Golden Bacterial “Do”…

OK, sometimes you run into something that just makes you push back from the keyboard and say “No Way! It just CAN’T be!!” yet “The facts just are. -E.M.Smith” so you look at it again. And again.

Well, two days into it. I’m thinking this is starting to look like at a minimum a “partial answer”, and maybe the major answer. Folks have found bacteria at great depths in the earth, living on what looks like mineral soup. Now this. Could there be bugs living in the earth “do”ing This?

So, do we need to redefine “Gold Bug”?

I’ll leave that for you to decide….

Gold ores have also been located along the mid-ocean ridges of the Atlantic and Pacific Oceans. One such deposit was found in association with the TAG hydrothermal field at 26o North latitude on the mid-Atlantic Ridge at the 3,670 meter water depth (Herzig 1991). The gold ores in these locations are associated with sulfide deposits formed by hydrothermal vents. These vents occur when the spreading seafloor allows water to percolate down in the crustal rocks and reach hot regions deep beneath the seafloor. The heated seawater dissolves mineral in much higher concentrations than can occur in cold water.
Much about the process of precipitation of gold and other metals from these solutions is unknown, however, it is believed that some sulfur-oxidizing bacteria of the genera Beggiatoa, Thiothrix or Thiovulum play an active role in this precipitation (Zierenberg 1990).

So far, so good. Mixed metals in a bulk of sulphide, and some sulphur eating bacteria remove it, concentrating the metals. OK, I’d heard of that bit before. Now comes the “hard left turn”…

These chemosynthetic bacteria derive energy unlike their surface dwelling relatives (assuming that they are related). Instead of deriving energy from the oxidation of organic mater, or from photosyntheses, they oxidize sulfide compounds directly from the scorching hot hydrothermal liquids. How these bacteria can live and even thrive at 200o C is a matter of much discussion and investigation, but evidence suggest that these bacteria can efficiently remove gold, silver, copper, and other metals and minerals from dilute aqueous solutions.

Other theories have been proposed regarding the role of gold precipitation from ore solutions by bacteria. Recent evidence suggests that most of the placer gold found in Alaska originated from bacterial scavenging. An analysis of the microstructure of Alaskan placer gold, and that of many of the epithermal deposits around the world, has revealed a fine structure of nearly pure gold microtubuals approximately 1 micrometer in diameter. It has been proposed that these hollow gold structures are the exact shape and size of the cellwall of bacterium genus Pedomicrobia (Watterson 1992). These bacteria are believed to derive energy from the precipitation of gold around themselves. A close examination of the microtubuals reveals branching structures of smaller diameters connected to the larger diameters. This observation is remarkable similar to the observed method of reproduction for Pedomicrobia. Instead of reproducing my fission, the splitting of the cell in two, these bacteria often reproduce by budding, a process remarkable similar in appearance to the gold microtubuals (Rennie 1992). The gold casings around the Pedomicrobia are extraordinary because of their high degree of purity, in excess of 98% gold (Pain 1988). It has been argued by these researchers that much of the Earth’s placer gold deposits, have originated from similar biological processes with these or other bacteria. It is believed that the bacteria can concentrate the gold around themselves in such massive amounts because of an electrochemical reaction whereby the gold is gathered on pecifically adapted membrane receptors to which the bacteria discharges excess electrons from its biological processesthus precipitating the gold out of solution (Watterson 1992).

The possibility that certain bacteria can concentrate gold in amounts sufficient to comprise a major share of the Earth’s gold ores suggest that with the right application, these or similar bacteria may be employed in the extraction of gold from low grade deposits or solutions. Already, there are commercial applications of bacteria in the mining of gold. Specifically, the bacteria Bacillus cereus is being used by the Canadian Genprobe Company to increase the yield of gold from pyrite ores (Anonymous 1989). In this case the bacteria are after the pyrite matrix that binds the gold and prevents economic recovery otherwise. Bacterial processing of these pyrite ores is relatively inexpensive and has increased yields from an average of about 65% to as much as 96% (Dworetzky 1988). Given the affinity that some bacteria have for the concentration of gold, the question arises as to whether it might be feasible to employ such a bacterium, or one specifically engineered for the task, to scavenge gold directly from the dilute concentrations present in sea water.

Even at the conservative estimates of 10 ppb of gold in seawater, there is a great deal of gold in solution in the oceans. Humankind has unearthed perhaps a total of 3.3 billion ounces of gold over the course of history, an amount equivalent To a cube of gold 55 feet on a side (Dworetzky 1988), but the sea water of the Earth’s oceans contain about 25 billion ounces of gold (Burk 1989). If the ability of some of these bacteria to concentrate gold around their cell membranes to the degree that they form massively dense agglomerations of hollow gold microtubuals, as the evidence suggests, then perhaps a similar bacterium may find a practical application in sea water.

So I’m sitting here with this mental image of a bacteria making its own gold jewelry…

That, and the pondering of what my spouse will say when I tell her that her gold is made of bug, er, um, “leavings”…

This is truly a very strange world…

Plastics. There’s a future in Plastics!

OK, so what brought me to that place? I was looking to see if anyone had done similar work on gold, as that done with Uranium, to extract it from the sea via a customized plastic. (Little did I now that bacteria had beaten us to the punch some billions of years ago…);2-E/full

New macroporous polymers for the selective adsorption of gold (III) and palladium (II). I. The synthesis, characterization, and effect of spacers on metal adsorption
J. M. Sánchez1, M. Hidalgo1, M. Valiente2, V. Salvadó1,*

Article first published online: 21 JAN 2000

DOI: 10.1002/(SICI)1099-0518(20000115)38:23.0.CO;2-E

Copyright © 2000 John Wiley & Sons, Inc.

polymer functionalization;spacer arm;Cyanex 471;triisobutylphosphine sulphide;heteroatoms;metal adsorption


New macroporous polymers with a functional group based on triisobutylphosphine sulphide are synthesized and characterized for the selective adsorption of gold and palladium. Five coordinating polymers are prepared from chloromethylated divinylbenzene polystyrene, by either direct attachement of the phosphine sulphide to the polymer or through a spacer chain that is modified to introduce O and S heteroatoms. The influence of the length and composition of the spacer chain on resin capacities is studied. The presence of O and S heteroatoms in the spacer increases the hydrophilicity of the polymers, and it is found to be essential for the adsorption of Au(III) and Pd(II). This is attributed to the coordination of the metal with the heteroatoms of the spacer.
© 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 269–278, 2000

OK, it’s not QUITE purely gold. You have to accept some palladium “contamination” as well ;-)


Ion exchange resins have been extensively used for the separation of noble metals.1–7 Unfortunately, the low selectivity of most commercially available ion exchange resins does not allow for effective separation without the use of elution solutions.

The use of coordinating resins solves the problem when the most suitable functional group is selected, as their selectivity is higher than that of conventional resins. Over the last few years there has been considerable research into the synthesis of coordinating resins with functional groups based on ligands presenting a high level of liquid–liquid extraction efficiency.8, 9

Polymers with covalently bonded functional groups containing donor sulphur atoms (such as thiol,10–14 thiourea,8, 15–20 dithizone,8, 21–23 thioglicolate,8 thiooxime,8 thiosemicarbazide,24, 25 and 2-mercaptobenzotiazol26) have been applied for the selective sorption of noble metals. Triisobutylphosphine sulphide (TIBPS, Cyanex 471) has demonstrated a high level of selectivity for gold and palladium in solvent extraction,27–34 supported liquid membranes,35–38 and solvent-impregnated resins.39 This ligand, bound to a microporous matrix,40, 41 can selectively separate gold, palladium, and silver from base metals. The use of a microporous matrix to prepare coordinating polymers presents some problems, as the swelling of this kind of matrix is highly dependent on the composition of the solution, thus making it difficult for data to be reproduced. Macroporous polymers, on the other hand, have higher capacities and are more highly selective than microporous resins, and they are not affected by the concentration of the external solution nor by the solvent.42

The reaction between the functional group and the metal, and the diffusion43 of the metals into the polymer, determine the success of coordinating resins in adsorbing metals. Steric hindrance by the polymeric matrix and the hydrophobic nature of the polymeric ligand sometimes limit the coordinating reaction.

This article describes the preparation and characterization of different waterinsoluble macroreticular polystyrenedivinylbenzene polymers functionalized with diisobutylphosphine sulphide groups (Fig. 1), which are selective towards Pd(II) and Au(III) ions.

For the rest, hit the link. The “bottom line”, though, it that it can be done. At $1500 an ounce, I think we’ll see folks doing it. This work was likely done back when gold was about $300 an ounce. A 5 fold jump can really boost your cost / benefit ratio ;-)


As a “sidebar” note, I also ran into an interesting approach to mining silver. Don’t know yet whatever came of it, but with current prices it would likely be a ‘winner’. Maybe someone ought to test the sediments of the Colorado in the Gulf of California and the sediments of the Sacramento where it dumps into the Delta / SF Bay for metal content… I know that at one point the silver from millions of folks photographs was washing into the SF Bay in quantities high enough they warned about silver poisoning in the area around Alviso…

No, not absorption, but mud concentration. This article is from 1982, so there has been a lot of price action since then.

Silver from the Sea

Written by Glyn Ford and Jonathan Simnett

In the Red Sea three years ago, Saudi Arabia and The Sudan jointly launched an experiment that, in the Middle Ages, might have been called alchemy: the transmutation of a common, worthless substance – mud – into a rare and valuable substance: silver. In the Red Sea, however, the process depends on technology rather than magic, and is extraction rather than transmutation.
What the commission is investigating are thick layers of mud – up to 30 meters (98 feet) – that have been collecting over the last 10,000 years in the deep depressions along the center of the Red Sea 90 kilometers from land (56 miles). Found beneath pools of dense, extremely hot brines-60°C (140°F)-that have formed in depressions two kilometers deep, these muds are rich in zinc and copper, smaller amounts of other metals, including gold, and — the main target-silver.

Since the 1880s, oceanographers have suspected that the Red Sea had hidden secrets. It was not until 1948, however, as the post-war boom in ocean research got underway, that the strange, high-temperature brines were found and recorded by the Swedish vessel Albatross. And it was not until about 1963 that scientists, in a burst of exploratory activity, obtained samples of the metalliferous muds.

Since then, 18 brine pools and associated mud deposits have been discovered. But from a commercial viewpoint only one of these is important: the Atlantis II Deep. The largest found so far, the Atlantis II Deep, named after the survey ship which discovered it, has a surface area of 60 square kilometers (23 square miles) and vast deposits of multi-colored muds, the consistency of soft toothpaste, containing, in the southwest basin, six percent zinc, one percent copper and 100 parts per million of silver.

The formation of these deposits came about, partially, as a result of the split in the earth’s crust between Africa and Arabia – the continuation of which may eventually turn the Red Sea into a full fledged ocean; it widens at the rate of 10 kilometers (six miles) every million years. When this thin ocean crust cracked, sea water poured onto the molten rocks below and formed salt solutions rich in metallic compounds. Carried upwards by convection currents, these solutions mingled with the colder water closer to the surface, where -since solubility is temperature dependent – the salts with the metallic components were precipitated – i.e. forced out of the solution – within the muds.

To be of commercial interest these deposits must, of course, be recovered economically. To determine costs, therefore, the governments of Saudi Arabia and The Sudan, in September 1975, established the Saudi-Sudanese Red Sea Commission to sponsor research into, and development of, these resources (See Aramco World, July-August 1981), and engaged Preussag to carry out a $28 million, five-year feasibility study.

Preparations for the study took time, of course, but by March, 1979, Preussag had readied the Sedco 445, a large mining ship equipped with a 2,200-meter steel drill-string (7,200 foot) with a suction head attached to the end of a standard oil drilling pipe. Lowered into the deeps, the suction head, with a motorized vibrating attachment, broke up the mud and pumped it to the surface; between March and June 1979, 15,000 cubic meters (68,190 cubic feet) of muds and brines were pumped to the surface for processing.
Engineers, therefore, had to be sure that the process could function in the Red Sea’s frequently rough weather. This was assured by tests run by the Warren Spring Laboratory in Britain, in which a ship’s motion simulator reproduced Red Sea conditions on land-so successfully that the commission’s pre-pilot test achieved concentration factors of eight to10 times, with an overall recovery rate of up to 70 percent and a final product containing 32 percent zinc, 5 percent copper and 0.07 percent silver.
Technical optimism aside, Saudi Arabia and The Sudan must also consider the economics – and they are as tricky as the technology. To be sure, the latest estimates of Atlantis II Deep suggest a tremendous potential: 1.95 million metric tons of zinc, 400,000 metric tons of copper, 4,000 metric tons of silver and 60 tons of gold worth some $4 billion at current prices. But metal markets are highly volatile. At today’s prices, for example, almost half the revenue would come from zinc – which has recently been steadily rising in price – while copper revenues would be much smaller.

As for silver, the target metal, commission experts have to keep in mind such upsets as the 1980 fiasco when prices gyrated wildly during an attempt to corner the market – and then crashed. On the other hand, the silver market is usually less vulnerable than other metals and now seems assured of a long-term upward trend.
So far, fortunately, detailed environmental monitoring has shown little adverse reaction. During the tests, the German research vessel Valdivia tracked the tailings plume as they were pumped down to 400 meters (1,300 feet) through a steel sewage pipe attached to Sedco 445’s bow anchor line – to be sure the tailings neither contaminated the water nor reduced light penetration, an important factor in the biology of the sea. In addition, LANDSAT satellite-sensors that have been monitoring the tailings (See Aramco World, March-April 1982) and post-test investigations showed that so far neither the coral reefs nor the fauna within the surface layers have been affected. Recently, the commission also received a report – from a Saudi doctoral candidate studying in San Francisco – saying that fine zinc particles discarded in the Red Sea develop a thin layer of oxide that makes them sink faster than originally thought-virtually eliminating danger to marine life from this source.
Glyn Ford and Jonathan Simnett are members of a research group at Manchester University in England, now studying the future usages of oceans.

This article appeared on pages 22-25 of the September/October 1982 print edition of Saudi Aramco World.

I find it interesting that they are simply discarding the zinc …

At any rate, it looks like there’s another place with loads of metals to mine.

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About E.M.Smith

A technical managerial sort interested in things from Stonehenge to computer science. My present "hot buttons' are the mythology of Climate Change and ancient metrology; but things change...
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33 Responses to Golden Bacterial “Do”…

  1. Adrian Vance says:

    Every cell of Macrosystis kelp contains one small crystal of iodine. How much genetic engineering would it take to change that to a crystal of gold? There is more gold in one cubic mile of sea water than claimed to be in Fort Knox, if we have been told the truth…

    For common sense, science and humor see The Two Minute Conservative at Also on Kindle.

  2. Scarlet Pumpernickel says:

    Plants can be used to find gold deposits sometimes. In Australia there are certain trees which seem to grow in areas of gold deposits. Sometimes its the gold uptake but sometimes it is areas of faults because more water accumulates and hence brings the gold into that area…

  3. Scarlet Pumpernickel says:

    Another interesting heavy metal or element is radioactivity. Radioactivity is higher around volcanoes, they emit radioactivity from deep in the earth be interesting to see what the levels are.

    Some areas have lots of minerals in hydrothermal springs.

  4. R. Shearer says:

    I like the kelp idea, but who said there was any gold left in Ft. Knox?

    Anyway, it appears that organic substitutes for aqua regia with tunable selectively for gold and nobel metals could prove useful.

  5. Tom Bakewell says:

    Thomas Gold proposed that most hydrocarbons were actually generated deep withn the earth’s crust. Hydrogen seems to leak up fro the core, and we know diamonds come from some source quite deep within the earth in diatremes.

    So it’s not unreasonable to have biogeochemistry at work as a concentrator. Some of the Lead _Zinc deposits in the tri-state district are hosted in carbonate reefs as remnants of the shales dewatering and transporting the base metals to an home.

    What a fascinating place we’ve been parked in to pass our lives.

  6. Scarlet Pumpernickel says:

    I love Thomas Gold’s work. I think he’s right. Time will tell, but really him and the Russians are the only ones with the proper model at the moment.

  7. Soronel Haetir says:

    Can you imagine the environmental outcry if gold concentrating bacteria were let loose in the ocean at near surface depths?

    Of course, I would also be interested to know if bugs that evolved for deep ocean vents could actually compete at the surface layers. I would suspect not, that the sulfur reactions they use require that extremely hot water to occur quickly enough to matter. OTOH, at the surface there wouldn’t be anything else trying to make a go of that particular energy source and they have the added benefit of likely being poisonous to anything in the photosynthesis chain.

  8. E.M.Smith says:

    @Soronel Haetir:

    I don’t see much problem putting a “bug house” on the bottom of the ocean over a hydrothermal vent. Come back once a year to collect the “bug do” and give them any needed repairs / special treat feedings…

    Also, we can make similar temperature / pressure conditions in factories today. So put them in a pressure cooker and turn on the gas!

  9. pascvaks says:

    This stuff is gooder than Sci-Fi! (Always liked SF. Always thought SF writers like Azimov were a blast. What a fantastic Universe;-) Don’t suppose anyone will find too much gold and silver and ruin the market do you? How will we know the value of a buck, or euro, or that Brit thing? Too much isn’t good.

  10. oldtimer says:

    While telling your wife about her gold ring, you might be well advised not to remind her that the colour of her lipstick relies on squashed beetles.

  11. PhilJourdan says:

    Come back once a year to collect the “bug do” and give them any needed repairs / special treat feedings…

    One man’s treasure is another man’s trash! Goes for the amimal kingdom too!

  12. H.R says:

    These bugs sound a little like my brother-in-law.

    He can live anywhere under extreme conditions that no one else would find habitable and eat anything that no one else would find edible… so long as it’s all free.

    The difference is his waste products have almost no value except for the astonishing amount of methane produced. (I’m thinking maybe I should harness this guy and save a little on utilities… get some of my money back.)


  13. tckev says:

    Would appear those tiny critters have beaten us at every step to an industrial process.
    I had read of something similar in Australia a couple of years a go but here is the only reference I can find.

    There was also an article about bacteria making very radioactive waste into lower grade radioactive waste but again I can’t find the original article, and can’t remember the specific details of who, where, and when, to allow me to search for it.

  14. R. Shearer says:

    I don’t buy abiotic oil theory. It has huge problems in that it can’t explain C isotope ratios and biomarkers.

    Certainly, there are abiotic sources of hydrocarbons, methane on moons and other planets are good examples, but on earth methane is mainly biologically derived as is coal – you can find fossilized leaves, etc. in coal.

    Biomarkers are molecular remnants of clear biological origin. The C12 to C13 ratios in crude match those of plants and plankton, depending on the oil source. Now I could accept some abiotic oil made via Fischer-Tropsch type chemistry, but I do not believe this has been shown.

    Of course, the only thing that matters with regard to Peak Oil is whether reservoirs can be replenished at rates greater that the rate of oil extraction. Proponents of abiotic oil theory tend to believe that Peak Oil is the product of conspiracy. However, despite demand and high price, oil production appears to have hit resistance between 85-90 million barrels/day. If that barrier cannot be broken at current high prices and demand, and in the next several years, I would suggest that this is evidence supporting “Peak Oil.”

  15. E.M.Smith says:

    @R. Shearer:

    Oil can be made in the lab from carbonate rocks with heat and pressure (and some water IIRC). So subduct some ocean floor with all the biological “goo” on it, send it back up as oil. What isotopic ratio will it have?

    The assumption that all biological origin carbon will have the signature of “now” and all geologic cabon is “4.5 Billiion years primative” is not accurate. There is a “middle ground” of a few hundred thousand to million scale years at subduction zones. Which just happens to be where we find loads of oil…

    (Saudi. California, Indonesia, …)

    Now take that oil and shove it to the surface through a lot of bacteria laden rock. What happens? Oh, it gets a bunch of bio-markers in it…

    So, for my money, since BOTH have been demonstrated in the lab in conditions known to exist on the planet, we are likely getting oil from both sources. Since it all gets mixed in the environment, we get the endless bickering over “IS vs IS NOT” when we ought to be looking at “What percentage?”…

    North Sea, for example, looks like it’s pretty well guaranteed to have been a shallow algae laden anoxic sea that got burried in sediments.

    Deep Water Gulf of Mexico is “way hard” to explain as biological. Especially that “depleted” well that has been refilling from a deeper source (visualized on some kind of sonar) and with a different isotopic signature…

  16. Pingback: Is there anything bacteria cannot do?…even deposit GOLD. | pindanpost

  17. pascvaks says:

    Ref – Oldtimer, 22 April 2011 at 5:08 pm

    Shhhhhhhhh! Wish you hadn’t said that. I just know someone’s going to spill the beetles.

  18. pascvaks says:

    Sounds like we need MORE ‘schoshi chingos’ to make gold, silver, plastic, oil, and eat CO2 in the process to get more O2. Got it!

  19. R. Shearer says:

    EM, yes hydrocarbons can be made from carbonate via FT following Anderson Shultz chain-growth mechanism, but this chemistry produces molecules of simple structure, not the complex biomarkers that are found in all crudes. The issue around contamination from biological “goo” counters this of course but at least not to my satisfaction.

    I used to do biomarker analysis for a major oil company that is involved in exploration and production all over the world including the Gulf of Mexico. I never saw or heard of a crude oil that does not contain biomarkers. It would seem that some would be found if abiotic theory were correct. I’d like to get a sample of oil that is refilling the deep well that you mention.

    I agree with your reasoning regarding IS vs. IS Not. The quantitative aspects of this are more complex. I just haven’t seen enough convincing evidence to overturn the conventional wisdom that oil companies use on a daily basis.

    New mass spectometer technology is becoming available that can analyze the isotopic ratios of individual molecule species, as opposed to a “whole” sample. It would be interesting to see what this technology in finding.

    With regard to subduction, etc. if this occurs more than once, then there could be sandwiches of old vs. newer layers and of course the newer layer can be below the older layer. This complicates it even more.

    My interest is piqued now.

  20. E.M.Smith says:

    @R. Shearer:

    Don’t have time to find the academic references right now, but this “popular” article has a fair number of person and university names that in a search key will tend to find a bunch of the more technical stuff:

    Oil Fields Are Refilling…
    Naturally – Sometimes Rapidly
    There Are More Oil Seeps Than All The Tankers On Earth
    By Robert Cooke
    Staff Writer –

    Deep underwater, and deeper underground, scientists see surprising hints that gas and oil deposits can be replenished, filling up again, sometimes rapidly.

    Although it sounds too good to be true, increasing evidence from the Gulf of Mexico suggests that some old oil fields are being refilled by petroleum surging up from deep below, scientists report. That may mean that current estimates of oil and gas abundance are far too low.

    Recent measurements in a major oil field show “that the fluids were changing over time; that very light oil and gas were being injected from below, even as the producing [oil pumping] was going on,” said chemical oceanographer Mahlon “Chuck” Kennicutt. “They are refilling as we speak. But whether this is a worldwide phenomenon, we don’t know.”
    Kennicutt, a faculty member at Texas A&M University, said it is now clear that gas and oil are coming into the known reservoirs very rapidly in terms of geologic time. The inflow of new gas, and some oil, has been detectable in as little as three to 10 years. In the past, it was not suspected that oil fields can refill because it was assumed the oil formed in place, or nearby, rather than far below.

    According to marine geologist Harry Roberts, at Louisiana State University, “petroleum geologists don’t accept it as a general phenomenon because it doesn’t happen in most reservoirs. But in this case, it does seem to be happening. You have a very leaky fault system that does allow it to migrate in. It’s directly connected to an oil and gas generating system at great depth.”

    What the scientists suspect is that very old petroleum — formed tens of millions of years ago — has continued migrating up into reservoirs that oil companies have been exploiting for years. But no one had expected that depleted oil fields might refill themselves.
    “No one has been more astonished by the potential implications of our work than myself,” said analytic chemist Jean Whelan, at the Woods Hole Oceanographic Institution, in Massachusetts. “There already appears to be a large body of evidence consistent with … oil and gas generation and migration on very short time scales in many areas globally,” she wrote in the journal Sea Technology.

    “Almost equally surprising,” she added, is that “there seem to be no compelling arguments refuting the existence of these rapid, dynamic migration processes.”

    The first sketchy evidence of this emerged in 1984, when Kennicutt and colleagues from Texas A&M University were in the Gulf of Mexico trying to understand a phenomenon called “seeps,” areas on the seafloor where sometimes large amounts of oil and gas escape through natural fissures.
    “On the first trawl, we brought up over two tons of stuff. We had a tough time getting the nets back on board because they were so full” of very odd-looking sea.floor creatures, Kennicutt said. “They were long strawlike things that turned out to be tube worms.

    “The clams were the first thing I noticed,” he added. “They were pretty big, like the size of your hand, and it was obvious they had red blood inside, which is unusual. And these long tubes — 3, 4 and 5 feet long — we didn’t know what they were, but they started bleeding red fluid, too. We didn’t know what to make of it.”

    The biologists they consulted did know what to make of it. “The experts immediately recognized them as chemo-synthetic communities,” creatures that get their energy from hydrocarbons — oil and gas — rather than from ordinary foods. So these animals are very much like, but still different from, recently discovered creatures living near very hot seafloor vent sites in the Pacific, Atlantic and other oceans.
    The discovery of abundant life where scientists expected a deserted seafloor also suggested that the seeps are a long-duration phenomenon. Indeed, the clams are thought to be about 100 years old, and the tube worms may live as long as 600 years, or more, Kennicutt said.

    The surprises kept pouring in as the researchers explored further and in more detail using research submarines. In some areas, the methane-metabolizing organisms even build up structures that resemble coral reefs.

    It has long been known by geologists and oil industry workers that seeps exist. In Southern California, for example, there are seeps near Santa Barbara, at a geologic feature called Coal Oil Point. And, Roberts said, it’s clear that “the Gulf of Mexico leaks like a sieve. You can’t take a submarine dive without running into an oil or gas seep. And on a calm day, you can’t take a boat ride without seeing gigantic oil slicks” on the sea surface.

    Roberts added that natural seepage in places like the Gulf of Mexico “far exceeds anything that gets spilled” by oil tankers and other sources.

    Although the oil industry hasn’t shown great enthusiasm for the idea — arguing that the upward migration is too slow and too uncommon to do much good — the search for new oil and gas supplies already has been affected, Whelan and Kennicutt said. Now, companies scan the sea surface for signs of oil slicks that might point to new deposits.

    “People are using airplane surveys for the slicks and are doing water column fluorescence measurements looking for the oil,” Whelan said. “They’re looking for the sources of the seeps and trying to hook that into the seismic evidence” normally used in searching for buried oil.

    Similar research on known oil basins in the North Sea is also under way, and “that oil is very interesting. There are absolutely marvelous pictures of coral reefs which formed from seepage [of gas] from North Sea reservoirs,” Whelan said.

    Analysis of the ancient oil that seems to be coming up from deep below in the Gulf of Mexico suggests that the flow of new oil “is coming from deeper, hotter formations” and is not simply a lateral inflow from the old deposits that surround existing oil fields, she said. The chemical composition of the migrating oil also indicates it is being driven upward and is being altered by highly pressurized gases squeezing up from below.

    This upwelling phenomenon, Whelan noted, fits into a classic analysis of the world’s oil and gas done years ago by geochemist-geologist John Hunt. He suggested that less than 1 percent of the oil that is generated at depth ever makes it into exploitable reservoirs. About 40 percent of the oil and gas remains hidden, spread out in the tiny pores and fissures of deep sedimentary rock formations.

    And “the remaining 60 percent,” Whelan said, “leaks upward and out of the sediment” via the numerous seeps that occur globally.

    Also, the idea that dynamic migration of oil and gas is occurring implies that new supplies “are not only charging some reservoirs at the present time, but that a huge fraction of total oil and gas must be episodically or continuously bypassing reservoirs completely and seeping from surface sediments on a relatively large scale,” Whelan explained.

    So far, measurements involving biological and geological analysis, plus satellite images, “show widespread and pervasive leakage over the entire northern slope of the Gulf of Mexico,” she added.

    “For example, Ian MacDonald at Texas A&M has published some remarkable satellite photographs of oil slicks which go for miles in the Gulf of Mexico in areas where no oil production is occurring.” Before this research in oil basins began, she added, “changes in reservoired oils were not suspected, so no reliable data exists on how widespread the phenomenon might be in the Gulf Coast or elsewhere.”

    The researchers, especially the Texas team, have been working on this subject for almost 15 years in collaboration with oil industry experts and various university scientists. Their first focus was on the zone called South Eugene Island block 330, which is 150 miles south of New Orleans. It is known as one of the most productive oil and gas fields in the world. The block lies in water more than 300 feet deep.

    As a test, the researchers attempted to drill down into a known fault zone that was thought to be a natural conduit for new petroleum. The drilling was paid for by the U.S. Department of Energy.

    Whelan recalled that as the drill dug deeper and deeper, the project seemed to be succeeding, but then it abruptly ended in failure. “We were able to produce only a small amount of oil before the fault closed, like a giant straw,” probably because reducing the pressure there allowed the fissure to collapse.

    In addition to the drilling effort and the inspection of seeps, Whelan and her colleagues reported that three-dimensional seismic profiles of the underground reservoirs commonly show giant gas plumes coming from depth and disrupting sediments all the way to the surface.

    This also shows that in an area west of the South Eugene Island area, a giant gas plume originates from beneath salt about 15,000 feet down and then disrupts the sediment layers all the way to the surface. The surface expression of this plume is very large — about 1,500 feet in diameter. One surprise, Whelan said, was that the gas plume seems to exist outside of faults, the ground fractures, which at present are the main targets of oil exploration.

    It is suspected that the process of upward migration of petroleum is driven by natural gas that is being continually produced both by deeply buried bacteria and from oil being broken down in the deeper, hotter layers of sediment. The pressures and heat at great depth are thought to be increasing because the ground is sinking — subsiding — as a result of new sediments piling up on top. The site is part of the huge delta formed over thousands of years by the southward flow of the massive Mississippi River. Like other major deltas, the Mississippi’s outflow structure is continually being built from sands, muds and silts washed off the continent.

    Analysis of the oil being driven into the reservoirs suggests they were created during the so-called Jurassic and Early Cretaceous periods (100 million to 150 million years ago), even before the existing basin itself was formed. This means the source rock is buried and remains invisible to seismic imaging beneath layers of salt.

    In studying so-called biomarkers in the oil, Whelan said, it was concluded that the oil is closely related to other very old oils, implying that it “was probably generated very early and then remained trapped at depth until recently.” And, she added, other analyses “show that this oil must have remained trapped at depths and temperatures much greater than those of the present-day producing reservoirs.”

    At great depth, where the heat and pressure are high enough, she explained, methane is produced by oil being “cracked,” and production of gas “is able to cause sufficient pressure to periodically open the fracture system and allow upward fluid flow of methane, with entrapment of oil in its path.”

    Copyright © 2002, Newsday, Inc.

    The strange bit left out of the article (but that I’ve seen elsewhere) is that the depth of the proposed oil is below the depth at which classical theory says you can have oil. It is supposed to have all been broken down by that depth.

    Also of note is that you have miles of bacteria laden rock, then a whole zoo of oil consuming life of great variety, befor you get to the surface. Plenty of opportunities of some bacteria or other to “mark” the oil or gas with “bio markers” (who’s isotopic mix will depend on the source carbon, not the surface carbon…)

    My own comment is that these communties of oil eating critters took time to evolve. But where? They had to be consistently getting some food to survive… This isn’t going to be some new phenomenon just recently. Oil has been seeping up for a very very long time to have such a diversity of critters living on it. That means a lot of oil, and not just some donosaur rotting under a mile of rock and salt dome far from life…

    So “Something is afoot”. We just don’t know what…

    IIRC, Eugene Island was the one that was refilling. They found the source vent on sonar and were unwilling to poke it to see (fearing the goose would stop giving eggs of oil). This story makes it look like someone got greedy and decided to “drill the hole bigger” and shut it off…

    A search on Eugene Island ought to be interesting.

  21. R. Shearer says:

    Thanks. I appreciate your breadth of interests, some which I share. I spent a couple hours on this today. Since you cited Rense, I found the link below from Heinberg, the conclusion of which I tend to agree.

    I need to get hold of Thomas Gold’s book before making a stronger judgement but in general I find that the abiotic proponents (on the web) tend to spew pseudo-science. That doesn’t mean they are wrong, but as a chemist I find sound scientific arguments to be more persuasive. See this paper for example.

    Click to access brocks2004.pdf


  22. E.M.Smith says:

    @R. Shearer:

    I’m more or less in agreement with the “rense” link. I lean a bit more toward “it could be possible” and a bit less toward “no way”, but generally think “abiotic is possible, with issues”.

    With that said, reading the link, I came to realize that there is really a “3 way” spread of views (and maybe 4…) not just “aboitic vs biotic”:

    1) PRIMORDIAL oil. Some folks seem to be saying oil is from the formation of the planet 4.5 Billion years ago. “I don’t think so Tim” comes to mind… Present lunar formation theory holds that the proto-earth got whacked hard and the volatiles got vaporized. The “condensate” was volatile poor on the moon, but not zero. So where is the trace lunar oil? Even if you allow that somehow the methane gets all loaded onto Earth or stripped from the moon, “light stuff floats” and oil is lighter than water, and a lot lighter than rock. It would (should?) be up where the newly forming life would eat it. So I lean against the notion of anything other than trace primordial oil hanging around. CO2, sure. Maybe even some methane, but not a lot.

    2) Pure Biotic oil: We know much oil is biotic. (Heck, some algae make up to 50 % body weight oil in nitrogen poor ponds, then die and sink. All it takes is an anoxic sedimenting zone. And as you well know, we’ve got the geologic history and biomarkers to show such history clearly happened. North Sea, for example.) But is there ONLY biotic oil? I see lots of evidence for it being dominant, but little way to prove it is “only”…

    3) Geologic Oil: Or what might be called “subduction oil” or “natural FT oil” or any of a thousand other names. At subduction zones, huge slabs of rock get subducted. We know a load of carbon gets sucked down as a load comes back out as CO2 from the volcanoes that form. We know that various carbon rich gasses can be turned into gasoline and oil like molecules via rock catalysts such as zeolites. It’s not a ‘big stretch” to suppose that some zeolites and subducted carbonates react to make petroleum chemicals. But does it happen “in real life”? Not seen yet…

    4) Deep Rock Bio-oil: I could also see a case for CO2 or Methane of primordial or even subduction origin being food for some bacteria that excreets oil. We’ve made bugs like that in labs. We’re still learning about all sorts of odd bugs that live in the earth (like the gold bugs in this article).

    Then, of course, you could mix and match these…

    So my only position is that while we’ve shown most oil is from biotic sources, we not shown it couldn’t be a #4 in some cases, and we’ve not shown that a #3 couldn’t be picking up “bug juice” along the way. (Who knows what the marker profile would be for an unknown set of bacteria). So I remain cautiously curious.

    I do fully agree with the notion that it’s not going to suddenly result in a perpetual oil supply. Even if subduction FT oil were proven real tomorrow:

    1) It would be way deep and painfull to drill. (Easier to just pick it up as it refills traditional fields over the top of it anyway). So no net economic impact.

    2) Crust does not subduct all that fast, and most of what does is not carbon bearing. That is going to be one slow run rate of production… Would be nice to know about, but when you are blowing through millions of years of production per decade, it’s not going to fill the tank even if real.

    So I see it more as an intellectual curiosity. It would be “way cool” to find that some particular porous rocks acted as a molecular sieve to subducted “bottom ooze” and made crude at 200 C over a 1000 year period. Just like it was ‘way cool’ to find the natural nuclear reactors in Africa. Useless, but cool!

    At that same time, if someone managed to drill a core through to the CO2 creation zone of a subduction zone and showed that there just were no bugs living on the CO2 in that core and no oily stuff either, it would not surprise me one bit. I’d be a bit disapointed at “nothing new?”, but that’s about it. And if someone else showed that carbonates are too light to subduct and always get scraped off and folded in place, their biologics turning to oil and the carbonates to limestone, well, that’s the default thesis as I understand it. Dull and ordinary but “The facts just are. -E.M.Smith”…

    So I suppose all that is just a very long way to go around the mountain to say “No worries, I’m not one of those folks who thinks the world is made of primordial oil”… I’m just one of those folks who would like to see a natural FT reactor, even if a tiny one ;-)

  23. Hugo M says:

    The most interesting insight in context of the controvery on the origin of oil is that the origin of life may not have happened in occassionally warm surface puddles, but in a warm, chemically rich layer around 10 km thick below surface, which provides an protected environment stable for eons. Various Archaea species had been discovered by the Deep Ocean Drilling program, now even “glass eating” bacteria are suspected:

    Until recently, conventional wisdom held that Earth’s subsurface was a sterile place, devoid of life. Exciting new results, however, indicate that this is far from the truth. Scientists have discovered evidence of organisms deep beneath Earth’s crust on both continents and ocean floors. By studying new microbial life-forms, and the incredibly wide range of environments in which they live, we gain a much better understanding of how life began and evolved on Earth, and possibly other planets. To this end, ODP has led the way in collecting subseafloor microbes to evaluate the exciting new paradigm of the so-called deep biosphere. The size of this biosphere is difficult to determine, and will require additional drilling to constrain. The concentration of living material in the oceanic crust is small, but because of the huge global volume of this material, it may contain a significant fraction of Earth’s biomass [Parkes et al.,1994]. About 5% of oceanic crust consists of volcanic glass, intuitively a material inhospitable to life. Nevertheless, new microscopic examination and application of molecular genetic techniques on DSDP and ODP basalts collected near the Mid-Atlantic Ridge [Bougault et al., 1985] suggests that the rocks contain ample evidence of microbial life. The idea is that microbial activity, indicated by pitting of the glass, and the formation of intricate and branching burrows, helps weather and erode this volcanically derived material. The microbes may even be “eating” the glass, using it as an energy source. The most typical texture observed microscopically is thin irregular channels, about one µm in diameter and extending 20 to 40 µm into the glass (see photomicrograph). A better understanding of Earth’s subsurface biosphere will result by examining other crustal rocks and new samples from future drilling that are free of contamination and are specially preserved immediately after collection. Microbes in volcanic crust may turn out to be important catalysts of chemical change. In this role, they would help regulate the cycling of elements between seawater and the oceanic crust. Microbes that derive their energy from inorganic chemical reactions suggests that life may thrive in previously unsuspected places, such as on Mars and Europa.


  24. E.M.Smith says:


    Talk about your ‘connections moment’…

    I’m looking up “cold season vegetables” to make plans for future gardens (as here in California we’ve got a definite cold streak going on compared to the last 1/4 century) and I’m running down the Chenopods…. (“Goosfoot” family, that someone has now renamed just to confuse things…) and run into:

    Silver and Gold nanoparticles synthesis:

    Chenopodium album plant leaves are used in biosynthesis of Ag and Au nanoparticles.This pristine method is rapid,facile,convenient,less time consuming,environmentally safe and can be applied in a variety of existing applications.
    19. Amarendra Dhar Dwivedi, K. Gopal, Biosynthesis of silver and gold nanoparticles using Chenopodium album leaf extract, Colloids and Surfaces A: Physicochemical and Engineering Aspects, 369, 27-33, 2010.

    So it looks like it’s not just bacteria that do things to gold. While not the same as excretion, it’s still an interesting thing to realize that gold is subject to impact from metabolic chemicals and processes…

  25. E.M.Smith says:

    @Hugo M:

    How bizzare. A bug that may eat glass? …

  26. Hugo M says:

    @E.M. Smith:

    maybe he only dissolves glass using energy from another process. One would also bet that this still uncharacterized species must be able to produce hydrofluoric acid.

    An in-situ hybridazation experiment of thin sections of this glass was positive for DNA and archaeal ribosomes stained with Arch344-FITC indicated the presence of archaea.

  27. E.M.Smith says:

    @Hugo M:

    Don’t think it needs hydrofluoric acid. Plants already use silica and have the needed enzymes to absorbe and transport it.

    Diatoms, Silicon and Carbon

    From this article:

    Click to access abjc18feb0502.pdf

    we have in the opening paragraph:

    Diatoms are the world’s largest contributors to biosilicification and are one of the predominant contributors to global carbon fixation. Silicon is a major limiting nutrient for diatom growth and hence is a controlling factor in primary productivity. Because our understanding of cellular metabolism of silicon is limited, we are not fully knowledgeable about intracellular factors that may affect diatom productivity in the oceans.


    Here we are smack up against all that “settled science” again. Predominant carbon fixer. Don’t know what controls its productivity. Understanding is limited. Silicon is limiting (and I wonder just how much work has been done on the “silicon cycle” to see how it controls the carbon cycle via diatoms… a google of ‘life “silicon cycle”‘ gave about 5700 articles and a lot of them are ‘misses’ where the terms are there but the topic is different. I think the diatom and silicate guys are missing out on the AGW Gravy Train here. Someone needs to send them the memo… ).

    From Bamboo and grasses to diatoms, life already uses silicon and silicates.

    It looks like even people may metabolize it:

    During the 20th century, progress was made by pioneering researchers and scientists such as Carlisle, Butenandt, Iler, Bergna, Kervran, and Schwartz. Edith Carlisle’s work in the 70′s through the 90′s at the UCLA School of Public Health, perhaps more than any other, demonstrated the necessity of having silica in the body for proper growth and development. As a result of her research, we know that silica is absolutely essential for the body to create and maintain collagen. What was dramatically shown through Carlisle’s research was that when silica is withheld from normal nutrition, gross abnormalities develop and normal growth does not take place. While Carlisle’s work was done with chickens and mice, humans have also been experimenting with silica.

    So maybe we need to have some more “sand sandwiches”

  28. Hugo M says:

    @E.M. Smith:

    But plants and diatoms take up silicon hydroxide (silic acid) in an already dissolved form, which is assumed to have been physically weathered from land. But how the Archaea turn SiO2 into the dissolved form?

  29. Jason Calley says:

    Regarding silica, we have discussed the use of diatomaceous earth (which is about 90% silica) for insect control, but you are correct to point out the nutritional use as well. It is sold as a food supplement and also taken to kill intestinal parasites.

  30. @Jason Calley Silica for insect control is “burnt” silica, i.e. crystals of SiO2, silicon dioxide, while silica used in agriculture is H3SiO4 (Silicic Acid=Silica Gel-dried or wet-).
    Diatoms have its celullar protein nucleus preserved, thus this nuleus is food.

  31. E.M.Smith says:

    @Hugh M:

    A BING! search of “silica soluability limits in water” shows silica has a limit of 0.12 g/L which means it DOES disolve. Now all you need is for the bugs to be able to tansport it, or put some moisture on the surface and such it off of a different surface. (i.e. make a pump picking up water at one end and dumping it at the other, washing the silica along for the ride…)

    Also, this paper looking at the tranport of highly insoluable iron froms finds it may be the silicon forms that is helping to move it. That implices the silicon forms are already in existence in these natural geologies:

    YOKOYAMA, Takushi, BAZILEVSKAYA, Ekaterina, WATANABE, Yumiko, and OHMOTO, Hiroshi, Astrobiology Research Center & Dept. of Geosciences, The Pennsylvania State Univ, 435 Deike Bldg, University Park, PA 16802,

    Iron is one of the most insoluble elements in oxygenated water because ferric iron is easily hydrolyzed and precipitated as ferric hydroxides with extremely low solubilities. Therefore, anoxic environments have been considered essential for the transport of Fe as ferrous iron. However, we have found that up to ~5 ppm of ferric iron dissolves in near-neutral oxygenated water containing high concentrations (~800 ppm) of silicic acid. Using spectrophotometry and gel chromatography, we have investigated the dissolution of ferric iron in solutions containing various amounts (75 – 800 ppm) of silicic acid at ~20 to 90°C. The dominant form of silicic acid changes from monosilicic acid to monosilicic and polysilicic acids when the concentration of silicic acid exceeds the solubility value of amorphous silica. The amount of ferric iron dissolved in solutions increases with increasing concentration of silicic acid. We have also recognized ferric iron dissolves in silicic acid-bearing solutions as two forms of stable colloids that are composed of ferric iron and silicic acids. Based on the Si/Fe ratios and UV absorption spectra of the colloids, we suggest the first colloid form (termed ISAC-I) is composed of particles of ferric hydroxide with adsorbed silica and the second colloid form (termed ISAC-II) is composed of particles of silicic acids with adsorbed ferric hydroxides. ISAC-I and ISAC-II form when the silica content of solution is below or above the saturation of amorphous silica, respectively. Our study suggests significant amounts of Fe can be transported for a long distance in oxygenated water in some environments containing high silica, such as the surface discharge of geothermal fluids.

    So looks to me like it’s just “Take silica, add water, get various forms of silicic acid”. And it is present in “geothermal fluids”…

    I’m not seeing the problem with getting silica mobilised.

    Sidebar from the Wiki on Silicic Acid

    Silicic acid is a general name for a family of chemical compounds of the element silicon, hydrogen, and oxygen, with the general formula [SiOx(OH)4-2x]n.[1][2] Some simple silicic acids have been identified in very dilute aqueous solution, such as metasilicic acid (H2SiO3), orthosilicic acid (H4SiO4, pKa1=9.84, pKa2=13.2 at 25°C), disilicic acid (H2Si2O5), and pyrosilicic acid (H6Si2O7); however in the solid state these probably condense to form polymeric silicic acids of complex structure.

    Silicic acids may be formed by acidification of silicate salts (such as sodium silicate) in aqueous solution. When heated they lose water to form silica gel, an active form of silicon dioxide.

    In the oceans, silicon exists primarily as orthosilicic acid (H4SiO4), and its biogeochemical cycle is regulated by the group of algae known as the diatoms. These algae polymerise the silicic acid to so-called biogenic silica, used to construct their cell walls (called frustules).

    Continuing research of the correlation of aluminium and Alzheimer’s disease has in the last few years included the use of silicic acid in beverages, due to its abilities to both reduce aluminium uptake in the digestive system as well as cause renal excretion of aluminium.

    So looks to me like take silicate rocks, apply acid solution: silicic acid. Metabolize.

    That last note is also interesting. Maybe I need to feed Granny some sand ;-)

  32. Jason Calley says:

    @ Adolfo Giurfa

    Well, I have certainly been wrong many times before, (and this may be another time!) but I think we may be talking about differing things here. There is a form of diatomaceous earth (often sold as a filtering material for pools, etc.) which has been fired at a high temperature, “burnt” as you say, and that variety is not suitable for consumption. It may in fact be good for insects, but I have not personally used the burnt product. What I have used is the food grade diatomaceous earth, which is the accumulated silica skeletons of diatoms left as deposits to be mined from the earth. This is a softer, not so hard or abrasive sort of silica, and is pretty much 90% silica with no living component or intact nucleus. It can be added to grains, rice or other food to allow storage without insect infestation, and because it is food grade it can then be safely eaten by humans, along with the grain. It can also be used agriculturally or in the garden to kill or discourage insets. It is also taken by some people as a nutritional supplement.

    I am not familiar with the use of H3SiO4 in agriculture. Is it used as a mineral or pH supplement to correct for soil conditions, or is it used to kill insects?

  33. Jason Calley says:

    @ E.M. “A BING! search of “silica soluability limits in water” shows silica has a limit of 0.12 g/L which means it DOES disolve.”

    It does dissolve — but slowly! I have a pretty good collection of tektites, including some Libyan Desert Glass with a 98% or so silica content. Dating their ages is rather problematic, but I have noticed that the older varieties, especially the Moldavites, have much deeper pitted and fluted shapes. I do not have a source on this, (it may be in one of the few books on the subject) but I seem to remember that not only are the flutes a result of silica dissolving in ground water, but it seems to dissolve preferentially along the areas of highest stress in the glass.

    Going farther out on a limb — but still in keeping with the subject — about 20 years ago, an old friend of mine, a research scientists for a major corporation, told me that he had put a slice of tektite under an electron microscope. He claimed to have seen what he thought were nano-bacteria, something similar to the suspected cause of the NASA reported “Martian bacteria tracks” in meteorites. Personally…I respect my old buddy, but I have a hard time swallowing bacteria in tektites. Still, he was an interesting guy!

    Also, if you are going to feed sand to Granny, remember that a lot of radiator and head gasket leak-repair additives are mostly sodium silicate, aka “water glass.” Just make sure Granny is not hot and under a lot of pressure when you give it to her. Safety first!

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