Evolving Bioreactors

This story was inspired by Ed Young’s post, “With evolutionary rocket fuel, bacteria give peas a chance,” about the ImuABC genes in the symbiotic bacteria found in plant root nodules.  

This is a short science-based fiction.

It had taken Andrew and his team five years to develop the complex web of interconnected glass panels and sleek cylindrical bioreactors that were currently bolted to the exterior walls of their off-the-grid Montana test house.

It ran beautifully through the fall, providing more than enough energy for four adults to call the house a home.  Then the first winter storm hit.  Now they couldnt even keep the lights on for an hour.

“Did all of these panels get tested in the lab before we brought them out to the field?” Andrew had his gloves off and was squatting down in front of one of the lower panels, near a bioreactor.  He had unscrewed the bottom of the bioreactor, where algae collects, and was examining its contents.  Snow crusted his thin beard.

The panels covered the exterior walls, ground to roof.  They were made of two pieces of glass sandwiched together, separated by just a half-inch gap.  That gap was filled with water, algae, and millions of tiny carbon dioxide bubbles that fed the algae.

“They weren’t all filled and tested, if that’s what you are asking,” Cory replied, stamping his boots in the snow to bring feeling to his numb toes.  Cory was the lead genetic engineer on the project, and had just arrived from California after power supplies had dwindled at the Montana house for three straight weeks following the storm. “We did a routine strength test on the panels, and decontaminated them before the install.” Invading bacteria had been an early problem when they designed the system.  Get the wrong bacteria mixed in with the algae and everything in the system dies.  Its a major drawback to a living power source.

So far, no group had successfully powered a building entirely on algae.  But every lab test Andrew’s company ran indicated that their system could do just that. Now they had to prove it was true.

“Well, I would guess the problem is biologic.  The equipment is all functioning fine.  We have two full CO2 tanks, air is moving through the panels, things look clean.  The lines to the bioreactors are not frozen over, and the algae are clearly getting in here,” he paused to screw the bottom back on the bioreactor.  Do you think the algae could have slowed their growth rate?  Or maybe they aren’t storing up enough energy.  Andrew mused, tapped his finger against one of the glass panels as the algae inside did their lazy dance.

The key to success, they had learned, was the algae.  Any number of people could design an efficient bioreactor, and make panels of the right dimension for optimal algal growth.  Hooking it all up, and figuring out how to capture that energy had been no small feat, but they had done it.  Then they naively filled their panels with standard algae and watched as they got the same result as everyone else in the field: not quite enough power.

Enter Cory.  He genetically engineered the algae and tweaked their microenvironment for three solid years.  After rounds of exhaustive testing, elimination of what didn’t work, and reinforcement of what did, he generated their proprietary strain of algae that could store up enough energy, in the form of fats, to sustain a typical household.

Cory crossed his arms and stared at the panels along with Andrew.  The house was working fine when we set it up in July.  I think the snow is doing us in, but I dont know why.

Only one way to figure it out.  Andrew pulled ten tubes out of his jacket pocket and passed half of them to Cory.  You get samples from the west side of the house.  I’ll collect from the south.”

Cory traipsed off through the snow, pulling his gloves off with his teeth.   He knew this algae inside and out, had practically examined it gene-by-gene.  He wondered what was causing this apparent temperature sensitivity.

He plugged a thin length of rubber tubing into a valve in one of the panels and drew off a twenty milliliter sample.  He did the same in four other panels, moving as quickly as his hands would allow in the cold.

Andrew had driven a generator out, for emergency use only, when their power resources started dwindling.  Cory powered it up on his way back inside.

They got to work in the makeshift lab that occupied one of the bedrooms. Cory did a quick nuclear stain and put the algae on a microscope slide.

Peering through the objective lenses, he saw the problem as soon as he had the cells in focus.

“We lost the symbiont,” Cory announced.

They were the first ones to discover how to best grow algae for use in bioreactors.  It was a discovery they had fought tooth-and-nail to patent.  The trick, it turned out, was not in the algae itself.  It was in a symbiotic bacteria.  Cyanobacteria, to be precise.  Algae and cyanbacteria need to be grown together.  It is a mutually beneficial relationship.  The bacteria fixed nitrogen for the algae, which let the algae grow faster.  The algae paid the bacteria back in the form of energy.

“Which algae-bacteria symbiont pair did you use when you seeded the panels?” Andrew asked.

“Y2147.  It’s what we are planning on for commercial use.

Andrew pulled that pair up on his computer.  Cory landed on the Y2147 pair after years of evolving and engineering.  To patent his work, they had to provide a full genomic sequence of both algae and bacteria to the USPTO.  Its very hard to patent living things, but by proving that this was a creation engineered in the laboratory, and never found in nature, they eventually won.

Andrew spent ten minutes quietly poring over data in the spreadsheet on his computer.  He sighed and shook his head.  “I was afraid of this,” he muttered.  Then told Cory, Let’s see what happens if we flush the panels and put A2147 in them.”

“A2147?  That was one of the earliest.  Why would we go that far back? You are talking about throwing out more than three years worth of work.  Y2147 performed better in every test.”

Andrew gave a rueful smile. Sure, in every lab test.  But the lab is not the real world.  The lab is a well-controlled, reproducible environment.  And we now find ourselves in the real world.  Remember the ImuABC genes?”

Of course Cory remembered them.  Those three genes had been the bane of his existence.  They were responsible for some of the sloppiest DNA copying Cory had ever seen.  They made the bacteria unpatentable because they changed so fast.

In nature, ImuABC made the cyanobacteria extraordinarily successful.  They evolved in mere days to coexist in a successful symbiotic relationship, and could quickly adapt to living with many different species.  Cory deliberately axed those genes so that he could be in control.  It was the move that decisively won their legal battles.

“The ImuABC genes get turned on whenever the bacteria are stressed.  Apparently winter is kind of stressful, because they are all dead.” Andrew said.

You want to let the bacteria evolve, to adapt to the real world?  Cory sat down on a nearby chair to mull this over.  He shook his head.  They will just keep evolving, though.  We cant patent that.  I didnt realize these bacteria would be so temperature sensitive.  I can fix this.  I can insert a few genes to deal with different temperatures.  It will take me a month, tops.

But there will always be something, right?  Were setting this system up for failure by not letting it evolve.  We are ignoring nature’s most robust adaptation.  Lets get the ImuABC-containing strain in the panels, see how the system performs.  I bet it will be back to full capacity in a few weeks.

No.  That idea destroys our business model.  We have to sell something patentable.  You know that.”  Cory thrummed his fingers against his leg.  Realizing the importance of the bacteria was a major breakthrough.  But could they improve on nature and engineer something that was more robust?  They needed those bacteria for one specific purpose: nitrogen fixation.  “We need to evolve the bacteria out of our system.”

Andrew raised an eyebrow.

Cory got out a piece of paper and started drawing out the relationship between the algae, the cyanobacteria, and the bioreactors in their current system.

The algae need sunlight and carbon dioxide to make energy.  They give some of that energy to the cyanobacteria, in exchange for nitrogen.  We take the rest of the energy and power the house, he was laying his idea out in broad strokes.  “We only need the bacteria for the nitrogen, right?

“As far as we know.” Andrew was always cautious when making assumptions about how living things work.

What if we designed a bioreactor for each panel, now Cory was drawing a panel, and another rectangle the of same size to fit inside.  that lets us eliminate the cyanobacteria?  In their place, we make a film of proteins that can fix nitrogen for the algae, and take energy in exchange.  Even better, we can capture that energy to power the house.  Of course, we’ll still use the algae to power the house, too.  We would waste nothing.

You’re suggesting that we take only the parts we need from the cyanobacteria and build them into our bioreactor? asked Andrew.

Exactly.  We would blur the life-machine boundary if this works.  And we can engineer the algae to work perfectly with this system.  No one is doing anything like this, Andrew.”

Excited, Cory began to make a list of all the proteins they would need for nitrogen fixation and energy capture.  This bioreactor would be the product of millions of years of evolution.

His mind wandered to what this could mean for the future of machines if it worked.  They could pick and choose proteins and subcellular machinery from bacteria, right on up the evolutionary chain.  The next generation of machines could emulate any biological function by drawing on life, itself.

“Would it be alive?” Andrew asked.

Cory’s knee-jerk reaction was “no.”  But as his list of proteins grew, he began to wonder the same thing.


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