Note (12/2015): Hi there! I'm taking some time off here to focus on other projects for a bit. As of October 2016, those other projects include a science book series for kids titled Things That Make You Go Yuck! -- available at Barnes and Noble, Amazon and (hopefully) a bookstore near you!

Co-author Jenn Dlugos and I are also doing some extremely ridiculous things over at Drinkstorm Studios, including our award-winning webseries, Magicland.

There are also a full 100 posts right here in the archives, and feel free to drop me a line at secondhandscience@gmail.com with comments, suggestions or wacky cold fusion ideas. Cheers!

Tectonic Plates


· Categories: Physics
What I’ve Learned:

Tectonic plates: Putting the 'rift' in 'continental drift'.
“Tectonic plates: Putting the ‘rift’ in ‘continental drift’.”

The Earth — or the bits of it we live on, anyway — is like the Kardashians.

(A chilling premise, I know. Feel free to roll around in the fetal position for a bit while that sinks in. I’ll wait — and then I’ll explain.)

The Earth’s surface is made up of independent sheets of planetary crust called “tectonic plates”. Parts of these plates — and some entire plates — lie under the ocean, but there are some rocky bits that manage to peek out above the surface of the waves. Scientists call these bits “land”.

(So does everyone else, obviously. Scientists just like to feel official about things.)

It’s these stretches of land, divided into continents, that share some traits with the Kardashians. So Europe is, I don’t know, Khloe. And South America can be Kim, with her high-Andean-altitude ass. Maybe Kourtney is Greenland, and…

Well, those are all the Kardashians I know, actually. Is Krusty one? Or Katzenjammer? Tito? Like all things Kardashian, it really isn’t important. Assign your land masses however you like.

The key things to know is that there are seven or eight major tectonic plates, depending on whom you ask, and another few dozen minor ones. Hangers-on, if you will. Distant cousins. Papparazzi.

(That’s one, right? I totally remember Papparazzi Kardashian being pulled over by cops for something. It was on all the channels starting with T-M, probably.)

Three hundred million years ago, all the tectonic plates containing land were huddled together like a big happy family in one supercontinent called Pangaea. They stayed together for about one hundred million years — so, slightly more seasons than the Kardashians managed — before finally breaking apart.

(And what’s more, it wasn’t the first time the whole family had come together. Geologists think there were at least four supercontinents mushing together all the land masses throughout prehistory, going all the way back to two billion years ago. It seems reunion specials and reboots have always been in vogue.)

It wasn’t constant in-fighting that drove the tectonic plates in Pangaea apart. Rather, the continents drifted due to geologic, tidal and gravitational forces tugging them into the configuration we know today. But the interactions between those plates as they moved along would be familiar to any Kardashian or reality TV fan. Specifically, there was:

Converging – where two tectonic plates came at each other (bro), one was pushed underneath the other in a sort of intercontinental cat fight. This can create ridges and even mountain ranges (like the Andes), where the “winning” plate is lifted up over the other. In plate tectonics, it’s usually the denser plate that’s thrust down, in a process called subduction. (In reality TV, sadly, the denser you are, the more camera time you’ll probably get.)

Diverging – where two plates drifted away from each other, with one never calling or writing or joining up for mani-pedi spa days any more, a rift would form between them. When it happens under the ocean, new material from under the Earth’s crust will rise and fill in; this is how we get new sea floor. When it happens in the entertainment world, some new bunch of idiots will rush in to plug the void; this is how we get Jersey Shore.

Transforming – sometimes two plates constantly rub and grind against each other — or against Lamar Odom, possibly. This causes friction and instability, and can lead to something called “transform faults” (like the one in San Andreas) where earthquakes frequently arise from all the tectonic jostling. Which is almost certainly less catastrophic than the product of all the Kardashian rubbing and grinding, which is usually more Kardashians.

So that’s the story of tectonic plates. Perhaps not the geologic migration process we wanted, but at this point probably the geologic migration process we deserve. Downton Abbey, it ain’t.

Actual Science:
Bucknell University – Plate tectonics
National Geographic – Plate tectonics
Nature – Earth science: how plate tectonics clicked
PhysicsWorld – Geophysicists blast their way to the bottom of tectonic plates
Scientific American – What happens to Google Maps when tectonic plates move?

Image sources: Ella-Rose’s Learning Portfolio (tectonic plates), Too Funny Chicks (tug of Kardashians), HefferBrew (rubbing Lamar), Kontrol Girl (template for Pangaean posers)

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Alu Element


· Categories: Biology, Genetics
What I’ve Learned:

Alu element: The crowd's not boo-ing, they're Aluuuuu-ing.
“Alu element: The crowd’s not boo-ing, they’re Aluuuuu-ing.”

This is one of those times when being a baseball fan can help you learn something about science.

(All the other times either involve knuckleballs or an obscure branch of physics dedicated to explaining what the hell has kept C.C. Sabathia’s pants up for most of his career. So this one is the best, obviously.)

Back in prehistoric times, before most anyone was born probably, people were playing baseball. I’m talking way back, like 1960 or so. It was around that time that major league baseball was invaded by the Alou family. First came Felipe, then his brother Matty — and then his other brother Jesus. And just when you thought there were no more, another Alou family member, Felipe’s kid Moises, joined the league. And Felipe stuck around as a manager, after his playing days were over.

Basically, Alous were everywhere in baseball. You could scarcely swing a dead Louisville Slugger around the majors without thwacking an Alou element. Not that anyone did that, of course. It would be unsportsmanlike.

A similar thing happened long ago in our genomes. Tens of millions of years ago, some furry little ancestral critter hiccuped, mutationally speaking, and produced the first Alu element. These Alu elements are short snippets of DNA that got erroneously copied out of a gene, mangled, and jammed back into the genome. The DNA bits couldn’t hit a curveball or shag fly balls, but they did have one major-league talent:

They could make copies of themselves, which could then set up shop in other spots in the genome.

Just like the Alous, who didn’t enter the league at the same time or always play for the same team, the Alu elements gradually spread themselves around. The species in which they first popped up was an ancestor of a set of mammals called Euarchontoglires, or “supraprimates”; these include, among other beasts, rodents, tree shrews and primates — including humans. That means that all these species — again, including humans — have Alu elements hanging out on their genomic rosters. Lots of them.

It’s like the Alous signed on — and then made clones of themselves, until they were everywhere all over the field. Real Bugs Bunny vs. Gas-House Gorillas stuff. Only with less cigar-chomping lunks, and more transposable DNA elements.

In total, Alu elements make up more than ten percent of the human genome, and there are more than a million of them in every person’s DNA right now. A few thousand of those are unique to humans, but most can be found in other animals, like those shrews and monkeys and such mentioned above. That’s how we know Alu elements jumped into the game a long time ago; all of these species still list Alus on the roster.

Most copies of the Alu elements don’t do much, since they’re located in stretches of DNA between genes. By hopping willy-nilly around the genome, Alu elements do increase our genetic diversity — and recent reports suggest they may help defend against toxins and viruses. The many copies can mutate over time, however, and they can insert into some pretty inconvenient places. These buttinski Alu copies have been linked with diseases from hemophilia to Alzheimer’s to type II diabetes to several types of cancer.

Which is where the parallel with baseball breaks down. So far as I know, no Alous ever scrambled anyone’s DNA, or made opposing pitchers more susceptible to developing cancer. Getting sent down to the minors, maybe. But never cancer.

So the Alous and the Alus have a few things in common. They’ve both been around for nearly forever, and there are a zillion of each, all a little bit different. But one is a family of All-Stars and sluggers, while the other is hitching a ride in our DNA like a pack of self-cloning subnuclear stowaways.

No wonder the Alous are the ones on the baseball cards.

Actual Science:
DNA Learning Center – How Alu jumps
Science Over a Cuppa – Alu transposable elements and the human genome
Phys.org – Jumping genes have essential biological functions
ScienceDaily – Orangutans harbor ancient primate Alu
Northwestern University – The evolution of Alu-mutations – a clever defense

Image sources: Genome News Network (Alu element), Suite / Kevin Schindler (Alous, Alous everywhere), Business Insider (so much Sabathia), HLNTV.com (Gas-House Clone-rillas)

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Radioisotopes


· Categories: Chemistry, Physics
What I’ve Learned:

Radioisotopes: When they have a meltdown, you might, too.
“Radioisotopes: When they have a meltdown, you might, too.”

Chemical elements are exactly like people: there are almost two hundred of them, and only a handful you’d want to invite to a dinner party.

(Okay, it’s possible there are more than two hundred people. But the second part still stands.)

The other way elements are like people is that they both have baggage. With people, it’s a messy divorce, or a predilection for making their pets wear sweaters. Or being an outlier on the Bell curve charting “frequency of parental hugs”.

With elements, it’s neutrons. Nothing else. Just neutrons, little uncharged subatomic bits of schmutz. You would think that would take all the drama out of having baggage.

You would be wrong. It’s like the Real Housewives of the Periodic Table down there. Here’s why:

You can dump extra neutrons onto an atom, no matter how small. Take hydrogen, for example — the runtiest little element of all. It’s got just one proton — the other bit of atomic schmutz that has a positive charge, to offset the negative electron circling the nucleus — and no neutrons at all. Hydrogen is simple that way, like a monk or a wise old hermit or that kid who used to shine shoes on Parks and Recreation, before he got married and buff and went into outer space with that tree and the rodent and the rest of them.

You can pile a neutron onto a hydrogen atom, and it’s mostly fine. This atom is called an isotope, because it’s got more (or less) than the usual number of neutrons — and it’s called deuterium, because that’s what hydrogen atoms with one neutron like to be called.

(I don’t know what sort of nicknames its friends give it. “Deutie” seems fraught with issues. “Deut”, maybe? “Terie”? No idea.)

But deuterium, laden with baggage though it is, is very stable. Makes good decisions. Keeps a steady job. Probably doesn’t even have a therapist — unless it lives in L.A., because pretty much everybody has a therapist there, but still. Deuterium isotopes are chill.

Until you feed them another neutron.

Then those isotopes become tritium, which is a radioisotope. And radioisotopes are atoms where the baggage has gotten to be too much, and it gets unstable. These are the atoms with the crazy eyes, and — like most anyone with too much baggage — they’ll eventually dump it out on those nearby. Explosively.

For radioisotopes, this means radioactive decay — a release of stored energy which brings the atom into a more stable state. Tritium, for instance, decays into an atom of helium-3 (two protons, one neutron), which is completely stable, and fine to invite over for parties or to babysit the kids. But the energy and particles released by decaying radioisotopes can be bad news — or extremely useful, depending on the atom.

Some forms of radioactivity can cause radiation poisoning, cancer or fish with an uncomfortable number of eyes. The rate at which radioisotopes blow their atomic stacks is measured as a half-life — that is, the amount of time it takes for half the atoms in a sample to go completely batshit and decay. Knowing this half-life (and the type of decay — alpha, beta, gamma or other) can come in handy where just the right amount of radioactivity is helpful — like americium-241 used in smoke detectors, or gadolinium-153 used for certain kinds of X-ray tests and osteoporosis screens.

But the most temperamental and energetic radioisotopes — the Kardashians of the atomic world — can cause problems for centuries or longer. Carbon-14 and strontium-90 from nuclear bomb tests, for instance, with a half-life of nearly six thousand years, or nuclear reactor output like cesium-137 and iodine-131 (which can also be used as a cancer treatment, under carefully controlled conditions).

So the next time you decide to dump baggage on someone — or unload some of your own on innocent bystanders — take a moment to think of the radioisotopes. Some of them are just as unstable as you. Only they wig out and break down because of science, and not a tragic hug imbalance. Neat.

Actual Science:
Universe Today – Radioisotope
Carleton College – Radioactive decay
American Chemical Society – Production and distribution of radioisotopes at ORNL
Nature – Radioisotopes: the medical testing crisis
WHOI / Oceanus – Radioisotopes in the ocean

Image sources: NOAA Ocean Explorer (radioisotope decay), Organizational Excellence (Bell curve for hugs), Splitsider (stoked Andy Dwyer), KnowYourMeme (crazy-eye girl), Into the Deep (Simpson’s several-eyed fishies)

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Zinc Finger


· Categories: Biology
What I’ve Learned:

Zinc finger: When you're a protein, it's good to get the finger.
“Zinc finger: When you’re a protein, it’s good to get the finger.”

Frogs have given us many things over the years. There’s Kermit the Frog. And… uh, frog legs. And Froggy, from the Little Rascals.

So, three things. Frogs have given us three things. But it turns out there’s a fourth: frogs have also given us the finger. Which is nice.

That’s because the finger in question is something called a “zinc finger”, an important motif in many useful proteins, and it was first identified in a species of African clawed frog that scientists often study when they get tired of squinting at lab mice and fruit flies.

But what is a zinc finger, exactly? In frogs — and most everywhere else, including in people — it’s a set of different regions in a protein that fold together into a finger-like protrusion, which is held in place by various separate bits binding to a single zinc ion. This keeps the “finger” rigid, and the structure stable. The zinc is like the hair scrunchie holding bits of ponytail together, or the plastic doohickey on top of a six-pack.

That’s the classical zinc finger setup, anyway. Since the first, researchers have found other ion-binding interesting structures, including the zinc ribbon, the treble clef and the gag knuckle, which sounds like something out of Fifty Shades of X-Ray Crystallography. They all look a bit different, but have a more or less similar function.

And that function is to reach out and grab onto other things, as fingers are wont to do. Many zinc finger proteins bind to DNA, where they perform (or help other proteins perform) helpful functions like replicating DNA, transcribing DNA into RNA and regulating cell growth, function and hairstyle.

Wait, no. The scrunchy does the hairstyle. But the zinc fingers do all the other stuff.

It’s not just DNA these zinc fingers wrap their sticky selves around, though. Some of them grab onto RNA, others onto specific proteins, and still others grab small molecules of various kinds that float around living cells. Without the zinc fingers, these proteins couldn’t hold on to any of these bits. And if they couldn’t hold on — and there were no microscopic six-pack holders handy to replace them — then our cells wouldn’t get much of anywhere. And we wouldn’t be around to make unsettling science-based Fifty Shades jokes.

Clearly, it would be a world diminished.

If you’re a fan of zinc fingers — and by now, you must be — then you’ll be happy to know that scientists are now able to put them to good use in the lab. With a bit of molecular fiddling, researchers can vary the specificity of zinc fingers for DNA or proteins, to enable new (or limit old) functionality. And they can snip the zinc finger-coding portions out of genes and glom them onto other genes, creating new proteins that can bind and cut specific DNA sequences, for instance. Scientists then use these fingered-up proteins to silence or activate genes and study the effects on cells.

That’s very clever — like taking one of those six-pack rings and making them into, I don’t know, a dress. Only the dress can’t do science. We hope.

So the next time your DNA or protein does something useful, remember the zinc finger proteins and all we’ve discovered about them. And be happy that once upon a time, frogs gave science the finger. Those little rascals.

Actual Science:
RCSB PDB-101 – Zinc fingers
Zinc Finger Consortium – Scientific background
Virology Blog – HIV gets the zinc finger
ScienceBlogs – The knock-out punch: zinc finger nucleases
HDBuzz – Giving Huntington’s disease the finger?

Image sources: StudyBlue (zinc finger), Animal New York (fingering frog), Img Arcade (scrunchie Deb), Sue Woodall (six-pack fashion)

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Ionizing Radiation


· Categories: Physics
What I’ve Learned:

Ionizing radiation: Hide your electrons, 'cause they ionizin' everybody out here.
“Ionizing radiation: Hide your electrons, ’cause they ionizin’ everybody out here.”

Science is hard. Even when something in science sounds straightforward, it usually isn’t.

And mostly it doesn’t sound straightforward at all. Even the names of scientific concepts are hard. Like “endoplasmic reticulum”. That’s just a jumble of Scrabble tiles, no matter how you break it down. Or “Schwarzschild radius”, which sounds like part of an equation you’d use to calculate how much cream cheese you’ll need for that bag of bagels you just bought.

But occasionally, science throws us a nomenclatural bone. Like “ionizing radiation”. Those words actually make sense; you can suss from the name that this is “radiation that ionizes”. Simple, right?

Weeeeeeell…

Start with ionization. An ion is an atom or molecule that has either more electrons or less electrons than you’d expect, given its properties like size and composition and pants size. Because electrons have a negative electric charge, that means this electron-lopsided thing also has a charge — positive if it’s missing electrons, negative if it’s hoarding them like some A&E channel reality show weirdo — and it’s called an ion.

With ionizing radiation — more on the “radiation” bit in a sec — electrons are not hoarded. They’re knocked off at (or near) the speed of light, chucked away like a Hefty bag on trash day. Or a kid out of Mom’s basement after graduation. Or John Travolta out of Hollywood after Battlefield Earth.

One way to think of the effects of ionizing radiation is that the resulting ion is still intact, more or less, but now it’s missing something. If you see a car without hubcaps or a fender lashed on with bungie cords, it’s still a “vehicle”, technically. It’s just a shitbox ion. A house with peeling paint and a hole in the roof remains a “dwelling” — but it’s a crapshack ion. Something’s missing. A little off. Busted.

So if you don’t want your precious atoms and molecules ionized — and you don’t — what sorts of radiation do you need to watch out for? Well, radioactive decay, for one. Whether it’s alpha particles, beta particles or high-energy delta-delta-delta-can-i-help-ya-help-ya-help-ya particles, they’re all ionizing radiation. Ditto for gamma rays, cosmic rays, X rays, ultraviolet rays and seemingly every other ray besides Rachel.

(Okay, that’s not precisely true. From an ionizing perspective, visible light rays, microwaves, infrared and even some ultraviolet rays are safe.

Also, Rachel Ray will probably eat you with her enormous mouth. Which isn’t “ionizing”, exactly. But it can’t be good.)

That’s what ionizing radiation is — but what does it do? Several bad things, and a couple of good. On the negative side, ionizing radiation can break chemical bonds, create free radicals and turn substances radioactive, among other things. Those effects are pretty bad for materials like metals and polymers and semiconductors, and really terrible for materials like you. In people and animals, high ionizing radiation doses cause radiation burns, DNA damage, chronic sickness, cancer and death. It’s no party.

On the other hand, ionizing radiation can be put to good use. The effects are critical for X-ray imaging, smoke detectors, some food sterilization, radiochemistry, medical tracers and lots of other applications. The key is to be careful, and balance dangerous exposures with practical use.

Also, don’t let Rachel Ray near any of the stuff. I don’t know what a dose of radioactivity would do to her — but I’ve seen Spiderman, and I do not want to find out.

Actual Science:
World Health Organization – What is ionizing radiation?
Environmental Protection Agency – Ionizing and non-ionizing radiation
Physics Central – Ionizing radiation and humans – the basics
Astrobiology Web – Effects at Earth’s surface following astrophysical ionizing radiation events
OnCancer / MSKCC – Scan safety: a radiation reality check

Image sources: Mammography blog (ionizing radiation), CinemaBlend (Battlefield John), Hulu (“Delta Delta Delta!”), SoGood (gaping Ray)

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