A Rip in Reality

Finding a rip within reality’s fabric
Strange how your perception of the world changes. When I was in kindergarten a toy could make the difference between a good and a bad day. Later, when I was in high school my world consisted of friends, grades and defining myself. When I was studying molecular biology I thought I knew who I was and what I needed to do to follow my dreams. And now? All has changed again.
I was never interested in a social life and I was wondering about the relation of me and the world. I wasn’t really feeling human since I was no social being. Who am I, what forces govern the world and is there a way to understand it, predict it? All my life I’ve been a skeptic, wanted to know this world I was thrown into. This desire made me pursue a scientific career. Soon I focused on universal concepts of biology and physics to explain the wonders I came across since religion always had an artificial aftertaste.
After I graduated with medicine, biology and chemistry as majors I had my answers. I could explain everything, knew the structure of matter, knew the forces holding molecules together, knew how genetic predetermination and environmental influences shape every existence. But I could neither predict nor manipulate it as I wished; there were so many influences on every scale from the smallest orbital interactions to the exchange of information that is so essential in a social world that the results of changing even the slightest factor in such a complex system could have any result since you don’t know what else plays a role. And when you don’t know the reaction of a given action, how do you want to predict it?
Having not much family, not many friends and looking for answers being frustrated is quite a good base for doing good science. I gave up trying to understand me, focused on building an existence in a dominant social world that felt so alien. Already in high school I noticed that my personality was not suited for such a life. I was impolite since I disregarded social codes, got into fights regularly because others disregarded my values which they didn’t share. I dealt with that problem by splitting apart a big chunk of my personality to form an adaptor, a mental suit allowing me to get in contact with this social world translating and buffering influences on both sides.
So there was I, frustrated with an unsatisfying answer to life and facing grad school. I didn’t have any preferences concerning grad school as long as it contributed understanding life. So I choose studying bio films. You might ask yourself why I did so since that’s an odd direction when you want to understand life. Why not a molecular biology group? As I said, I didn’t have preferences. And I enjoyed the undergraduate lectures of Professor Samson, the head of the bio film group. Bio-films are really interesting. Yeah, you have them on your teeth, inside your veins, your heart: bacteria that settle down and colonize a surface. Samson’s lab had studied industrial applications of colonizing bacteria for pharmaceutical and hazardous waste processing.
One night our team had lab club again; we were all meeting in our lab to talk about results and ideas. And Samson would bring beer and order sushi.
“So guys, what’s new?”, Samson opened the session.
“Got that Miniprep to work,” Saph, another Ph.D. student reported, “The sequence we got from our collaborators in Berlin is in the construct, the colonies are growing over night and I’ll start polymerization tomorrow.” Some guys in labs on the same floor were joking, that we would be the lab of strange names. Being named like a stone Saphira was used to comments. She once explained that her parents were hippies and somehow this influenced their decision for her name. I couldn’t claim to have that excuse. My father was a diving fanatic which was the reason for my name. Not that I would complain. I like it. Even more now then back in those days. Professor Samson’s first name was Henry but everybody called him Samson. Must have been his tall athletic appearance in combination with a rather unusual beard covering most of his face.
“Sounds great. If that works we can wrap up that story and send it out for publishing”, Samson said. “And your project, Glauca?”
I didn’t have as much luck with my experiments as Saph. “I’m still struggling with their adhesion properties.” I previously had managed to generate bacteria with catalytic properties that might one day be used in kidney dialysis. But they didn’t want to stick to the plastic surface of the capillaries which caused me problems for the last three months. “Things look slightly better for the UV block for plastic surfaces. But I’m still trying to increase the ion concentration in the upper layers of cells. I’ll try to make the cells express another copper channel to get more copper into the film.”
“Good, good. Guys, I wanted to talk with you about an idea I’m thinking about. I want to shift our lab’s interest a bit more into clinical applications. We have enough funding from our patents and competition concerning applications for bio-films is getting quite strong. We’ve beaten most groups so far but there are just too many groups fighting for funding and since we have been one of the pioneer groups in this field I think we have enough experience and funding to do the next leap. I want to use bio-films for noninvasive medical treatment.”
Silence. We were both somewhat baffled.
“Sounds exciting”, Saph diplomatically replied.
“Boss, you’re sure we have that background? We don’t know enough of clinical studies.” I said.
“We haven’t, that’s right. But we can always collaborate. We were in contact with that group in Boston in that fermenter coating paper. And they also look into applying bacteria though they don’t have our background.”
Slowly fascination caught fire in me. It was a huge leap for such a small lab but Samson had proofed to have a nose for the trend in the field before. And since I had not chosen my Ph.D. topic yet this new idea sounded fresh and promising.
During the next months we finished our running projects and added details to Samson’s idea. We wanted to shoot for a melanoma treatment. A strain of bacteria should be generated coating the patient’s skin, delivering specifically a programmed retrovirus to the carcinoma cells.
And that was the first source of frustration; we didn’t want to cause a systemic shock due to bacteria entering the skin and blood system. And our first experiments with rats showed, that the retrovirus caused more cancer than it cured.
Help came unexpected from another workgroup. They had developed a mini genome, containing only what was essential for bacteria to grow. We bought a colony of that strain and reprogrammed it with genetic material from bacteria already on our skin. So the danger of a systemic shock was solved. We just needed another way to get that genetic material from the bio-film to the skin cells; the commonly used retrovirus caused too much abnormal growth. Again we were lucky. A pore forming shuttle protein was discovered that opened the pathway from nucleus to nucleus of neighboring cells, which was in our case the skin cell and the bacteria film. We combined it with priming sequences that defined which part of the sequence is transferred and where it is introduced into the cancer cell causing it to be reprogrammed.
We could cure skin cancer in rat models and were all extremely excited and dreamed of prizes and a bright future.
Happiness always has a price. That much I learned. While there is sunshine after rain, there is also rain after sunshine. And so it was then. The rats we had treated died after two months.
We were out of ideas. We had solved all the logical problems; it should have worked. Yet it didn’t.
When I went home that day I went down the stairs with Saph. “What do you think it is?” she asked.
“I don’t know. I really don’t know. An immune reaction, some enzymes blocked or something more general. There is so much that could go wrong.”
“I guess the leap was a bit too far for us then. I just wonder what we do for our Ph.D.s then. Hey, we can always become mechanics or gardeners if this doesn’t work out.”
That was a joke we shared. I had come to enjoy Saph’s optimistic nature that sometimes seemed to hide behind an acid sarcasm. I was wondering if there was something hidden behind that sarcasm, whether this ironic view reflected her view of the world. I had the feeling that she was also looking for an alternative.
I certainly was. I went to work to unravel the mysteries of the world without even glancing at the questions in myself. I went home, shoveling in some quick dinner, spending the evening by reading. I don’t drink, because I’m afraid of it. I feared that my longing and frustration would wreck me when fueled by alcohol. Frequently a book failed to catch my thoughts and they would wander. What if I could find another form, another place, another purpose? I had my purpose back then: I needed to find one. I buried the longing for another form thinking it would be a childhood fantasy. But without knowing I was looking for a place. So far home had been where I was. I left my birthplace without a second thought and went were I wasn’t before. I quickly learned that there are special places. I found several. I went to the Sarek region in Sweden. It felt like flying, this open space, green-gray mountains, boulder fields, cold wind, heavy rain and rough hikes keep population thin up there. That was home.
Sorry, I guess I get distracted. I guess retrospectively it’s feelings that I remember more than how I came to change. It’s hard since none of the lab stuff matters anymore.
The specimen were dead, the lab in a bad mood and my private struggle for answers in a dead end as well. Since science is frustrating by nature frustration and stalled projects were nothing new for us. Samson was doing dry thinking, background searches and checking with other groups, Saph checked the bacteria and the virus while I had the weird idea, that it might be some unexpected interaction of bacteria and host. I thought I could check that by using another species for tests, something with a more regenerative skin. Not really scientific and an absolute shot in the dark but it was an easy and quick experiment since we had a lizard lab right across the corridor and they offered specimen and animal care.
So I applied the same bacteria-virus combination and waited, took blood and tissue samples and waited some more.
A week went by and they were still alive, another week, a month, six weeks and eight weeks. They didn’t die. We couldn’t test these specimen for cancer reduction since it was just a test for survival, whether it is species related or not but still I was glad to have positive results. One day after almost four months I was once more in that narrow room taking out animal after animal, getting some blood with the syringe, scraping off some mucus from the skin and cutting off a small portion of the tail when that little black and red sucker bit me. I’ve never worked with lizards before and was astonished how strong their bite is. Took me a while to pull it off to return it to its box. Went right through the thin gloves. I didn’t think much of it then. I guess I was a bit naïve it was a potential hazardous animal contaminated with genetically altered bacteria and a retro virus analogue. But that’s how it was.
Samson was not happy about my findings. He would have preferred an error in our procedure or something unrelated to the species. There is no money in curing cancer in lizards. But he was still confident that we would be able to figure out the factor that allowed one species to survive the treatment while the other died.
Meanwhile I had some insight about how the bio-film worked from the blood and tissue samples I collected from my lizards. The speed with which the bacteria were spreading was extreme. I found the whole body dominantly coated with our bacteria already 48 hours after application. The gene transfer was somewhat slower. It took three weeks until all cells had successfully undergone gene replacement.
More alarming was something I had stumbled across at week 5. The bacteria on the lizard’s surface did not have the same genetic material as those we used in the first place; they had changed. Designing this experiment we had made a mistake. While a retro virus delivers sequence mostly one way, from virus to cell the extent of retrograde transport of genetic material, from cell to bacteria through the shuttle protein was much larger than expected. The bacteria contained DNA from the host, the lizard. Should have rung a bell when I was bitten. It didn’t. I began to worry when my finger turned black two days after the bite.
There was another thing I found from what I scratched from the lizard. The bacteria were using the lizard genes to form a tissue matrix and were actually penetrating the skin. I found them practically everywhere; in the skin, muscle, heart, intestines, brain, eyes, everywhere. Well, it didn’t do any harm to the lizard since these cells were almost indistinguishable from their environment since they expressed a large number of the lizard’s genetic material. But what would it do with me? I panicked.
I went to campus, euthanized and burned all specimen and disinfected my workspace. I was a ticking time bomb and potentially infectious. I started wearing gloves out of fear to contaminate others indirectly. I called Samson and told him about the bite and my results. There was this weird silence. Neither of us really knew what to do. He urged me to go to a doctor but keep things quiet if possible. Meanwhile he would check with others what one might do to stop it.
If you want to understand Samson walk in his shoes: He ran a very productive lab, leading in the field. He takes a leap, a huge risk… and generates a contagious disease. It’s the end of his career. To describe that situation as uncomfortable is a euphemism, I guess.
I did go to a doctor. But was not completely truthful. I said it would be a contagious bacterial disease so he prescribed antibiotics.
I stayed at home from then on. My black finger tip hat become a black finger. And something was strange. First I thought the black color would be due to necrosis, dying flesh. But it was alive, felt almost normal if a bit hot as if inflamed and oozing slime.
I couldn’t go out and not really calm. I was in PANICK. Even more so when I noticed that the antibiotics didn’t work. What did I expect? We had changed these little suckers; we must have changed the targets for the antibiotics as well. I was doomed I thought.
I wanted company, somebody to talk to. I called Saph.
She wasn’t panicked. She was calm. Still wonder why. I guess it’s her nature. Feels good to have some wonders left.
I didn’t want to talk about that black thing that crawls up my hand. Instead we talked about our lives. Each of us shared his or her special moments and we found that they were strangely similar. I told her of Sweden, about that waterfall I found one evening and spend the night beside, about the feeling of hiking through the Icelandic desert, of the turmoil inside me, the need for a special place and purpose. I didn’t mention the form since that would just have brought back the panic.
She also enjoyed hiking, went to Peru and remembered a special night on the shore of a large mountain lake admiring the reflection of the white mountains on its surface, that she was a stargazer and that she planned to return to that solitude once she knew she would not do so to run away but to have managed to sail the waters of society, leaving them behind.
Resonance. I wasn’t aware of it but her words could have been mine, now that I heard them they gave shape to my unrest and purpose to my behavior of the past years. I was a fool to have ignored her all these years. And so changed my view of the world once more. I noticed that my world was self-centered and while I thought I would be trying to understand the world it was always with the same eyes, always in my context. I never tried to understand her with her own eyes instead of from the perspective of a lab colleague.
“What are you going to do now?” She asked me. That ripped me out of the clouds so conveniently hiding the ground of reality.
“The drugs don’t work and it’s spreading. I don’t know. From what our experiments indicate I wouldn’t give me much time till the little beasts get the best of me. Humans are closer to rats than to lizards. On the other hand, the bacteria have changed. I don’t know what will happen. I know it’s much to ask but could you bring me to Sweden? I don’t want to spend my last days here; I want to go home. Besides, having me out of the country might be the best for the lab.”
“You still think about the lab? The lab is of no consequence to you now. Let Samson take care of it. The question is, what do you want from life?”
“A place, a form, a purpose. It would be nice if the purpose would be to prolong a moment. But then I’m not so sure whether I could enjoy paradise.”
“Take what you get. I can’t help you with form and purpose. But I’ll accompany you to Sweden.”
Two days later the black skin hat reached my torso. Every joint in my arm was aching and my skin was hanging loosely in flaps from my arm. I was miserable, my head was burning and I was so weak I could barely stand. Saph packed some gear for us, a tent, provisions, the usual equipment and drove us to the airport. I was so tired. On the plane I had fever dreams, half a wake, half buried beneath a mucus of pain and terror. The train ride to Abisco was long, longer than 24h. An eternity and the black skin was spreading further. By the time we stumbled out of the train Saph half carried me and the black front had reached my chin. How she managed to carry the pack and support me I don’t know. I wasn’t really awake by then. I lost consciousness , either that day or the next. It all became a blur.
I periodically woke up from weird dreams. Sometimes I was hot, sometimes cold. And every bone hurt. It was not a stabbing pain but an intense blunt pain associated with my bones and joints. And I remember waking up once looking at my hand seeing a black claw. I sunk back to sleep thinking it would have been a fever dream. And every time I woke up she was there. I took comfort in her smile, wanted to erase the worries from her eyes. Couldn’t even say a word, my neck was swollen.
Slowly the pain subsided. The dreams became slower, clearer, comforting.
I woke up and saw her. Gratitude bubbled up inside me. I was lying on my stomach and the sleeping bag was open and laid over me. Why wasn’t it closed and I inside it? Why was I able to see it in the first place lying on my stomach? I sat up fully alert. Several things happened at the same time. I jumped with my front legs ten inches in the air trying to sit up… and fell right back. Front legs? Something in front of my face hit the fabric of the tent. My face bulged out where my nose and mouth should be. Subduing the first surges of panic I tried to calm down and take a look at my situation. I was still in the tent, the fabric filling my whole field of view. I turned my head. Another sleeping back. And a leg. My leg. Strange angle, strange skin. Strange hand. Out of my shoulder came shortened limb, black, loose skin covering it, ending in a five digit hand. But my shoulder was further away than before. My neck must be longer I figured. I tried to turn around but something behind me stuck the tent and prevented that maneuver. So I crawled back out rear first since I figured that what I hit trying to turn must have been the open tent entrance. Finally, free of the tent. I was on a stony plateau, boulders everywhere. It was a pass of sorts, very smooth ridges flanking the valley. So she found it. The waterfall was just a few hundred yards from here. I took another look at my body. It was elongated, covered in black scales on loose black skin. And I had a tail. To judge from that view almost as long as my torso and head together. The hind legs where similar to those I had the pleasure to greet first. But not quite. I still had a thumb. How convenient, I thought. But I couldn’t stand up. So that was lost to me. Somehow I felt at home in that body. I was looking for Saph. This body was fast. And the sun felt good. I found Saph sitting next to the waterfall and had to grin. Could I speak? “Chi Sath!” Not very well it seems.
She turned around with a glad grin. “Finally awake I see. Took you long enough.”
“Cho chong?”
“A month. Glad you made it. How are you feeling?”
“Oh che… Thanchs Sath.”
That my speech was impaired was a bit frustrating but Saph seemed to understand me well enough. That day I just enjoyed lying there on the rock next to Saph and the waterfall. It was so deeply satisfying.
But reality soon caught up with us. Saph hat to return several times to stock up provisions and returned then to the lab, tying loose ends she said. I didn’t ask whether she would come again. Maybe she would take care of my things; maybe she did it to do her Ph.D., maybe to find her own place, her own paradise.
For my part I came to enjoy my new life. First I feared how long I would have to live since I still considered it freakish luck to be still alive and not covered with cancer growth. But why should I ruin a good day with worry? I have what I wanted. I have a place, a form suiting my soul. And my purpose? Enjoying life is purpose enough.
The provisions helped me through the first months until I learned to sustain myself. I’ve come to enjoy my solitude here. But even here society found me: The other day kids from a nearby Samen village found me. They teach me some of their language and I play with them. So far no adult has come for which I’m glad. Maybe the kids keep it a secret or their parents don’t believe them. Either way keeps them from ruining a perfectly good day.
And so I found what I would never have dreamed to find: The rip in realities fabric, where dreams don’t shatter on reality’s laws. I cannot say whether this is real or not. I don’t care. It is too precious to analyze it. To analyze means to alter what is analyzed. I just want to enjoy. And wherever Saph is at the moment: Good luck. I wish I could help you find your heaven the way you helped me into mine.