What really counts as a “microbe”?

Just a brief pre-post before the main one I’ve got brewing now (which will be posted either later today or tomorrow).

A tapeworm: Since when does 30-36 feet long count as 'micro'???Microbiology is the dominating topic of this particular blog, but I don’t think I’ve ever addressed what I consider to really count as “micro”biology. This isn’t necessarily an obvious topic. My old “Microbiology” book from 8 years ago, plus the textbook from last year’s “Pathogenic Microbiology” class both contained large sections discussing organisms that are visible without a microscope. Heck, the “Pathogenic Microbiology” text even had a whole section on spider and insect bites. And, tapeworms? Since when is “over 30 feet long” considered “micro”? As I like to say: It’s time for Microbiology to grow up and move out of Medicine’s basement.

So: Here are the defining features of what I consider to be a “microbe”, at least for purposes of what I tend to discuss here on the blog:

  • Obvious: the organism cannot be effectively examined visually without a microscope and individual organisms can virtually never be observed by the “naked eye”.
  • In nature, a full normal population of a microbe can and will develop from a single live cell, and isolated individual cells are reasonably commonly observed.
  • Microbes do not “eat”.

It’s that last point that prompted me to write this post, mainly because it’s such an important part of why microbes work and how they affect their surroundings, especially when it comes to food microbes. What I mean by “do not eat” is that they are incapable of taking large (microbially speaking) chunks of material into themselves to use. Any cell nutrient for a microbe must be in the form of small molecules, like sugars, small peptides or individual amino acids, and so on that can be easily transported across the cell membranes and through the cell wall where applicable.

The importance of this is that for a microbe to grow on a complicated substance like meat or bread (for example), they have to excrete specialized enzymes that break down the substances out in the environment into simpler components like sugars or small peptides. If a microbe cannot secrete a protein-digesting “protease” enzyme, it can be surrounded by tasty, nutritious proteins and still starve to death. If a microbe can’t secrete an amylase (starch-digesting) enzyme, it doesn’t matter that starch is made of nice yummy glucose molecules because they’re all wadded up into long chains of starch that the microbe can’t get at.

And that, finally, is important because it brings up issues of growing multiple microbes together to accomplish something. Sake, for example, is made by fermenting rice, but rice is made primarily of starch. Saccharomyces yeasts don’t make amylases, so in order to make sake, you also have to add a kind of mold (Aspergillus oryzae, one of the types of white-mold-with-little-black-specks that you may see growing on the bread you’ve left sitting around for too long). A. oryzae is also a microbe and therefore can’t “eat”, but it does produce amylase. Since the amylase is breaking down the starches outside of the cells, this means the released glucose is also available for the yeast to use.

Admittedly, my definition above isn’t perfect. On the one hand, it leaves out protozoa (like amoebae and the well-known Paramecium, both of which actually do take in “chunks” of food, but both of which most people would normally consider to be “microbes”. It also leaves IN things like mushrooms, which are not usually thought of as being “microbes” by people who aren’t microbiologists. And, of course, it leaves me with no excuse not to go and learn something about eukaryotic (“plant”) algae (as opposed to bacteria-algae, a.k.a. cyanobacteria) and diatoms. Suggestions for updating my definition may be left in the comments…

Just something that came up while I was assembling what will be the next post. Stay tuned.

Drugs make you stupid. And so does fear.

Ignorance breeds fear. Fear breeds terrorism. Terrorism breeds interruption of homebrewing. There was a disturbing article that came up today. Evidently, someone’s burglar alarm went off, so the security company drove by to check it out. They opened the garage (where I guess the alarm indicated an attempted break-in or something) and thought they saw a “still”. Naturally, anything that looks science-y with copper tubes or whatever can only be for one thing: drugs, right?

A bunch of police officers in both marked and unmarked cars AND the fire department later, somebody finally finds out it’s just somebody’s (completely legal!) homebrewing setup. Of course, officials describe the panic as “an appropriate response”. You might think this was in notoriously over-reacting Boston, but no – it was Hamilton, New Zealand.

My first thought was that it probably wasn’t even a “still”, which due to unrepealed prohibition-era laws is still treated pretty much the same that meth-lab equipment would be in terms of legality here in the US. I kind of assumed it was probably just the owner’s fermentation container, or possibly a wort-chiller (see image – click for context). Without some apparently-rather-expensive permits, it’s extremely illegal to have distillation equipment in the US, and I’m under the impression that most places around the world still criminalize home distillation. It’s worse, though – apparently New Zealand repealed the ban on home distillation for personal use over a decade ago. Even if what the panicky security guys saw really WAS a “still”, it’s STILL a completely legal piece of equipment there. And yet, surrounding the guy’s house with marked and unmarked police cars and firefighting equipment was “appropriate response.” Because somebody said “drugs”. The original article may be found here.

In fairness to the public officials, it sounds like once the police and fire department showed up, they actually talked to someone at the house (no tasing or teargas required) and had no trouble figuring out that nothing illegal was actually going on, so the damage was pretty much limited to the time wasted by the police and fire-department in responding. What I want to know is why the “security” company gets a free pass on causing all this fuss by reporting a completely legal piece of vaguely science-like equipment as a “clandestine drug lab”? At the very least, I’d expect people to want to know which “security” company is supposed to be protecting their houses but cannot tell the difference between legal homebrewing equipment and real criminal activity.

As a fairly hardcore nerd with an interest in intentional food microbiology (brewing, cheese, etc.) this kind of thing worries me. I intend to build myself a fairly decent science-lab setup for doing food microbiology. I’m already planning to label everything as though it were part of a public museum exhibit, just in case some idiot happens to see it and assume it’s some kind of terrorist drug lab or something.

Here in the US, I consider “amateur” science and technology to be part of the very foundation of my country’s greatness. Think Thomas Edison. Nikolai Tesla [yes, he was a naturalized American citizen]. Benjamin Franklin. And no doubt many, many others who are less famous but nonetheless made major contributions to the advancement of their country. When we set about attacking that, we’re harming our country – yes, you people outside the US, this applies to you, too.

The moral of the story is this: Please, people – science and technology are fun. Yes, there are many of us out here who quite happily set up “science-lab stuff” to play with food, or rocks, or plants, or electronic circuits or whatever else in a completely safe and legal manner. Sure, it’s a good thing when good police-work closes down some drug-crazed freak’s meth-production setup – I don’t want some idiot blowing up my neighborhood with unsafe chemical activity nor attracting violent criminals anywhere near where I live. All I’m asking is, will people please stop panicking and screaming “drugs!” or “terrorism!” every time you see some glass tubes or blinking lights? Please? Thank you.

This Public Service Announcement has been brought to you by the popular drug 1,3,7-trimethylxanthine. We now return you to your regularly scheduled (and, it should be emphasized, completely legal) nerdity.

Why you really do or don’t want me as a student…

Of the classes I took this last semester, there’s only one I haven’t blogged about at least once.

Masochist that I am, I went and took “Applied Calculus”, even though I’d gotten approval to count my previous semester of calculus (about 8 years ago) as fulfilling the mathematics requirement for graduation. The “applied” in the title of the class caught my eye, and after speaking to the instructor before the semester to find out what the class was like I decided that if there was time and money left I’d take the class. So I did.

Although I’d rank it as only the second most useful “Mathematics” course I’ve taken so far, Dr. Wolper was one of the best mathematics instructors I’ve had up to this point, so I’ve got no regrets for having spent the time and money to take it. I suspect I’ll remember a lot more of it than I did of the previous calculus class.

Anyway, getting to the point of this post:

There are times when I am unable to restrain myself and answer homework or exam questions in a terse, boring manner, regardless of the subject. If you’re an instructor and are wondering if you want me in your class, here is something to judge by.

Calculus (for those who don’t know) is more or less the math you use to deal with when, how, and how fast things change. In practical terms, when dealing with real-world applications this often means dealing with a graph of some data. A number of homework (and exam) problems this semester dealt with questions along the lines of “what would a graph of such-and-such a situation look like and how would you interpret it?”. Here’s one from early in the semester:

This was my answer:

You may judge for yourself whether this is a good answer or not…

#1 on Google!

Over on scienceblogs.com’s The World’s Fair, the author has started an amusing meme.

It goes like this: the challenge is to find 5 sets of search terms for which your own blog or site is the #1 hit on a Google search. Note that it is acceptable to quote specific phrases but of course it’s more impressive if you don’t. Here are 8 that (as I type this) for which this blog is the #1 hit (links go to the blog address that is the hit):

There was at least one other which I’m having trouble remembering at the moment. Perhaps I’ll update later if I remember what it was.

A short update…

I’ve got an Art History exam in the morning which has been consuming my time, but I wanted to get some kind of post up. Especially since it almost looks as though I just don’t post on Thursdays. I swear the recent several weeks of “no post on Thursday” is purely coincidental.

I’m still waiting to hear if This Week In Science got the audio file I sent them and whether or not they liked it. I did manage to find a legally-free embeddable flash-based audio player that I can use, so I’ll probably post it for listening to online or for downloading soon.

Meanwhile: One of my competitors in the College Blogging Scholarship 2007 competition had an interested post up the other day. Famous neuroscientist Shelley Batts of Retrospectacle posted about a bunch of computer people getting together to have a “hackfest”, where they all work on their projects and exchange ideas. She wonders if something similar might not be possible for scientists.

I have regularly found myself thinking about the possibility of a similar gathering for scientists. I wonder – would an international society of Peripatetic Scientists be feasible? What I envision would be a combination of “Science Cafe’” and “Semi-spontaneous field trip” (or even perhaps a “Flash Mob of Nerds”).

I picture groups of scientists, engineers, and other interested people converging on relatively short notice (say, no more than a week or so) to explore something together, whether it’s a section of a national park, or an observatory, or a grocery store, or even to just wander around in a public space discussing some topic. Rather than a carefully planned and organized event where people take turns “giving presentations”, I tend to suspect a more spontaneous exploration by a group of diverse people like this would result in much better horizontal meme transfer potential. It’s so much easier to participate and listen when one isn’t busy focusing on one’s own presentation material…

How many of you reading this might be interested in participating in this sort of thing?
(UPDATE: TO clarify, I mean how many of you, if you heard something like this was happening where you are, would be interested, not how many people are so incredibly impressed by me that they would travel across the world to be where I am…)

Electricity-breathing bacteria! (Microbial fuel cells)

I made a 90-second “pod”cast of why microbial fuel cells work. I don’t yet know if This Week in Science is or was interested in playing it. [Update: this was featured in the November 6, 2007 broadcast! Hooray!] Either way, once I find a way to make it available without killing my bandwidth I shall. I’ll probably do more of them – if nothing else I obviously need the practice.

It was oddly difficult getting myself to actually talk to the microphone – more so than actually publically speaking to real people. I’m not sure why. It strikes me as something I’ll get over quickly once I’ve done it a few times, and my voice won’t sound quite so bland in the future.

In any case, microbial fuel cells are possibly the topic that got me really interested in a college education in applied biotechnology. I’ve been meaning to do a post on why they work for a while, so here’s one, in somewhat more detail than the 90-second audio version.

First, some quick review: We all remember that atoms are made of positively-charged protons, uncharged neutrons, and negatively-charged electrons, right? Protons and usually neutrons in the middle, and electrons hovering around. When atoms chemically react with each other, they’re really just having a fight over who gets to keep the electrons. When the reaction is over, some kinds of atoms or groups of atoms will have gained at least partial custody of electrons that used to belong to some of the other atoms or groups of atoms. The ability of a kind of atom to take electrons away from other atoms is called “electronegativity”. The second most electronegative element in the universe just happens to be a major part of our atmosphere – Oxygen.

As bacteria break down food molecules to get biological energy, there are electrons left over along the way. The bacterial cells have specific carrier molecules that take these extra electrons away, where they can be later dumped elsewhere into any of a variety of other useful biological reactions that need them. The one we’re concerned with today is called the Electron Transport Chain.

In many bacteria, and in the mitochondria of plants, fungi, and animals, the Electron Transport Chain regenerates a huge amount of a cell’s biochemical energy. The extra electrons get sucked into the beginning of this chemical chain, and as they are pulled along, the force of this pull drives a process which regenerates the cells’ main energy-carrying molecule, called ATP. This process is “respiration”, and it’s also exactly the reason you need to breathe oxygen. Humans need so much energy just to remain alive that we couldn’t survive without the huge amount of extra energy that respiration provides.

What drives this whole chain is some chemical at the other end pulling the electrons out. In aerobic organisms, this is oxygen. Some bacteria can use other chemicals, like nitrates, sulfates, and ferric iron (yes, there are bacteria that can breathe rust…) None of these chemicals provide quite as much energy as oxygen does, but it’s better than nothing and gives bacteria that could be damaged by oxygen something to breathe.

Normally, this last step happens inside the cell, but some bacteria have ways of extending this last step so that the final hand-off of the electrons happens outside itself. Some bacteria even make electrically-conducting biological “nano-wires” that this can happen through. Others make “shuttle” molecules that can pick up electrons, dissolve out of the cell, hand off the electrons somewhere outside, and then dissolve back into the cell to pick up more.

Now, we can make a microbial fuel cell. An electrode is put where the bacteria are growing – without oxygen – and a wire runs from this, out of the area where the bacteria are and to another electrode which is exposed to oxygen. It’s like an electric snorkel for bacteria. From the electrode and through the wire, the oxygen sucks electrons away from the bacteria. An electrical device stuck between the ends of the wire can use this energy exactly the same way that it could use the energy from electrons being sucked from one end of a battery to another.

Interestingly, the common “simple stain” Methylene Blue can also act as an artificial “shuttle” molecule. When reduced (carrying extra electrons) methylene blue is actually colorless, and I would swear I’ve seen protocols somewhere that use this to measure just how active a yeast culture is, and one of the demonstration microbial fuel cell setups actually uses a culture of yeast in methylene blue rather than a microbe that can naturally breath through electrodes.

By the way, if you thought you could tell a human from a realistic humanoid robot bent on world domination by the fact that only humans eat, I’ve got bad news for you. One interesting application of microbial fuel cells is Gastrobots. Literally, robots with digestive systems, where bacteria breaking down the contents of the “stomach” act as a microbial fuel cell to power the robot.

I hope you find this explanation useful and interesting. If you have (or even if you haven’t) please let me know. I can’t necessarily tell if I’m doing anybody any good without feedback!

Yatta! I Fail to Reject the Null-Scholarship!

(Oops, got so excited I got carried away with the title. Fixed now.)

I am thrilled to notice this morning that I am in the running for the College Blogging Scholarship, honestly, if this even attracts a larger population of active readers, I’ll consider that alone an excellent “Runner-Up” prize.

Not that the scholarship money wouldn’t be much appreciated…but more about that later.

For the moment though: Hello, current and new readers, to the internet’s self-proclaimed foremost authority on Expired JellO, among other things. I suppose that since I’m asking people to vote for me, I should probably give a quick description of myself and this blog. I’ll keep it short for the moment:

My actual name is Sean Clark; the explanation for the “Epicanis” handle deserves a post of its own. I am a “non-traditional” student at Idaho State University, working on finishing my long-overdue B.S. in Microbiology. This is actually the 5th college institution I’ve attended. It’s not that I’ve been kicked out of the others or anything, just that I keep having to move and start over. I’m finally in one place here long enough to actually finish the degree. Where I end up doing my graduate work depends on where (and if) we end up moving next year – I’ll post about this if anybody’s interested.

My primary interest is in “applied” microbiology, particularly non-medical biotechnology. I’ve been convinced for many years that non-medical applications of microbial biotechnology are underappreciated and somewhat neglected, and I’d rather people not have to get sick before they can benefit from whatever I might come up with…

Incidentally, Hillary Clinton agrees with me (“we should increase investments in non-health applications of bio-technology” – see paragraph 23). Whether that helps or harms my position no doubt depends on your political opinions, but still, I appreciate that someone with some kind of official authority agrees with me. And, hey, maybe this means I’ll be able to find a decent job during or after graduate school. Anybody think the Office of Technology Assessment will be hiring again soon?…

This blog itself is primarily concerned with sharing some of my education, and science in particular, as an exercise in communicating science. I, for one, think I’ve gotten better as the blog has progressed.

A couple of important points: This is a blog, not a magazine: participation is encouraged. If nothing else, the voting for the scholarship looks like it goes on for a couple of weeks, so if you are thinking to yourself “Gosh, I’d vote for you, but you don’t talk enough about X” or “you talk too much about Y” or “I hate the background color of the webpage” or whatever, now’s your chance to speak up. You do not need to be logged in to comment (but I do screen comments, so spammers: you’re wasting both your time and mine), so please do. Also consider subscribing to the RSS feed, found in the upper-right area of the page.

I try to update at least a couple of times each week, though lately I’ve managed to maintain a nearly daily pace. Participation helps here, as comments from readers helps me come up with additional topics to post on. I’m getting a lot of enjoyment out of blogging, so I’ll post as often as I reasonably can…

One last quick note on using this blog: I try to put title tags on most special bits of posts, like images and links. And…bits of text like this, which you might think of as “inline footnotes”. If you hover over anything with that thick-dotted-underline, you should see some additional information. As of a week or two ago, if you click on them, the entire extra text will pop up in a separate box where you can read it all, assuming you don’t have javascript turned off. I haven’t yet gotten around to going back and doing this to the previous bits like this, but I will eventually.

So, again, welcome. Comments, questions, and suggestions will help me improve the blog, and are therefore strongly encouraged. Oh, yes, and please vote for me. Otherwise, I’m going to have to resort to selling blood plasma and begging outside of scientific conferences. Thanks.

Libel! Blasphemy! Slander!…

Injustice! Perfidy! HUMBUG!

Periodically, someone puts up a “could you pass a grade-school science class” quiz. The one linked to the image below goes to one that I just broke down and took, purely out of curiousity. Take a look at this outrage!:

JustSayHi - Science Quiz

Oh, sure, it LOOKS good, but what you don’t see is that it only gave me a 96%, implying that I missed one (it was a short quiz)! Sure, the quiz was very much in the modern fashion for “standardized testing” (aka the “No Child Left Awake” project) where the emphasis is on memorizing stuff for a test rather than actual comprehension. So, I thought, maybe I hadn’t correctly memorized which word was correct for one of the word-memorization questions. But, no, according to the “answer sheet”, the one I supposedly got wrong was this one:

(Note: If you’re planning to actually take that quiz, do so now before you read on and I give away one of the answers…)

“How do mammals respire?”

The options were:

  • Aerobically
  • Anaerobically
  • Both aerobically and anaerobically

Come on, I may hardly ever concern myself with perverse eukaryotic systems but…never mind just “mammals”, as far as I know, all eukaryotes (animals, plants, and fungi) only possess aerobic (oxygen-requiring) respiratory systems.

However, the “answer sheet” for the quiz claims that the answer is “Both aerobically and anaerobically”.

So….they’re wrong. I’m pretty sure what what they were intending to ask, given this answer, is “what kind of metabolism do mammals have?”, in which case their answer is correct.

See, “respiration” is only one part of the cellular energy-generating system. Specifically, it’s our friend, the Electron Transport Chain, which (to grossly oversimplify) harnesses the energy of oxygen sucking electrons off the end of the chain various biochemicals to recharge molecules of ATP. That’s not the only way a cell can get ATP, though. What the quiz authors are presumably alluding to is that there are non-oxygen-requiring biochemical pathways that animal cells can take to make energy – such as the one your muscles use when they can’t get enough oxygen, which involves production of lactic acid, which in turn gets blamed for the “burn” sensation you get when you work your muscles hard.

So, the authors of this quiz are bad, bad people, besmirching my reputation and harming my precious self-esteem by giving me less than 100% on that quiz!

On a related subject: breathing causes cancer in Sprague-Dawley™ rats!

No, seriously, it’s true – try raising one group of Sprague-Dawley™ rats with air, and one group with no air, and examing both populations 150 days later. I guarantee you’ll find many more cancerous growths in the “with air” group than in the group that was denied air to breathe…

What brought this outburst on? It was this blog article. “No, It’s for Real: Aspartame Causes Cancer”, the post proclaims. They’re talking about This study(pdf). Go ahead, take a look, but in particular, look at the tables of actual data, not the paper’s abstract. In particular, take a look at Figure 1, especially “D” and “E” (showing survival rates for the different groups of Sprague-Dawley™ rats as the study progressed), and at the number of “tumor-bearing animals” in Table 2.

Notice that at around 120 days on the survival graphs, the groups with the highest percentage of members still alive were the groups receiving the most aspartame in their feed. It’s worth noting that the highest-Aspartame group there was getting roughly the equivalent of a human drinking <em>thousands</em> of cans of diet soda every day. Also note, in fairness, that both graphs seem to show little difference between the groups, so rather than assuming that Aspartame makes Sprague-Dawley™ rats live longer, I would tend to assume that there’s really not much difference.

Notice also that in terms of the percentage of Sprague-Dawley™ rats that developed one or more tumors, there were fewer of them in the group that got the equivalent of 500 mg/kg of aspartame: which scaled up to human terms means about 200-250 cans of diet soda EVERY DAY worth of aspartame.

You may be wondering why I keep mentioning Sprague-Dawley™. It’s because this is a particular commercially-bred strain of rat that’s popular with labs for this kind of thing. One point that isn’t always mentioned is this: Sprague-Dawley™ rats are known to be prone to developing cancer spontaneously. This can be handy if you’re doing studies of “borderline” carcinogens. The hope is that if something has even a tiny ability to cause cancer, you’ll be able to measure the effect in a population of critters known to get cancer at the drop of a metaphorical hat, when in a human population the incidence might be so rare that you can’t distinguish it from random chance. To my admittedly-not-big-on-the-biochemistry-of-perverse-eukaryotes mind, this study really seems to show that there’s little or no effect – and certainly no dose-dependent effect – of aspartame even on cancer-prone lab rats.

I don’t know what it is, but “artificial sweeteners”, and especially aspartame, seem to generate such passionate hatred in some people. It reminds me a great deal of people’s reactions to “genetically modified” crops. People just really want to hate it. The authors of this paper are obviously trying REALLY hard to show somehow that aspartame is a dangerous poison, despite the inconclusive-appearing actual results. Though I suppose one could argue that they showed Aspartame to be at least as much of a deadly poison as Expired JellO®.

And now that I have exposed my readers to several times the Recommended Daily Allowance of Humbug, I bid you all a good night – I have Art History and Philosophy to attend in the morning…

Environmental Chemistry Field Trip – Day 1, part 3

Overview of Narrow Gauge Spring
Our final destination of the day was Narrow Gauge Spring, which is on the backside of the Mammoth Terraces area. Apparently, there’s only one other place in the entire world – somewhere in China – that has exactly the same kind of conditions as this place.

The process of making this kind of formation requires rainwater, healthy microbe-supporting soil, limestone, and heat. It goes something like this: rainwater seeps down through the soil, where lots of healthy microbial activity uses up the oxygen in it and excretes plenty of extra carbon dioxide into it, making it more acidic. The water sinks into the ground and runs into the limestone, which is Calcium Carbonate (CaCO3). Calcium Carbonate doesn’t dissolve well in plain water at all, but there are two things that make it dissolve better: acid and heat. The heat from the magma under the park and the acidity of the water combine to dissolve a whole lot of the limestone. Then, somewhere, the heated water gets forced back up to the surface through a crack.

Where the water comes back in contact with the air, it can let off the extra carbon dioxide and heat. This doesn’t happen very fast in a deep pool, since this can only happen in a thin area near the top. Where the water overflows, though, it’s very shallow, and the carbon dioxide and heat can escape very quickly into the air. This makes the water suddenly become less acidic and less hot, and all that extra calcium carbonate can no longer stay dissolved. It crystallizes, making a hard calcium carbonate “shell” along the edge of the pool. The edge can end up growing some much over time that it forms an overhang with stalactite-like formations underneath it:

Another view of Narrow Gauge Spring

You can just make out an overhanging area in the upper-left of the photograph.

It was fun taking measurements of the water here. Water freshly removed from a pool initially showed up off the scale on our “Total Dissolved Solids” meters, but if you waited a few seconds the reading would drop down to where the meters could read it, and keep falling. Out of the pool, the water was cooling off quickly enough that the extra dissolved Calcium Carbonate was un-dissolving out of the water in tiny bits even as we stood there.

The water appeared to be about 56°C at the top of the pool where it was initially emerging. If you want an idea of not only that I am a nerd but what kind of nerd I am, I will mention that I think of this as “stewpot temperature”, and often wonder if there is any useful or tasty effects to be discovered in the microbial processes done by thermophilic microbes that live in these conditions. I’ll find out one of these days…

Oh, and a couple of bits of trivia about the Apollinaris Spring area from a couple of posts ago. Firstly, it was apparently named after a spring in Germany with the same name. Secondly, we briefly discussed the chemistry of carbon dioxide in water in class this week, and it turns out that the pH of 5.9 that Apollinaris Spring has is probably more basic than plain distilled water would be.

Now, anyone who’s had basic chemistry is probably a little baffled by this – after all, isn’t a pH of 7 that of pure water by definition? The answer is yes, but we’re not talking about pure water, we’re talking about water exposed to the air, where carbon dioxide can dissolve into the water. Working through the mathematics involved showed that distilled water should end up with a pH of about 5.6-5.7, at least at “standard temperature and pressure” (roughly sea-level air pressure and a temperature of around 72°F.). I have a suspicion as to why the Apollinaris Spring water seems less acidic than I might have expected, though.

They actually took our Apollinaris Spring water and ran it through an analytical instrument of some kind (I wasn’t there for it, but the description of the results made it sound like it was a “liquid chromatography” type of device). They found NO nitrates or nitrites in it. Since we’re talking about spring water percolating through healthy soil, I would have expected some nitrogen. I noticed, though, that although they checked for nitrite and nitrate, they didn’t check for reduced nitrogen – that is, ammonia.

I managed to score a tiny vial of the water during lab last Wednesday. When I get a chance to hit the pet store for some ammonia testing supplies, I’ll check that. If it’s there, it might explain the possibly slightly higher than expected pH. Similar to what happens to carbon dioxide and water, when ammonia (NH3) is dissolved into water(H2O), there tends to be some recombination of the atoms to make “ammonium hydroxide” (NH4OH), which is basic.

I don’t know if that’s what’s going on, but I intend to check.

There’s one more post worth of Field Trip stuff, and then I’ll be back onto other topics. Here’s a hint of what might come up, though: can anybody tell me what the effective pore size of pectin and cornstarch gels might be?…

Environmental Chemistry Field Trip – Day 1, Part 3

There were two more stops on the first day of the field trip. After Appolinaris Spring, we stopped off at the “Sheepeater Cliffs”, named after the local natives’ use of mountain-goats for food. I did get a picture of the small cliff, but who cares. You’ve seen one columnar basalt formation, you’ve seen them all, right?

Oh, well, in case you haven’t seen even one yet, here’s one:

Columnar Basalt Formation: Sheepeater Cliffs, Yellowstone National Park

It’s actually kind of interesting – despite the fact that Yellowstone is essentially one gigantic crater left by a volcano explosion, lava doesn’t seem to be a common feature at all. The reason seems to be that the volcanic explosion was an explosion of steam, not melted rocks. Put simply, water seeps down into the ground and gets trapped on top of magma, which is naturally extremely hot. The water can’t boil away as steam, though, because it’s trapped under all that rock, which keeps the pressure high enough that it stays liquid even when it’s superheated. Then, one day (about 600,000 years ago, if I remember correctly) somewhere a crack opened up enough to start letting the water flow out. When it got out from under all the rocks, the reduction of pressure let the superhot water suddenly explode into a cloud of steam. As the water shot out as steam, it let off some of the pressure on the water still trapped underground, which could then also explode into steam….and the whole area got flung into the air on the exploding, superhot steam. Kind of like the way a perfectly innocent looking bottle of heavily carbonated beverage can suddenly erupt in a spray of bubbles if you open it too suddenly.

Or at least, that’s my I’m-not-a-Geologist understanding of the process. The point is, melted rocks aren’t really a big part of the park area’s surface, so it’s interesting to see the basalt cliffs here. The giant hexagonal columns are actually huge crystals of that formed as the melted rock solidified.

This was just a brief stop, though. We piled back into the field-trip vehicles and headed for the Mammoth area of the park. I was originally going to cram that stop into this post, too, but I’m still editing it down to make it less pedantic. Unless my Vast Horde of Loyal Readers would LIKE pedantic…

Incidentally, the College Blogging Scholarship submissions are done as of midnight tonight. Or midnight tomorrow morning, depending on whether you think of midnight as the end or beginning of a day. Finalists get announced on Monday. Here’s hoping I’ll be one of them. That also means that if anyone has any suggestions or comments about how I’m running the blog, the topics I’m picking, and so on, now would be a good time to speak up…

Meanwhile, a couple more posts on the field trip coming up (possibly another one later today) and then I’ll move on to other topics.