Short Story Contest Winner: "The Gerry Program"
It's an odd sensation knowing you're going to die, but it was a feeling Gerry Ferguson had become relatively acquainted with over the past two years. What most perplexed the terminally ill, he observed, was not the concept of death so much as the continuation of all other life.
Gerry's secret project had been in the works for two years now, ever since they found the growth.
Who will mourn me when I'm gone? What trait or idiosyncrasy will people most recall? Will I still be talked of, 100 years from now?
But Gerry didn't worry about these questions. He was comfortable that his legacy would live on, in one form or another. From his cozy flat in the west end of Glasgow, Gerry had managed to put his affairs in order and still find time for small joys.
Feeding the geese in summer at the park just down from his house, reading classics from the teeming bookcase in the living room, talking with his son Michael on Skype. It was Michael who had first suggested reading some of the new works of non-fiction that now littered the large oak desk in Gerry's study.
He was just finishing 'The Master Algorithm' when his shabby grandfather clock chimed six o'clock. Time to call Michael. Crammed into his tiny study, Gerry pulled his computer's webcam close and waved at Michael's smiling face.
"Hi Dad! How're you today?"
"I'm alright, son. How're things in sunny Australia?"
"Hot as always. How's things in Scotland?"
"I'd 'ave more chance gettin' a tan from this computer screen than I do goin' out there."
Michael chuckled. He's got that hearty Ferguson laugh, Gerry thought.
"How's the project coming along?" Michael asked. "Am I going to see it one of these days?"
"Of course," grinned Gerry, "I designed it for you."
Gerry's secret project had been in the works for two years now, ever since they found the growth. He had decided it was better not to tell Michael. He would only worry.
The two men chatted for hours. They discussed Michael's love life (or lack thereof), memories of days walking in the park, and their shared passion, the unending woes of Rangers Football Club. It wasn't until Michael said his goodbyes that Gerry noticed he'd been sitting in the dark for the best part of three hours, his mesh curtains casting a dim orange glow across the room from the street light outside. Time to get back to work.
*
Every night, Gerry sat at his computer, crawling forums, nourishing his project, feeding his knowledge and debating with other programmers. Even at age 82, Gerry knew more than most about algorithms. Never wanting to feel old, and with all the kids so adept at this digital stuff, Gerry figured he should give the Internet a try too. Besides, it kept his brain active and restored some of the sociability he'd lost in the previous decades as old friends passed away and the physical scope of his world contracted.
This night, like every night, Gerry worked away into the wee hours. His back would ache come morning, but this was the only time he truly felt alive these days. From his snug red brick home in Scotland, Gerry could share thoughts and information with strangers from all over the world. It truly was a miracle of modern science!
*
The next day, Gerry woke to the warm amber sun seeping in between a crack in the curtains. Like every morning, his thoughts took a little time to come into focus. Instinctively his hand went to the other side of the bed. Nobody there. Of course; she was gone. Rita, the sweetest woman he'd ever known. Four years this spring, God rest her soul.
Puttering around the cramped kitchen, Gerry heard a knock at the door. Who could that be? He could see two women standing in the hallway, their bodies contorted in the fisheye glass of the peephole. One looked familiar, but Gerry couldn't be sure. He fiddled with the locks and pulled the door open.
"Hi Gerry. How are you today?"
"Fine, thanks," he muttered, still searching his mind for where he'd seen her face before.
Noting the confusion in his eyes, the woman proffered a hand. "Alice, Alice Corgan. I pop round every now and again to check on you."
It clicked. "Ah aye! Come in, come in. Lemme get ya a cuppa." Gerry turned and shuffled into the flat.
As Gerry set about his tiny kitchen, Alice called from the living room, "This is Mandy. She's a care worker too. She's going to pay you occasional visits if that's alright with you."
Gerry poked his head around the doorway. "I'll always welcome a beautiful young lady in ma home. Though, I've tae warn you I'm a married man, so no funny business." He winked and ducked back into the kitchen.
Alice turned to Mandy with a grin. "He's a good man, our Gerry. You'll get along just fine." She lowered her voice. "As I said, with the Alzheimer's, he has to be reminded to take his medication, but he's still mostly self-sufficient. We installed a medi-bot to remind him every day and dispense the pills. If he doesn't respond, we'll get a message to send someone over."
Mandy nodded and scribbled notes in a pad.
"When I'm gone, Michael will have somethin' to remember me by."
"Also, and this is something we've been working on for a few months now, Gerry is convinced he has something…" her voice trailed off. "He thinks he has cancer. Now, while the Alzheimer's may affect his day-to-day life, it's not at a stage where he needs to be taken into care. The last time we went for a checkup, the doctor couldn't find any sign of cancer. I think it stems from--"
Gerry shouted from the other room: "Does the young lady take sugar?"
"No, I'm fine thanks," Mandy called back.
"Of course you don't," smiled Gerry. "Young lady like yersel' is sweet enough."
*
The following week, Mandy arrived early at Gerry's. He looked unsure at first, but he invited her in.
Sitting on the sofa nurturing a cup of tea, Alice tried to keep things light. "So what do you do in your spare time, Gerry?"
"I've got nothing but spare time these days, even if it's running a little low."
"Do you have any hobbies?"
"Yes actually." Gerry smiled. "I'm makin' a computer program."
Alice was taken aback. She knew very little about computers herself. "What's the program for?" she asked.
"Well, despite ma appearance, I'm no spring chicken. I know I don't have much time left. Ma son, he lives down in Australia now, he worked on a computer program that uses AI - that's artificial intelligence - to imitate a person."
Alice still looked confused, so Gerry pressed on.
"Well, I know I've not long left, so I've been usin' this open source code to make ma own for when I'm gone. I've already written all the code. Now I just have to add the things that make it seem like me. I can upload audio, text, even videos of masel'. That way, when I'm gone, Michael will have somethin' to remember me by."
Mandy sat there, stunned. She had no idea anybody could do this, much less an octogenarian from his small, ramshackle flat in Glasgow.
"That's amazing Gerry. I'd love to see the real thing when you're done."
"O' course. I mean, it'll take time. There's so much to add, but I'll be happy to give a demonstration."
Mandy sat there and cradled her mug. Imagine, she thought, being able to preserve yourself, or at least some basic caricature of yourself, forever.
*
As the weeks went on, Gerry slowly added new shades to his coded double. Mandy would leaf through the dusty photo albums on Gerry's bookcase, pointing to photos and asking for the story behind each one. Gerry couldn't always remember but, when he could, the accompanying stories were often hilarious, incredible, and usually a little of both. As he vividly recounted tales of bombing missions over Burma, trips to the beach with a young Michael and, in one particularly interesting story, giving the finger to Margaret Thatcher, Mandy would diligently record them through a Dictaphone to be uploaded to the program.
Gerry loved the company, particularly when he could regale the young woman with tales of his son Michael. One day, as they sat on the sofa flicking through a box of trinkets from his days as a travelling salesman, Mandy asked why he didn't have a smartphone.
He shrugged. "If I'm out 'n about then I want to see the world, not some 2D version of it. Besides, there's nothin' on there for me."
Alice explained that you could get Skype on a smartphone: "You'd be able to talk with Michael and feed the geese at the park at the same time," she offered.
Gerry seemed interested but didn't mention it again.
"Only thing I'm worried about with ma computer," he remarked, "is if there's another power cut and I can't call Michael. There's been a few this year from the snow 'n I hate not bein' able to reach him."
"Well, if you ever want to use the Skype app on my phone to call him you're welcome," said Mandy. "After all, you just need to add him to my contacts."
Gerry was flattered. "That's a relief, knowing I won't miss out on calling Michael if the computer goes bust."
*
Then, in early spring, just as the first green buds burst forth from the bare branches, Gerry asked Mandy to come by. "Bring that Alice girl if ya can - I know she's excited to see this too."
The next day, Mandy and Alice dutifully filed into the cramped study and sat down on rickety wooden chairs brought from the living room for this special occasion.
An image of Gerry, somewhat younger than the man himself, flashed up on the screen.
With a dramatic throat clearing, Gerry opened the program on his computer. An image of Gerry, somewhat younger than the man himself, flashed up on the screen.
The room was silent.
"Hiya Michael!" AI Gerry blurted. The real Gerry looked flustered and clicked around the screen. "I forgot to put the facial recognition on. Michael's just the go-to name when it doesn't recognize a face." His voice lilted with anxious excitement. "This is Alice," Gerry said proudly to the camera, pointing at Alice, "and this is Mandy."
AI Gerry didn't take his eyes from real Gerry, but grinned. "Hello, Alice. Hiya Mandy." The voice was definitely his, even if the flow of speech was slightly disjointed.
"Hi," Alice and Mandy stuttered.
Gerry beamed at both of them. His eyes flitted between the girls and the screen, perhaps nervous that his digital counterpart wasn't as polished as they'd been expecting.
"You can ask him almost anything. He's not as advanced as the ones they're making in the big studios, but I think Michael will like him."
Alice and Mandy gathered closer to the monitor. A mute Gerry grinned back from the screen. Sitting in his wooden chair, the real Gerry turned to his AI twin and began chattering away: "So, what do you think o' the place? Not bad eh?"
"Oh aye, like what you've done wi' it," said AI Gerry.
"Gerry," Alice cut in. "What did you say about Michael there?"
"Ah, I made this for him. After all, it's the kind o' thing his studio was doin'. I had to clear some space to upload it 'n show you guys, so I had to remove Skype for now, but Michael won't mind. Anyway, Mandy's gonna let me Skype him from her phone."
Mandy pulled her phone out and smiled. "Aye, he'll be able to chat with two Gerry's."
Alice grabbed Mandy by the arm: "What did you tell him?" she whispered, her eyes wide.
"I told him he can use my phone if he wants to Skype Michael. Is that okay?"
Alice turned to Gerry, who was chattering away with his computerized clone. "Gerry, we'll just be one second, I need to discuss something with Mandy."
"Righto," he nodded.
Outside the room, Alice paced up and down the narrow hallway.
Mandy could see how flustered she was. "What's wrong? Don't you like the chatbot? I think it's kinda c-"
"Michael's dead," Alice spluttered.
"What do you mean? He talks to him all the time."
Alice sighed. "He doesn't talk to Michael. See, a few years back, Michael found out he had cancer. He worked for this company that did AI chatbot stuff. When he knew he was dying he--" she groped in the air for the words-- "he built this chatbot thing for Gerry, some kind of super-advanced AI. Gerry had just been diagnosed with Alzheimer's and I guess Michael was worried Gerry would forget him. He designed the chatbot to say he was in Australia to explain why he couldn't visit."
"That's awful," Mandy granted, "but I don't get what the problem is. I mean, surely he can show the AI Michael his own chatbot?"
"No, because you can't get the AI Michael on Skype. Michael just designed the program to look like Skype."
"But then--" Mandy went silent.
"Michael uploaded the entire AI to Gerry's computer before his death. Gerry didn't delete Skype. He deleted the AI Michael."
"So… that's it? He-he's gone?" Mandy's voice cracked. "He can't just be gone, surely he can't?"
The women stood staring at each other. They looked to the door of the study. They could still hear Gerry, gabbing away with his cybercopy.
"I can't go back in there," muttered Mandy. Her voice wavered as she tried to stem the misery rising in her throat.
Alice shook her head and paced the floor. She stopped and stared at Mandy with grim resignation. "We don't have a choice."
When they returned, Gerry was still happily chatting away.
"Hiya girls. Ya wanna ask my handsome twin any other questions? If not, we could get Michael on the phone?"
Neither woman spoke. Gerry clapped his hands and turned gaily to the monitor again: "I cannae wait for ya t'meet him, Gerry. He's gonna be impressed wi' you."
Alice clasped her hands to her mouth. Tears welled in the women's eyes as they watched the old man converse with his digital copy. The heat of the room seemed to swell, becoming insufferable. Mandy couldn't take it anymore. She jumped up, bolted to the door and collapsed against a wall in the hallway. Alice perched on the edge of her seat in a dumb daze, praying for the floor to open and swallow the contents of the room whole.
Oblivious, Gerry and his echo babbled away, the blue glow of the screen illuminating his euphoric face. "Just wait until y'meet him Gerry, just wait."
Jamie Rettinger was still in his thirties when he first noticed a tiny streak of brown running through the thumbnail of his right hand. It slowly grew wider and the skin underneath began to deteriorate before he went to a local dermatologist in 2013. The doctor thought it was a wart and tried scooping it out, treating the affected area for three years before finally removing the nail bed and sending it off to a pathology lab for analysis.
"I have some bad news for you; what we removed was a five-millimeter melanoma, a cancerous tumor that often spreads," Jamie recalls being told on his return visit. "I'd never heard of cancer coming through a thumbnail," he says. None of his doctors had ever mentioned it either. "I just thought I was being treated for a wart." But nothing was healing and it continued to bleed.
A few months later a surgeon amputated the top half of his thumb. Lymph node biopsy tested negative for spread of the cancer and when the bandages finally came off, Jamie thought his medical issues were resolved.
Melanoma is the deadliest form of skin cancer. About 85,000 people are diagnosed with it each year in the U.S. and more than 8,000 die of the cancer when it spreads to other parts of the body, according to the Centers for Disease Control and Prevention (CDC).
There are two peaks in diagnosis of melanoma; one is in younger women ages 30-40 and often is tied to past use of tanning beds; the second is older men 60+ and is related to outdoor activity from farming to sports. Light-skinned people have a twenty-times greater risk of melanoma than do people with dark skin.
"When I graduated from medical school, in 2005, melanoma was a death sentence" --Diwakar Davar.
Jamie had a follow up PET scan about six months after his surgery. A suspicious spot on his lung led to a biopsy that came back positive for melanoma. The cancer had spread. Treatment with a monoclonal antibody (nivolumab/Opdivo®) didn't prove effective and he was referred to the UPMC Hillman Cancer Center in Pittsburgh, a four-hour drive from his home in western Ohio.
An alternative monoclonal antibody treatment brought on such bad side effects, diarrhea as often as 15 times a day, that it took more than a week of hospitalization to stabilize his condition. The only options left were experimental approaches in clinical trials.
Early research
"When I graduated from medical school, in 2005, melanoma was a death sentence" with a cure rate in the single digits, says Diwakar Davar, 39, an oncologist at UPMC Hillman Cancer Center who specializes in skin cancer. That began to change in 2010 with introduction of the first immunotherapies, monoclonal antibodies, to treat cancer. The antibodies attach to PD-1, a receptor on the surface of T cells of the immune system and on cancer cells. Antibody treatment boosted the melanoma cure rate to about 30 percent. The search was on to understand why some people responded to these drugs and others did not.
At the same time, there was a growing understanding of the role that bacteria in the gut, the gut microbiome, plays in helping to train and maintain the function of the body's various immune cells. Perhaps the bacteria also plays a role in shaping the immune response to cancer therapy.
One clue came from genetically identical mice. Animals ordered from different suppliers sometimes responded differently to the experiments being performed. That difference was traced to different compositions of their gut microbiome; transferring the microbiome from one animal to another in a process known as fecal transplant (FMT) could change their responses to disease or treatment.
When researchers looked at humans, they found that the patients who responded well to immunotherapies had a gut microbiome that looked like healthy normal folks, but patients who didn't respond had missing or reduced strains of bacteria.
Davar and his team knew that FMT had a very successful cure rate in treating the gut dysbiosis of Clostridioides difficile, a persistant intestinal infection, and they wondered if a fecal transplant from a patient who had responded well to cancer immunotherapy treatment might improve the cure rate of patients who did not originally respond to immunotherapies for melanoma.
The ABCDE of melanoma detection
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Clinical trial
"It was pretty weird, I was totally blasted away. Who had thought of this?" Jamie first thought when the hypothesis was explained to him. But Davar's explanation that the procedure might restore some of the beneficial bacterial his gut was lacking, convinced him to try. He quickly signed on in October 2018 to be the first person in the clinical trial.
Fecal donations go through the same safety procedures of screening for and inactivating diseases that are used in processing blood donations to make them safe for transfusion. The procedure itself uses a standard hollow colonoscope designed to screen for colon cancer and remove polyps. The transplant is inserted through the center of the flexible tube.
Most patients are sedated for procedures that use a colonoscope but Jamie doesn't respond to those drugs: "You can't knock me out. I was watching them on the TV going up my own butt. It was kind of unreal at that point," he says. "There were about twelve people in there watching because no one had seen this done before."
A test two weeks after the procedure showed that the FMT had engrafted and the once-missing bacteria were thriving in his gut. More importantly, his body was responding to another monoclonal antibody (pembrolizumab/Keytruda®) and signs of melanoma began to shrink. Every three months he made the four-hour drive from home to Pittsburgh for six rounds of treatment with the antibody drug.
"We were very, very lucky that the first patient had a great response," says Davar. "It allowed us to believe that even though we failed with the next six, we were on the right track. We just needed to tweak the [fecal] cocktail a little better" and enroll patients in the study who had less aggressive tumor growth and were likely to live long enough to complete the extensive rounds of therapy. Six of 15 patients responded positively in the pilot clinical trial that was published in the journal Science.
Davar believes they are beginning to understand the biological mechanisms of why some patients initially do not respond to immunotherapy but later can with a FMT. It is tied to the background level of inflammation produced by the interaction between the microbiome and the immune system. That paper is not yet published.
Surviving cancer
It has been almost a year since the last in his series of cancer treatments and Jamie has no measurable disease. He is cautiously optimistic that his cancer is not simply in remission but is gone for good. "I'm still scared every time I get my scans, because you don't know whether it is going to come back or not. And to realize that it is something that is totally out of my control."
"It was hard for me to regain trust" after being misdiagnosed and mistreated by several doctors he says. But his experience at Hillman helped to restore that trust "because they were interested in me, not just fixing the problem."
He is grateful for the support provided by family and friends over the last eight years. After a pause and a sigh, the ruggedly built 47-year-old says, "If everyone else was dead in my family, I probably wouldn't have been able to do it."
"I never hesitated to ask a question and I never hesitated to get a second opinion." But Jamie acknowledges the experience has made him more aware of the need for regular preventive medical care and a primary care physician. That person might have caught his melanoma at an earlier stage when it was easier to treat.
Davar continues to work on clinical studies to optimize this treatment approach. Perhaps down the road, screening the microbiome will be standard for melanoma and other cancers prior to using immunotherapies, and the FMT will be as simple as swallowing a handful of freeze-dried capsules off the shelf rather than through a colonoscopy. Earlier this year, the Food and Drug Administration approved the first oral fecal microbiota product for C. difficile, hopefully paving the way for more.
An older version of this hit article was first published on May 18, 2021
All organisms have the capacity to repair or regenerate tissue damage. None can do it better than salamanders or newts, which can regenerate an entire severed limb.
That feat has amazed and delighted man from the dawn of time and led to endless attempts to understand how it happens – and whether we can control it for our own purposes. An exciting new clue toward that understanding has come from a surprising source: research on the decline of cells, called cellular senescence.
Senescence is the last stage in the life of a cell. Whereas some cells simply break up or wither and die off, others transition into a zombie-like state where they can no longer divide. In this liminal phase, the cell still pumps out many different molecules that can affect its neighbors and cause low grade inflammation. Senescence is associated with many of the declining biological functions that characterize aging, such as inflammation and genomic instability.
Oddly enough, newts are one of the few species that do not accumulate senescent cells as they age, according to research over several years by Maximina Yun. A research group leader at the Center for Regenerative Therapies Dresden and the Max Planck Institute of Molecular and Cell Biology and Genetics, in Dresden, Germany, Yun discovered that senescent cells were induced at some stages of regeneration of the salamander limb, “and then, as the regeneration progresses, they disappeared, they were eliminated by the immune system,” she says. “They were present at particular times and then they disappeared.”
Senescent cells added to the edges of the wound helped the healthy muscle cells to “dedifferentiate,” essentially turning back the developmental clock of those cells into more primitive states.
Previous research on senescence in aging had suggested, logically enough, that applying those cells to the stump of a newly severed salamander limb would slow or even stop its regeneration. But Yun stood that idea on its head. She theorized that senescent cells might also play a role in newt limb regeneration, and she tested it by both adding and removing senescent cells from her animals. It turned out she was right, as the newt limbs grew back faster than normal when more senescent cells were included.
Senescent cells added to the edges of the wound helped the healthy muscle cells to “dedifferentiate,” essentially turning back the developmental clock of those cells into more primitive states, which could then be turned into progenitors, a cell type in between stem cells and specialized cells, needed to regrow the muscle tissue of the missing limb. “We think that this ability to dedifferentiate is intrinsically a big part of why salamanders can regenerate all these very complex structures, which other organisms cannot,” she explains.
Yun sees regeneration as a two part problem. First, the cells must be able to sense that their neighbors from the lost limb are not there anymore. Second, they need to be able to produce the intermediary progenitors for regeneration, , to form what is missing. “Molecularly, that must be encoded like a 3D map,” she says, otherwise the new tissue might grow back as a blob, or liver, or fin instead of a limb.
Wound healing
Another recent study, this time at the Mayo Clinic, provides evidence supporting the role of senescent cells in regeneration. Looking closely at molecules that send information between cells in the wound of a mouse, the researchers found that senescent cells appeared near the start of the healing process and then disappeared as healing progressed. In contrast, persistent senescent cells were the hallmark of a chronic wound that did not heal properly. The function and significance of senescence cells depended on both the timing and the context of their environment.
The paper suggests that senescent cells are not all the same. That has become clearer as researchers have been able to identify protein markers on the surface of some senescent cells. The patterns of these proteins differ for some senescent cells compared to others. In biology, such physical differences suggest functional differences, so it is becoming increasingly likely there are subsets of senescent cells with differing functions that have not yet been identified.
There are disagreements within the research community as to whether newts have acquired their regenerative capacity through a unique evolutionary change, or if other animals, including humans, retain this capacity buried somewhere in their genes.
Scientists initially thought that senescent cells couldn’t play a role in regeneration because they could no longer reproduce, says Anthony Atala, a practicing surgeon and bioengineer who leads the Wake Forest Institute for Regenerative Medicine in North Carolina. But Yun’s study points in the other direction. “What this paper shows clearly is that these cells have the potential to be involved in tissue regeneration [in newts]. The question becomes, will these cells be able to do the same in humans.”
As our knowledge of senescent cells increases, Atala thinks we need to embrace a new analogy to help understand them: humans in retirement. They “have acquired a lot of wisdom throughout their whole life and they can help younger people and mentor them to grow to their full potential. We're seeing the same thing with these cells,” he says. They are no longer putting energy into their own reproduction, but the signaling molecules they secrete “can help other cells around them to regenerate.”
There are disagreements within the research community as to whether newts have acquired their regenerative capacity through a unique evolutionary change, or if other animals, including humans, retain this capacity buried somewhere in their genes. If so, it seems that our genes are unable to express this ability, perhaps as part of a tradeoff in acquiring other traits. It is a fertile area of research.
Dedifferentiation is likely to become an important process in the field of regenerative medicine. One extreme example: a lab has been able to turn back the clock and reprogram adult male skin cells into female eggs, a potential milestone in reproductive health. It will be more difficult to control just how far back one wishes to go in the cell's dedifferentiation – part way or all the way back into a stem cell – and then direct it down a different developmental pathway. Yun is optimistic we can learn these tricks from newts.
Senolytics
A growing field of research is using drugs called senolytics to remove senescent cells and slow or even reverse disease of aging.
“Senolytics are great, but senolytics target different types of senescence,” Yun says. “If senescent cells have positive effects in the context of regeneration, of wound healing, then maybe at the beginning of the regeneration process, you may not want to take them out for a little while.”
“If you look at pretty much all biological systems, too little or too much of something can be bad, you have to be in that central zone” and at the proper time, says Atala. “That's true for proteins, sugars, and the drugs that you take. I think the same thing is true for these cells. Why would they be different?”
Our growing understanding that senescence is not a single thing but a variety of things likely means that effective senolytic drugs will not resemble a single sledge hammer but more a carefully manipulated scalpel where some types of senescent cells are removed while others are added. Combinations and timing could be crucial, meaning the difference between regenerating healthy tissue, a scar, or worse.