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!

Ubiquitin


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

Ubiquitin: It's everywhere you want to be (and several places you don't).
“Ubiquitin: It’s everywhere you want to be (and several places you don’t).”

This is one of those times where you can learn about science by knowing a little English. Like how you figure out the dinosaur brachiosaurus was made out of grandma candy, or that the element proactinium will cure your acne, probably.

Sorry. This time will be better. I promise.

The protein “ubiquitin” was so named, back when it was discovered in the 1970s, because it was ubiquitous — in other words, everywhere. Every tissue scientists studied, every microscope they looked in, ubiquitin was there. Probably with enormous lapels and feathered hair, humming Jim Croce ballads. But it was there. Ubiquitously.

But what is it, exactly? Ubiquitin is a small protein that’s now been found in nearly every eukaryote — that is, most anything more evolved than a bacterium. It’s in most every type of tissue, and its job is to be glommed onto other proteins as a sort of targeted messaging system. Think of ubiquitin as the “Kick Me” sign of the cellular schoolyard.

Basically, it works like this: special proteins produced in our cells latch onto ubiquitin proteins and activate them — like writing the message on the sign. Then the ubiqiutin is hooked onto a different specialized protein in a process called “conjugation”. This gets it ready for the final step, like attaching a piece of tape to the top of the sign.

(Hey, genetics was invented before we had Post-It notes, all right? If you wanted to stick a sign to something back in the old days, attaching the tape was a separate step.

And yes, we walked uphill in the snow to do it, and we liked it. Shaddup.)

The final step, ligation, sticks the ubiquitin to whatever target protein is supposed to receive the message. Sometimes one ubiquitin is slapped on; sometimes, it’s a whole chain, like a bunch of latched-together plastic monkeys. Depending on which, and exactly how they’re hung on, determines exactly what fate lies in store for the poor unsuspecting tagged protein.

The most well-studied kind of ubiquitination (or ubiquitylation, if you’re really going for the Scrabble words, Einstein) involves a chain of ubiquitins strung together in a certain way, then tagged onto a protein. The result? That tagged protein is doomed to destruction. The message here is “Kick Me, Hard“, and the intracellular bullies are happy to comply.

But ubiquitination isn’t always a Mafia-style kiss of death. Some ubiquitin tags lead to a protein’s activation, or to being transported to a different part of the cell. So “Kick Me On”, or “Kick Me Over There”, if you like. It all depends on the message, and how it gets delivered. Uniquitin’s not bad; sometimes it’s just attached that way.

Ubiquitin thus plays a whole set of important roles in cells — keeping materials moving, cleaning up waste and flipping switches throughout a cell’s development. That makes it crucial for survival, and also something for infectious agents (like the flu virus) to try and exploit.

For figuring out the ubiquitin signalling pathway leading to protein degradation, three scientists were awarded the 2004 Nobel Prize in Chemistry. Two of them were from Israel, and the third was a researcher from the United States.

Because of course he was, right? Those guys are everywhere.

Actual Science:
WiseGEEK – What is ubiquitin protein?
Baldwin-Wallace University – The ubiquitin system
YouTube / Scottish Enterprise – Ubiquitin proteasome system programme
Bioscience Technology – Applying proteomics to Parkinson’s
Futurity – How the flu gets cells to crack open its shell

Image sources: Osaka University (ubiquitination diagram), Gold Country Girls (Brach’s old people candy), Dates with Kate (“Kick me”), Calvin’s Canadian Cave of Cool (monkeys, monkeys, monkeys!)

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Exosphere


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

Exosphere: It's where the innie space becomes an outie.
“Exosphere: It’s where the innie space becomes an outie.”

The earth’s atmosphere is sort of like a family. Everybody stays pretty close… but some stay closer than others. So the troposphere, the nearest layer, is like that aunt who comes over every weekend you can’t get rid of. The mesosphere, you maybe see at holidays, and it sends you stupid-looking sweaters for Christmas.

Or pictures of itself in stupid-looking sweaters. The mesosphere’s side of the family was always a little weird.

But the exosphere? No. The exosphere is the black sheep of the atmospheric family — and it likes it that way. You might get the exosphere to RSVP “NO!” to a family reunion, but that’s about it.

In planetary (as opposed to familial) terms, the exosphere is the outermost layer of influence, where individual molecules are still bound by gravity, but there’s nothing you could call an “atmosphere” to be found. Around Earth, the exosphere contains hydrogen, with a little bit of helium, carbon dioxide and oxygen flitting around. But not in a crowded way. It’s less “Times Square at rush hour”, and more “fans at a Miami Marlins baseball game”.

The spot where the exosphere begins is called the thermopause. That might sound like a fancy name for “hot flashes” — and if you happen to be a planet, that’s not too far from the truth. The thermopause marks the boundary of the Earth’s energy system, and the exosphere doesn’t have enough molecular oomph to be part of that.

Of course, the planet has good and bad days, just like the rest of us. So on a high-energy day — maybe it’s summer, or the sun is flaring, or Earth got its ass out of bed early for yoga — the exosphere might start six hundred miles or more above the surface. On days with less energy — Sundays, I’m assuming, and the day after Thanksgiving — the exosphere might start half that high, around three hundred miles up. Some days it’s just harder to push yourself up against outer space, you know?

Where the exosphere ends depends on how you feel about outer space. Or at least how you feel about defining it. If you prefer your outer space to start where the radiation from earth ends — light, heat, the glow from Ryan Seacrest’s front teeth, all of that — then your exosphere ends six thousand miles above the earth, give or take a few hundred miles.

If you want to be all technical about it, and consider where the gravitational pull of the earth on atoms of hydrogen gives way to radiation pressure from the sun, letting those atoms escape out into the ether, that’s a different story. That happens a wee bit further out — say, a hundred and twenty thousand miles up the chute. Or halfway to the moon, if we’re getting other celestial objects involved now.

Speaking of which, other globs of space rock — including our moon — have exospheres, though at lot of them don’t have much of anything else. So an exosphere is sort of the bare minimum possible, in lieu of something more substantial.

Kind of like Ryan Seacrest, apart from his teeth — or the stands at a Marlins game. Neat.

Actual Science:
Universe Today – Exosphere
University Cooperation for Atmospheric Research – Exosphere – overview
Science Daily – How the moon gets its exosphere
CBS News – NASA moon mission targets lunar dust, “exosphere”
University College London – Dione’s thin oxygen exosphere

Image sources: Surfline (atmospheric layers), (Christmas sweater), Buzzfeed (Marlins fans [both of them]), The Richest (Tom Cruise’s shiny, angry, shiny teeth)

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Gene Drive


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

Gene drives: sometimes CRISPR is the best accessory.
“Gene drives: sometimes CRISPR is the best accessory.”

When you shop for a new outfit, you’re looking for a number of things. It has to fit. It has to look nice. The accessories should match. And ideally, it should be malaria-free.

Genetic scientists don’t shop for clothes much (lab coats never go out of style), but they do struggle with problems like that last one — reducing the impact of diseases around the world. Malaria and others are transmitted via mosquitoes, affecting hundreds of millions of people and killing more than one million worldwide every year. But what if there was a way to genetically alter the blood-sucking little bastards to prevent these infections? And what if it was as easy (relatively speaking, for the lab geek set) as picking out a cute hat to match that kicky new jacket?

Enter the gene drive, which could bring the concept of the extreme makeover to the chromosomes of bugs and pests and maybe even humans all over the world. It works using a system nicknamed CRISPR, which stands for a bunch of long sciency words that no one bothers to remember. The important thing is how it works, which comes below.

(Stick with me here. The beginning doesn’t seem to have much to do with malaria, but it gets better and then all comes together in the end. It’s like the anti-Matrix trilogy.)

Some bacteria have a very clever protein that helps them avoid virus infections. The bacterial cells keep snippets of viral genes around (the structure these are stored in is the thing actually called CRISPR), and this protein — called Cas9 — recognizes the viral sequence as a target, or “guide”. Whenever Cas9 sees this sequence, like when a virus barges in and starts throwing it around the joint, Cas9 cuts it right down the middle and ruins it. No viral genes, no virus, and the bacteria go on to lead long, happy, fulfilling tiny lives. Or not. They’re not really important to the rest of the story, so screw ’em.

The key is, this Cas9 protein doesn’t really care what guide sequence it’s given. So scientists can yank the Cas9 gene out of the bacteria and engineer it into other organisms. Like mosquitoes. They can also engineer in custom guide sequences matching that organism’s DNA — like one for mosquitoes’ immune response to malaria, for instance — and thus effectively delete or mutate just about any gene they like.

With a little extra fiddling — like a perfect scarf that ties the ensemble together — scientists can also use CRISPR and Cas9 to introduce new genes. Better still, those genes can be inserted in particular spots in the genome that have a genetic “competitive advantage”, meaning they get passed on to offspring more readily than most. That means these gene drives could spread through a population faster than the latest French runway fashion. And look damned good doing it.

Gene drives specifically in mosquitoes could be theoretically used in a number of ways. We could make the bugs resistant to malaria and other diseases. We could alter genes that allow insects to pass the disease on. Or we could go all snarky fashion critic on them and wipe them out completely — like skewing their offspring to be nearly all male.

See, “Raining Men” is one thing. But when it rains only men for a few generations, your species got a problem, yo.

The opportunities for gene drives are near-endless. Any species that reproduces sexually — which is most animals, up to and including (most) humans — could theoretically be CRISPR’ed, and convinced to “say yes to the gene”. There are one or two (or thousands) of ethical kinks to work out first, of course. But in terms of the science, we can rebuild those mosquitoes (and nearly everyone else). We have the technology. We can make them less malarial than they were before. Better. Stronger. CRISPRier.

Actual Science:
eLife – Emerging technology: concerning RNA-guided gene drives for the alteration of wild populations
NOVA Next – Genetically engineering almost anything
Scientific American – “Gene drives” and CRISPR could revolutionize ecosystem management
The Scientist – Opinion: on the irreversibility of gene drives
UCLA / John Marshall lab – Gene drive systems for spreading refractory genes

Image sources: Science (mosquito family tree), PRWeb (totally matching accessories), Digital Journal (perfect scarf), Joy Reactor (men, raining [hallelujah])

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Pauli Exclusion Principle


· Categories: Physics
What I’ve Learned:

Pauli exclusion principle: If you're anything like me, then get the hell out.
“Pauli exclusion principle: If you’re anything like me, then get the hell out.”

The Pauli exclusion principle sounds like some rule a big Italian bouncer would use to keep you out of a swanky club, or maybe the reason Hollywood doesn’t let Pauly Shore make movies any more.

(That last one doesn’t really need a special name. The reason Pauly Shore isn’t allowed to make movies any more is all of them.)

But the Pauli exclusion principle is something else entirely. In the 1920s, physicists kinda-sorta understood something about the nature of atoms, and the electrons whizzing around them. They knew how many electrons the atoms of each element contained — one for hydrogen, two for helium, five for Milla Jovovich, et cetera — and they knew that some of those elements were more “stable” than others.

In physics terms, this stability meant that atoms of these elements didn’t share electrons with other atoms. They had no extras to give, and no empty electron-sized holes on their knickknack shelves to fill. These elements seemed to have atoms that were “full” of electrons — but no one knew exactly what that meant, or what kept the atoms in that “full” state.

A lot of people guessed it was those godawful Carl’s Jr. Thickburgers. But those didn’t exist yet — so it was probably something else.

Enter physicist Wolfgang Pauli, who simplified matters by making things more complicated. Because this is quantum physics, and that’s how it works most of the time.

At the time, electrons in an atom were characterized by three characteristics, or “quantum numbers”. Together, the values for these numbers described (roughly) the distance, shape and orientation of the electron’s orbit around the atom. And it took a hell of a lot of work to figure those three coordinates out.

Pauli decided that wasn’t enough, and added a fourth. He didn’t know what it was, exactly, but it was some characteristic with one of two possible values, like “on” or “off”. “Shirts” or “skins”. “Team Edward” or “Team Jacob”. Take your pick.

To make up for all the extra math, he then tacked on his Pauli exclusion principle: taking all four characteristics into account, no two electrons in an atom can have the same values. An electron orbital is “full” with two electrons in it — one with each possible value for Pauli’s fourth number. They can’t have the same number — and a third wheel can’t slip in, because both possible numbers are taken.

With that, it all came together. Atoms have different numbers and types and sizes of orbitals, but applying the Pauli exclusion principle explains which ones are “full”, and when the whole atom is “full”. The predictions lined up exactly with what scientists had already observed about atomic behavior. With one simple rule (well, relatively simple, for physics), Pauli gave physics a cornerstone of quantum mechanics and atomic physics. And in 1945, physics gave him back a Nobel Prize for it.

In the following years, Pauli’s fourth quantum number was identified as the “spin” of the electron, which for typically-complicated reasons has a value of either 1/2 or -1/2, but never anything else. All those physicists who bet on “boxers” versus “briefs” were apparently wrong.

But the impact of the Pauli exclusion principle didn’t end with electrons and atoms. The rule applies to all fermions (subatomic particles with half-integer spin), and also explains the characteristics of conductors and semiconductors, shows why matter is stable and takes up volume, and helps astrophysicists describe why white dwarf and neutron stars don’t collapse into black holes. Not bad for a scientific idea that basically started out with electrons picking “heads” or “tails”.

Actual Science:
The Physics Mill – Binary unity: the Pauli exclusion principle
The Physics of the Universe – Spin and the Pauli exclusion principle
David Yerle – A physics challenge: explain Pauli’s exclusion principle
NASA Astronomy Picture of the Day – Pauli exclusion principle: why you don’t implode
NanoWerk – New insights into the world of quantum materials

Image sources: StudyBlue (Pauli exclusion principle), Vevo (Pauly Shore, outside looking in), Kristy Lish (Leeloo / Fifth Element), Synotrip (Paris with a mouthful of Carl)

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Convergent Evolution


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

Convergent evolution: When great genes think alike.
“Convergent evolution: When great genes think alike.”

There’s no commandment in nature saying, “Thou shalt not covet thy neighbor species’ competitive survival advantage.” Mother Nature plays it pretty fast and loose with the rules.

For instance, say you’re a tree frog living high in the branches of some verdant tropical forest. Maybe some of your chittery squirrel pals have adapted their flappy limb skin and learned to glide gracefully from treetop to ground, whereas your species’ method for quick descent ends with a splat and an unfortunate frog-innard mess. Have you missed the gliding boat, simply because you decided to hop off the evolutionary squirrelhood branch before gliding came up?

Not at all, wartyballs. Because you can still develop gliding abilities on your own — completely separate from those showoff squirrels — in a process known as convergent evolution.

As processes go, convergent evolution is really just evolution, in an encore presentation. When the same environmental pressure is applied to different species, they may adapt in ways that appear similar, but are actually unique and occur entirely independently. So just because the tree rats figured out one way to glide doesn’t mean that the frogs can’t find another and glide alongside them. The squirrels don’t hold the patent on the technology; anybody with a flexible genetic code and a few millennia to burn can follow in their footsteps. Even Italian plumbers, apparently. Mother Nature’s not picky.

Are there other examples of evolution going back to the well over and over to solve the same problem in similar ways, like Jonah Lehrer barfing out a thousand words of recycled New Yorker fluff? You betcha.

For starters, there are animal wings. Bats, birds and prehistoric flying dinosaurs don’t have a lot in common — except that they all learned to fly, and grew their own appendages to do so. But in shape and structure, all those wings are different; the adaptations they made were in response to the same need for flight, but unique to the type of animal yearning for air time.

There are plenty of other instances of convergent evolution, too. Like eye structures in vertebrates versus squid, or echolocation in bats and dolphins, or fruit production in a variety of plants. It also happens at the molecular level — some enzymes converge on similar configurations of active site pockets, and some specific DNA and amino acid changes have been found (in the case of sonar-using bats and dolphins) to have occurred in separate species, independently helping to enable the same biological function.

Seriously, that level of convergence is straight-up crazy. Mother Nature goes completely off the rails sometimes. I really think the old girl should switch to decaf.

Actual Science:
University of Texas, Austin – Convergent evolution
University of California Museum of Paleontology – Vertebrate flight: the three solutions to flight
ScienceDaily – Genetic similarities between bats and dolphins discovered
ExtremeTech – Scientists unravel the genetic secrets of caffeine’s evolution in coffee

Image sources: Mr. Kubuske’s blog (wings, wings, wings!), FlippySpoon (Rocky the flying squirrel), The Ultimate Gamer (Mario the flying Italian plumber), Spoonful (crazy-Lee Mother Nature)

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