Monthly Archives: September 2018

Microscopic Monsters – The Age of Discovery, Chapter 18: The Bottom Ooze

Day 14: 1100 hours…

Crisis!

I am loath to report that we are stranded, now mired to the gunwales in the bottom ooze – and I have only myself to blame.

The accident occurred in the middle of a strategizing meeting with naturalist Lyra Saunders and engine master Barron Wolfe. They were elucidating me on their well-reasoned plan to modify Cyclops’ fuel production by utilizing the product and by-product of photosynthesis (starches and oxygen) to fashion a fuel supply that would be emission-free, resulting in no carbon excess, making us undetectable to the predators of the pond micro verse.

As proposed, our menagerie of green algae cells, which has provided the bulwark of our oxygen production, could also be utilized as a starch farm. The starch would be processed to make a clean fuel for the boiler. Combustion would provide heat to drive the turbine, and the carbon gas waste product channeled back to the algae cells, which with the addition of sunlight, would continue the cycle. The idea was nearly perfect… the single stumbling block being that we had yet to discover how to easily convert the starch, which was itself combustible, to a higher energy-yielding fuel.

We were, in fact, discussing this very issue when there came a loud report, a metallic ‘BANG’ from aft.   The interruption hung for a moment in the cabin air as we looked at each other with a range of expressions, puzzled to concerned.

“Skipper, better get up here…” came Gyro’s stern declaration over the voice pipe.

Barron was bound for the engine room without a word. I raced for the wheelhouse, Lyra at my heels. In that moment I knew I had been remiss: following our run-in with the planarian, and more recently with the hydra – both of which were taxing to the ship’s constitution – I should have ordered a stem-to-stern inspection. But I neglected to do so, caught up in the excitement of new discoveries, and now some important piece of equipment had failed.

We charged into the pilothouse, found Gyro clutching the ship’s varnished oaken wheel with his left hand, his right pulling futilely on the elevator control lever.

“Control cable snapped,” he shouted in a matter-of-fact greeting. “She won’t pull up!”

Yes, I thought with alarm and self-recrimination, something that likely would have appeared plain as day in a cursory inspection… if only I had ordered one.

The following moments are a blur… of alarm bells… of desperation to regain control… of the pond bottom rising up from the shadowy depths as Cyclops plummeted deeper and deeper.

“Hang on!” shouted Lyra, but her warning was unnecessary. My knuckles, bone white, were locked around the safety railing in an iron grip. Around us, water roared past the observation panes with the sound of a hurricane. Ahead, the terminus of our steeply sloped path loomed with ever-increasing detail.

And then we met with the bottom. Iron howled, steel screamed, wood trembled. Cyclops’ downward motion was turned into forward motion in an instant, and momentum threw me over the railing and into a forward pylon separating two glass panels. I lay on the deck, looking up at the glass panes through which a dense cloud of bottom detritus was roiling around the ship – but to my surprise, no collision came then or ever.

The bottom, it turned out, was soft as goose down. Cyclops came to rest on a vast pillow of spongy ooze – the term given to the bottom micro habitat: a layer made up of dead plants and animals that rained down from the upper levels of the pond, home to the tireless decomposer organisms that constantly converted organic matter back into basic molecules for re-entry into the food chain.

As the cloudy water cleared from around the stranded ship, our immediate surroundings became perceptible in the murky light. The motionless silhouettes of hulking dead micro crustaceans littered the bottom-scape to the edge of visibility, like monstrous prehistoric invertebrates transformed into mountains. Periodically the body of a daphnia, or copepod, would drift down from above, land amongst the carcass-littered bottom with a small puff of cloudy detritus.

1330 hours…

“Jonathan, this is interesting,” says Lyra from where she tends the environmental sampling station in our laboratory. “The water down here is much lower in oxygen than near the surface. And the carbon dioxide levels much higher.”

“That is indeed curious,” I say in agreement. “I hope that we have an opportunity to discover what might account for such conditions.”

Lyra begrudgingly accepts my clumsy change-of-subject, and turns to greet Gyro and Barron.

The crew and I have gathered in the lower deck laboratory to assess our situation. We are in one piece, thankfully – more a tribute to Cyclops’ stalwart construction, than any clever action taken by her skipper. We have survived our ungraceful landing with only minor structural damage. To avoid another oversight like the one that now finds us stranded on the pond bottom, I have ordered ship-wide inspections of all mechanical systems.

Engine master Barron has already begun repairs on the damaged elevator control cable that put us here, and as he enters the lab reports that repairs will be complete in half a day. But a larger problem looms. A storage tank was ruptured in the crash and the last of our fuel oil is all but gone.

“And in summation, we have just enough fuel to spin the dynamo and keep the lights on,” explains Barron, adding, “for a little while.”

“And then what?!” inquires Gyro. “We won’t survive down here for long… there’s got to be a meter and a half of water between us and breathable air!”

“And not much sunlight getting through that water to energize our photosynthetic algae herd,” adds Lyra. “Which means oxygen will soon be in dwindling supply.”

“What about the starch bodies they’ve been producing all this time?” I ask. “What will it take to convert it to useable fuel?”

Barron grumbles. “There’s plenty of starch – the little critters keep cranking it out, but it will have to be desiccated. It’s going to be difficult to remove all the water without a dehydration chamber for focusing low steady heat and dry air. And I’m not sure we have enough fuel remaining to run such a thing…”

Lyra interjects: “Sorry, Barron, I don’t mean to interrupt… “ she looks around the lab, as if searching for something undefined. “But… well… does anyone else hear that?”

For a moment there is silence, then, as our hearing adjusts to the quietness, a rustling, brushing sound can be heard coming through the hull.

“Open the crash shutter,” I suggest, “and let’s have a peek.”

Barron inserts a handle into the shuttering mechanism and slowly cranks the shutters open.

The porthole reveals the source of the strange scraping and sliding sounds we are hearing: a microbe, about the size and shape of a large watermelon, is pressed against the glass. Beyond the cell, to the limits of sight, tens of thousands, no, millions, of other similar microbes litter the pond bottom. Some twist and writhe, moving by way of flagella or finger-like projections, others lie still in layer upon layer of identical microbes. The world of the pond bottom is a world swarming with a fantastic diversity of bacteria!

“Well that explains the CO2 levels! “ A glimmer comes to Lyra’s eye. “Jonathan, “ she begins, but I stop her.

“You most certainly are not going out there,” I announce firmly. The others cease their duties and direct their attention to us to see if Lyra is going to press me with one of her entertaining justifications for going out for a dip.

“Why in heaven’s name would I want to do that,” she chides. “Especially when it’s much easier to bring a bacterium on board for study!”

1410 hours…

With the use of a manipulator claw, capturing one of the plentiful cells was not difficult.

The cell’s shape is oblong, and has a lazily whipping flagellum at each end. It is now bathing in our examination tray, a large raised rectangular tub about the size of a large dining table. The bath is filled with pond water and the bacterium is idling near one end, its flagella occasionally disturbing the surface with a gentle rippling sound.

Initial observations: The cell appears much simpler than previously studied microorganisms, such as the ones we have been tending for oxygen production. Unlike the more complex single cells the bacterium has no nucleus, and very few internal organ-elles, just a few fuzzy bundles inside a gelatin-like cloud.

“But make no mistake,” cautions Lyra, “there is a lot of chemistry going on in there.”

Another difference from other single cells is the presence of a semi rigid wall surrounding the bacterium’s cell membrane: a cell wall, which we theorize serves as a protective shield from harsh environmental conditions.

“Such protection might allow bacteria to thrive in some of the most inhospitable places on Earth,” I conclude.

“Jonathan, look!” cries Lyra. “The examination tray is dissolving!”

To our astonishment the bacterium appears to have a destructive effect on our examination pool!

“Curious… what is the tray made of?” I ask.

Lyra considers for a moment, then: “Plant cell walls, easy to come by and perfect for this application, or so I thought.”

“We need a closer look,” I say as I swing a magnifying view lens over the affected area of the try.

“Would you look at that,” whispers Lyra, peering down through the lens. “Large molecules appear to be leaving the bacterium through those pores in the cell wall. Digestive enzymes, I should think. And look! The enzymes have a caustic effect on the tray, breaking it down into smaller subunits – which are absorbed by the cell.   Those digestive enzymes react with dead plants and animals everywhere down here, reducing them into molecules that the bacterium can use to build more enzymes and other molecules of life.”

A harsh scent suddenly stings my nostrils. “Do you smell that?”

Lyra sniffs at the cabin air. “Jonathan… I’ll bet my grandmother’s mule that that’s alcohol!”

1500 hours…

Using a low flame of diatom oil, a coil of copper tubing, and a beaker filled with sample water from around the bacterium, Lyra has fashioned an effective still. She is about to test the product, a clear fluid in a glass phial. She inserts a cotton wick into the phial and sets a burning match to the end. It flares brightly with a clean blue flame… the tell tale sign of alcohol.

Lyra looks up excitedly. “Well Jonathan, I do believe you are the luckiest skipper ever commissioned. Our fuel problem is solved!”

2300 Hours…

Working tirelessly into the night, Barron has been modifying the boiler to burn alcohol, which will allow steam to generate faster, while requiring substantially less fuel than before. Meanwhile, Lyra, with my assistance, has collected two-dozen of the fermentation bacteria, and has moved them into culture tanks where they will convert starch from our green algae cells into alcohol. We are expending the last of our now obsolete oil reserves to fuel lamps set around the algae pens, so that photosynthesis can kick-start the process. By morning we should have enough pure distillate to fire up the boiler, work up a head of steam, and resume our voyage.

At the approach of eight bells, I retire to my small, corner study and set about organizing the various logs and journals of the past few days. As I stow an etching of the captured bacterium and an accompanying diagram of the chemical process by which we now power the Cyclops, I reflect on how our new system, a renewable system, so perfectly echoes the cycles of matter and energy in the living world.

I have come to the inescapable conclusion that bacteria provide perhaps the most important role in life’s grand saga. They are the never-ending recyclers of nutrients – tireless, ubiquitous. These simplest of living things break down dead organisms, then become food themselves for larger single cells. And those become food for larger organisms yet.   Down here in the shadowy murk of the bottom ooze, we have discovered the beginning of a food chain.

As I gaze out my small porthole into blackness, lost in the elegance of Earth’s living cycle, a shape momentarily appears in that encircled frame – but my mind cannot comprehend it, its form or its very presence, until the shape, a moment later, vanishes from sight.

It was… though I can scarcely pen the words… a face.

Microscopic Monsters – The Age of Discovery, Chapter 17: The Immortal Monster

Day 13: 0900 hours…

Last night passed, at least for myself, with little sleep. Slumber was kept at bay by a mind overly occupied, pondering the dilemma we now face of generating steam to drive our engine, but doing so without emitting carbon gasses. We’ve learned from our observation of single-celled pond life and from our recent run-in with the flatworm, that most aquatic microorganisms have the ability to detect the presence of CO2 – the universal product of aerobic respiration. These organisms are adept at locating prey by following a trail of carbon dioxide – an ingenious evolutionary adaption. Our own engine, which burns oil to generate heat, to in-turn boil water for steam, has the same effect on predators. I am amazed that we aren’t now digesting in some micro beastie’s belly!

I am faced with the inescapable conclusion that it is only by luck and fast-thinking that we have avoided such a fate. Surviving these encounters has given us invaluable observational data, and I now feel that we better understand how organisms locate prey, and how carbon dioxide plays a role in photosynthesis and respiration. Therefore it is imperative that we find an alternative source of fuel that when burned, won’t smell to the lions, tigers, and bears of the microcosm like the sound of a dinner bell!

0940 hours…

I have just announced my new directive to the crew, and I am pleased to report that they are wasting no time seeking a solution. There is a general consensus that the only way to produce heat without a carbon waste product is to fashion a closed system requiring little more than sunlight.

“Barron,” says Lyra to our engine master, “we are already raising several of those green photosynthetic algae for oxygen. There must be a way to convert the starch bodies they produce into a clean fuel.”

“And starch, like sugar, is made up of carbon molecule chains. You might be onto something there,” rumbles Barron. “Not bad for a biologist,” he adds with a wink.

Deep in thought Lyra ignores the jest. “Carbohydrates,” she says with precision, as if to one of her students back at Cornell. “But how to convert it to a more efficient, high-energy fuel?”

“That’s the question,” I insert. “Sounds like we have promising start. Please have plans and proposals on my desk for review by first bell tomorrow.”

With affirmations from each, Barron and Lyra disappear through the companionway.

I turn to Gyro and instruct him to find us a way free of the aquatic weed forest and the perils therein. “And keep us out of the shadows,” I add. Those flatworms don’t like sunlight, and may be hiding on the underside of these elodea leaves. Best speed, helmsman.”

“Aye sir,” answers Gyro, then relays the message for all hands to take their stations.

1015 hours…

The ship rocks gently to port, then to starboard, as Gyro weaves a path through the monstrous plant stems, ever closer to the deeper pond region where the aquatic jungle gives way to the open water. My awareness is keen and my apprehension remains high as long there is danger of encountering another predator of the weedy shallows, but outside, the forest is beginning to thin, and my concerns along with it.

At our current cruising depth, about twenty centimeters, sunlight from the surface is increasing. Green microorganisms streak past the ship. Through the panes of the observation dome I watch the enormous trunks and branches of the aquatic weeds pass astern, every verdant surface abuzz with microbial life. Larger organisms, so distant as to be discernible only as blurry shadows, dart in and out of awareness.

We are almost clear of the forest, almost free from the worry over monsters, when the hand railing slams backwards into my mid section. The panes of the observation dome skew suddenly to starboard as the outside world tilts on its ear. Cyclops comes to an unceremonious stop.

Metal groans. A complaint of our engine vibrates up from below decks. Gripping the rail to keep myself from tumbling across the pilothouse, I scan our surroundings to fathom some inkling as to what has interrupted our escape from the weed forest. It is as the aquatic jungle refuses to let us go.

Before I am able to cast a whispered curse at these perilous weedy shallows, a fleeting shadow of a tendril passes over the watery light above us.

Lyra stumbles from the companionway looking like her trip up from the lower deck laboratory was unusually difficult. “What happened?” she shouts over the protest of iron and wood.

“I haven’t a clue, but it’s like we ran into a wall, or a net,” announces Gyro. “And now we’re stuck.”

“Let’s try to break free,” I tell Gyro. “Ahead, half speed.”

“Answering ahead, half speed,” acknowledges Gyro, then pulls the lever on the engine telegraph.

The deck slips beneath my feet as the ship lurches forward for a breath – then stops.

“It’s like we’re trapped,” declares a frustrated Gyro.

“That’s exactly what it is,” states Lyra from the aft window of the observation dome. “And now I know exactly what has us trapped. Look!”

I turn my gaze to the aft panes. Beyond Cyclops’ tail assembly, a mouth surrounded by six tentacles looms far too close for comfort. Four of those limbs are now wrapped tight around the hull of our ship, and are pulling it closer and closer toward that ring-shaped mouth.

“What is it?” I ask.

“That,” explains Lyra, pointing, “is Hydra, first identified by Carl Linnaeus, father of modern scientific taxonomy, in 1758. And we are in serious trouble.”

As if to emphasize her warning, the hydra’s tentacles tug decisively on the ship. All hands braced themselves as Cyclops lurches half a ship’s length toward the animal’s sphincter-like maw.

“Let’s try again,” I announce, then into the voice pipe I call down to the engine room: “Barron, we are going to try pulling free of the hydra’s grip. We will need as much power as your boiler can muster, mister.”

“All ready down here,” came the engine master’s voice. We are at full steam pressure.”

“Ahead, full!” I announce.

For a moment I can feel momentum pressing me backwards as the sturdy ship drives forward, then a sudden braking as the hydra’s arms reach full extension and responds by pulling us back towards the animal’s mouth, now closer than ever.

“Barron, more power!” – I bark into the voice pipe. But I know that our engine is already laboring as hard as it is able.

Barron’s basso booms back. “The boiler is at critical, skipper. Any more of this and boiler will blow and take the back half of the ship with it.”

I reluctantly turn to Gyro, nod, and watch him ease the engine telegraph level back to half speed. The hydra’s tentacles pull us a full ship’s-length closer to its mouth.

“Jonathan,” offers Lyra, “the hydra is a very simple animal. No muscles, just a network of nerves giving it the ability to retract its tentacles to pull prey into its mouth. Maybe a simple jolt of electricity would confuse its nerve net and make it release us.”

“Get below and help Barron wire the dynamo to the outer hull,” I answer. “Hurry!”

“Skipper,” says Gyro, “if this doesn’t work…”

“If this doesn’t work,” I say, “then we are going to get an amazing view of the inside of a hydra’s gut.” As I speak these words, I have no idea of how prophetic they will turn out to be.

1030 hours…

The animal has rotated the Cyclops so that we are now being pulled headfirst toward its mouth. We stare helplessly down the gullet of the hydra, namesake of the many-headed serpent of ancient Greek mythology, a fictional beast that is no more frightening that the real one we currently face. With its next contraction, the monster will pull us into its craw, which even now, is stretching wide to accommodate Cyclops and her crew.

Lyra appears in the pilothouse entranceway, is stunned by the looming nearness of the monster, shakes herself from the momentary shock, then shouts: “It’s ready! Throw the switch!”

“Now, Barron, now!” I boom into the voice pipe. “Contact!”

With the zap of electrical current, the lights of the pilothouse dim. Ozone stings my nostrils. Outside, strings of wavy lightning do a worm-like dance across the hull. The hydra’s tentacles maintain their coiling grip for a count of one, two, three…and just when I start to accept that our plan has failed, the tendrils loosen, jerk back from the ship, leaving Cyclops drifting freely.

“It worked!” celebrates Lyra.

“Full reverse,” I tell Gyro, “and keep us clear of those tentacles!”

1130 hours…

Hiding beneath a aquatic plant leaf we observe the hydra, now safely beyond the reach of its tentacles. There is so much we do not know about this monster. We may not have another opportunity like this one for detailed observation. Closer magnification through my telescope reveals some unusual movement on the creature’s skin.

Then we see them – single-celled organisms cover the hydra! These disc-shaped single-celled organisms are ciliates, adapted for living on the hydra’s skin. They use their cilia to create feeding currents for pulling in bits of food, and for walking and hanging onto the hydra.

Lyra postulates that these single-celled partners scavenge bits of food captured by the simple animal. “This helps to keep the hydra free of pesky bacteria. Quite a beneficial arrangement if you think about it. In exchange, the hydra provides its tiny guests a home safe from other predators.”

How, we wonder, does a baby hydra become home to these partners? Which begs the question: where do baby hydras come from?

1215 hours…

What luck! We have just seen a nearby hydra capture a red copepod. The crustacean’s battle to escape hydra’s tentacles is short-lived. The unfortunate copepod struggles for a moment, then becomes still.

“Watch carefully,” says Lyra. “Hydra’s tentacles have a stunning effect on the copepod. They are lined with stinging cells! Like other animals in this family, like the jellyfish and sea anemone, those stinging cells inject the captured animal with a paralyzing agent. Luckily the iron hull protected us during our close call.“

We gaze upon the drama with open-mouthed fascination as the utterly immobile copepod is drawn into the hydra’s mouth…alive.

“Jonathan,” shouts Lyra, spinning away from the observation glass. “This is the moment we’ve been waiting for! We have a chance to observe the digestive process from the inside!”

“What are you suggesting,” I inquire with no small degree of apprehension.

Lyra suggests a daring mission, bold even by her usual standards of recklessness, but I listen with interest. “I’ll take the diving bell, and anchor it to the copepod’s carapace, and get a free ride right down into the hydra’s gut!” she explains with unbridled glee.

“Oh, nothing crazy about that idea,” mutters Gyro.

“It’ll be perfectly safe,” Lyra quickly adds after seeing the scowl forming on my face. “The diving bell will stay tethered to Cyclops. If there is any trouble, just pull me out!”

I have to admit: this was an unprecedented opportunity to observe how the hydra digests its copepod dinner. I know that the diving bell is a sturdy vessel, so I grant permission for this bold venture.

1330 hours…

It took Barron the better part of an hour to equip the diving bell with the necessary equipment for Lyra to effectively monitor conditions inside the hydra’s gut.

Now we watch with with no small measure of uneasiness as the hydra completes its devouring of the live copepod – and anchored to it, our diving bell with Lyra tucked inside.

Day 13: 1345 hours…

Excerpt from Naturalist’s Log…

What an incredible opportunity! Surrounded by the safety of the diving bell, I am now inside the hydra’s gut! Following the complete engulfment of the copepod into the hydra’s gullet, I have released the anchor hooks so that the diving bell is now drifting freely within the predator’s stomach. Through the portholes I can clearly see cells lining the hydra’s stomach produce a caustic soup of digestive chemicals and enzymes. The crustacean is beginning to dissolve.

My litmus-o-meter is reading a rapid rise in hydrogen ions outside, indicating that acid is building up quickly in the hydra’s stomach. I believe that the stomach lining excretes acid, which digests the meal. As the crustacean’s soft tissue breaks down, its basic molecular nutrients are absorbed into the gut lining, completing the process of digestion.

But there is a problem for the hydra: the copepod’s protective shell is not digestible. How does hydra manage the indigestible exoskeleton?

Further observation into this digestive dilemma is cut short when the diving bell’s chemical alarm rings! The hydra’s stomach acid is beginning to dissolve the bell’s hatch seals (made of frog slime) – and if it does, it will digest me as well!

Day 13: 1430 hours…

“She is signaling!” calls out Gyro.

Just a moment earlier we were observing Lyra’s progress from the Cyclops. The diving bell was clearly visible through the thin dermal layers of the hydra, the copepod dissolving before our very eyes, and then Lyra’s semaphoric flash signaling an emergency of some kind.

I restrain from announcing that “I knew this was going to happen.”

“Pull her out of there – but gently,” I instruct Gyro.

Cyclops inches forward, slowly taking up the slack in the tethering cable. In a moment the cable becomes taut, but fails to pull the diving bell out of the beast’s throat.

“It won’t let her go!” exclaims Gyro. “We have to get her out of there. We need more power!”

“If we pull harder,” I reason aloud, “the cable will snap and Lyra will be digested along with the copepod. No Gyro, I think the hydra itself will come to our aid.”

Gyro gives me a puzzled expression.

“I don’t know why I didn’t see it before,” I muse. “The hydra’s entire digestive system is quite simply a mouth connected to a sack. And, to put it delicately, there are no other openings – it is, so to speak, a sack, instead of a tube. Therefore, it is safe to assume that whatever goes in, and cannot be digested, must come back out…”

“…the same way!” shouts my exuberant steersman.

“Precisely,” I tell him with a friendly clap on the shoulder. “I will make an anatomist of you yet!”

“And here she comes!” heralds Gyro.

Before our eyes, the hydra disgorges the now chemically scoured shell of the digested copepod, and the diving bell with it.

1500 hours…

Minutes later, Lyra is safely aboard the Cyclops. She comes to call in my small study where I am rendering the hydra’s capture of the copepod in pen and ink.

“Well, Jonathan,” she says with a sobriety not normally heard in my young naturalist’s usually chipper enthusiasm, “I was storing the observation logs from the diving bell and realized that we have now completed nearly every imperative on our mission check list.”

“And is that not cause for celebration? I believe we still have a couple bottles of that very smooth Kentucky sour mash.”

“I’ll tell the men,” she said, her eyes distant.

“Is everything all right?” I ask softly.

“I wasn’t ready… didn’t expect to feel… I guess I am saying that I’m going to miss this,” she says, forcing a brief smile. I know what she means. The micro world, despite all its perils, has become our world – and the Cyclops our traveling home within it. Leaving behind so much beauty and life is difficult to accept. “I’ll fetch the bourbon,” she adds, leaves me alone in my study, closing the door behind her.

I turn to the porthole above my tiny writing desk. I press my nose to the thick cool glass. The deep infinite of immeasurable liquid blue-green-amber stretches to an impossible horizon… and I feel like leaving it will shred my heart to tatters.