The Soul of the Matter

by Bruce Buff

  Taking the keyboard, Trish typed, What about the journals? When can I see them?

  Dan took the keyboard back and wrote When we get back and then shut the cover. All of a sudden, he wondered if his diminished state of mind had once again caused him to be easily manipulated and to share more than he should have.

  He decided to turn to small talk. That was much safer. “Tell me about your background. What makes you believe what you do?”

  “I don’t know. I go with what feels natural. My parents didn’t try to instill any particular beliefs in me. My mother is French Protestant and my father is an Italian Jew. Both are agnostic. They’re reformed hippies from the early seventies who went mainstream in their occupations but never really gave up their contrary personalities, though they did mellow. I think the two things I got from them are a lack of anger and a desire to make a difference.”

  “That’s an interesting background. Have you been in therapy long?” Dan said with a playful smile.

  “What are you searching for?” Trish replied.

  “You mean other than the few small things I mentioned earlier, such as a cure for Ava, finding out what happened to Stephen, and recovering his work?”

  “Yes, bigger than all those things.”

  “I’m looking for answers that matter. Something that tells me life is more than what it seems. Is that what you meant?” Dan said.

  “About what I expected.”

  “Well, that’s a remarkable expectation. Now, how about you?”

  “Not sure. I think I’m looking for a question.”

  “I’ve got plenty of those. Probably not the one you’re looking for.”

  “Time will tell,” Trish answered and then looked out the window.

  It took Dan a few moments to realize that she was lost in her own thoughts. Suddenly tired, he put his head back and closed his eyes. He hoped that they both found all they were looking for, including whatever awaited them at the Salk Institute.

  Chapter 52

  DAY 12

  TUESDAY MORNING

  He had seen pictures of the Salk Institute, but its beauty, perched on cliffs bordering the surf below, still surprised Dan. Stunning architecture wasn’t something he normally associated with a major scientific research center.

  The Salk Institute for Biological Studies had been established by Jonas Salk, lead developer of the vaccine that ended the scourge of polio in 1955. The Institute opened in 1963 in La Jolla, California, outside San Diego. The complex was designed by Louis Kahn, known for his innovative designs. Two long buildings opposed each other across a rectangular plaza bisected by a narrow channel of water that was aligned with the sunrise and sunset at the equinoxes.

  The buildings had six floors, two of which were belowground though illuminated with light wells. In the fifty years since its completion, the complex’s architectural accomplishments were well recognized.

  The institute’s scientific stature and achievements greatly outshone even the architecture. With over eight hundred researchers in over sixty research groups spanning the biological sciences, the institute was one of the top biomedical research centers in the world.

  The overall impression the institute gave was of majesty and goodness, and it boosted Dan’s hope of finding a treatment for Ava inside. It was also a decent location for potentially encountering Galileo and then accessing Stephen’s work one way or another. With a spring in their steps, Dan and Trish entered the institute.

  • • •

  “Thank you for seeing us on such short notice,” Trish said to Dr. Chamberlain, president of the Salk Institute. They were inside his well-appointed office, with striking views in almost every direction.

  “Not at all, Dr. Alighieri. We’re happy to meet with a colleague of Dr. Bishop’s who’s trying to continue his research. He was a giant in the genomics field, and it was our great regret that we couldn’t recruit him ourselves,” said Dr. Chamberlain, gesturing to chairs in front of his desk.

  As Dr. Chamberlain turned to walk around his desk to his chair, Trish glared at Dan. She had not been pleased when Dan introduced her as someone involved in pediatric cancer research who had been collaborating with Stephen in his genomic-based treatment research at HBC. Both were deep areas of interest to the Salk Institute, so Dan knew it would get them in the door, but she had been angry about the lie.

  After they all sat down, Dr. Chamberlain said, “Dr. Bishop’s loss will be felt by many. We’ll do anything we can to help.”

  Hearing the words again about Stephen’s loss, the once sharp blade of sorrow, since dulled by too many thrusts, entered Dan again, but not as deeply. The pain felt abstract, as though he knew it was happening but its impact was lessening. It bothered him to think that someday it wouldn’t hurt enough.

  Trish paused, as if she too felt something at hearing the words. Then she said, “Thank you. Regrettably, I had started working with Dr. Bishop only recently. There are a few pieces missing in our knowledge of his research, and we’re hoping someone here may have collaborated with him and can help us fill in the gaps.”

  “What specifically are you looking for? To the best of my knowledge, no one here was working with Dr. Bishop,” Dr. Chamberlain replied.

  “Genetically repairing and reprogramming a leukemia patient’s own stem cells to produce healthy bone marrow,” Trish replied, using a story she had worked out with Dan based on conversations both had had with Stephen that made it almost true, at least true enough for her not to feel bad saying it.

  “Yes, that would be a wonderful treatment. Dr. Bishop did talk with Dr. Marc Senter about it. Dr. Senter leads our efforts in both the genomics and cancer research areas. Over fifty percent of our research is focused on cancer. They had a memorable discussion,” Dr. Chamberlain said with a you-had-to-see-it-to-believe-it look. “I’ve already given him a heads-up that you’d probably want to talk with him. We can walk over to his office. It’s nearby.”

  • • •

  Inside Dr. Senter’s office, after introductions, including respectful ack­nowledgments about Stephen’s death, Trish began. “Dr. Bishop was working on a leukemia treatment for patients with highly sensitive immune systems. I believe, but am not sure, that it was for patients who required treatment with only their own cells, whose weakened condition from prior treatments also meant they could not withstand aggressive treatments. He might have been pursuing a treatment whereby a patient’s own stem cells were extracted and then genetically corrected.”

  “This is the objective of a lot of researchers these days,” Dr. Chamberlain said.

  “Yes. The idea is that the corrected cells would be used to generate sufficient quantities of healthy bone marrow cells in preparation for the patient. Meanwhile, the patient’s own immune system cells would be programmed to eradicate the patient’s faulty bone marrow stem cells. Both the now-healthy marrow and the programmed immune cells would be injected into the patient, where they would simultaneously destroy and replace diseased cells with healthy ones—without any side effects or need for further treatment,” Trish said.

  “It will be wonderful when such a treatment can be provided to all patients, for all types of cancers.”

  “It would be a one hundred percent cure, without any threat to the patient or traumatic side effects. Almost anyone could sustain this treatment. Did you discuss this with Stephen, Dr. Senter?”

  Dr. Senter took a slow, deep breath before he answered. “Yes, we had discussed this conceptually. While the treatment makes sense, and there is a lot of research showing promise in these areas, we have a tremendously long way to go before anyone will be able to try anything like this. Perhaps others researchers are closer, but that would be remarkable news to us. Frankly, I’m astounded to hear that Dr. Bishop may have already been piloting this—it would be highly unorthodox if he was.”

  Dan’s heart sank. But perhaps Sente
r could still point them in the right direction or help them find Galileo, whether Senter was aware of the treatment or not. The institute was large, and any type of research could be going on there without others being aware of it.

  “Is any of this being researched somewhere else that you know of?” Dan asked.

  “Although initial research is being conducted today, here and elsewhere, as far as I know— and I’m well connected to research in all of the relevant areas—nothing is close to a pilot. In particular, we need a much better understanding of the genome so we can correct defective . . . programming,” Senter said, with a noticeable pause before programming, and a glance at Chamberlain.

  Trish said, “What were the discussions with Dr. Bishop like?” She sounded as disappointed as Dan felt.

  “We met with several of our leading genome and cancer researchers. The discussion began innocuously enough, and initially covered the areas you described, though in more detail. People found the ideas stimulating and exciting. Then Dr. Bishop started to veer off in a direction that some found disturbing,” Senter said, looking back and forth between Dan and Trish, seemingly assessing whether their sympathies aligned with Stephen’s views, which some of the institute researchers had found troubling. Senter continued cautiously, “We were fine with exploring the idea of genome expression and the possibility of algorithmic-like processing. It was when Dr. Bishop implied that algorithmic genome expression begged the question of the manner of its origin. He asked about its impact on genetic mutations producing beneficial adaptations, as opposed to destructive malfunctions, and that’s when the wheels came off. I’m afraid that, at that point, the discussions ended quickly, and poorly. We tried to return the topic back to understanding the genome, but that discussion was limited and the air strained. The meeting concluded shortly thereafter.”

  “I don’t understand. It was acceptable to say that algorithmic processing may be involved in genetic expression, but not to discuss the implications? You folks understand DNA as well as anyone in the world. What do you think the implications are?” Dan said, channeling his disappointment into aggression.

  With a sigh, Chamberlain said, “The implications of what Stephen was presenting were too much for most people in the room; though he never came out as a creationist, he was headed in that direction.”

  “Did Stephen actually say anything about God, a creator, or spirituality?” Trish asked.

  “It wasn’t necessary. He implied it when he said that DNA had no direct information content without something preexisting to interpret it; that an algorithm had to take a small amount of DNA to generate a large amount of instructions; that these instructions then needed a mech­anism to direct biological development; and that all these things had to be present independently, from the beginning, for life to have formed. He entered the realm of intelligent design, and all bets were off. We’re a science center, not an institution for faith-based, antiscience ideas.”

  Dan decided to ignore the temptation to explore Senter’s definition of antiscience, because he was still holding out hope they’d find something helpful at the institute. Instead, he asked, “What happened next?”

  “One of our researchers directed Dr. Bishop to the Crick-Jacobs Center. It’s part of the institute. I’m sure you’re familiar with Francis Crick, codiscoverer of the double-helix structure of DNA. He also believed that DNA was too complex to have evolved unaided. In his view it’s alien in origin.”

  “So it’s not acceptable to leave open the possibility of God, but it’s okay to attribute everything to aliens,” Trish said mildly. “Who created them?”

  “Dr. Alighieri, attributing human origin to aliens is not what people in this institute ascribe to. I was simply recapping what took place that day.”

  “I’m sorry we’ve veered off topic ourselves. Let’s get back to the science, which is solely where our interests lie,” Dan said while looking at Trish, pleased that she picked up the cue and nodded her head in agreement. “Is there anyone else we can talk with about research they may have participated in, or know of, with Dr. Bishop? Even someone who was once involved with the institute but fell off the beaten path?”

  “We had limited contact with Dr. Bishop. I know none of the people he met that day have collaborated on research with him,” Senter said with an edge to his voice.

  “Do you think it’s worth our time checking out the Crick-Jacobs Center?” Dan asked.

  “Different research areas. Can’t see it helping you. But it’s an impressive center. You’ve come this far so, if you have the time, it’s worth visiting,” Chamberlain said.

  “Before we head over there, does this mean anything to either of you?” Dan asked, showing them a display on his smartphone of the characters of the symbol Stephen had drawn.

  “Looks like an equation of sorts. No idea what for,” Chamberlain said.

  “Likewise,” said Senter.

  “Thanks anyway,” Dan replied.

  • • •

  The Crick-Jacobs Center for Theoretical and Computational Biology housed a vast array of interdisciplinary research into the functioning of the human brain.

  It was a short walk from Senter’s office. Stepping into the plaza, Dan scanned the surroundings. All he saw were people moving in a casual but purposeful manner, all seemingly oblivious to him.

  With a puzzled expression, Trish asked, “What does the Crick-Jacobs Center have to do with finding a treatment for Ava?”

  “Probably very little. But Stephen, knowing my beliefs and state of mind, had made it a point to tell me that he was going to prove to me that I had a soul, that I was more than physical matter. He also wrote about consciousness in his journal. While we’re here, it seems like a good opportunity to find out more about those things. And perhaps someone here will know about others who worked with Stephen.”

  “Sounds intriguing, especially the part about your having soul,” Trish said, barely suppressing her amusement.

  He thought of correcting Trish’s usage of “soul,” but then realized that she knew exactly what she was saying.

  They looked toward the Pacific as they approached the Crick-­Jacobs Center’s main entrance, but a flash of reflected sunlight caught Dan’s eyes. He turned and saw two figures, too far away for him to see clearly, wearing dark clothes that seemed out of place in the California sunshine. One of the figures lowered his hands from his face, then placed his right hand behind his back along with whatever he was holding. Dan was left with the feeling that the person was holding binoculars that had been used to view him. He proceeded with almost no reaction, giving no indication he was concerned about anything. Dan held the door for Trish as she entered the building.

  • • •

  “Welcome to our Center. I understand you only have a short time. We have a quick video that will give an overview of the Center’s mission and work. After that, I can answer whatever questions you have.”

  “That would be very helpful,” Trish said with a warm smile that the director appeared to appreciate.

  Sitting down in the media center, they watched a ten-minute video that explained that the center was dedicated to understanding how all the different parts of the brain work together to produce behavior and cognition. Most of the video presented illustrations and images of current research. None of it explained how the brain actually worked. Brain research was still in its infancy.

  After the video ended, Dan asked, “This center is focused solely on the operations of the brain?”

  “Yes. We look at things from the molecular level to the systems level and try to understand how that gives rise to behavior. We also work with another branch of the institute, that’s focused on visual perception, the most complex of the senses. Once that is understood, the rest of the senses should fall into place.”

  “And then comes cognition,” Dan added.

  “That’s right. B
ut we’re a long way off and need better tools. Right now, we’ve only been able to see rudimentary activity at the neuron level. Watch this,” the director said. “What you’re seeing are individual neurons firing in response to visual stimuli showing the locations in the brain associated with the corresponding mental processes. It’s quite exciting, actually.”

  “What did Dr. Bishop think when he saw this?” Dan asked.

  “Like you, he was only here briefly. He had one interest. I remember it because of the conversation I heard he had before he came by and because of the discomfort the topic seemed to give those he discussed it with. He wanted to know what we thought about the basis of consciousness. We actually have a good understanding of it. Francis Crick wrote a book on it called The Astonishing Hypothesis. Basically, it’s about how quantum mechanics effects inside neurons generate consciousness.”

  “You’ve proven this?” Trish asked.

  “Not yet, but it’s only a matter of time. Almost all scientists in this field recognize that discrete, individual particles consisting only of objective states, such as the spin of an electron, cannot, by themselves, generate whole, subjective experiences. There has to be something that ties the individual states and processing together. The only thing that can do that is quantum mechanics–based. In time, we’ll be able to demonstrate the scientific basis for it.”

  “You mean since there is no soul, no immaterial mind, the cause must be material, and you just have to keep looking to find it,” Dan said, remembering what Stephen had written in his journals.

  “Absolutely correct. No spiritualism to fill temporary gaps in scientific knowledge. Only natural causes for natural effects,” said the director emphatically.

  “Which means all we are is just biological robots with the illusion of meaning, purpose, love, free will, morality, and intrinsic value,” Dan added.

  The director shifted in his seat. “I wouldn’t say it that way, but yes, in the end we’re temporary collections of atoms.”