Category: Grossly Oversimplified Science

Extra-simple explanations of natural phenomena

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official “expiration date” shown, given the “expected shelf life” of 24 months, this package is approximately 2 years out of date.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…

Okay, this is completely bogus…

The folks over at BBspot are callously spreading microbiological misinformation (click for full-size):

This is just plain irresponsible and utterly wrong. Surely everyone can see the obvious problem here, right?

When this happens, the flame is blue, not orange.

Uh, or so I’ve heard.

(If it isn’t obvious – what you do in this situation is calmly take the spreader out and set it on your nice, flameproof benchtop, and set something non-fragile and non-flammable on top of the flaming jar of alcohol, which will then go out quickly as the oxygen gets used up. All the labs I’ve been in lately use “canning” jars for the alcohol in this application, complete with lids which can be set on top to extinguish the flame.)

“Teh Deth Kitteh!”

Run! Itz teh Deth Kitteh!

The prestigious New England Journal of Medicine reports (Dosa, DM: New England Journal of Medicine; 2007; 357:4; pp 328-329 ) on the case of a single eukaryotic organism – a specimen of Felis catus – who is reported to identify People Who Are About To Die (insert ominous thundercrash here).

It is presented in a tone that is a mixture of “OOOo, spooky, mysterious!” and standard issue “Human Interest Story“, as though it was a baffling or unexplainable phenomenon. Honestly, didn’t modern science explain this long ago?

Obviously, Oscar the Cat is simply waiting around to devour the souls of the departed as they are exhaled on the last breath. Or as “Mike, the Mad Biologist” puts it:

Shouldn’t the situation be obvious? I mean, come on, did ALL of these journalists sleep through Biology 101? Even if they did, surely at least some of them own cats and already know about this….

There are, of course, numerous examples in the scientific literature documenting the tendency of the cat to steal the breath of the living. See, for example, Bener A, Galadari I, Naser KA.”Pets, allergy and respiratory symptoms in children living in a desert country”;Allergie et immunologie;1995 Jun;27(6):190-5…

Interestingly, as I was trying to find a more explicit reference in PubMed to this folk-belief, I ended up stumbling upon an article entitled “Micturition and the Soul” [Holstege G.”Micturition and the Soul.” J. Comp. Neurol. 2005 Dec 5;493(1):15-20.]. I love browsing databases of scientific papers. Where else could you go looking for a folk belief and find an article about the neurology of peein’?

I know I don’t normally discuss freakish, perverted Eukaryotes on this blog – hey, CHILDREN could be reading this! – but I found the article (and the responses to it) interesting, and it serves as filler until I can finish putting together my “Gram Stain Article To End All Gram Stain Articles” post.

Search Queries That Came To This Site, Part 2: Odd but coherent

There have been a few queries that somehow led to this blog which weren’t actually bizarre, as such, but which were kind of unexpected…

Someone in Maryland was trying to find out “why does alcohol rub work?”, for example. The answer is, it’s a “counter-irritant”. The effect is somewhat similar to rubbing a sore spot, stretching a sore muscle, or scratching an itch. The mild “burning” of the alcohol helps deaden the soreness. Beyond that, it’s some medical/physiology-of-freakish-gigantic-multicellular-eukaryotes thing, so I’ll defer a detailed explanation to someone who’s more of an expert on such things.

Someone in New Jersey wanted to know “what does a gram of nutmeg look like”. Well, I’ve never actually measured it but I’d guess a gram of ground nutmeg is probably about half-a-teaspoon of coarse (sand-grain-sized) light-brown-and-tan bits.

Pakistan wanted “total molecules of universe”. Doesn’t everyone know this? It’s exactly 2.379×10some-really-big-number. To 4 significant figures, of course. Oh, and the last digit of pi is “3”.

Colorado (I think) consulted the oracle of Google for “Why does immersion oil work”. It’s a refraction thing. Simplistically, when light goes from one substance to another – like the glass of the slide, to your sample material, to the air, to the objective lens of the microscope – it’s direction gets bent slightly. Different substances cause a different amount of bend. The immersion oil causes less bend than air does, and when you’re operating at really high magnification, it’s important to keep as much of the light as possible getting into the lens of the microscope instead of ending up “bent” away from it. Unless I’ve badly mangled my understanding of it, this is also part of why the light in the microscope seems to get dimmer as you increase the magnification.

Possibly from Florida came a query on “Scientific How Enzymes work to get stains out of carpet”. Even more simplistically than the previous explanation: Everything wants to fall apart, but is usually too lazy to just do so, so a little bit of extra energy (the “activation energy”) needs to be added to push-start it. Enzymes are catalysts – they each make a specific kind of reaction able to happen with less activation energy. If the enzyme is good enough, you reach the point where the ordinary ambient heat supplies enough energy to get things going – like breaking down those large, ugly, dark-colored chunks of protein and stuff in stains into smaller, invisible bits.

California asked Google about “eugenol clove isolation”. I suspect that if you want some kind of extreme high purity thing, you might be better off just approaching it as an Organic Synthesis problem. Otherwise, why cut out any other components of the clove buds that may add subtle flavors to the mix? If you’re just trying to separate the clove flavor from the chunks of dried evergreen-bush-flower-buds, though, there are a few ways to do it. Eugenol’s a phenol-like compound, and it’s soluble in ethanol. Go to the local liquor store and buy some vodka or EverClear™, soak the clove buds in it for a while, and pour it off. You could conceivably also try distilling it directly from the buds, as some people do to extract perfume oils from flowers.

Luxembourg sought “+homebrew +LED +Flashlight”. If anybody’s interested in that, it deserves a separate post, but it’s pretty easy. I’ve been planning to make an infrared one to do some IR digital photography, and to modify an 8-white-LED flashlight to turn it into a UV flashlight anyway.

Somewhere in Michigan, some concerned soul wanted to know “does beer have red dye in it”? Well, I’d argue that definitely, no real beer does. It’s possible that some mass-market commercial swill does, though I suspect even then it might only happen as A)a ‘novelty’ beer (like Green beer on St. Patrick’s day) or B)places like China or any other country where there seems to be a lot of unnecessary prettification of alleged foodstuffs. Now, I’m no Rheinheitsgebot zealot or anything, but beer ought to at least be reasonably “natural”…

There were a couple of queries on why Bunsen burners work, for some reason. Well, they’re essentially just tiny little carburetors for making variable flames instead of feeding a combustion engine.

Someone in Ghana wanted to know “How to make something disappear scientifically?”. Well, you can’t. But you can change something into something else. You can’t (scientifically speaking) make water disappear, but you can turn it into a gas by heating it. You can’t make oxygen gas “disappear” but you can combine it with hydrogen so that you end up with water but no molecular oxygen gas. And so forth.

Illinois wanted advice on “what to cook when you are bored and sick”. I think it depends on what kind of sickness you’ve got and how soon you expect to recover, and whether you’re cooking because you’re bored or specifically because you want something to eat that won’t make you feel sicker. Make some yogurt. Bake some bread. Or mild ginger cookies. Or make some “Jell-O™” (or other brand of instant-flavored-gelatin, for that matter). All easy to digest stuff. Or, you could make some Pepto-Bismol™ Ice Cream

Texas wanted to know “Food science- why chill the dough”. The details depend on the context (cookies? Pie crust?) but generally it seems to be to make sure the fats in the dough stay solid. In pie crust, chilling the dough makes sure the bits of butter or lard stay chunky instead of getting spread evenly throughout the dough – when they cook and melt, this leave little areas in the dough that aren’t solid, making the crust flaky. In cookies, this might help keep the dough from flattening too quick when you cook them.

Hmmm. More of these than I realized. For tonight I’ll stop on this one: Pennsylvania was trying to find out: “what does the Giant Microbe factory look like”? I don’t actually know the answer to this one, but since the Giant Microbes headquarters looks like it’s just an office in an office building, they probably contract out to someone else to actually make the giant plush microbes. I’m guessing they probably renew their contracts every so often, and maybe shop out different runs to different factories, so there isn’t necessarily a single “Giant Microbe” factory…

I suppose that’s enough for one evening. I’ve really got to catch up on my sleep…

Poisoning Prokaryotes in the Park

(Well, okay, it was a “Pathogenic Microbiology Lab”, not a “Park”, but whatever).

Antibiotic Susceptibility of a Poor, Innocent Microbe

Objective:Experience the awesome power of the mighty Antibiotic Susceptibility Test, wielded against an unsuspecting bacterial organism!

Introduction:

Every day, billions of innocent bacteria are ruthlessly slaughtered by antibiotic substances introduced into their callous, inconsiderate hosts. Condemned to death as nuisances due to nothing more than the potential inconvenience of debilitation, tissue necrosis, death, halitosis, and other minor problems, the unstoppable might of all medical science is focussed on our prokaryotic friends like medical professionals around the world focussing the rays of the sun through a thousand magnifying glasses to obliterate innocent prokaryotic “ants”.

The ?-lactam antibiotics – the blahblahcillins (Penicillin, Ampicillin, etc.) and the Cefablahblah compounds (Cephalosporin, Cephalothin, Cefuroxime, etc.) all interfere with the formation of the bacterial cell wall – loosely analogous to the human epidermis. This treatment viciously targets the hardest-working, actively-reproducing bacteria, spilling their guts as they attempt binary fission, while leaving the lazy, dormant microbes alone. Gram-negative bacteria are somewhat protected from this torture by their outer membrane, but some (such as ampicillin) can affect even some of them. Gram-positives, with their simple structure, are hardest hit. A few microbes have learned to counter this by secreting an enzyme which disables many of these drugs, though medical science has countered with clavulanic acid – an inhibitor of the ?-lactamase enzymes. Enzymes resistant to inhibition by clavulanic acid are being developed as part of this continuing arms race.

Chloramphenicol is an artificially manufactured bacteria-poisoning chemical synthesized in laboratories (though it was originally obtained during interrogation of a captured Streptomyces species) which interferes with protein synthesis at the 50s ribosome. Erythromycin has the same affect, by a slightly different mechanism, and is a macrolide – a class of large molecules with lactone rings which resemble in shape the poisoned ninja throwing-stars seen in movies. Both of these chemicals are bacteriostatic rather than bacteriocidal, but are broad-spectrum. Chloramphenicol’s devious action sometimes backfires on a small number of people, causing potentially fatal aplastic anemia.

The Sulfonamides are also bacteriostatic, and are competetive inhibitors of enzymes that convert the nutrient PABA into biochemical products vital for prokaryotic health. Much like a hypoglycemic person with diarrhea given a “cupcake” made entirely out of Olestra® and Sucralose, the microbial victim of this chemical ingests it but finds that it merely inconveniences the metabolic processes rather than feeding them.

Tetracycline (the first of the Tetracycline-type antibiotics) and Tobramycin (an Aminoglycoside) both jam the gears of protein synthesis, inhibiting the action of the ribosome in the former case, and actively causing erroneous protein formation in the latter. The latter effect is outright bacteriocidal, causing the poor bacterium’s protein assembly systems to make broken enzymes until the cell’s protein factory is bankrupt and has to lay all the enzymes off. Tetracyclines appear to only slow down the cell, but in the cutthroat competition for cellular activity in the human body, this stumbling can be a death sentence for the business of prokaryotic replication.

In order to determine which of these lethal agents to deploy against the oppressed bacteria, a medical professional may capture a microbe and torturously test various agents on it, watching without emotion to see which ones destroy the microbe most efficiently. This awful, coldly clinical process is standardized in the Medical Microbiologist Field Manuals on Interrogation as the “Kirby-Bauer”[1] antibiotic susceptibility test. In these tests, 6mm diameter paper disks soaked with various antibiotics in specific amounts, is pressed onto a growing young microbe culture to see which ones are most destructive, leaving desolate areas devoid of life in the culture…

Recently, we got to do this..

Materials and Methods:

A colony of Pseudomonas aeruginosa was lured into a culture tube with the promise of free candy. Happily replicating, this culture was transported to a secret location containing Mueller-Hinton agar. 100?l of this culture was told that it had won an all-expense-paid stay at a four-star hotel with room-service, and was plated onto the agar. The culture was then strapped down and tortured for its secrets by application of 12 antibiotic-soaked disks. The torture was performed at 37°C for 24 hours, and the results measured with a ruler.

Results:

The defiant Pseudomonas organism bravely withstood the application of Ampicillin, Cephalothin, Chloramphenicol, “Triple Sulfa”, Nafcillin, Cefazolin, Amoxicillin with clavulanic acid, Cefuroxime, and Penicillin G. Erythromycin seemed to cause the subject some discomfort. It was not quite able to grow to the edge of the antibiotic disk all the way around but was able to get within less than a millimeter of it, even touching it in a few spots. Tetracycline was unbearable to the subject, who was limited to a 11mm (diameter) zone of inhibition around the Tetracycline-containing disk. Finally, Tobramycin (zone of inhibition approximately 23mm) finished breaking of the subject, who then confessed to several murders of immunocompromised individuals, robbing a “Wal-Mart”, and once molesting an archeaean of the genus Thermoplasma. Investigations may already be underway to determine the authenticity of these confessions. Then again, they may not.

Conclusions and Discussion:

Pseudomonas aeruginosa is a hardy little bugger who can put up with a wide variety of antibiotic insults. Its weak point appears to be its ribosomal machinery, as this was the target of the three drugs which had any apparent effect. Should intelligence indicate the threat of attack by the terrorist Pseudomonas organization, ribosome-targeting, protein-synthesis-inhibiting agents should be deployed as a countermeasure.

References:

[1] – Bauer AW, Kirby WM, Sherris JC, Turck M, “Antibiotic susceptibility testing by a standardized single disk method” Am J Clin Pathol. 1966 Apr;45(4):493-6

[2] –Tortora GJ, Funke BR, and Case CL, “Microbiology – An Introduction (sixth edition)” 1997, Benjamin/Cummings Publishing Company, Menlo Park, CA

The “Electron Transport Chain”, Grossly Oversimplified

Why does breathing work, anyway? And can I possibly explain it in a couple of paragraphs? I don’t know, but I’m going to try…it leads into the subject that got me interested in majoring in Microbiology in the first place. It’s probably kind of foolish to try to cram in this explanation in the half-hour or so before midnight (and hence the informal deadline for getting a post up every day for “Just Science week”), but here goes:

First, a bit of really simplistic background. Since the fundamental principle of the universe is basically that stuff likes to fall apart (dang lazy molecules), in order for a cell (bacterial or otherwise) to make new proteins and strands of DNA and so on, it has to have some kind of energy that it can use to pay for the increasing orderliness that it’s causing. The chemical that’s usually used to provide this energy is ATP. The energy comes from a string of three Phosphate (PO4) groups that are attached to it. The third phosphate in the chain comes off really easily, releasing a bit of energy in the process, like a spring uncoiling. A lot of enzymes work by attaching to ATP, letting ATP fall apart (becoming the slightly more “relaxed” ADP in the process), and using the released energy to power some other process.

In order for this to work, the cell has to be constantly re-charging ADP, cramming that third phosphate back onto the end along with putting back the bit of chemical energy.

The point of this post is a major way that cells provide the energy to reassemble ATP. There are actually a number of ways, but one of the more effective is the “Electron Transport Chain”.

In simple terms, the cell takes an electron from a simple “food” molecule of some sort, and passes it along to a type of protein that reaches through the cell’s membrane. This protein passes the electron along to another protein, but in the process, it goes through a series of changes in shape that allows it to pump a few hydrogen ions (“protons”) from the inside of the cell’s membrane to the outside. Depending on how much energy (as “electrical potential”) was released along with the electron by the “food” molecule’s electron donation, there may be enough energy to shove the electron through up to three different proteins that do this “proton-pumping” trick with each electron.

This process causes there to be a buildup of protons outside of the cell membrane. Since the universe is lazy, it doesn’t want to hold all those crammed-together protons in place – it really wants to shove them back inside the cell so there’ll be an even concentration of them on both sides of the membrane.

The cell has a special sort of gate which lets the protons shove their way through back to the inside of the cell – but in the process, they make part of the ‘gate’ mechanism rotate. The rotating part essentially grabs ADP and loose phosphate and virtually crams them back into place – the energy to do this comes from the force of the protons shoving their way back into the cell.

But what about the electron? Well, at the end, there has to be something that will pull the electron off of the last protein. One of the best “electron acceptors” is oxygen. Oxygen is the second most electron-loving kind of atom there is. Half of an oxygen molecule (O2), a couple of spare protons, and two electrons make a nice, relaxed, stable molecule of H2O.

The reason I find this interesting is because some bacteria can use something besides oxygen, if oxygen isn’t available. They don’t get quite as much energy out of the process since these other “electron acceptors” don’t pull the electron out quite as hard at the end, but it’s better than suffocating. Sulfate-respiring bacteria, for example, can use sulfate (SO4) as the place to dump the electron, converting it to sulfite (SO3) in the process – and eventually converting it to plain “elemental” sulfur (just “S”) or even in some cases using the elemental sulfur in place of oxygen and making H2S – which is that ‘rotten-egg’ smelling gas.

There are some even more exotic “electron acceptors” that some bacteria can use…which will be the topic of another post.

(And, again, please let me know if you spot anything wrong here, and please ask questions if I’m not making any sense – I’m pretty sure I need the practice explaining this kind of thing…)

The Entire Universe Explained Part 2: The Most Fundamental Observation

“The Universe is Powered by Laziness”

(I obviously need more practice – I’m still not sure how coherent this explanation is to anyone but me. Comments welcome here – or if you prefer, you can contact me via XMPP (“Jabber”, “Google Talk”) at XMPP:epicanis@enzymestew.dogphilosophy.net )

There you have it, the big secret that is at the heart of every single thing that happens in the natural world. Everything is the result of the Universe’s laziness. This is more or less what the Second Law of Thermodynamics says. In more proper language, it’s the observation that the total “disorder” in the universe is continually and unstoppably increasing.

I like to think of the universe as a big, fat, obnoxious sports fan. Picture him slouching in his couch. In one hand he’s holding a gigantic can of the most awful “lite beer” you can think of – you know, the one that only losers like – and in the other he’s got a giant foam hand with the logo of that team that only complete weenies like. He doesn’t even bother cheering – he just sits there, slouching as much as possible, maybe drooling a little, and wishing he could relax until he was nothing but an ever-spreading lump of flab…

So, what does this mean? Firstly, that there are always some “losses” whenever something happens. Basically, the universe can never manage to open a fresh can of that awful Lite Beer that it drinks without spilling at least a little bit of it on the floor. Secondly, that any bit of the universe you might happen to look at always wants to slouch a little further if it can.

That first part is what accounts for the “losses” in light of the “nothing magically disappears” observation previously mentioned. In the real world, no matter how carefully you build something, you can never quite get as much energy out of something as you put into it. You might get nearly all of it back out if you’re really careful, but no matter how carefully you hand 12 ounces of beer to the Universe, it always seems to end up with only 11.999999999 ounces of beer to drink. Or a lot less. It didn’t “disappear”, it just ended up soaked into the Universe’s filthy carpet where it is no longer available for anyone to drink. That beer-spillage is what physicists call “Entropy”. Or, “Heat no longer available to do Work“, if you want the proper physics definition.

The second part relates to the fact that there is a certain amount of “energy” inherent in the way any kind of matter is arranged. Matter, being part of the universe, is lazy, and doesn’t like having to hold onto all that energy. If you give it an opportunity, a piece of matter will tend to want to rearrange itself so that it’s not holding onto as much.

As an example, if you mix together some chemicals that will burn together if you light them, then seal them completely in a solid container, and set them off (by adding just a little bit of energy), you’ll find that the weight of the sealed container stays the same before and after…but it got really hot. That means there was energy released, and apparently a lot more than the little bit that started the whole thing – where did it come from?

The answer is that it was “built in” to the structure of the chemicals. Setting them off with a little bit of energy shoved the chemicals together just hard enough to let them recombine in a way that they didn’t have to hold on to all the energy they had up until then. All the energy the lazy chemicals let go showed up as heat. The little bit of energy you had to put in to get things started is what chemists call “activation energy”. It’s just there because those molecular slackers sure weren’t going to put out any extra effort to start rearranging – but once a couple of them are shoved together hard enough to make them get started, the energy they release is enough to shove a few more molecules together and get them to release more energy…and so on.

Because cool science types seem to avoid using whole words whenever possible, this energy that comes out is referred to as ?G. The total amount of energy that is “built in” to a particular molecule is referred to as “Gibbs’ Free Energy” (named after William Gibbs.)

So, for the last horrible analogy for now, let’s return to our big fat slob of a Universe slouching on his sofa. He’s been drinking that disgusting beer of his all night, and his bladder’s full. He’d really like to go to the bathroom but, eh, it’s too much effort to stand up. However, if you get behind him and shove hard enough to push him off of the sofa, then he figures while he’s up he might as well hit the bathroom before he sits back down. And, yes, I suppose that means it is my fault if next time you go camping, you end up waxing poetic and describing the nice, comfy campfire as “urinating heat and light on everybody”.

Microbiologically, that means that for a microbe to be able to live on some kind of “food”, it’s got to be possible to convert the food into substances with less energy built in, in such a way that it can capture and store some of the released energy in the process for its own use. It also means that if the microbe needs to make more of, say, some kind of enzyme (a more “ordered” combination of smaller molecules) it’ll have to shove in some energy to make up for the increased “order” while it assembles the parts.

Finally, what enzymes (or any other kinds of catalysts) do is reduce “activation energy” for a particular reaction, so bacteria don’t have to burst into flame in order to “burn” sugars for energy (for example).

And now I think I ought to go back to Microbiology posts before I get myself lynched by angry chemists and physicists for making a mess of this explanation…

The Entire Universe Explained: Part 1. The Most Important Observation

This is just a downright flippant Gross Oversimplification™ of some things that I’ve noticed over the years which seem to come up in every science class, though occasionally they are described in slightly different ways or under different names. The more I’ve thought about it, the more I find these principles always buried, somewhere, in every observation of the natural world.

I present them here mainly for people who don’t have a background in science, though I’m hoping those who do will at least find this mildly amusing. Essentially, I just want to mention these things now on the assumption that it might help some people understand some of the basic reliable assumptions that science uses. Since they also then explain the underlying principles that drive the biochemistry that’s important to the microbiology that I want to get into, and I’d like as many people as possible to understand what I’m talking about when I do.

Therefore, I’m going to attempt to describe, using my Super Undergraduate Writing Skills, in very brief terms, everything you need to know to understand basic biochemical processes that I plan to try to explain to the best of my current ability later. I apologize in advance to any serious “hard science” types who may suffer blurred vision, seizures, dizziness, upset stomach, or psychiatric anaphylaxis from reading this.

(As always, if I get something outright wrong here, please say so…)

Part 1. The Most Important Observation of the Natural World: “You can’t get something from nothing – or vice versa”. Or in other words, nothing ever magically appears or disappears. If something appears where there previously wasn’t something, it came from somewhere. If something disappears, it went somewhere – it hasn’t simply ceased to exist. This is more or less all that is meant by “The First Law of Thermodynamics” in physics. In practice, this is what’s being invoked whenever you hear someone describing a scientific “Conservation of [whatever]”. You can still chemically combine things to make completely different substances, melt solids into liquids, bubble gasses away or dissolve solids, turn one kind of energy into another (like turning electrical force into light), and so forth, but in the end the amount of material and energy at the end should be the same as when you started. (It’s even possible to turn material directly into energy and energy into particles of matter, but as far as I know this only actually happens in conditions that matter to people like high-energy physicists and such, not in biological systems.)

This is a handy principle – it lets you measure things indirectly. If, for example, you’re studying some kind of chemical reaction that makes hydrogen gas, you can measure just the amount of hydrogen that comes out when you mix the chemicals together and be confident that this will tell you exactly how much hydrogen was chemically combined into the original ingredients that reacted. Or if you put a three-ounce cricket in a cage with a 12-ounce snake, then come back a few minutes later and discover that the cricket has “disappeared” but the snake now weighs 15 ounces, it should be obvious what’s happened without having to give the snake an MRI.

I’ll pause here for comments before I get to parts 2 (regarding the 2nd law of thermodynamics) and 3 (tying the first two parts together to make Equilibrium and such), both of which I’ll try to get to tomorrow, unless it turns out that I’m completely butchering this whole explanation and have to fill in with something else while I rework it…