Harry Potter and the Sciency Words of Molecular Dissociation

July 20, 2018

Okay, I’m going to try something a little different for this week’s episode of Sciency Words.

I’ve been a huge fan of the Harry Potter novels for a long time now.  Learning new and interesting scientific terms, as we do here on Sciency Words, can feel a little like learning new magical spells.  Sometimes scientific terms even sound a little like the kinds of spells they might teach at Hogwarts.

So today, we’re going to discuss the magical art of molecular dissociation, and we’re going to learn three spells which can cause the dissociation of molecules to occur.  In other words, we’re going to learn three ways to break molecules apart.  Ready?

Photolysis is one of the very first “magical spells” I leanred, and I think it’s a really good one to know about.  “Photo” comes from the Greek word for light, so photolysis is the breaking of chemical bonds using light.

Typically this is done using higher energy wavelengths of light, like the Sun’s ultraviolet rays.  As an artist, it’s important for me to know how to cast shield charms against photolysis, because photolysis can (and will) destroy the chemical pigments in my art work, causing the colors to fade.

As you might have guessed, electrolysis is when you break chemical bonds with electricity.  You may have assumed astronauts are muggles.  You can be forgiven for that assumption, but astronauts definitely know how to perform at least this much magic.

And in the not-so-distant future, space explorers on the Moon and Mars and out in the asteroid belt will probably use electrolysis to split water molecules into hydrogen (useful as rocket fuel) and oxygen (useful for breathing and also as rocket fuel).

“Pyro” means fire, so pyrolysis is the breaking of chemical bonds using heat.  This is probably the most common and most obvious of these molecular dissociation spells—what do you think Bunsen burners are for?—but for some reason I don’t see this term being used very often.

In fact the first time I ever saw the word in print was in this paper about the Curiosity rover on Mars.  I guess Mars rovers have magical powers too, because Curiosity cast pyrolysis on a weird sample it had collected in order to figure out what the sample was made of.  Turned out it was made of complex organic compounds, the kind of compounds that may (or may not) be associated with Martian life.

* * *

Of course there are still so many more scientific terms… I mean magical spells to learn.  I’m hoping I’ll find another of these molecular dissociation spells that fits the photolysis, electrolysis, pyrolysis pattern.  If I do, I promise to draw someone in Slytherin colors performing the spell.

Sciency Words: Aromatic

July 6, 2018

Today’s post is part of a special series here on Planet Pailly called Sciency Words.  Each week, we take a closer look at an interesting science or science-related term to help us expand our scientific vocabularies together. Today’s term is:


At some point when I was a little kid, I discovered that gasoline doesn’t smell terrible.  In fact, it has an almost sweet aroma to it.  I got in a lot of trouble for this because, for obvious reasons, my parents didn’t want me sniffing gas fumes.  But still, that subtly sweet smell is there, and it’s caused by a chemical known as benzene.

Apparently I’m not the only person to take note of benzene’s smell.  German chemist Augustus Wilhelm Hofmann is credited with the first usage of the word “aromatic” to describe benzene, along with a whole host of other sweet-smelling chemicals.

Hofmann seems to have realized not only that these chemicals smelled similar but also that they had similar chemical compositions.  “Of this series,” Hofmann wrote in 1855, “few members are at present known, but the group of aromatic acids is itself very imperfect and limited.”  In other words, Hofmann predicted the existence of more “aromatic” chemicals that should fit the pattern.

And more chemicals of this series were later discovered, and we now know what they really have in common: a flattened, ring-like chemical structure, as pictured below:

As an adult, I know better than to sniff gasoline, and as an artist I know better than to sniff my art supplies.  But the xylene used as a solvent in some pens and markers does have that same vaguely sweet aroma as benzene. However, not all of the chemicals we call “aromatic” smell so nice, or smell at all.  It’s the flattened, ring-like structure that defines aromaticity today.  The odor is no longer considered relevant.

You might be wondering then why we still call these chemicals aromatic, if their aromas aren’t important.  This seems to be another case of scientists naming something before they really understood it.  The same thing happened with the word organic.  The term was used so often in scientific literature and became so deeply ingrained in the scientific lexicon that we’re now unable to change it.

The ring-like structures in aromatic chemicals are incredibly strong and unlikely to break apart during chemical reactions. That makes them really good structural components for the large, complex molecules that make life possible here on Earth—and may have once made life possible on Mars.  But we’ll talk more about that next week!

Molecular Monday: Carbon vs. Silicon

June 4, 2018

I recently completed a certain long anticipated manuscript, and I’m currently in the process of rewriting and revising it. Editing this thing has me thinking about a certain line from Macbeth, which I’ll paraphrase as: I have walked so deep into blood that, should I go no farther, returning will be as tedious as continuing onward.

That’s morbid, I know.  What do you expect?  It’s Shakespeare!  But simply replace the word blood with red ink, and I think you’ll understand how the editing is going for me.

Anyway, I’ve waded so far into that “red ink” that I haven’t had much time for research; so for today’s episode of Molecular Monday I thought we’d take a look back at one of my older posts.  A very old post, from all the way back in 2011, long before I really knew what I was talking about with regard to organic chemistry.

And yet despite my ignorance and inexperience, I think I still got the general idea right with this one.  Also, this post includes one of my very first attempts at science illustration, so I hope you’ll enjoy that!


It’s often suggested that the aliens from the Aliens movies, sometimes referred to as xenomorphs, are silicon based rather than carbon based like us.  There are a lot of silicon based aliens in science fiction, but no one knows if such a thing is really possible.

Carbon and silicon have one thing in common: they both have four bonding sites, meaning they can bond with up to four other atoms when making a molecule.  Other than that, they’re completely different.  Silicon is a metalloid; carbon is a nonmetal.  Carbon is much lighter and more flexible, and it’s ten times more abundant in the universe.

If the idea of silicon based life is simply to replace carbon atoms with silicon, it wouldn’t work.  Take breathing for example.  We breath oxygen in, and exhale carbon dioxide.  When a silicon based alien breaths in oxygen, it will have a hard time exhaling silicon dioxide; silicon dioxide is better known as quartz crystal.

I don’t remember any xenomorphs hacking up quartz crystals in the movies, but maybe they use silicon for something else.  Carbon has to be part of their biochemistry anyway, or they wouldn’t be able to grow inside human hosts.

Humans are not only carbon based.  We also depend on oxygen, nitrogen, hydrogen, phosphorus, and sulfur.  Not only that, but we need traces of iron, sodium, potassium, etc as well.  So maybe the xenomorphs can be carbon based and silicon based at the same time.

Molecular Monday: Dihydrogen Monoxide

May 21, 2018

Welcome to another episode of Molecular Mondays, a special biweekly series here on Planet Pailly where we take a closer look at the atoms and molecules that make up our physical universe, both in reality and in science fiction.

I had a really bad time in high school chemistry.  That was the closest I ever came to failing a class, and the experience sort of traumatized me. But there was one lesson from my high school chemistry class that I did learn well.  It involved a chemical with the very scary sounding name dihydrogen monoxide.

The teacher gave us a handout to read, laying out the case that dihydrogen monoxide (also known as DHMO) is a horrifyingly dangerous chemical that should be banned.  DHMO has been found to be present in cancer cells, and yet it continues to be incorporated into our processed foods.  It’s one of the chemical components of acid rain, and yet we keep putting more of it into our atmosphere.  Inhaling DHMO has caused deaths, the U.S. Navy has conducted weapons tests using DHMO, etc, etc, etc…

My teacher seemed a bit like an aging hippie and probably an environmentalist too, so I thought I understood why he was having us read this.  I had the vague suspicion that I was being scammed somehow, that this article about dihydrogen monoxide might not be telling the whole story.  But when the teacher asked us what should be done, I went along with the crowd and voted to outlaw DHMO.

Everyone in the class voted to outlaw it, except one kid: the stereotypical super smart, super nerdy kid (every class has one, I think).  He just sat there with a big grin on his face.  The teacher, who was also grinning at this point, asked what was so funny, and the smart kid of the class proceeded to explain that “dihydrogen” means two hydrogen atoms, and “monoxide” means one oxygen atom: H20.  We’d just voted to outlaw water.

Going back through everything it said in the handout:

  • DHMO is found in cancer cells… yes, it’s found in all your cells.
  • It’s in processed foods… sure, unless your food’s been dehydrated.
  • It’s in acid rain… because acid rain is still rain.
  • We’re putting it into the atmosphere… yes, everytime we boil water.
  • Inhaling it can kill you… that’s called drowning.
  • The U.S. Navy uses it… obviously!

I guess the lesson I learned that day had more to do with linguistics than chemistry.  Just because something has a scary-sounding name, that does not necessarily mean it’s a scary thing.  People may try to deceive you while hiding the truth in plain sight. This is especially true with science, where you can rely on the science illiteracy of the general public.

So stay skeptical, and whenever you’re confronted with a strange and unfamiliar word, don’t be afraid to ask what that word actually means.

P.S.: High school students aren’t the only ones who’ve fallen for the DHMO hoax.  At least one politician, when confronted with similar facts about this very dangerous chemical, called for outlawing water.

Molecular Monday: Making Rocket Fuel on Mars

October 30, 2017

Today’s post is part of a bi-weekly series here on Planet Pailly called Molecular Mondays, where we take a closer look at the atoms and molecules that make up our physical universe.

As most of you now know, I am on a totally-for-real, not-making-this-up mission to visit the planet Mars. Now if you’re planning a mission to Mars, one of the first things you need to figure out is how to get back to Earth. Unless you’re not planning to come back, which is apparently an option.

But if you do want to come home, you’ll probably need to refill the fuel tanks of your spaceship using only the natural resources Mars provides. Believe it or not, this is surprisingly easy to do using a process called the Sabatier reaction (discovered in the early 20th Century by French chemist Paul Sabatier).

In the Sabatier reaction, hydrogen and carbon dioxide mix together to produce methane, with water being produced as a byproduct. The chemical equation looks like this:

CO2 + 4H2 –> CH4 + 2H2O

Liquid methane makes a decent rocket fuel, but you still need an oxidizer. To get that, all you have to do is zap that byproduct water with electricity, creating oxygen and hydrogen.

2H2O –> 2H2 +O2

Liquid oxygen is pretty much the best oxidizer you can get, and the “waste” hydrogen can be put back to work keeping the Sabatier reaction going.

I first learned about the Sabatier reaction in Robert Zubrin’s book The Case for Mars, coming soon to my recommended reading series. The only problem, according to Zubrin, who was writing in 1996, is hydrogen. Mars’s atmosphere is almost completely CO2, but Mars is severely depleted of hydrogen. Zubrin’s solution in his book is to import hydrogen from Earth (still cheaper than trying to ship rocket fuel to Mars).

But since 1996, we’ve learned that Mars has more water than previously thought, most of it frozen just beneath the planet’s surface. So when I read about the Sabatier reaction again, this time in Elon Musk’s paper “Making Humans a Multi-Planet Species,” published in 2017, the hydrogen problem was no longer a problem. We can get it through the electrolysis of Martian water.

Of course for my own Mars mission, I don’t have to worry much about rocket fuel. My spaceship is fueled by pure imagination! But still, if something were to go wrong with my ship, it’s good to have a backup plan.

Sciency Words: Island of Stability

October 13, 2017

Today’s post is part of a special series here on Planet Pailly called Sciency Words. Each week, we take a closer look at an interesting science or science-related term to help us expand our scientific vocabularies together. Today’s term is:


According to Star Trek: Voyager, in the 24th Century there will be 246 elements on the periodic table. In one episode, the Voyager crew discovers element 247, and to their astonishment that element is stable.

Here in the 21st Century, on modern day Earth, there are only 91 naturally occurring elements. Element 43, technetium, and everything above element 92, uranium, have to be produced artificially. And these artificial elements are all unstable. Some of them, especially the really, really high numbered ones, are so unstable that they’re effectively useless.

When an atomic nucleus gets too big, the so-called strong nuclear force is no longer strong enough to hold the whole thing together. You can also run into problems if you don’t have a comfortable balance of protons and neutrons. At that point, when atoms are too big or improperly balanced, they start shedding nuclear particles until they can stabilize themselves. This process is called radioactive decay.

If you want, you can draw a chart with the number of protons in an atom along one axis and the number of neutrons along the other. But charts are boring, so let’s draw a map instead.

Physicist Glenn Seaborg (for whom element 106, seaborgium, is named) was apparently a big fan of maps. I imagine he and J.R.R. Tolkein would have gotten along well. In the 1960’s, Seaborg started referring to groups of atomic isotopes by “geographical” names, and these names have stuck.

On the map above, the landmass stretching up from the bottom left corner represents all the stable and semi-stable isotopes. This “Peninsula of Stability” is surrounded by a “Sea of Instability.” But somewhere out in that sea, according to Seaborg and others, certain very large atoms might theoretically become stable. These atoms would have just the right balance of protons and neutrons to hold themselves together despite their extreme size. These “magically” stable isotopes are represented by the Island of Stability.

Physicists have been trying to find the Island of Stability for decades now, but it seems to be perpetually just over the horizon. It was once predicted that elements 110 and 114 might be stable. They’re not. I remember reading that element 118 might turn out to be stable. It didn’t. Now there’s a prediction about element 120. We’ll have to wait and see about that one.

Also there’s a possibility that we’ve been skirting along the island’s coast, so to speak. Maybe if we just add a few more neutrons to some of the unstable elements we’ve already found, they’ll stabilize. Maybe. More on that in next week’s Molecular Monday post.

Personally, I think Star Trek: Voyager was on to something. My prediction is that the Island of Stability will be found all the way out at element 247, and I recommend the IUPAC name it Janewayium.

Molecular Monday: Boron Isn’t Boring

October 2, 2017

Welcome back to another edition of Molecular Mondays, a special biweekly series here on Planet Pailly combining two of my least favorite things: chemistry and Mondays.

At some point long, long ago, I read a book about the periodic table of the elements. Chapter five was about boron, and what I remember learning was that boron is kind of useless. Certain boron-containing compounds are used in cleaning detergents, and while boron is not particularly toxic to humans, it’s deadly to insects, so it makes a good insecticide.

And that was basically it. Nothing more to know. Time to move on to chapter six: carbon.

So when the news came out that the Curiosity rover had detected boron on the surface of Mars, my initial reaction was “who cares?” But then I read more, and I soon realized that I’d been grossly under-informed about the fifth element from the periodic table.

First off, finding boron on Mars posed a real challenge. The Curiosity rover used an instrument called ChemCam, which basically zaps rock samples with a laser and performs a spectroscopic analysis on the resulting rock vapor.

According to this paper published in Geophysical Research Letters, scientists were looking for two spectral lines, both in the ultraviolet part of the spectrum, which are characteristic of boron: 249.75 nm and 249.84 nm. Annoyingly, iron also produces a spectral line at 249.96 nm, so ChemCam can only confirm boron’s presence in samples that have low iron content, which are hard to come by on Mars. Iron oxide is basically everywhere.

But despite this difficulty, boron was detected. Why should I or anyone else care? Because it was detected in veins of sedimentary rock, meaning that at some point long ago when Mars still had lakes and rivers and oceans of liquid water, boron must have been mixed into that water (likely in the form of borate, a compound of boron and oxygen).

Again, why should anyone care? Because some of the fragile molecules necessary for life decompose in open water, but borate can help stabilize those molecules, allowing them to combine to form RNA. Boron itself is not incorporated into our modern DNA, but its presence here on Earth may have helped life get started—and if boron was present on Mars, mixed into ancient Martian waters, it could have helped life get started there too.

Could have. We still don’t know for sure, but as I’ve hinted previously I am planning a little trip to Mars aboard my imaginary spaceship. Stay tuned. I’ll be sure to let you know if I find anything.