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!

Retrovirus


· Categories: Biology
What I’ve Learned:

Retrovirus: when it comes back, you don't really want to be there.
“Retrovirus: when it comes back, you don’t really want to be there.”

“Retro” is in right now.

Of course, retro is always in. In the ’70s, people pined for the ’50s. In the ’90s, they wanted the ’70s back. And now, it’s ’90s nostalgia. So is a “retrovirus” just a cold bug that dresses like Blossom and listens to Nirvana CDs?

No. For the love of everything holy in this world, it is not.

A retrovirus is instead a virus that uses a process called reverse transcription. Because retroviruses — like Blossom, but without the goofy hat — just had to be different.

Nearly every organism on the planet follows what biologists call the “central dogma”. That’s the rule that says genes coded in DNA get converted to RNA, and that RNA is then read to make proteins, which are the building blocks for cells, people, animals, plants, Joey Lawrence and the cotton inside grungy flannel shirts. Among other things.

That’s the way life works — DNA to RNA, in a process called transcription, and RNA to proteins, which is called translation. It’s a solid system, and everybody follows the same rules.

That includes most viruses, who are little more than a few scraps of DNA and maybe a protein shell to hold it all together. These viruses infect cells, get their DNA converted to RNA by the cell’s machinery, then to protein, package themselves up and look for the next cell to invade.

Nobody ever said viruses live fulfilling lives. They’re like an old retired couple with an RV, wandering aimlessly in search of early bird dinners and cheap campground fees. There’s no point, exactly, but it keeps them busy.

And in the virus’ case, it also keeps them causing flu, smallpox, herpes, warts and sometimes cancer. It’s not a perfect analogy. Old people aren’t quite as harmful as all of that. Mostly.

Retroviruses, though, refuse to play by the rules. A retrovirus doesn’t pack its DNA on road trips; it bundles up RNA instead. It also packs a special type of enzyme called reverse transcriptase. This protein flips the central dogma upside down, and can make DNA out of the retroviral RNA. This new DNA then worms itself into the host genome, where it gets converted to RNA and protein, as usual.

So retroviruses aren’t so much like the retired RV couple scoping out campsites. They’re more like a biker gang that invades your neighborhood, squats in your house and drinks from all your toilets. And not in the nice way.

Because they randomly insinuate themselves into chromosomes, retrovirus DNA can sometimes cause cancer by disrupting an important gene. And that’s on top of the diseases they cause to begin with, which include AIDS and related diseases, equine infectious anemia, avian wasting disease, encephalitis in sheep and goats, and several others.

Not all retroviral infections are harmful, though — or even active. Sometimes, a retrovirus inserts its DNA into a “silent” stretch of DNA and it’s never heard from or activated again. Like Ugly Kid Joe and Starter jackets. These “endogenous” retroviruses are so common, in fact, it’s thought their sequence makes up 5-8% of the human genome.

So when it comes to retroviruses, they’re much like “retro” trends: better left buried and forgotten than dug up, reawakened and unleashed on anyone or anything you care about. And if a retrovirus should get loose? Hide the Blossom hats and Nirvana CDs; you’re in for a rough ride.

Actual Science:
HHMI / BioInteractive – Retroviruses and viral diversity
The Scientist – Repurposed retroviruses
Small Things Considered – Retroviruses, the placenta and the genomic junk drawer
Virology Blog – Retroviruses R us
Quanta – Killer virus is invading koala DNA

Image sources: MedPageToday (HIV virion), StyleBlazer (big-hat Blossom), RantGizmo (RV retirees), Crudely-Drawn Filler Material (Hell’s Satans commode chugger)

· Write a comment
· Tags: , , , , , ,

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)

· Write a comment
· Tags: , , , , , , ,

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)

· Write a comment
· Tags: , , , , , , , , , ,

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)

· Write a comment
· Tags: , , , , ,

Viroid


· Categories: Biology
What I’ve Learned:

Viroid: the simplest is as the simplest does.
“Viroid: the simplest is as the simplest does.”

Everyone I know is trying to “simplify”, in any way they can. They’re downsizing their houses. Giving away old clothes. Cutting out cable. (But not Netflix, because come on, Unbreakable Kimmy Schmidt, already.)

Pretty much anything short of donating their kids to science and moving into a zen garden, these people are doing in the name of simplicity. And you know what?

They’re amateurs.

Because how “simple” are you, really, when you’re still human? There are all sorts of complicated things going on inside us — and I’m not just talking about our Facebook relationships or the way we feel about Charlie Kaufman films.

Human bodies are all kinds of intricate. You’ve got circulatory systems and immune cells, respiratory tracts and reproductive organs — and that’s just the tip of the person-berg. “Simplify” all you like, but if you’re holding on to all that bodily baggage — with your fingers; don’t even get me started on fingers — then you’re not very simple at all.

And what’s more, if you think you need all of that — or any of it — to live in the world, grow up and pass on your genetic material, then you’re wrong. You can do all that with less. Much less. If you really want to simplify, take a cue from a viroid.

Viroids are about as small — and simple — as a reproducing bit of schmutz can get. Classified as “sub-viral pathogens”, viroids have almost none of the fiddly biological bits even most tiny organisms hold dear. Take amoebas, for instance; these microscopic little one-celled critters still have tiny tails to move around with, a way to take in nutrients and a nucleus for their genome. Ain’t no viroids got time for that.

Bacteria are even smaller than amoebas, but they at least have a cell membrane, and enzymes and stuff kept handy in pockets, for when they’re needed. Viroids got no enzymes, no pockets, and no cell to keep them in.

Viruses are tinier still, and are mostly just made up of a few genes on a strip of DNA. But at least — at least, for crissakes — they have the decency to cover up their genetic material with a membrane of some kind, and to code for a protein or two.

But viroids? Nuh uh. They’re nothing but naked RNA, single-stranded genetic material all folded in on itself. No membranes, no cell walls, no nothing. They don’t even code for proteins — they’re just themselves, the epitome of “simple”. Viroids are out there. And they’re lovin’ every minute of it.

Of course, living simple has some downsides. So far as we know, no viroids have Twitter accounts, for instance. Also, they can’t reproduce by themselves — we’ve all been there, amirite? — but need to infect a living cell to “borrow” its machinery to make more copies of its RNA. Most of those living cells are in plants; viroids have been identified that infect potatoes, eggplants, avocados and coconuts, among others.

Because they can’t reproduce by themselves — or in ugly-RNA-bumping pairs — viroids aren’t considered to be “alive”, exactly. But they may provide a hint as to how life ultimately began on the planet. Making copies of oneself — with help, and before one really has a “self” to speak of — isn’t much, perhaps. But it’s an important step on the way to truly living, and might have been critical to the formation of the very earliest life forms.

And today, viroids can still float around a farm field, dig into crops and pass along their genetic material to new generations. From what I’ve seen of the “simplify” crowd, most of those people would love the viroid lifestyle. Or near-lifestyle, as the case may be.

Of course, that “lifestyle” also involves running around naked, mooching other peoples’ equipment and using vegetables for sex.

I’m not saying that would deter any of the hippies pining for a life change. But suddenly, viroids don’t sound so “simple” to me.

Also, that Netflix queue of mine isn’t going to watch itself. I’ll pass.

Actual Science:
Virology Blog – Viroids, infectious agents that encode no proteins
Small Things Considered – Smallest Things Considered
New York Times – A tiny emissary from the ancient past
Science Magazine / Origins – Fast-mutating viroids hold clues to early life
Washington State University – Hop stunt viroid research

Image sources: Nature Reviews (viroid structure), Neptune Society (kids with signs), QuickMeme (Kramer, LOVIN’ it!), The Snipe (sexy, sexy eggplant)

· Write a comment
· Tags: , , , , , , , , ,

« Older articles
Newer articles »