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A Study in Emerald, Part II [PLOT]

Posted on Thu Jul 19th, 2018 @ 8:12am by Captain Malcom Llwyedd & Lieutenant Laree Desai

Mission: Mission 3: The Galilei Conundrum
Location: Galilei sickbay
Timeline: 26 June, 2394 - 1000 Hours

Continued from A Study in Emerald, Part I

Of course this sickbay has a fancy computer Desai thought as she sat down at the doctor’s desk in sickbay. Soft corners and shiny surfaces dominated the space, but the tech was state of the art--if you want to make a wiz-bang presentation. Which was pretty much exactly what Desai wanted to do.

She needed to think. And to think she needed to visualize. So she pulled up the computer’s 2D holodisplay and made a list:

Emeralds (beryllium aluminum cyclosilicate)
Organ failure
Stress hormones
Savin vs. Tajor?
Fungal spores?

Each of the items she placed in a box, then arranged the boxes in a rough circle on the display. She drew an arrow from the “Emeralds” box to the “Organ failure” box, because at this point they were sure that the growth of the emerald crystals was what caused the organ failure. She drew a line from “Stress hormones” to “Savin vs. Tajor,” because Savin’s hormone levels were elevated but Tajor’s weren’t. She stared at the beginning of her network diagram. Could she draw any more connections? She thought the fungal spores were probably responsible for the emerald crystals, but she wasn’t sure yet so she drew a dotted line only. Then she stared at the network again. It was too sparse, but it was the best she could do for now.

She downloaded the diagram into the computer on the biosuit, still thinking. Nora was working on a treatment for the crystals, Jillian was analyzing blood samples, and Vaun was working in the lab. Maybe they could help her add more connections, help her build the network that would describe and explain exactly what was going on here.




Jillian looked up as Desai moved through sickbay. "I'm glad you are here. I have been thinking about why the patients with red blood react different to the illness than those with green blood."

Desai raised an eyebrow. "And what are you thinking about why the patients with red blood react differently than those with green?" Vials and slides and chemical reagents--the evidence of Nurse Mox's industry--littered the counter over which Jillian stood.

"I've been trying to find differences in the spores between red blood versus green blood: size, or color, or, well, anything." Jillian flicked open a holographic display of the spores, gently rotating above the table. "Every property I've measured shows the samples to be identical, within a reasonable tolerance. But then, I should have recognized it sooner but in all the excitement, the running around..." She paused to take a deep breath, "I mean, the crystals. They haven't formed in any of the samples of green blood. I'm running an analysis to see what other chemical differences the blood has." Jillian also wondered how the contagion would affect Emily, and how many parents on board must also be suffering in silent fear for their loved ones.

Desai drew her eyebrows together in concentration. Differences between red blood and green blood? "Hmmm," she said, thinking out loud. "Red blood is red because it uses hemoglobin as an oxygen acceptor. Green blood uses vertinagen." She looked up at Jillian. "That could be the key difference. Thank you, Jillian. I'll have Vaun take a closer look. In the meantime..." Desai looked over at Nora. "Doctor Morrison is focusing on the crystals. But it's starting to look like the underlying infection might be fungal. Let's assume that's true for a moment. Medically speaking, how do you cure a fungal infection?"

"I have a few ideas." Jillian mused. "I'll keep working on it."

Desai smiled at the thoughtful expression on Jillian's face. "If anyone can do it, you can," she said. "Let me know when you have something. I need to go check in with Vaun." She nodded at Jillian, then turned and left sickbay.




The tricorder beeped. All flight controls were with acceptable ranges. Releasing a huge sigh Gantt rolled out from under the flight console. His back ached. He'd lost track of the failed attempts to correct the controls; fewer than the number of times T'Sai had accidentally kicked him while he worked. In mid stretch when the door from the bridge opened. Gantt jerked towards his phaser before recognizing Lieutenant M'rron encased in a Federation biosuit.

"Greetings, Lieutenant M'rron," said Gantt, returning to his stretching.

"Good to see you, Gantt," M'ndi rejoined. "Wish I could stay and chat. Just here for a blood sample."

"Sure, go right ahead." Gantt stepped out of the way but she followed him. "Oh, from me? IF you're sure you want my blood." He shrugged, half hoping M'ndi would change her mind.

M'ndi smiled apologetically. "Sorry, doctor's orders." She held out her hand expectantly.

He turned to give her easy access to the suit's Biometrics menu. "What is the sample for? None of us have been exposed." His hand rubbed the collar joint of the bio-suit. "Have we?"

"Not that we know of," M'ndi reassured. "We just need control samples for each species among the exposed." She hit a few buttons on the electronic menu on the suit's side, and a small vial full up with Gantt's blood came out as he grimaced in discomfort. "Thanks," she said.




Vaun was bent over a growth chamber when Desai arrived in the science lab. Eighteen blinking, humming, transparent boxes rested in neat rows on the workbench, labeled in Vaun’s familiar shorthand. Desai examined two of the chambers while she waited for Vaun to finish her readings. An amorphous mass of differentiated tissues pulsed inside the growth chambers, blood vessels visible through the shapeless body. In one of the boxes, green crystals pierced the epithelial layer and red blood oozed around the sore. Desai pulled over the magnifier, and sure enough, black spheres floated in the blood and caked the skin around the eruption.

“The crystals are the source of the spores?” she said to the room, still staring at the sample in the growth chamber.

Vaun answered, also without looking up. “I don’t think so, actually.” Silence fell again as Vaun finished making notes on her PADD and Desai continued her observation. When Vaun was done tapping, she straightened up and joined Desai on the other side of the bench. “This sample is from M’ndi. Red blood, and you can clearly see the crystals. But look over here…” Vaun moved two chambers to the right. “This sample is from T’sai.”

Desai straightened, but didn’t move next to Vaun. “Let me guess. No crystals.”

Vaun looked at Desai in surprise. “How did you know?”

Desai nodded. “Jillian found the same thing when she was looking at blood samples from patients. Green-blooded humanoids aren’t affected by the crystals. And there’s more. Savin has highly elevated levels of stress hormones in his bloodstream—215% higher than normal. Tajor… doesn’t.”

“Green blood versus red blood,” Vaun mused.

Desai punched buttons on the arm of her suit, and the lab’s 2D display lit up with Desai too-sparse network. Vaun examined the boxes: Emeralds (beryllium aluminum cyclosilicate), Organ failure, Stress hormones, Savin vs. Tajor?, Fungal spores? She noted the lines, solid and dotted. She looked over at Desai and asked, “May I?”

Desai gestured toward the display. “Be my guest.”

Vaun stood in front of the display and edited the box “Savin vs. Tajor?” so that it read “Green blood vs. Red blood.” She stepped back, frowning, then reached over and edited it again, splitting it into two boxes: “Green blood” and “Red blood.” She moved the line from “Stress hormones” so that it only connected to the green blood box, then she drew a line from the red blood box to “Emeralds.” When she was done, she looked over at Desai. “What do you think?”

Her brows creased in concentration, Desai nodded again. She reached toward the display, and under the words “Red blood” she added “hemoglobin.” Under “Green blood” she added “vertinagen.” “Those aren’t the only differences between red and green blood,” Desai said, “but if I were a pathogen, the oxygen carrier would seem like an awfully good target to me.”

Now it was Vaun’s turn to nod. “I agree.”

Desai pointed to the dotted line between “Fungal spores” and “Emeralds.” “Tell me why you think the crystals aren’t connected to the spores,” she said.

“Oh, I think they’re connected,” she said. “They have to be. But I don’t think the crystals are the source of the spores.”

“Correlation versus causation,” Desai said ruefully. She almost smacked herself on the forehead for making such a freshman mistake. ‘There’s a third thing responsible for both.”

“That’s what I think,” Vaun said. “But I need to let these samples grow out a bit more before I can be sure.” Vaun paused, thinking. “You said Savin has highly elevated levels of stress hormones in his blood stream?”

“That’s what Jillian found.”

“There’s a signaling molecule I isolated from the green bloods that I’ve never seen before. It looks like it might work with the MAP kinase pathway, which…”

“…is crucial to the stress response in many humanoids. Including Vulcans and Romulans.” Desai understood immediately.

“I didn’t look at it too closely—I had more promising leads to follow. But it sounds like it might be important. I was able to isolate and sequence the amino acid structure, but the molecule itself broke apart when I tried to image it directly. So I have no idea what it looks like in 3D.”

Desai looked at Vaun and Vaun looked at Desai. They both knew what needed to be done, and they both understood that it was an almost impossible task.

“How long is the sequence?” Desai asked.

“Short for a protein, but long for a combinatorics problem. 79 amino acids.”

“79 factorial is…” Desai reached for the computer.

“Too many for us to model.”

8.946182 E116 popped up on the display and Desai whistled. “9 times 10 to the 116th power. You’re right. Too many possibilities for us to model before everyone on the ship dies.”

“Starfleet’s advanced AI’s might have a shot,” Vaun said, “but this is an NP hard problem and in four hundred years of research we still haven’t made much progress on predicting protein folding. There’s no way Starfleet’s Big Blue Brains could get it to us in time.”

But Desai hadn’t heard anything after “advanced AI’s.” She looked up at Vaun, a twinkle in her eye. “I think I know just the AI’s to help.”




“Gentlemen,” Desai declared, focusing down at the PADD in her hand. Her walk from the science lab to sickbay had been brisk. Three taps later she had uploaded a file into the memory banks of the two EMH’s. “I just sent you a protein sequence.”

sp|P25098|ARBK1_HUMANOID Beta-adrenergic receptor kinase

MAD LEA VLA DVS YLM AME KSK ATP AAR ASK KIL LPE PSI RSV MQK YLE DRG EVT FEK IFS QKL GYL LFR DFC LNH LEE ARP LVE FYE EIK KYE KLE TEE ERV ARS REI FDS YIM KEL LAC SHP FSK SAT EHV QGH LGK KQV PPD LFQ PYI EEI CQN LRG DVF QKF IES DKF TRF CQW KNV ELN IHL TMN DFS VHR IIG RGG FGE VYG CRK ADT GKM YAM KCL DKK RIK MKQ GET LAL NER

“I know,” Desai continued, matter-of-factly, “that protein folding is an NP-hard problem, so this may be beyond even your capacious abilities. I’d like you to give it a try, though, if you’re willing. First we need to determine this protein’s tertiary structure. Then we need to identify the molecular subunits, especially the ligand binding site. Once we’ve modeled the structure, we need to reverse-engineer an inhibitor that will plug that hole."

Clothed in frank professionalism, she looked at the two doctors expectantly. “I know it’s a lot to ask, but you two probably have the best chance of any of us to figure this out. Would you be willing to give it a try?”

The Firebird's EMH crossed his arms. He still felt strange on the stricken cruise ship without his portable holo-emitter. Still he had to admit that he'd never looked better. He made a mental note to request the re-installation of the Firebird's holo-emitters. "Frankly, lieutenant, I'm not sure why we need the assistance of this," he said, gesturing to the Galilei's EMH, who was dressed in civilian clothing. "Antiquated EMH."

The Galilei's EMH smiled. "It sounds like someone got up on the wrong side of the bed," he said in a cheerful tone. "I know I might not have some of your updated medical databases, but I do have access to all of the data I processed before you showed up in a johnny-come lately fashion."

Both EMHs looked at Desai expectantly.

Desai suppressed a smile. She wished she could sit down with a bag of popcorn, but alas she had lives to save. "Well then," she said, "I'll take that as a 'yes.' Please let me know as soon as you find anything." She straightened, her expression serious. "Good luck, gentlemen." She turned snappy on her heel and didn't laugh until she was in the corridor.

"This is preposterous," the Firebird's EMH said. He began pacing around the small Chief Medical Officer's office. "Its as if I am being forced to collaborate with a child," he said to himself.

The Galilei's EMH nodded. "Isn't it fascinating that I feel the same way?"

The two stared at each other. They were physically similar, of course but beyond that they could not have been more different. One wore a crisp Starfleet uniform and the other wore long casual shorts and a black t-shirt.

"How can anyone take you seriously when you appear so unprofessional?" The Firebird EMH said.

"Your programming is limited when it comes to doctor patient interactions," The Galilei EMH said and continued, ignoring the horrified look on his counterpart's face. "My program has been updated and modified by the most talented programmers, with emphasis based on serving my clients needs in the most humane fashion possible."

"That sound horrible. You've been warped by some civilian hacks and assume that you're improved. You poor, poor program."

The Galilei EMH sighed and covered his face with a hand. "Perhaps we can both agree that focusing on the work is the most important thing on our agenda?"

"Fine. We can use the computer system on the Firebird to help work the problem since the Galilei's computer isn't as smart as young Emily Mox."

The Galilei EMH frowned. "I don't know who Emily Mox is but this ship's computer is more robust than you know. It also has a remarkable lack of anything to do. We should split the data processing and thus arrive at a solution more quickly."

"Fine. Let's get to work."

To be concluded in A Study in Emerald, Part III


Lieutenant Laree Desai
Chief Science Officer
USS Firebird NCC-88298



Lieutenant M'ndi M'rron
Assistant Chief Science Officer
USS Firebird NCC-88298



Lieutenant Nora Morrison M.D.
Chief Counselor
USS Firebird NCC-88298



Jillian Mox
Nurse
USS Firebird NCC-88298



Lieutenant Junior Grade Soto Gantt
Structural/Environmental Specialist
USS Firebird NCC-88298



Chief Warrant Officer (Grade 2) Amara Vaun Jr.
Biologist
NPC
By Lt. Laree Desai and Lt. Comm. Yumi Han

Lieutenant Commander Emergency Medical Hologram
Chief Medical Officer
NPC
By Captain Malcolm Llwyedd

 

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Comments (2)

By Lieutenant JG Murril Na on Fri Jul 20th, 2018 @ 1:53pm

My favorite bit so far has been: "...but this ship's computer is more robust than you know. It also has a remarkable lack of anything to do."

It's good because it seems more funny-foreshadowing-clever than funny-fluffy-haha. It never dawns on us as the audience that from a computer's POV, using a tiny fraction of what it's capable of could be akin to asking a physician to spend all day adding two and two together, over and over.

Also, I like how immediately after mentioning an obnoxiously long number, the speaker restates it in easier-to-understand terms for herself in the next sentence. (After all, how many readers are actually going to drop everything to go look up what that capital E means? Yet, it's a smooth way to educate without being insulting nor preachy nor awkward.)

By Cadet Freshman Grade Gianna Djokovic on Mon Jul 23rd, 2018 @ 7:07am

I just smile every time I read the EMH and so this is EMH^2 and it makes me so happy. <3 -Liam