Category: Freakish Eukaryotes

I normally discuss NORMAL (prokaryotic) organisms on this blog, not perverted Eukaryotes.

Why “Perverted”? Well, as a society, we tend to think inter-SPECIES mating is pretty perverse, but eukaryotes derive from inter-PHYLUM mating…and an orgiastic one at that, according to my own pet hypothesis regarding how eukaryotes came to be…

I should be getting more done…

Im Name des Nudelmonster! It’s been over a week since my last post!

“Someone” seems to have located a replacement original disk of a game I had many years ago (but lost when I loaned it to someone) and bought it for me. Now, in addition to a variety of issues I need to deal with related to moving over the next few months, I have this delightfully surreal old computer game beckoning at me. ARGH! MAKE IT STOP!

Meanwhile, I’ve been trying to put together topics for next week’s “Just Science 2008”. We’ll find out who, besides me, is interested in fermentation once it starts. I think I’ll have to start off the series with a post on evolution, however, since it really does play a fundamental role when it comes to yeast culture. I also think I may be able to work JellO® into at least one of the posts, too…

Internet connection will be spotty the rest of this week as we travel towards the area that is to be our New Home, but I should have posts assembled in time for next week.

If I get a chance, there will hopefully be at least one more Geostrings post, possibly with a sample mp3 and/or Ogg/Vorbis audio file.

More on geotagging

Some good comments came up in the last post on georeferencing. I thought a followup post was
merited.

The itch I’m trying to scratch here is that I want to be able to georeference just about any kind of data,
and I want to be able to embed the georeference information directly in the data file, whether it’s a
graphic, or audio, or video, or gene sequence data, or anything else. I want to have a standard form for tagging any of these files. And I don’t want to store the location metadata in a separate file.

What I think I need, then, is a standard, simple way of making geographic notations in a terse, concise format that is both easily parsed by and readily recognizeable to a computer, is reasonably human readable, and can be made to fit just about anywhere that arbitrary text is allowed.

Right now, there are only two types of files that have some way of embedding geographic information into them that I know of. The obvious one is that EXIF data in JPEG files can contain “GPS” tags. For hardcore GIS people, GeoTIFF is the other one. Both are for photographs or other still-image data only. What about the rest?

A variation of one of the current geotagging XML formats like the W3C (“<geo:lat>41.4354840</geo:lat><geo:lon>-112.6660845</geo:lon>”) or GeoRSS is an obvious possibility. XML has two potential problems though, as I see it. First, it’s not very terse – the markup substantially increases the amount of space the information takes up. I think in most cases that wouldn’t necessarily be a problem, but I suspect there are a few file formats out there with only comparatively small spaces set aside for a “comment” or “description” field.

The second potential “problem” is something odd that occurred to me today: it’s hard to pronounce out loud. There are some popular audio formats (e.g. “.wav”) that as far as I know have no space whatsoever for arbitrary text…but if my little standard was something that could be distinctly spoken, someone making a recording could literally speak the metadata in a format that a speech-to-text engine (like Sphinx) might be able to recognize and convert to a compatible string of text which could be parsed just like data from anywhere else. This is something of a corner case, I admit, but I think it’s at least worth considering.

Another good point that came up was what you do if your data extends beyond a single point. For example, if I want to georeference an audio recording I might make while narrating what I’m seeing out the window of a speeding train, it makes good sense to at least try to store line segments rather than just a point. That way, if someone wants to find the spot within a several-mile stretch where I suddenly exclaim “Hey, wow, look at that!” they can. The ability to define areas with a polygon or a point-and-radius seems like it would be handy, too, though obviously much more optional.

So, let’s see, I’m looking for a format with minimal markup, but which is easily recognized, is made of plain text which could be crammed into, say, a PNG tEXt chunk, an mp3 comment frame, a Genbank “Source” field, or any other field which allows arbitrary text. I want a form that’s minimally objectionable to anyone else who might be willing to use it. And I think I want it to be able handle points consisting of at least latitude, longitude, optional elevation, optional timestamp, and possibly even an optional heading and angle, and can handle more than one point per file (for the case of lines). Am I forgetting anything?

Besides “going to bed before 3am”?

’tis the season to be greedy

Members of my immediate family start asking around this time of year about what kinds of things I’d like for Christmas presents this year.

This strikes me as a good way to break the week-long bout of blogstipation I’ve been having. Here, then, is what I want for Christmas, Xmas, Hannukah, Kwanzaa, Cephalopodmas, or whatever gift-giving winter holiday you prefer (each category is sorted roughly in order of desire at the moment):

Ridiculously Expensive Stuff

Which I only list on the off-chance that someone wins the lottery or happens to find an amazing bargain on “e-bay®” or something.

Relatively Expensive Books

Other kinda-expensive-but-maybe-you-can-find-it-at-reasonable-price stuff

Relatively Cheap Stuff (but still spiffy)

I know there was more, but my brain seems to have gone on break right now…

“Does beer and ice cream make gas?”

I get some odd Google searches hitting this site. Once in a while, however, I see one asking a question of vital importance and great usefulness to the general public. Today’s brief topic is this query: “Does beer and ice cream make gas?”.

I’m assuming the searcher did not mean gasoline. Biodiesel is all well and good, but who the heck would waste perfectly good beer and ice cream on such a thing? No, I assume the searcher wanted to know if eating these two fine foods together would expose one to the risk of increased flatulence.

Sad to say, the answer is most likely “yes”.

Flatulence gas (from humans, at least) is made up mostly of carbon dioxide and hydrogen gas[1], and for some people (but apparently not all!) methane. It’s worth noting that none of these components have any odor. All of the offensive smell comes from comparatively tiny amounts of sulfur-containing chemicals – most notably plain old Hydrogen Sulfide, and maybe a few molecules of indole-type compounds such as skatole which can make the origin of the stench obvious.

These main gases come from two sources – swallowed gases (air and carbonated beverages) and microbial fermentation. Obviously this is one place beer comes in – the carbonation adds to the amount of gas entering the digestive tract. Secondly, the beer probably contains some amount of remaining malt which some intestinal bacteria, like the yeast that made the beer in the first place, can break down and eat, possibly generating more carbon dioxide in the process. Beer also has small amounts of sulfur compounds in it which give it some of its flavors. It’s possible that some of this sulfur can end up as smelly by-products of microbial action as well.

I tend to assume that problems one might have with ice cream are mainly related to the lactose from the cream. Lactose is actually a combination of two kinds of “simple” sugar molecules linked together in pairs – glucose and galactose. Many unfortunate human beings are cursed with a lack of production of lactase, which is an enzyme that breaks lactose into its two simple sugars which can be easily absorbed and digested. Many bacteria which can live in the human intestine, on the other hand, make their own lactase. If the human eating the ice cream doesn’t make their own lactase so as to absorb and use up the simple sugars, it all gets down to the intestines where the intestinal bacteria can turn it into a major feast. Many bacteria generate a lot of carbon dioxide when eating these sugars, too, and this adds to the gases that build up in the intestine. This is similar to the issue with beans[2] and similarly ‘indigestible’ substances which can appear in food[3] – humans don’t use them up, so the bacteria get it all and make a huge amount of gas in the process of eating it.

Milk also has at least some sulfur in it[4], like just about any protein-containing food, but I’m not sure if it’s enough to add to the smell problem.

So, yes, beer and ice cream probably do make gas.

Incidentally, it seems as though methane production in humans only happens in some people. Methane is only produced by certain kinds of archaea, and not all humans have them growing in their intestines along with the regular bacteria. Don’t quote me on this, but I would tend to suspect that this would actually reduce the amount of gas that actually results in the end. Methanogens actually make the methane out of the other two major flatulence gases: carbon dioxide and hydrogen. I haven’t looked up the biochemistry, but I suspect the other byproduct is water. Since the pressure of a particular bubble of gas (and therefore its volume when your container is stretchable, like an intestine) is dependent on the number of actual molecules of any kind of gas in it, if you have methanogenic archaea in your intestines they should be taking a molecule of carbon dioxide plus more than one molecule of hydrogen gas, and producing just one molecule of methane out of it (plus some liquid water), so where you once had three or more molecules of gas you end up with just one. I’m sure somebody somewhere has done some kind of study on this, maybe I’ll go dig for it at some point. While I’m at it, perhaps I should look at patenting the use of archaeal “natural flora” as a probiotic?…

The picture at the head of this post, incidentally, came from this blog post of odd signs – apparently this one’s from an advertisement for some kind of backache treatment. Still, I couldn’t pass up putting it here…

[1] Furne JK, Levitt MD: “Factors influencing frequency of flatus emission by healthy subjects.” Digestive Diseases and Sciences, 1996; 41:8; pp 1631-1635
[2] Rockland LB, Gardiner BL, Pieczarka D: “Stimulation of Gas Production and Growth of Clostridium perfringens Type A (No. 3624) by Legumes.” Journal of Food Science; 1996; 34 (5); pp 411–414.
[3] Cummings JH, Macfarlane GT, Englyst HN: “Prebiotic digestion and fermentation” American Journal of Clinical Nutrition; 2001; 73(2); pp 415-420
[4] Ramsdell GA, Whittier GO: “Composition of Casein in Milk” Journal of Biological Chemistry; 1944; 154; pp 413-419

Give a man a fish, and you feed him for a day…

…but teach a man to fish, and he’ll sit in a boat and drink beer all day.

-== We interrupt this blog post to bring you this important announcement: Happy Birthday, Dad!==-

(His birthday was actually yesterday, but this week of school has been grinding me pretty hard and I’d forgotten all about it. He must be so proud – his son can handle a couple of semesters of biochemistry, complex microbial science, working with dangerous chemicals in a lab…but doesn’t seem to know how to use a simple calendar…I am filled with shame.)

We now return you to your regularly scheduled blog post:

This here critter is our resident fish. “He” is a classic specimen of real, old-fashioned, Honest-to-Aquaman Carassius auratus auratus – the Goldfish. And not one of those poor mutant freaks who can barely swim, either. No this here fish was rescued from the overcrowded “feeder goldfish” tank of a local Wal-Mart®. Handsome, ain’t he? I had a tough time getting even this good of a picture – every time I get near the tank he swims back and forth in front of me frantically, perhaps worshipping me as the magical fishfood god. He’s been here for about three years now, so I think he’s having a much longer life than most of them.

I’ve had no time to get into it, but part of the reason for having a fish is that I have a casual interest in aquaculture. That is, while I don’t currently have any intention of becoming a professional full-scale fish-farmer, the subject is interesting and, I think, very important in the near future. Once we figure out where we’re going to end up living next year and get settled in somewhere, I have considered trying to do the aquaculture equivalent of a backyard garden, though.

I think aquaculture is going to become extremely important in the relatively near future, as we run into the combination of overfishing of natural stocks, water shortages, contamination of natural waters with pollutants that build up in naturally-existing populations of fish, and the overall effects of climate change. I think understanding how to raise healthy and nutritious aquatic food without wasting water or causing environmental problems is going to be a useful set of knowledge to have. (There, see, not only do I love kittens and puppies and want to make the world a better place, but I’m also interested in Sustainable Environmental Practices™. While feeding the hungry. [Uphill. In the snow. With no shoes…]).

You may be wondering what interest an ex-professional-computer-nerd microbiologist would have in tending a pond full of eukaryotes. Well, aside from the obvious “Hey, I can have more than one interest, you know”, there actually is a lot of microbiological activity involved in the natural processes of the fishes’ homes. Plus, of course, the aforementioned beer doesn’t ferment and bottle itself, you know.

Since one of my interests in this context is water conservation, my main interest is in figuring out how to maintain a healthy “closed” system. In an aquaculture context, a “closed” system is one that you don’t normally add substantial amounts of water to. (An example of an “open” system might include raising fish in pens floating in a natural lake, or having a constant stream of fresh ground or river water pumping through your tanks). This poses certain problems, since you have to feed the fish, and this adds an ever-increasing load of potentially uneaten fishfood and especially of eaten fishfood – that is, fish wastes.

Fishfood being digested by either fish or bacteria ends up adding ammonia to the water, which is poisonous to the fish (and crawdads and whatever else is in there). Also excreted is carbon dioxide, which makes the water more acidic, and unused food also dumps sulfur and phosphorous into the system.

If you’ve ever had a fishtank, you may know about the ammonia. Certain kinds of Oxygen-using bacteria can actually get some of their biochemical energy from turning reduced nitrogen into oxidized nitrogen, ultimately turning the ammonia (NH3) into much less poisonous nitrate (NO3). These bacteria tend to colonize the tank’s filter, where they do their thing using the oxygen in the water that flows through. Even nitrate is dangerous if it builds up too much, though. In an aquarium, they usually recommend just taking out some of the tank’s water and replacing it with fresh water every week or two to get rid of the build-up. I’d show you pictures of the bacteria, but I still can’t afford a decent microscope. (sniffle.)

Anyway, I want to build a denitrification column one of these days. There are bacteria that can “breathe” nitrate in place of oxygen, and in the process they can reduce the nitrate back down to plain old harmless nitrogen gas, which just bubbles out of the water. If you build a long, tall tube full of something like gravel that bacteria can grow on, and then pump the water through it slowly, oxygen-breathing bacteria near the bottom of the tube rapidly use up the oxygen in the water, leaving the nitrate. With no oxygen further up the tube, bacteria that can breathe the nitrate instead can grow like crazy, and exhale the extra nitrogen out of the system.

That’s one way of avoiding the need to use up as much fresh water as you’d need if you relied only on replacing the water to get rid of the nitrate.

I’ll save the sulfur and phosphorous parts for another day. Meanwhile, I think the next podcast or two will deal with MRSA, since it’s been in the news so much lately. I normally find the neglected non-medical microbiology more interesting, but the biochemistry and genetics involved with Methicillin Resistant Staphylococcus Aureus (not to mention S. aureus itself) is pretty interesting, and I find the media discussions of it unsatisfying.

Stay tuned…

Electricity-breathing bacteria! (Microbial fuel cells)

I made a 90-second “pod”cast of why microbial fuel cells work. I don’t yet know if This Week in Science is or was interested in playing it. [Update: this was featured in the November 6, 2007 broadcast! Hooray!] Either way, once I find a way to make it available without killing my bandwidth I shall. I’ll probably do more of them – if nothing else I obviously need the practice.

It was oddly difficult getting myself to actually talk to the microphone – more so than actually publically speaking to real people. I’m not sure why. It strikes me as something I’ll get over quickly once I’ve done it a few times, and my voice won’t sound quite so bland in the future.

In any case, microbial fuel cells are possibly the topic that got me really interested in a college education in applied biotechnology. I’ve been meaning to do a post on why they work for a while, so here’s one, in somewhat more detail than the 90-second audio version.

First, some quick review: We all remember that atoms are made of positively-charged protons, uncharged neutrons, and negatively-charged electrons, right? Protons and usually neutrons in the middle, and electrons hovering around. When atoms chemically react with each other, they’re really just having a fight over who gets to keep the electrons. When the reaction is over, some kinds of atoms or groups of atoms will have gained at least partial custody of electrons that used to belong to some of the other atoms or groups of atoms. The ability of a kind of atom to take electrons away from other atoms is called “electronegativity”. The second most electronegative element in the universe just happens to be a major part of our atmosphere – Oxygen.

As bacteria break down food molecules to get biological energy, there are electrons left over along the way. The bacterial cells have specific carrier molecules that take these extra electrons away, where they can be later dumped elsewhere into any of a variety of other useful biological reactions that need them. The one we’re concerned with today is called the Electron Transport Chain.

In many bacteria, and in the mitochondria of plants, fungi, and animals, the Electron Transport Chain regenerates a huge amount of a cell’s biochemical energy. The extra electrons get sucked into the beginning of this chemical chain, and as they are pulled along, the force of this pull drives a process which regenerates the cells’ main energy-carrying molecule, called ATP. This process is “respiration”, and it’s also exactly the reason you need to breathe oxygen. Humans need so much energy just to remain alive that we couldn’t survive without the huge amount of extra energy that respiration provides.

What drives this whole chain is some chemical at the other end pulling the electrons out. In aerobic organisms, this is oxygen. Some bacteria can use other chemicals, like nitrates, sulfates, and ferric iron (yes, there are bacteria that can breathe rust…) None of these chemicals provide quite as much energy as oxygen does, but it’s better than nothing and gives bacteria that could be damaged by oxygen something to breathe.

Normally, this last step happens inside the cell, but some bacteria have ways of extending this last step so that the final hand-off of the electrons happens outside itself. Some bacteria even make electrically-conducting biological “nano-wires” that this can happen through. Others make “shuttle” molecules that can pick up electrons, dissolve out of the cell, hand off the electrons somewhere outside, and then dissolve back into the cell to pick up more.

Now, we can make a microbial fuel cell. An electrode is put where the bacteria are growing – without oxygen – and a wire runs from this, out of the area where the bacteria are and to another electrode which is exposed to oxygen. It’s like an electric snorkel for bacteria. From the electrode and through the wire, the oxygen sucks electrons away from the bacteria. An electrical device stuck between the ends of the wire can use this energy exactly the same way that it could use the energy from electrons being sucked from one end of a battery to another.

Interestingly, the common “simple stain” Methylene Blue can also act as an artificial “shuttle” molecule. When reduced (carrying extra electrons) methylene blue is actually colorless, and I would swear I’ve seen protocols somewhere that use this to measure just how active a yeast culture is, and one of the demonstration microbial fuel cell setups actually uses a culture of yeast in methylene blue rather than a microbe that can naturally breath through electrodes.

By the way, if you thought you could tell a human from a realistic humanoid robot bent on world domination by the fact that only humans eat, I’ve got bad news for you. One interesting application of microbial fuel cells is Gastrobots. Literally, robots with digestive systems, where bacteria breaking down the contents of the “stomach” act as a microbial fuel cell to power the robot.

I hope you find this explanation useful and interesting. If you have (or even if you haven’t) please let me know. I can’t necessarily tell if I’m doing anybody any good without feedback!

Do Not Taunt Happy Fun Park

Here’s a brief interlude for my new readers. Members of my immediate family have seen this before elsewhere, but what the heck, I may as well share with you all.

Related to my recent posts about this year’s field-trip to Yellowstone National Park, I am reminded of a trip my wife and I took last year to Norris Geyser Basin in the same park.

I’ve heard of “communing with nature”, when the natural world seems to speak to you and put you at ease. Well, on this occasion it didn’t just seem to be speaking to me, and it hardly put me at ease. The conversation between me and the park went something like as follows that day. (Forgive all the scrolling, it WAS a several-hour conversation after all. If it bugs you, feel free to say so in the comments…)

Sign:No Restroom in Geyser Basin

Well, okay, I don’t smoke, I didn’t bring a bicycle, we left the dog at home. And I guess we can hold it until later. It’s a small price to pay to go out to nice, happy, peaceful trails, away from, for example, all the annoying road construction.Traffic cone, in the middle of the trailWow! Look at that! Do I spy the Fruiting Body of the rare Yellowstone Giant Orange Holewarning Mushroom?!?!?No, wait…that’s just a traffic cone over a hole in the trail! What the heck? I thought I was getting away from road construction!

Well. Maybe things will get more natural-looking once we get a chance to walk off into the wilderness. Maybe the map’ll show where we can go.

Map of Norris Geyser Basin, with Warning to Stay On Designated Trails
Ah, look at all the lovely trails. Plenty of space to roam around in.
What? I can’t leave the trails?
sign:Stay On Designated Trails

Can’t I take a mere step or two off? Just a little bit???

Sign:Stay on TrailSign:Stay On WalkYeah, yeah, whatever. What are you going to do if I don’t – have me arrested?

 

Sign:Unlawful to Leave Walkway
What kind of criminal act could possibly be involved with just leaving the silly walkway? Littering? Vandalism?
Sign:It is UNLAWFUL and UNSAFE to: Leave the walkway in thermal areas or throw objects into or deface thermal features

Oh, come on! Look, there’s a beautiful green pool over there, full of no doubt fascinating little animalcules. Can’t I just go over and take a little look?

Sign:Keep Off - Thermal Area
“Thermal Area”? What the heck is that supposed to mean? It’s a little windy and chilly today, maybe I want to be warmed up a little. So, why not? What’s so bad about a “Thermal” area?

Sign:Hazardous Ground - Thin Crust - Boiling Water

What’s that supposed to mean?

 

Sign:Dangerous Ground -with illustration of kid falling into ground and getting broiled-
Children are prone to explode out of the ground unexpectedly?Walkway shown crossing the top of the steaming opening of Green Dragon SpringWhat the heck? Is Green Dragon Spring actually devouring the ground under that walkway?!?! Oh! I get it – you’re saying the park itself can swallow you up and and cook you?
So everything here is flaming hot death, then, right?

Sign:Warning: Trail My Be Icy

Is there no end to the dangers this place threatens innocent visitors with? Can there possibly be anything else this park can do to us?!?!?

 

Solfatara: Very Dangerous Landscape spewing Sulfuric Acid Gas!
“Thin Crust”? “Boiling Water”? Broiled flesh cooked in acid? Ice?
Is this a park, or the kitchen at a Chinese restaurant? Is this how “Hot and Sour Soup” is made?!?!? Is there nothing that can stand in this realm of violent burning chemical death without fear!?!?!?
Fearless Geyser

But what of us poor, fragile fleshy people? We aren’t safe here!That does it! I’m getting out of here! No more of these horrible Killer Thermal Death Areas of Doom for me! I think maybe I’ll just go look at the nice cuddly animals that Yellowstone is also famous for.
Sign: Caution - Wild Animals are Unpredictable and Dangerous!
This whole friggin’ place wants to gore, dismember, maul, cook, devour, and digest me! That does it. No more of this dangerous stuff for me – I think I’ll just go read a nice book for a while…
Bookstore:Closed
NOOOOOOOOOOOOOOOOOOOOOoooo!!!!!!

Libel! Blasphemy! Slander!…

Injustice! Perfidy! HUMBUG!

Periodically, someone puts up a “could you pass a grade-school science class” quiz. The one linked to the image below goes to one that I just broke down and took, purely out of curiousity. Take a look at this outrage!:

JustSayHi - Science Quiz

Oh, sure, it LOOKS good, but what you don’t see is that it only gave me a 96%, implying that I missed one (it was a short quiz)! Sure, the quiz was very much in the modern fashion for “standardized testing” (aka the “No Child Left Awake” project) where the emphasis is on memorizing stuff for a test rather than actual comprehension. So, I thought, maybe I hadn’t correctly memorized which word was correct for one of the word-memorization questions. But, no, according to the “answer sheet”, the one I supposedly got wrong was this one:

(Note: If you’re planning to actually take that quiz, do so now before you read on and I give away one of the answers…)

“How do mammals respire?”

The options were:

  • Aerobically
  • Anaerobically
  • Both aerobically and anaerobically

Come on, I may hardly ever concern myself with perverse eukaryotic systems but…never mind just “mammals”, as far as I know, all eukaryotes (animals, plants, and fungi) only possess aerobic (oxygen-requiring) respiratory systems.

However, the “answer sheet” for the quiz claims that the answer is “Both aerobically and anaerobically”.

So….they’re wrong. I’m pretty sure what what they were intending to ask, given this answer, is “what kind of metabolism do mammals have?”, in which case their answer is correct.

See, “respiration” is only one part of the cellular energy-generating system. Specifically, it’s our friend, the Electron Transport Chain, which (to grossly oversimplify) harnesses the energy of oxygen sucking electrons off the end of the chain various biochemicals to recharge molecules of ATP. That’s not the only way a cell can get ATP, though. What the quiz authors are presumably alluding to is that there are non-oxygen-requiring biochemical pathways that animal cells can take to make energy – such as the one your muscles use when they can’t get enough oxygen, which involves production of lactic acid, which in turn gets blamed for the “burn” sensation you get when you work your muscles hard.

So, the authors of this quiz are bad, bad people, besmirching my reputation and harming my precious self-esteem by giving me less than 100% on that quiz!

On a related subject: breathing causes cancer in Sprague-Dawley™ rats!

No, seriously, it’s true – try raising one group of Sprague-Dawley™ rats with air, and one group with no air, and examing both populations 150 days later. I guarantee you’ll find many more cancerous growths in the “with air” group than in the group that was denied air to breathe…

What brought this outburst on? It was this blog article. “No, It’s for Real: Aspartame Causes Cancer”, the post proclaims. They’re talking about This study(pdf). Go ahead, take a look, but in particular, look at the tables of actual data, not the paper’s abstract. In particular, take a look at Figure 1, especially “D” and “E” (showing survival rates for the different groups of Sprague-Dawley™ rats as the study progressed), and at the number of “tumor-bearing animals” in Table 2.

Notice that at around 120 days on the survival graphs, the groups with the highest percentage of members still alive were the groups receiving the most aspartame in their feed. It’s worth noting that the highest-Aspartame group there was getting roughly the equivalent of a human drinking <em>thousands</em> of cans of diet soda every day. Also note, in fairness, that both graphs seem to show little difference between the groups, so rather than assuming that Aspartame makes Sprague-Dawley™ rats live longer, I would tend to assume that there’s really not much difference.

Notice also that in terms of the percentage of Sprague-Dawley™ rats that developed one or more tumors, there were fewer of them in the group that got the equivalent of 500 mg/kg of aspartame: which scaled up to human terms means about 200-250 cans of diet soda EVERY DAY worth of aspartame.

You may be wondering why I keep mentioning Sprague-Dawley™. It’s because this is a particular commercially-bred strain of rat that’s popular with labs for this kind of thing. One point that isn’t always mentioned is this: Sprague-Dawley™ rats are known to be prone to developing cancer spontaneously. This can be handy if you’re doing studies of “borderline” carcinogens. The hope is that if something has even a tiny ability to cause cancer, you’ll be able to measure the effect in a population of critters known to get cancer at the drop of a metaphorical hat, when in a human population the incidence might be so rare that you can’t distinguish it from random chance. To my admittedly-not-big-on-the-biochemistry-of-perverse-eukaryotes mind, this study really seems to show that there’s little or no effect – and certainly no dose-dependent effect – of aspartame even on cancer-prone lab rats.

I don’t know what it is, but “artificial sweeteners”, and especially aspartame, seem to generate such passionate hatred in some people. It reminds me a great deal of people’s reactions to “genetically modified” crops. People just really want to hate it. The authors of this paper are obviously trying REALLY hard to show somehow that aspartame is a dangerous poison, despite the inconclusive-appearing actual results. Though I suppose one could argue that they showed Aspartame to be at least as much of a deadly poison as Expired JellO®.

And now that I have exposed my readers to several times the Recommended Daily Allowance of Humbug, I bid you all a good night – I have Art History and Philosophy to attend in the morning…

Environmental Chemistry Field Trip – Day 1, part 2

Our next stop was Appolinaris Spring, which seems to be an uncommon thing in Yellowstone National Park: ordinary springwater. No sulfuric acid, no steam, just plain old water that sinks into the ground and then comes back up later. For most of the park’s history, it seems like this used to be a popular place to stop to get a drink of water.

water emerging from small copper pipes
Although the signs around the spring now all suggest that you really shouldn’t drink it, at least not without filtering it first, I’m kind of kicking myself now for not having tasted it. Perhaps I’ll have to go back on my own time and try it.

Our on-site tests showed a pH of 5.9 (slightly acidic: milk is normally around 6.8 or so, Root Beer somewhere around a more acidic 4.0, cola beverages around 3.0, for reference…), relatively low TDS of about 100ppm, coming out of the ground cool (about 7°C, or 43°F), with very little dissolved Oxygen (about 6.0ppm) and faintly carbonated (300ppm CO2). It reportedly didn’t taste too good, but having foolishly missed out on tasting it, I don’t know why.

There were hints that perhaps contamination from surface water – like rain trickling through bison poo – but quite some time ago they sealed the spring up to protect it from that kind of thing. This is the actual spring now:

Appolinaris Spring is a concrete box in the ground with locked metal tops...
Even so, the signs still try to discourage people from drinking the water coming from the pipes that lead out of the spring, which I take to be the park service covering themselves just in case someone claims to get sick from it. (“Hey, we TOLD you not to drink it!”).

Appolinaris: This spring water has been used by visitors since early days of the park. However modern water tests show periodic contamination. Park waters, even though clear and running are subject to pollution by wildlife. As with all untreated water, purify before drinking.
Periodic pollution by wildlife? What the…

The northern end of a south-bound bisonOh, right. Natural bottled-spring-water flavor. Hey, it’s natural, it’s got to be good for you, right?

And to end this post on a complete and totally baffling non-sequitur: the student lounge I’m sitting in right now has a television constantly tuned to some cheesy mass-media channel. Today it’s “E!®”. I overheard something on it just now that made me sit up and take notice: Evidently “Leprechaun” made a profit. Wow.

One never knows what kind of amazing things one might learn at college…

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.