Michael: People value gemstones for all sorts of reasons. They’re usually rare, pretty durable, and most of all, they’re shiny and sparkly. They can have multiple colors, streaks of light, weird inside-out shapes, and all kinds of other qualities.

The things we consider gemstones are often made up of minerals arranged into different types of crystals, although a few are made up of molecules that are arranged totally randomly. But either way, their properties come from their specific chemical structure. At the atomic level, it’s simple geometry, but it leads to some of the most beautiful natural materials on Earth.

When you look at a gemstone, probably the first thing you notice is its color. Some gems, like tourmaline and fluorite, can come in practically any color you can think of. And often, those colors come from transition metals that are incorporated into the mineral’s crystal structure — metals like copper, iron, and zinc. The transition metals are the metals in the middle part of the periodic table. Those elements tend to take on bright colors because the way their electrons are arranged lets them absorb visible light with certain wavelengths.

With those wavelengths gone, we see a complementary color. Sometimes, a specific metal is an inherent part of a mineral’s structure, so the mineral always takes on that color. Malachite, for example, has copper in its chemical structure, which turns it green.

Other times, the metals aren’t an inherent part of the mineral. Instead, they’re sort of hitchhiking in its crystal structure, occasionally taking the place of whatever element would normally be there. Ruby and sapphire, for example, are actually the same mineral, called corundum, with a chemical formula of two aluminums and three oxygens.

When some iron and titanium atoms replace a few of the aluminums, the mineral is brilliant blue. That’s what we call that a sapphire. But when the hitchhiking atoms are chromium instead, the mineral turns red and you have a ruby.

But there’s more to this color thing, because gems aren’t always just one color. Some look like they change color when you view them from different angles, an effect that’s known as pleochroism. See, crystals are made up of atoms arranged in repeating patterns.

The patterns form blocks called unit cells, which can be different shapes, like cubes or pyramids. Geologists classify crystals by assigning three axes to the unit cell. Depending on whether those axes are at right angles to each other or not, and whether they’re the same length or not, crystals will have different shapes and properties. It’s kind of like the difference between building a tower with cube-shaped blocks and building one with pyramid-shaped blocks. They’re gonna be different.

If the axes are all the same length and at right angles to each other, like in a cubic unit cell, nothing very interesting will happen to the light passing through the crystal. But when the axes are different, the light can get split into multiple paths as it travels through the crystal. Different paths might absorb more of different colors of light. So for example, light traveling along one path might seem more green, and along another it might look more brown.

And when you rotate the crystal, you change the paths the light takes. So pleochroic crystals seem to change color as you move your head, or rotate them in your hand. Depending on their exact geometry, you can get either two or three different colors.

Not all non-cubic gems are pleochroic, and even when they are, the color change isn’t always noticeable to our eyes. But it’s a pretty common property. Sapphire, for instance, is often pleochroic. So is topaz. It’s just light interacting with atomic geometry. But it looks awesome.

Then there are gems that are attracted or repelled by a magnetic field. You can’t just walk up to your refrigerator and stick a garnet to it or anything, but strong magnets will attract certain kinds of gems. In fact, the same transition metals that give gems their color can make them drawn to magnets.

Often, the metal responsible is iron, but rare earth elements like neodymium can do it too. Those trace elements make the mineral magnetic because they have odd numbers of electrons. Electrons have a property called spin, and two electrons with opposite spins pair up and cancel out.

But when an electron isn’t paired, its spin goes un-canceled, and it’s free to be attracted by a passing magnetic field. That’s called paramagnetism. On the other hand, a material with all its electrons paired up is slightly repelled by a magnetic field, because when the electrons move around in an atom, they make magnetic fields of their own, which repel other magnets. That’s diamagnetism.

Bismuth, for instance, is diamagnetic, so it’s always repelled by a magnet. When unpaired electron spins line up parallel to each other, you get ferromagnetism, or a mineral that’s an actual magnet. Very few minerals are ferromagnetic, but hematite is one example.

Sometimes, a gem that’s normally repelled by magnets will have bits of iron inside it, which will make it attracted to magnets instead. So magnetism isn’t a perfect tool for figuring out what a gem is made of, but it’s often a helpful clue.

Sometimes you’ll see gems cut into facets, but other times, they’ll be polished into a round shape called a cabochon. And sometimes, a round-polished gem will look like it has a bright streak of light across its surface, like the vertical pupil in a cat’s eye.

It’s called chatoyance, and it happens because of little thread-like pieces of a mineral, like rutile, inside the gem — what scientists call silk. As these crystals form, the impurities are forced to line up along the axes of the crystal’s structure, so the pieces of mineral end up parallel to each other. Those parallel pieces reflect light in a way that creates a bright line perpendicular to the threads.

And it’s not just gems that do this — a spool of silk thread will do the same thing, where there’s a streak of light perpendicular to the wound-up thread. But unlike a spool of thread, gems can have inclusions going in different directions, based on the crystal structure of the mineral. That creates a streak of light perpendicular to each axis, which looks like a star with four, or six, or even more points. The star effect is called an asterism.

When a gem has these threads, cutting it into facets might make it look kind of muddy. But when it’s polished into a round shape, you get gorgeous streaks of light.

Polymorphic minerals don’t always have the same structure. Even if they have the same chemical composition, the temperature and pressure when they form can lead to different shapes.

Carbon is probably the most famous example of this. Depending on how its atoms are arranged, carbon can form soft, slippery graphite or basically-indestructible diamond. Silica, the mineral that makes up sand and quartz, also has lots of different polymorphs. Its molecular formula is always the same: one silicon atom and two oxygen atoms. Its molecules form tetrahedral shapes -- that’s a triangular pyramid, or a d4 if you’re into tabletop RPGs.

Tetrahedrons can stack into different shapes as changes in temperature and pressure juggle them around. At the temperatures and pressures humans find comfortable, silica makes the alpha, or so-called “low”, form of quartz. But as temperature and pressure increase, it can become things like cristobalite, which is found in lava flows, or stishovite, which is in meteorite craters.

Even a single polymorph of silica can take on a huge variety of forms. Alpha quartz can look like scepters, rounded pebbles, or clusters of needles. It all depends on the growth conditions: like how fast the crystals form, how much space is available, and how much material there is to make crystals.

The unit cells stack together in the same way, but sometimes an impurity will cause them to take off at an angle or make them more likely to stick to one part of the crystal than another. Quartz is so varied that tons of gems -- like amethyst, chalcedony, agate, and citrine -- are all made of silica.

Organic matter can be slowly replaced by minerals to become a fossil. Often, the mineral involved is kinda drab, but sometimes the conditions are just right to produce something spectacular. And in rare cases, petrified wood, shells, teeth, and even bones of extinct organisms are made of opal.

Opalized fossils are most often found in Australia, along with most of the world’s opal in general. One of the most famous specimens is a pliosaur nicknamed Eric, an almost-complete marine reptile preserved in opal.

Like quartz, opal is made of silica. But unlike quartz, it doesn’t have a crystal structure. Instead, it’s made of little spheres of silica all bunched together. These tiny spheres scatter light, giving opal its characteristic rainbow sheen.

Geologists have a few different models for how opal might form, but it could come from silica weathering out of rocks in an acidic environment. Australia used to be partially covered by an inland sea. And as that sea dried up, it left acidic, silica-rich gel behind. Bits of silica settled into the gel and then grew into the spheres that make up opal.

Sometimes, that gel was stuck in bones or bits of wood that had already started to fossilize, so the silica trapped in there formed opals in the shape of those organic structures. The resulting fossils have both aesthetic and scientific value, and in 1993, Eric the pliosaur was almost made into jewelry by a broke owner looking to sell and potentially break up the pieces. But a crowdfunding campaign rescued Eric and got him a place in the Australian Museum.

Hopper crystals are probably some of the strangest-looking crystals. They’re shaped into a weird stair-stepped, hollow kind of pyramid known as a hopper. The shape comes from a quirk of chemistry as the crystal is forming.

When the growth rate and saturation of the crystal-forming solution is just right, new molecules will tend to be more attracted to the edges of the growing crystal than the inner flat surfaces. That makes the edges grow out of control while the flat faces mostly stay the same, so the crystals grow in a lopsided way that leads to that fascinating inside-out shape.

Bismuth hopper crystals have to be grown in the lab, but hopper crystals have also been found in nature, in minerals like rose quartz. Bismuth is pretty easy to get your hands on and has a low melting point, so you can actually try to make your own hopper crystals, if you’re feeling adventurous.

Some materials that are culturally prized as gems aren’t minerals or gems in the strictest geological sense: things like amber, jet, coral, and pearl. Instead of being made up of crystals, all these materials have more amorphous chemical structures, and they come from living things — that’s why they’re called amorphous organics.

But the way they form makes them look a lot like the classic crystal gems. Amber is fossilized tree resin, and can actually preserve organisms that get stuck in it. When the resin gets buried in calm, wet, low-oxygen environments, it slowly turns to amber.

Jet is practically the same thing as coal in some ways. But while coal forms in big seams from huge amounts of plant material, jet is formed from small bits of wood that get buried in sediment and compacted. Jet can be cut and polished to a gem-like shine, but it doesn’t have a rigid crystal structure — at a microscopic level, it can actually preserve the cellular shapes of the plant it used to be.

Coral is made up of small colonial animals, with calcium carbonate skeletons. The skeletons are usually white, but the precious coral that’s often considered a gem is a species that includes reddish-orange carotenoid pigments.

Pearls contain a mixture of protein and calcium carbonate secreted by certain types of molluscs. Different species will produce different colors of pearls, and impurities in the water can also affect the color.

Like all of the gems on this list, amorphous organics look the way they do because of the way their atoms are arranged. The regimented structure of a crystal and the laid-back chaos of an amorphous solid both affect the way they interact with light, magnets, and other materials. It’s the sparkliest kind of geometry.

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