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Organically Grown Diamonds

Secretions can be the oddest things
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Start with an organism that likes to eat methane gas (among other things). The methane molecule consists of one carbon atom connected to four hydrogen atoms.

We do not necessarily need a lot of genetic engineering here, depending on the organism's ability to evolve.

The first thing we need to do to the organism is modify/encourage it to extract the hydrogen for fuel energy (combine with environmental oxygen), and to use the carbon ONLY for internal biological structures ("organic compounds"). We want to limit the organism's access to all other carbon-containing molecules, so that it will lose any ability to burn excess carbon for energy, in preference to using carbon for internal compounds.

After the first step is achieved, the next step is to introduce extra carbon in the organism's diet. For example, the propane molecule consists of a simple chain of 3 linked carbon atoms, and 8 hydrogens attached to them. That's the equivalent of two methane molecules, plus an extra carbon atom. If the organism is given the ability to digest the propane molecule, after being "biologically tuned" to not need that extra carbon, what will the organism do with that atom?

And what if a lot of those extra carbons become available as a result of switching the organism's diet from mostly methane to mostly propane?

Note that in the realm of speculative nanotechnology, it is proposed to assemble structures of diamond, pure carbon, one atom at a time. Note also that biology at the molecular level is a sort of "natural nanotechnology".

I think it would not be a great leap for an organism that had extra carbons available, and no biological machinery for burning them with oxygen for energy, to treat the carbons as a waste product. And in general, when an organism has some waste to dispose of, it doesn't do it one atom at a time; instead it assembles a mass of waste and secretes it as a lump.

So, biologically produced diamonds, anyone?

Vernon, Apr 02 2010

Also organic, from the other end of the life-cycle http://www.crematio...From-Ashes-c39.html
(ignore the missing apostrophe) [swimswim, Apr 02 2010]

Diamonds from methane http://www.apollodi.../linares-021506.pdf
There is a "sweet spot" in a vacuum chamber, with some heat added (to small amounts of gas, not to the diamond!), that allows diamond to grow fairly quickly. Note that if the quantity of heated material is small enough, then even a lot of heat can be, in total, only a small amount of energy. [Vernon, Apr 02 2010]

More on Apollo Diamonds http://www.wired.co.../11.09/diamond.html
The sixth page of the article specifies natural gas, CH4, which is methane. [Vernon, Apr 02 2010]

Evolution of a new trait http://esciencenews...ch.evolution.unfold
The scientists conducting the experiment didn't know how the bacteria were going to deal with a particular environmental challenge. [Vernon, Apr 05 2010]

Nanotech and diamond http://en.wikipedia...nd_mechanosynthesis
Remember that molecular biology is Natural Nanotechnology; if we can devise molecule-sized machinery to do this like a macroscopic factory makes things, then we can probably get living organisms to manipulate atoms that way, too. [Vernon, Apr 05 2010]

Diatoms http://www.hsu.edu/content.aspx?id=2102
Remember that silicon dioxide CAN have a chemical-bond structure (in quartz) that is similar to diamond (if the oxygen atoms are ignored). I'm quite sure that organic catalysts are used to manipulate those fairly-high-strength SiO2 bonds (they are stronger than the bonds between two carbon atoms in a diamond), to form diatom shells, even if the result here is more amorphous (glass-like) than crystalline. Diatoms most certainly do not make glass by melting silica! [Vernon, Apr 05 2010]

Nanotech Learns from Nature http://www.iupac.or...1/pdf/7303x0459.pdf
Anyone who thinks that tools devised for one purpose (say, nanotech diamond manufacture) can only be used for that purpose (never in biology), needs to think again! [Vernon, Apr 06 2010]

Bacteria can produce longish fibers http://www.rense.co...ryofamorgellons.htm
As mentioned in an annotation [Vernon, Apr 08 2010]


       This would be biological, not organic. Except in the original sense of the word, in which case all diamonds are.   

       It's also unlikely. Carbon doesn't like forming diamond, you'll get graphite unless there is a massive energy input.
MechE, Apr 02 2010

       [MechE], it actually doesn't take lots of energy to make diamond. See link. In biology, I expect an appropriate catalyst would work fine. Life-forms tend to use catalysts for almost everything.   

       Also, "organic" has other meanings.
Vernon, Apr 02 2010

       Strictly hydrogen for energy is doable. Carbon for synthesis is what we all do.   

       However, converting carbon to carbon is enzymatic and I am unaware of any biological reaction that handles stray carbon molecules by hooking them to other carbon molecules with no hydrogen or oxygen involved. If such things did occur one would predict geologic bands of carbon as graphite / diamond etc as a result of microbial deposition since pure carbon is biologically inert.   

       Maybe such things exist. On googling graphite I turned up "hydrothermal graphite" occurring around deep sea vents which all know occur at sites of High Microbial Magick. Perhaps there are critters that produce graphite. One could test this hypothesis by analyzing carbon isotopic ratios in the graphite as opposed to surrounding water - enzymatic action often has isotope preferences wheras plain abiotic crystalization should not.   

       Diamonds are ancient and so isotopes might decay and conceal any possible biologic origin. If new natural diamonds can be found then isotopic analysis could be done on them too.
bungston, Apr 02 2010

       Fascinating, but think fullerene and thermal vent modified electric eels crossed with silk worms.   

       //realm of speculative nanotechnology//   

       If that isn't a journal now, it soon will be.
MaxwellBuchanan, Apr 02 2010

       After thinking it over, I've decided to tweak the title.   

       I admit this Idea is a bit sketchy as to details, but that is far from abnormal here at the HalfBakery. Also, please note this Idea was posted to the Genetic Engineering category mostly because I could not find any other category for biological technologies. Did anyone note the LACK of stress on using that, near the start of the main text?   

       Also note that failure of imagination means nothing --just because we don't know exactly how something might become possible, doesn't mean it is impossible. See link!   

       [bungston], organisms on this planet have a long long history of oxidizing carbon. In a way this Idea is an experiment; if the ability to do that is removed from an organism, what will it do instead, with excess carbon? Certainly it might secrete graphite, but it seems to me that if that much can be achieved by evolutionary biology alone, then THAT is the time where a little genetic engineering (imitating the nonbiological nanotech approach to making diamond) might yield the desired results.
Vernon, Apr 05 2010

       vernon please your rebuttal is weak. this IS using genetics as a cover for having no mechanism to make your idea work and it IS fair to point out that this goes far beyond what is currently even approachable in GE, including the construction of new metabolic pathways FROM SCRATCH. And you can call me crazy but it seems UNLIKELY that an organism would spend much effort building a diamond out of waste carbon when it COULD metabolize it. Finally I don't see how the "diamond" will ever be larger than a single celled organism. Also appealing to the unknown is a fallacious argument, while i cannot prove the null case, you cannot use that as a basis for overcoming objections. This idea: Feed magic GE nano chickens a propane rich diet and they will poo diamonds. Even if the chickens are single celled organisms and the diamonds are tiny micro diamonds you still have no idea how this would be done.
WcW, Apr 05 2010

       you also failed to point out that, generally speaking, when confronted with a situation where an organism is lacking a critical adaption to the environment the response is to die, and it might take billions of years to accidentally hit on the adaption (pooing out tiny diamonds) that you want and another solution (oxidizing that carbon to CO2) might arise sooner, possibly inevitably, leaving the unlikely solution that you describe an impossible outcome.
WcW, Apr 05 2010

       [WcW], you are confusing the things that can qualify as "metabolic pathways"; some are much simpler than others. I do say that genetic engineering can help REMOVE the existing metabolic pathways regarding oxidation of carbon. You agree that existing GE techniques are good at removing genes, don't you?   

       Next, every organism already has a pathway for excreting waste, PLUS excreting incoming "dirt", stuff that cannot be biologically processed. The notion that something new and complicated must be added, just to get rid of extra carbon atoms, is ridiculous. Something new might be needed to get those carbons to join the rest of the excrement, but that is not going to be complicated!   

       The basic new thing here is the notion that AFTER all the preceding "setup" work has been done, THEN we seek ways to encourage the organism (and please note I am not ruling out the possibility of working with multicellular critters, not just bacteria) to separately handle that carbon. You seem to think I'm proposing the entire thing to be done all at once, and you are quite wrong. Our current ignorance will require a one-step-at-a-time approach, toward the goal of this Idea.   

       Since this is the HalfBakery, who cares if an Idea takes billions of years to reach fruition?   

       I'm fairly sure that if an organism has had removed from it all the biology associated with oxidizing carbon, it will not easily get that back, or reconstruct it from scratch.   

       Finally, remember that a pearl is a way for an oyster to deal with a particle of irritating grit, and also a way for it to excrete/secrete calcium carbonate mineral, separately from other wastes.   

       Diatoms are organisms that build shells out of silicon dioxide, and since that is practically always a long-chain substance (not to mention actually being a 3-dimensional grid, like diamond), you can bet the organism has a way of connecting new individual SiO2 molecules to the chain/grid. See link.   

       Your teeth were grown, also, one molecule at a time, by a group of cells working in concert. I daresay that if an organism, even if merely bacterial, "stuck" to its waste carbon, a nice-sized lump could eventually be grown, especially after additional bacteria became stuck to the same lump. Sure, there will be details regarding the way each carbon atom is added to the lump. Graphite may be simple, but diamond is more space-efficient...(a living cell can put more carbon atoms in one area before having to expend energy to move to another area).   

       [WcW], your opinions are invalid, regarding this Idea.
Vernon, Apr 05 2010

       how are you going to put the Carbon into the diamond allotrope? considering the amount of heat/pressure involved to get it right.
FlyingToaster, Apr 05 2010

       [FlyingToaster], I'm sure this is where an appropriate catalyst would come in handy. I'm thinking that this catalyst would be the biological equivalent of the mechanism that the nanotech folks have in mind, for making diamond objects one atom at a time. See the nanotech link. I recognize that genetic engineering may be needed to get the organism to make that catalyst. So? It is merely the final step of the chain proposed in the main text.
Vernon, Apr 05 2010

       I am thinking of the halophiles who deal with excess salt by crystallizing it. I suppose something analogous could happen with carbon. But pure C would not be a problem because it would not enter the cell. As regards carbon waste, if I can use C for biosynthesis I can biosynthesize a carbon waste product and poo it out - maybe some nice amino acid.   

       The interesting thing to me is whether this is actually going on. I think given the availability of carbon and the durability of diamond, if biological processes could produce diamonds we would see a lot of diamonds: diamond shells, diamond teeth etc. But graphite could have a place too: it is biologically inert and so could serve as a shell. I think known shells are calcareous or silicate. If raw materials were scarce (perhaps because of pH conditions?) maybe graphite could be used as a shell?
bungston, Apr 05 2010

       [bungston], carbon is most typically found combined with other elements; the carbon I'm talking about here would be inside an organism because the organism would have stripped off and used the other elements, and the carbon is simply "leftover", because the total of carbon compounds that went into the organism contained more carbon than the organism needed for molecules used for such things as cell-wall structures, internal scaffolding, DNA, etc.   

       An excess of any substance could of course be expected to build up and interfere with normal biological operations, unless that substance is secreted/excreted. The first part of this Idea is all about manipulating an organism's biology until it can do this, for carbon.
Vernon, Apr 05 2010

       So what's the idea here? A magical enzyme that makes diamonds?   

       Furthermore, even if this did exist, how are you going to make a reasonably sized diamond without rupturing the cell?
Cuit_au_Four, Apr 06 2010

       [Cuit_au_Four], the nanotech people who want to construct diamond objects one atom at a time have a plan for accomplishing it. I don't know the details, but whatever molecule-sized "levers" and "grippers" their nanomachines will use to do that, similar levers and grippers can exist for living cells to do the same thing. No magic!   

       Next, you apparently missed the word "secretion" that has been employed here a number of times. Why, therefore, would you assume any diamond produced must be inside a cell?
Vernon, Apr 06 2010

       // Who cares if an Idea takes billions of years to reach fruition?
Vernon, Apr 06 2010

       1) Aerobic metabolism of propane and methane yields less energy than the oxidation of elemental carbon. The bond energy of carbon in a diamond is higher than the bond energy in the substrate "food".   

       2) Biology abhors waste. Building high energy molecules for no good reason is a huge waste of energy, not something that selection or evolution is going to encourage barring some smart special conditions not found on earth. This goes for the building of high energy no real purpose structures outside the cell. Most extra cellular structures (shells) are constructed out of local materials at a low investment organizing energy.   

       3) Levers and grippers??? REALLY?   

       4) There is no real idea here (which is what the MFD for genetic magic is for) if you were working in the field, proposed a real model with a plausible chemical rationale (a waste product with more energy in it than the food????) then you might float this idea. Otherwise this is just   

       "genetically engineer a goose that eats mine tailings and shits golden eggs"
WcW, Apr 06 2010

       [WcW], Your statement (1) is flawed because you don't specify quantities of atoms involved. You are ignoring the hydrogen; we know that there is a lot of energy available to an organism by the hydrogen-oxygen reaction; I'm saying here it should be possible for an organism to get enough energy from that alone, and not need the energy from the carbon-oxygen reaction. The first part of the Idea involves specifically tailoring an organism toward that end.   

       Regarding (2), this is true ONLY because of evolutionary competitive pressures. This need not be true in a controlled environment that allows an organism to be wasteful (because wastefulness is not associated with death, in that environment).   

       Regarding (3), it remains true that the nanotech people want to assemble objects from diamond, constructed one atom at a time. Regardless of what the appropriate nanoscopic tools are called, that will do that, they will have purposes not very different from what I called them.   

       Regarding (4), it remains perfectly true that if the nanotech people can manage to do what is described in (3), then equivalent molecules can be used by organisms. Have you not noticed how we are studying the nanoscopic tools already being used by organisms, to design certain macroscopic industrial systems? (See link, not to mention, look at the Diatoms link, too.) There is NO magic intended here; just a couple of unknown things that should be quite discoverable, given enough time.
Vernon, Apr 06 2010

       [Vernon] threatening to delete annos is no way to conduct a debate. Saying //your opinions are invalid// is just rude, and repeating it thrice just makes it thricely rude. I expect better from you.   

       I tend to agree with [WcW] - his point is not that he, personally, does not know of a possible mechanism, but that you, as poster of the idea, do not, and nor does humanity/science as a whole, and that you have in fact not even remotely proposed or described a mechanism, beyond handwavium/a wizard did it.   

       This is what puts it in the realm of magic, bad science and not-an-idea.   

       Reading onwards, into your annotations, you do describe some similar mechanisms in nature, and I can see that, plausibly, they could be adapted and/or mimicked to create diamond. But this comes ~after~ [WcW]'s challenge to you, not before. When he says //This idea: Feed magic GE nano chickens a propane rich diet and they will poo diamonds// - he is quite right, up to that point in the discussion. It is only afterwards that you explain your thinking further.   

       And still, even to now, you have not proposed an actual, specific, mechanism which results in diamond. When and if you do, I expect you to take the inevitable challenges seriously.   

       If I propose to fling myself to the moon with a giant rubber band, and someone can SHOW me than my physics is laughably wrong, then so be it. In the battle between theory and reality, reality wins every time.   

       It's up to you to explain your idea, not up to the reader to assume the steps along the way, in between, before, or after what you actually write.
BunsenHoneydew, Apr 06 2010

       [BunsonHoneydew], I did not propose specific details because it was not necessary.   

       How many times do I have to remind people that this is the HalfBakery, and complete details are never required here? The opinons of [WcW], when they conflict with that primary aspect of this place, are indeed invalid!   

       For this Idea it was only necessary to indicate that the nanotechnologists expect to be able to manipulate carbon one atom at a time, to make diamond --and to indicate that molecular biology is directly equivalent to the smallest proposed nanotechnologies.   

       Those things were indeed pointed out in the main text.   

       The net result is, because molecule-sized tools are still tools, and are independent of the user, HOWEVER the nanotechnologists think they can manipulate carbon one atom at a time, to make diamond, it is extremely likely, the details of that process can also be performed by a biological organism.   

       If you want to say it can't be done, or can only be done by magic, then I suggest you start by telling the nanotech crowd it is impossible to manipulate carbon, one atom at a time, to make diamond. ONLY if you manage to convince them of that might I accept an MFD for this Idea. Not before!
Vernon, Apr 06 2010

       no mechanism=no idea. Let me be clear that i do understand that material engineering and genetic engineering offer amazing potential in the future, potential that we do not today imagine with any clarity. But this sort of speculation was essentially banned from the site due to a proliferation of junk nano and GE ideas. These ideas have no real content and rely on "brilliant minds in the field" to fill in all the details. I feel that this is a 'text-book' example of the MFD for using science as an analog for magic. As long as the idea utilizes a "black box" of genetic engineered organisms without a VERY clear mechanism (adding florescence to the coding for hair proteins by transcription as an example that was shot down at least once, seemed fine to me) then the idea does not belong.
WcW, Apr 06 2010

       [WcW], I've made it plain that the nanotech people DO seem to think they know a way to manipulate carbon atoms to make diamond; they've even published books about it. I am not making that part of this Idea up!   

       What I am doing is referencing it, and claiming that if such manipulations can be done nonbiologically, then they can also be done biologically --because we KNOW that biological organisms can and do manipulate various atoms one at a time, on occasion, using molecular machinery that WOULD be called nanotechnology if humans had invented it first!   

       So, again, if you want to insist that there is no mechanism here, then go to the nanotech people and tell them they have no mechanism, either.
Vernon, Apr 07 2010

       No, [Vernon], you go to the nanotech people and get them to come on the halfbakery to explain how this idea could work.
pocmloc, Apr 07 2010

       Artificial flight can be done nonbiologically. If anything, it's more thoroughly baked than artificial diamond synthesis.   

       If it can be done nonbiologically, it can be done biologically too, so "Genetically engineer lobsters to have wings" is obviously a valid halfbakery idea.
Wrongfellow, Apr 07 2010

       Um, nanotech people are not trying to construct diamond in an environment that has all sorts of contaminants and other interesting issues. They are also not using "levers and grippers". They are creating conditions under which diamond is likely to form and then attempting to shift atoms into likely positions, more likely through magnetic or electrical manipulation.   

       I'm not sure you understand the scale involved. At this level probability and guesswork replace absolute manipulation. You cannot "grip" an atom simply because the gripping surface is not solid at this scale.   

       You therefore, are proposing that a high purity, low chemical probability process that has to be extremely carefully controlled, occur in a very contaminated and low control environment. It won't happen.   

       Oh, and why are you trying to produce diamond anyway? It's cheap and common to start with, and the only thing that it's useful for is either artificially inflated sales pricing or a low wear hard edge coating. For which you want, ideally, a single crystal deposition, which you will not get from an organism.
MechE, Apr 07 2010

       [MechE], apparently you haven't studied biological catalysts enough. They DO exhibit fine control over molecules, pieces of molecules, and sometimes even atoms.
Vernon, Apr 07 2010

       For that approach to work, you need to have an attachment site that will bond both to your catylyst and then prefferentially to it's final location. Good luck finding one that works with isolated carbon atoms.   

       There is also the fact that it is definitely probabalistic. W number of catylsts encounter X number of target molecules and bond with Y of them, and transfer them to the next Z target sites. Where W>X>Y<Z, which isn't going to work real well for precision placement in a crystalline matrix.
MechE, Apr 07 2010

       Maybe maybe not. The chemistry of life is inherently limited by the conditions it developed under. Some kinds or reactions may be incompatible with those conditions. The less specific you are about NANO and GE the more they are simply the lubrication of fantasy. This is not an invention it is a speculation. This speculation might find a more comfortable and supportive home elsewhere.
WcW, Apr 07 2010

       /Some kinds or reactions may be incompatible with those conditions/   

       Enzymes are biologic catalysts. Some enzymes might optimally work at temperatures incompatible with the rest of the organism. For example the Taq polymerases run hot because the bug they are from lives hot. The polymerase is used exvivo. Could one tweak Taq to optimally perform even hotter and so faster? You could hammer away at Taq ex vivo, changing one AA at a time, evolving it to work at higher temperature.   

       One could do something of the sort with diamond production. I think it would be quicker to evolve this enzyme exvivo then engineer bugs to make it. Some evolutionary steps have such a high energy of activation that it is unlikely to happen - Vernon I have this idea you have written on optimizing RUBISCO here which is an example of this.   

       Re criticisms / fighting words - pretty standard stuff here for a Vernon idea, in my opinion. Neelandan even used more colorful language back a few years ago.
bungston, Apr 07 2010

       Yeah, I saw the part about the secretion, but what are you going to secret? Assuming this magical enzyme can actually produce diamond nanocrystals, there is a limit to how big they can grow before they tear open whatever organism you are using. I suppose you could use a frog egg or something massive, but you might as well just take a test tube, grind up carbon and pour enzymes on it.
Cuit_au_Four, Apr 08 2010

       [Cuit_au_Four], why are you assuming the organism must always totally surround a growing diamond crystal? There are bacteria that can produce significant lengths of fibrous substance (see link). That means the bacterial cell makes some, partly secretes/excretes it, but stays attached in a way that allows it to gradually extend the length of the fiber.   

       In this case we could imagine various variants, such as starting with a diamond "seed", letting appropriate bacteria grow on it, and those bacteria would, by secretion, simply add layers of diamond to the seed.
Vernon, Apr 08 2010

       "simply add layers of diamond to the seed."   

       This will produce polycrystaline diamond or have to be done in a seriously inert atmosphere, as hydrogen, oxygen, not sure what else, will quite happily bond to exposed diamond surfaces before the bacteria can add the next layer.
MechE, Apr 08 2010

       [MechE], you have a point. The organism needs oxygen in its environment to metabolize hydrogen, after all, and we don't want that oxygen reacting with loose carbon bonds at the surface of the diamond.   

       There may still be a fairly simple solution, though. If the extra carbon is not fully detached from hydrogen, before being added to the diamond, then the organism can strip off a hydrogen from the surface of the diamond, and add a new carbon-attached-to-a-hydrogen at that bond site.   

       Net effect, the organsims eventually consume all the hydrogen that was initially attached to the carbons (see propane suggestion in main text), while still secreting diamond.   

       Note to detractors: this approach gives the organism a bigger thing to manipulate (a "CH" fragment), than just a pure carbon atom.
Vernon, Apr 08 2010

       "carbon is not fully detached from hydrogen, before being added to the diamond"   

       yea, the cells can use duct tape to hold it down until they get back to it. Failing that we could add "bailing wire" to their DNA and that would be even stronger. We can give them tiny scuba gear to deal with the oxygen and hydrogen (and water!) free environment and then they can all go to a technical school and get BA's in Diamond Tech. There's nothing that can't be solved with a little creativity and an open mind.
WcW, Apr 08 2010

       I would humbly point out that bailing wire is far inferior to a bucket for that particular job.
bungston, Apr 08 2010

       Pondering this again: probably the place this might happen is in deep earth petrochemical deposits. Lots of lots of carbon bound to hydrogen and not a lot of stuff to react with exposed diamond surfaces.   

       I visited this idea because I could have sworn Vernon had a scheme to optimize RUBISCO; I even mention it in an anno up there. I was going to link it to a poorly fleshed out new idea on optimizing photosynthesis. But I cannot find the Vernon idea. Maybe it was taken down because he is working on it in earnest.
bungston, Mar 09 2011

       //Carbon doesn't like forming diamond//
Perhaps we need to explain to carbon the profits that could be made and get it to shape up a little
AbsintheWithoutLeave, Mar 09 2011

       [bungston], I think you are mistaken about me thinking about "RUBISCO". I don't know what that acronym stands for....
Vernon, Mar 09 2011


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