The 366 daily episodes in 2014 were chronological snapshots of earth history, beginning with the Precambrian in January and on to the Cenozoic in December. You can find them all in the index in the right sidebar. Now, 2015, the blog/podcast is on a 3 or 4 per month schedule with diverse topics.

Tuesday, January 20, 2015

Episode 367 – Kidney stones

Today I want to talk about some of the youngest minerals on earth – kidney stones. Some might argue whether these should be considered minerals at all, since part of the definition of a mineral is other than man-made, but that’s usually phrased as “naturally occurring” and these mineral deposits really are natural, even if they are not welcome.

My first professional job was analyzing kidney stones. My mineralogy professor, Carl Beck at Indiana University, had died, and his wife asked me, his only grad student, if I would continue the analytical business he had been operating. I said yes, setting out on a four-year, 20,000-kidney-stone start to my geological career.

First, please accept this disclaimer. I am not a medical doctor. I’m not even a geological doctor. So don’t take anything I say as medical advice.

Apatite is a common mineral in nature. Chemically it is a complex calcium phosphate with attached molecules of hydroxyl (OH), fluorine (F), and sometimes other elements. Apatite is the fundamental mineral component in bones and teeth, and when apatite has fluorine in its crystal structure, it is stronger. This is why fluorine is added to water and toothpaste. In kidney stones, carbonate (CO3) substitutes for some of the phosphate, making a mineral that is relatively poorly crystallized. Its formula in kidney stones is usually given as Ca5(PO4,CO3)3(F, OH, Cl). Well-crystallized or not, apatite often forms the nucleus upon which other urinary minerals are deposited. It usually occurs as a white powdery mineral deposit, one of the most common components of kidney stones.

Two minerals that are really common in human urinary stones but that are exceedingly rare in nature are whewellite and weddellite, calcium oxalates. Oxalate is C2O4, not too different chemically from carbonate, CO3, the common constituent of limestone.

Whewellite (CaC2O4.H2O) is known to occur in septarian nodules from marine shale near Havre, Montana, with golden calcite at Custer, South Dakota, and as a fault filling with celestite near Moab, Utah. It is found in hydrothermal veins with calcite and silver in Europe, and it often occurs in association with carbonaceous materials like coal, particularly in Saxony, the former Czechoslovakia, and Alsace. Whewellite was named for William Whewell, an English poet, mathematician, and naturalist who is credited with the first use of the word ‘scientist,’ in 1833.

It is one of the most common kidney stone minerals, where it typically occurs as small, smooth, botryoidal – which means like a mass of grapes –  to globular yellow-green to brown, radially fibrous crystals. Whewellite stones larger than ½ inch across are quite unusual. Often whewellite is deposited upon a tiny nucleus of apatite, which may form as build-ups on the tips of tiny papillae in the kidney. Those papillae are little points where ducts convey the urine produced by the kidney into the open part of the kidney.

Weddellite, CaC2O4.2H2O, was named for occurrences of millimeter-sized crystals found in bottom sediments of the Weddell Sea, off Antarctica. Unfortunately the sharp yellow crystals that urinary weddellite forms are often much larger than that, and they are frequently the cause of the pain experienced in passing a kidney stone. Rarely, weddellite crystals may occur that are nearly a half inch on an edge, but most are somewhat smaller. The yellow crystals are commonly deposited upon the outer surface of a smooth whewellite stone. Like whewellite, weddellite is a calcium oxalate. They differ in the amount of water that is included in their crystal structures, and this gives them very different crystal habits. Occasionally, weddellite partially dehydrates to whewellite, forming excellent pseudomorphs of grainy whewellite after weddellite's short tetragonal dipyramids. Together, apatite, whewellite, and weddellite are probably the most common urinary stones.

Struvite is a hydrous magnesium ammonium phosphate, Mg(NH4)(PO4).6H2O, that forms distinctive coffin-shaped crystals. Often masses of tiny crystals grow together with powdery apatite to form huge branching stones called "staghorns," which may be several inches long. They may even fill up the entire open area of a kidney. Struvite stones are sometimes associated with bacterial infections of the urinary system. They also require non-acid systems to form, as indicated by the presence of ammonium (a basic, non-acidic compound) in the crystalline structure. The only common occurrence of struvite outside the urinary system is in bat guano. Certain dogs (especially Dalmatians) can produce remarkable large, smooth, milky-white tetrahedrons of well-crystallized struvite.

Brushite is a calcium phosphate compound, CaHPO4.2H2O that is very similar to the common mineral gypsum (calcium sulfate, CaSO4.2H2O). Gypsum finds its greatest use in sheetrock and other wallboards used in home construction. Brushite is a rare mineral outside the urinary tract, and even there it probably occurs in fewer than 10% of all stones. It is a soft, silky mineral, usually honey-brown and showing a fine radial fibrous structure. It can only crystallize in a limited range of pH (acidity), so treatment may include changing the acid-base balance of people who make brushite kidney stones.

Whitlockite is very rarely found in the urinary system, but it is the most common mineral found in prostate stones. It is a calcium phosphate with small amounts of magnesium, Ca9(Mg,Fe)H(PO4)7, or Ca9(Mg Fe)(PO4)6(PO3)OH and its occurrence may be stabilized by trace amounts of zinc. Prostate fluid has a very high zinc content. The mineral is a resinous, brown, hackly-fracturing material, and it commonly forms multiple small stones in the prostate. It also sometimes precipitates as deposits on teeth in cases of periodontal disease. In nature, it’s pretty rare – it wasn’t formally described until 1941. It occurs in pegmatites, igneous bodies that often contain complex and unusual minerals, and in lunar samples and meteorites, where it is known as merrillite. Whitlockite also forms in bat guano.

The other moderately common crystalline compound in kidney stones is cystine, the amino acid. It forms maybe 1% of the total spectrum, and crystallizes as beautiful, soft, honey-colored hexagonal masses. It is the least soluble of all the amino acids which is probably why it can form kidney stones. So far as I know it never occurs outside of biological systems.

There are a handful of really uncommon kidney-stone minerals, including newberyite and hannayite, both magnesium phosphates, monetite, a calcium phosphate, and calcite and aragonite – calcium carbonate, really common in nature but really rare in kidney stones. Chemical analysis sometimes reports calcium carbonate in kidney stones, but that’s probably wrong. The analysis picks up the CO3, carbonate, that is incorporated in the apatite crystal structure. The chemicals are there, but not the minerals. And that can make a big difference in treatment.

If you have kidney stones, you have my sympathy! Drink lots of water.

My kidney stone web page (source of most of the text here, and more photos)
—Richard I. Gibson

Friday, January 16, 2015

The Precambrian - the daily episodes from 2014 combined

For 2014, the podcast consisted of daily productions averaging about 5 minutes each. The individual episodes for each month are now being assembled into packages for each month, representing various spans of time in the history of the earth.

This episode is the first package, which combines the 31 daily episodes for January, covering the Precambrian – the time from the origin of planet earth up to about 543 million years ago. This episode is an hour and 15 minutes long and includes all the individual daily episodes from January 2014.

If you listened to last year’s daily episodes, you’ll find that I’ve re-recorded some of them. Especially in early January, when I was just getting started, some of the episodes were technically lacking. I hope I have improved on that for this assembly of 31 episodes covering the Precambrian. Thanks very much for your interest in this project. As the year continues, there will be new episodes, maybe every week or two, in addition to these monthly assemblies.

If you have questions or comments, please let me know, either here on the blog – there’s a page for Question of the Week – or contact me by email at rigibson at I’ll try to respond.
—Richard I. Gibson

Wednesday, December 31, 2014

December 31. The 6th Extinction

So we’ve made it to the end of our geological year, covering 4.6 billion years of geologic time. 366 episodes, close to 180,000 words and a total of about 25 or 30 hours of programs. I hope you’ve enjoyed it! The podcast will not end, but the structure will change as we go into next year. It won’t be daily any more, sorry to say – there were times when it was really touch and go in terms of me getting the episodes out, but I’m happy to say I managed. Thanks for your interest – that was my main motivation once things got going. 

I’m not certain exactly what sorts of topics next year will bring. I’m not going to try to cover “current events” in any particular way because there are many good blogs and podcasts that do that. I expect I may do a few more that use my own work as a basis, and some posts will probably be based on topics in my other book, What Things Are Made Of. I want to try to do a few interviews with geoscientists working on interesting topics, and that may give it a Montana-centric flavor, but we’ll try to make things pertinent to a wide audience. Since I only covered 366 topics – and they were selected largely based on my own prejudices – there’s certainly plenty more that we can look at. Feel free to submit questions or suggestions, either through the blog or email me at rigibson at You’ll get a spamblocker message, but I’ll find your email. I’m not going to make any promises, but I am going to shoot for at least one episode every week or ten days next year. 

I also will be assembling the existing podcasts into single recordings. I’m not sure how it will work in terms of file sizes, but I’m hoping that I can make each month of the previous series into one or two packages – without the repetition of the intro music and exit tagline. I’ll try to edit the episodes into those assemblies early in the coming year and make them available in the usual way, through the blog. 

To close the year, I thought I might address what has been called the Sixth Extinction. Of all the mass extinctions in earth history, only five have been really, really devastating. Those are the ones at the end of the Ordovician, in the Late Devonian, the biggest of all at the end of the Permian, the Triassic-Jurassic extinction, and the one that ended the Cretaceous Period and the Mesozoic Era. The case has been made that we are presently in the midst of another mass extinction, the Sixth great one.

There is an entire book, titled The Sixth Extinction: An Unnatural History, by Elizabeth Kolbert. It just came out in 2014, and I recommend it highly. The New York Times Book Review listed it as one of the ten best books of 2014. The book makes the case for a present-day massive die-off of organisms, ranging from bugs and bats to corals and rhinos. We’ve seen in the podcasts in this series that things like climate change certainly affect extinction rates, and there is no question that earth’s climate is changing at high rates right now. There’s also no question that human activities are affecting many of the things that contribute to climate change. It’s happening.

Kolbert integrates our knowledge of past extinctions, such as the disappearance of the ammonites, which you have heard about in this podcast series, as lessons for the present.

We don’t really know how many species of plants and animals exist on earth today, although we have good ball-park estimates. New species, even new large animals, are being found all the time. So it’s hard to say with certainty what kind of extinction rate is in progress, but some estimates say that as far as we can tell, extinction rates today are as much as 1,000 times those that typified most of earth’s history. We might argue about whether what’s happening now is on a scale comparable to the Big Five Extinctions, but at some scale, an extinction event is assuredly in progress.

The big, charismatic animals, like rhinos, elephants, tigers, and whales, that need extensive spaces for their lifestyles, are probably most threatened by human pollution and invasion of habitat, but who knows what’s going on in the insect world or the frog world? Those who study frogs are concerned. Is it possible to help all, or even most, species survive in a human-dominated world? I certainly don’t know. Should we even try? From both the altruistic and selfish points of view, it would probably be advantageous to try. Even human-centric people can’t deny the continual discoveries of beneficial products that come from obscure plants and animals.

For me as a geologist, I sometimes take the long view – the earth does not care. If humans kill off lots of things, including perhaps themselves, earth, and life, will continue. It always has, and until the sun burns out or some incredible catastrophe happens, it always will.

Thanks for joining me on this journey. If you’ve learned a tenth of what I have learned in putting these talks together, you’ve learned a lot! I hope it was fun!

—Richard I. Gibson

Extinction rates

Animals that went extinct in 2014