Episode 395 Connections

This episode is about some of the interesting connections that arise in science.

We’ll start with me and my first professional job as a mineralogist analyzing kidney stones. My mineralogy professor at Indiana University, Carl Beck, died unexpectedly, and his wife asked me as his only grad student to carry on his business performing analysis of kidney stones. Beck had pioneered the idea of crystallographic examination to determine mineralogy of these compounds because traditional chemical analysis was misleading. For example, some common kidney stones are chemically calcium phosphates and calcium carbonates – but they are hardly ever calcium carbonate minerals. That makes a big difference in terms of treatment, because calcium carbonate minerals can be dissolved with acids, while calcium phosphate cannot. The carbonate is actually part of the phosphate mineral structure, partially substituting for some of the phosphate. Other subtleties of mineral crystallography can distinguish between different minerals and can point to specific kinds of treatments, more than just chemistry can.

One of the most common minerals in kidney stones is called whewellite – calcium oxalate, CaC₂O₄ with a water molecule as part of its structure. In kidney stones it usually forms little rounded blobs, but sometimes the way the mineral grows, it makes pointy little things called jackstones, for their similarity to children’s’ jacks. And yes, those can be awfully painful, or so I’m told.  Whewellite is really rare in the natural world beyond the urinary system, but it does exist, especially in organic deposits like coal beds. Whewellite was named for William Whewell, spelled Whewell, a true polymath and philosopher at Cambridge University in England during the first half of the 19^th century. He won the Royal Medal for his work on ocean tides and published studies on astronomy, economics, physics, and geology, and was a professor of mineralogy as well.

Mary Somerville, 1834 painting by
Thomas Phillips - source

Whewell coined many new words, particularly the word “scientist.” Previously such workers had been called “men of science” or “natural philosophers” – but Whewell invented the new word scientist for a woman, Mary Somerville. Somerville researched in diverse disciplines, especially astronomy, and in 1835 she became one of the first two female members of the Royal Astronomical Society, together with Caroline Herschel, discoverer of many comets and nebulae.

In 1834 Somerville published “On the Connexion of the Physical Sciences,” a synthesis reporting the latest scientific advances in astronomy, physics, chemistry, botany, and geology. William Whewell wrote a review in which he coined the word scientist for Somerville, not simply to invent a gender-neutral term analogous to “artist,” but specifically to recognize the interdisciplinary nature of her work. And even more, according to Somerville’s biographer Kathryn Neeley, Whewell wanted a word that actively celebrated “the peculiar illumination of the female mind: the ability to synthesize separate fields into a single discipline.” That was what he meant by a scientist.

Somerville was born in Scotland in 1780 and died in 1872 at age 91. Her legacy ranges from a college, an island, and a lunar crater named for her to her appearance on Scottish bank notes beginning in 2017. Besides the mineral whewellite, William Whewell is also memorialized in a lunar crater and buildings on the Cambridge campus, as well as in the word scientist, included in the Oxford English Dictionary in 1834, the same year he coined it. He died in 1866.

—Richard I. Gibson

LINK:

Article about Whewell and Somerville 

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