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!

Junk DNA


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

Junk DNA: there's a whole lotta junk in ALL of our trunks.
“Junk DNA: there’s a whole lotta junk in ALL of our trunks.”

Comparing yourself with other people is tricky. George Carlin famously pointed out that “their stuff is shit, but your shit is stuff“. Which is great, if you’re comparing music collections or wardrobes or childrens’ refrigerator art.

But there’s another thing we have in common with other people: our DNA. And when it comes to genetic material, it turns out everybody’s is mostly junk. Yes, even yours. And George Carlin’s.

(Well, at this point, certainly George Carlin’s. Unless you count half of Kelly Carlin. Which you probably should.)

But don’t feel too bad about your junky genome. “You are what you eat,” as the saying goes — so if you’ve ever shoveled down a McRib or a whole bag of powdered mini donuts down your gullet, then you knew some “junk” was probably in there, somewhere.

The question is… how much? No one is entirely sure.

Regrettable food choices aside, the degree of “junkitude” in a species’ DNA was first measured in a very simple way. Somewhere within that DNA are a number of genes — regions that are transcribed into RNA messages, and then translated into proteins, which perform most every function in living cells.

Different species have different sized genomes, and varying numbers of genes. Back in the ’60s or so, scientists took a hard line concerning “junk DNA”: if it can produce a protein, it’s useful. If not? Junk.

That leaves many species with an awful lot of so-called junk DNA — and it makes humans look like downright hoarders. Using this definition, roughly 98% of our DNA is pointless garbage. Expired Fruitopia coupons. Porky’s Revenge Betamax tapes. Last year’s newspapers. Or really, any newspapers.

But a funny thing happened on the way to our deoxyribonucleic intervention. As scientists dug deeper into how our genomes work, they discovered something interesting. Our non-protein-coding DNA may be “junk” — but that junk DNA… is not.

Not junk, that is. At least, some of it isn’t. Because while genes — actual, protein-producing sequences — only make up about 2% of our DNA, other regions are pretty important, too. Like telomeres, for instance — little fiddly bits of DNA that “cap” chromosomes to protect the squishy ends. Or for that matter, centromeres — repetitive sequences where two halves of each chromosome are held together, and which are critical during cell division.

But it’s not just structural elements hiding in the junk DNA. There’s other stuff in that shit, too. Thousands of regulatory sites, for instance. All those protein-encoding genes are great — but on their own, they’re kind of dumb. If you don’t want intestine genes turned on in your brain, or adrenaline released along with melatonin — and seriously, you do not — then something has to regulate how and when and where and why each gene gets expressed.

That “something” is a bunch of proteins, mostly — but they do their jobs by sitting down on stretches of non-coding DNA to direct traffic. Take away those “junk” DNA regions, and your gene expression suddenly goes all higgledy-piggledy. Congratulations, spring cleaner. You’re a sewer mutant now.

There are other important things happening in our “junk” DNA, but we’re still discovering what all of them are. Maybe 10% of our DNA is actually useful. Or 8.2%, according to one study. Maybe as much as 50%. But probably not more than that; nearly half our DNA is thought to come from transposable elements and integrated viruses, which are generally not so useful.

So Carlin wasn’t wrong, but he didn’t have the whole story. True, our shit is stuff, and their stuff is shit. But underneath, we’re all 50 to 98% junk. Sorta makes you want to mutter the seven words you can never say on television, dunnit?

Actual Science:
Scientific American – Hidden treasures in junk DNA
Live Science – People use just 8.2% of their DNA, study finds
io9 – What extraordinarily weird things are locked up in your junk DNA?
Quanta – A surprise source of life’s code
Scitable / Nature Magazine – Transposons, or jumping genes: not junk DNA?

Image sources: Biotechnology and Society (junk DNA), Amazing Spaces (Carlin, finding a place for his stuff), YouTube (powdered donut face), Daily Beast (sewer muties, wavin’)

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Ketone


· Categories: Chemistry
What I’ve Learned:

Ketone: We could make beautiful organics together.
Ketone: We could make beautiful organics together.

For years, I thought a “ketone” was a musical instrument played by new wave ’80s bands and hairsprayed Euros and one slightly unsettling busking bear. Needless to say, I was wrong.

(Well. I say “needless to say”. But if someone had told me, then my final exam answers in organic chemistry class might have involved a lot less Herbie Hancock. So, there’s that.)

Later, I started thinking of ketones as more like Oreo cookies — which, oddly, is sort of right. A ketone is an organic — which is to say, carbon-containing — compound with a particular sort of structure. On one end is… well, anything that includes a carbon atom, pretty much. A methyl. A benzyl. Hansyl. Gretyl. You name it.

On the other end is… pretty much any other carbon-including thing, or possibly even the same kind of thing. So basically, the ends aren’t important. Just like an Oreo cookie. But in a ketone, the sweet, sweet creme filling is a thing called a carbonyl — that’s a carbon and an oxygen atom double-bonded together. Or double stuf’d. If that helps you remember.

Ketones come in a few different classes, just like there are red velvet and creamsicle and watermelon Oreos.

(Actually, there are watermelon Oreos because apparently Nabisco as a corporation has fallen into an existential funk and disavowed the concept of rational meaning in the universe. This is what happens when you mix pastries and philosophy.)

Some ketones have two carbonyl groups; these are called “diketones”. Others are cyclic, meaning their two arm parts branching off the central carbonyl meet each other and form a ring. Sort of like an Oreo doughnut.

(Because apparently, that’s also a thing that exists. What, is Kierkegaard running a Krispy Kreme shop or something? Madness.)

Ketones know some cool tricks, too. For instance, if a ketone contains a carbon right next to the carbonyl group, and that next-door carbon is bonded to a hydrogen atom, then the hydrogen can often swap places and jump up to bind the oxygen of the carbonyl group, while the double bond slides down between the central carbon and it’s neighbor that just lost a hydrogen. It’s the same set of atoms; the hydrogen just hops back and forth like a ballet dancer. Or a hopscotcher. Or a subway-busking keytar bear.

When this hydrogen moves, the new molecule forms a tautomer. I got extremely excited when I learned about this process.

I was later told that “tautomer” is not, in fact, the animal that Han cut open to keep Luke warm in The Empire Strikes Back. And that the molecule formed by a ketone-hopping hydrogen is called an “enol”. Which is fun to say, but not nearly as much as imagining billions of microscopic reptomammals swimming around in a chemistry flask.

Anyway, ketones are pretty much all around us. A lot of sugars, including fructose, are ketones. Many biological processes — like photosynthesis — produce or break down ketones. And certain kinds form “ketone bodies” in the blood, an important diagnostic readout for several health conditions. On top of that, we make industrial ketones to use as organic solvents, pharmaceuticals and as building blocks for synthetic polymers.

So ketones are pretty cool, I suppose. And also important for life and society as we know it. And, since they contain fructose, also Oreos. Take that, keytar bear.

Actual Science:
Chemguide – Introducing aldehydes and ketones
Master Organic Chemistry – A simple formula for 7 important aldehyde/ketone reactions
Berkeley Lab – Sweet smell of success: JBEI researchers boost methyl ketone production in E. coli
New Scientist – No need to starve to get fasting’s immune benefits
Tech Times – One in seven Scots have natural resistant to midge bites

Image sources: Hibbing Community College (ketone), Universal Hub (keytar Bruin, technically), Shut Up and Take My Money (watermelon Oreos, an actual real thing), Travel Recommended (tauntaun, suddenly seeing where this is headed)

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Quiescence


· Categories: Biology
What I’ve Learned:

Quiescence: how much less growth could there be? None. None less growth.
Quiescence: how much less growth could there be? None. None less growth.

Isaac Newton said a body at rest tends to stay at rest. That’s the First Law of Motion.

My mother said a body at rest had better tend to get his lazy teenage ass off the couch and mow the lawn before his father gets home, if he knows what’s good for him. I’m not sure that’s a “law” of anything, but it always got me moving. Eventually.

Inside your body are trillions of cells, and right now many of those are also at rest, in a state known as quiescence. What they tend to do next depends on what sort of cells they are, and how they got into that state to begin with.

Like teenagers, most cells go through phases. But instead of “goth skateboarder” or “sparkly vampire”, your cells go through phases of the cell cycle. The cell cycle is a set of steps cells go through to divide, because reproducing requires very careful planning.

If a cell went through the division process without a roadmap, anything could happen. It could split before it’s ready, and produce deflated Whoopie cushion cells that aren’t helping anyone. It could get its DNA scrambled, and serve it to the daughter cells, family-style. Or it could divide into fourteen cells at once, none quite the way they should be. Like Duggars. It’s terrifying. Thank goodness for the cell cycle.

But a cell’s life isn’t all spent thinking about reproducing. This isn’t college. Sometimes, cells need to exit the rat race of dividing over and over, and rest in quiescence. Take heart muscle cells, for instance. Once your heart has grown to full size during development, you don’t want it getting any larger.

(I know people like to think they have a “big heart”. But if it were big enough to squish your lungs between your ribs, you might reconsider that goal.)

To keep your heart from growing three sizes each day, the mature muscle cells are pulled out of the cell cycle right after a division, in a phase called G1. The “G” stands for “growth”, which is what cells typically do after dividing, but quiescence is a resting state, sometimes called phase G0. Because there’s no growth. Or dividing. Or anything else. The cells just sit there, doing their thing. Pumping blood, keeping you alive and leaving all the worrying about reproducing to you. If you’re into that kind of thing.

This also happens with neurons and other cells that stop growing after development; they enter quiescence, and basically never come out. But other cells can slip into the G0 phase from G1, for just a little post-division breather. Think of it as microscopic maternity leave.

Except that once cells divide, there’s no “parent” cell left. So really, it’s the children who were just produced that get a rest. Lazy kids. That grass is never getting mowed.

These “paused” cells — and in theory, any cells — can be pulled out of quiescence under the right set of circumstances. That could be a growth factor released in the body, or some other growth-goosing signal. Or maybe there are little mothers running through our bloodstreams, telling cells to get busy and do their chores.

The textbooks are silent on that last one. But sometimes, it’s the only thing that works. You do not want to be in the quiescence phase when your father gets home.

Actual Science:
Boundless – The cell cycle and the G0 phase
BioMed Central – Proliferation/quiescence: the controversial “aller-retour”
Stanford Medicine – On alert: study identifies cell-cycle phase that primes stem cells for action
Jackson Laboratory – Forcing quiescent leukemia cells to proliferate holds promise for acute myeloid leukemia (AML) chemotherapies
Medscape – Diabetes drug appears to eliminate residual CML

Image sources: University of Texas (cell cycle circle), Unilad (lazy, lazy teen), Mom This Mom That (Grinchy heart growth), Life as a Divorced Dad (quiescent kid, uncut grass)

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Love Wave


· Categories: Physics
What I’ve Learned:

Love wave: It's DEFINITELY not the motion of the ocean.
“Love wave: It’s DEFINITELY not the motion of the ocean.”

When you see the term “Love wave”, you might think it’s any number of pleasant things. Some kind of humanitarian pay-it-forward deal. A page for really flexible people from the Kama Sutra. How hippies say hello.

Hey, I said “pleasant”. I never said “freshly showered”.

As it happens, a Love wave is none of these things. A bunch of physicists got to the phrase first, so now it means something much more serious — and not nearly so pleasant. Or in any way love-ly.

The Love wave is actually named for Augustus Edward Hough Love.

(And with a name like that, it seems unlikely he was familiar with either the Kama Sutra or hippiedom. I bet he never even went to Burning Man.)

Love was a British mathematician who in 1911 made a prediction about waves traveling along a surface. Not all surface waves, though — just one specific type, on a very particular sort of surface. You wouldn’t see these waves where the usual surface waves show up — on ponds, or in glasses of water when T. rexes are nearby, or when somebody farts on a waterbed. Those waves are boring; they just travel in a straight line away from the origin, moving the surface up and down as they pass with no razzle-dazzle at all.

But Love had another surface in mind. He imagined waves not on water, but on a surface sitting atop other layers of material. If the top layer is “low-velocity” — that is, a material the wave moves through more slowly, compared to the layer(s) below — Love predicted a different sort of wave could form. A sexy wave that wouldn’t rock the surface up and down, but instead would shake it side to side, like a Polaroid picture.

Only Polaroids weren’t invented yet when Love worked out the math for all this, so the analogy probably wouldn’t have occurred to him.

(Possibly he said his waves “shake like a quick-drying daguerreotype”, but that’s way harder to work into song lyrics, so what’s even the point, really?)

If you live on a pond — or, say, Waterworld — then Love waves probably aren’t of much interest. But if you’re a landlubber, then you’re living on a low-velocity layer atop a bunch of other layers. Most of us call that “earth”, and when it shakes around a lot, we call that an “earthquake”. And Love waves are one of four major types of wave that spread out from earthquake events, just as A.E.H. Love predicted.

In fact, Love waves can be the most damaging type of seismic wave produced by earthquakes. Two of the types — P-waves and S-waves — are “body waves”, which travel quickly through the solid body of the earth and may affect the surface less if they’re sufficiently deep. The “boring” sort of surface wave — called Rayleigh waves after Lord Rayleigh, pip pip, indeed, Bob’s your uncle — undulates the ground as it passes. That’s no picnic for buildings and bridges and such, but at least the movement is fairly regular, and relatively slow.

Love waves, on the other hand, are transverse surface waves, so they shear the surface in layers, side to side — and they’re a little faster than Rayleigh waves, too. In culinary terms, if Rayleigh is a “rough chop”, Love is a fine mince. And considering all the waves come at you during an earthquake, it’s no surprise the aftermath often looks like it’s been through a blender.

So there’s no reason to love Love waves, though it might be helpful to know about them. They’re the side-to-side jostling most people feel during an earthquake — and the best you can hope for at that point is that you’re sharing a bed with someone you love, and hoping that’s why “the earth just moved”.

Preferably with the Kama Sutra. But not an unwashed hippie.

Actual Science:
Michigan Tech UPSeis – What is seismology?
PSU Department of Geosciences – Seismic waves and Earth’s interior
AllShookUp.org – Types of earthquake waves
ABC Science (Australia) – Earth hums while making ‘Love’ waves

Image sources: Earthquakes blog (Love wave schematic), Laurie Conseils (“Aw, C’mon Sutra”), Gizmodo (T. rex water), Complex (The Love Haters, shakin’ it)

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Immunoglobulin


· Categories: Biology
What I’ve Learned:

Immunoglobulin: even your immune system has door greeters.
Immunoglobulin: even your immune system has door greeters.

I took an immunology class back in college. I’m not sure why, exactly — maybe I thought it said “immortality” and I was looking for the secret to eternal life.

What? I went through a Highlander phase. We’ve all been there.

Anyway, it quickly became clear this class was something completely different — and completely hard. Everything about immunology is complicated as hell. There are, like, nine hundred different kinds of immune cells, a billion marker proteins and pathways out the wazoo. Stuff gets activated. Things turn into other things. Some cells remember crap, some cells spread the word about crap, other cells kill crap… it’s exhausting.

Then they told us about immuno-goblins. And finally, something made perfect sense. It was a couple of months into the semester, the middle of October just like now. Halloween was looming, so goblins were on everyone’s mind.

So when the professor explained these immunogoblins are produced in enormous hordes within the body, each on the lookout for a specific interloper, it made sense. When she told us each immunogoblin’s individual characteristics comes from mutations… well, duh. And when she said they either neutralize invaders or mark them for others to overwhelm — yeah, that sounds exactly like a bunch of goblins.

I went into that test full of answers. Basically, my body is Mordor. It pumps out goblins by the billions, looking out for viruses and bacteria and, I don’t know, effeminate ring-bearing halflings? I didn’t really study for those Tolkien exams, either.

Long story short, I got a 12% on the test, failed the class and apparently there’s not a little tiny Saruman living inside of me, releasing hordes of goblins.

(Turns out it was heartburn. Booo-ring.)

But all that stuff about immunogoblins — sorry, I was informed in red ink those are “immunoglobulins” — is apparently true. These are proteins produced by our immune cells in huge numbers, with millions of different kinds. The tips of each protein contain regions called paratropes, shaped to specifically recognize one specific antigen. Like an elbow of an influenza virus, or a tuberculosis pinky toe.

Binding of an immunoglobulin to its antigen may take the baddie out of commission. But just in case, it also triggers the immunoglobulin to signal to the rest of the immune system to get its ass in gear and come help.

That’s less of a “goblin” thing that immunoglobulins do, I guess. It’s more like a Wal-Mart greeter. Assuming the Wal-Mart was staffed by sentient killer cells ready to surround you, break you in half and eat you. Which, as I understand it, is most Wal-Marts.

In the end, I did learn a couple of things about immunoglobulins. So if you’re ever stuck staring down an immunology exam, just remember these three things:

1. When an immunoglobulin is glommed onto an immune cell, it’s just called an immunoglobulin. But when it’s farted out into the bloodstream to look for victims, it’s called an “antibody”. Personally, I would have gone with “Globs the Bounty Hunters”. This is probably why no one ever asks me to name things.

2. That “paratrope” bit that makes immunoglobulins unique has nothing to do with paratroopers, even if you have an awesome story about your great-grandfather dropping into occupied France to storm… uh, Nazi baguette bunkers or whatever. History was also not a thing I was good at.

3. Immunoglobulins are not like goblins, which means your body is also (probably) not like Mordor. Instead, they’re like evil greeters, which makes your body a Wal-Mart built on a hellmouth. Which seems redundant, and also mostly the same as Mordor, but I’m not the one grading these tests, so give the professors what they want, I guess.

Like I said: immunology is complicated.

Actual Science:
WebMD – Immunoglobulins
Study.com – The five classes of antibodies
University of Arizona – Immunology problem set
The Biochemistry Questions Site – Immunoglobulins: structure and functions
Science Clarified – Antibody and antigen

Image sources: MedGadget (immunoglobulins), Wikia (Tolkien goblins), Pop Cult Assault (beware, Dog), Walmart Wall (terrifyingly friendly greeter)

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