Molecular Monday: Carbon vs. Silicon

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

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: Transparent Aluminum

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.

As a lifelong Star Trek fan, I’ve known about transparent aluminum since I was a little kid.  It’s a see-through material that’s incredibly strong while also being incredibly lightweight.  In fact, it’s kind of unrealistic how strong and light it’s supposed to be.

But last week, while I was searching for something molecular to write about for today’s post, I found out that transparent aluminum is a real thing.  It’s more commonly known as ALON (or AlON, with a lowercase L).  The name, I take it, is based upon the substance’s chemical composition: Al for aluminum, O for oxygen, and N for nitrogen.  The more technical sounding name is aluminum oxynitride.

According to this video from Wonder World, aluminum oxynitride starts out as a white powder.  It’s pressed into a mold and heated for several days, after which it comes out looking cloudy white.  It’s then polished to make it clear.

ALON is now a product manufactured by Surmet, and according to Surmet’s website, ALON is 85% transparent to electromagnetic radiation between the near-ultraviolet and mid-infrared, a range which includes the full spectrum of visible light.  Its scratch proof and shatter proof, and relatively thin sheets of ALON do a better job stopping bullets than much thicker sheets of bullet-proof glass. Based on that, I presume it would also be good for making spaceship windows that can resist micrometeor impacts.

Surmet claims they acquired the rights to ALON in 2002 following a laboratory demonstration, but I was able to find video of the actual invention of this material dating back to 1986. Enjoy!

Molecular Monday: Mr. Asteroid’s Organic Delivery Service

A lot of what I write about on this blog, and also a lot of what I hope to do as a science fiction writer, comes from reading actual scientific research. Over the years, I’ve gotten pretty good (I think) at wading through all that scientific jargon. But sometimes I invest my time in reading something and… well, it just doesn’t give me a whole lot to work with.

There’s been a lot of press lately about how asteroids and comets deliver loads and loads of organic material to Mars, and what that may mean for our search for Martian life. I thought this would make an excellent Molecular Monday post (today’s post is part of a biweekly series called Molecular Mondays, blah blah, you know the spiel).

But after reading the actual paper, I can’t help but feel that this research has been overhyped.

Don’t get me wrong! It’s good research, as far as I’m able to judge, without any of the usual red flags I’ve learned to watch out for. But it’s based on a computer simulation, a simulation that depends upon quite a few assumptions about asteroid and comet populations in our Solar System. The authors are upfront and honest about this, and they do a good job explaining why they believe their assumptions are justified. This article from IFL Science calls these assumptions “reasonable assumptions,” and that may be true.

But still… this paper makes a lot of assumptions!

The general idea that asteroids and comets deliver organic material to Mars (and other planets) makes sense to me. The conclusion that we should search impact craters on Mars for organics seems sensible enough. It’s just… I don’t know, maybe I’ve missed something important (it wouldn’t be the first time), but with so many assumptions in play, I can’t take any of the specifics from this paper too seriously.

P.S.: I didn’t really talk about chemistry in this post, which is sort of off brand for Molecular Mondays. So I’ll just remind everyone that the word organic does not mean what you may think it means. You can have organic chemicals and organic chemistry without having living organisms.

Molecular Monday: The Imaginary Sulfide Ion

Just when I feel like this chemistry stuff is starting to make sense to me, I learn something new that makes me feel like I don’t understand it at all. Maybe I’m not the only one. Maybe even the professional chemists feel the same way sometimes. With that in mind, it’s time for another episode of Molecular Mondays.

This month (February, 2018), a paper was published by the Royal Society of Chemistry that casts doubt on a longstanding assumption made by chemists. It involves the S-2 ion in aqueous solutions.

First off, this may have been the most amusing scientific paper I’ve ever had the pleasure of reading. No, the authors didn’t make any references to unicorns, but they did mention something about fairies at the bottom of a well, and then there was this delightful quote: “[…] there has been a growing awareness amongst solution chemists that the S-2(aq) emperor may have no clothes.”

As I understand it, the existence of an aqueous S-2 ion is the kind of thing that makes sense on paper. It allows chemists to easily balance their chemical equations, and it’s been included in textbooks and chemical computer databases for so long now that everyone just takes it for granted that the thing exists.

But apparently the experimental evidence of this particular ion was lacking, and aqueous solutions incorporating several different sulfide compounds did not produce any S-2 ions. At least not according to a Raman spectroscopic analysis.

Now as I’ve written before, papers like this should NOT be interpreted as final proclamations handed down from the ivory tower of science. Rather, this kind of paper should be understood as the beginning of a conversation among scientists. Does this S-2(aq) ion exist or not? If not, how many prior scientific studies need to be reexamined?

There will be further research, and perhaps a rebuttal will be published. Then there will be a rebuttal to the rebuttal, and so forth. But I think, regardless of how this plays out, that this is a good reminder that in science—as in life—what makes sense on paper does not necessarily work in the real world.

Molecular Monday: Quasar-Induced Chemistry

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 a science fiction writer, one of the things I’m really doing with my research is trying to find excuses to break the laws of physics. So anything that might produce a previously unknown material substance, a substance that might be imbued with properties that are useful for storytelling purposes… that sort of thing is of great interest to me. With that in mind, I recently read a news article about quasars and the weird, unexpected chemical reactions they can cause.

Quasars are black holes with disks of superheated gas and dust swirling around them. Due to the intense heat of the disk, the extreme gravity of the black hole, and the crazy electromagnetic field the two produce together, you end up with these twin laser-like jets of super-accelerated particles shooting away from the quasar in opposite directions.

According to this research paper published in the Monthly Notices of the Royal Astronomical Society, and according to this slightly less technical summary from Physics World, any molecules that happen to get caught in a quasar’s laser beams are ripped apart by a process known as photolysis. Then, after these quasar-zapped particles have had some time to cool off, they can recombine to form new molecules.

I was led to believe by the initial news report I read that this sort of extreme scenario might also cause atoms to recombine in ways that they normally wouldn’t. Unfortunately I don’t see anything in the actual research to back that up. For the most part, quasar chemistry produces fairly ordinary molecules like hydroxyl, carbon monoxide, and molecular hydrogen.

Still, for the purposes of science fiction, some sort of quasar-induced chemical reaction producing strange, new, potentially valuable chemical substances… that may be too awesome of a concept for me to pass up.

Molecular Monday: Top 5 Chemicals on Mars

For today’s Molecular Monday post, I thought I’d try something a little different. I’m counting down my picks for the top five chemicals on Mars. These are chemicals that, in one way or another, are important to helping us understand the Red Planet better.

#5 Possible Methane
Several robotic probes have detected burps of methane on Mars, which could indicate ongoing biological or geological activity—either one of which would be a huge surprise on a world long thought to be both biologically and geologically dead. However, the methane could also be a contaminant leaking from the robots themselves. We’ll have to wait and see with this one.

#4 Hematite
Hematite is a rusty red colored mineral, also known as iron oxide or iron (III) oxide. Almost the entire surface of Mars is covered in hematite, giving the planet its distinctive color. But questions remain about where all this hematite came from. One thing we can be certain about is that Mars’s red color is only skin deep. When the Curiosity rover drilled a hole in the ground, it found the underlying layer was grey.

#3 Carbon Dioxide
Mars’s atmosphere is almost all carbon dioxide, which should help keep the planet warm, but the air is too thin to produce much of a greenhouse effect. As a result, Mars is a little too cold for human comfort. There’s also plenty of frozen CO2 (also known as dry ice) at the poles. Maybe someday we can release all that excess CO2­ and do to Mars what we hope not to do to Earth.

#2 Perchlorate Salts
The most noteworthy perchlorates on Mars are calcium perchlorate and magnesium perchlorate, but there are plenty of other flavors besides those two. Based on data collected all over Mars, it seems these perchlorate salts make up 0.5% to 1.0% of the Martian regolith; that makes the regolith extremely toxic to humans, and we need to figure out what to do about this problem before we can begin any serious colonization efforts. On the other hand, in the unlikely event that life already exists on Mars, perchlorates might (might!) make a good source of chemical energy, similar to the way oxygen is a good source of chemical energy for us.

#1 Water
Humans on Mars will not suffer from a lack of water. There are vast quantities of H2O frozen at the poles and buried in underground glaciers. And there’s little doubt that liquid water once flowed over the planet’s surface, carving river channels and chemically altering the rocks. However, a wet and watery Mars would have looked very different from modern Earth. Rather than standing lakes and rivers, Mars seems to have experienced violent flash floods, perhaps caused by melting and refreezing glaciers, followed by long periods of dryness. Still, the liquid water was definitely there, and there’s a distinct possibility that microorganisms could have started to evolve before the planet dried up completely.

So those are my picks for the top five most interesting and/or important chemicals on Mars. Let me know what you think of this list in the comments, and if people like it, maybe I’ll do something similar for other planets.

P.S.: Honorable mention to the polycyclic aromatic hydrocarbons (PAHs) from the Martian meteorite ALH84001. Like those methane burps, PAHs could either be an indicator of Martian life or a hugely embarrassing scientific mistake.

Molecular Monday: Jarosite on Mars

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.

Over the last few months, I’ve been trying to get to know the planet Mars better. There’s some pretty clear evidence that Mars used to be a different kind of planet, a wetter and more watery sort of world… but perhaps not in the way you might have expected.

Many of Mars’s rocks seem to tell a similar story about that wet, watery past. That story usually begins something like this:

We’ve already looked at Mars’s sedimentary basaltic rocks. Such a thing would be almost a contradiction in terms on Earth. Sedimentary rocks are made by flowing water; basalt is destroyed by water. So how could a rock be both basaltic and sedimentary?

Now let’s take a look at another rock that’s almost self-contradictory: jarosite. Jarosite is a potassium/sulfur/iron-containing mineral with the chemical formula KFe3(OH)6(SO4)2. It typically forms in wet, acidic environments by the oxidation of iron sulfides. If you don’t understand what that means, that’s okay; I don’t fully understand it either. The important thing is that jarosite forms in water; but jarosite is also destroyed by water. It breaks down into simpler compounds if exposed to water for long periods of time. That makes jarosite pretty hard to find on Earth, but of course it’s surprisingly common on Mars!

In 2004, the Opportunity rover discovered jarosite—lots of jarosite—in the Meridiani Planum region (incidentally, the same region where Airy-0 is located). According to a NASA press release at the time: “Jarosite may point to the rocks wet history having been an acidic lake or an acidic hot springs environment.”

But whatever was happening in Meridiani Planum, the region must have dried up pretty quickly. According to the abstract of this paper, also from 2004, “[…] the presence of jarosite combined with residual basalt at Meridiani Planum indicates that the alteration process did not proceed to completion, and that following jarosite formation, arid conditions must have prevailed.”

Before I started all this Mars research, I imagined ancient Mars as a very Earth-like place, with standing oceans and lakes and gently flowing rivers. I guess there still could have been a time like that in the very beginning, but most of Mars’s history with water seems to have been far more sporadic and violent than that, with lots of flash flooding (perhaps caused by melting glaciers) and very brief wet spells followed by long periods of dryness.

At least that’s my impression at this point in my research.

Molecular Monday: Mars Burps Methane

Happy New Year’s, and happy Molecular Monday too! I can’t think of a better way to start off 2018 than with a blog post about molecules. Well, no… I probably could, but my schedule says this is what I’m supposed to blog about today, so here we are!

If you’re looking for life on other planets, one of the most common pieces of advice you’ll get is “follow the water.” That is, of course, assuming you can find any liquid water in the first place. But maybe another option is to follow the methane.

The planet Mars seems to have a bit of a methane mystery going on. Mars will sit there, all quiet and normal, for years at a time, but then suddenly…

… and then suddenly all this methane shows up in the planet’s atmosphere.

The most notable of these methane burps occurred in late 2013 and early 2014, when the Curiosity rover started detecting methane levels ten times higher than normal. Where did all this methane come from?

One boring possibility is that it came from the rover itself, a result of some kind of leak. It’s also possible that a meteorite just happened to land near Curiosity, and that this meteorite just happened to be carrying a lot of organic material. Or maybe there was some kind of surprise geological activity nearby that vented methane from somewhere underground.

But the most intriguing possibility is that the methane was produced by biological activity. That is, after all, how most atmospheric methane is produced on Earth. And I recently found this paper offering a possible way to determine once and for all (maybe, hopefully, fingers crossed) if Mars’s methane really does come from a biological source.

From what I gather, having only skimmed through this paper (sorry, I was trying to read this on New Year’s Eve, and there were margaritas), the key is to follow the methane then follow the hydrogen. So the next time Mars burps up some methane, the ratio of methane to hydrogen in the air might reveal the methane’s true source.

Molecular Monday: Perchlorate Salts on Mars

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.

It’s hard to imagine how anything could survive long on Mars. This has been especially true ever since 2008, when the Phoenix Lander conducted the first ever wet chemistry experiment on Martian regolith and detected a chemical called calcium perchlorate.

I haven’t looked into how this wet chemistry experiment worked, but I’m guessing it involved mixing water with a sample of Mars dust and then running a spectroscopic analysis.

Of course when this calcium perchlorate was detected, the first question was: did Phoenix contaminate its own sample? On Earth, perchlorates are an increasingly common pollutant produced by (among other things) rocket fuel. But if there was any serious contamination of the Phoenix landing site due to Phoenix’s landing rockets, we’d expect to find ammonium perchlorate, not calcium perchlorate.

Also subsequent experiments and observations by the Spirit and Opportunity rovers, the Mars Odyssey orbiter, and other Mars missions have found that chlorine is scattered all over the planet. Most of that chlorine is likely bound up in perchlorate form, and it’s now estimated that calcium perchlorate, magnesium perchlorate, and other perchlorate salts make up anywhere between 0.5% and 1% of the Martian regolith.

For humans, that’s an alarmingly high percentage. More than enough to kill you, or at least to cause you serious thyroid problems. But if you’ve been following along with my blog, you know I’ve been living on the surface of Mars and growing my own food here for over a month now. So why am I not dead?

Well… it turns out there is life here on Mars, and the natives have been surprisingly helpful. More about that in my next post.