Category: Science Philosophy

Thinking about science

Are “Acid-Fast” bacteria Gram-positive or Gram-negative?

I was wondering what today’s post ought to be – but a Google™ search that reached the page posed an interesting question and made it easy.

Someone from a Miami, Florida college got to this site after asking Google:
“Assuming you could stain any cell, would an acid-fast [bacterium] be gram-positive or gram-negative?”

Therefore, today’s post will deal with some Microbial Physiology.

The easy answer is, of course, “no“.

A more useful answer, though, is that it depends on what you mean by “Gram-positive”.

If one takes the “Assuming you could stain any cell” part of the question to mean that you’ve done whatever it takes to get the Crystal Violet/Iodine into the cell wall, and you mean “will the cell still look purple instead of pink at the end of the Gram Stain process”, then I’m pretty sure the answer would be yes, that it would be “Gram Positive”. It actually IS possible to stain “acid-fast” bacteria with the Gram stain. The catch is that it takes 12-24 hours of staining (according to Gram’s original paper) rather than a minute or so. This still counts as Gram-positive, though, and in fact the whole Phylum of Actinobacteria (including the Mycobacterium genus) is considered “High G+C Gram-positive”. (If the query was for an exam or homework problem, this is probably the answer you’re looking for.)

On the other hand, if you mean “does the cell wall structure of an acid-fast bacterium better resemble Gram-positive or Gram-negative bacteria?”, you can make an argument that instead of a nice simple “inner membrane surrounded by a thick peptidoglycan-layer cell wall”, the “acid-fast” bacterial cell wall looks more like a complex gram-negative-type cell wall, having multiple layers, with special proteins that form channels through them to let substances in and out of the cell through the otherwise penetration-resistant outer layer, just as Gram-negative bacteria have through their outer membrane. (On yet another hand, those outer layers are tough like a gram-positive bacterium rather than fragile like a gram-negative bacterium’s outer membrane, and don’t dissolve in alcohol.)

Therefore, if you’re speaking in terms of taxonomy, and by “Gram-positive” you mean firmicutes which, as far as I know at the moment, are really the only class with the simple, officially-gram-positive-type cell wall structures and therefore are usually what is meant when someone says “Gram-positive” (someone please correct me if I’m wrong here), the obvious differences with “acid-fast” type cell walls can at least make a good argument that they are “not ‘Gram Positive’ bacteria”.

But if you put that on your homework or exam answers, don’t blame me if you get marked wrong…

I actually found a pretty nice illustration on the University of Capetown website showing the differences in cell wall structures here, which might help.

So, to summarize – Officially, they’re either “neither” or “Gram-positive”. Unofficially, you can probably argue either way. Hmmm. I should try to work in a post on bacterial taxonomy one of these days.

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…

Just a little over an hour…

“Just Science” blogging week starts tomorrow, which is to say, in a little over an hour where I am. Starting sometime in the next 24 hours or so, all of the participants are supposed to post at least once each day, and only about scientific topics, for the whole week. Of course, I intend to do my part.

I haven’t decided what to start with yet, though. Depending on how much time I can afford to devote to it, I may either make my ambitious attempt to, in one post, explain the workings of the entire natural world (in Grossly Oversimplified form, of course – e.g. “The Universe is Powered by Laziness“), or I may just start out with a simple post or two on staining methods or how to cheat and quickly identify the “Pseudomonas” cultures when you have to do the “Unknown” identifications in basic microbiology labs, or something like that.

If I can get through the Three Basic Observations that (I boldly claim) describe pretty much everything in the natural world, plus a Grossly Oversimplified explanation of how chemistry works (hint: it’s nothing more than the aforementioned Three Basic Observations plus electricity) then maybe I can get into things like the Electron Transport Chain, the Sulfur, Nitrogen, and Phosphorus cycles, why microbial fuel cells work, and things like that.

Any requests?

About this blog, Part 1: Me.

I thought it’d be useful to do a couple of posts explaining who I am (this post) and what I’m hoping to accomplish with this blog.

Don’t worry, I’ll try to be concise.

In a metaphorical nutshell: I’m a general-purpose nerd with a 15-year history of being a reasonably hardcore computer geek. I’m now escaping that field, and am a continuing undergraduate (at least as of right now.) who’s been painfully puttering part-time through college for many years off and on until recently – they don’t seem to make much provision for ““Non-traditional” students in US colleges. I’m now hoping to actually finish and graduate this summer – and then find an appropriate graduate program in whatever part of the country I end up in afterwards.

My area of academic interest is Environmental and Industrial (“Applied”) Microbiology. Medical microbiology, which seems to get all of the attention and funding, is somewhat interesting, but I’d rather people be able to benefit from anything I learn without having to get sick first.

In particular, at the moment I’m interested in exotic modes of respiration in prokaryotes. Or, more colloquially, fun (and preferably useful) ways of playing with live bacteria and electricity at the same time.

I’ve also got some interest in science history, public policy, writing and other forms of mass communication, public access to science, travel, food and food science, and at least casual interest in a wide variety of other areas. As such, you can generally expect that most of this blog will focus on microbiology and microbial biotechnology related topics, but will occasionally veer off in odd directions.

I also hope very much that someone besides me will get some pleasant usefulness out of this blog, so I strongly encourage comments, suggestions, corrections, and so forth.

Phlogiston and Aether

No, that’s not the name of an obscure pair of mythological Greek characters. Nor do they really have much to do with microbiology, either, but they’re kind of interesting, now-obsolete scientific theories. And since I mentioned them both in the last post, I may as well say something about them.

It’s worth mentioning that being a “theory” is a big deal, scientifically. I means something that’s been examined and tested repeatedly and still appears to correctly describe and predict natural events.

Phlogiston seems really bizarre in a modern context. Phlogiston was supposed to be a sort of “fluid” that came out of things when they burned. It was invented to explain the observation that if you burn something in a sealed container, it will only burn so much and then stop, until you give it fresh air. The theory held that the air could only hold so much of the phlogiston, and when it was saturated with it (“phlogisticated”) it simply wouldn’t support combustion any more.

You can test this, of course. If this hypothesis is accurate, then if you have a lot of air but just a LITTLE bit of material that you burn in it, then the air will still be partly “dephlogisticated” and if you then add more fuel it, too, will still be able to burn. Naturally if you actually try this, that’s exactly what you see – the theory accurately predicted what would happen.

Of course, modern chemistry knows that what’s really happening is that oxygen in the air is combining with the fuel being burned – “stuff” is going from the air to the fuel. (That’s not the first time a popular scientific theory turned out to be exactly the opposite of correct.)As chemists did more experiments they were able to show more cases where phlogiston theory no longer predicted correctly, and it was abandoned.

Aether (I spell it that way rather than “ether” do better distinguish it from the modern meaning, which is used in organic chemistry) has to do with light. Leaving out all the historical details around it, since light seems to be a wave (okay, AND a particle, but never mind that for now), and since waves have to travel through some kind of medium (like sound travelling through air, or a wave travelling through water in the ocean), there must be some kind of “stuff” that light waves are going through, right? Well, that “stuff” was referred to as “luminiferous aether”.

This one is somewhat trickier, but basically, fancy experiments with lasers which ought to have shown some effects of “aether” if it existed didn’t show anything. I’m not a physicist, so I’ll stop here before I badly butcher an attempted explanation of what was tested and how it failed to demonstrate existence of “aether”. If you’re interested, the relevant experiment is the Michelson-Morley experiment. Of course, if the universe actually IS geocentric, then the test results merely demonstrate that the aether is fixed with respect to the Earth…

I’m not even going to attempt to explain the whole “it’s a wave AND at the same time it’s a particle” thing. It’s kind of like how Schroedinger’s Cat is both dead AND alive at the same time until somebody checks on it. I think to really explain it you have to fluently speak a specialized made-up nerd language because normal speech doesn’t seem to handle it very well…

Actually, in the unlikely but not impossible event that someday, a physicist happens to read this who can explain “wave-particle duality” comprehensibly using only plain English prose I’d be interested (I ‘get’ how light is both a wave and a particle simultaneously, I just don’t get why.)

Ye Olde Science Paper?

As I finished up the report for the second Pathogenic Microbiology lab, I found myself – again – wanting access to a classic scientific paper.

I mean really classic. I mean, all professional microbiologists know what a Gram stain is, but how many have actually read Gram’s “Über die isolierte Färbung der Schizomyceten in Schnitt- und Trockenpräparaten” Published in “Fortschritte der Medizin” in 1884.

I wonder what would happen if I asked the college library to get me a copy via Inter-Library Loan?

A short post on what the heck “Schizomycete” means may be in order later, too.

Ah, a good-natured rant

One of the sources of my daily metaphorical firehose of information that I try to take in is the RSS feed for the blogs at Scienceblogs.

One of the sources of my nearly-daily metaphorical itchy rash of irritation that I encounter along my studies is the fact that as far as most people are concerned (including, most importantly, the people responsible for the required “Microbiology” degree curriculum), “Microbiology” is essentially the study of diseases.

These two collided today when a professor of Epidemiology who is a blogger on Scienceblogs posted offering “Everything you want to know about Microbiology and Epidemiology[…]”. A perfectly reasonable post (downright laudable, actually – it’s part of an effort by several of the bloggers there to be try to get posts going offering explanations of basic concepts in their respective fields). Nonetheless, I couldn’t resist mentioning that what I wanted to know was what it would take to get people to quit assuming microbiology was about diseases (while acknowledging that an epidemiologist was probably not the most sympathetic person to ask…). Hopefully the mini-rant came across in as good-natured a manner as I’d intended.

Those bored enough to care can read it here (the main post is here).