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Chapter 6
The meeting with Professor Camble had gone well Jack thought. He had explained that he wouldn’t be able to come back for at least six months, doctor’s orders. Professor Camble had been understanding and told Jack he had his full support and that Jack's health was the most important thing. Jack left the meeting feeling confident that someday he would be able to return to his research at the university.
Jack went looking for Phylicia, finding her in her office. They decided to get a cup of coffee in the cafeteria before her next appointment. “How did the meeting with Professor Camble go?” asked Phylicia after they were seated.
“He was actually very understanding. I was afraid that he might be upset when I told him I would have to take six months off.”
“Six months!” exclaimed Phylicia before she could catch herself. “I'm sorry Jack, I didn't mean to, I mean it is such a long time.”
“That's okay Phylicia, I should have told you more about my condition before.” Jack then told Phylicia the details of his illness. He found it easy to talk to her and ended up telling her the story of his past few years. It was the first time he had opened up to someone since Miri had died.
After he had finished Phylicia said, “Jack, I just want you to know that I will help in whatever way I can, even if you just need someone to talk to.”
“Thanks Phylicia. I appreciate your concern, and I will let you know if there is anything you can do.”
They talked a bit more before Phylicia had to get back to her office. Jack returned to his apartment.
It was the following evening that he got an email from the university research committee. It informed him that his research had been suspended. That it was the property of the university and that he should not use or claim any of the results as his own. And that Jack had been taken off the roll of Ph.D. candidates. If he should wish to renew his application for Ph.D. he would need to reapply with the proper forms. The email wished him well and mentioned that official paperwork would follow.
At first, he was a bit stunned at the bluntness and speed with which the committee had seemed to make its decision. After talking to Professor Camble he expected a more tactful approach to be taken. But he knew how competitive research positions had become in the past few years, especially following the employment crisis.
Though young at the time Jack remembered that the crisis had started as the automation of jobs became more common in the developed world. Transportation was automated, jobs were lost. Fast-food was automated, jobs were lost. Retail was automated, jobs were lost. By the time automation spread into the developing world, the crisis was too visible for governments to dismiss it. To quell the rising unrest governments all over the world had no choice but to establish a guaranteed lifetime income. The income was to be paid by a tax on automation, a tax to which businesses vociferously objected but became resigned to pay as they realized that without purchasing power people simply couldn't buy the goods the now automated businesses produced.
Conservative pundits predicted that a government-provided life-income would lead to a majority of the population spending their time in virtual pursuits such as gaming. And while a lot of people did spend their days in virtual worlds others, feeling liberated from the immediate need to earn a living, were pursuing learning and advanced degrees as an outlet for their energies. This had created a huge demand for positions in undergraduate and graduate programs. Universities found they could pick and choose the students they admitted to their programs.
By the time Jack entered graduate school many disciplines had stiff competition for admittance and continued enrollment. He had seen others lose their positions in labs because they were deemed not to be serious enough about their research. Or because they hadn't put the hours in or because they had questioned their assignments or they had questioned their adviser's motives. Anyone that didn't show complete devotion was subject to immediate dismissal without recourse. Jack knew he wasn’t unique.
It was decided then, he thought. He went out for a walk.
His Annie alerted as he reentered his apartment. It was Phylicia. “Hi Jack, this is Phylicia. I was just calling because I heard what happened with your research.”
“You found out already?”
“Well, I was in the lab when they buttoned up your experiment which I found disturbing, so I started asking around. I guess I've developed some good sources over the years, it didn't take long to find out what was going on.”
“Then you know that I've not only lost control of my experiment, I've also lost my standing in the doctorate program and any use of the results of my research.”
“They kicked you out of the program too? I didn't know that. I don't understand, I mean how could they do that?”
“Supposedly it is in the agreement we signed when we entered the Ph.D. program. If for any reason we abandon our research we can be required to forfeit our place in the program. The research committee claims that my request for a six-month sabbatical constitutes abandonment. But I guess it's to be expected, you know how competitive research positions are today. I wouldn't be surprised if they don't replace us all with research Annies.”
“Jack that is so unfair! They just want to get their hands on your research, that's what I think.”
“I've been thinking I haven't made as much progress as I should have and besides,” Jack paused, her words sinking in. “Why do you think that someone is trying to appropriate my research?”
“Because, no matter what you say, you've made more progress than all the others. There is a lot of jealousy in that lab. Someone has decided to take this opportunity to steal your research.”
“Do you think steal is the right word?”
“I'm afraid it is the right word. That is the state of university research these days. Did you know that most of the research done in that lab can't even be reproduced? I've tried and I for one question their results. I wouldn’t be surprised if Kenneth doesn’t take over your research, he’s always been Professor Camble’s favorite and Camble is under pressure from the administration to show some results out of his lab. That's probably why he didn't stand up for you.”
“Well, I don’t like to think of science being practiced like that but you may be right, I’ve seen others treated not much better. I will just have to do what I can to keep my research alive while I recuperate.”
“Jack, if you need anything from the lab or the university just call. I’ll be glad to help you with any research you pursue.”
Chapter 7
The long flight from LAX to Guangzhou, China was over. Now it was only another hour until landing at Tang Son Nhat International Airport in Ho Chi Minh City.
Dr. Roberta Hughes of the CDC was going to Vietnam to investigate a viral outbreak in the western part of southern Vietnam. The virus seemed highly contagious but not life-threatening. Out of the hundreds of cases Vietnam health authorities were monitoring, only one person had died.
That was different from the virus outbreak that her colleague Dr. Williams had investigated in South Sudan the month before. There the virus was highly virulent but not so contagious. Unfortunately, he had lost his samples trying to leave the country during a tribal uprising and apparently the virus had run its course, so the CDC had not been able to make a definitive classification except for what Dr. Williams' Annie had analyzed.
Dr. Hughes drifted off to sleep and was awakened by one of the flight attendants upon landing. The entire trip had taken nearly thirty hours including layovers.
In the modern terminal, Dr. Hughes saw someone holding up a sign with her name on it. The person turned out to be Dr. Cam Nguyen.
“Hello, I'm Roberta Hughes.”
“Hello, I am Cam Nguyen. I work with the Health Ministry and will be your guide during your stay in Vietnam. I hope you had a pleasant flight?”
“Yes, too long, but overall not a bad flight.”
“Good, let us get you through immigration and then pick up your luggage downstairs.”
With the help of Cam, it didn't take long to be processed through immigration. Dr. Hughes had her passport and visa in order. Baggage claim was typical of any large airport, harried but workable.
Dr. Hughes had nothing to declare in customs, and she and Cam passed on through and out of the terminal. Dr. Nguyen looked to her left and waved, a small SUV started toward them. The driver loaded Dr. Hughes's luggage and they were on their way to the hotel that Cam had booked for Dr. Hughes. Coming out of the terminal it was only a short drive-up Bach Dang to the Palm Hotel.
It was late afternoon, and Dr. Hughes remarked how busy the streets were, with cars and SUVs and the ubiquitous motorbikes passing on the right.
“Yes,” said Dr. Nguyen. “And this is as light as the traffic gets today I'm afraid.”
After making sure Roberta was checked into her room Dr. Nguyen said good night and that they would start for Chau Doc early in the morning.
Roberta ate some dinner in her room and studied the reports Cam had given her. Chau Doc was a fishing village on the Hau River in An Giang province, close to the Cambodia border. It seemed to be the epicenter of the breakout. Three-hundred and fifty-three people had been infected so far with still only one death. The CDC had been called in at the request of the World Health Organization (WHO) which the Vietnamese had appealed to. So technically Roberta was there representing WHO and not the CDC, but she really didn't care for the fine politics. She was just intent on getting samples and field intelligence and getting back to the CDC for analysis. She put the reports back in her bag and went to bed.
Early the next morning Roberta and Cam were on the road with their driver Huynh Hoang. Roberta noticed the driver was completely quiet though apparently competent.
“The traffic is incredible,” remarked Dr. Hughes. “Is it always this bad?”
“This is typical for a morning rush hour,” said Dr. Nguyen. “We should make better time once we clear Ho Chi Minh outskirts. It shouldn't take more than four or five hours to drive to Chau Doc.”
“I have to say that Ho Chi Minh City is quite modern and beautiful. I really didn't know what to expect but thought it would be much older. What will Chau Doc be like?”
“Yes, Ho Chi Minh has changed much in the last couple of decades. Very much development and very much population increase. Much of the old city has been redeveloped except the outskirts. Now Chau Doc is a much smaller city. It has only a population of about one-hundred fifty-thousand. The Hau River flows through town to the Mekong. The floating city, houseboats as you would say, is quite famous. It is also excellent for fish and sauces. We will try them tonight?”
“Sounds good,” said Roberta.
Roberta and Cam talked most of the way to Chau Doc, discussing their professional careers and educational experiences and the current viral outbreak. As they talked Roberta noticed the changing scenery. From city to town to more rural. She noticed the houses became fewer but still were located close to the road with fields stretching out far behind. She also noticed that while the roads ran very straight they had to turn many times to apparently make their way to the few bridges that crossed the many watercourses between Ho Chi Minh City and Chau Doc.
It was eleven-thirty in the morning when the SUV pulled into the Victoria Chau Doc Hotel. After lunch at the hotel, the driver dropped off Roberta and Cam at the Binh An Hospital where they went on rounds with the hospital's Medical Director. Roberta took notes and made pictures with her Annie. Blood samples were provided by the hospital personnel in a small sample satchel. Roberta did not bother to analyze these with her Annie as she could do a much more thorough job at the CDC in a couple of days. It was late in the day when they arrived back at the Victoria.
“We will go to dinner in thirty minutes; I will take you to the floating cafe?” asked Cam.
“Yes, I'll meet you in the lobby.”
They arrived at what appeared to be a floating barge, the sign said Con Tien Restaurant. The driver dropped them off, Dr. Nguyen arranged for him to be available by phone. They were seated on the upper level which was open to the air with a curved roof above.
The menu was mostly fish or chicken served with a selection of Vietnamese fish sauces. Roberta chose fish, Cam had chicken. Several fish sauces came with the meal including 'Red Boat' which became Roberta's favorite.
“This is excellent,” said Roberta.
“I'm so glad you like it,” said Cam. “As you can taste it's very important to find a fish sauce you like to highlight the meal.”
They spent their dinner mostly discussing the viral outbreak. When they had finished their meals Cam called the driver while she and Roberta drank a glass of wine. The drive back to the hotel was uneventful. Roberta was soon asleep.
She knew something was wrong as soon as she awoke the next morning.
Chapter 8
After the shock of losing his research wore off, Jack started to think about his future. He was determined not to give up on his goal of a cure for virus infections. But he would have to redirect his efforts into something like software design and simulation, something he could afford since he no longer had access to a well-stocked biology lab. He could do a few simple DIY tests on his synthetic biology constructs but most of the in-depth lab work and testing would be done by others, he hoped.
Jack felt confident his virus detection circuit would have worked. So his first step would be to program and simulate such a circuit using standard synthetic biology components.
Next, he would pursue an idea that had occurred to him about how to stop a viral infection. He knew that one way the human body responded to a virus was by generating antibodies that mimicked cellular receptors and would bind to the virus-associated protein (VAP) of the virion (a viral package before cell infection). With all its binding sites occupied the virion was effectively prevented from anchoring itself to a cell and causing infection.
Jack believed he could do something similar by creating what he called blocking molecules. These would mimic the cellular receptors and attach themselves to a virion's VAPs and neutralize the virus.
Once his virus detector identified the virus-associated protein he would use genetic tools to assemble DNA snippets into blocking molecules for that VAP. The current strategy of developing such molecules was quite expensive because of its trial and error aspects. Jack hoped that his design-oriented approach would reduce the cost significantly.
The delivery vehicle to get his virus neutralizers into the human body would be similar to the branching molecules called dendrimers. These were symmetrical three-dimensional self-assembling molecules. They currently served as excellent spherical 'cages' to deliver RNA and DNA into cells. Jack reasoned he could build upon the software that he had written for the design of three-dimensional integrated circuits to build his dendrimer inspired delivery cages, d-cages, as he came to call them.
Finally, he would use the techniques of ANI available as a package through one of the cloud providers to make the software smart. The ANI would be able to help researchers set up and interpret the software solutions. Once trained it would also be able to offer ideas for further investigation to the researchers.
All he needed was access to a synthetic biology component database, an ANI cloud provider, and support for publishing his software, and Jack thought he knew someone who could help.
He called Phylicia and told her what he needed. As expected, she had a contact in the IT department at the university, give her a few minutes she said and she would find out what resources were available. She hung up.
A few minutes later Jack’s Annie announced a caller. “Hi Jack, this is Phylicia, here is what I have found. My friend tells me we could use the university’s 'Open Access Program' to request the use of university computer resources. The program is ostensibly a public outreach program that was designed to encourage high school students with their science projects but there have been cases where others were also allowed into the program. My friend assures me that your request is a proper fit for the program's objectives. She will put in the necessary paperwork and let us know when it’s available.”
“Wow, that is great Phylicia, you really came through. I think that deserves at least a dinner, what do you say?”
“Well I didn’t do it for a reward but a dinner would be nice, thanks.”
“Okay, I’ll call you soon, thanks again.”
“Um, okay Jack, bye.”
Chapter 9
Roberta definitely felt something was wrong. Her head was pounding, and her mouth was very dry. Her eyes itched, almost burning in intensity. She quickly showered and dressed. By the time she called Cam's Annie, she felt feverish.
"Good morning, Cam, this is Roberta. I'm sorry to be calling so early but I'm not feeling very well, I was wondering if you could come to my room?"
"I'll be there as soon as I can get dressed."
Roberta put the few things she had into her bags so that she would be prepared to leave. She then lay back down on the bed to wait for Cam. She was sure she had a fever. There was a knock at the door.
Roberta opened the door to let Cam in. "That was fast,” she said.
"So you feel bad. Have you used your Annie to check your vitals?"
“No. Funny but I hadn't thought about it. It's in my bag there.”
A minute of silence passed as Cam used Roberta's Annie to check her vitals. "Temperature one-hundred," said Cam. "You definitely have a fever. Heart rate elevated, blood pressure elevated. Are there any other symptoms you've noticed?"
"Yes," said Roberta. "I have a headache and my eyes are burning."
"But no nausea?"
"No, not yet anyway."
"Okay," said Cam putting the Annie back in Roberta's bag. "Let's get out of here and on our way to Ho Chi Minh, I want Dr. Dao to check you."
Cam called the driver explaining that Dr. Hughes wasn't feeling well and they needed to leave immediately.
"What is wrong with her?" asked the driver.
"I don't know. Could be just a little food poisoning but we need to get her back to Ho Chi Minh as soon as possible."
"Yes," said the driver. "Okay I'll be there in twenty minutes."
Roberta and Cam were waiting outside the hotel, the dawn was just breaking when the driver drove up. He quickly put the bags in the vehicle, all the time watching Roberta. As Cam started to help Roberta into the SUV she suddenly became limp and collapsed to the sidewalk.
"Help me!" yelled Cam.
The driver looked around from the back of the vehicle and saw Roberta on the sidewalk. Instead of moving to assist Cam he turned and ran the other way. He was in the SUV and racing away before Cam knew what had happened.
A guest of the hotel came out and assisted Cam in getting Roberta back inside. By this time Roberta had recovered from her faint. A hotel staff member started assisting Roberta and this allowed Cam to call the Health Ministry back in Ho Chi Minh.
After finishing her call Cam came back to Roberta.
“How are you feeling Roberta?”
“I'm better though my head is still throbbing.”
“You probably missed it but the driver took off. I think when he saw you faint it scared him into thinking you might have the Chau Doc virus. Anyway, I've called the ministry and they've agreed to send a plane to pick us up at the local airport. They should be here in a little over an hour. Do you think you can make it?”
“I'll be okay. As long as I can sit down while waiting.”
The hotel arranged for one of their employees to drive Roberta and Cam to the local airport.
Sitting in the airport waiting on the plane Roberta started drifting in and out of consciousness and talking nonsense to Cam.
“Aunt Lucy will be here anytime Kimmy,” said Roberta. “We should just wait here, mom won't like it if we wander off.”
Cam was disturbed but played along. “Okay Roberta, we'll wait here.” This is moving fast, thought Cam. I have to get her to the hospital and soon.
Roberta had fallen into a fitful sleep by the time the plane arrived. A stretcher was brought into the airport waiting area and Roberta was carried onto the plane by a couple of orderlies. Dr. Dao was waiting and started an IV immediately. Cam was relieved to see the doctor.
“Oh thank you Dr. Dao for coming. I was really getting worried, her fever is very high and she started hallucinating and then became listless and unresponsive.”
“You've done well Dr. Nguyen. I'm hopeful that the IV will help her and we will be able to get her back to the hospital where we can further treat her. It certainly appears that she has caught the infection she was sent here to study. How ironic.”
Roberta spent a week in the hospital intensive care and then another week in a private room before recovering. After a week of staying with Cam at her apartment, she was scheduled to fly back to the States. She would meet someone from the CDC at the airport to assist her if needed.
The driver and SUV had still not turned up so Roberta had nothing to take with her to the airport. She only had the new clothes that Cam had bought for her that week. She had her papers replaced by the American Embassy in Ho Chi Minh with the Vietnamese government helping with the red tape. Cam promised to send new samples to her as soon as possible, but Roberta still felt dejected about losing the first batch.
As they were finishing at immigration Roberta saw someone she recognized in the crowd. It was Wesley Williams. Wesley ran up to Roberta and hugged her.
“You don't look sick at all,” said Wesley.
“I'm sure glad to see you Wesley. Let me introduce you to Dr. Cam Nguyen, she's the reason I'm doing as well as I am.”
Wesley and Cam shared greetings. Then Wesley said they should get on board the plane.
Roberta and Cam hugged, and Roberta said how grateful she was to Cam for all that she had done.
As they sat down in their seats on the plane Roberta turned to Wesley and said, “I lost everything Wesley, my samples, my Annie, everything."
She seemed about to cry when Wesley said, “Well the important thing is that we still have you.”
“That's kind Wesley, but I feel like such a failure.”
“No, you don't understand what I mean, and I thought you were supposed to be the smart one,” he smiled. “We have you and the antibodies in your blood. You see we have everything we need to ID this virus.”
“You're right Wesley. I've been so despondent I haven't been thinking straight. You're right,” she smiled.
Chapter 10
Jack began working to the exclusion of all else, even forgetting the dinner he had promised Phylicia. But Phylicia didn’t forget Jack, she helped him move to a cheaper apartment and continued to check in with him and even contributed some of her expertise to his research.
He worked for weeks programming and simulating his virus detection idea. When finished he put the resultant software, V-Detect, up on the web site.
Next, he started modifying his old IC software to build his delivery vehicle, d-cages. Research in a corner of science called foldamers (self-assembling molecular folding structures) was helpful with this step.
His approach proposed to use two spherical cages, one inside the other. The outer cage would be covered in virus detectors. Once attached to a virus the cage would exactly mimic the topology of the virus. The synthetic biology tool would then identify the virus-associated protein and create a program for the blocking molecules.
Inside the inner cage DNA snippets (held there so that they could be protected from the identification tools of the outer cage) would be assembled according to the program created by the synthetic biology tool until the blocking molecule was complete. When finished the blocking molecule would be released into the body.
Unlike integrated circuits, his d-cages would self-organize. He would have to add to the software so that the primary structure, the arrangement of atomic composition and chemical bonds needed for the desired result, could be predicted. Then he would add simulation of the self-assembly of the cage in different solvent baths and extract the resulting size parameters.
It was a few more weeks until he first put the software, D-Cages, up on the website provided by the school.
Next, he integrated his software with the ANI cloud expert provided by the university. This consisted mostly of running many design iterations and training the ANI until it could propose, set up and run its own designs. Surprisingly this took more time than anything else.
Finally, with the help of Phylicia, he put up his proposal for the DNA assembly of the blocking molecules. This part of the design was necessarily the most sketchy as Jack had never been able to test any of its ideas.
When finished Jack decided to promote his site. He posted announcements to all the biology magazines that had an online presence and an open blog. Finally, he made the announcement on a biocoder blog page, a page that a lot of the DIY biology community outside academia and some academics frequented.
He hoped that his open software approach would attract researchers with whom he could establish a relationship and maybe encourage them to pursue his complete program. The response was encouraging, especially from the biocoder community, which led to his next problem.
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