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!

Agonist


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

Agonist: It always gets the best reception.
“Agonist: It always gets the best reception.”

If you read a lot — or watch movies, because let’s face it, this is America and words are hard — then you might be familiar with the term “antagonist”. That’s the villain of the story. The rogue billionaire. The dirty cop. The Hamburglar.

You might think if you change the “ant(i)-” to “pro”, you’d get “protagonist”, and that would be the story’s hero. And you’d be right! From Sherlock Holmes to Pippi Longstocking to the velociraptors in Jurassic Park movies, these are the characters we root for to solve mysteries, teach valuable lessons and rip enemies to shreds with their powerful claws.

Not necessarily in that order.

But where does this leave the root word? If antagonists are bad and protagonists good, what are regular plain old agonists? Hollywood doesn’t have an answer. That’s where biochemistry steps in.

In strictly scientific terms, an agonist is a chemical that is recognized by a protein on the surface of a cell, and causes some response within the cell. The cell surface proteins are called “receptors”, because their main job is to sit there peeking outside the cell, waiting for these agonists to come along and be recognized.

Basically, receptors are like security guards in an office building. Maybe the guard knows you, and you get to go inside. Or maybe you’re delivering pizza, so the “receptor” guard calls upstairs and signals someone to hoof it down to pay you. Maybe you’re the Hamburglar, and the response is to call the cops on you. Or Mayor McCheese. Or velociraptors. I’m not really sure how corporate security works, frankly.

The point is, as an agonist, you’ve been recognized, and that’s kicked off some sort of response. That happens inside our cells all the time, and there are thousands of types of agonists (or more) produced and used by our bodies themselves.

Dopamine, for instance, is a neurotransmitter important for several brain functions, and also an agonist for a family of (aptly-named) dopamine receptors, which bind dopamine on the surface of cells and kick off various responses. But there are many others. The agonist estrogen has estrogen receptors. Agonist androgens have androgen receptors. Agonist growth factors, growth factor receptors. And so on.

That’s the textbook definition (more or less), and all true (except the part about velociraptors, probably). But the above only describes endogenous agonists, meaning those that are produced naturally — and that’s probably not the ones you’re most likely to hear about. Because we don’t just make agonists with our bodies; we also make them with our laboratories.

If you ever read about an “agonist” in a medical or science blurb, it’s probably describing an exogenous agonist, which is usually lab-generated. These are chemical compounds and molecules that behave like natural agonists, when it comes to specific receptors in the cells. So a “dopamine agonist” would bind dopamine receptors, and when it did, the cell would kick off the same response as if it were actually binding a “real” dopamine molecule.

Think of this back in the office building. You’re not delivering pizza now — but maybe it’s falafel. The call goes upstairs just the same. Or maybe you can use someone else’s ID card to fool the guard. That might not work every time, so it’s not completely reliable. But it’s close.

Exogenous agonists work the same way. They’re not always perfect matches, but the good ones get the job done. And for some diseases and conditions — particularly where patients have a deficiency of the natural agonist — these “close-enough” agonist drugs can be a huge help when they’re able to fool the cell’s “security guard” receptors.

Just watch out when they don’t. Because even tiny little attack velociraptors are terrifying.

Actual Science:
WiseGEEK – What are receptor agonists?
Biology in Motion – Receptor and signal as “lock and key”
Virtual Chembook / Elmhurst College – Drug receptor interactions
MedScape – GLP-1 agonist alters brain response to seeing, eating food
Medical XPress – Study finds connection between age-related cognitive decline and dopamine levels

Image sources: StudyBlue (), CNN (hushy Hamburglar), Pyxurz (friendly office security guard), Daily Dot (ruminating raptor)

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Doppler Effect


· Categories: Physics
What I’ve Learned:

The Doppler Effect: yet another reason to run from screaming children.
“The Doppler Effect: yet another reason to run from screaming children.”

Most science happens in a laboratory or a particle accelerathingy or inside the brain of some bushy-eyebrowed theory geek. The applications don’t make it far into the real world. Like, why do we never see nonhomologous recombination in the newspapers? Or a cartoon starring Schrodinger’s cat?

Which would presumably be a fan of lasagna, but not so much of Mondays. Just based on previous observations of animated feline behavior.

But once in a while, we’re thrown a bone — a science bone — and we get to see what the eggheads are talking about in their fancy journals and proceedings. Like the Doppler effect, which we can observe on a regular basis — or daily, depending on your neighborhood — and also hear about on the local six o’clock news. That’s more public exposure than Jeremy Piven gets.

Although, to be fair: it’s Jeremy Piven. So.

Anyway, the Doppler effect has to do with waves, and the way they change in frequency relative to motion. Sound waves, for instance. Imagine a toddler in a mall throwing a tantrum, and screaming “MOMMY!” at one-second intervals. As toddlers do.

Now, if you’re moving toward the child — maybe you’re “MOMMY”, and you have the binky that will end this meltdown — the sound of those one-per-second screams will reach your ears faster. If you could run fast enough (and please do; we’re trying to shop here, ma’am) in the direction of the kid, you’d notice the frequency of those screams getting closer together. The child’s still shrieking them once a second, but you’re plowing toward them, so you get to the next one faster than, say, some guy just sitting in the food court with breadsticks shoved in his ears.

That change in frequency is the Doppler effect, and it’s a result of relative movement between the source and the receiver of the waves in question. So if you’re sitting still — because “Mommy’s tired”, obviously — but the squirt comes screaming toward you, the effect will be the same. On your ears, anyway. If not necessarily your Xanax prescription.

The Doppler effect works in the receding direction, too. If your relative motion is away from a wave source, the frequency will decrease as you move further away. With sound waves, pitch varies with frequency, which is why sirens — or toddlers — coming toward you sound high-pitched as they approach, then normal as they pass and lower-pitched as they speed past.

But autotuning ambulance noises and screaming tots isn’t the only trick up the Doppler effect’s sleeve. Light is a wave, too — depending on the time of day and which theoretical physicist you’re talking to — and astronomers can use observations of starlight to determine whether those stars are moving toward us or away from us. But rather than changing pitch, light undergoing a Doppler effect shifts color instead. So light sources coming at us skew toward blue wavelengths, or are “blueshifted”, while light from stars streaking away shows a “redshift”.

And what about the Doppler effect horning in on the local news? Well, radar is another type of electromagnetic wave, and works just the same as light and sound. That “Doppler radar” the weatherman gets so excited about determines the speed and direction that storms are moving by measuring the Doppler effect on radar waves bounced around the atmosphere.

There are plenty more examples, but you get the idea. Also, that kid’s not going to cram his own binky in his mouth, apparently, so maybe you could take care of that now, mommy. Mommy. MOMMY!

Actual Science:
The Physics Classroom – The Doppler effect
Exploratorium / Hubble – Physics 101: redshift and the expanding universe
AAAS – A Doppler effect for distant planets
Gizmodo – This webpage uses centuries-old physics to let anyone scroll hands-free
Physics World – Doppler shift is seen in reverse

Image sources: CK-12 (it’s the Doppler coppers!), CinemaBlend (pouty Piven), Ramblin’ Mama (kid, keening), Twilight Language (randy radar reading)

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Glycosaminoglycans


· Categories: Biology
What I’ve Learned:

Glycosaminoglycans: you'll take two sugars, and like it.
“Glycosaminoglycans: you’ll take two sugars, and like it.”

Some words in science just sound completely made up — like “glycosaminoglycans”, for instance. That sounds like something you get when your cat walks across the keyboard, not something your body makes so you can bend and heal and see.

And yet. That’s what glycosaminoglycans do, apparently. So… thanks, kitty, I guess?

As for what glycosaminoglycans are, it’s actually all right there in the gibberish-looking name. You just have to break it down into parts to make sense of it. The prefix for “sugar” in biochemical speak is “glyco-“.

(I assume this is because sugars of various kinds come up a lot in biochemistry, and the scientists don’t want to be yelling “sugar” back and forth in the lab at each other, lest their significant others hear about it and get jealous.)

(Of course, I’m kidding about the reason. That’s obviously not how it works.

I’m not even sure biochemists have significant others. Just for starters.)

So if you take the last part of the word, “aminoglycan”, that describes something called an “amino sugar”, which is… I don’t know, a sugar that drinks those amino acid shakes, maybe? Could be it’s a bodybuilding sugar. Or it’s beefing up for sugar swimsuit season. Search me.

Anyway, stick this “amino sugar” with the “glyco-” — that is, a second sugar — from the beginning of the word, and you’ve got two sugars glommed together in one molecule. That’s what scientists call a “disaccharide” — “di-” for “two”, and “saccharide” for “hey, screw you people learning about science; we can have as many damned words for ‘sugar’ as we feel like, so nyah“.

(Biochemists are really petty, vindictive people sometimes. Maybe it’s all the significant others they don’t have.)

So, that’s what glycosaminoglycans are — long chains of two sugars latched together, and then repeated over and over. Our bodies make all different sorts of them, mixing and matching sugars and chain lengths in a process much more willy-nilly than most things our cells synthesize. DNA, RNA and proteins, for example, follow very strict recipes; glycosaminoglycans are pretty much thrown together from whatever happens to be in the pantry at the time. Glycosaminoglycan production is definitely less “paint by numbers”, and more “happy little trees all over”.

Also, now that we’ve sweated the glycosaminoglycan term for all it’s information, I’m going to stop typing it. I’m starting to get carpal tunnel on top of the carpal tunnel I developed three paragraphs ago. Instead, I’ll use the common abbreviation: GAG.

(Which also happens to be the sound you make if you try to say glycosaminoglycans three times fast. The more you know.)

So what are these GAGs good for, anyway?

First off, because of their long structure and chemical polarity, GAGs are great at sucking up water. So anywhere the body needs hydration, GAGs often come to the rescue, carrying water with them. This includes inside our corneas, where keratan sulfates keep us seeing sharp, and in the fluid in our joints, which are lovingly lubed by other GAGs called hyaluronic acids.

That fluid hauled around by GAGs can come in handy in other ways, too. Another type, heparin, can prevent blood from clotting. And those keratan sulfates, when they’re not watering up the insides of our eyes, keep cells and other structures from sticking together by forming a slippery, squishy preventative layer between.

If you’ve ever tried to have sex with someone with a dog in the room, you know exactly how this works.

But like the morning of a really bad hangover, the GAGs aren’t done yet. They also play roles in blood vessel growth, brain development, regulating cell division, cell surface binding, collagen stabilization and many other processes.

So glycosaminoglycans may be a tongue twister. But when it comes to all the ways our bodies need GAGs, that’s the real mouthful.

Actual Science:
TutorVista – Glycosaminoglycans
The Medical Biochemistry Page – Glycosaminoglycans and proteoglycans
VCA Animal Hospitals – Glycosaminoglycans
Elsevier Blogs – Glycosaminoglycans: from “cellular glue” to novel therapeutic agents

Image sources: SlidePlayer / Jeff Esko (GAG me!), Pussington Post (crazy-eye cat on keyboard), Flavorwire (happy little Bob Ross, and trees), Bee on Film (canine-blocked)

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Transcendental Numbers


· Categories: Mathematics
What I’ve Learned:

Transcendental numbers: weird stuff happens when pi and yoga get together.
“Transcendental numbers: weird stuff happens when pi and yoga get together.”

I’ve heard mathematicians say that learning math is like peeling an onion. I assume what they mean is that there are outer layers built on more basic ones, with patterns and fundamentals that go all the way to the core.

But all I get out of it is that math will probably make you cry. And if you eat too much of it, no one will want to kiss you.

Take transcendental numbers, for instance. Those might sound like numbers that have turned on, tuned in and dropped out of the number line — possibly to hand out flowers at a local airport — but that’s not exactly true. Technically speaking, transcendental numbers are numbers that aren’t “algebraic”.

(In other words, numbers that have nothing to do with algebra. Lucky bastards. I tried that in junior high school, and they made me repeat a grade.)

Specifically, algebraic numbers are those you can plug into an equation with plain old integers or fractions, and make the result come out to zero. Or, for the protractor-and-pocket-protector crowd, numbers that are roots of finite, non-zero polynomials in one variable with rational coefficients. And gesundheit.

So 4 is algebraic, then, because if you take the equation “3x – 12 = 0” and plug in 4 for “x”, it all works and you get that zero out the other end, like you wanted. Of course, “4” works for a bunch of other equations, as does “9” and “42” and “1/17” and “2,641,835”.

All the everyday plain old numbers we know are algebraic as hell (not an official mathematical term), but it only takes one solvable equation (outside of multiplying by zero to get zero, you sneaky devil, you) to make a number algebraic. It’s easy. What self-respecting numerical concept wouldn’t bother to be algebraic? I ask you.

Well, for three-point-one-four-one-five-nine things, pi.

Pi is weird in a bunch of ways. But one of its oddball properties is that you can’t plug it into any equation containing only integers or fractions (aka, “rational numbers”) and make the thing equal zero. It can’t be done. Smart people have tried, with computers and abacii and everything, and it’s not happening. Pi r stubborn.

That also makes pi a transcendental number. But lest you think it’s some kind of lone wolf — a rogue bad boy who won’t play nice with the other numerical kids — get this: the set of transcendental numbers is, mathematically speaking, uncountably infinite. And if that doesn’t make your Euler shrivel up inside you, then you probably don’t want to hear that we don’t even know which numbers are which.

Oh, some numbers are safe. The rational numbers are all algebraic. But lots of irrational numbers — which, like pi, can’t be written as a ratio of two integers — might be transcendental. Nobody knows. Is there some weirdo pretzeled-up equation that a particular irrational number might fit, making it algebraic?

(Sometimes. Take the square root of 2. It’s not rational; can’t be written as a ratio of two integers. But it nestles nicely into the equation x2 – 2 = 0, so it is algebraic.

But that’s an easy one. Numbers are like Tinder dates — the irrational ones aren’t usually nearly so accommodating.)

A few other (totally irrational) numbers have been outed as transcendental. Like “e”, the base of the natural logarithm. Esoteric weirdos like the Gelfond-Schneider constant, the Fredholm number and the Liouville constant (which really got the transcendental Bingo ball rolling back in the mid-1800s).

But most irrational numbers — which can be “real” like pi, or “complex” (which is to say, half-imaginary) like 2 + 3i, where “i” is the imaginary unit equal to the square root of -1, which isn’t a thing that exists in the actual world of onions and shriveled Eulers and unkissable mathematicians — might be algebraic, or they might be transcendental numbers. Like, is ee transcendental, or just weird as hell? What about pi – e, or pi/e? Today, no one can say. Maybe someday, smart math people will figure out some way to tell for large swaths of these bizarro half-made-up numbers of theirs.

In the meantime, I’ll be huddled over here in the corner. Crying on my onion slices and watching out for irrational transcendental numbers. And I thought eighth-grade algebra was scary.

Actual Science:
Good Math, Bad Math – Irrational and transcendental numbers
Math Lair – Transcendental numbers
University of Wisconsin / Cliff Pickover – The 15 most famous transcendental numbers
Gizmodo – What the hell is a transcendental number?

Image sources: Mind Your Decisions (transcendental pi love), MNN (onion cryer), MemeGenerator (totally rational date), Brown Sharpie (tie-dye pi [and also e])

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Apoptosis


· Categories: Biology
What I’ve Learned:

Apoptosis: it's cell biology to die for!
“Apoptosis: it’s cell biology to die for!”

You might know that roughly sixty percent of your body is made of water. Slightly more if you’ve been floating in a swimming pool all day, and probably a lot less if you were double-fisting tequila shooters last night.

But perhaps you didn’t know this: you’re also made of trillions of little tiny cells, many of which behave like hysterical widows from a weepy Victorian novel. Which is to say, at the first sign of stress they throw up their subcellular hands in lamentation, beat their microscopic breasts and end it all in a suicidal cell process called apoptosis, or “programmed cell death”.

(Before we go any further, I should point out that there are two camps of scientists when it comes to the pronunciation of “apoptosis”. One group calls it “a-POP-toe-sis”, while the other (including the people who yanked the word out of ancient Greek to use it again) call it “a-po-TOE-sis”.

The first group argues that’s how the Greeks would pronounce it, and anyway, we don’t ride in “he-li-COE-tors” or on the Love Boat with “CAE-tain Stubing”. The other side says it’s a compound word and if you can’t handle a silent “p” at the beginning of “ptosis”, then you should see a psychiatrist. Or a psychologist. Or a pterodactyl. Pick your poison.

Or for fun, go tell some neckbeard scientist you have a “GIF showing apoptosis in a potato-tomato chimera”. No matter how you pronounce all that, you’ll get an argument about something.)

The actual process of apoptosis is a long chain of events kicked off by a cell; that cascade can be interrupted — if the cell finds a reason to live for, presumably, like maybe a new McRib sandwich promotion or something. But left unchecked, apoptosis means the bitter end for the cell that starts it. So why would it?

It turns out, cells apoptotically off themselves for a whole range of good reasons. Some cells are slotted to die during development — like those in the webs between our embryonic fingers and toes. Also, if a cell is damaged, malfunctioning or infected with a virus, say — better to put it out to apoptotic pasture than let it poison the other cells in the neighborhood. In all, between 50 and 70 billion cells die inside you every day, self-whacked by apoptosis.

Strangely, none of them has ever left a note. Dun-DUN-DUN!!

The nice thing about apoptosis is that it’s very tidy. None of your cells are jumping off high rises downtown or running into freeway traffic. When cells die unexpectedly, they more or less explode, exposing nearby cells to proteins and bare DNA and shattered organelles that they’ll never be able to unsee. (And more important, that could royally foul up their cellular livelihood.) The “programmed” part of “programmed cell death” gets around this; apoptotic cells essentially implode, breaking into little balls of broken-down material that can easily be cleared away. It’s cellular suicide that supplies its own body bags. Neat.

Deadly as it seems when it’s working right, the real problems with apoptosis come when it goes all wonky. If too many cells drink the Kool-Aid and try to join the mother ship, you could develop a degenerative disease that eats away your body tissue. That’s bad. On the other hand, if cells find a way to bypass apoptosis, they can grow and live forever. That’s cancer, and that’s no good either.

So you don’t want the apoptosis inside you to run too hot or too cold; it’s got to be just right. Sixty billion distraught little tragic Victorian characters a day seems about right, give or take a Bronte sister novel. Get cracking, weepypants.

Actual Science:
The Oncologist – Apoptosis
Bitesize Bio – Life or death? Apoptosis in healthy organisms
ALS Association – Cell death and apoptosis
The Scientist Magazine – Ancient apoptosis
Phys.org – Dying cells can protect their stem cells from destruction

Image sources: Stanford University (apoptosis in white blood cells), Decor to Adore (weepy Victorian), Logophilius (concerned Cap’n Stubing), Red Bubble (hangin’ with apoptosis)

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