Thank you for your detailed response as well, it's always heartening to see people chipping at these problems. FWIW I've met plenty of crackpots and you are not one of them. You become a crackpot when you can't tell the difference between what is true and what you want to be true, not when your ideas are "out there".

Regarding your experiment with the fish, I suspect this is a difference in your environment, as you alluded to. I'm out here in the desert, and it is sunny and it is hot, and if you're maintaining a low evaporation rate there's no where for that heat to go. Algae don't usually mind though. If you deploy a tube out here it'll only be so long until it gets warped and won't accept a pig (basically a plug that moves along a pipeline & cleans the sides), so I'm very interested in this idea of having the fish clean the tube. But I suspect that the same technique would go belly-up for me, pun fully intended.

I completely agree with your evolutionary approach and with using ecosystems that are already functioning. I did the desert equivalent and found my attached growth culture under a rock.

I was not aware of Living Machine but thanks for pointing it out. I think a lot about a similar concept called Algae Turf Scrubbers (http://algalturfscrubber.com/) (also trademarked), which mimic coral reefs.

You clearly have put a lot of thought into this so I hope I'm not rehashing ideas you've already dismissed, but here it goes.

You may want to consider using fungi. They are the matchless experts in breaking down toxic material, and my inkling is that they will be the ones to crack the problem of digesting plastics. Some organisms have started to do this already. Fungi have the ability to learn and adapt as individuals, so they're more friendly to this sort of engineering than most complex lifeforms. Microalgae are of course fantastic because they evolve on human timescales.

Keep in mind that plastics aren't really pure hydrocarbons. It would be very nice if they were. But they'll come with paints and stabilizers and such, and you'll end up with heavy metals and other contamination (I won't pretend to understand the intricacies here). If this ends up in your biomass then it cannot be used for agriculture. Dirty biomass is usually fine for fuel production, however. I'm sure you've thought of this though and that I would see your reasoning if I understood MSO reactors better. What happens to this waste when it leaves your reactor is another big question.

Gas separation is hard. You might consider separating the nitrogen and calling that good. The more conventional approach would be to use a pressure swing absorber but I'm taking the impression you want to use your vortex tube for cooling as well as separation. I've never tried pumping pure CO2 through an algae culture, but I believe it will become toxic at some concentration.

Rather than feeding it to worms, you might consider an anaerobic digester. You'll still produce fertilizer but you'll also be able to capture methane, which you can blend with your H2 and send to a generator instead of a fuel cell. While they have the same problems with shading as aquaponic systems, AD effluents are a very good fertilization ratio for algae. (I'm remembering a lecture here so I don't have a source to cite & don't recall the ratio, I'm afraid.) Another advantage is that they can accept wet biomass, and harvesting is often the most expensive part of the process. The methane could be blended with hydrogen and fed into an off-the-shelf natural gas generator. But I imagine that you did choose fuel cells for a reason. My personal view is that developing technologies are expensive in terms of liability, and that you can only pick a few of them. So if I were you I wouldn't put fuel cells and a novel approach to gas separation in the same design. Of course methane can be converted to hydrogen through steam reformation, or it can also be used in a fuel cell. Maybe you can even put them in the same fuel cell, I don't understand this technology whatsoever.

I've also got some more open ended questions you might find interesting to think about.

Are you planning to do this on a barge or derrick? How will your process effect the chemistry of the ocean around you? How will that effect the marine life around you?

If you're concentrating metal contamination and taking water in from the ocean, can you recovery dissolved metals? Perhaps you can combine this with desalination?

Is there a way your project can help with ocean acidification?

This talk seems to paper over a lot of problems with this system (its one of those "CO2 to methane" systems), as a TED talk does, but it's an interesting idea & related to your problem space.

https://www.youtube.com/watch?v=X-HE4Hfa-OY

You're probably aware but some people are producing hydrogen from algae. Could enhance your yield.

https://en.wikipedia.org/wiki/Biological_hydrogen_production