Where Was I? – Page 6 – The Big Room (and the little things in it)

Environmental Chemistry Field Trip – Day 1, part 1

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

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

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

sampling water from the Madison river

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

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

Sulfur-encrusted pipe at Beryl Spring

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

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

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

This weekend should be worth at least one decent post…

This weekend, one of the two of this semester’s classes that I have not yet used for a “what I learned in school today” post took a field trip.

Yes, Our “Environmental Chemistry” lab went to Yellowstone National Park and (legally – we had a permit and everything) did some water sampling. We got some on-site lectures about the types of water systems in the park, considerations involved in sampling things, and so on. All in all, I thought it was pretty interesting, but after spending the entire weekend either driving to or from the park or walking around in the park I’m a bit exhaustipated. Plus, bummed out that I can’t afford a good portable field microscope to go with the regular microscope which I also can’t afford. Woe unto me. I imagine the permit we had would have allowed me to also dangle some slides in the water to look at.

I did record a GPS track of both days field-trips, I got ICBM addresses for our sampling sites, and a number of photographs with my cheap and ancient digital camera along the way. Give me some time and I’ll get at least one real post out of it.

Meanwhile, a bit of trivia: “The Microsoft Network” search system is pretty Fupped Duck. I do get the occasional obviously relevant hit from one of their searches, but the great majority seems to be “hits” from random one-word searches, many of which seem to refer to words that appear nowhere on the site (and others of which are so broad I have no idea how many pages some MSN user would have to click through before hitting my site. For example, while I like to think I’m making a reasonable effort to do interesting science blogging, I’m having trouble imagining that this blog would show up in the first few pages for a search consisting solely of the word “science”…which one of the recent hits seemed to show.

Actually, this probably has less to do with users than with Microsoft itself – the hits for this don’t appear to be loading real views (it pulls one page and doesn’t reference, for example, images) though it is coming from “The Microsoft Network” addresses. Perhaps Microsoft has one of their bots masquerading as a real user (the user-agent string looks like regular “Internet Explorer 7″)…even the IP address resolves to a bogus name ” bl2sch1082217.phx.gbl.”, for example) which doesn’t resolve back the other way. Of course, it’s also possible the hit is ENTIRELY bogus and the “referer” tag that seems to indicate this is also faked. Perhaps it’s time to start blocking Microsoft…or maybe just messing with them. This apparent standards abuse and obfuscation of what exactly it is that they’re trying to do with my blog (and messing up my logs!) kind of bugs me. (Moral of the story is probably “Everybody should just use Google“…)

Sure “Cardboard Sarcophagus Instructions” is a pretty weird search, too, coming from Google, but at least I know why THAT one got here. I doubt the searcher – possibly from the Memphis, Tennessee area – was really searching for metaphors for expired JellO boxes.

The Oldest Microbiology Book (that I own)

There’s this thing that some people do sometimes when they’ve been getting stressed out in one place for a while. I hadn’t done it in so long I can’t remember what it’s called. You know, where you Leave the area and then avoid it for a while. Oh, yes, that was it, a vacate-shun. Anyway, leaving the barren desert wastelands of the West, we headed east, and spent a few days admiring the area around the midpoint of the Appalachian Trail: Harpers Ferry, West Virginia. (Incidentally, I can recommend the “Angler’s Inn” Bed and Breakfast there, and the whole time there was incredibly delightful to me. I think I’d love to move to the area.).

I was delighted to note that there was an Old Book store in downtown Harpers Ferry. One thing about the Eastern US is that it’s been settled by book-using folks for somewhat longer than the West, so it would seem it’s easier to find really good Old Books. I found a publication of a 110-year-old microbiology book. In decent condition, for just over $20, no less! Not counting the (relatively modern) reprint of Micrographia that I picked up from a library sale, this makes it by far the oldest microbiology book I own now.

Oh, yes, did I mention I collect (casually) old books, especially old scientific and technical books?

The book in question, published in 1897, is “Story of Germ Life”, by Herbert William Conn. Not to be confused with Harold Joel Conn of “Conn’s Biological Stains” fame…who happens to be Herbert William Conn’s son. To be fair, the book *I* got was actually a republication from 1904, so only 103 years old…back when copyright was more rational (7 years, plus an OPTIONAL 7 more years. Thus explaining why my republication came out 7 years after the original.) It appears to have been part of a series called “Library of Valuable Knowledge”. The bookstore actually had another one of them, but I don’t remember what its topic was.

“Story of Germ Life” isn’t really a textbook so much as an overview of the subject of “Bacteriology” (as understood in 1897) for otherwise well-educated people – the kind of book I don’t think there are enough of these days. The Gutenbook project actually has a plain-text-only version of the book online here. Of course, then you miss out on the incredibly useful illustrations:

I always find it interesting to go back and see the earlier stages of scientific endeavors – especially as relates to my own interests. There always seem to be things that have since been forgotten, abandoned, or glossed over in them.

H.W. Conn seems to have been most interested in dairy microbiology, so there is a substantial amount of space devoted to it. I’ve heard of “blue milk” before (Yummy!….Pseudomonas?), but not Red or Yellow milk. He also devotes space to discussing the affect of “good” (and “bad”) bacterial cultures on butter, cream, and cheeses. I’m not even sure if butter is cultured these days, or if they just churn it up fresh and cold with minimal growth. Dangit, one of these days we’re just going to have to move somewhere we can keep a miniature dairy cow so I can do some experimentation with real unpasteurized fresh milk.

Bacterial phylogeny was so quaint back then. “Bacillus acidi lacti.” Ha! I love it. Interestingly, the term “Schizomycete” doesn’t appear anywhere in the text, though that may or may not be because it was considered unnecessarily technical for the intended audience. There’s actually very little about microbiological methods, too, which is the one major disappointment for me. Oh well, still interesting stuff. Conn actually mentions various “industrial” uses of bacteria including retting (soaking fibrous plants like flax or hemp so that bacteria eat the softer plant material to free the fibers), the roles of different bacterial cultures in curing tobacco, and even a fermentation in the production of opium (which Conn says is fungal rather than bacterial).

Also, much to my approval, the first 2/3 of the book is not about diseases. Only the last third of the book discusses “parasitic bacteria” and related topics. I leave you with this quote from the book’s 1897 Preface, which I think is still relevant today:

“Few people who read could be found to-day who have not some little idea of these organisms and their relation to disease. It is, however, unfortunately a fact that it is only their relation to disease which has been impressed upon the public. The very word bacteria, or microbe, conveys to most people an idea of evil. The last few years have above all things emphasized the importance of these organisms in many relations entirely independent of disease, but this side of the subject has not yet attracted very general attention, nor does it yet appeal to the reader with any special force. It is the purpose of the following pages to give a brief outline of our knowledge of bacteria and their importance in the world, including not only their well-known agency in causing disease, but their even greater importance as agents in other natural phenomena. It is hoped that the result may be to show that these organisms are to be regarded not primarily in the light of enemies, but as friends, and thus to correct some of the very general but erroneous idea concerning their relation to our life.” — April 1, 1897

“Where Was I?” Femto-episode 20070109 – Astronomy or Microscopy?

I got a chance to check out a bunch of my Gunnison Bay anaerobic iron-reducing cultures in the microscope.

I did a “Live/Dead stain and took a look:

Here you see an image from the Hubble Space telescope of a nebula called…oh, wait, that’s from the microscope. Never mind.

These are the (allegedly) “live” cells. The bright circles are out-of-focus cells – this is a “Wet mount” with huge chunks (from a microscopic point of view) of iron oxides in it, which makes the sample thick enough that it’s hard to focus on more than one part at a time. The vague blur that looks like a gas cloud in a nebula is what you can make out of the chunk of what is more-or-less just wet rust.

This particular specimen is from the positive control of my ongoing experiment (in what I estimate to be roughly 18% salinity, assuming my original Gunnison Bay samples were around 25-26% salinity). If you look close, you can barely make out the bendy/spiral shaped cells almost in focus in a few spots. I believe that this might be the iron-reducing organism that I’ve been trying to isolate. In one of the other samples I checked, I managed to spot one actually actively swimming around, corkscrewing its way around the slide.

I checked one of the experimental specimens that my hypothesis predicts will be growing at least one (and ideally ONLY one) kind of organism and it, too, has a lot of “live” cells growing on the rust-chunks.

I think I shall designate this as-yet-unidentified strain “Bendy Benjamin“…

Other samples from the same place (but not subjected to precisely the same conditions) also seem to have some long straight rod-shaped bugs and some short (straight) rods also still alive in them, so even in the pretty specialized high-salt/no-oxygen iron-oxyhydroxide-being-reduced environment I would guess I’ve got at least three different viable organisms that MIGHT be doing the iron reduction that I’m trying to track down the cause(s) of.

Any questions? No? Does this mean you’re all ready for the quiz?…

“Where Was I?” Femto-episode: “Im in ur kitchen, eatin ur c00kiez”

No, You Can't Have a Cookie - Not Yours

Or: “All Your Bake Are Belong To Us”

Yes, tonight “Where I Was” was in my kitchen.

Introducing “Righteous Fire of Purification Ginger Cookies”, version 1.1! Now with more Culinary Grace! And before anyone asks – no, I don’t have any idea what possessed me to combine internet memes with cooking in this post.

New Features:

Reduced pH
New Flavor:Lemon Juice!

Source Code: Dry Ingredients

3 Cups of “All-Purpose” bleached flour
1 tsp baking powder
3 Tablespoons (Yes, Tablespoons) Ground Ginger
1.5 Tablespoons (Yes, Tablespoons) Ground Cloves
Around 3 teaspoons Cassia Powder
A teaspoon or two of Mace (or Nutmeg)

Wet Ingredients:

A couple of teaspoons of vanilla extract
2 Large “Grade A” Eggs
0.75 Cups of Molasses
A tablespoon or two of lemon juice

Not really “Wet” but treated as such:

About 1.25 Cups of Unsalted Butter
2 Cups of Granulated White Sugar (Sucrose)
About 0.3 Cups of Brown Sugar (Sucrose with a little bit of Molasses added back to it)

How to Compile:

Cream the sugars into the butter
Add the rest of the “wet” ingredients
Add all of the dry ingredients and mix them in thoroughly – add the baking powder LAST (the order of the other ingredients doesn’t matter).
Stick the dough somewhere cold to chill
Put some baking parchment on a cookie sheet – sprinkle it with sugar.
Once chilled, scoop out balls of dough onto the cookie sheet.
Sprinkle some more sugar on top of the proto-cookies.
Bake 12 minutes at about 350�F
Sprinkle more sugar on top of the cookies immediately before they cool.

Installation:

Pick up a cookie
Insert as much of the cookie into your mouth as will comfortably fit in a manner that would not be considered obscene or freakish
Bite off portion of cookie. Chew.
Savor the sensations. Be sure to notice and appreciate how the flavors explode on the tongue, like an orgy of purification, preparing your palate for paradise (or at least gratuitous alliteration)
Swallow. Repeat the previous two steps until cookie is completely devoured and has become a part of your very being.
Visible shudders and audible moans of pleasure and “MMMM!” noises are optional, but recommended.

The only mortal flaw imposed upon these otherwise unmarred cookies is that they keep coming out “crispy-chewy” instead of “soft-chewy” as I want. I was hoping the added acid would help keep the cookies firmer and prevent flattening as they baked – as Tako, the Octopus mentioned in the “Chocolate Chip Cookies” episode – but no luck. Or at least not much. However, as I’d hoped, the lemon juice flavor goes PERFECTLY with the ginger. The texture is a minor flaw (and is actually preferred by some people. Not that there’s anything wrong with that.)

Oh, I know, SOMEBODY is bound to recommend that “shortening” or “margarine” crap instead of butter, since they don’t melt as suddenly as real butter. Feh! Those are An Abomination Unto The Cook! There has to be another way – I refuse to defile these cookies. (Hmmm, how does the melting temperature of lard compare?)

Incidentally, I was completely wrong when I was guessing that the ginger pungency meant it had a mustard-like flavor chemical. It’s nothing of the sort – in fact it turns out that several of my favorite spice flavors have very similar structures – Eugenol (clove), Vanillin (vanilla), Zingerone… All of them have the same sort of “ortho-methoxy phenol” type shape in them. If you look up Zingerone, Vanillin, and Eugenol on Wikipedia, you can compare the chemical structure and see the similarities around the “ring” that I’m talking about.

Oh, and for the internet meme references:

See “im in ur base, killin ur d00dz” (Numerous parodies exist – such as This One, though for some reason most of them have cats in them – like this one. (Ran into this one on BoingBoing
The picture parodies a picture that appears to be turning into a cliche’ on fark.com. You can see the original here. Incidentally, the photo I used to make this parody comes from “strph” on flickr.com (Original here) released under Creative Commons “Attribution/Share-alike” terms – so if for some reason you can’t resist remixing my masterpiece here…go for it. Just give me credit and allow others to remix yours as well.
I’m pretty sure “All Your Base Are Belong To Us” is well covered by the “Internet History” class you have to take to be allowed on the intertubes nowadays, right? No? Well, Wikipedia has the details.

And there you have it – Where I Was�, some food science, and some Internet Nerd History lesson, all in one post. You’re welcome.

“Where Was I”, episode 3 (Now Updated with Lots More Stuff!)

Where Was I, Episode 3 – “It’s a Small World After All” (now updated!)

Study is sucking up most of my time, but that doesn’t mean I never go anywhere any more. Recently, I went to the “Edson Fichter Nature Area”.

Yeah, that place. But look closer.

No, no, I mean go inside and look closer. Down there, by the river.

Down by the river
No, no, go closer.

A closer look, down in the river
CLOSER!!!
Microbes!

There, that’s a closer look. Incidentally, as you can see, the trick of setting the camera for close-up photos and sticking the little lens opening into the eyepiece of a microscope actually does work. Conceivably, then, the same trick ought to work with any kind of scope, which I’ll have to keep in mind for the next time we go to visit the Bruneau Observatory. But I digress…

I have no idea what all these neat-looking funky things are. Well, not besides the fact that they’re little animalcules with cilia and stuff swimming around and that they’re pretty big as far as microbes go.See, I’m not really into eukaryotes. Needlessly complicated, I say. I’m interested in the cool stuff. Useful stuff.

No ponderous huge protozoans for me, I’m hunting Our Friends, the Bacteria.

See them in there? No, no, you have to look even closer. What do you mean you still can’t see them?

Same stuff, now heat-fixed to the slide. Fire is our friend.

All right then, here, let me dry the sample out and heat fix it, then I’ll Gram Stain them for you.Wow. I guess soft, wet, squishy protozoal cell membranes don’t like being heat-fixed, do they? Ouch.

I’m not sure how much of that is bacteria and how much of that is exploded protozoan guts.

Let me look around elsewhere on the slide…

Ghostly, mangled bodies of diatoms litter the landscape Okay, technically at least some of these things are diatoms rather than “protozoa“.

Kinda neat and creepy at the same time, ain’t it?

Okay, enough staring at hollow shells of dead things, let me see if I can find some bacteria…

ah, here are bacteria Now, months later, I’m still not sure how much of the debris on those original slides was bacteria and how much was just crud from the samples. I did, however, get pictures of the 10 isolates that I wanted to try to identify (and of which, as you know from my entry on Willy Bacillus, I so far only know one…)

Of the variety of isolates we got, I pulled out seven that showed some degree of fluorescence under my homebrew UV-LED flashlight, one that was growing in media containing 10mM of a zinc salt, one that was growing in scalding-hot conditions (55�C – which is about the temperature that “melts” collagen into gelatin and makes that tough stew-meat moist and tender), and of course, Willy Bacillus who grew in 10% salt.

Pyotr, Paul, Olga, Ursula, Peggy, Penny, and Ada (the fluorescent bacteria) and Castor (the zinc-tolerant bacterium) all looked more or less like this when I gram-stained them:
Peggy the Possible Pseudomonas Penny the Possible Pseudomonas
I think the Gram-biguous effect is more because of my technique than the bacteria. I believe these are all probably really gram-negative.

There’s a portrait of Willy Bacillus in the other post. Horace was the other interesting-looking culture:
Horace the Hothead
I’m not sure what’s causing the funny spore-like spots or the bulging of the cells. It might be normal, or it might be an effect of the heat-fixing or being in the “cold” (room temperature) or something. I’d be interested to find out what it is.

More fun facts:

Olga and Ursula both grew in the ‘fridge (4�C)
Ada’s fluorescence was different from the others – it was a dim blue rather than a bright blue-green.
Ada also seemed to grow fine on media without nitrogen in it.
Peggy was also releasing a green substance into the media.
The quick-and-dirty metabolic tests we did (with Enterotubes� did seem to imply differences between these different isolates.

One lesson driven home this semester was that you just can’t identify bacteria based on simple things like what they look like or a few simple observable traits. However, I still suspect there’s a good chance that everyone but Ada (and maybe her, too) is a Pseudomonas of some flavor, and all of them in any case are probably Gamma-proteobacteria, just based on the fact that when I went looking for information on fluorescent bacteria, nearly everything I found was about species of Pseudomonas, and the ones that weren’t were all still Gamma-proteobacteria. Plus, the media and techniques we used (and possibly the site itself) seemed to heavily favor the isolation of gamma-proteobacteria. If anyone’s bored enough to care, I can post something more about where we got the bacteria and why I wonder if the site had an influence on the heavily slanted taxonomy of our isolates this semester.

And that’s Where I Was.Where Will I Be next? Will my next post be something exciting, interesting, and insightful? Or will I just bore the holy living crap out of everyone with a couple of quickly-crammed-together trips with a couple of minimally interesting pictures? Even I don’t know! Tune in next time and find out!

Meanwhile, as always, questions, comments, and suggestions are welcome.

Remember “Where Was I, Episode 3?”

Hi! My name is Willy Bacillus!

“I came from the Portneuf river in Pocatello. I grew in 10% NaCl and I look like slime-coated sausage links. I’m purple in this picture because I’ve been Gram stained. People used to think I was just a strain of Bacillus subtilis, but I’m really Bacillus atrophaeus“.

Yes, I named my bacterial isolates. I figured if we had to give them some arbitrary designation, naming them like hurricanes was just as good as some bizarre system with names like “ZXKUQYB276” or something equally boring.

Unfortunately, we had so much trouble getting the PCR reactions to work we ended up just pooling the class’ sequences rather than having all our own. That means I only got this one. (Actually, it looked like one of my others worked, but not well enough to give enough DNA to sequence.)

I’m trying to talk the instructor into letting me do a 1-credit “Independent Study” session next semester to try to finish getting good sequence identification of Pyotr, Paul, Olga, Ursula, Peggy, Penny, Ada, Horace, and Castor.

The first seven of those all produced fluorescent stuff (probably siderophores, I’m guessing) and while I suspect they’re probably all Pseudomonas species, and almost certainly all gamma-proteobacteria, I was told they actually could be quite different, and I’d really like to find out just how different they really are. Plus, Horace the Thermophile was just kind of neat-looking in the microscope.

Yes…I am a nerd.

“Where was I” Femto-episode 4.1

Just a tiny bonus update and a test of a trick I’m trying to do…