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Chemical Biology

Rewiring Plankton. And Reality.

OK, the “Silicon Valley Meets Biotech” subject has come up around here numerous times, most recently here, about a startup out of YCombinator called Verge Genomics. But several people have called my attention to this proposal over at (yes) YCombinator, so by gosh, it’s coming up again. Because this is just too much to believe.

It’s not strictly biopharma – this is a “request for a startup” to take a look at engineering plankton for better carbon sequestration. That’s not an insane idea per se, although it’s certainly a big risky one, but the worldview behind the proposal is perhaps the purest example of what I’ve called the “Silicon Valley Sunglasses” effect: the way that writing code and building hardware can give a person the illusion that everything else works the same way, that physical reality is there for you to re-engineer if you’re just smart enough and fast enough.

If we could figure out a way to solve phytoplankton’s mineral requirements, the entire ocean could become a powerful carbon sink, as well as a new frontier for economic growth. There are two ways of solving this problem – either get the missing minerals where they are needed (fertilization) or eliminate the need for minerals all together. We will start with what’s possible today and wade into what some might consider sci-fi. Either way, current biology won’t do the trick.

True. So far we are not in disagreement. The site starts off by talking about engineering phytoplankton to form “megastructures” to pull up more nutrients from the sea bed. How does one do that? Why, it’s just programming, you know:

When people talk about programming biology, they usually mean re-writing DNA to add some new feature. In this context, when we are talking about programming biology, we mean actually writing a complex, responsive biological programs with if/else statements, inputs and outputs that respond to a variety of different signals etc. We imagine something like a biological or biochemical Turing machine/computer instantiated at the level of a microbial cell. Actual programming. We imagine something like a more engineering or applications-oriented version of systems biology, where something approximating a multi-line python script could be instantiated in an organism.

That is actually what synthetic biology would like to achieve, and I agree that amazing things could be done when we get to that point. But no one is anywhere near it. Not within a million miles. We can hijack the natural systems inside cells, up to a point, and use the routines and structures that a billion or two years of evolution have left us. But there is no way to build a complex architecture from scratch. We don’t know how the ones we have work, and we don’t know how to make another that works, either. That paragraph is getting close to the Platonic ideal of the Valley view of how to do biology. I will leave for the reader to examine the attitude that we know enough about ecological systems to assume that turning plankton loose to make completely new megastructures in the ocean will work out fine because we clearly can work out the consequences beforehand.

But there’s more. You may be wondering about that earlier “eliminate the need for minerals” part, since those minerals are things like iron that are essential components of key enzymes. Or are they?

As we mentioned, mineral limitations are a major problem for using phytoplankton as a CDR tool. Many of these minerals are metals. These metals are used in various enzymes called metalloenzymes. All organisms have metalloenzymes. This may be leftover from life’s early evolution and may not necessarily be a necessity for biochemistry. For examples, the organisms Borrelia burgdorferi (lyme disease) and Lactobacillus plantarum (yogurt) have eliminated all iron from their metalloenzymes and instead use a different metal called manganese. This suggests that there is some flexibility with how metalloenzymes do their job. It might be possible to eliminate metals from these metalloenzymes all together.

Well. Some wheeled vehicles have spokes, while others have solid wheels, suggesting that it might be possible to eliminate wheels altogether and have cars that just sort of skid along the ground. You’ll get further in a wheel-less Tesla than you will with cells that have eliminated their requirements for all metal centers, I can tell you that. I don’t know quite where to start with this, only to suggest that this is the sort of idea that can only occur to a person who doesn’t actually know much chemistry. The reactivity of metal centers as they switch oxidation states would seem to be a very difficult thing to replicate by other means. I’m having trouble even imagining the beginnings of an idea, and honestly, I have a pretty vivid imagination.

Here’s the closest thing I can find to realism:

All of these approaches come with significant financial and technical risks. Even if all the technology was developed, it is entirely possible that the solution might not perform as expected. More modeling is required to get a higher resolution answer on this. In addition, all of these approaches rely on the release of genetically engineered phytoplankton into the ocean. Some folks might not be too keen on that idea.

That section does go on to mention that many of these things are currently beyond our abilities, but I detect a certain amount of “Well yeah, but the iPhone used to be beyond our abilities, too!” in there. What I really like is the idea that you can model your way to an answer for questions like these – that’s also an extremely revealing look into the worldview of the folks who wrote this. This is a sort of digital fundamentalism: everything comes back to 1s and 0s, because that’s all there is. Philosophically, would that be “Binism” instead of Monism? In the beginning was the bit, and it was capable of being a 1 or a 0, and Flipping of the Bit was the morning and evening of the first day? Hack the genome, hack biochemistry, hack ecology, hack the laws of chemistry and physics. We are not yet as gods, not even out in Mountain View.



87 comments on “Rewiring Plankton. And Reality.”

  1. anonymous says:

    It may sound eerie and juvenile. The whole topic gives me the impression of the Alien movies –David, the A.I android, saunters in the music of Wagner ( the Entry of A.I. Gods into Valhalal) — Alien: Prometheus and Alien: Covenant.

  2. Marcus Theory says:

    This reminds me of the Craft sequence that I’ve been really enjoying recently.

    “Two things are happening at once”: our planet is dying, and Silicon Valley has money to burn!

  3. Hap says:

    1) Apparently, the only thing we learn from history is that we don’t learn from history, or maybe that “There’s a fool born every minute.” and “A fool and his money are soon parted.”

    2) Even if it were a pure computing system, could you be sure of predicting the consequences? I thought Godel kind of shot a large hole in omniscience about formal systems.

    3) I didn’t think the people as gods thing tended to work real well, although I guess it works well for the would-be gods (at least for a little while), and that’s all that matters?

    1. Ben Mills says:

      The reasons it hard to predict the consequences in his case come more from complexity theory than Godel, who showed that there would always be true statements that could not be proven.

    2. Pete says:

      Just following up the pure-programming idea: If it was a pure undisturbed computing system, you could be sure what happens; just run it in simulation, speeded up a thousand times, for a year, and you’re happy nothing bad is coming even in the relatively long term (this is, by the way, about as far past the current possibilities of computers as the proposal is past the current limits of biotech).

      But this is a system which receives huge amounts of external inputs and the outcome is dependent on these. In principle you are still able to simulate, but this time you’d need to simulate all the possible external inputs. That’s not even remotely possible – just to write down every time the simulation worked out well would need more particles than in the known universe.

      The other way to do it would be to try to prove that the system cannot have bad results within a given time (say 1000 years). Neither Goedel’s theorem nor Turing’s theorem (which is the one that actually relates to computation) says anything about whether this is possible, because in principle it is. But the proof might get a bit long…

      In any case, any half-decent computer scientist would tell you that the answer will certainly be that bad things can happen, and given half an hour they would probably figure out how.

  4. Isidore says:

    There’s a Monty Python skit, a spoof of TV shows, called “How to do it”. Here’s an excerpt:

    Alan: Well, last week we showed you how to be a gynaecologist. And this week on ‘How to Do It’ we’re going to learn how to play the flute, how to split the atom, how to construct box girder bridges and how to irrigate the Sahara and make vast new areas cultivatable, but first, here’s Jackie to tell you how to rid the world of all known diseases.
    Jackie: Hello Alan.
    Alan: Hello Jackie.
    Jackie: Well, first of all become a doctor and discover a marvelous cure for something, and then, when the medical world really starts to take notice of you, you can jolly well tell them what to do and make sure they get everything right so there’ll never be diseases any more.
    Alan: Thanks Jackie, that was great.
    Noel: Fantastic.
    Alan: Now, how to play the flute. (picking up a flute) Well you blow in one end and move your fingers up and down the outside.
    Noel: Great Alan. Well, next week we’ll be showing you how black and white people can live together in peace and harmony, and Alan will be over in Moscow showing you how to reconcile the Russians and the Chinese. Til then, cheerio.

    1. Dr. Manhattan says:

      You beat me to it. I was going to insert the following:
      “We imagine something ….where something approximating a multi-line (Monty) Python script could be instantiated in an organism.”

      As a (micro)biologist, I agree wholeheartedly with Derek. We are far, far away from being able to accomplish this in any biological system. And predicting the consequences if you could somehow accomplish this??

      1. Emjeff says:

        That’s the other thought I had – this crowd probably won’t eat anything that is not certified non-GMO, but they are willing to unleash genetically-altered plankton into the ocean?

        1. Nat says:

          The reflexively anti-GMO crowd tend to not be people working in the tech industry.

          1. Valley View says:

            You would think, but they are surprisingly anti-vaccination…

      2. lynn says:

        Yup – far from this. I’m just imagining some “megastructure” encoded within a bacterium [OK, then, not so mega]. I would think mutations leading to improved fitness [less energy expenditure] would lead to its destruction in short order.

  5. myma says:

    Just the other day, we were talking at the dinner table about horseshoe crabs and their blue blood due to having copper instead of iron. But still a metal there, not nothing.

    1. Ben Mills says:

      The blue blood of the lowly horseshoe crab is such a perfect example of something we can quite easily harvest from nature yet can’t even dream of synthesizing ourselves!

  6. Emjeff says:

    Let me guess; the prospectus for this will feature a bunch of confident, Silicon-Valley types with their arms folded , looking confidently into the camera. Some will have dropped out of UCSF/Berkeley/Stanford to join this amazing venture. And the money will come pouring in…

    1. SirWired says:

      Well, Elizabeth Holmes is available, and this wouldn’t be an industry she’s legally barred from joining, though she can’t be in charge of the joint for a while.

      1. Mad Chemist says:

        Maybe they’ll let her work from prison.

  7. Anonymous says:

    There is one quote from the proposal that sums up how little they actually know about biology:

    “While most other ideas involve a lot of scientific research, this idea is foremost an engineering/infrastructure problem (though engineering a phytoplankton capable of driving CO2 into bioplastics will require development).”

    Right. Good luck with that.

    1. Ben Mills says:

      Wel in their defense humans did spend a few centuries jumping off cliffs before we learned how to fly.

  8. SirWired says:

    What this guy is asking for would be like writing a proposal for the development of the iPhone in a world without the integrated circuit or the LCD.

    There’s just so far between “here” and “there”, with a whole lot of fundamental basic science and engineering that doesn’t even exist, that an entire industry could be built on just a small part of the pre-requisites for the final solution.

    1. zero says:

      Ask these people how hard it would be to write a port of Linux that runs natively inside Windows 3.11 using only assembly code on a hardware architecture that randomly reassigns the function of various commands at random times. They get 4k of magnetic core memory, unlimited drum storage and a processor with 65534 cores (but no cache) running at 1 Hz.

      1. Some idiot says:

        Perfect! Thank you!!! 🙂

      2. myma says:

        on punch cards

        1. Some idiot says:

          Even better…! (-:

      3. Adam Brunet says:


  9. ScientistSailor says:

    If you look at the other proposals on their site, this one does not seem to be an outlier…

  10. polyalanine says:

    If the organisms could do without the metals would not they already have a tremendous advantage? The selection pressure for what is proposed seems plenty strong enough already at least for carbon sequestration.

    1. Hap says:

      If you can do it, then yes, but there’s already a lot of organocatalysis in the enzyme world, and that would likely be the replacement for metal chemistry. Metals are likely more stable to redox manipulation, as well, so replacing a metal with an organic cofactor is possible but really hard (organic radical ions and cations are susceptible to decomposition if they’re reactive enough to do interesting stuff).

      Not done doesn’t mean impossible, but since lots of things are mutating for the purpose of getting ahead, this likely is being tried – either organisms are stuck in a historical sink (they can’t get there from here) or it’s really hard to evolve a metal-free enzyme to do currently metal-mediated biochemistry. The selective advantage would also mean that you’d want to be sort of careful about what you get – don’t call what you can’t put on hold.

  11. Bob says:

    Some wheeled vehicles have spokes, while others have solid wheels, suggesting that it might be possible to eliminate wheels altogether and have cars that just sort of skid along the ground.


  12. Peter S. Shenkin says:

    They are building a Touring Machine: a device you carry around in an attache case when you go on tour to visit investors. When activated, the machine tricks them into giving you money.

  13. __anon says:

    They also want to build 1000 nuclear powered ships, which is only 5x the number that currently exist in the world, *and* think they can do it for $10M each, which barely buys a conventional container ship.

  14. SP says:

    One problem with the SV approach is that they take criticism as a sign that they’re special, unique, you might say Thinking Different. Look at all these commenters on a chemistry blog saying how impossible our idea is- well that’s a 20th century mindset, it just shows that we’re Thinking Outside the Box and can do things everyone else says is impossible!

    1. Postdoc says:

      Exactly! After that you just have to wait for the omnipresent, misattributed Gandhi quote about how people first laugh at you and then you win, or that sort of nonsense…

  15. Some Commenter says:

    Yes, and if we could just figure out that affordable cold fusion thing and antigravity we could do a lot of cool things as well. Just imagine! Not even the sky is our limit, with the aid of your investor funding…

    1. Skeptical says:

      In fact, if we could just get Mr Fusion working, we wouldn’t need to muck about with plankton and biotech. Free energy for everyone. We’ll just suck that pesky carbon right out of the air!

  16. Hap says:

    Maybe this is a new level of Dunning-Kreuger, with extra arrogance? They appear to be solidly in the “don’t know what we don’t know” square of the Rumsfeld hierarchy.

    Alternatively, maybe it’s just a bigger version of “Anything is easy if you don’t have to do it yourself.” Someone (else) will figure out the pieces, and then they can come along to put them together and cash the checks. That’s a somewhat more common affliction.

    1. eub says:

      This is classic “bad software architect” behavior. In software development you get some people who have years ago evolved past the necessity to build anything themselves, and then past the necessity of concrete well-founded designs for others to implement. They have reached the heaven of pure software architecture, and the funny thing is, in Dunning-Kruger style, they often don’t realize as programmers they’ve been dead for ten years. (I know because I interview them for programming positions after they get laid off.)

      They reach this point where they can just spin out some airy technical blather, and someone else will implement it, or else someone else won’t but that’s not their fault. Their corporate environment enables this behavior like a soft forgiving womb, until somebody very senior finds a way to cut them off. But then the better ones of this class will find a way to deploy their skills in a startup — where there’s no way to fail yet, and they can provide real practical value by convincing money men to give you money that you might even use to ‘pivot’ into something useful and unrelated.

      Or, here, a way to deploy their skills in a whole different technical world where their peers can’t check their work. Derek can, but they don’t hear from Derek.

    2. Some Dude says:

      Is misspelling Dunning-Kruger part of the Dunning-Kruger effect?

      1. Hap says:

        Maybe that’s the Donning-Kroogur Effect.

  17. C says:

    Driving dynamic growth of the word “instantiated” will be their pivot

  18. Chem2Bio says:

    One thing that strikes me here is the lack of concern about what if they succeeded? I understand that the request is preposterous (replacing the need for trace minerals in life), but even some form of forced plankton bloom is not exactly a good thing. We would reduce CO2 (potentially too much) at the cost of what? Algal and plankton blooms are ecological disasters when they naturally occur.
    This line of thinking (or lack thereof) feels reminiscent of tech companies building other technologies like social media that are really impressive, but have had major negative externalities that were not thought through.

    1. Hap says:

      To be fair, tech people aren’t the only ones with a lack of ability to foresee consequences.

  19. myma says:

    I know! How about we just plant plants. Plants are an excellent CO2 sink.

  20. Wavefunction says:

    Ignorance of the difference between science and engineering strikes again.

  21. Earl Boebert says:

    Reminds of the time I did a top-down systems design of an antigravity machine. It was all there, control system, operator interface, reactor power unit, gravity vector reversal module. But I did it long ago, when such things were universally recognized as a joke. If I did it today somebody might throw money at it. Hmmm…

    1. Ian Malone says:

      You just need to define the API.

  22. MoMo says:

    I agree with Chem2Bio. What if they create a FrankenPlankton that sucks all the CO2 out of the atmosphere? Plants will then die off leaving us all to whither along with them.

    These SV types cant even keep servers from breaking and our enemies from hacking us and our political parties. You cant even release GMOs unless you are Monsanto, and even they are having a hard time of it these days, so they tell me.

    But keep spending money SV on your dream-state projects.
    American scientists and researchers and the Economy don’t mind at all, I can assure you.

  23. Ian Malone says:

    They have an excellent understanding of applied natural selection. Natural systems aren’t designed or intended to do something, they just adapt to optimise reproductive success. Similarly, startup pitches might have originally been intended to create successful businesses, but the ones who succeed are the best, not at running a business or achieving a vision in their prospectus, but at separating investors from money. (I suppose they might have a vision of that…)

  24. John Wayne says:

    Huh. If we could draw infinite CO2 from the air and make anything I would produce food, plastic, lubricants, fuels, and feedstocks for other industries.

    Or, you could dump it into the ocean. Different strokes I guess.

  25. Just askin' says:

    Isn’t it just easier to make either a battery that was 5x as effective or that nasty old room-temperature semiconductor people have been looking for for decades? No mucking about with squishy, wet things…

  26. Paul says:

    surely this counts as “Things I won’t work with”… by which I mean Silicon Valley startups?

  27. Ffgjjjgdddfggggvvc says:

    Things I won’t work with……my PIs startup. Funny story, my PI from an unnamed San Diego institute actively discouraged us to submit patents during grad school and then developed them into a startup. He sued us to keep us quiet with a large San Diego law firm.

    1. Anonymous says:

      PI = RAH, per chance?

      1. Butane Research Institute says:

        My money is on BFC III or DLB

  28. Joe Hazelwood says:


    (cue Sam Cooke – shortened verse…)

    Don’t know much about biology
    Don’t know much about chemistry
    Don’t know much about oceanography

    And I know that if you pay me to
    What a wonderful world it would be

  29. Chris Phoenix says:

    “Some wheeled vehicles have spokes, while others have solid wheels, suggesting that it might be possible to eliminate wheels altogether and have cars that just sort of skid along the ground. You’ll get further in a wheel-less Tesla…”

    Ironically, Elon Musk’s “hyperloop” design does not run on wheels. His original proposal had air bearings, but it looks like it’s moving in the direction of maglev.

    “In the beginning was the bit, and it was capable of being a 1 or a 0, and Flipping of the Bit was the morning and evening of the first day?”

    Ironically, there’s reason to think that evolution can’t work without a digital information substrate – analog can’t make perfect copies, so designs would devolve faster than they improved. (As Pirsig said, you have to have static structures to latch what your Dynamic Quality comes up with.)

    Neither of these, of course, provides any support for the proposal being criticized here. (In the software industry, we call that kind of thing “vaporware.”) And neither of these is meant to criticize Derek – his points and analogies are spot-on. I’m just amused by the coincidence of outside-the-box semi-counterexamples.

  30. eub says:

    You’ve forgetting quantum dots! Who needs metal ions when we can program our own atoms nowadays!

    Oooh, and what happened to those vibrational fruitbats? These guys could get together with those guys and use the vibrational signatures of iron to do the work.

  31. Sue says:

    Throughout the history of science, there’s a bunch of dudes standing back, arms folded, going, “This will never work.” Vast swathes of ocean are devoid of nutrients, primarily iron, that plankton need to bloom. Plankton have reduced greatly in recent decades – their presence in the ocean drives all life there. Seeding iron strategically is a great idea – it’s a plan. What do any of you propose to solve our existential problem? No, please do go on about your computer theories.

    1. Derek Lowe says:

      Interestingly, iron-seeding has already been experimented on, not that there’s a reference that I saw in this proposal to that past work. But they go straight to “massive fleet of vessels”, which is still the sanest part of the whole deal.

    2. Ian Malone says:

      There are real technologies around that can sequester carbon, or produce energy without burning fossil fuels. Making them economically feasible and work at the scale we need is a challenge, hopefully an attainable one, but it will take hard work of the type that frightens off people who just want to write science fiction proposals to get funding for a few years.

      As Derek says, iron seeding is a thing people have tried and can work. There are logistical challenges to solve, and serious environmental problems if you’re going to start doing it at scale. Tackling those, finding a business model that would work and getting it off the ground are real challenges someone could have a shot at.

      That’s not what’s being proposed by these people. They are suggesting from the ground up genetically engineering plankton in ways nobody has the faintest idea how to do, just to get to a point where you face those hard-work problems that real technologies have. Plankton needs iron? No problem, just make plankton that doesn’t. How to get it where you need it? No problem, just tow it around with a massive fleet of ships. How to get the carbon stored permanently? No problem, just program the behaviour of the organism at the genetic level to achieve exactly the results you need. “This technology could be programmed to have some really useful behavior. One side of the massive tube could float towards the sea surface and sprout leaf-like structures, while the other side might sink to the bottom of the ocean and attach itself into the ocean floor, putting out “roots.” We would have essentially built a primitive tree-like entity.”

      That’s a “computer theory”, from the Ocean Phytonplankton people, not anyone here: “In computers we use little switches called transistors. Engineering complex behavior into phytoplankton will require many biological switches that can be combined to create artificial biological behaviors.”

      Already quoted by another commenter, but bears repeating:
      “While most other ideas involve a lot of scientific research, this idea is foremost an engineering/infrastructure problem (though engineering a phytoplankton capable of driving CO2 into bioplastics will require development).”
      They are here passing off an order of magnitude or two change in our understanding of biology and genetics as, “will require development”.

      1. Ian Malone says:

        Though to be fair to them, by the time you get to the “Estimated costs” section, it looks more like a piece of student coursework than a genuine proposal

      2. Sue says:

        I see and agree. The best solution is often the simplest. Like using soil conservation techniques to sequester carbon – zero-till, cover crops, rotational grazing. All of which we could switch to tomorrow – soil has immense sequestration potential.

        1. loupgarous says:

 is a review of various carbon sequestration schemes, including Freeman Dyson’s proposal to use deciduous forests to improve on the 8% of the atmosphere’s carbon dioxide currently captured by trees, planting vast plantations of them, and eventually redesigning the trees to capture CO2 more efficiently.

          The review article takes the best perspective – no one way of sequestering CO2 will answer all objections possible to raise. Several ought to be actively considered.

          1. loupgarous says:

            pardon, I meant “evergreen forests”. Firs, Pines, fast-growing trees.

      3. loupgarous says:

        When I was young, someone proposed making windmills for electrical power on submerged towers (like those supporting navigational beacons in ship channels) off the Gulf Coast. The idea was to ring these with metallic mesh cylinders, connected to the windmills by insulated cables, and to electrochemically cause calcium carbonate to form on the mesh – the lazy man’s way of making reinforced concrete.

        Eventually, one would put more windmills on the towers that formed, and then place piping to exploit the temperature gradient between deeper ocean and the surface within the towers… and generate electrical power that way. I can’t remember whether it was proposed to run cables to shore to capture that power, or make hydrogen electrolytically and compress it for shipment ashore.

        But it seems to me one might capture those gigatonnes of carbon in that way. It wouldn’t be immediate, but it would happen, pursued over a long enough period of time.

        The ecological effects of electrochemical carbon sequestration in carbonate deposits from ocean waters would, of course, have to be studied. But that would take much less time than re-designing plankton, and I’d be willing to bet the ecological harms would be small compared to the potential harms of an entirely new form of plankton made specifically to sequester carbon.

    3. metaphysician says:

      There’s a fairly simple and straight-forward solution to greatly reducing global carbon emissions, that somehow nobody ever seems to watch to acknowledge:

      Build. More. Nuclear. Plants.

      No requirement for inventing entire new technologies. Just a willingness to put aside superstitious dread of radiation.

      1. Druid says:

        I agree with you, subject to some simple and obvious rules like “Don’t build them on earthquake or tsunami zones”. Then integrate them into a combined grid-power and fuel process – make hydrogen or methanol during periods of low demand, to replace fossil fuels. Let nature, natural weathering of rocks, take care of carbon dioxide. All the ideas I have seen here are disturbing (to the environment). As I recall, iron is not the only nutrient in short supply in the sea – nitrogen and phosphorus are also limiting. So, by seeding with iron or artificial plankton which don’t need it, you are likely to further deplete phosphorus and wipe out a lot of life. No phosphorus = no DNA.

      2. loupgarous says:

        Agree as long we abandon the archaic uranium/plutonium rod designs and go to molten salt reactors , which can be made very meltdown resistant (intrinsically safe designs were tested out of Oak Ridge in the 60s-70s) and use much more abundant thorium as fissionable fuel (you’d save U-235 as a neutron source to “warm up” thorium reactors).

        All of natural thorium can be burned in nuclear reactors, not just the 0.7 percent of uranium which is U-235 that requires enrichment to create usable reactor fuel. Fission products that now sit in spent fuel rods near operating reactors (because someone decided to renege on the government’s promise to open Yucca Mountain to store them) can either be burned in molten salt reactors, or chemically separated from the stream of molten salt fuel continuously for much more efficient disposal than replacement and storage of entire spent fuel rod assemblies.

        1. Shazbot says:

          Don’t forget about breeder reactors when mentioning the 0.7% number. If several thousand were built, I’d assume the majority would be breeders of some type.

          1. loupgarous says:

            Not so sure about breeders. The issue there is that they’re machines for making plutonium, so there’s a legitimate concern about a power source that makes weapons-grade fissiles. To be honest, the thorium fuel cycle makes uranium-233, also a fissile, but usually made along with some really nasty gamma-emitters. No one’s going to be separating out U-233 for bombs from irradiated thorium from a power reactor, whistling while he works, unless he’s got the lead windows and waldoes from the old plutonium shop at Rocky Flats and an overpowering death wish.

            There are indications (not just rumors, but DoE documentation and radiochemical evidence in the Columbia River) that DoE’s Hanford plant had a brief production run of relatively “clean” U-233
            in the 1960s-1970s (the reason being its bare crit is as low as plutonium’s, so you can make lighter nuclear devices without all the joy of handling plutonium.

            Using actinides as power sources at all entrains some nuclear weapons proliferation risk. We’re long past shutting the barn door on proliferation, now, so it’s possible to compare the certain ecological harm of relying on carbon fuels for dense energy to a chance of ecological harm if fissiles from actinide nuclear fuel streams are diverted to make nuclear weapons. If we’d done that calculation back in the late 1970s when ERDA/DoE decided to walk away from breeder reactors, it’s possible we’d be closer to lowering global CO2 levels now.

          2. loupgarous says:

            The wikipedia article “Uranium-233” contains the reason why we don’t really need to worry as much about diversion of nuclear weapons-grade fissile from the thorium nuclear fuel cycle as we do about plutonium recycle from uranium-fueled breeder reactors.

            While Pu-240 made in power reactors (including breeders) makes the resulting plutonium less than ideal weapons material (predetonation from internal neutron source limiting efficiency in implosion weapons and totally precluding use in gun-type weapons), the decay chain of U-232 (made from small amounts of Th-230 in natural thorium) immediately produces a number of strong gamma emitters:
            232U (α, 68.9 years)
            228Th (α, 1.9 year)
            224Ra (α, 5.44 MeV, 3.6 day, with a γ of 0.24 MeV)
            220Rn (α, 6.29 MeV, 56 s, with a γ of 0.54 MeV)
            216Po (α, 0.15 s)
            212Pb (β−, 10.64 h)
            212Bi (α, 61 m, 0.78 MeV)
            208Tl (β−, 1.8 MeV, 3 m, with a γ of 2.6 MeV)
            208Pb (stable)

            I flippantly talked about the “lead windows and waldoes” at Rocky Flats, but actually, plutonium was processed at Rocky Flats in glove boxes, because gamma rays weren’t so great a concern there (while Am-241, the big worry in weapons plutonium re-processed at Rocky Flats, is an alpha emitter safely worked in glove boxes, or so they thought).

            The lead windows and/or remote closed-circuit TV and waldoes were used at Hanford while cutting uranium rods up for plutonium production. But the Hanford production runs of U-233 were from “clean” thorium-232, supposedly. Plain old natural thorium, while safe within a molten salt fuel loop in a power reactor, would produce that really hot decay chain workable only with waldoes behind stout walls – not what you could use to make bomb-grade U-233.

            So the thorium fuel cycle guards itself against diversion of fissiles. You’d need a dedicated fissile breeder project to make usable U-233 from thorium, and it’s easier and safer just to make weapons-grade plutonium from uranium. Thus, thorium’s got economic and safety advantages over U-Pu breeder reactors.

  32. Ken says:

    That paragraph is getting close to the Platonic ideal of the Valley view of how to do biology.

    It’s also pretty close to the premise of Greg Bear’s 1983 Hugo-winner, Blood Music. The short story ends with the modified bacteria using humanity for raw materials. Fortunately we’ve learned a lot about software quality since then and won’t make that mistake when programming the plankton.

  33. dipthroat says:

    And I thought my unsuccessful Y Combinator proposal was too far off, too risky to be taken into consideration.
    Instead, it turns out I didn’t go banana crazy enough!

    Let alone, my idea was based on solid science, while this and Verge “business” models seems based mostly on cheap scifi and pseudo/wishful science.

  34. While it is possible that YCombinator would actually throw a few bucks toward someone with a good slide deck along these lines, I suspect that this is largely positioning/marketing.

    YC wants you to know that they are not just funding stupid virtual-reality lolcat social sharing apps, they are Big Thinkers. This helps them raise money, which they will primarily use to fund virtual-reality lolcat social sharing apps.

  35. Anonymous says:

    How about programming plankton or algae to selectively sequester ppt gold (Au) instead of CO2? There may be around 20 million pounds (or tons, depending on which source you choose) of gold in the oceans. $400 B or $770 T (depending on which source you choose). Send out your gold-sucking microbes programmed to return to the nest with their mother lode (or load) of Au.

    Others have already hit on other points. As the plankton suck the CO2 out of the atmosphere (400 ppm, 350, 300, … 100) and we revert to another Ice Age, the coal companies will just crank up production (and prices) to keep the temperature up and agriculture afloat. But the price of plankton will plummet so maybe we’ll just have to learn to enjoy detoxified planktonburgers, planktonflakes cereal, and plankton smoothies. (Yes: humans have been eating plankton for centuries but it is currently a niche market: GNC Spirulina, etc.)

    Derek (and others) had some great analogies, above. I was LOL. Yet, the proposals get funded. I was QQQ.

  36. thedude says:

    “convert CO2 into an ultra-stable carbon sequestration medium”

    that sounds like utter scientific poppycock

    phytoplankton is just a temporary carbon sink that gets rapidly recycled

    that article looks like dumb and dumber made a baby

  37. gippgig says:

    “I’m having trouble even imagining the beginnings of an idea”
    See radical SAM enzymes.
    I think it would almost always be possible to have metal-free substitutes for metalloenzymes but they would often be less (wildly variable how much) active and plankton not requiring metals would be possible but slow growing.
    It is worth noting that particular-nutrient-requiring proteins are known in some cases to have alternates that do not require or require much less of that nutrient, i.e., nitrogen fixation uses Mo but if there’s no Mo there’s an alternative that uses V, and if there’s no V either there’s yet another variant that just uses iron, and there are low-sulfur versions of light harvesting proteins in some cyanobacteria that are expressed under low sulfur conditions.

  38. Jacob Bauer says:

    I am somehow reminded of JBS Haldane’s essay “Daedalus, or, Science and the Future” which was written in 1923. Somewhere in the last third he begins speculating, in a relentlessly optimistic way, about a strain of genetically engineered algae which escapes into the oceans, causes them to partially solidify, and turns them purple (amongst other things).

    1. Derek Lowe says:

      Haldane was a very strange guy. He also wrote what must be the only impassioned pro-chemical-warfare essay ever published (“Callimachus”).

      1. secret sauce says:

        reminds me of Edward Teller and his advocacy for peacetime uses of nuclear weapons (e.g. nuking hurricanes – what could go wrong?)

  39. drsnowboard says:

    What’s in it for the phytoplankton….?

  40. loupgarous says:

    When I was young, there were proposals to electrochemically cause carbonate to form on metal meshes in order to make structures in the oceans. While this also has imponderables – we just don’t know how it’d affect surrounding sea life – it’s almost a benign undertaking compared to creating a recombinant species of plankton and unleashing it on the oceans.

    The first things that occurred to me reading this post were the vast hazards of introducing re-engineered plankton into the oceans, and
    (a) creating new, toxic plankton that might either kill species of fish and cetaceans that eat them or consume fish that eat them (say, plankton that move those crucial nutrient minerals up from the sea bed but retain them in toxic amounts in their bodies)
    (b) creating plankton that out-compete existing plankton that are crucial to fish, cetaceans and other marine organisms as a food source.

    Just as we don’t know everything there is to know about metabolic/biochemical pathways in plankton, we’re probably ignorant to a large degree about how various species of plankton figure in diets of other marine organisms. Necessarily, we’re entirely ignorant about how a recombinant species of plankton might disrupt those food chains.

    Purposefully shifting the number of plankton in the Earth’s oceans in hopes of sequestering CO2 from the atmosphere in gigatonne amounts is a massive alteration of the oceans’ chemistry – their pH balance (since we’re eventually also fooling with dissolved CO2), changing the equilibrium and partial pressure not just of CO2 but likely O2 and other dissolved gases and minerals. The minerals desired to make plankton in general grow and sequester CO2 will also change the oceans’ chemistry, upsetting countless chemical equilibria.

    How will this affect every other living thing in the ocean? We do not know.

    Our experience as the supreme tool-users on the planet ought to have taught bright people like the guys at Ycombinator the hazards of changing environments we don’t understand accidentally.

    It really ought to made them very cautious about changing the ocean environment to change the way it uses carbon dioxide and moving other minerals from the sea bed to where they become available not just to plankton, but other sea life.

    1. The one thing to keep in mind here is that the people at YCombinator are not bright. They are glib, but not bright.

      1. loupgarous says:

        That was, of course, meant facetiously. The objections made to their request for a startup were well-founded and we took fairly little time to comprehensively shoot it down on a variety of grounds.

  41. Anonymous says:

    1. Sometimes, the authors of papers Derek highlights in Pipeline join in the discussion here. Very recently, the MicroED authors, and others added comments. I assume that the YCombinator authors (and reviewers) are aware of Pipeline … but maybe not? How about sending them an invitation to join in?

    2. I don’t see a place for public comments at YC. YC should open up their site to public comments. That would save them the trip over to Pipeline to address many of the points raised here.

    3. Someone above pointed out that P and N also become limiting (Redfield ratio: 106 C:16 N:1 P:0.1-0.001 Fe), as does dioxygen, O2, hence the hypoxic DEAD ZONES in our oceans. (Those blooms can kill off other ocean life.) Not to fear! The YC group should hook up with Felisa Wolfe-Simon (wikipedia) to engineer ARSENIC based lifeforms (arsenate backboned DNA vs phosphate backbones) to scavenge and sequester As and then more CO2. Even tho’ arsenate-DNA is several orders of magnitude less stable than phosphate-DNA, every engineer knows that you can just add more struts, buttresses, or other reinforcements. Write it into the program!

    Attempts to change the preferences of life forms can be very difficult. E.g., even when they thought they were growing GFAJ-1 arsenic bacteria under phosphate free conditions, the bacteria managed to find trace P and utilize it and grow. I can’t access the literature, but some essential nutrients (Zn, Se, …) have been periodically de-essentialized by poor research until it is shown that “pure” reagents contain enough traces of the micronutrients that the organisms will find them and thrive. Some attempts to engineer metal preferences of some metalloenzymes have been undermined by the inability to remove 100% and maintain 0.0% of the original (preferred) metal from the system.

    That said, if YC wants to fund my project to mine ocean gold with engineered plankton, I’m all in. The first task will be to hire a Silicon Valley PR firm to design a logo with happy-faced algae wearing hard hats and carrying nano-pickaxes made from carbon nanotube shafts and nanometal spikeheads.

    4. The conclusions drawn from the ocean fertilization with iron experiments (and volcanoes) are rather mixed. There can be blooms, but they are temporary. The changes in CO2 and O2 don’t persist. Some see the glass half full or better, others see it half empty or worse.

    (5. Pipeline would be much easier (for me 🙂 ) to follow, search, etc. if it was built on forum software instead of blog software. Derek? Science? Pipeliners? Anybody agree?)

    1. Druid says:

      Dammit! – happy-faced algae in hard hats carrying pickaxes – you’ve gone and made me want one! Maybe an emoji for a beguiling idea which attracts great publicity but is really really stupid. I could mark project proposals with it.
      Speaking of arsenicals – you know that Paul Ehrlich gets credited with “Magic Bullets” to describe Salvarsan? Well his “Zauberkugeln” was also translated as “Bewitched Balls”. Next time you hear magic bullets …

    2. joe gamman says:

      YC comments/discussion happen on Hacker News. On average one of the highest quality discussion sites I know of on the web. the ‘on average’ part of the previous sentence is important though.

      relevent discussion thread:

  42. Mark says:

    The really irritating thing is that synthetic biology is a valid area that has great promise. The trouble with stupidly over-optimistic, ill-informed proposals is that they raise expectations, and undermine long-term faith in the technology.
    Back when I was a youth (bah! I’m becoming a grumpy old man), photosynthesis research was put back decades by people running round saying they were going to sort out rubisco and stop it from using oxygen and that would make plants more productive and the world would be a better place. At the time, no one had a clue where to start, no one managed, and after a while, no one could get funding for anything that mentioned rubisco.
    Again in that era, we could add a gene to some unsuspecting plant and it wouldn’t do what we expected, so with enormous effort we could add another. Now, genuinely, we can (probably, often, with the wind behind us, and a bit of good luck) express quite a complex pathway in a different organism, and even manipulate what it makes by mix-and-match selection of enzymes with similar-but-not-identical properties, and all this is Really Useful. But it’s small and realistic: all we’re doing is using the bits that nature provided, to do what we know they’re capable of doing, but we’re enlarging the context. It’d be a real pity if this technology, which could genuinely make bioactive complex small molecules much more available, got a negative press because it can’t make metal-independent super-plankton solving the world’s CO2 problems with almost-certainly-non-existent chemistry.

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