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.

Molecular Monday: The Four Elements

September 18, 2017

For some reason, I’ve been thinking a lot lately about the original elements, the four elements Aristotle wrote about many millennia ago: fire, water, wind, and earth. Of course we no longer think of these as elements in the chemical sense. Instead we have the periodic table of elements, with well over a hundred elements identified so far.

But just for fun, I thought I’d try to find a way to connect the old Aristotelian elements to the first four modern chemical elements: hydrogen, helium, lithium, and beryllium. Here’s what I came up with:

  • Hydrogen: Let’s start by associating hydrogen with “water.” The word hydrogen actually means “water maker.” It got its name because in 1783, Antoine Lavoisier demonstrated that the oxidation of hydrogen gas produced water (this experiment also proved that water is not elemental).
  • Helium: Helium was first detected in the solar spectrum in 1868 and was thus named after the Greek word for “sun.” The Sun is pretty fiery, so my first instinct was to make helium represent “fire.” But I’m going to go with “air” instead, because of helium’s use in balloons and airships.
  • Lithium: As I’ve written about previously, lithium was first discovered using a method called a flame test. When a chemical substance is burned, the color of the flame can be used to determine the chemical’s identity. Lithium burns with a characteristic bright crimson flame. Therefore, I’m choosing to associate lithium with “fire.”
  • Beryllium: Beryllium was first identified in 1798 as a component of the mineral beryl, specifically a form of green beryl we all know as an emerald. So I think I can safely wrap this little game up by connecting beryllium with “earth.”

So how did I do? Do you agree with the connections I came up with? Are there other connections we could think up that might work better?

Okay, maybe this was more of an exercise in creativity than science. I’m okay with that. And besides, in the half-hour I spent researching for this post, I learned a few things about the first four elements of the periodic table that I didn’t know before. That’s always a plus.

Anyway, next time on Molecular Monday, we’ll be talking about boron. Now I wonder if I can find some way to associate boron with the girl from The Fifth Element.

Sciency Words: Spectroscopy

September 2, 2017

Welcome to a special Saturday edition of Sciency Words, because sometimes life gets in the way of regular blogging schedules. Each week (normally on Fridays) we take a closer look at some science or science-related term so we can all expand our scientific vocabularies together! Today’s term is:


What color is it? It sounds almost like a childish question, but as we look out into space, trying to study the Sun and other stars and distant planets, we can learn a great deal just by figuring out what color things are.

The science of spectroscopy has a long history, beginning with Isaac Newton. In the late 1600’s, Newton demonstrated that pure white light can be split apart into a rainbow of color using a prism. Newton called this a spectrum, from the Latin verb specto, meaning “I observe” or “I see.” (According to my trusty Latin-English dictionary, the noun spectrum also meant “apparition” or “ghost.”)

Over the decades and centuries to come (click here for a detailed timeline), scientists used increasingly sophisticated combinations of lenses, mirrors, and prisms to study Newton’s spectrum in greater detail. They also experimented on a wide variety of light sources: sunlight, starlight, firelight, and even electrical sparks.

An especially noteworthy experiment in 1752 showed that burning a mixture of alcohol and sea salt produced an unusually bright yellow band in the middle of the spectrum (we now know this to be a emission line for sodium). And in 1802, another experiment on sunlight revealed multiple dark bands in the Sun’s spectrum (which we now know are absorption lines for hydrogen, helium, and other elements in the Sun’s photosphere and corona).

All the colors of the rainbow, except a few are missing. This is an absorption spectrum.

It wouldn’t be until the early 20th Century, with the development of quantum theory and, specifically, Niels Bohr’s model of the atom, that anyone could explain what caused all these spectral lines.

No rainbow, just a few specific colors. This is an emission spectrum.

In Bohr’s atom, the electrons orbiting an atomic nucleus can only occupy very specific energy levels. When electrons jump from one energy level to another (the true meaning of a quantum leap), they either emit or absorb very specific frequencies of light. The light frequencies are so specific that they act as a sort of atomic fingerprint.

And so today, as we look out into the universe, seeing the glow of stars and the absorption patterns of planetary atmospheres, it’s possible for us to identify the specific chemical elements we’re seeing, even across the vast distances of space, simply by asking what color is it?