I Was Nominated (and Accept)

Confabler nominated me for a Sunshine Blogger Award!

My distant, yet close friend Confabler has nominated me for the Shiny Shiny Sunshine Award. I love her imagination and sense of whimsy; she lets her muse du jour lead and she follows. There’s a wonderful freedom to that which is (1) difficult to allow in the rational process of “writing” and (2) enjoyable to find.

1. If you were to choose an insect that would take over the world after human extinction, who would that be?

It sort of depends on our route to extinction. If it involved an epidemic, the population of flies might see a giant uptick. This would be a good one:

Gauromydas heros

If it is a slow process, then I nominate the Japanese Rhinoceros beetle because it would be awesome if creatures  with such improbably fashioned protuberances were to be the alpha species (Megasoma and Titan beetles would be acceptable alternatives):

Allomyrina dichotoma

 If our extinction took all other terrestrial life along for the ride, I would like to see this enormous isopod (a relative of our terrestrial roly-polies) rule the seas (note inclusion of actual human hands for sense of scale):

The underside of a male Bathynomus giganteus, a species of giant isopod captured in the Gulf of Mexico in October 2002.

2. How old were you when you first read Harry Potter? And your favorite author of course?

I was pretty old when I read my only Harry Potter book (the first one). I didn’t enjoy it enough to complete the series, although I’ve seen all the films and enjoyed them well enough. In the period I read that first one, I was typically reading a lot of history and didn’t find that it was a good use of my time. When I was really young, I read the Classics Illustrated versions of novels, which were quite good at introducing a curious young mind to the wonders of literature without having to do the work (sort of illustrated CliffsNotes (I didn’t use these in school though), if you will). When I was a little older, I read Robert E. Howard, Sax Rohmer, John Carter of Mars, H. Rider Haggard, Stanley Weinbaum, George McDonald fantasies, etc.

My favorite author is Gabriel Garcia Marquez for One Hundred Years of Solitude and Love in the Time of Cholera. His writing is so rich, amusing, full of simple wisdom and abundant humanity it is hard to believe he was just a human being writing about the lives he saw playing out around him. I literally would read some passages and have to put the book down as if I had just sipped the richest chocolate elixir in the world and needed to savor it until I sipped again. His Spanish-to-English translators did a good job in getting it right; Gregory Rabassa (OHYoS translator) was even praised by Garcia Marques himself!

3. If you were invisible what is the craziest thing that you would do?

Here’s an odd one: Go and hang around bigots, transcribe their conversations, and publish them for the world to see how terrible people speak when they think no one is listening (but, oh yeah, we have the internet so this already happens). If I could walk through things, which seems fair since I’m invisible, I would go around seeing what it felt like to do that—see if there were different textures to different things on the inside than on their surface.

4.what food makes you feel like a hungry hyena?

This has changed so much over time! These days, I don’t get this kind of urge anymore. In my early adult (late teen?) years… ICE CREAM!!!!

5. A song that makes you dream?

Gymnopedie #1 by Erik Satie

6. Have you ever planted a tree?

Yes. Unasked but answered: quite a few!

7. Choose your man: superman/ Spiderman/ iron man and if he was your best friend one thing that you would make him do?

Can I choose Supergirl? If I can, I would have her take me around to various places in the world, build shelters so I could stay there and visit free, then whisk me off to the next place on “our” list (she would be enjoying the sight-seeing with me, of course! What kind of boor do you think I am?!?!).

8.How much time do you spend in front of the mirror everyday?

As little as possible, which involves shaving and brushing my teeth. I find that shaving my teeth first helps with the brushing.

9.why you started blogging and tell us about the post enjoyed the most making.

I was having a bunch of conversations with people who did not seem to understand the wonderful humility of learning and doing science and wanted to see how well I could write about how science is a discipline that can assist us all in not leaning out too far over our skis (getting ahead of ourselves and pretending we know stuff we don’t). Blogging has become so much more than that since my first post on June 22, 2016, and I have had so much fun writing fiction and revisiting some poetry I wrote several decades ago (and finding them easier to “fix” than I remembered).

I’m not sure which of my posts I enjoyed the most. They’re all my children so I like them all? I probably like the odd bits of fiction that I had no idea were inside me when I woke up and then found them on the page looking up at me. I like The Big Day of these. Of the science posts, I like The Mess: Parts 1 & 2 and the Appendix 1 items best (maybe). Of the historical pieces, I like Risk Management. Of the life pieces, I like Building Blocks the best. Anyone who reads this is encouraged to make up their own mind; I am hopelessly biased.

10. Which social media platform are you addicted to (including WordPress)?

I don’t do much social media except WordPress. I don’t like Facebook at all and deleted my account. WordPress is addicting but in a very healthy way! You get to create something and share it with new friends from all over the world. That’s a great addiction have.

Now the rules:

1.thank the person that nominated you.

Thank you, Confabler. You are a true virtual friend, and I don’t mean that in any Pokemon way either!

2. Answer the questions from your nominator.


3. Nominate fellow bloggers you follow.

Hereinafter lie the following nominees in no particular order (order, of course, being an illusion):

Confabler – it would be completely wrong not to boomerang this thing back at her; how could I like what she writes and like that she nominated me but ignore why we share interests at all?

November_child –  in her poetry, every word is judiciously considered for its various meanings and the images they stir and she makes great short stories that are deep and playful and serious all at the same time

anonymouslyautistic – for doing an AMAZING job of writing about this misunderstood spectrum of living – and for inviting others who share her interest to contribute

English Lit Geek – because she searches the web and her library for poems that communicate her inner soul to us all out here in the ‘sphere and I appreciate this!

Wiser Daily – because this guy writes REALLY well about every single subject he wraps his mind around, because he is not a scientist but writes extremely clearly about science, because he is just a damned good writer!

Breathmath – because they are doing an astonishingly serious job of trying to get the world to see the beauty in mathematics

Sheryl – because she’s written a book, is working on others, has great tips for doing the same, and kindly visits my offerings fairly often

The Nexus – because he writes REALLY well about physics and does a great job of doing what I set out to do, whether I’m doing it on any given day or not

The Biology Yak – because she is passionate about biology and shares her passion in every word on every topic she chooses

afternoonifiedlady – even though I have no idea what it is to be an afternoonifiedlady, I love her rants about living with and without her ex and trying to wrestle with notions of romance – she is very witty and amusingly pissed off!

Yaskhan – for her lovely, succinct way with words

urbanagscientist – because she is at least as worried about the misunderstanding of science as I am

Luke Atkins – because he writes really well about difficult subjects and he writes like the stuff matters a lot, which it absolutely does!

And there are more in my list of 119 writers that I am following but this is enough for now.

4. Give them 10 questions to answer.

If you wish (and I clearly cannot impose this on any of you, please respond to confabler’s funny questions. I enjoyed them, maybe you will too!

Kind regards, MSOC


It was Generous of confabler to choose me. Now I have to Jump off and do other stuff!

Today is Brought to You by the Letter “Tzett”

Z – The Sequel

There are loads of naturally occurring and synthetically created organic molecules (usually compounds composed of carbon and hydrogen but often containing other elements as well). As chemists got busy discovering these substances, they also started coming up with ways to name them in increasingly systematic ways. Very early in an organic chemistry course (or very late in a general chemistry course), students learn that organic chemistry is as much a language course as a science course. Bright students with good language skills figure this out and apply the grammar and syntax accordingly; bright math students sometimes wonder what the heck happened? The way chemical compounds are named is called nomenclature, which means (oddly enough) “name calling” from Latin roots. Before the end of any organic course, some portion of the class usually gets quite busy calling names, although not those of the organic compounds they’ve come to despise (silly students! Succumb! Breathe in that fresh and unusual knowledge!). The professors bear the brunt of the name calling, although teaching assistants and anyone else nearby will do nicely. I probably fell in love with organic chemistry when I realized the nomenclature was systematic and could be applied logically rather than learned by rote memorization. And then there is the rich, rich symbolic language that goes along with the words! So spare and simple! So full of endless possibilities!

Anyway, among the structural idiosyncracies posed by increasingly insightful physical and chemical tests chemists developed was that some organic compounds contained single carbon-to-carbon bonds, some contained shorter double carbon-to-carbon bonds, and some others contained triple bonds between carbons, which were shorter than either of the other two types. Typically, carbon requires four bonds to other elements (carbon, hydrogen, oxygen, nitrogen, sulfur, etc.). When there was a double bond between carbons, the two carbons with the double bond between them only needed another two bonds—a total of three bonds instead of four. When the two carbons had a double bond, the other elements on either side of the double bond were sort of locked in place by the relative rigidity of that double bond (triple bonds are even more rigid). If there were only two carbons in the molecule and each of the carbons were bonded to two hydrogens as well as each other, there was no problem in naming that little nugget. It was called “ethene.” Just to give you something to relate this to, if you take off one of those hydrogen “H” atoms and put on an hydroxyl “OH” bit, this little guy magically becomes ethanol, fuel of dreams, liver-pillager, starter of fights and trips to the ER.

Ethene (also known as ethylene)

When the chemical moieties are something other than hydrogens, the naming game gets a touch more difficult. For instance, if we are presented with a four-carbon compound that has a double bond between the second and third carbons, it would generally go by the name “but-2-ene” or the arguably simpler 2-butene (there is a global chemistry naming organization called the International Union for Pure and Applied Chemistry (IUPAC) that gets together and sorts this stuff out; but-2-ene is their preference and they have a really colorful website, so let’s go with their approach, which I also adopted with “ethene,” although “ethanol” is the IUPAC name for ethyl alcohol). Here’s but-2-ene:


Oops! But that’s TWO molecules. Yes it is. The thing with that rigid double bond is that once a molecule has one, and there are a sufficient number of carbons or other sufficiently complicated moieties hanging off one end of the double bond or the other, there are two possibilities. The top symbol represents the cis- form, by which it is meant that the two methyl groups (each CH3– group is known as a “methyl” group) are on the same “side” of the double bond as each other (by the way, the double bond makes all of four of the carbons lie in the same plane as each other, so it is essentially a “flat” molecule, although the hydrogens on the methyl groups sort of spoil that by spreading out in their typical tetrahedral patterns). The bottom symbol represents the trans– form, by which it is meant that the two methyl groups are on different “sides” of the double bond. They are two different molecules with different physical properties: cis-but-2-ene boils at 3.7°C, while trans-but-2-ene boils at 1°C (they melt at -138.9°C and -105°C, respectively—a pretty huge difference in melting points for two molecules with exactly the same chemical formula (C4H8)).

For a more three-dimensional look at the difference between cis– and trans-but-2-ene, take a look at the following pages, which allow you to rotate molecular models of these distinct chemicals and shows their “flatness” better than the structures shown above:

CIS: https://chemapps.stolaf.edu/jmol/jmol.php?model=C%2FC%3DC%5CC
TRANS: https://chemapps.stolaf.edu/jmol/jmol.php?model=C%2FC%3DC%2FC
(Just click on each with your left mouse button and wiggle them around)

That naming convention worked just fine… until more complicated substituents were inevitably discovered mucking up the nice cis- and trans- simplicity. As an example, let’s look at 1-bromo-2-chloro-2-fluoro-1-iodoethene:

Two conformers (configurational isomers) of 1-bromo-2-chloro-2-fluoro-1-iodoethene

The way this new rule works is that we must take into account the atomic masses of the ethene substituents (ethene (we’ve met before) being that two-carbon-double-bonded bit in the middle of all these halogens (e.g. F, Cl, Br, and I)). Let’s rank these halogens in decreasing atomic mass: iodine (~127 daltons or amu), bromine (~80 amu), chlorine (~35.5 amu), and fluorine (19 amu); (in science, the tilde (~) is used to mean “approximately). The rule is this: if the moieties with the highest atomic masses are on the same side (not the same end, mind you!) of the double bond, then they are “together” or “zusammen,” the German word for “together.” If the highest amu moieties are on different sides of the double bond, they are opposite or “entgegen.” It would be sort of laborious and annoying to spell out “zusammen” and “entgegen” prefixed to every molecule for which this naming convention applies, so instead the letters “Z” and “E” are used. This means compound 9 (above) is named (E)-1-bromo-2-chloro-2-fluoro-1-iodoethene, while compound 10 is named (Z)-1-bromo-2-chloro-2-fluoro-1-iodoethene.

If you’d like to know who to thank for this naming convention, make sure you give credit to R.S. Cahn, C.K. Ingold, and V. Prelog, without whom the Cahn-Ingold-Prelog Rule would not exist. It can be applied in an equivalent manner to any compound in which conformational isomers around a double bond raises some ambiguity about nomenclature. Here is one last picture that shows you how it might apply to other substituents around a double bond:


And, by the way, the Germans (responsible for the words zusammen and entgegen) call the letter “Z” “tzett,” which is close to how those English-speakers on the other side of the pond (i.e. the British, but also Australians, Kiwis, and for that matter, Canadians, who are just across the Great Lake ponds) say it – “Zed.”

If you want to know a bit more, listen to the dulcet tones of Sal Khan as he goes through a few more examples.


Special thanks to my German tutor November Child, who writes excellent poetry and had no idea I was writing about this today.

Featured image: ©2009 Martin Fisch (Some rights reserved).



When we see a galaxy being born, we are viewing several jaw-dropping phenomena all at once…

When we see a galaxy being born, we are viewing several jaw-dropping phenomena all at once:

  1. We are seeing an event that started transmitting light outwards from its location some number of light-years ago; before it got here (and all of the other places it went), there was nothing for us to see in that bit of space
  2. We are seeing the birth and evolution of something like 100,000,000,000 (100 billion) stars (± some billions, but who’s counting?!?)
  3. We are seeing fantastically large clouds of ionized gas light-years across in their own right, glowing with the overwhelming energy that initiated with the generation and evolution of that galaxy, however many light-years ago
  4. The ionized clouds may or may not eventually condense into new dense forms, thus making yet more stars; all of that energy will turn into a local galactic phenomenon much like our own sun or planets, perhaps larger and more ferocious or smaller and meek
  5. Somewhere in all of that brilliance of stars and ionized gaseous forms of hydrogen, helium, isotopes thereof, and of heavier elements and their isotopes (not to mention naked bits of sub-atomic stuff zooming around), there may be planets condensing from the astonishing catastrophe that initiated that galaxy, settling into white-hot (ultraviolet-hot! x-ray hot!! gamma ray hot!!!) clouds of dust with poorly defined orbits around the gravity centers closest at hand, then condensing further over time into molten elements (or ultra-cold matter balls), then really hot dust with a metal core (or a big chunk of methane, etc. ice), then something coalescing further into a blisteringly hot (or supremely cold) planet, perhaps with an atmosphere of whatever gases stuck around and got pulled into the new planet’s own gravity

That thing we are witnessing from so far away in light-years once happened here roughly 4.5 billion years ago. As the Milky Way condensed into a circulating system and ionized gases condensed into stars and planets started their lazy ellipsoids around those brand-new gravity centers staggering out towards the edge of each tiny solar system, the system settled down into something wild but that followed more deliberate rules than it had initially. Among the planets formed was our little blue world, although it was once more amorphous than it is today and it wasn’t blue until much later in its evolution. It was brutally hot and as it coalesced, solidified chunks of various sizes plummeted into it at accelerated speeds. There are plenty of these solidified chunks out there crashing into our atmosphere even now; NASA estimates that 100 tons (200,000 pounds) of meteoroids hit our atmosphere each day and burn up. Cornell University astronomer Dr. Lynn Carter estimates that 84,000 meteors with a mass of at least 10 grams (about 2 level teaspoons of table sugar) hit the earth each year. While our galaxy was forming, these processes were far more common. With our telescopes—earth-bound, satellite-based, and outward-bound—we see this happening all the time, although paradoxically long ago.

Space.com has lots of great articles elaborating on these processes. For a brief article and video about the formation of planets in our solar system, go here:


For some information on what our early earth was like, go here:


The wonderful and talented folks at khanacademy.org have a series focused on these processes. Here’s the first in a series of five video units.

Inevitably, there are varying hypotheses and timelines associated with exactly how our galaxy, solar system, star (the Sun), and planet came into existence. Is there variation among the hypotheses? Sure. That’s part of the scientific method. Will we ever be able to go back in time over 4.5 billion years and watch the process happening for the next 4.5 billion years? Highly unlikely (in fact, absurd, but it would be the only way to know with certainty; can you imagine being part of a (1) backwards time travel expedition that (2) was stationed somewhere in our portion of the Milky Way to watch, over billions of years, how the process actually progressed?). What we are left with is an enormous data set collected by telescopes that cover every portion of the electromagnetic spectrum scanning the inner, middle, and outer fringes of all the space that surrounds us, trying to watch how it all works. The following is an animated model of how a starburst galaxy forms based on data collected relatively recently by the Hubble Space Telescope’s Advanced Camera for Surveys. This particular galaxy is “only” 300 million light-years from the Hubble.

To close, Hubble has gathered so many images of the universe and of galaxies surrounding our own that its earthly handlers at NASA were able to put together a composite video of our nearest galactic neighbor—Andromeda. It is “only” 2.5 million light-years away—spittin’ distance—just over yonder, etc. Watch this astonishing video composite; it is available in resolutions up to 4K HD, so set your YouTube gear to the highest resolution your video card and monitor can handle and prepare to lose your mind! Each point of light is AT LEAST one star; we cannot be absolutely sure as the point resolution this far from (this close to) Andromeda cannot provide certainty.

And here’s a logarithm-based (our solar system in the center and distances out from our solar system scaled logarithmically) image of the entire known created from NASA data by artist Pablo Carlos Budassi:


Every day, we can view this celestial wonder and try to comprehend its complexity. For me, it is preferable to know that humankind is unlikely to ever understand even a small fraction of this profundity than it is to dismiss it as something comprehended and explained away by oral traditions conceived well over 5,000 years ago and eventually written down and codified as the single explanation to life, the universe, and everything.

With apologies to actual astronomers everywhere.

Featured image: http://www.nasa.gov/sites/default/files/thumbnails/image/hubble_friday_07152016.jpg



Everyone thought it was an illusion, a mass hallucination, and no one mentioned it to anyone else.

Everyone thought it was an illusion, a mass hallucination, and no one mentioned it to anyone else.

Then it was obvious that something was going on and that whatever had been would no longer be.

Sometime around that time the tides started placing boats on the ground and if they were placed back in the water, replacing them somewhere else. The tides started knocking the piles out from under beach houses and floating away docks built at some point to watch the water come and go and exert its slow, gentle magic on the torments of the human mind. Fish were left on shore, gawping at this irregularity and at their abbreviated lives. And then people started getting grabbed by the tides and taken out and away into deep watery ravines that would open and shut with a shattering clap hundred of meters or kilometers towards the horizon. Ships would get devoured in one gulp in these hungry seas. Islands that once communicated with the large islands of the Americas, Africa, and Eurasia (as the deserts between them were washed away never to return) went silent and were believed gone forever. The waters would rise further today than they did yesterday, sweeping areas of the shoreline that had never seen tides and never been drenched except in rain. And each time they rose curious people who had come out to see where all the water had gone were surprised to see the water coming for them faster than they could run. The local authorities told people to flee inland and all of the roads were packed with cars that could go no further until the cars ahead of them had moved on to higher ground. Sometimes and for some people, the cars no longer worked as they had run out of gas and become obstacles to the onslaught of cars and people fleeing the ravening waters and some begged rides, which were either given to them or, when there were too many useless cars and too many fearful people, not. So the people walked uphill and inland until they couldn’t and hoped that would be far enough. It was for some and not for others, who were pulled back to the deeps increasingly cloudy with lives.

And sometime around that time it occurred to the people who watched such things that the smiling face of the full moon no longer beamed down upon them but had turned, at first imperceptibly, then more dramatically, then quickly and presented all its faces, one after another, as if they were frames in a hand-drawn animation from a hundred years ago. Click-click-click, the faces went, a new face every hour, then minute, then second. And the moon started wobbling as it orbited, as a top running down wobbles at both ends as it is about to drop to the floor and flounder through a couple of useless cycles before it comes to a halt. But the moon wasn’t stopping, it was spinning faster and wobbling faster and its ellipsis around the earth was pulling the tides higher and higher, nearly emptying the ocean at its perigees and sucking the shorelines dry at its apogees.

Then the earthquakes started. Mountains split and deserts disappeared in the raw wounds festered into them. Water washed through them and disappeared, returning in plumes of steam and ash. Volcanos shuddered from their naps and spat mud and lava into the clouds, hanging there like giant question marks over the earth.

Then it became terrifying. The moon’s ellipsis shifted subtly and then it was obvious what was happening. It would get further away at apogee but at perigee, it became a huge, leering, spinning, cackling face grimacing into the hearts of those who remained alive, like the corpulent, round-faced relative playing a discomfiting game of peek-a-boo with a newborn; “WHO’S your uncle? WHO’S your uncle? WHO’S YOUR UNCLE!!!”

But all of that was nothing when it finally came so close that it started brushing the edge of the atmosphere with its pock-marked visage. Tendrils of fire trailed behind its circuit and the tendrils were bits of the moon’s face so the craters became more numerous and deeper and the face became more angry and unpleasant with every orbit and more trails of fire became more rocks falling through the sky and pointing incandescent fingers at the places they would impact if they ever arrived. But they didn’t. They just burnt by the hundreds, then thousands and then millions every day as the moon swung closer in its perilous orbit. And the people who were left realized that this was not going to end well. Not at all.

But those who watched such things noticed something odd about the moon as this all happened. They noticed that way up near what was once the reliable north cap a hole appeared, first fairly small, then wider, then deeper, or as deep as the watchers could tell with their telescopes and satellites, which were rapidly being splattered against the hard dome of the air like bugs on a windshield. It was when it became deeper that the wobble had shifted and the orbit had changed and they had seen that there was some kind of apparatus near the north cap and that the hole was extruding a plume of dust up and back onto the surface around the hole. And there may have been some kind of vessel but it was hard to tell as the dust seemed to mask that part of the picture, so maybe there was no vessel or apparatus but the moon was surely doing its prolate dance and scraping the atmosphere and sending these torrents of rocks into the air.

Then the day came when it came too close and the air turned to fire around the moon as the rocks crumbled off and burned into the earth, larger and larger until they did hit the huge remaining islands or the catastrophe of the seas leaping from their abyssal canyons. And the moon braked further and slowed until, finally, the atmosphere joined the fire and burnt as well. And the moon crashed, splitting the earth open and disgorging both cores.

Sometime near the end, it came to make sense to those who watched. They had wondered what had happened to the moons around Neptune and Uranus, Saturn and Jupiter and Mars, and what had happened to those planets before they had disappeared.

The vessel and its apparatus came in, swept up what remained, and moved on.


Under Pressure (The Mess Pt 2 App. 1)

When we say we are “under pressure,” we should intend that to be a positive thing.

Introductory note: Anyone who has really thought about their chemistry or physics classes, rather than just endure them, has realized (perhaps in other words) that the seemingly endless equations that define our physicochemical universe (which includes the biological universe 😉 ) are a bit like those Russian matryoshka nesting dolls. If you define one phenomenon with an equation, you are probably well on your way to “nesting” that equation within several other equations that all define some aspect of what you were defining. This article is going to be like that and it is pretty inescaple. Have patience and enjoy.

When we say we are “under pressure,” we should intend that to be a positive thing. If we weren’t, we would be more diaphanous than outer space. Short of that meaning we have become a hive-mind of neutrinos, we should celebrate being under pressure! You could say that being pressured is the opposite of being vacuous but that might be unkind.

I’ve written two of three posts on The Mess (Part 1 and Part 2 so far). In Part 2, I spent a good bit of time using the word “vacuum” but I didn’t end up talking about what that means, except that a complete vacuum has never been achieved and it is difficult to achieve high vacuum (aka low pressure) without leaks occurring. The more I thought about it, the more I wanted to rectify that issue.

Our earthly pressure is due to the force that the weight of atmospheric gases (dry air is a mixture comprised mostly of nitrogen (78.09%) and oxygen (20.95%); “wet” air includes varying amounts of water and is lighter due to the lower atomic mass of water (18 amu) vs. nitrogen (28 amu) or oxygen (32 amu)) place on us. Since we experience the weight of the atmosphere, we also feel a force that is inextricably linked to our experience of pressure; that force is gravity and is related to the masses of objects interacting with each other over a distance and to the gravity constant, defined by Sir Isaac Newton.


Mass and weight are different. Mass is a physical constant related to the number of protons and neutrons in atoms of various elements and their isotopes (electrons, although very important, add negligible mass and are ignored here). Weight is the mass of an item (the sum of all of its constituent atoms) multiplied by the force exerted upon it by gravitational acceleration (gn), or:

W = m * gn

Mass, then, is weight divided by gravitational acceleration. By the way, because stuff like gravity is usually complicated it is worth stating that it is not constant but changes with latitude and altitude on earth (and between planets, stars, galaxies, etc., but that folds the theory of relativity and we are not going there). As r2 is larger for a person standing on top of Mt. Everest, even though the mass of the earth is larger at that point, the acceleration due to gravity is less, although the mass of the person remains constant (ignoring any hypothermic dehydration that is going on).

Gravity vs Altitude

The mass of earth’s atmosphere – all those speedy, invisible molecules of nitrogen, oxygen, argon, and water racing about and colliding with each other – is estimated at about 5.15×1018 kg. That’s a mass-ive amount of air! And all of that air is multiplied by the force of gravity pulling it towards the nickel-iron alloy center of our planet. To reprise, that is atmospheric pressure. Imagine a square inch on top of your skull, roughly postage stamp-sized (stamp size may vary with special editions and countries and may be larger than they appear in your rear view mirror). The atmosphere extends about 12 kilometers above your head (this varies with your location, etc.). There are, therefore, 1,200,000 cubic centimeters of air above your head and that contains a hole bunch of molecules of “air,” which is a mixture of gases. Every day at sea level, with variations due to latitude, that square inch of skull experiences 14.7 pounds (6.7 kg) of pressure from the weight of all that column of air pressing down upon you. The square inch is sort of misleading as it is really a COLUMN of air reaching all the way to where the atmosphere on this planet fades off into space. All of those molecules in a miles-high column with an area of a square inch – 14.7 lbs (14.7 pounds per square inch (psi) or about half to a third of the pressure in your car tires). And each square inch of your body that points skyward, whether you are standing, prone, supine, or lying on your side, gets this same treatment. If there were no gravity, the air would way 1/6th as much and the pressure would be reduced (if there were no gravity, the atmosphere would have dissipated into space so I wouldn’t have to explain this).

That’s atmospheric pressure. In a volume of air enclosed in a metal vessel within a scientific instrument, that same pressure is present if the instrument has not been hooked up to vacuum pumps and the air evacuated, in other words, if the instrument has just been assembled but not initiated for use. Scientists don’t use psi as a useful measurement. Instead, they use 1 atmosphere as the pressure at sea level; it is one of two measurement standards folded into virtually all chemical and physical measurements. The measurements are “standard temperature and pressure (STP)” and are 1 atmosphere (or 760 torr or 760 mmHG or 101,325 Pascals (101 kPa) or 1.01325 bar (1,013 millibar) and 273.15 Kelvin (K) or 32°F or 0°C (the Kelvin scale, based on absolute zero, does not use the “°” sign). The different units make use in some physics and chemistry a little easier, hence the large number of pressure and temperature scales. There is also a “standard ambient temperature and pressure,” which uses 298.15 K as the standard temperature; that is often more useful as it is a comfortable laboratory temperature. Standardization and calibration of scientific instruments to consensus measurements allow experiments to be compared conveniently between laboratories. Even if SATP (or STP) is not used in every laboratory, it can be used to understand how conditions might need adjustment to replicate results lab-to-lab.

As Parmenides said in about 485 B.C.E. “Nature abhors a vacuum,” although I’m pretty sure he said it ancient Greek. Again, we find that so long ago the Greeks were constructing rules of the universe that would not be proven for a few millennia but they were correct. This idea, of the implausibility of a complete vacuum in the universe, got many people thinking, among them Empedocles, Plato, Aristotle, and so forth into the present era where attempt at achieving a complete vacuum will continue until attained. It’s in our nature.




How is this done? Using various kinds of pumps. How does that work? If you pump water, you know quite well how it works. The water goes up a tube, through the pump, which has an object in it of various designs intended to exert a change in pressure on the material to be moved. The devices are sort of like tight-fitting fan blade in a water- (or gas-) proof housing. As it turns, it exerts a force on the water and the “pumpate” (to coin a word) is moved from point A to point B. If the water source was finite and can be inspected after pumping, you will see some volume of water left in the source. Move the tube around and try to “vacuum” it up and it will run up the tube a little bit and trickle back down. The same kind of thing happens with gases.


There are a bunch of different pump mechanisms, all of which are fascinating in their own right but the same principle applies to all of them: move something from one place to another by exerting a superior force against an inertial force (e.g. gravity, magnetic, electric, normal, air resistance, friction (viscosity), tension, spring). Vacuum pumps move gases.

For ease of calculations, let’s pretend the volume with our exotic scientific instrument (a x-ray photoelectron spectrometer (XPS)) is 22.4 liters (L). To make this relatable for people still using the U.S. “customary unit” system rather than metrics, 22.4 L. is about a gallon more than the typical upside down water jug found in various offices. Imagine such a space at the center of the following instrument (the actual analytical volume in which samples are analyzed is much smaller than 22.4 L.):


In this version of an XPS with the 22.4 L. volume of air at SATP (standard ambient temperature and pressure), there are Avogadro’s number of individual gas molecules in the vessel at 1 atm pressure. Avogadro (1776-1856) was an Italian scientist who worked out that there would be 6×1023 molecules of any gas in 22.4 L. if the temperature and pressure were kept constant. This is a HUGE number of molecules but if they are molecules of gas they will always occupy 22.4 L. at SATP. This number of molecules is called a mole and correlates the number of molecules, by way of its atomic mass, in a mole of molecules. It is a constant number, just like there are always 12 of an item in a dozen or 144 of an item in a gross.

Let’s compare some other, more visible molecules. Because (in part) a molecule of water has a mass of 18 atomic mass units (amu) a mole of water molecules weighs 18 grams and occupies a volume of about 18 milliliters (0.018 L.). You could put 55 moles of water in a 1 L. container (55moles x 18 milliliters) – and 1,244.4 moles of water in a 22.4 L. container. Why? One of the reasons that water is a liquid between 0C and 100C is because all of them hydrogen bond to each other.

Gases at SATP do not make friendly clusters of molecules; instead, they bounce against each other and against the walls of any container with maddening speed, like bumper cars at the fair driven at blinding speed.

A property called the root mean square velocity of gases can be calculated, a measurement which is temperature and mass-dependent; gases with low masses move at higher speeds than those with higher masses. A molecule of hydrogen (it occurs in nature as a molecule with two covalently bonded atoms of hydrogen, or H2) has a velocity (speed) of 1,920 meters per second (m/s) or 4,295 miles/hour. A molecule of oxygen has a velocity of 485 m/s or 1,085 miles/hour, right around one-fourth the velocity. This makes sense as one molecule of hydrogen is one-fourth the mass of a molecule of oxygen. If we were to look at fluorine, also diatomic, with an atomic mass of about 19 amu we would see a velocity somewhat slower than oxygen at about 424 m/s. Why do I tell you all of this? Because the pressure (1 atm) in that vessel is related to the mass of all of those molecules but it also related to all of those invisible particles smashing into each other and into the walls of the container at those mind-imploding speeds.

XPS plumbing around the intro port
XPS Plumbing and Sample Intro Ports (Attribution)

We have our 22.4 L. vessel in the middle of the XPS instrument and it has 6×1023 molecules of air in it. To do our surface analysis experiments we are going to have to reduce the pressure in that vessel from 1 atm to as low as we can go, which will probably be between 9.87×10−13 and 9.87×10−16 atm. We will have two pumps connected in series (one after the other): (1) roughing pump and (2) turbomolecular pump. The purpose of the roughing pump is to reduce the air pressure in the xps instrument and in the turbomolecular pump to around 1×10−5 atm. After this is achieved, the turbomolecular pump is activated and it can reduce the pressure due to remaining gases to somewhere in the range of 9.87×10−13 to 9.87×10−16. The following video does a reasonable job of showing how a turbomolecular pump functions, although there are other videos available that examine the moving parts of these pumps.

In these ultra-high vacuum conditions it is important to remove as many of the gas molecules as possible. This is done with various types of ion pumps. The remaining gases are bombarded with energy sufficiently high to create positively charged ionic versions of the gases that then collide with the walls of the pump and react. The gases are no longer gases and no longer add to the pressure inside the apparatus being evacuated.

Placing aside the ion pump from our considerations, a couple of big problem lies at the heart of achieving an absolute vacuum – a vacuum in which there are literally zero gas atoms remaining in a volume (HxWxL or its cylindrical equivalent). The pumps are achieving a truly significant reduction in pressure but as they do there are fewer gas molecules and the mean free path of the individual molecules involves fewer collisions and more randomness. You will recall that these molecules are traveling at enormous speeds; as they approach the exit orifice attached to the pumps, they are no longer flowing as was possible at low vacuum, they are moving in increasingly random patterns. Some of these patterns direct the molecules back into the vessel we are attempting to empty.

Gas Flow Patterns due to decreased pressure
Attribution and In-depth Explanation

I watched a duck herder with his collies at a state fair some decades ago. The dogs had been trained remarkably by the herder and I assume that the ducks had also worked with these non-duck lifeforms previously. As the herder and the collies positioned themselves in ways to coerce the ducks into a cage, three ducks would enter but as the fourth duck approached, one duck would pop out, then another, then two ducks would go in and another would exit. This went on for a while and, perhaps because I had never seen it before, I found it to be extremely entertaining and funny. I also thought of the problem of trying to eat the remaining green peas in a metal bowl using only a knife (no pea-stabbing please!). The difference between these analogies and teasing the last gas molecules out of an evacuated volume is that the ducks eventually enter the cage and the peas will be eaten.

The reason I bring this up is that “herding” gas molecules out of a volume is a lot like this. Some exit, but others sort of bump around at the exit port and return to the cylinder to play a few more games of hyper-bumper cars with the walls of the vessel. As I read for this article, I saw some ultra-high vacuum wizards talk about how it is invevitably the hydrogen molecules that will not leave. These have the highest gas velocity and the lowest mass. They are also the most present element in the universe; about 74% of mass fraction of the universe composed of mass (only about 5% of the universe, the rest being composed of dark matter and dark energy) is made up of hydrogen.

To sum up:

  1. Atmospheric pressure is the force created by all of those gas molecules above your body being pulled towards the earth’s center of gravity (F=m*g);
  2. There are a whole bunch (6×1023) of gas molecules in a 22.4 L. container at SATP;
  3. Getting most of those gas molecules out of the container involves some spectacular types of pumps;
  4. Getting absolutely ALL of those gas molecules out of the container has never been achieved to date.

I have glossed over a huge and beautiful realm of gas laws in the above. These roll up into the enormous topic of thermodynamics  and kinetic theory. I will leave it to you (and future posts) to explore these further. They are a wonderful set of nesting dolls!


The Mess (Part 2: Drilling Down)

There was a pretty jovial guy in grad school who was working on surface analysis of materials.

[Part 1 can be found here – updated Aug. 12, 2016 @ 07:15PM EDT]

There was a pretty jovial guy in grad school who was working on surface analysis of materials. There was a problem. His initial tasks all had to do with creating a sufficient vacuum so that he could do his spectroscopy (I’m not sure which of the surface analysis techniques he was attempting; generally, I was too busy reading organic chemistry literature and trying to create new types of metal ligands, but (again) I digress). Every time I’d see Mr. Smythe-Terwilliger (a fictional name to protect his innocence), I’d ask him how it was going. “Oh, I got the apparatus down to about 1×10-15 atmospheres (a measurement of pressure; at sea level, we experience about 1 atmosphere or 760 torr) and it sprung a leak.” He was achieving REALLY low pressures, and it would take him days to achieve those, but they would get stuck at some pressure above where he needed to be.

Pressure vs Time

If somehow, we were to instantly find ourselves at a pressure of 1×10-15 atm (the abbreviation) we would go through explosive decompression. Whenever he would get close to his goal, some tiny, previously undetectable pore between the metal gaskets or flanges he had tightened down with impressive looking bolts would start inhaling molecules of air into his nice vacuum. Air, being a collection of elements, is among the many substances you do not want around when you are trying to characterize the surface of a material. The material you hope to study is already going to be far from perfect and that will be a nice problem to have, but until that happens, he would have to shut off the valves to the huge vacuum pumps (pumps that pull most of the gas molecules out of his instrument), then shut off the pumps themselves. If he shut off the pump first, its oil would go slithering up the vacuum hose into his relatively pristine, ultra-high vacuum instrument and he would probably spend his remaining years on earth swabbing oil out before he could pump it down again (and find yet another leak). Here is a chart of relative pressures achieved or observed and a paper discussing how to achieve ultra- and extremely high vacuum conditions.

Pressure ranges of each quality of vacuum in different units
Vacuum quality Torr Pa Atmosphere
Atmospheric pressure 760 1.013×105 1
Low vacuum 760 to 25 1×105 to 3×103 9.87×10−1 to 3×10−2
Medium vacuum 25 to 1×10−3 3×103 to 1×10−1 3×10−2 to 9.87×10−7
High vacuum 1×10−3 to 1×10−9 1×10−1 to 1×10−7 9.87×10−7 to 9.87×10−13
Ultra high vacuum 1×10−9 to 1×10−12 1×10−7 to 1×10−10 9.87×10−13 to 9.87×10−16
Extremely high vacuum < 1×10−12 < 1×10−10 < 9.87×10−16
Outer space 1×10−6 to < 1×10−17 1×10−4 to < 3×10−15 9.87×10−10 to < 2.96×10−20
Perfect vacuum 0 (theoretical) 0 (theoretical) 0 (theoretical)

The whole exercise seemed very exciting in a way, but in slow motion. I’m too impatient to do this kind of thing, but Mr. S-T was always fairly cheery about it all. He reminded me, I suppose, of a well-adjusted Sisyphus, the tricky Greek king punished for pissing off Hades and condemned to roll a large boulder up a mountain every day, just to watch it roll down the other side. “Repeat for eternity, please, Sisy old boy. Do not call, do not write. Thank you, Hades.” There is something very prescient in this myth as much of what scientists do on most days is do experiments that do not result in any useful advancement of knowledge. Experiments fail, fail often (just to make sure the first ten were true failures), are redesigned, refocused, fail again and often, and are redesigned until they succeed or that path to new knowledge is abandoned to other groups and/or other future times or altogether by everybody previously working on it. The experiment is rolled up the “hill,” falls down the other side, and is dutifully pushed again, this time with a few micro-grains of stone polished away. It is kind of crazy to do… until it rewards persistence with the tiny gleam of something new, something to be affirmed and passed into the literature to be replicated, confirmed, or rejected by others.

There are many instrumental methods for materials analysis. There are a substantial number of surface analysis methods that require insanely high vacuums and all of the asymptotic refinements in technology (pumps, metal, plastic, ceramic, and adhesive purities, for instance) that must improve to get there. The rapid evolution of nanoelectronics and the desire to create quantum computers have been critical driving forces towards improvements in these methods but before there is any application in science there is an exploration of theories and techniques. What is possible? How can the formerly impossible be attained?

To convince you further of the truth found in my lede for The Mess (Part 1: Too Much Mess! (to wit, “There is nothing superficial about surfaces”), let us explore three of those methods: X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM), along with its quantum-empowered sister scanning tunneling microscopy (STM). This stuff gets heady very quickly so there will be much generalization and extreme hand-waving.

The XPS (aka ESCA) system is illustrated below, along with a cartoon of what is happening in the surface atoms (blue box) and the resulting graphical output showing the number of electrons blasted out of their energy levels. It shares characteristics with many electromagnetic analytical techniques in that a beam (“ray”) of some chosen energy is aimed at a sample, the sample responds in some way, and a graph of response versus physicochemical property is gained. The particular sample of copper illustrated seems to be quite pure as electrons from other elements are not produced during the experiment. If there had been other metallic or organic impurities present, they could have been revealed in the spectrum as well. This method is able to detect impurities in the parts per thousand (ppt) and parts per million (ppm) range. Purified silicon is required to make quality semiconductors but to get this material to function as a conductor it must be purposely contaminated with trace phosphorus, boron, and other “dopants.” XPS is one means of determining whether the silicon is adequately pure and appropriately doped.


To give the truly inspired reader something to ponder, I have included the following video in which the contours of a typical XPS instrument are lovingly caressed by several supplicants. While I have never known the fickle love of an XPS, I have appreciated that of other large, expensive instruments. Alas! No more!

But XPS (aka ESCA) and its affiliated methods provide data that is deconvoluted and interpreted to arrive at an insight into some aspect of a material’s quality. The really mind-blowing achievements in surface analysis (to the extent that I can cover in this post) come with SEM and STM. Let’s start with SEM.

As with XPS, a beam is propagated from an electron-producing device and focused through a range of lenses, apertures, and magnetic deflection coils to optimize and narrow the beam as it speeds towards the sample. Once the beam strikes the sample, electrons are scattered off the sample and detected by various types of detectors, depending on the configuration of the microscope. This type of microscope is responsible for providing some of the most intriguing views into many of the tiny realities among which we stomp, giants in a universe of delicate details. I am particularly intrigued by electron photomicrographs of bug heads. Well, any bug part, really.


To extend this fun further, please watch the following portion of a much longer video about microscopy in general.

STM takes these explorations down to individual atom resolution. It works by achieving just the right voltage difference between the scanning tip and the sample surface to cause electrons to quantum tunnel their way through the vacuum between them. This makes the atoms in the surface develop a three-dimensional aspect that allows very close inspection of materials. The truly remarkable feat that STM allows is the rearrangement of individual atoms on the surface of – or within – a material! Pick it up, put it down “here, please!”



The following video goes into greater detail as to how this is accomplished. Please enjoy.

Archimedes animated this film for the Max Planck Institute of Microstructure Physics. The film explains, how scientists observe surfaces at the atomic level with a scanning tunnelling microscope. An extremely fine tip “feels” its way over a surface at a constant distance of a few atomic diameters. The distance between the tip and the surface is regulated with the aid of what is called a tunnelling current, which flows between the tip and the sample when a voltage is applied between them.

There’s an incredible array of these electron photomicrographs (and even just light photomicrographs) out there on the web. Here are two sites that run annual competitions to select the best images from the previous year. It is important to note that all of the SEM and STM images and perhaps some of the light images use the art of false color imaging, a technique also used to great effect in the Hubble, and other satellite images. In effect, it takes images produced from non-visible portions of the electromagnetic (EM) spectrum, or from black and white images, and assigns colors within the visible spectrum to them so we can have some comprehension of their appearance. It’s a useful illusion but we would only be able to see the real thing if, somehow, our eyes and the brain to which they’re tethered could see the entire EM spectrum. It would probably result in minds shattering into some huge number of pieces, so false color it is!

Galleries from an annual electron photomicrograph competition

Astonishing light photomicrograph competition galleries from Nikon (dig around on the site for amazing video micrography)

To wrap, I provide a few SEM and STM videos, plus a playful explanatory video about the size of atoms to give some general perspective.

A link to a whole bunch of other “Zoom into…” videos:


Plus a mosquito eye!

A cluster of atoms!

And the promised explanatory video!

To conclude, there is nothing superficial about any of what you see around you. Do your own searches using some of the key words and phrases provided above. Discover more about the world you live in than you may have ever imagined before. It’s pretty beautiful, particularly if we are safe from the pincers, proboscides, and mandibles of all those tiny insects. Have a look around!

Featured image attribution: By Heiti Paves (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0)%5D, via Wikimedia Commons


The Mess (Part 1: Too much mess!)

There is nothing superficial about surfaces.

There is nothing superficial about surfaces. While there are many objects that appear smooth, most of what we see is all about nooks and nicks, crannies and pores, pleats and folds, imperfections and inconsistencies, hooks and dips, bumps and craters. We live in a world of beautiful deformations, of breath-taking imperfections, and we should celebrate all of them. Simultaneously. In one globally cavitating “YAWP!” at least once a day.

I first read about close packed structures in high school. I found it fascinating. I can’t explain being fascinated. It is one of those dovetailing moments when your own individual, completely unique brain that is also just like all the other human brains finds something that it likes for whatever impossibly complicated reason and latches onto it. It is a concept with which all of you have more familiarity than you think.

Have you ever shopped for oranges? Not just an orange but a box of oranges. The first layer sits in the box and reveals a uniformity of depressions where each orange touches two (at the corners) or three (at the sawtooth edges) or four (at the straight edges) or six (anywhere besides the places above). Those depressions are an invitation to add another layer of oranges. Or not. You can add that next layer to the enticing curve-edged triangles that have appeared between oranges or you can add them directly above the oranges you’ve already added to your box. If you add them to the dips between oranges, you are making a close packed structure of oranges and they will all sit very comfortably in those dips until you get them home, their imperfect skins pressed against their friends like tiny butts in triangular swing seats.


Take a look at that first layer of white, imaginary spheres and pretend they are oranges…

From this illustration, you see the first, second and third layers and two possible arrangements: hexagonal close-packed (left) and face-centered cubic or cubic close-packed arrangement (right). So orderly! So nice!

The thing is that nature is not orderly and nice. What happens to the stacks of oranges if we add in a grapefruit in one of the layers, right in the middle, and then a couple of divots later we add in a grape or seven? Then we add a variety of apples, plums. and kiwi fruit on top of that? Let’s put a cantaloupe into our lattices, but keep piling up and pushing in the oranges wherever spaces are left. And we do this kind of craziness, not for two or three layers, which would still be a sub-microscopically thin collection of atoms (but a good box of fruit); we go for a trillion cubic layers of atoms (the fruit thing has just become an impossible and fairly useless analogy; let’s put them all back in the grocery already). Atoms don’t always sit in a single layer with other identical atoms. Atoms are paired (or tripled, etc.) with disruptors to these simple lattices (“lattices” is what these formations of atoms are called). Sodium atoms (ions actually, but that is a rat hole I will not go down – yet) are paired with chloride ions (still atoms, just with an additional electron, stolen (perhaps) from the sodium). Sodium and chloride – atom center to atom center – has a lattice constant of 564 picometers (5.64×10-10) meters, a very small but critical distance that helps make those nice cubic crystals you see when you look at a grain of salt with sufficient intent. If you grow your sodium chloride crystals in a vacuum from absolutely pure water that includes nothing but pure sodium and pure chlorine, they will probably be gems of perfection. If they grow in the real world – on a beach or rocky shore at the high tide line or in evaporation ponds used since pre-history to harvest salt, those little crystals will probably include other ions. These are called inclusion impurities or coprecipitates. They may be ions or organic substances that got muscled into the crystallization process in spite of their differences or they may have sufficient affinity with one or another of the primary ions in the substance to bind simply because no energetic reason not to do so. The shape of the crystals will not be so perfectly face-centered cubical and their color might even shift, depending on what is included and to what extent.

In virtually any water you can imagine except the purest water (but we might as well start talking about unicorns now), sodium ion, which has given up an electron to have a single positive charge, a single electron-shaped absence in its uppermost and typically populated energy level, badly wants to fill that hole with almost any substance that comes along with a spare electron in its uppermost and fully populated energy level (we’ll just put the concept of energy levels aside with the notion of ions, although we are now revisiting ions after I promised to delay them). If a fluoride or bromide or iodide atom floats by, they will fill the bill quite nicely but water molecules will do the job by pairing its comparatively electron-rich oxygen (negatively charged) with the momentarily electron-poor sodium ion (positively charged). The water is just lending its cloud of electrons through a process called hydrogen bonding, illustrated forthwith:


Schematic representation of the aqua ion [Na(H2O)6]+.

Instead of this “flat” representation, the sodium ion sits at the center base of two four-sided pyramids defined by the oxygens from the water molecules; this is known as an octahedron. To illustrate, we have the structure on the right, although instead of rubidium ion (Rb+) at the center we have sodium ion (lithium is smaller and only requires four waters for its solvation shell, thus forming tiny floating tetrahedrons all linked to other tetrahedrons through other waters).


Li- and Rb-water omplexes
Water-solvated lithium ion (left) and rubidium ion (right)

To further illustrate, here is a stripped-down diagram of six waters binding  to an ionized metal (M) at the inner center of the octahedron. The diagram also shows how this hydrogen bonding continues by oxygens in the next sphere out from the metal binding through the hydrogens in the waters affiliated with the metal ion.


But again I have digressed! Water – pure, unadulterated by absolutely anything water – will dissolve anything onto which it can place its tiny hydrogen bonding mittens. If no sodium ion (or any of the other group 1 alkali metals) is available, a group 2 alkali earth metal – or almost any ionizable metal from the transition metals or lanthanides or real-world actinides will suffice, thank you. And we haven’t even touched on all of the polyatomic ions that water will cluster about like electronically ambiguous fanatics looking to rub shoulders with their i(c)ons. Water will grab anything with an electron or more missing and will grab anything with extra electrons as well. If there is soluble lead in a water pipe, the lead is grabbed by water and whisked along to your tap. It will grab organic compounds (table sugar, vitamin C, short-chain alcohols and acids, for instance), charged or not, to the extent that they are mixable (miscible) with water; if the organic compounds aren’t miscible, they will form a very tight interface. You have probably seen this interface in oil-vinegar salad dressing, although that is an imperfect example. If you have some mineral oil in the medicine cabinet, remind yourself what an immiscible interface looks like.

To provide a visual example, the following is a photograph of air bubbles in foam. Notice the irregularity of the bubbles. This is not exactly like imperfections in crystals or  dissolved substances, but will suffice as an analogy to the irregularity of materials dissolved in water. All water-metal solvation does not form octahedrons and not all waters surround positively-charged ions; they also surround negatively-charged ions, neutral materials, and are surrounded by other waters as well. It’s messy.


Order and chaos of air-bubbles in a foam: from order to chaos or from chaos to order? Hexagonal packing of spheres due to regularly sized spheres, transitioning to disorder due to spheres of differing size.

If water has a difficult time being pure, what about the rest of the world? The rest of the world is more like the composition of minerals than it is about absolute purity and pristine structures. What do I mean? Here is a mineral, or rather here is a photograph of at least three minerals (Uvarovite, Malachite, Azurite) sharing space.

A proliferation of minerals

Uvarovite has the chemical formula Ca3Cr2(SiO4)3. Malachite’s formula is Cu2CO3(OH)2. Azurite goes by the alias Cu3(CO3)2(OH)2. When they are blended together as they are in this formation, bits of each stick into the lattices of the other – a copper (Cu) infiltrating the chromium (Cr), a silicate ion ([SiO4]4−) latched onto a copper, an hydroxide (OH) here, a carbonate (CO32-) there, an intrusion of calcium (Ca2+) toying with the affections of a carbonate, although there may be patches that are as pure as nature allows. And there is always the promiscuous water molecule and its tendency to complicate matters with its waters of hydration to consider. See the wave-like shapes in the chunk of history above? There’s a really good chance that this occurred because the various minerals were once suspended in water and somewhat slowly, for whatever reason, the water dried out or the minerals were in a sufficiently concentrated solution that they precipitated out. The blue stuff in the middle? See the little bumps? Those are tiny crystals. This is where all the stuff about water solvating various ions of various sizes and the solid surfaces of rocks kind of come together.

And this is the sort of world that surrounds us. A world of appearances that are far more complicated than they seem. Surfaces that are even more complicated than diligent study reveals. Scientists, after all, are looking for rules, patterns, predictability (however chaotic at first blush the predictability may seem) at the heart of the messiness. It would not make sense to take an item like the pictured jumble of minerals and break it down – the only unique “it” that “it” is – and determine EXACTLY how all of the minerals fit together and where the inconvenient atom that is “none of the above” has interloped into something already impossibly complex. The scientist studying any facet of the universe looks for the through-line that links the messy with its fundamental characteristics and helps us understand what a predictable, impossible universe surrounds us.

(Updated, extended, clarified, polished, and propagated afresh: 12:21PM EDT Aug 12, 2016).

(Further updated with the addition of the following videos 7:15PM EDT Aug 12, 2016).

Hydrogen bond rearrangement dynamics in liquid water by molecular dynamics simulation. 1 second in the movie corresponds to 1 picosecond in reality. The blue spheres represent oxygen, aqua spheres represent hydrogen and the yellow connectors represent hydrogen bonds.

Featured Image: https://commons.wikimedia.org/wiki/File:Ductile_Iron.png