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!

Knockout Mouse


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

Knockout mouse: one lab animal that really goes to the mat for science.
“Knockout mouse: one lab animal that really goes to the mat for science.”

The late author Douglas Adams once said a thing about cats:

If you try and take a cat apart to see how it works, the first thing you have on your hands is a nonworking cat.

He was making a point about how living things are extraordinarily complex, even more so than things like alarm clocks and carburetors and the London Bridge — which, while also complex, can in fact be taken apart and reassembled into reasonable working order.

(By people who are not me. I struggle to reassemble a hamburger after I’ve taken the top off to adjust the pickles.)

Note that the esteemed Mr. Adams never said anything about mice.

Since 1989, scientists have been able to produce essentially the non-cat (and mostly un-messy) equivalent of what Douglas Adams described: a mouse that’s been taken apart to see how it works — and then put back together, with one of the pieces missing.

Unlike your average neighborhood mechanic or electrician, however, the missing bits of these mice are left out intentionally, to find out what they do. And before visions of Frankenmice or other murine monstrosities skitter through your head, let’s clarify that we’re talking about “pieces” at the genetic level. Nobody’s hacksawing the ears off your favorite Disney rodent.

Well. Not for science, anyway.

The term for one of these genetically-altered mice is “knockout mouse”, which sounds like someone Jessica Rabbit shares an apartment with. Or some remedial schlub you have to fight in Punchout if you get your ass kicked by Glass Joe.

Happily, it’s neither. The “knockout” part of the name refers to the knockout of a specific gene. To create a knockout mouse, scientists recreate the sequence of a mouse gene in the laboratory — but with a fatal flaw. They alter the gene sequence so that it can’t produce the functional protein it normally would. They then introduce this broken gene into stem cells collected from mice.

Because the mucked-with gene is still nearly the same sequence as the normal version, some of the stem cells will integrate the new copy into the same spot in the genome, via a process called homologous recombination. It’s a rare occurrence — the cell’s DNA has to need repair in just the right place, when the engineered gene copy happens to be handy — but researchers have designed ways to know when it happens, and to retrieve those few cells where the gene has nestled in just right.

Since each cell contains two sets of chromosomes, the engineered stem cells have one “good” copy of the target gene, in addition to the scrambled one they’ve just picked up. Those stem cells get inserted into an early-stage mouse embryo, which is then implanted into a female mouse to grow. If all goes well, the embryo grows into a baby mouse containing cells from both the original embryo and the injected-in cells. This is called a chimera. And if all goes really well, the sex organs on those baby chimeric mice will come from the injected cells, with one wonky copy of the target gene.

From there, it’s just a hop, skip and a few tiny Barry White albums to a knockout mouse. The chimeras with one wonky copy of the gene in their sperm or eggs are bred, and some of their offspring will inherit that wonky gene — along with a normal copy from the other parent. But, cross-breed a few of those single-copy mice together, and eventually you’ll come up with a mouse with a non-functional copy inherited from both parents. That’s a critter where the gene essentially doesn’t exist any more — and that’s a knockout mouse.

There are now thousands of different types of knockout mice, each demonstrating the effects a particular gene has — by its absence. Knock out one gene, and the mice without it become more susceptible to cancer. Knock out another, and they lose their hair. Another, and the mice grow huge and chubby.

Scientists use knockout mice because many of their genes are similar to ours, and often function in the same way. It’s not a perfect model, but “knockout people” are generally frowned upon in the medical community, so it’ll have to do. And knockout mouse models have been used to study everything from aging to arthritis to obesity to cancer, so they’re extremely useful as research tools.

They might also, according to Douglas Adams’ books, be hyper-intelligent pan-dimensional beings who’ve set up the Earth as a grand cosmic experiment. And he was pretty spot-on about the cat thing, so it’s worth mulling over.

Actual Science:
NIH/NHGRI – Knockout mice
NobelPrize.org – Gene modification in mice
Nature Scitable – Scientists can analyze gene function by deleting gene sequences
Speaking of Research – Lung cancer immunotherapy, from PD-1 knockout mice to clinical trials
Science Daily – Potential role of leptin in diabetes discovered

Image sources: Science Alert (leptin KO mouse), S M Ong (D.N.A., looking devious), Carton-Online (Mickey, missing something), One Gamer’s Thoughts (Monsieur Joe, mid-taunt)

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Uncertainty Principle


· Categories: Physics
What I’ve Learned:

Uncertainty principle: you'll never be a know-it-all; you can only be a know-it-half.
“Uncertainty principle: you’ll never be a know-it-all; you can only be a know-it-half.”

The uncertainty principle is an important tenet of quantum mechanics, first stated by Werner Heisenberg in 1927. And, like most concepts in quantum mechanics, it’s best explained with an analogy to a scene in Cool Hand Luke.

(No, seriously. I’m pretty sure ninety percent of Richard Feynman’s lectures involved stories about eating fifty hard-boiled eggs. You can look it up.)

In a nutshell, what the uncertainty principle says is this: at the quantum level, there are certain pairs of properties of a particle — like position and momentum, for instance — that cannot be accurately determined at the same time. The more precisely one property in such a pair is determined, the less certain one can be about the other.

That’s a fairly textbook definition of the uncertainty principle, which means any of us who ever took a class with an intro to quantum mechanics once slept through a very similar paragraph, probably drooling on our desks. Therefore: Cool Hand Luke.

Say you’re out there in the prison yard like Luke, wearing leg irons — double irons, to be precise — and the guards have decided to break you. Boss Position says you got a bunch of your dirt in his ditch, and you’d better get it out. So you go to work, and you dig it out.

Then Boss Momentum comes up, and asks what the hell you’re doing. Get your dirt out of his yard, he says. So you shovel your dirt back into the ditch. At which point, Boss Position comes back and yells at you to get your dirt out of the ditch, and somebody smacks you with a walking stick and you get your mind right for a while until you and George Kennedy ride off in a dump truck together.

Okay, some of that bit has nothing to do with physics. It’s just a really good movie.

The point is, you’ve got a ditchful of dirt, which stands for your ability to measure. You can put all your dirt in the ditch and measure position to a T — but then you’ve got no dirt left over to measure momentum. Or you can dump all your dirt in the yard and nail down momentum, but then position is a mystery. Or you can split the dirt, half-ass an estimate for both, and then nobody’s happy. It’s your choice. But there’s no more dirt to work with.

Also, the man with no eyes will probably shoot you in the end, either way. Because in quantum physics, nobody gets their mind right for very long.

One last important thing about the uncertainty principle: it’s not solely a result of the way you do your measuring. Some people — including Heisenberg — explained the uncertainty principle in a way that made it seem the ambiguity came from the act of measuring.

(Probably because Cool Hand Luke hadn’t been made yet in 1927. I think we can all agree that would have saved everyone a lot of time.)

And while it’s true that measurement will often alter the properties of a particle under study — a photon from a microscope changing a particle’s path is a classic thought experiment example — that’s not the same thing. That’s called the “observer effect”, and beyond any ambiguity that brings to the party, there’s still a fundamental, no-getting-around-it, baked-into-the-universe uncertainty principle lurking underneath. Even in a perfect world, with a measuring device that leaves a particle entirely undisturbed, you still can’t know both the position and momentum (for instance) of a quantum particle with complete certainty.

It’s almost as though what the two properties have is… a failure to communicate. Talkin’ physics over heah, boss.

Actual Science:
American Institute of Physics – Uncertainty principle
Nature – Proof mooted for quantum uncertainty
LiveScience – Wacky physics: new uncertainty about the uncertainty principle
Scientific American – Common interpretation of Heisenberg’s uncertainty principle is proved false
NY Times – Nothing to see here: demoting the uncertainty principle

Image sources: Clear Science (uncertainty principle), Information Processing (Feynman, obviously lecturing about a hard-boiled egg), Wars and Windmills (Luke and his ditch dirt), Northwestern University and Dewey21C (Werner and Luke staring down the man with no eyes)

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Lysosome


· Categories: Biology
What I’ve Learned:

'I'm the lysosome. I solve subcellular problems.'
“I’m the lysosome. I solve subcellular problems.”

Everybody has a mess that needs cleaning up, and you usually know who to call to get it taken care of. If you’re staring at the crumby remnants of your BLT, you call the waiter. If the backseat of your car is dirty, you call an auto detailer.

(Or, if the backseat of your car is really dirty, you call Harvey Keitel.)

And if your cell is getting cluttered full of junk, you call the “cleaner” of the microscopic world: the lysosome.

Lysosomes are basically emergency cleaning supplies that (almost all of) your cells keep around, just in case a mess breaks out. That makes sense. You or I might stash a can of Pledge under the sink, or cram some napkins in the glove box. (And straws. Why so many stupid straws?) If things go sideways, at least you have something on hand to do some cleaning.

Your cells are much more hardcore. Or possibly OCD. The cells’ strategy for mess management is essentially to hoard baggies filled with acid and enzymes. These “baggies”, the lysosomes, have a spicy pH of around 4.8, compared to the rest of the cell, which is typically a bland and neutral 7.2. When the cell encounters something it wants to be rid of — a virus, say, or a broken-down mitochondrion, or its mother-in-law — it dumps it into a lysosome, and lets nature take its course.

Where “nature” refers to the acid and more than fifty different kinds of destructive hydrolytic enzymes. And “take its course” means breaking the mess into its molecular components so hard, even its own mother wouldn’t recognize it.

Like I said, cells are hardcore.

Lysosomes are enclosed by the same sort of lipid membrane that covers the cell itself, and can merge together to make bigger “baggies”, as needed. Overall, lysosomes can vary in size by a factor of about ten. And when it comes to cleaning messes, they don’t discriminate; they’ll take care of anything you throw their way. Phagocytosis — the uptake of microscopic critters? Check. Endocytosis — the accumulation of external large molecules and detritus? No problem. And autophagy — fusing with a failing internal cell component to get rid of it? Clean as a lysosomal whistle.

And like most good cleaners, the only time you really notice lysosomes is when they’re not doing their job. Mutations in one of several key enzyme genes can lead to conditions called lysosomal storage diseases. Where these mutations render the lysosomal genes inactive, those enzymes can’t do their job. Certain materials can’t be broken down, and pretty soon the messes back up and clutter the whole cell. If you’ve ever seen an episode of Hoarders, you know that’s pretty bad.

And if you haven’t, then I’ve just told you it’s pretty bad. So now you know.

But mostly, lysosomes quietly do their thing in the background, like an attentive busboy at a restaurant. Or like Winston Wolfe. You may never see the lysosomes in action. But you’ll know when they’ve been there. Because everything will be so clean.

Actual Science:
The Almighty Cell – Lysosome
KUMC Cell and Tissue Biology – Introduction to lysosomes
NTSAD – Lysosome pathology
ScienceDaily – Detecting lysosomal pH with better fluorescent probes
YaleNews – Failure of cells’ ‘garbage disposal’ system may contribute to Alzheimer’s

Image sources: Molecular Expressions (lysosome), Miramax (the Wolf), My Blissful Space (straws in the glove box, yo), Psychology Today (hoarder’s hovel, needs a shovel)

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Noble Gases


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

Noble gases: They are SO not into you.
“Noble gases: They are SO not into you.”

When you hear the word noble, it conjures many thoughts. French aristocracy. Those starch-shirted tea-sippers on PBS. “Barnes and”. But what is it exactly that these “noble” things have in common?

For starters, they really don’t like dealing with people. They’re not into sharing or helping or customer service. Or customers. Or anyone they consider peasants. Which is all of us.

But this notion of noble isn’t limited to the Antoinettes and booksellers and creepy Crawleys of the world. It’s also pretty much the way noble gases behave: hands-off, aloof and rarely intermingling with the common folk. Not while anyone is looking, anyway.

In atomic terms, this means that atoms of the noble gas elements — helium, neon, argon, krypton, xenon and radon — almost never form molecular bonds with other elements.

(And unlike some “noble” families, they don’t often bond with their own kind, either.

Yeah, that’s right. I’m lookin’ at you, Habsburgs, ya interbreeding jaw-jutters.)

The reason noble gases don’t readily form molecules is that their outermost electron shells are “full”. Atomic bonding — like all bonding, according to Bert and Ernie — is about sharing. In this case, sharing of one or more electrons.

But atoms are built with “shells” of certain sizes, and the outer one is where the interatomic electron love is most likely to happen. If that outer shell already has as many electrons as it can hold, like a dozen eggs in a carton, then it’s got no room for a spare shared from another atom. And having that full shell gives the atom stability — so it’s in no hurry to loan an electron out and break up the set, either.

All the noble gas elements have atoms in this exact situation. They’ve got everything they need, and a place for everything they have. They don’t want to talk to you, nor to some chatty hydrogen ion. And especially not some clingy bonder like carbon. Carbon atoms make up to four atomic bonds at the same time.

That would never do for a noble gas. Noble gases probably hire atoms to make their dirty atomic bonds for them. Indeed. Quite. I say.

Of course, being “noble” gives the noble gases a set of unique properties. (Which, happily for them, don’t include hereditary haemophilia and chronic haughtiness.) First — as if to prove how little they want to do with you — all noble gases are colorless, odorless and tasteless. As the name suggests, they’re all also gases at normal temperatures and pressures — helium, in fact, is the only element that can’t be cooled into a solid without also applying pressure. As in, twenty-five atmospheres of pressure. Nobles really are a stubborn lot.

While it is possible — though never easy — to get the noble gases to play nice and bond with other elements, it’s actually their uppity ways that make them most useful. Helium is added to deep-sea scuba air tanks to prevent the bends, since it’s not easily absorbed into tissues. And because it’s inflammable, it’s replaced hydrogen gas for blimp filler since that whole Hindenburg “oopsie” a few decades ago.

Non-reactivity makes noble gases useful in light bulbs, too. Halogen lamps include krypton, incandescent bulbs use argon and neon lights… well. Loners or not, let’s just say Las Vegas wouldn’t be Las Vegas without a helluva lot of noble gas in its signs. And they find use in arc welding, medical and industrial lasers, MRIs, Antarctic ice dating and gas chromatographs, among many other applications.

Which might be the oddest thing of all about these elements. For a bunch of atoms too snooty to mingle with us commoners, noble gases sure do get around.

Actual Science:
Science Clarified – Noble gases
PhysicsWorld – First noble-gas molecules found in space
National Science Foundation – Krypton-dating technique allows researchers to accurately date ancient Antarctic ice
PNNL – A noble gas cage
Phys.org – Curiosity sniffs out history of Martian atmosphere

Image sources: Chemhume (noble gases), Buzzfeed (disapproving dowager), American Museum of Natural History (“holy Hapsburg jaw, Charles II!), Shrimpdaddycocoapuff (noble gas cat)

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Zombie Computer


· Categories: Computers
What I’ve Learned:

Zombie computer: beware the night of the living Dells.
“Zombie computer: beware the night of the living Dells.”

Zombies are kind of a big deal these days. If you’re a fan of TV or movies or video games, you’ve surely seen them — and like actual zombies, they’re still multiplying. It’s like somebody ran a zombie through a Dr. Seuss-ifier:

You’ve got fast ones and slow ones and now one with an ‘i’.
They crave brain, feel no pain and just want you to die.

There are zombies that walk and zombies that talk and zombies that grin like Fairuza Balk.
Some zombies dance and others fight plants and by now, one of them might be Jack Palance.

(Sorry. Too soon?)

The point is, zombies are everywhere in fiction — but they’re also everywhere in real life, in an insidious form you don’t often hear about. I’m talking about zombie computers, and there are millions upon millions of them just waiting to eat your… well, not brains, exactly. But probably your bandwidth. And these days, that’s just as bad.

A zombie computer — or just zombie, if you like — is a device that’s been taken over by a malicious user or bit of software, and now unquestionably does the bidding of its nefarious master. Once the machine is hacked into or infected with a virus or Trojan horse or computer worm, it can become a zombie without anyone around it ever knowing.

(Unlike zombie humans, zombie computers apparently don’t decompose, start to smell or shuffle down the street mumbling, “CPUUuuuuus, CPUUuuuUUUUSSss…” So they’re harder to identify.)

And while Dr. Frankenstein used his “zombie” to terrorize the townspeople or a voodoo priest might use a zombie army to, I don’t know, make a really big batch of jambalaya, maybe, controllers of zombie computers usually have much, much more sinister stuff in mind.

Like spam.

The puppet master of a bunch of zombie computers can coordinate them into something called a “botnet”, which is just a big gaggle of infected computers doing whatever they’re told. And some people tell them to send billions upon billions of junk emails to people all over the world.

Security experts estimate that roughly two-thirds of all email sent is “spam” of some kind, and much of that — up to eighty percent, according to one study — comes from zombie computers in botnets. It’s thought that a ten-thousand computer botnet — which is not particularly large; botnets have been seen with over one million zombie computers — can send up to fifty billion emails in a single week.

That’s “billion”, with a “b”. Kinda makes those zombie hordes on TV look like a couple of kindergarten kids, eh?

Of course, zombie computer masters can do worse than flood a few (billion) inboxes. Botnets can also be used to artificially generate hits on websites, to generate so many simultaneous hits that sites effectively shut down — known as a DDoS, or distributed denial of service attack, very nasty — identity theft, bank fraud, extortion, espionage and, of course, to recruit more victims. What good would a zombie computer be, if it didn’t reach out and bite a few uninfected innocents?

So enjoy the science fiction shows and films and games featuring “scary” zombies that can’t actually crawl out of the grave and get you. But be wary of that laptop or PC that you’re watching or playing on. That could be a real zombie, sitting in your very own living room. Maybe even on your lap.

EEEEEEEKKK!!

Actual Science:
New York Times – Attack of the zombie computers is growing threat
PC World – Cleaning up botnets takes years to complete — if ever
ZDNet – DDoS botnet makes slaves of your home and office routers
Wired – Connected home: a next-gen botnet army?
Newsweek – FBI issues $3 million bounty for Russian hacker

Image sources: Pocket Fives (zombie computer botnet), Design and Trend (i[cecream]Zombie), Socialite Life (Balk, batty), The Var Guy (botnets after your braaaaaaains…)

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