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!

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

X-linked inheritance: sometimes chromosomes aren't X-actly as they should be.
“X-linked inheritance: sometimes chromosomes aren’t X-actly as they should be.”

We humans have a bunch of chromosomes — balled-up tangles of DNA — lying around our cells. Forty-six of them, in fact, in twenty-three pairs. We get one chromosome of each pair comes from our mother and one from our father — though they may smush together and intermingle during the fertilization process.

(That’s the chromosomes, not our parents. They smushed and intermingled right before the fertilization process, obviously. Also, Barry White was probably involved, which you don’t typically find at the chromosomal level.

Most DNA strands are more into Marvin Gaye.)

The last chromosome pair — the “sex chromosomes” — is special. Males get one copy each of an “X” chromosome and a “Y” chromosome. And females double up on “X” chromosomes, leaving out “Y” altogether.

(The chromosomes get those names because under a microscope, they look a little like the alphabet letters.

To whom, I don’t know. Maybe Elmo from Sesame Street is in charge of naming biological structures.)

Put another way, if a fertilized egg gets the “Y” chromosome from the father (and one of the mother’s “X” chromosomes), the child will be male. If it gets the father’s “X” (and a second “X” from the mother), it’ll be female. Genes on these chromosomes will kick in during development, to determine the sex of the child.

(That’s how it works in humans, anyway, and most other mammals. Some animals have different sex chromosomes — like chickens, where hens have ZW and roosters are ZZ. Or grasshoppers, where females get XX and males get one X, nothing else, and are told to suck it up and stop whining.

Or platypuses, which have ten sex chromosomes, because of course they do. Platypuses are freaking weird.)

The XX versus XY choice has consequences down the line. Many genetic traits are “recessive”, meaning if just one of your two chromosomal copies is defective, you’re fine. Only if both are screwy will you have the trait or disease. For genes on, say, chromosome 3 or 12, that’s okay — everyone’s got two copies, so it’s rare to get both mucked up at once.

But X chromosome genes are trickier. Males only get one copy of X — from their mothers, remember, because to even be male, they had to get a Y from their fathers. If a gene on that lonely X chromosome happens to be horked up, they’re out of luck. There’s no backup, no “chromosome on the cloud” or flash-drive file to recover. One X chromosome, one chance to get all of “X-linked inheritance” right.

Sometimes, it doesn’t happen. If a recessive trait is X-linked and the father has a wonky copy, his daughters will all inherit it — but one bad copy doesn’t hurt. They’ll still get a “normal” X from Mom, and hopscotch happily away. If the mother is affected, all her kids have a 50% chance of catching the bad copy — but again, in girls, it’s covered by a healthy X (this time, from Dad). Only the sons, with mother’s lone mangled chromosome, get dinged by recessive X-linked inheritance.

(Daughters can also get the diseases. But it takes both an affected father and mother — and a bit of bad luck — to be so dinged. It’s like the sperm and egg walked a black cat under a ladder or something.

There’s also “dominant” X-linked inheritance, where even a single defective copy of a gene causes a disease. Females are more likely than males to inherit these conditions, but they’re pretty rare. Overall, X-linked torpedoes still sink males more often.)

So what issues can X-linked inheritance cause? Common recessive disorders include hemophilia, color blindness and certain types of muscular dystrophy. And the rarer stuff includes even nastier syndromes and diseases you wouldn’t wish on your worst newly-fertilized enemy.

So however many X’s you happen to have, be happy that the dice of X-linked inheritance probability didn’t roll snake eyes for you. Unless they did, and then curse the cocked-up chromosomes that combined to mark the mutant-X spot. If only you’d been a platypus, this might not have happened.

Something much weirder, probably. But not this.

Actual Science:
Medline PlusSex-linked recessive
NCBIAn introduction to genetic analysis / human genetics
Science PrimerX-linked inheritance
NHS UKX-linked conditions
Wellcome TrustX-linked diseases

Image sources: Madical School (X-linked inheritance), AllMusic (White ‘n’ Gaye), Aussie Pete II (Elmo [and Norah Jones!] and Y), Try Nerdy (platypus sex [chromosome] appeal)

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

Mitochondrial Eve: Making DNA from an ooooooold family recipe.
“Mitochondrial Eve: Making DNA from an ooooooold family recipe.”

Imagine your DNA is a brown bag lunch. Your parents packed it with everything you need. A banana, if you like those. PB&J, maybe — unless your particular DNA makes you allergic to peanuts, in which case, I don’t know. Pizza? Fish heads? Who am I, Andrew freaking Zimmern?

The point is, your DNA comes from both your parents, in more or less equal amounts, and it’s stored in each of your body’s cells in something called a nucleus. That’s the bag in this analogy. Or the kick-ass Tardis lunch box, if you prefer.

Anyway, as she often does, your mother left you a little something extra.

But instead of a “love you” note or an extra Twinkie, our moms gave us something else: a bonus stretch of DNA, passed down only from mothers to children. This DNA is housed in a separate subcellular sack called a mitochondrion. Mitochondria do some pretty amazing things, but that’s a whole other bucket of lunches, so let’s stick to the DNA.

Because mitochondrial DNA is passed straight from mother to child, it can be traced back to earlier generations. Variations in DNA occur at a steady rate, and these get passed down, too. By comparing mitochondrial sequences between individuals, scientists can estimate how closely related they are — the more variations they share, the closer they are. If their DNA variations don’t overlap, it indicates they’re swinging on different branches of the old family tree. When a branch diverges enough to represent a unique DNA signature, it’s called a “haplotype” — a pattern of DNA variation shared by all the members of that branch.

Back in the 1980s, scientists tested mitochondrial DNA from more than one hundred people from different populations and found something unexpected: the variations between subjects suggested that they were all related, anthropologically speaking, by a common female ancestor who’d passed her mitochondrial DNA down the line. The research suggested that everyone in the entire human race shares the same great-great-great-lots-and-lots-more-greats grandmother. And we’re all rocking gently-used, slightly-mutated versions of her mitochondrial DNA.

This ancestral individual is technically called our matrilinear most recent common ancestor, or MRCA, but is more informally known as “mitochondrial Eve”; her maternal genetic makeup is represented in all of our DNA. She’s also been described as the “lucky mother”, since she wasn’t the only woman walking around and having babies at the time. Rather, her lineage — including mothers having daughters, since mitochondrial DNA is only passed by mothers, remember — is unbroken through history, while other childbearing ladies of the time had only sons, or no children, or their daughters didn’t produce more daughters down the line.

The idea of mitochondrial Eve shook science to its lunchtime Twinkies, because it implies a couple of things about human history. First, there was a time (or several) when our population must have been very small, maybe on the verge of extinction. For only one woman’s genetic imprint to have survived, rather than many, suggests there weren’t a whole bunch of humans running around the planet already, with haplotypes of their own. Our species went through some rough times, and only one branch of the tree survived.

The DNA also tells us roughly when this mitochondrial Eve existed. Based on the variability between contemporary humans’ DNA and the rate at which DNA glitches occur, mitochondrial Eve probably lived around 100,000 to 150,000 years ago. And since other evidence suggests that early humans didn’t migrate from Africa until about 95,000 years ago, our ur-granny most likely lived there. And cooked up some nice bits of DNA we’re still using today.

(For the record, we can also trace an “ultimate grandpa” via male lineages and the men-only Y chromosome. The “Y-chromosome Adam” may have lived around the same time as, or tens of thousands of years before, mitochondrial Eve. Their DNA’s early paths are completely independent.)

So next time you’re eating a sack lunch, root around in the bottom a little. Not only might you find a nice note — or a delicious snack cake — but you might discover some 100,000-year-old genetic material, courtesy of mitochondrial Eve. DNA appetit.

Image sources: Alvin’s Enviro Blog (mitochondrial Eve map), Sierra Club (fishy Zimmern), ThinkGeek (Tardis lunchbox), PlanetKris (mitochondrial mom joke)

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· 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 is 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 joyriding genomic gypsies.

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

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

Z-DNA: Because everybody needs a little time to unwind.
“Z-DNA: Because everybody needs a little time to unwind.”

Maybe you’re familiar with the fundamentals of DNA. A pair of organic biopolymer strands composed of covalently-bonded nucleotide molecules, wrapped together in a double helix. It’s not exactly simple. But the basics are pretty well established, thanks to Watson and Crick (and Franklin, and Gosling, and a bunch of others). If that’s as complicated as it gets, super.

Naturally, it gets more complicated. The universe is a smug little infinitely-large bitch, yo.

One way DNA gets harder is the way that pair of helices wrap around each other. You’d think there’d just be one way to fit, like Legos clicking together. But no. A DNA double helix is more like a jigsaw puzzle: if you get really frustrated and smush the pieces into those little holes, it’ll go together just about any way you want.

In nature — which in this case means, in you — DNA comes in (at least) three forms. The usual, vanilla, run-of-the-mill DNA in most of your cells is called B-DNA. I don’t know what the B stands for, but almost all DNA looks like this, so I’m guessing it’s Boooo-ring.

Moving on to something sexier.

A-DNA is similar to B-DNA structurally; they’re both wound in a “right-handed” orientation, and spoon together like desperate freshmen on a third date. But A-DNA is scrunched up even tighter, like an overwound Slinky. That’s not especially surprising, because you only see this form in DNA that’s dehydrated. I don’t know how your last hangover felt — but twisted up, jumbly and curled in on yourself is probably not a bad description. That’s probably why they call this A(lcohol-soaked-bender)-DNA.

But it gets even weirder.

The third form of naturally-observed DNA is called Z-DNA, and it’s pretty freaky. Like, up is down and right is left and Team Edward and Team Jacob living together in sparkly harmony freaky. First of all, it’s not right-handed. The two strands flip directions and twist the other way around each other, like some genetic freakshow oozing out of Ned Flanders’ Leftorium.

Z-DNA is also ganglier than the other forms, twisting every two base pairs instead of one. It’s not a great look. And the Z stands for “zig-zag”, which is only about a half-step above naming a DNA confirmation “humpback”. Or “pizzaface”.

In the end, you sort of feel sorry for Z-DNA. It looks like some kid accidentally broke a real DNA molecule and tried to rubberband and bubblegum it back together, but there are pieces left over and none of the cracks line up right. It’s the Steve Buscemi of the deoxyribonucleic acid world.

But don’t feel too bad for Z-DNA. Despite it’s lopsided ugly-lefty-ducklingness (or maybe because of it), Z-DNA may actually turn out to be pretty important. Scientists are still exploring its role in biology, but it’s thought that regular old B-DNA can somehow drunken-Twister itself backwards into Z-DNA at spots where transcription occurs in the genome. And since transcription is where the DNA template gets read as RNA, which then becomes the proteins that every cell needs to survive, that’s kind of a big deal. If not for this temporary unwinding into Z-DNA, all our DNA might scrunch up together, winding tighter and tighter like a raging genetic-scale hangover. Even tequila shooters can’t hurt you that bad.

So we should all appreciate our letter-coded DNA double helix friends. B-DNA, steady and boring and essential — the plain white underpants of our genetic material. And A-DNA, which reminds us to hydrate at parties, and also not to get too wound up over things. But especially Z-DNA, the southpaw oddball of the group. Z-DNA demonstrates that even the strangest-looking among us have a role to play, and no matter how weird left-handed people are, we shouldn’t kick them out of the nucleus.

Also, we shouldn’t feed them through a wood chipper, probably. But it is about time to watch Fargo again on Netflix. Thanks, Z-DNA!

Image sources: Neuroscience News (“Now I know my A, B, Z…), Nothing Is Going to Last (nailed-in jigsaw piece), Leftorium.com (Leftorium, the store), Dawson Reviews (gimme Buscemi)

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

Splice junctions: snipping ads out of your favorite programs since many millions of years ago.
“Splice junctions: snipping ads out of your favorite programs since many millions of years ago.”

Your DNA is crap.

Well, mostly it’s crap. But so is mine, and so is everyone else’s. For all the wondrous and amazing things our genetic code can accomplish, most of the really good stuff comes from a tiny little fraction of the genome. The rest is poorly understood, variable in quality and dubious in value.

In other words, your DNA is like cable TV.

Think of it this way: imagine all of your genetic material — three billion DNA base pairs tucked into every one of your cells, and responsible for making you “you” and not me or a goldfish or a head of iceberg lettuce — laid out in a line, like a TV program schedule. The “shows” are the genes — twenty to thirty thousand snippets of code that actually mean something. These can be read to produce proteins, which do just about all of the important work in your body, from grabbing the oxygen you breathe to growing toenails to helping you decide how much of that Buffy the Vampire Slayer marathon to sit through.

(All of it. Duh.)

But what’s between those shows you like, in the great abyss of “five hundred channels and nothing on”? Well, a couple of things. First, there are “pseudogenes” — stretches of DNA that look like they might do something interesting, but which have been mutated and mangled past the point of being useful. These are your knockoff shows and half-assed sequels: Who Wants to Be a Thousandaire?. Seinfarb. Home Alone 9: The Alonening. No good can come from these, clearly.

There are other bits of fluff, too. Near-endless repeats — possibly important in DNA for structure; used in TV as an excuse for USA to cram another NCIS rerun on the schedule. And long, droning stretches of apparently random sequence — the overnight informercials of the human genome.

But back to the genes. These are structured like TV shows in another important way: our genes contain commercials. In the genome, these are called “introns”, and are bits of DNA in between the important parts (which are called “exons”). When the gene is finally translated into a protein, these bits are snipped out in a process called splicing. And the edges of each intron in the line contain a short code called a splice junction, which tells the translation machinery where to snip the nonsense out.

So if a gene is like a television show, then a spliced gene is like watching with TiVo. Which is clearly better, because you can skip the commercials. And it’s made possible at the genetic level by splice junctions.

These splice junctions are tiny two-base sequences — usually GU (in RNA-speak) on one end, and AG on the other — that mark the intron they surround for snipping. But it’s not always a simple matter of lopping out the “commercials”. Many of our genes undergo a process called alternative splicing, where chunks containing multiple introns (and the exons between them) can be yanked out, producing multiple proteins from the same gene — sometimes with very different functions.

Think of alternative splicing as watching through the setup of, say, your favorite cop drama, then skipping to the end when they catch the perp. All that stuff in the middle is just filler and dusting for fingerprints, right? Much better.

So the next time your body translates a gene into a protein — which is all the time, obviously — give a little thanks to the splicing, and splice junctions, that make it possible, by editing out the crap in your cable lineup of a genome.

And then get back to that Buffython. Season 5 isn’t gonna watch itself, sunshine.

Image sources: Wikipedia (splicing), The Mental Elf (TV watcher), Uncoached and TimeToast (intron-snipping TiVos), Jack of All Trades… (Buffy squeal)

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