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!

Frameshift Mutation


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

Frameshift mutation: be VERY careful with your threesomes.
“Frameshift mutation: be VERY careful with your threesomes.”

Imagine you’re a Subway “sandwich artist”.

(I know, it’s very depressing. I’m sorry. It’ll only take a minute, and I promise you won’t run into that Jared guy. Because, yikes.)

As a sub Salvador Dali — or if you prefer, po’ boy Picasso, grinder Van Gogh or hero Edward Hopper — you follow three steps to create each “munch-sterpiece”:

  1. Slap down the spongy bread.
  2. Lay in the meatlike substance.
  3. Sprinkle various wilted veggies to taste.

That’s the procedure, one two three, into eternity.

(Or until school’s back in for the fall. Or you get fired for having mayo-balloon fights. As one does.)

But what happens when you get the sandwich dance wrong?

A simple screw-up — substituting the bread with cardboard, for instance — would ruin a single sandwich. (Or not. Possibly no one would notice.) Ditto for getting the steps out of order, slapping your meat on your pickles or some such thing.

But what would really throw things into a state of hoagie higgledy-piggledy would be to skip a step (or add an extra), without changing the overall pattern. If you had bread and meat ready, for instance, and momentarily forgot that vegetables existed.

(Hey, this is America. It happens.)

You’d know there’s a third step to the sandwich, so maybe you’d move on to bread and create a bread-meat-bread order. But now you’ve already done the bread step, so even if you remember the veggies — hello, lettuce! — your process is out of sync. Your next sandwich would be meat-veggies-bread, and so would the other subs after it, until you found a way to make an adjustment. Or until the manager fired you, because you’re making sandwiches like a crazy person.

What you’ve just done — apart from the important public service of encouraging people to eat somewhere better than Subway — is called a frameshift. When it happens in a sandwich shop, it gets a little messy. When it happens in your DNA, it’s called a frameshift mutation, and it can be very, very bad.

That’s because of the way that information in DNA gets used to code for proteins, which do most of the important jobs around our cells. Most of the genes in our DNA code for proteins, but the DNA information goes through another form called RNA to make it happen. The RNA gets created directly from the DNA, “word-for-word” as it were. So if a frameshift mutation occurs in the DNA — one missing bit of information, or one extra — it doesn’t make much difference here. The RNA is just a little longer or shorter than it ought to be.

Making RNA into proteins is trickier, though. Here, three bits of RNA information code for individual amino acids, the building blocks of proteins. And just like with the blimpie Botticellis above, if a triad stutters out of frame, everything afterward goes to hell. The wrong protein gets built, shorter or longer and unable to function the way it’s supposed to. It’s basically a Franken-protein, and all because of one little frameshift mutation.

While frameshift mutations are relatively rare, they can have huge consequences thanks to the complete horking-up of proteins they cause. Frameshift mutations can cause conditions ranging from Tay-Sachs disease to Crohn’s disease to cystic fibrosis to cancer, and more. Any of which are significantly worse than not getting lettuce on your footlong Italian.

You can reduce your risk of developing frameshift mutations by staying away from suspected DNA mutagens. Cigarette smoke. Ultraviolet radiation. Possibly, Subway food. So keep those DNA frames in sync and if you forget the veggies, then for heavens sake, start over. Sandwich safety first, kids.

Actual Science:
Penn State University / Microbiology – Frameshift mutations
San Diego State University / Stanley Maloy – Frame-shift mutations
Study.com – Effects of frameshift mutations: definitions and examples
Baylor College of Medicine – Looking for a shift could provide molecular diagnosis in rare disease
GenomeWeb – Exome sequencing uncovers new monogenic form of obesity

Image sources: Slideplayer / From DNA to Protein (frameshift mutation), The Commercial Curmudgeon (Subway sista), Domestic Geeks (frameshifted sandwich), RedBubble (“the only good way this ends” shirt)

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Birthday Problem


· Categories: Mathematics
What I’ve Learned:

The birthday problem: because nobody wants (or gets) to celebrate alone.
“The birthday problem: because nobody wants (or gets) to celebrate alone.”

Birthdays often have problems. Whether it’s the annual reminder of impending mortality, Grandma getting you the totally the wrong Teenage Mutant Ninja Turtle action figure or Marilyn Monroe failing to jump out of your cake to wish you happy birthday.

(Actually, regarding that last one, it would create a whole bunch of additional problems if she did. So stop wishing for that.

There’s always Marilyn Manson, if you just can’t shake the idea. Good luck with that.)

None of these issues is the birthday problem, however. The specifically-named “birthday problem” is actually a mathematical exercise — two words which you probably wouldn’t want to hear, in any combination, on your actual birthday. Assuming it’s not your actual birthday right now, here’s what the mathematical exercise asks:

Among a group of randomly-chosen individuals, what is the probability that at least two of them will share the same birthday?

The “randomly-chosen” bit is key, of course, since including certain individuals would muck up the math. The Olsen twins, for instance, would totally ruin everything.

(Presumably, this is not something you need mathematics to tell you.)

Assuming a full-on rand-o crowd, the question gets a little more interesting — to non-probability theorists, at least — when asked in this way:

How many people do you need to have a better than 50% chance of two people sharing a birthday?

That’s a trickier question than it looks. Most people can narrow down the range of possible answers a bit. If there’s one person in the room — scary Olsen or not — then there’s zero chance of sharing a birthday with the nobody else in attendance. And if (ignoring leap days, because ain’t nobody got time for that) 366 people are mingling, then the chance is 100% that at least two of them share a birthday. There’s only so much calendar to go around.

You might think that the number to get 50%, then, would be right in the middle. You would be mistaken.

Then again, a few minutes ago you wanted Marilyn Manson to hop out of a cake and sing to you. You don’t exactly have a track record for making good decisions.

The real answer (spoiler alert!) to this version of the birthday problem is 23. According to combinatorics probability theory — and some nifty math — with just 23 people in a room, the odds are slightly better than 50% that two of them share a birthday. If you want to increase the odds to 99.9%, you’ll have to make a few more phone calls — but your meeting hall still only needs a capacity of 70 people.

That’s nothing. They get bigger crowds than that at the Pawnee, Indiana town hall. And Ron Swanson doesn’t share his birthday with anyone.

This surprising result to the birthday problem is important for three reasons. First, maybe it instills in some young minds a wonder and love for math, and they’ll go on to become professional mathematicians. Which is great, because somebody has to take that bullet. And numbers make my head hurt.

Second, there are computer hacking strategies — called “birthday attacks” — that take advantage of the math behind the birthday problem to wreak certain kinds of digital havoc. These brute-force cryptographic manipulations are often aimed at using hash collisions to the hackers’ advantage. In other words, no birthday cake for you.

And finally, this demonstrates that there’s a big difference in calculating a 50/50 that any two people will share a birthday, versus the same odds that somebody in a crowd shares your birthday. For the latter, you’d need at least 253 people, which reminds us that probability is tricky, the obvious answer is not always the right one, and for crissakes stop making everything about you, ya town hall-cramming Olsen-loving Manson-caker.

And oh, yeah: happy birthday. Freak.

Actual Science:
Damn Interesting – The birthday paradox
Better Explained – Understanding the birthday paradox
NPR / Math Guy – The birthday problem
Hack This Site – Hash collisions and the birthday attack
University of Waterloo – Invasive species use landmarking to find love in a hopeless place

Image sources: Math.info (birthday match graph), Photobucket / taintedXarts (birthday Manson), The Gloss (Olsen twin powers, irritate!), FanShare (in Spanish!) (Pawnee powwow)

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Albedo


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

Albedo: upon further reflection, it keeps getting better.
“Albedo: upon further reflection, it keeps getting better.”

I used to think “albedo” was a term for sex drive in people without skin pigmentation. This led to some very uncomfortable conversations. And, as someone who doesn’t tan very well, a lot of unsuccessful pickup lines.

As it turns out, albedo means something a little bit different. It’s another word for “reflection coefficient”, which is the ratio of light reflected off an object to the amount of light pumped in. For a highly shiny object — Gwyneth Paltrow’s forehead, say — then you have a high albedo, close to 1. On a much darker surface — where light rays check in, but they don’t check out — the albedo will be very close to zero.

A partial list of substances on the low end of the albedo scale:

A 7-11 asphalt parking lot: 0.12
Charcoal: 0.04
Vantablack carbon nanotube substance: 0.00035
C. Montgomery Burns’ shriveled heart: 0.002
Black hole: 0(-ish)
Spinal Tap’s Smell the Glove album (revised cover): 0.000000001

(How much more black could it be? The scientific answer is: negligibly more black, allowing for measurement variability and prevailing experimental conditions. Nigel Tufnel wasn’t so far off.)

The albedo of most objects is affected by two things: the angle and the wavelength of light streaming in. Light glancing past is easier to reflect, and some materials have a preference for absorbing or bouncing back light of various colors.

In fact, that’s how we perceive objects as having colors; we only see the wavelengths bouncing off them that they neglected to absorb. If every substance sucked up every wavelength of light like some kind of solar paper towel, then they’d all be completely black.

Unlike non-solar paper towels, which are white. Because the Brawny man will clean up your coffee spills. But he’ll never take away your sunshine.

In astronomy, albedo is an important characteristic of faraway objects, and can be used to determine what they’re made of. One of Saturn’s moons, Enceladus, has a surface of nearly pristine ice, and an albedo of 0.99. You could basically use Enceladus as a mirror to see if there’s spinach stuck between your teeth, except that its 750 million miles from your bathroom and your face would freeze if you got anywhere close to it.

This week’s flyby — or more accurately, screamingwhooooshby — of Pluto by the New Horizons spacecraft is providing details and answers to a question first raised by albedo measurements of Pluto and its largest moon, Charon. These bodies (as well as Pluto’s other moons) are thought to have formed from a collision of two large objects many millions of years ago. But looking at light reflected from them, Pluto has an albedo in the range of 0.49 – 0.66, while Charon is much darker, at 0.36 – 0.39.

Why the difference? Are the two made of different substances, after all? Did somebody polish Pluto up to try to get it reinstated as a planet? Or is Charon just going through a “goth” phase?

These are answers that albedo alone can only hint at, for objects at the edge of our solar system and for planets many, many light years away. It’s not a perfect tool for astronomical discovery — but for the places our probes (and horny albinos) can’t reach, it’s an awfully good start.

Actual Science:
Universe Today – Albedo of the Earth
Lake County Astronomical Society – Albedo effects
io9 – Strange alien planet is impossibly black
Discover Magazine – A new record linked to climate change was just set in Greenland. It may seem esoteric, but it’s really important.
Washington Post – Fenway Park groundskeepers clear the snow with black sand. Brilliant.

Image sources: University of Washington (albedo spectrum), ChaCha (Gwyneth aglow), Brass Collar (“none more black”), Got a Nerdy Mind? (the Brawny menagerie)

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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)

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Acoustic Levitation


· Categories: Physics
What I’ve Learned:

Acoustic levitation: be uplifted by the sound.
“Acoustic levitation: be uplifted by the sound.”

Imagine you found an insect in your bathtub — a beetle, say. And also imagine that you’re a kind and compassionate soul — or maybe you actually are, in which case bully for you, Gandhi — and you want to move the beetle outdoors without harming it. That’s where the situation gets a bit complicated, because:

You don’t want to grab the bug, because you might accidentally bend a leg or antenna or something.

Also, you don’t want to catch the bug in a box or glass, because that’s cruel — and we’ve already established you’re a tree-frenching envirohippie paragon. At least for the duration of this thought experiment.

And really, you don’t want to touch the bug at all, because it’s gross. I don’t care how you feel about Mother Nature’s skittering nightmares. Nobody’s touching them on purpose. Ew.

So what do you do? It seems like yelling at the beetle to get the hell out of your bathtime sanctuary wouldn’t help — but actually, it might. If you could yell in a very specific and consistent way, and get the insect in just the right spot, and also maybe have a machine do the yelling for you, to make it less stressful for everyone.

(After all, what did that disgusting little bug ever do to you, other than rubbing its filthy thorax all over your tub?)

If you could produce just the right sort of sound waves, at a high enough volume and a suitable frequency, you could actually lift that beetle off its porcelain perch into mid-air, without ever physically touching it. The process is called acoustic levitation, and can be a lifesaver for manipulating things you don’t want to touch. Even with a Kleenex.

Acoustic levitation — or sonic levitation, as it’s sometimes called — relies on the force of sound waves colliding with an object. Under normal circumstances, this force is tiny. It might nudge a few atoms around, but it’s too weak to get anything fancy accomplished.

However. If you concentrate enough sound waves together, then channel your inner Nigel Tufnel and turn the volume all the way up to 11, those puny nudges multiply into a force that can defy gravity — at least when applied small objects, like that bathtub beetle. Or a computer chip. Or an unstable chemical.

Of course, it helps to use “ultrasonic” signals — those outside the range of human hearing — lest you blast out your own eardrums trying to float a butterfly off your medicine cabinet. Typical volumes for effective acoustic levitation signals are 150 decibels and higher.

That’s basically the equivalent of listening to a NASA rocket launch from the comfort of a chair that’s been strapped to the bottom of the solid fuel booster. Or sharing an elevator with Donald Trump. But because human ears can’t “pick up” ultrasonic frequencies, we’re not deafened by the prodigious ruckus being created by acoustic levitation experiments. We’re also too big to be lifted off the floor by those experiments — and that’s where the beetles and other small objects come in.

There are many advantages to holding something in the air using only sound. Those computer chips, for example, could be examined — or even manufactured — with a complete panoramic view, and no worries about using electromagnetic forces for levitation, either. Chemicals can be mixed or tested without fear of breaking their container, because there is no container. And yes, maybe you could get an insect out of your bathroom without needing a desperate shower yourself.

Mostly, scientists are working on the computer chips and chemicals sort of applications for acoustic levitation. But maybe a beetle crawling up some egghead’s shower head will get them moving on the last one, too. We can only hope.

In the meantime, researchers have managed to move objects around with sound, too. With the right mix of frequencies, sources and intensity, levitated objects can be made to dance, move and travel around the acoustic field. This opens up huge possibilities for what acoustic levitation can do in fields from manufacturing to medicine. Maybe someday, we’ll all have kits that will float those bathroom beetles right out the window to freedom, No muss, no fuss.

In the meantime, I suggest yelling at the bugs as loud as you can. That might not get rid of them, but at least other people will probably come running. They’ll probably know what to do. Or at least bring a Kleenex.

Actual Science:
Wired – How do you levitate things with sound?
io9 – Yes, you can levitate objects with sounds
National Geographic – Scientists move levitating objects through space for the first time
Phys.org – Gravity-beating ultrasonic tweezers provide a sound route to bioengineering
Nerdist – Acoustic levitation is even cooler when it explodes stuff

Image sources: LiveScience (acoustically-levitated beetle), Cool Advices, Brooklyn Magazine (Nigel Tufnel, going to 11), Salon (Trump, mid-dump)

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