R&R Fiction: Prologue and Chapter 1

San Francisco Institute for Comprehensive Rejuvenation and Repair introduction and Dr. Amanda O'Neal

Imagine:

• Mini suicide drone swarms are guided by VR goggle wearing specialist pilots, switching to self-piloting mode for the final diving attack after locking on to speeding special forces astride motorbikes.

• Surface to air ballistic missiles climb into the stratosphere and are shot down by interceptors in outer space. Laser cannons are at the early stages of replacing such systems at borders and on ships for the purpose of shooting down smaller missiles.

• Netrunning hackers write code utilizing advanced AIs, driven remotely on space-age computing tech with built-in deep-learning optimized CUDA architecture, to decode encrypted messaging and breach enemy networks.

Call of Duty Black Ops 2154? No, it’s a slightly dramatized yet not inaccurate description of 2025 warfare happening now. Humans, wittingly or unwittingly, have often turned future technology into reality through fiction, decades in advance. It can be dark and scary as with warfare, nifty and cool as with VR headsets and flying cars, or generally economically useful as with manufacturing robots etc making the world more productive and plentiful. Regardless, in many ways it is rapidly arriving as outlined in this excellent blog post. But sadly, both the science and science-fiction of therapeutic advancement lag far behind that of the cyber and space domains. Why don’t we start similarly imagining into being a world where medicine truly works for people?

Thus, this multi-chapter fiction series follows the lives of 5 doctors and their trainees in the late 21st century working at the “San Francisco Institute for Comprehensive Rejuvenation and Repair”, a theoretical multifaceted medical institute catering to all people and utilizing future technologies for optimum effect.

It focuses not on a dream of absolute societal utopia, but rather on a world where rejuvenation & repair approaches as well as other therapeutic and diagnostic technologies can lessen the dystopian aspects of the cash and labor-strapped 2025 medical establishment. And, where personal age plays a much smaller role in determining your identity and lifestyle. What would the world look like if medicine grew at the rate of software and robotics? Let’s go to the Institute and find out…

Prologue: Lunch Break

DIIIING

Saira’s buzzer vibrated violently, rudely interrupting her feast of egg salad and chocolate milk.

“Damn it, I was hoping recess would come after lunch! All this Medical School training and my life quality is worse than in 3^rd grade”.

“Well, you did choose this labor of love for yourself honey” said Amanda, an appreciative lack of empathy for her friends problems in her smiling eyes. “We all did, after all.”

“Yeah, and you know, as my grand pappy Dr. Bernstein told me, they used to have to drive patients through the STREETS before suturing their wounds with their OWN HANDS” scoffed James, leaning back on his chair with folded arms and pursed lips.

“James, you’re literally 35. Your grand pappy and I probably threw snowballs at each other when we were walking 15 miles to school up hill both ways” Saira lambasted, rolling her eyes.

The posse of long-time colleagues laughed, except for Saira who sat rapidly chugging her chocolate milk before returning to her duty. 5 of them sat there, all almost ready to start there shift again. James, the bio-manufacturing specialist. Amanda, the Internal Medicine specialist and self proclaimed House wannabe. Saira, the hilariously unstoic ER Doctor. Juan Carlos, the medical implant engineer “Ripperdoc” (who clearly chose his specialization as a fan of Cyberpunk literature). And Akira, the nurse who basically held the group (and the hospital floor) together.

“Okay guys. Half the day left and then tomorrow we get to go hike and climb in Joshua Tree and have some fun in our AirBNB in Palm Springs” noted Akira resolutely.

“Yes, we’ll party like it’s 2065 again. Bro, I can’t wait!” said Juan Carlos.

Saira wiped a thin film of milk from her upper lip “ME NEITHER! Oh man…”

James giggled “Yup, and now that you had all your calcium for the day Saira, your 78 year old bones might even make it through the whole hike!”

“DUDE! When was the last time you saw a patient with osteoporosis, of all things? It doesn’t matter, I’ll drink you under the table and you’ll go crying back to your gen epsilon or whatever frat buddies about how you can’t keep up with your old lady friends”.

Akira, who had easily the most time lived (with formative memories all the way back to the 20^th century) and the least time for bullshit, tapped her watch. “Let’s get on with it guys. Continue this conversation tomorrow at 8:00, yeah?”

They all nodded and dispersed, some shifting silently but visibly back to professional mentality, others simply looking forward in curiosity to the rest of what had thus far been a typically non-typical day at the San Francisco Institute of Rejuvenation and Repair.

Chapter 1: Dr. Amanda O’Neal (and Deng)

Amanda started at her case list floating across her left most screen. She had finished her meetings for the day in the morning and now had the next 6 hours to sort through as many cases as she could manage. Her med student trainee, Deng, sat politely next to her as he waited for her to start discussing the puzzles of the afternoon.

“Okay Deng, first case, just came in. Patient is a previously healthy 4-month-old male infant presenting to the ED with progressive lethargy, poor feeding, and irritability over the past 36 hours. Parents report that he was well until this morning when he became increasingly difficult to rouse for feedings. This morning, they noticed episodes of vomiting and unusual breathing patterns.

Vitals:

• Temperature: 37.2°C

• Heart rate: 160 bpm

• Respiratory rate: 50/min

• BP: 78/45 mmHg

• Oxygen saturation: 94% on room air

• Blood culture negative for signs of infection

• Physical Examination”

  • General: Lethargic, responsive only to painful stimuli

  • HEENT: Fontanelle slightly full, no nuchal rigidity

  • Respiratory: Tachypneic with periods of irregular breathing

  • Cardiovascular: Tachycardic but no murmurs

  • Abdomen: Mildly distended, hepatomegaly 2 cm below costal margin

  • Neuro: Decreased tone, hyperreflexia, intermittent myoclonic jerks.

What do you think it could be?”

Deng sat and thought for a moment. “Well, I’m assuming a genetic disorder. Maybe a Urea Cycle Disorder? But why exactly would this come to us? Shouldn’t the automated universal metabolite assay have caught the hyperammonemia immediately? No one misses these types of diseases in 2087.”

“Not bad! The ammonia was degraded in the first sample turns out, and the case automatically got forwarded to us.” She smiled “Of course they re-ran the sample and found it out but the case still came to us. Thought I’d give you a warmup though”.

“Why would the AI monitoring system make that error?”

“Never assume human error doesn’t exist Deng. It was from a pop-up clinic in a Doctors Without Borders camp, a lot more chaotic then here. Claude 17.2 and GPT 6o1.2a mini high guessed the problem, but they wanted an extra human in the loop to double check as they ran the next test.”

“Okay anyways Dr. O’Neal. Let’s go on to a harder one.” sighed Deng.

“Sure. Look here:”

• Patient is a 19-year-old male presenting with a 5-month history of progressive visual disturbances, declining academic performance, and increasing clumsiness. Previously an honor student and competitive swimmer, he initially complained of difficulty reading small print, attributed to eye strain. Over the past 3 months, he has developed an unsteady gait, occasional myoclonic jerks, and family reports personality changes including inappropriate laughter and apathy.

• His personal background is mostly unremarkable, but his family history is remarkable for paternal uncle with "early-onset dementia" in his 30s, died at age 42.

• Physical Examination:

  • General: Alert but with delayed responses to questions

  • HEENT: Subtle cherry-red spot on fundoscopic exam, subtle supranuclear gaze palsy

  • Respiratory/Cardiovascular: Unremarkable

  • Abdomen: Normal

  • Neuro: Dysmetria on finger-to-nose testing, dysdiadochokinesia, positive Romberg sign, occasional subtle myoclonic jerks, hyperreflexia in lower extremities with bilateral Babinski signs

• Diagnostics:

  • MRI brain: Subtle hyperintensities in bilateral thalami and cerebellum on T2-weighted images, cerebral and cerebellar atrophy not consistent with age

  • EEG: Periodic sharp wave complexes at 1-2 Hz

  • CSF analysis: Normal cell count, protein 60 mg/dL (mildly elevated), glucose normal, negative for infectious pathogens, 14-3-3 protein positive

  • Routine labs (CBC, CMP, TSH, B12/folate, ANA): Unremarkable

  • Ophthalmology assessment: Subtle macular cherry-red spots, no Kayser-Fleischer rings

“Thoughts Deng?”

Deng winced. “Hmm. You didn’t mention one obvious thing. Family history of something marginally similar to this suggests genetic issues, and a lot of these symptoms could be associated with some disorders like juvenile Huntington’s, Wilson’s disease, Niemann-Pick C, etc. Maybe the last one fits best”. He paused. “But why were they not detected by genotype or sequencing? You’re a world leading internal medicine specialist, why would someone send a genetic disease case to you? They’re practically never misdiagnosed in this era and they’re easily corrected through gene therapy. Maybe prion disease?”

Amanda stared, slightly frustrated her trainee wasn’t getting the point of the lesson. “Listen Deng. What did I just mention previously. Don’t discount human error, people’s unique situations, and don’t assume resources are limitless.”

Deng straightened up. “Okay Dr. O’Neal. Do they have genotype data?”

“At first no. The patient didn’t want his genotype or sequencing data taken at his hometown for some reason. So he came here.”

Deng looked at her confusedly. “Why?”

“I don’t know Deng. You figure out. Now we have the DNA sequence though, he finally consented. Why don’t you run it?”

Deng slid over to the 3-monitor setup, pulling up the .seq file and dropped it into the automatic assessment program. “Hmm...no standard alleles detected. Maybe something de novo? Let’s try the structure determination algorithm for the proteins related to the three diseases I mentioned...oh wow. Yup, missing a cysteine in NPC1, and a critical disulfide bond forming one. Definitely that.” He winced. “Why didn’t he just have this tested a while ago? They should have his sequence from birth practically”.

“They did Deng. But it disappeared from the database 5 months ago. Mysteriously.”

“Hmm. I saw a case like this before. Guy requested sequencing data from all major databases be removed… they did, and then later they found out he had pulled it right after accidentally fathering a child with a woman he had met the same night on a work trip.”

Amanda smiled. “That’s my bet too Deng. Freshman year spring break gone wrong. But we’re bound by HIPAA laws to keep our noses out of that and not run any genetic similarity cross-checks on the database.” She looked him deeply in the eyes. “Do you understand the lesson? In the world of AI and big data based diagnosis, everything is solvable until it isn’t. Luckily 99% of these things are solved by algorithms and treated promptly nowadays, which is why we can get through all the outstanding cases in an afternoon. But the ones that are left – well, human error adds up. And that’s where your training comes in.”

Deng nodded, finally appreciating the lesson deeply. “Okay. You’re right. Then, diagnosis is Niemann Pick C, suggested solution is CRISPR based single base addition gene therapy to correct the cysteine deletion. Let’s put in the order to the novel gene therapy division and I think they should be able to manage this one in...a week, ten days maybe? It’s high urgency as a degenerative neurological condition and it’s a clear SNP so it’s mostly going to be a matter of going ahead with the guide RNA manufacture and running the necessary QC assays.”

“Sounds good Deng. Now come on. We have 8 more cases before 7:00pm and you’ve got an exam tomorrow”. Amanda smiled, reclining in her chair and spinning back to her screen to read the next puzzle.