Geological Theory Challenges

Please forgive me if this is not specific to gemstones, but I think it is relevant and I am curious to hear others thoughts on this.

Over the past couple of decades, it is becoming more and more clear that microorganisms (bacteria, largely) play a central role in the formation of minerals, and a number of other geological processes (erosion, etc). To date, geological theory has focused on geothermal and non-biological processes (heat, pressure, etc.) but multiple papers are published each year which challenge that theory, or at least suggest a need to rethink many of the fundamental assumptions of that field of science. For additional information search ā€œMICPā€ (microbial induced calcite precipitation) or simply ā€œbiomineralizationā€.

The relevance to gemstones I believe is significant. Since gemology rests largely on geological theory, and it is becoming clear that bacteria/microorganisms almost certainly played a significant role in the formation of minerals/gemstones, it will likely prompt revisions to everything from mining, to synthetic synthesis of gemstones, to various theories related to gemstones themselves.

I recognize this is a touchy subject in the field of geology, and I do not want to stir up non-constructive discussion, but I am curious to hear if this emerging research has found its way into the field of gemology, or if anyone has perspective on its potential impact.

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Although ā€œbiomineralizationā€ is very real, all the professional papers in support of this process are related to surface conditions and the formation of non-gem minerals… mostly calcium phosphates and carbonates. Most of the gem minerals we love (ruby, sapphire, diamond, tourmaline, topaz, garnets…etc.) have NOT been the subject of biomineralization because the thermodynamic data is overwhelming that the stability fields for their formation are indeed high temperatures and often high pressure. I find your statement of ā€œmultiple papers are published each year which challenge that theoryā€ is just not correct… none of the studies you cited are questioning the hydrothermal, igneous, or metamorphic origins of the vast majority of gemstones that we enjoy working with in our society.
I like Newton’s statementā€¦ā€œIf I have seen farther than others, it is because I have stood on the shoulders of giantsā€. New directions in science rarely negate previous sound research, but are built by extending the earlier results into unknown areas. The thermodynamics used in current biomineralization are built upon the same principles that were established in the research of the formation and stability of gemstone… the new direction is not producing contradictory or alternative origins for gems… but is exploring the field of low temperature (and low pressure) mineral formation by living organisms… This is a new field that is NOT questioning the well established processes of gemstone formaion.

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Thank you for the thoughtful reply, I appreciate your perspective. I certainly do not want to stir up controversy, I know this can be a touchy thing in geology. I certainly could have chosen differently terms in my post, but I am pretty confident the points I made are quite well supported by the research. Microbes and bacteria are indeed essential to a great number of geological processes that were once thought to be geothermal (ie, non-biological, in this sense). That is not to say that geothermal, climatic, etc. forces are not also essential factors in mineral formation (and processes like erosion, etc), I hope that was not how my post reads. My point is/was roughly that these non-biological factors are not at all sufficient to explain a a great number of such processes, including the bio mineralization of a rapidly glowing list of minerals, many of which are indeed considered ā€œgemstoneā€ or gemstone minerals (agate, carnelian, and even pearls, to name a few - see bottom link). The thing with discoveries like this is not so much the current state of knowledge (in this case of the absolute number of minerals and processes with essential biological dimensions), but the trend. Here’s a rough sense of those trends from Pubmed, the first a chart of the publication of papers on bio mineralization, the second on MICP (microbial induced calcite precipitation, a subset of the former, as I’m using the terms:


Of course, theae papers cover more than just gemstones or even minerals, but that speaks to the growing awareness of the breath of such processes, which is hard to really dismiss, IMHO.

It’s interesting to me that the role of microbes in the production of minerals and other hard, mineral like processes was quite well known in ancient times (Strabo and Horodotus both describe it, but not using thai term), so it’s not new knowledge, nor does it seem particularly controversial. I guess I was just interested in hearing what others may think of this topic in the gemstone world, and I appreciate your reply.

Here’s a few papers, just by way of context. There are many (I understated the number by using ā€œyearlyā€ in that sentence), and it’s a fascinating field:

https://www.sciencedirect.com/science/article/abs/pii/S1084952115001627

Pearls are indeed a biomineralized example of carbonate (85+% CaCO3). Coral is another and bacterial interaction is certainly not excluded as a component. I did my PhD in part on neo-diagenesis and found a clear link between organic matter and the precipitation of clays in very young sediment (bacteria are directly involved in this process).
However, this is not the same as the usual gem minerals like diamonds, emeralds, sapphires, garnets, etc… that are typically formed at temperatures higher than bacteria can survive. Agate, carnelian, and opal are all variants of quartz which can form under a range of temps from way too hot to just right for bacterial interaction. And, bacteria do interact with iron and sulfate mineralization at surface conditions and at depth. Nonetheless, most of what the folks on this site would call precious gems are formed at high temps (too high for bacteria).

Hi, thanks for the reply, it’s still a topic that interests me a lot, and I’ve done quite a bit of research on the topic (i’ll probably write a paper one of these days on the topic).

I’m not sure I agree with you, though. Since posting this, I’ve found pretty extensive ancient textual references to this process specifically, although the biology was not known as such, the process was as far more widely known than I would have guessed. Temperatures are not quite relevant in the sense that I think you are framing your reply. That is, although bacteria can survive on an astroid or in acid (and in very high temperatures), as a biological process, such high temperatures are not a factor, and to my knowledge, such processes can occur pretty much anywhere on earth (in any environment). I even tried it in my basement, it’s not at all difficult, and made something approximately basalt, it’s remarkably hard (density wise). Admittedly, that’s not a gemstone (although I’m quite pleased with the results, lol), but most known grow-able crystals do not require particularly high temps, and they don’t even require lab conditions, mother nature does most of the heavy lifting.

I think it’s hard to argue, just given the statistical rate of discovery of the central role of such processes versus the finite number of known minerals, that it’s just a matter of time before most, of not all, including gemstones, are understood to involve biological processes. That’s not my opinions, it’s sort of how the math works out. Anyhow, if you are interested I can forward the paper when it’s done. Thanks again!

Paul,
Interesting… Can you please list the precious gem minerals that form at low temperatures or surface conditions and that have documentable bacterial mediation for their formation? For carbonates, sulfates(ides), silica (including opal), and numerous other minerals that may not be considered precious gems… we may easily agree on a number of these minerals being bacterially mediated at temperatures bacteria can do their thing. When we get to garnet, tanzanite, topaz sapphire, emerald, diamond, etc… maybe not so much. Mother nature tends to do the heavy work with temperature and pressure for these (the lowest documented formation temps for these minerals is ~700 degrees F and higher (>melting point of lead). If you can do so with the right mix of bugs in your basement, there will be a LOT of folks here who will be extremely interested to see your results!

Sure (but I warn you, this will be a long reply, lol), as it’s a big topic and a lot is happening in research at a very fast pace.

Here are some ancient and mideival textual references, and some modern ones. It is important to note that in the ancient texts (which is the primary focus of my research, as contextualized with modern science) the authors, and likely the actual stone producers or lapidaries, are clearly not aware of the specific details of the biological or amorphous processes involved (none, for example, state the producer of said mineral/stone is ā€œintroducing biotic processes to precipitate calcitesā€, or such, of course, but in many cases, the processes are clearly described, involving material like uric acid (easily available, lol), ā€˜fermentation’, and similar processes over time, and the introduction of bacterial sources and often enzymes (from various sources, including soil, mushrooms, decomposed organic matter, etc). Many are even reproducible, I can show you some crazy results I’ve gotten attempting to replicate (not pretty, but pretty cool to me). Also, the names and classifications of ancient gemstones changes so much over time, what is described, although often explicitly described as a ā€˜precious’ stone, is not described in modern terms, but there is often good physical descriptions of colors, features, etc.

To be sure, if such references were rare and not consistent in many such descriptions, one could say (I would say) it’s simply ā€œalchemyā€, but they are neither, they are quite widespread across cultures and for many millennia. In this regard, the ancients have us beat by a long shot, lol.

Finally, as per my original post, it seems clear that we are learning more and more, at an increasing rate, of the central role of biotic processes in the formation of minerals that until recently, were considered purely abiotic. Is anyone brewing diamond or emeralds today? Of course not, but the more we learn, the more it become clear that crystaline structures regularly form through biological interactions at temps and pressures that can be, in many cases, ambient (or not at all extreme). I don’t know what the limit is for such things, that is, I have no clue how extensive such processes are, but if you consider the ancient record and both current research and the trajectory of insights it has produced, it seems quite certain that these processes (whether microbial mediation, and/or involving biogenic silica precursors at ambient temps) will be seen as central to more and more crystalline minerals. I could be wrong on that, but the trend seems to suggest it inevitable.

Ancient (the stuff I research):

Indian Rasaśāstra and lapidary texts detail not just heating, but soaking, fermenting, and fluxing stones to alter or improve them.

Pliny the Elder (Natural History, Book 37) explicitly describes

  • Dyes applied to emeralds and opals.
  • Heating carnelian to deepen color.
  • Fakes made from colored glass and treated quartz.
  • Also mentions various people of central Arabia using urine and other processes to harden soft materials to produce stone for construction.

Bį¹›hat Saṁhitā (Varāhamihira)

  • Though often interpreted as astrological, it also includes technical descriptions of gemstones, including mentions of stones that are manipulated or imitated.

Al-BÄ«rÅ«nÄ« (973–1050 CE) - goldmine of such descriptions.

  • Text: Kitāb al-Jamāhir fÄ« MaŹærifat al-Jawāhir (Book of Precious Stones)
  • Describes several human produced precious ā€œmoldedā€ gemstones (ā€˜Adhrak’ for example, resembling), often produced by earlier peoples, and various treatments involving such processes.
  • Describes various treatments to enhance color or features, or convert various raw materials into precious stones/precious stone-like features; regularly involving heating, but not to high temperatures, and regularly involving urine (often from specific animals), burying the combined substances for extended periods of time (which would invariably introduce naturally occurring bacteria and facilitate fermentation or de/recomposition process), etc.

Jābir ibn įø¤ayyān (Geber, 8th–9th ce)

  • Text: Kitāb al-Asrār (Book of Secrets), Kitāb al-KhamsÄ«n, and others in the Jābirean Corpus.
  • Content: Includes numerous recipes for the artificial generation of gemstones, crystals, and metals, including descriptions of combining earths, soaking materials, heating with sulfur or mercury, and long periods of ā€œcookingā€ or ā€œburying.ā€

Bencao Gangmu (ęœ¬č‰ē¶±ē›®) – Li Shizhen (16th c.)

  • Content: An encyclopedic Ming dynasty materia medica. Lists hundreds of stones, minerals, and synthetic preparations used in medicine, construction, and art. Notable examples - Descriptions of ā€˜stone powders’ mixed with animal glue to make polished tablets or imitation jades.Processes where ā€œearths are baked and steamedā€ to become hard like stone, sometimes for moxibustion or writing tablets. Some entries clearly describe heat-treated or chemically altered materials, not simply mined stones.

Pseudo-Democritus / Apollonius of Tyana (Arabic reception)

• Text: Kitāb al-Madkhal al-KabÄ«r (The Great Introduction) as translated/adapted in Arabic

• Content: Early Greek alchemical texts received into the Islamic world describe methods for growing or forming stones, often for magical or ornamental purposes. These were sometimes preserved in alchemical manuals focused on ā€œartificial stonesā€ (įø„ajar į¹£ināʿī).

Modern:

Opal production at ambient pressures/temps:

https://www.mdpi.com/2075-163X/14/10/969

Biotic processes in agate synthesis

https://www.mdpi.com/2075-163X/10/11/1037

Biogenic contribution to the process of quartz formation:

  • Microbial Mediation: Certain bacteria can facilitate the transformation of amorphous silica into crystalline quartz.
  • Biogenic Silica Precursors often involved

https://pubs.acs.org/doi/10.1021/acs.chemmater.4c01087