Search Engines appear to have found me…

Quick update: I just checked my logs – I just realized there have been a number of hits from Google searches in the last couple of days, from people trying to find information about staining and such.  I’ll try to throw in a post on search query topics that showed up in the logs in the next day or two as well.  Stay tuned…

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

(I’ve only got a couple more days before the start of “Just Science” week, so if I’m going to get this post up, I’d better get to it…)

Now that I’ve briefly explained who I am, here’s the bit about this blog itself.

My intended audience:
Anyone who’s interested. Okay, that’s kind of a cop-out. Essentially, I’m aiming at anyone who’s sufficiently scientifically-minded to be interested. I’m kind of assuming that if and when I’ve got enough readers to consider a “core audience”, it’ll be made up largely of interested science students, people who are inclined to read magazines like “Scientific American” or “Discover”, and just generally reasonably intelligent people with an interest in scientific matters, particularly but not only microbiology. I’m hoping that I’ll reach the point of being able to write so as to be interesting to some scientific professionals but still comprehensible to people without much of a scientific or technical background. This blog is, in part, an exercise in “public access to scientific information”, so if I write anything badly or fail to explain something, please comment and let me know.

How it works:
It’s easy: I think of something that I find interesting and that I think someone else might also find interesting, and I post something about it here. I expect to focus primarily on microbiology-related science, but a wide variety of topics might come up. I have a particular fondness for subjects that I think are underappreciated or ignored in other venues. Comments on whether or not things I bring up are interesting or boring will help guide the topics. I’ll tend to focus more on informal and hopefully pleasant to read style rather than a dry but detailed technical discussion – though wherever possible I’ll include links to that kind of information for anyone who’s interested (or perhaps thinks I’ve gotten it wrong.).
I also try to make the postings somewhat interactive – at the very least, I try to add extra information, explanations, and comments wherever I think they might be helpful or just entertaining. If you see words or phrases with thick dotted underlining, you should be able to “hover” your mouse cursor over it and get a little bit more information. I generally try to do the same with links and pictures. Maybe once in a while I’ll get bored and plant an Easter Egg or two.
Comments are welcome and encouraged, other than “spam”. What little information you’re required to give in order to comment is entirely to discourage spammers.

Really, this is mainly for personal gratification – I like to write. I like science. I’d like to share this interest, and I think scientific information would be interesting to many more people if more of it was presented in an interesting and accessible manner without making it seem otherworldly or dumbing it down to the point of uselessness. This blog is a cheap and easy way to get practice.
It’s also a cheap and easy way to get free learning for myself – I find trying to explain something helps me recognize when I don’t know something as well as I thought, helps me understand things better, and occasionally is a handy way to find out when something that I think I know is wrong.

Addendum: Yes, my Mom reads my blog. No, she does not wear combat boots. No, she does not dress me funny.

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.

Wow, I guess everything IS bigger in Texas…

…including, at least for today, my audience.

After being linked to from The Tangled Bank I’ve gotten hits from all over. Mostly using Firefox, I notice, and a large number of Mac users (plus at least one and possibly two fellow Penguinistas.)

Hits coming from all over – A few from Canadian colleges, Michigan, California, New York, the U.K., the Sydney, Australia area [update: Oh, and now India – Hello, India!]…and a surprisingly large number from Texas.

Interesting selection of institutions, too. Colleges, research institutions, government agencies…I just want to assure the readers from the disease and mental-health organizations (there was at least one from each) that I’m perfectly healthy and sane. For certain values of “perfectly”, anyway. At least, I’m not 5150 nor afflicted with any sort of terminal condition.

Since at least a few people seemed to come back and look at the rest of the site, I’ll endeavor to put up a post tomorrow on what exactly I’m trying to do in this blog and such (in case anyone’s thinking “that’s nice, but does this get better?…”).

But for now it’s bedtime – early morning Pathogenic Microbiology Lab tomorrow. Goodnight, all.

They did it!

Thanks to our library staff and the people at the University of Illinois at Urbana-Champaign (from whom this comes) I was able to get a copy of the original “Gram Stain” paper…

Beginning of the original Gram Stain paper

I don’t know whether to be annoyed (that someone else beat me to it) or happy (because now I’ll be able to double-check my translation) but it appears the ASM actually already has a translation of the paper online. Interestingly, the attached commentary states that the Gram stain even works on bacterial protoplasts. If that’s true, then all this stuff I keep getting told about the action of the Gram stain being due to the cell walls themselves is incorrect. I wonder, do Gram-positive bacteria also have thicker inner membranes? Or is the commentary full of it?

Why this article didn’t originally show up when I was poking around Google looking for it by the title, I don’t know.

Next request will be for the “Everything is Everywhere” paper…

“What’s the purpose of heat-fixing bacteria on a slide?”

I check my web server’s logs fairly regularly. Given that right now this is a brand spankin’ new blog with a pitifully small readership (Hi, mom!), seeing a new reader (even just a casual drive-by reader) is interesting to me.

I just noticed someone bounced by the site, having gotten here via a Yahoo search for the question above. Just in case they come back (or anyone else comes by and is interested, for that matter), here’s the answer – at least to the best of my knowledge.

Have you ever thrown a piece of meat into a hot pan or barbeque that wasn’t sufficiently greased? You notice how it sticks and doesn’t want to come off? That’s what heat-fixing is for. It basically “bakes” the bacteria to the surface of the slide, so that when you then soak the slide with stains and rinse it with water and/or alcohol and/or other substances (like the “acid alcohol” stuff used for the “acid-fast” stain for Mycobacteria) they don’t get washed off. This can be an issue, since some of the staining techniques have a whole series of “soak/rinse/soak/rinse/soak/rinse” kind of steps with different kinds of solvents, and it would be very annoying to go through all that work and find out you’ve rinsed the stuff you wanted to look at down the sink in the process. It’s also nice if you want to look at the slide with an oil-immersion lens.

You can’t really “glue” the bacteria to the slide with some sort of chemical, either, since anything you “glue” them with might cover them and interfere with stains that you’re trying to soak them with so you can see them in the microscope.

Actually, it’s probably worth mentioning that since most sources seem to unfortunately assume that “microbiology” just means the tiny fraction of a percent of microbes that cause diseases, a lot of sites will also say that the heat-fixing process is also “to kill the bacteria” (so that if you are overcome by an uncontrollable urge to lick the slide later or rub it on an open wound for good luck or something, you hopefully still won’t get the disease). While it’s true that heat-fixing ought to kill just about any microbe on your slide, I suspect that most of us who are looking at things that aren’t disease-related probably don’t consider this a “purpose” of the heat-fixing process. Still, if you’re answering a question like this on a “General (medical-centric) Microbiology”-type exam, you may want to mention this as well.
(UPDATE 2010-08-25 I dug up some Real Science™ on this “killing the bacteria” idea in “Stir-Fried Stochasticity Episode 4: TuberculosisBurgers“, which is an amateur podcasting project I’m dabbling in. I’d very much appreciate feedback on it!)

Hopefully that information will be of interest or use to someone…

Coming up next – some commentary on the history of staining bacteria, and why it seems like all of the classic techniques of microbiology – most of which seem to still be in common use – seem to have been invented entirely in or near Victorian-era Germany…

Also possibly coming soon: Discussion of the “Everything is Everywhere” concept, making chemicals with bacteria, and (if I can manage to get the thought into some organized form) a simple discussion of the concept of speciation, using science itself as an example. And various other things as I think of them and get time to type them up.

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.)

Obsolescent terminology: “Schizomycete”

I couldn’t resist doing a bit of research to track down what “schizomycete” meant. I can’t help it, it’s fun, and in this case also was both informative and amusing. Don’t tell the Psych department, though – I think the MMPI probably formally classifies this kind of thing as a perversion…

In any case, here’s what I’ve come up with.

First, a simple Google search turned up some online “medical dictionary” sites. Where they had a definition of the term, they just said it was “a class of bacteria” (or something similarly vague). However, neither the NCBI Taxonomy Browser nor the RDP Heirarchy Browser seemed to have any kind of category called “schizomycete” (or “Schizomycetales” or similar variant). Obviously, the term is no longer in use.

Although my academic interests are specifically not medical in nature, I do casually collect old medical (and scientific) books. So, I dug out my handy 1953 “Stedman’s Shorter Medical Dictionary (“Revised and Enlarged”)” and looked up the term. Here’s what it said:

“A class of vegetable organisms which reproduce by fission; fission-fungi or bacteria.”

Fission-fungi“???Okay, I can excuse such an obviously archaic term in a dictionary from 1953 – at that point, Watson, Crick, and Franklin hadn’t even puzzled out the structure of DNA yet (in fact there aren’t even entries for DNA or Deoxyribonucleic acid in this edition). What’s funny, though, is that I stopped in on the campus library and looked at the current edition of Stedman’s Medical Dictionary and the famous Physician’s Desk Reference. The current (2006) Stedman’s still has an entry for “Schizomycete”, as well as an entry for “schizomycetic”. “Schizomyces” now says:

“Member of class schizomycetes; a bacterium”

Even funnier, “Schizomycetic” says:

“Relating to or caused by fission-fungi (bacteria)”

Okay, the fact that they’re happily referencing a bacterial “class” that was rendered obsolete and nonexistent decades ago is funny enough…but they STILL refer to “fission-fungi”? Unless I’m mistaken, that would be like looking up a current “Dictionary of Chemistry and Physics” and seeing an entry that describes some optical phenomenon in such a way as to make reference to “the Aether”.

I was perversely even more amused to see that, as I recall, the famous “Physician’s Desk Reference” happily parroted the definition word-for-word.

Judging by the occurrence of the term in Pubmed, the term “Schizomycete” disappeared sometime in the mid-1980’s, and even then was used almost exclusively in Italian journals (presumably it was just slower to drop out of the language than in English). I did find, however, a series of articles on bacterial taxonomy which started in 1916, and included an entire article from 1917 on “Schizomycetes”[1]. Being 90 years old, this is a mature public-domain work so you can make, print, and share all the copies you want (Even in the U.S., believe it or not). Pubmed has a copy here if you’re interested.

In the end, though, here’s the summary:

Even when it was in common use, it seems like “Schizomycete” was an unreliable term. It seems to have been in use during a time when there was a lot of argument over how to categorize microbes. The 1917 article has a whole section discussing the historical meanings of the term and where various researchers drew the lines of what was a “schizomycete” or not. In general, it seems to have usually meant any relatively “ordinary” bacteria that didn’t produce chlorophyll (that is, wasn’t some kind of “algae“)

In honor of the completion of this batch of grueling and difficult research, I hereby declare by the power vested in me that henceforth “Schizomycetic” shall be defined as “pertaining to any relatively unremarkable-looking prokaryotic organism” and that all microbiology-related professionals should be compelled to use the term regularly. I further decree that the terms “aerobic” and “anaerobic” shall be replaced by “dephlogisticated” and “phlogisticated”, respectively.

Incidentally – Hello, “Tangled Bank” readers! Comments, suggestions, and corrections on any of my postings (or this blog in general, for that matter) are welcome and encouraged, in case that isn’t clear.

[1] – Buchanan RE, “Studies in the Nomenclature and Classification of the Bacteria: II. The Primary Subdivisions of the Schizomycetes.” Journal of Bacteriology. 1917 Mar; 2(2):155-64