Category: Why Does It Work?

How things work is usually much less interesting than why, in my experience.

Poor-boy science: should I build my own electrophoresis platform?

I want to build my own little electrophoresis gizmo to play with.

I did pick up a small tube of powdered graphite and some liquid tape. With this, I should be able to make a waterproof electrically-conducting glue that I can use for the electrodes. I’ve got numerous old “wall-wart”-type power adapters that I ought to be able to use for power supply.

The main thing I’m trying to work out in my head before I start trying to actually put this together is exactly how I’m going to arrange it so that I can have either a thin gel or a piece of paper or other fibrous material in between the electrodes so that I can best separate things.

I suppose it’s kind of bizarre, but this is actually part of the ongoing Expired JellO® projects. I was wondering to myself what actual changes might possibly occur in a packet of dry gelatin mix over time, and how would I be able to tell?  My previous experiments have shown no indication that there are any easily detectable differences (no obvious changes in taste or texture, no strange eerie glow, no acquisition of superpowers upon eating it…) so I’ll have to look more closely.

It occurred to me that just maybe over time the strands of protein that make up gelatin might get damaged by oxidation from the air in the pouch (or do they seal the pouch in a relatively inert gas, like argon or nitrogen?). This isn’t something one can really tell just by looking, obviously. One MIGHT be able to tell indirectly by making fresh and “expired” packets of gelatin with the same precisely-measured amount of water, poured on at the same precisely-measured temperature, and ideally with the same amount of mixing. Believe it or not, there are actually special scientific devices for measuring the firmness of gels like this. The hypothesis would be that expired gelatin might end up “degraded” into smaller strands of protein than a fresh packet, and that this would be reflected in a reduced firmness of the gel, or perhaps reduced water-holding capacity.

However, I don’t have access to precise devices for measuring things like that, and in any case since I suspect the difference would be pretty minimal, I’m not sure any difference in firmness would really be detectable with any kind of instrument I could cobble together on my own. What to do?…

I thought that if I had a way to subject a sample of dissolved gelatin to electrophoresis, I could then use a protein-staining substance to see how broad of a range of protein-fragment sizes were existent, or perhaps even spot distinct fragments if oxidative damage tended to happen at the juncture between particular amino acids or something.

I’m not quite sure why, but I have a strong desire to do this experiment from scratch as a “hillbilly biotech” exercise (including building the equipment and obtaining my supplies from grocery or hardware stores rather than specialty scientific supply places).

There are special protein staining compounds I can use at the end to see where my bits of protein ended up after electrophoresis. “Coomassie Brilliant Blue“, for example, but they don’t have that down at the grocery store. (And if you think that’s a funny name for a dye, consider “Light Green SF Yellowish”…)

Then, I ran into a post indirectly about henna over on scienceblogs.com. It seems the natural orange-staining ingredient in henna, called lawsone, may be specifically a protein-staining substance. I’m not certain about this, but a dark-orange protein-staining dye would work for my purposes I think. If so, that solves my need to get a protein stain from an ordinary store.

It’ll be a little while before I can try to put this plan into action, but I think I’ll be able to get to it in the next month or two.

In other news, I think I’ll try to post my “Microbial fuel cells in 90 seconds” audio sometime tomorrow. Then I can work on more. Anybody want to hear me attempting to explain something in 90 seconds? So far I’ve considered MRSA, and perhaps how cow flatulence threatens the world’s climate (which is also a microbiological topic). I’m sure there must be plenty of other possible topics. Any suggestions?

P.S. Who wants audio in Ogg Vorbis format in addition to mp3?

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!

Stir-fried random…

Just a few brief random comments for the moment:

  • Am I the only one who is already completely sick and tired of the word “spooky”?
  • I think I’ve figured out what Descartes’ problem is. He’s gone on this meditation where he’s convinced himself that as far as he knows, nothing exists…except for himself. I think what happens next is that he gets horribly lonely, so when he realizes that his thoughts also exist with him, that’s when he developed that unwholesome passion for them and inability to bear leaving them that I’d previously mentioned. “But what kind of thing am I? I’m a thing that thinks. A thinking thing is what I am. But what kind of thing is that? Oh, yeah, I already said, it’s a thinking thing. Did I mention I was a thinking thing that thinks thoughts?….”. Okay, Descartes, we got it the first time…
  • One of my fellow “college science bloggers whose obscurity currently keeps them low in the vote totals” actually has a pretty neat blog. The Biourbanist focusses on features and attributes of urban areas. Well worth adding to your RSS feeds, I think. After you’ve already voted for me, of course…
  • I am currently attempting to put together my first netcast, in which I shall attempt to crunch an explanation of why microbial fuel cells work, in a form hopefully comprehensible to anyone with a good junior-high-school science education (or a mediocre high-school education, which is probably sadly more common), that fits into 90 seconds. Wish me luck.

More to follow…
UPDATE: Got the “pod”/netcast done – a real blog post on the subject of Microbial Fuel Cells to go with it may be found here tomorrow (Tuesday, October 16th) sometime, so long as nothing unexpected happens…

“Dog Philosophy”

But first, a quick request for information for anyone who happens by: where you live, what is the job market like for Ph.D. Geologists (with a background in stratigraphy, mining, and petroleum, among other things) and what kind of opportunities for non-medical biotechnology graduate programs are in your local colleges?

(And a quick side-question: is it obvious to most people that you get extra information if you hover over or click on things that look like this? I’ve never formally checked the usability of this trick for normal people…)

No login required to answer – they’ll appear as soon as I’ve filtered out any spam. Okay, on with the meat of this post.

In case anyone’s wondering what the “Epicanis” handle is all about: it’s a pun on the concept of “Dog Philosophy”, based on the name of the famous Greek philosopher “Epicurus” and the word “Canis”. Yes, I know, “Canis” is Latin, not Greek, but I figured “Epicanis” would be more a more recognizeable pun to most people than “Epicynus”.

Properly defining “Dog Philosophy” involves a joke which necessarily incorporates mild profanity and adult situations. In case any of the readers are of more delicate sensibilities, I present instead a more matter-of-fact (but sadly less funny) version.

Plato once famously wrote that dogs were philosophers. Like all philosophers that I know of, dogs consider the nature of what is real (metaphysics). To the dog, everything that exists external to the dog can be assigned to one of four categories:

  • Food
  • Toys
  • Companions

    • and

  • Everything Else, which is generally useless except as a surface for territory marking

You may wonder what that has to do with “Applied Empirical Naturalism” or science blogging.

The explanation is simple: science is fundamentally a method for examining the natural world to determine how and why it works. That’s what I like about science. One can find novel or unexpected applications of any system or thing by learning how and why they work, or in other words, it’s a method for, among other things, taking things from the “useless” category to one of the “useful” categories. Finding ways to make otherwise-useless things beneficially useful for people strikes me as a particularly rewarding purpose in life.

In addition to wanting to make the world a better place, I’m also kind to puppies and kittens and I think people should be nicer to one another.

(This shameless display of sympathy-solicitation has been brought to you by my participation in the following competition:)

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.

Environmental Chemistry Field Trip – Day 1, part 1

I can think of a number of things to complain about with regards to living where I do. However, it is nice that we live near enough to Yellowstone to day-trip there. In fact, it’s close enough for my local college to take field-trips there – which we did.

Environmental Chemistry spent the weekend there, examining the area, discussing the chemistry of the natural waters and geothermal features, and collecting samples (yes, we had a permit for this…).

We started with a stop by the side of the Madison River to collect a sample of the surface water. Clear, cool (12°C, or about 55°F), mildly basic (pH of about 8.0), and a TDS reading of about 300ppm, which is roughly the same as mildly to moderately hard tapwater, I suppose.

sampling water from the Madison river

The sampling device -seen being hurled over the water here – is kind of interesting – it’s a hollow tube (a bit of plastic pipe) with two spring-loaded balls that slam shut on either end to trap the water inside when you tug on the string. That lets you throw the device out and trigger it when it gets to the precise spot that you want to take a sample from.

We made a brief stop at Beryl Spring afterwards. We didn’t do any sampling here, but we did talk about acid-sulfate water systems. “Reduced” sulfur – as Hydrogen Sulfide gas – comes boiling out from underground along with steam, and ends up being oxidized by oxygen from the air to become sulfate in the end – combining with the water and forming sulfuric acid.

Sulfur-encrusted pipe at Beryl Spring

Of course, it doesn’t go from sulfide to sulfate all at once. There’s a stop along the way as elemental sulfur. The whitish-yellow stuff here is crystals of elemental sulfur. The black stuff you see is…also crystals of elemental sulfur. The difference is just how the atoms of sulfur collect together. The black form is actually a little less stable than the yellow, so it tends to form first, but then slowly convert to the yellow form over time as the sulfur atoms settle into a more stable arrangement. Being a chemistry class, we didn’t really discuss the possible microbial activity that might be involved here. Note the small patch of dark-green there. I suppose this could be a “Green Sulfur Bacteria“, which does something like photosynthesis except that it makes sulfur instead of oxygen in the process. These are normally anaerobic but perhaps the concentration of hydrogen sulfide (H2S) and carbon dioxide gas coming out of the ground right there is enough to crowd out the oxygen. Alternatively, it could just be a heat-loving cyanobacterium or something.

I really wish I wasn’t too poor to buy a good field microscope to go along with the good lab microscope that I am also too poor to buy…

The last two stops of the day – Appolinaris Spring and Narrow Gauge Spring – will be in the next post…

Expired JellO®! Flee! FLEE FOR YOUR LIVES!!!!

Expired JellO®! Deadly Poison, or Merely Debilitating? Can a human being withstand the toxic load of an *entire box* of it? Would he suffer embarassingly loud and messy gastrointestinal distress, or would immediate organ failure set in before this could take place? STAY TUNED TO FIND OUT!…

Yes, loyal readers, as I type this I have subjected my own body to unthinkable risks to answer these very questions. That, dear readers, is how much I care about your health and welfare. You can thank me later…

…If I survive!

What does it mean to be an “Applied Empirical Naturalist”, anyway? As a naturalist, I look for natural explanations for natural observations. If I survive this ordeal, I will not explain it as being due to protection by supernatural forces, and conversely if I end up confined to an intensive care unit, my body ravaged by Expired-Gelatin-Syndrome, I will not seek to explain it as divine punishment for violating Kosher. As an Empirical naturalist, I investigate things by actual observation and direct testing wherever possible, rather than purely philosophical means. And – particularly important to me – Applied Empirical Naturalism is intended to convey that I am primarily interested in investigations with practical uses. Discovering the “Pineapple-Upside-Down Quark” with an umpty-brazillion-dollar particle accelerator and six months of supercomputer time to crunch the data wouldn’t do me, personally, much good. Knowing whether expired JellO® is safe to eat or not, however, has obvious practical application. Especially considering that I seem to have about 5 more boxes of the stuff in the pantry.

So, here I sit, perhaps writing my very last words ever before Expired-Gelatin-Shock causes my brains to swell up and explode messily and fatally from my ears like the popping of two superintelligent zits, in the service of Science. Here, then, is my story.

I begin by building my dire experiment around the following excessively-formal Valid Argument:

Upon expiration, JellO® becomes a deadly poison which causes great harm to those who dare ingest it
I prepare and consume an entire box of expired JellO®
Therefore, I suffer great harm due to its ingestion.

Last night, I plucked from the depths of my pantry an expired-2½-years-ago box of sugarless orange-flavored gelatin with which to begin this investigation. I blew the layer of dust off of the box, and carefully opened it, half-expecting to find some strange mutant gelatin-beast had developed in it over the years since expiration. One hand poised to protect myself should the creature leap from the box to eat my face in anger of being disturbed, I was both relieved and slightly disappointed to find nothing more than a foil packet containing what sounded like perfectly ordinary gelatin-powder. The packet proved to be intact, and the happy orange powder poured into a freshly-cleaned dish in a manner perfectly imitating that of wholesome non-expired gelatin. I dismissed the faint demonic snickering sound I seemed to hear as a figment of my fevered imagination and prepared the gelatin powder in the usual manner.

I took up my electric kettle, containing distilled water, and threw the switch. Seconds passed into minutes. Minutes passed into more minutes. Then, the water began boiling vigorously, and I applied one cup (8 fluid ounces) of this to the dish of powder, stirring it with a tablespoon. It seemed to take at least two minutes of continuous stirring, but the deceptively innocent-looking powder finally dissolved without the slightest scent of brimstone. As prescribed by the instructions on the box, I added a further 8 fluid ounces of cold water (from the tap of my kitchen sink), stirred briefly to mix, and placed the dish in the refrigerator to gel overnight.

I lay awake in bed for hours, wondering if I was doing the right thing. Was I insane? Did I not remember the tales of Jeckyll and Hyde? Of Doctor Frankenstein? Of Pons and Fleischman? What horrible fate was I setting myself up for? Finally, I dropped into a fitful slumber, disturbed only by dreams of amorphous orange demons stalking me to feast upon my soul…

Day broke, and this very afternoon I took the now solidified mass from the refrigerator. This was it. My last chance to avoid whatever hellish abuses this disturbingly orange substance had planned for me. But no…it was far too late to turn back now. I took up my spoon, and devoured every last bit of happy orange jiggliness.

This was approximately seven hours ago. In the intervening time, I have experienced the following symptoms: Occasional thirst, mild generalized anxiety about the near future, hunger, and an urge to write this blog post in a hyperbolic language more suited to an H.P. Lovecraft story than a scientific report. In other words…I appear to have been entirely unaffected, despite consuming an entire box of expired gelatin.

I’ve been taught that when hypothesis-testing, one considers the “null hypothesis”. That is, the hypothesis that would falsify the one that I’m starting with. In this case, it would be something to the effect of “I will suffer no harm whatsoever from eating expired JellO®”. Given the results in this experiment I must – in the tortured language of philosophical science – “fail to reject the null hypothesis”, because my results show no evidence whatsoever that I have suffered harm from eating expired gelatin. In other words, I cannot rationally cling to my original hypothesis as written, and must confess that perhaps expired instant gelatin still in intact packaging may, in fact, be harmless.

Ah, but I know what happens now. “Cad!”, you cry! “Fraud! Sham! This experiment is, like, totally bogus! This is not normal JellO® but a sugar-free impostor! And furthermore, this isn’t even JellO®-brand gelatin, but a cheap knock-off brand! How dare you, sir, feed us this crap, which proves nothing!”

I answer in two parts: Firstly, ladies and gentlemen who are my readers, I assure you that the contents of the less-famous brand and the official Kraft® Foods brand are essentially identical, and indeed, might conceivably have come from the same source. It’s common practice for one factory’s product to be shipped to multiple sellers who each offer it under their own label, as the wide variety of affected brands during the recent “salmonella peanut butter” scare demonstrated. And secondly: as it happens, I also have in my possession a box of JellO®-brand lime-flavored gelatin, WITH sugar, which although it lists no obvious “expiration date”, has a code stamped on the box indicating that it was originally packaged in late 2003, and therefore should have exceeded the expected 24-month shelf-life about the same time as today’s test subject did. I swear to you, dear readers, that I will repeat my experiment with this sample next.

Stay tuned: “Expired JellO II: Lime’s Revenge”, coming soon to a blog near you!

UPDATE: The Expired JellO® Saga continues here!

What I Learned In School: “Valid” arguments

The new semester has begun on this, my last schedules semester as a mere old Undergraduate. This semester’s primary purpose is to fill in the two vitally important “general education” goals for my current Institute of higher learning: Art Appreciation and Philosophy.

I added a “What I Learned in School Today” category to the blog just because of this semester. My loyal readers (all 2-4 of you…) can look forward to occasional posts on other aspects of my Higher Education as the semester goes along, besides microbiology. On the metaphorical menu over the next 16 weeks: “Introduction to Philosophy” (today’s topic), “History of Western Art“, Applied Calculus, and finally I have a chance to take Environmental Chemistry.

Prior to reading some Plato for next week, we started out “Philosophy 101” with a discussion of “Valid” arguments. In Philosophy, this has a very specific meaning. If you make an argument in the general form of “This, and that, therefore something”, the argument is “valid” when if “This” and “that” are both true, then “something” must also be true.

The thing that most of the class seemed to have trouble with is that being “valid” has nothing to do with whether or not the argument is “sound“, or whether the statements in the argument are true.

An example from the class:

All mammals have lungs.
Whales have lungs.
(Therefore) all whales are mammals.

This is an invalid argument, despite the fact that every statement is actually true. The reason is simply that the fact that whales are mammals does not automatically follow from the fact that they have lungs. (Chickens have lungs, too. Does this mean chickens are mammals?…)

It took two class sessions before most of the class seemed to “get” this. I felt as though I was in Junior High again…though I think this had more to do with watching the freshman girls in front of me passing notes during the class. Come on, kids, grow up! We adults are using IM for that now! Sheesh. Kids today…

On the other hand:

You’ve got to be some kind of genius to attend college and blog at the same time.
I attend college and I blog at the same time.
I am, therefore, a genius.

is a valid argument. As written, if both of the first two statements are true, then the third statement must be true. This is where the value of valid arguments come in – if it turns out that the conclusion is false, then one of the premises must also be false. If anyone were to discover that I am, in fact, not a genius, then either it’s unnecessary to be a genius to blog and go to college at the same time, or perhaps I’m paying someone else to write this stuff for me.

Who cares, I’m a science major, not a philosophy major, right? Except: a properly designed scientific hypothesis should be a premise in a “valid argument”, and an experiment is merely a test to see if the argument is unsound. For example:

All lactic acid bacteria, grown in otherwise sterile milk, will make yogurt.(the underlying hypothesis being tested)
I inoculate sterile milk with a culture of Pediococcus damnosus(the test performed by the experiment)
(Therefore) I obtain yogurt. (Expected results and conclusion of the experiment)

This is (as far as I can tell) a completely valid argument. Now, I haven’t actually done this experiment, but let’s pretend I did, and the end result was a smelly mass that kind of looked like yogurt except it turned out to be slimy rather than firm. I cannot in fairness call it “yogurt”, so my conclusion in the argument is false. Thanks to the magic of Valid Arguments™, I know that either my assumption is wrong (maybe not all lactic acid bacteria turn sterile milk into yogurt after all), or there was a problem with the experiment (perhaps the milk was contaminated with something and wasn’t really sterile, or I grabbed a culture of something other than P.damnosus by mistake.)

Assuming I carefully recheck the materials and repeat the experiment to confirm that I really am inoculating actually-sterile milk with a definitely clean culture of P.damnosus and continue to get the same results, then my hypothesis – the first premise in the argument – must be false. I have to then go back and revise my hypothesis and test again, until I have a hypothesis that seems to consistently generate true conclusions. Thus, the “valid argument” is the basic tool which allows hypotheses to grow up and become theories.

Incidentally, some Pediococcus damnosus strains are a cause of “ropy” wine, which is why I chose that example. I don’t actually know what, if anything, it would do to pure, sterilized milk, though.

Coming up next: I picked up a 100-year-old microbiology book while on vacation!