Tag: science

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.

The Unbearable Limeness of Being

I awaken. Am I alive? The temperature is neither extremely hot nor extremely cold, so I’m apparently not in some punishment-afterlife. And there’s no beer volcano or stripper-factory, so this obviously isn’t heaven. On the other hand, I am experiencing the usual persistent discomfort involved with waking up early in the morning. On the assumption that Catholic “purgatory” would be more dull, I will assume I am still alive, and had better get up and get to class.

Since my previous experiment, I have obviously had to revise my original hypothesis. Since the last caused me no ill effects, I had to abandon the notion that expired gelatin products become a deadly poison. Instead, as I consume this batch of official, non-sugarless Jell-O®-brand Gelatin (Lime flavored), I operate on a new hypothesis:

“Expired instant gelatin products from intact packaging will not harm me if I eat it.”

My precious stock of expired JellO® is depleted by one more box, the packet ripped from its cardboard sarcophagus, the contents prepared according to the standard instructions, and consumed hastily last night (the animation from the previous post is the actual container of prepared Lime JellO® made from digital photographs taken between helpings.). You can see the old-style date code on the box. According to Carolyn Wyman’s “JELL-O: A Biography”, the code indicates that it was packaged in 2003 (the “3” at the beginning of the code), on the 343rd day of the year, in the San Leandro (California) packaging facility. Although there is no official “expiration date” shown, given the “expected shelf life” of 24 months, this package is approximately 2 years out of date. And I ate it. I appear to have suffered no ill effects. Not even a decent sugar-rush: the entire box contains 320 calories, barely equivalent to a package of Twinkies®. The flavor even appeared to be perfectly normal. Mmmmmm, Lime JellO…

When I took it out to eat it, I did spot a beautiful if alarming sight, though:

The crystalline-appearing sheets of growth from the edge of the bowl into the gelatin was slightly disturbing. Was I crystallizing something odd out of the gelatin/sugar/flavor solution? The growth resembled infiltration of mold into the gelatin medium enough to slightly worry me. But only slightly.

In fact, as I had most suspected, these turned out to be ice crystals. Quite pretty, but they started slowly melting away after the bowl was allowed to sit at room temperature for fifteen minutes or so – plus, they crunched when I ate them just like ice. Thus encouraged, I ate the gelatin and went to bed. And here I am (sitting in the student lounge between “History of Western Art” and “Introduction to Philosophy”) happily blogging away, apparently unharmed.

Does this prove that expired instant gelatin is harmless? Well, no, not exactly. Scientists never really “prove” anything. Instead, we attempt to “falsify” our hypotheses and theories as best we can. This is where the concept of the “null hypothesis” comes in.

The “Null Hypothesis” here is the situation that, if true, falsifies my hypothesis. In this case, it would be “Expired instant gelatin products from intact packaging will harm me if I eat it.”. However, I did eat expired gelatin products from an intact package and was NOT harmed. Therefore I must “reject the Null Hypothesis”…and therefore my experimental evidence does not fail to support my hypothesis! SUCCESS!

If we are unable to find a condition which renders our hypothesis or theory incorrect after many and varied tests, ideally by several different researchers, then we can be confident that our hypothesis or theory is correct, but we don’t necessarily KNOW that there isn’t some odd undiscovered exception that we don’t know about.

Two samples (this one and the previous sugarless-orange one) is hardly a large number of trials. This doesn’t prove that expired JellO® is always safe, but since I know of no plausible way by which an intact package of instant gelatin could become hazardous I feel pretty comfortable that expired gelatin from intact packaging won’t harm me.

If the package is not intact and contains a fuzzy green lump instead of the usual powder, then it’s a whole other situation, obviously…

I do still have three or four more boxes of the sugarless generic expired gelatin – perhaps I can come up with some more tests. Meanwhile, I do hope that my incredibly brave, life-threatening experiments here will relax nervous expired-JellO eaters everywhere…

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!