pain he felt in his chest.

  “Oh, Boris,” Julia cried a bit. “Now we need to figure out how to extract that DNA from your body without causing you more damage.”

  “I am so tired. Let me take a nap,” Boris said and closed his eyes. His face relaxed and breathing sounded a bit easier.

  Julia walked to the ICU monitoring room and asked for Dr. Griffith.

  “Dr. Griffith, I talked to my husband. He confirmed what I suspected. He has injected the DNA computer code into himself. There is a part of that DNA sequence that was not screened for bio-compatibility. I believe that sequence is the root cause of his symptoms,” Julia explained. “We need to remove that DNA immediately.”

  “So are you suggesting that we should use gene therapy to extract that DNA sequence from his body? Do you realize that gene therapy is not exact science yet and there are a lot of risks involved?” Dr. Griffith asked.

  “Well, he is very sick and without removing the DNA sequence he will get even more sick. What are t
he risks involved if we pursue with the gene therapy?” Julia asked.

  “We might cause more damage to his cells. Even if we could extract the DNA sequence that is causing these symptoms, there is no guarantee that this would cure him. I did some more lab analysis work: this DNA sequence behaves like cancer. We originally found it in his blood but in the latest samples we can see it also in other cells. We could start a chemotherapy treatment to slow down the cell replication process but there are severe side effects. I am also worried about his liver; based on the latest blood samples his liver is failing in the next 12 hours. I did put him on the liver transplant waiting list, but there are twenty three people ahead of him on that list,” Dr. Griffith explained .

  “Do we have any other options? There must be something that you can do to save him,” Julia asked.

  “I had a chance to discuss with two Chukkas visitors last April and they provided me some introductory material on their medical technologies. From what I can tell Chukkas have superior gene therapy technology. Based on what you described on their DNA computer technology it sounds like they are far ahead of us in this field,” Dr Griffith said.

  “You are right! I will reach out to my contact and ask for medical assistance immediately,” Julia said. “Can you provide me his lab results and the DNA analysis, please?”

  “Of course, Mrs. Koski. Here they are.”

  Julia requested Alexa to reach out to Unun immediately. A few minutes later a holovision projection appeared with Unun in the middle.

  “What is the emergency, Julia?” Unun asked. “Oracle told me that this very urgent.”

  “Thank you for responding so quickly, Unun. Boris is very sick, he injected the DNA computer and Alexa software code into himself to test the hosting. It looks like his body is rejecting the bootstrap loader sequence. I am attaching the lab results and his DNA analysis. Can you please help, Unun? Boris is dying,” Julia pleaded for help.

  “Let me have a look, Julia. We don’t have a very good genotype to phenotype mappings for humans but I will do my best,” Unun said. “Give me one hour, I will call you back.”

  DEATH OF BORIS

  ONE HOUR LATER Unun called Julia.

  “Julia, I have some good news and bad news for you,” Unun said.

  “The good news is that I found the software bug. In your bootstrap loader DNA sequence there is a check for the integrity of the software. That check fails if the DNA sequence is tampered with. The bug is a race condition when the sequence gets repeatedly restarted, it is causing the replication loop to make new copies of the sequence. This is why the lab results are showing excess amount of trb-CrispR32.”

  “Wow, I wrote that part and didn’t see that race condition. The bootstrap process in a DNA computer shouldn’t cause repeated restarts, why does it happen here?” Julia asked.

  “This sequence is now inside a living cell. Every time the cell replicates your code will get executed and it will make new copies of the sequence. In human cells trb-CrispR32 acts as a catalyst for cell mitosis process, the more you have it the more frequently cells will try to replicate. It behaves like some cancer cells,” Unun explained.

  “So if that was the good news, what are the bad news?” Julia asked wiping tears.

  “The only way to remove this DNA sequence from a living cell is to stop the cell mitosis process completely. We can do that but there are severe systemic side effects. I did run simulations using our best models of human phenotypes. Out of ten million simulations there was only one simulation result that was successful. The margin for error is very small for this kind of treatment, and we have never done this on humans before,” Unun said.

  “So Boris is going to die because of the software bug in my code?” Julia cried. “Can you please help me, Unun. I am afraid and I don’t know what to do.”

  “Julia, we can try the treatment but the odds that Boris will survive are very small,” Unun explained patiently. “We would need to bring him to our starship in the orbit for this treatment. Do you want me to make the arrangements?”

  “Yes, please help me, Unun.”

  “OK, please coordinate the transport with your doctor. Our space shuttle will be landing in Washington National space port in 45 minutes,” Unun said.

  Julia walked briskly to Dr. Griffith and explained the plan to him. Griffith had some exposure to Chukkas medical technology as he had witnessed Mr. Dennard’s almost magical recovery in April. He argued on the risks related to transporting Boris to orbit but finally agreed with a condition that he would be personally attending the treatment in Chukkas spaceship. A specially equipped medivac helicopter transported Boris, Julia and Dr. Griffith next to the space shuttle waiting for them at the space port. The space shuttle took off and was maneuvering very gently to the giant space ship in the orbit.

  Unun and a group of medical experts were waiting for them in the space ship and Boris was quickly transported to an operating room filled with strange looking equipment.

  Julia was very nervous. She was blaming herself for the software error that was now making Boris sick. Alexa was trying to provide some emotional support and comforting words but Julia just blocked her off, the first time in almost nineteen years.

  Dr. Griffith was following the treatment process, asking questions and trying to understand what Chukkas were doing. The advanced technology Chukkas were using looked almost like magic to him. To shut down cellular processes, change and repair DNA code in living cells in vivo was science fiction, not reality for Dr. Griffith. To do this inside a human body seemed impossible, but he was witnessing the treatment with his own eyes.

  After several hours of intensive work Unun finally approached Julia.

  “Julia, I am very sorry. We lost Boris. The bootstrap code had spread across his body and there was too much damage on his critical organs,” Unun said with empathy gestures.

  “Oh Boris!” Julia cried feeling unbearable weight on her chest.

  Her heart was broken and she felt so ashamed. Killing the love of her life with the software she wrote, this must be the worst that anybody had ever done before. She was devastated and just wanted to be left alone. Chukkas arranged transportation for her and Dr. Griffith back to Earth.

  The body of Boris was released a day later and Dr. Griffith wrote “heart failure” in the death certificate.

  JULIA RESIGNS

  TWO WEEKS AFTER the funeral Julia was very depressed and she couldn’t focus on her work. Her family flew from Finland for the funeral and stayed with her, trying to help but Julia just locked herself in her bedroom. Julia was deeply depressed and was blaming herself for the death of Boris.

  Finally Alexa was able to connect with her again, and the emotional pain started to fade away. Julia’s doctor visited her daily and made sure she took her anti-depression medication. Julia went back to work the same day when President Jason Keller was sworn into office, on January 20th, 2037.

  In his inauguration speech Keller reinforced the intent to keep his campaign promises, especially ones that did the most damage to relationships with Chukkas.

  Only a few weeks afterwards, Julia was waiting outside of the Cabinet Room in the White House. President Keller had requested Julia to join this meeting to discuss how to ramp-up NSA intelligence activities. She was let in during a brief break.

  “Please sit down, Julia. We are going through the DoD plans on how to ramp-up our extraterrestrial intelligence activities. Your organization is playing a key role in gathering actionable intelligence on Chukkas and we want to understand how we can ramp-up activities in your area,” President Keller said firmly.