Category Archives: How it works

What Does an Atom Look Like? See For Yourself

How do you know when something’s real?  Is it enough that its existence is predicted mathematically?  What if you use an instrument to measure its effects on other things?  Or is seeing truly the only path to believing?  Atomism, the idea that all matter is made of fundamental, discrete, indestructible units, has been around for ages, at least since ancient Greece.  Back then, it was more of a philosophic idea rather than anything that could actually be tested.  The evidence for atoms began to stack up in the 1800′s, but they couldn’t actually be imaged until 1951, facilitated by the technique of field ion microscopy.

Today, showing off atoms is almost a novelty, as IBM has proven able to maneuver single bits of carbon around to create images and even a stop-motion film.  There’s no denying that atoms exist, baby.  The proof is in the pudding.  But is there pudding in the atom?  That’s what one historic model predicted.  Despite the romantic notions of foregone generations, atoms are not the indestructible bases for everything; there are other little scraps of matter that come together to form them.  So what does it look like inside the atom?  It’s been a subject of debate (and calculation), but thanks to an international team of researchers, we’ve finally been given our first real glimpse.

Still image from “A Boy and His Atom,” the nearly inconceivable stop-motion carbon atom film by IBM

John Dalton is credited by most as the originator of modern atomic theory, as he noticed that chemical elements always react in ratios of whole numbers.  That wouldn’t be necessary if a substance could be broken into infinitely small parts.  But that didn’t prove atoms weren’t themselves made up of smaller things.  In 1897, J. J. Thompson discovered that cathode rays are actually composed of tiny, negatively charged particles (eventually dubbed “electrons), and he hypothesized that they originated from within atoms, casting doubt on the indivisibility issue.  Since atoms have no net electrical charge, Thompson suggested as a counterbalance that electrons were distributed through a sea of positively charged material within the atom, as if they were raisins suspended in plum pudding.  A delicious yet ultimately inaccurate view.

A Christmas treat or the basic building block of everything?

Ernest Rutherford took the next high profile shot in 1909, hurling positively charged alpha particles at gold foil sheets, playing a hunch that bet against the Thompson model.  Sure enough, Rutherford saw what he wanted when most of the alpha particles slipped right through the foil, with a few being deflected at extreme angles J.J. wouldn’t have expected.  Like charges repel, so for the majority of alpha particles to pass through undisturbed, the positively charged parts of the gold atoms had to be almost vanishingly small compared to their atomic radius.  The plum pudding was dumped and we were left with the unsettling conclusion that most of the atom was nothing at all; negatively charged electrons orbiting a positively-charged nucleus at a distance much vaster than the particles’ sizes.  Turns out there’s not much more to see than empty space.

Niels Bohr continued the “solar system” idea of an atom, but with an important and freakish difference.  If an electron circling a proton (which is pretty much a hydrogen atom) were subject to regular electrostatic forces, it would rather rapidly spiral into the nucleus and we’d have no atoms at all.  Bohr instead proposed in 1913 that there were certain stable orbital paths surrounding the nucleus in which the electron wouldn’t lose energy and could perpetually stay put unless excited to a higher state.  The mind-numbing implication here is that when an electron changes energy levels (orbits), it literally DOES NOT EXIST from the time it leaves one and reappears at the next.  Planets don’t pull that kind of shit.  This was one of the first inklings of the revolutionary science of quantum mechanics and appears to reflect genuine reality, as Louis de Broglie mathematically refined the idea in 1924.

Don’t look for those electrons in-between.  From

But it gets even weirder!  The probability function of the Schrodinger Equation, the meat and gristle of quantum mechanics, predicts not circular but a SPHERICAL shell for the innermost electron orbit.  In fact, as you might have surmised from the term, you can only really guess at where the electron might be on that spherical shell, not really where it is at any one point.  That’s just the beginning, though.  Further orbitals take on completely unintuitive shapes with rings and squashed lobes.

How can you believe any of this stuff?  These are all necessary, mathematical consequences of quantum mechanics, a discipline the predictions of which are just too accurate to deny.  It’s so hard to contemplate because it’s alien compared to anything we’re used to seeing up here in our macroscopic world.  As mentioned above, IBM has taken the lead in imaging the infinitesimal, so that maybe it’ll all seem more real if we can actually see it for ourselves.  They obtained the first complete image of a molecule in 2009, molecular orbitals in 2011 and atomic bonds themselves last year, but they were scooped a couple weeks ago.

The First Image Ever of a Hydrogen Atom's Orbital Structure

That right there is a hydrogen atom’s electron wavefunction captured by Aneta Stodolna, Marc Vrakking and company using what’s called a quantum microscope.  They were able to produce the image through interference patterns after the hydrogen atoms were ionized.  Not quite like what Niels Bohr imagined, but probably still fitting for the 100 year anniversary of his model.

What Does This Mean?

If mathematical predictions aren’t enough for you, and you really have to see it to believe it, then there ya go.  We’ve gone from viewing atoms themselves all the way down to the fuzzy electron probabilities around the outside.  Our perception doesn’t always match reality, so it’s nice to know that with a little ingenuity, we can still see some fundamental truths for ourselves.

Okay, once and for all. What the hell is antimatter?

Well, it’s not dark matter.  I had that argument with a a co-worker whose father is a physics university professor, so he was sure he was right.  Don’t know where the miscommunication occurred.  Truth is, even though there’s almost 6 times as much dark matter as “ordinary” matter in the universe, it’s damn hard to figure out, as it only interacts gravitationally.  Light passes right through it, hence the name.  The “antimatter” moniker is also beautifully descriptive, but this time tells us exactly what the stuff is.  It interacts with light and everything else like usual, it just happens to have the exact opposite charge.  Antiprotons are the same mass as protons, but with a negative charge; antielectrons (better known as “positrons”)… well, I’ll let you guess.  While “ordinary” guys like you and me are scarily underrepresented next to dark matter, there isn’t much antimatter kicking around these days.  The reasons why are simple and yet puzzling.

The main reason is ANNIHILATION!  FUCK yeah!  When a particle and its corresponding antiparticle meet, E = mc² takes over and the bits are transformed explosively into energy, often in the form of photons.  Why this happens is a little murky, but you can kind of imagine that particles want to have as little mass as possible, and photons have zero mass.  Non-matched particles can’t annihilate each other because something wouldn’t be conserved, like spin or charge.  The deadly doppelgangers fit just right.

The opposite can actually occur through a process called “pair production,” when a high energy photon can spontaneously turn into an electron and a positron.  Holy shit!  Being in close proximity to each other, the two particles usually, you guessed it, ANNIHILATE each other and exit as quickly as they entered, but when the pair is produced near the event horizon of a black hole, sometimes the antiparticle will “fall in” while the other one flies off into space and sticks around, a phenomenon called Hawking radiation.  Freaky!

All right, so if matter and antimatter annihilate each other as soon as they come in contact, maybe the question isn’t “where’s all the antimatter,” but why is there… anything at all?  Doesn’t it stand to reason that if both kinds of matter exist, equal amounts of each would have been created?  That’s what the standard model of particle physics predicts.  So why wasn’t there a Big Boom that blew all our matter into energy?  Maybe the antimatter is still out there, but it’s hiding.  There can’t be large chunks of it in the observable universe, or we’d be able to notice the high energy photons from the annihilation at the “boundary” with all the regular matter.  It could be beyond the observable range, so far away that the light from those regions hasn’t yet reached the Earth, but why would it all be sequestered off in a corner somewhere?

If, alternatively, more matter than antimatter was created at the beginning of the universe, there must be fundamental differences between the two things we don’t yet understand.  Current experiments trying to find out if antimatter reacts differently to gravity or if the magnitudes of its magnetic charges deviate from those of normal matter at all could set us on the path to provide a backdoor reason for why regular matter eked out its counterpart.


This universe ain’t big enough for the both of us.  Image from

Even though there isn’t much antimatter, more is produced every day!  Cosmic rays smashing into the atmosphere create some through pair production.  Coming from the other side, positrons are also products of certain kinds of radioactive decay.  We take advantage of this process with Positron Emission Tomography, the PET scan that produces three dimensional images of functional processes in the body.  And if that’s not enough, we can even whip some up ourselves!  Antimatter is a not uncommon product of particle accelerators, and the wizards at the European Organization for Nuclear Research (CERN) have even been able to create and isolate entire hydrogen atoms of the stuff!


Given the tremendous amounts of energy released during matter-antimatter reactions, could we use those antiparticles for spaceship fuel or even weapons?  Well, you’d have to hold it first, and even with the best vacuums in the world, those antihydrogens don’t last very long before they find a partner to shuffle off this earthly coil with.  And you’d need A LOT of it.  According to CERN senior physicist John Eades in a 2012 Skeptical Inquirer article, if all the antiprotons EVER produced at the laboratory over its near 60 years of operation were somehow bottled and used as an energy source… it would power a sixty-watt light bulb for eight or nine minutes.  Not exactly enough to push us to the stars.  Making bombs would be an even worse proposition.  At the current viable bottling rate, you could muster enough antiprotons to make a hydrogen bomb-sized explosion in just about 10,000 times the age of the universe.

While we have a pretty good idea what antimatter is, why we don’t see much of it is an ongoing mystery.  The paltry particles we’re able to produce won’t likely even the scales anytime soon.

Older and Wiser: How the Age of the Universe Has Been Expanded and Refined Over Time

Isaac Newton was arguably the most brilliant scientist in history.  He was certainly unrivaled in his lifetime, during which he invented the reflecting telescope, developed his famous universal laws of gravitation (daring to unite the heavens and the Earth as governed by the same processes) and pioneered the use of mathematical equations in the scientific enterprise, constructing the realm of calculus in the process.  He also used the power of mathematics, and the Bible, to calculate that the Earth was created sometime around 4,000 BC.  Well, even the best can trip up.

This figure also assumed that the world had existed more or less as it is since that beginning, and that the great variations in landscape we see had been caused by catastrophic events such as floods and powerful earthquakes.  James Hutton proposed in 1795 that instead our great canyons and mountain ranges had been formed by the same processes of erosion and weathering we observe today, necessarily taking place over much vaster lengths of time.  Catastrophism thus gave way to gradualism, an idea further cemented by Charles Lyell, one of the pillars of geology.

So the Earth was much older than we thought, but how much older?  in 1897, Lord Kelvin assumed that our world began in a molten state and calculated it would need 20-40 million years to cool to its present temperature.  A helluva lot older than 6,000 years, but still not close by a longshot.  Kelvin didn’t know about radioactive decay, which contributes enormous amounts of heat that “fooled” him into thinking the Earth was younger than it is.  Thankfully we now understand the process well, so much so that we’ve used radiometric dating to finally get a good handle on the planet’s age, a whopping 4.5 billion years, a figure we still didn’t arrive at until the 1950′s.

Okay, okay, so the Earth has changed drastically over time, but the universe – now THAT’s eternal and unchanging!  Right?  I mean, that’s what Einstein thought.  He wanted the universe to remain static so badly that when his own theory of relativity showed that it must be expanding, he threw in a MacGuffin called the “cosmological constant” to fudge the numbers!  And if there’s one thing we’ve learned, it’s that the most brilliant scientist of his time can’t be wrong!  Wait…

Edwin Hubble refined the first numerical estimates for the universe’s expansion made by George Lemaître, and by combining that with the known distances to certain astronomical features, he arrived in 1929 at a cosmic lifespan of 2 billion years, a figure he himself called “suspiciously short,” as many stars seemed older than that and the geologists had already brought the age of the Earth to at least 3 billion years.  Better distance measurements to Cepheid variable stars and quasars in subsequent decades continued to raise the age of the universe, from 6, to 10, to 12 billion years.

In 2008, the Wilkinson Microwave Anisotropy Probe (WMAP) revealed the most precise appraisal yet, further aging the universe to 13.7 billion years.  And now the European Space Agency’s Planck spacecraft has used the same primordial quantum fluctuations to kick it a tiny bit more, for a final figure of 13.82 billion years.


Thanks in part to the Planck spacecraft, the universe if billions of years older than it was a century ago


The continuing changes to a single piece of information may seem damning at first blush, but it’s really a monument to how beautifully self-correcting science is.  No ideas are sacred, no matter who came up with them,  and all positions are open to revision when new or better evidence is presented.  If the argument of an iconoclast is sound, it cannot be ignored.  Not all institutions are so democratic or flexible.

But then again, the wiggly, fiddly findings do also reinforce that science can only offer approximations of the way things are.  No one can provide true certainty, but through the advancement of ideas and technology, our approximations of reality become ever better and the picture of our vast, ancient universe becomes clearer.

“Do you know how fast you were going?” Law-abiding neutrinos give a glimpse at the scientific process

Neutrinos are funny things.  Their existence was first hypothesized in 1930 by Wolfgang Pauli as a way to explain how a certain kind of radioactive decay doesn’t violate well-established physical principles.  Ironic then that 80 years later the poor little guys would themselves be fingered as lawbreakers.  We already knew that neutrinos zip around at ridiculous speeds, close to that of light, enabled by their nearly non-existent mass, but could they actually surpass that cosmic speed limit?  Of course it’s since been confirmed that the original, supernaturally suggestive findings from the OPERA detection project in Gran Sasso, Italy were erroneous, but could the relativity reprisal have been real?  What implications would that have?  And what does the huge, hollow hubbub tell us about how science is done and how it’s reported?


The Oscillation Project with Emulsion-tRacking Apparatus (OPERA) detector, which finished construction in 2008, was designed to measure the phenomenon of neutrino oscillation.  It turns out that being the smallest and fastest particles in the universe isn’t enough for the bewildering bastards, as they ratchet up the weirdness by actually changing between their three different types while traveling through space.  This realization solved a major problem in the standard model of how the Sun operates, as earthbound measurements only observe between a third and half of the electron neutrinos predicted to be produced by solar activity.  Who would’ve guessed they’d be altering their identities on the way here?!

So that’s two cosmic mysteries the mighty yet tiny neutrino had helped to clear up.  Okay, their presence actually kind of precipitated the “solar neutrino problem” but hey, they were vindicated in the end.  The roguish particles seemed poised to make history again when OPERA announced in September of 2011 they had measured the arrival times of neutrinos produced at the CERN supercollider in Switzerland to be 60 nanoseconds faster than if they had been traveling at light speed.  That might seem like a small discrepancy, but in physics a few billionths can make the difference between ordinary and iconoclasm.


The error was identified in March of 2012 as a faulty GPS cable connection, but that’s only part of the story.  It does show that scientists are human and capable of making mistakes like the rest of us, as with the embarrassing unit conversion mishap that scuttled the Mars Climate Orbiter in 1999.  Don’t be fooled though; awry equipment isn’t always the answer when measurement discrepancies have amazing implications.  The original confirmation of the cosmic microwave background radiation, the best piece of evidence we have for the Big Bang, was attributed to an accumulation of bird shit before the antenna was cleaned and the experiment repeated.

And that’s one of the primary tenets of science.  Reproducibility.  Fool us once, Universe, shame on you.  We’ll work harder and come together so we won’t be fooled again.  The real story here is how tentative the potentially revolutionary results were presented, and how the physics community proceeded.  Relativity is one of the most robustly supported theories in science.  Its mathematical confirmation helped give Einstein the celebrity status he still enjoys today.  Your GPS wouldn’t work right without it.  So instead of immediately proclaiming the king to be dead, the OPERA scientists asked the rest of the community, “Uh, could you take a look at this?  It doesn’t look right.”  Sure enough, three different experiments refuted the new data, and even OPERA’s numbers came back to reality once the equipment issue had been resolved.  This is not just a clear-cut victory for Einstein, but for the scientific process itself.

If there are victors in this instance, we can’t ignore the losers.  Antonio Ereditato, OPERA’s spokesperson, resigned after the flap following a “no confidence” vote from other project leaders, even though he himself had criticized the media for over-sensationalizing the initial story.  It’s plain to see that the disconnect between how science works and how it’s communicated is still in effect.  We should take mainstream reports of scientific findings with a grain of salt and try to look for primary sources and accounts whenever we can, as too often our journalists seem to prefer getting it fast to getting it right.

And the cranks banging out homemade manifestos on how relativity is wrong should probably give it a rest.  If billions of dollars of equipment and the brightest minds in the world can’t do it, chances are you didn’t stumble upon revolution from your studio apartment.